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-rw-r--r--README.md4
-rw-r--r--app-text/zotero-bin/Manifest1
-rw-r--r--app-text/zotero-bin/metadata.xml11
-rw-r--r--app-text/zotero-bin/zotero-bin-5.0.96.ebuild53
-rw-r--r--dev-java/netcdf/Manifest1
-rw-r--r--dev-java/netcdf/netcdf-4.2.ebuild78
-rw-r--r--dev-lang/conceptual/conceptual-1.5.1b.ebuild2
-rw-r--r--dev-libs/optix/Manifest1
-rw-r--r--dev-libs/optix/optix-7.2.0.ebuild37
-rw-r--r--dev-ml/lacaml/lacaml-11.0.8.ebuild4
-rw-r--r--dev-perl/BTLib/BTLib-0.19.ebuild3
-rw-r--r--dev-perl/BTLib/BTLib-0.20.ebuild3
-rw-r--r--dev-python/av/Manifest1
-rw-r--r--dev-python/av/av-8.0.3.ebuild24
-rw-r--r--dev-python/av/metadata.xml8
-rw-r--r--dev-python/bokeh/Manifest2
-rw-r--r--dev-python/bokeh/bokeh-2.3.2.ebuild85
-rw-r--r--dev-python/cadquery-pywrap/Manifest1
-rw-r--r--dev-python/cadquery-pywrap/cadquery-pywrap-7.5.2_rc20210526.ebuild70
-rw-r--r--dev-python/cadquery-pywrap/metadata.xml (renamed from dev-java/netcdf/metadata.xml)8
-rw-r--r--dev-python/cymbal/Manifest1
-rw-r--r--dev-python/cymbal/cymbal-1.0.0.ebuild34
-rw-r--r--dev-python/cymbal/metadata.xml13
-rw-r--r--dev-python/dnaio/Manifest1
-rw-r--r--dev-python/dnaio/dnaio-0.5.1.ebuild22
-rw-r--r--dev-python/gffpandas/Manifest1
-rw-r--r--dev-python/gffpandas/gffpandas-1.2.0.ebuild29
-rw-r--r--dev-python/gffpandas/metadata.xml (renamed from sci-biology/StarORF/metadata.xml)4
-rw-r--r--dev-python/kmapper/Manifest1
-rw-r--r--dev-python/kmapper/kmapper-2.0.1.ebuild42
-rw-r--r--dev-python/logzero/Manifest1
-rw-r--r--dev-python/logzero/logzero-1.7.0.ebuild18
-rw-r--r--dev-python/logzero/metadata.xml13
-rw-r--r--dev-python/meshio/Manifest1
-rw-r--r--dev-python/meshio/meshio-4.4.6.ebuild26
-rw-r--r--dev-python/meshio/metadata.xml13
-rw-r--r--dev-python/numba/numba-0.53.1.ebuild18
-rw-r--r--dev-python/persim/Manifest2
-rw-r--r--dev-python/persim/persim-0.3.0.ebuild28
-rw-r--r--dev-python/persim/persim-0.3.1.ebuild28
-rw-r--r--dev-python/pybind11-stubgen/Manifest1
-rw-r--r--dev-python/pybind11-stubgen/pybind11-stubgen-0.8.7.ebuild24
-rw-r--r--dev-python/pynndescent/Manifest2
-rw-r--r--dev-python/pynndescent/pynndescent-0.4.8.ebuild27
-rw-r--r--dev-python/pynndescent/pynndescent-0.5.1.ebuild27
-rw-r--r--dev-python/pynndescent/pynndescent-0.5.2.ebuild8
-rw-r--r--dev-python/pyvista/Manifest1
-rw-r--r--dev-python/pyvista/metadata.xml13
-rw-r--r--dev-python/pyvista/pyvista-0.31.1.ebuild32
-rw-r--r--dev-python/pyzotero/Manifest1
-rw-r--r--dev-python/pyzotero/metadata.xml12
-rw-r--r--dev-python/pyzotero/pyzotero-1.4.20.ebuild39
-rw-r--r--dev-python/schema/Manifest1
-rw-r--r--dev-python/schema/metadata.xml13
-rw-r--r--dev-python/schema/schema-0.7.4.ebuild28
-rw-r--r--dev-python/scooby/Manifest1
-rw-r--r--dev-python/scooby/metadata.xml13
-rw-r--r--dev-python/scooby/scooby-0.5.7.ebuild16
-rw-r--r--dev-python/texext/metadata.xml6
-rw-r--r--dev-python/transforms3d/Manifest1
-rw-r--r--dev-python/transforms3d/metadata.xml13
-rw-r--r--dev-python/transforms3d/transforms3d-0.3.1.ebuild23
-rw-r--r--licenses/netCDF31
-rw-r--r--media-libs/embree-bin/Manifest1
-rw-r--r--media-libs/embree-bin/embree-bin-3.13.0.ebuild58
-rw-r--r--media-libs/libgfx/files/1.1.0-gcc-4.3.patch24
-rw-r--r--media-libs/libgfx/files/1.1.0-gcc4.3.patch11
-rw-r--r--media-libs/libgfx/files/1.1.0-libPNG-1.2.5.patch24
-rw-r--r--media-libs/libgfx/libgfx-1.1.0.ebuild18
-rw-r--r--net-misc/cernbox-client/Manifest2
-rw-r--r--net-misc/cernbox-client/cernbox-client-2.8.2.4246.ebuild (renamed from net-misc/cernbox-client/cernbox-client-2.7.5.3180.ebuild)0
-rw-r--r--profiles/package.mask10
-rw-r--r--profiles/updates/2Q-20211
-rw-r--r--sci-biology/KING/KING-2.2.7.ebuild (renamed from sci-biology/KING/KING-2.2.5.ebuild)12
-rw-r--r--sci-biology/KING/Manifest4
-rw-r--r--sci-biology/StarORF/StarORF-9999.ebuild29
-rw-r--r--sci-biology/cutadapt/Manifest1
-rw-r--r--sci-biology/cutadapt/cutadapt-3.3.ebuild42
-rw-r--r--sci-biology/cutadapt/files/cutadapt-3.3-skiptest.patch13
-rw-r--r--sci-biology/dcm2niix/Manifest1
-rw-r--r--sci-biology/dcm2niix/dcm2niix-1.0.20201102.ebuild24
-rw-r--r--sci-biology/dcm2niix/dcm2niix-1.0.20210317.ebuild41
-rw-r--r--sci-biology/dcm2niix/files/dcm2niix-disable_find_git.patch19
-rw-r--r--sci-biology/dcm2niix/metadata.xml5
-rw-r--r--sci-biology/dipy/dipy-9999.ebuild2
-rw-r--r--sci-biology/fsl/Manifest1
-rw-r--r--sci-biology/fsl/files/fsl-6.0.4-cuda_buildsettings.patch12
-rw-r--r--sci-biology/fsl/files/fsl-6.0.4-eddy_cuda.patch21
-rw-r--r--sci-biology/fsl/files/fsl-6.0.4-fdt_cuda.patch14
-rw-r--r--sci-biology/fsl/files/fsl-6.0.4-flameo_std.patch11
-rw-r--r--sci-biology/fsl/files/fsl-6.0.4-fsldir_redux-p1.patch240
-rw-r--r--sci-biology/fsl/files/fsl-6.0.4-fsldir_redux-p2.patch254
-rw-r--r--sci-biology/fsl/files/fsl-6.0.4-gcc10_include.patch11
-rw-r--r--sci-biology/fsl/files/fsl-6.0.4-melodic_std.patch11
-rw-r--r--sci-biology/fsl/files/fsl-6.0.4-remove_fslpy_collisions-p1.patch303
-rw-r--r--sci-biology/fsl/files/fsl-6.0.4-remove_fslpy_collisions-p2.patch348
-rw-r--r--sci-biology/fsl/files/fsl-6.0.4-setup.patch174
-rw-r--r--sci-biology/fsl/fsl-6.0.2-r1.ebuild10
-rw-r--r--sci-biology/fsl/fsl-6.0.2.ebuild6
-rw-r--r--sci-biology/fsl/fsl-6.0.4.ebuild217
-rw-r--r--sci-biology/jellyfish/jellyfish-1.1.12.ebuild7
-rw-r--r--sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild2
-rw-r--r--sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild2
-rw-r--r--sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild2
-rw-r--r--sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild2
-rw-r--r--sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild2
-rw-r--r--sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild2
-rw-r--r--sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild2
-rw-r--r--sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild2
-rw-r--r--sci-biology/nilearn/nilearn-9999.ebuild2
-rw-r--r--sci-chemistry/MotionCor2/MotionCor2-1.4.0.ebuild10
-rw-r--r--sci-chemistry/MotionCor2/metadata.xml1
-rw-r--r--sci-libs/ciftilib/ciftilib-1.6.0.ebuild6
-rw-r--r--sci-libs/ciftilib/files/ciftilib-1.6.0-version.patch27
-rw-r--r--sci-libs/ensmallen/Manifest1
-rw-r--r--sci-libs/ensmallen/ensmallen-2.16.2.ebuild28
-rw-r--r--sci-libs/fox/fox-4.1.2-r2.ebuild2
-rw-r--r--sci-libs/mlpack/mlpack-3.4.1.ebuild2
-rw-r--r--sci-libs/mlpack/mlpack-3.4.2.ebuild2
-rw-r--r--sci-libs/nipy/nipy-9999.ebuild2
-rw-r--r--sci-libs/pytorch/Manifest23
-rw-r--r--sci-libs/pytorch/pytorch-1.9.0.ebuild321
-rw-r--r--sci-mathematics/gap/gap-4.11.0.ebuild6
-rw-r--r--sci-mathematics/gappa/Manifest1
-rw-r--r--sci-mathematics/gappa/gappa-1.3.5.ebuild5
-rw-r--r--sci-mathematics/gappa/gappa-1.4.0.ebuild42
-rw-r--r--sci-visualization/forge/Manifest1
-rw-r--r--sci-visualization/forge/forge-1.0.7.ebuild54
-rw-r--r--sci-visualization/scidavis/Manifest1
-rw-r--r--sci-visualization/scidavis/files/scidavis-build.patch39
-rw-r--r--sci-visualization/scidavis/files/scidavis-tests.patch10
-rw-r--r--sci-visualization/scidavis/metadata.xml24
-rw-r--r--sci-visualization/scidavis/scidavis-2.3.0.ebuild93
-rwxr-xr-xscripts/check-duplicates.sh2
-rwxr-xr-xscripts/setup-and-run-repoman.sh4
-rwxr-xr-xscripts/setup-master-gentoo.sh2
-rw-r--r--sys-kernel/dkms/Manifest1
-rw-r--r--sys-kernel/dkms/dkms-2.8.4.ebuild41
-rw-r--r--sys-kernel/dkms/metadata.xml22
-rw-r--r--x11-libs/qwt/Manifest1
-rw-r--r--x11-libs/qwt/metadata.xml18
-rw-r--r--x11-libs/qwt/qwt-5.2.3_p20200902.ebuild88
-rw-r--r--x11-libs/qwtplot3d/Manifest1
-rw-r--r--x11-libs/qwtplot3d/files/qwtplot3d-doxygen.patch28
-rw-r--r--x11-libs/qwtplot3d/files/qwtplot3d-examples.patch125
-rw-r--r--x11-libs/qwtplot3d/files/qwtplot3d-gcc44.patch12
-rw-r--r--x11-libs/qwtplot3d/files/qwtplot3d-profile.patch27
-rw-r--r--x11-libs/qwtplot3d/files/qwtplot3d-qt-4.8.0.patch34
-rw-r--r--x11-libs/qwtplot3d/files/qwtplot3d-sys-gl2ps.patch31
-rw-r--r--x11-libs/qwtplot3d/metadata.xml16
-rw-r--r--x11-libs/qwtplot3d/qwtplot3d-0.2.7.ebuild66
151 files changed, 3160 insertions, 1086 deletions
diff --git a/README.md b/README.md
index 29e518d33..99fcfe316 100644
--- a/README.md
+++ b/README.md
@@ -2,7 +2,7 @@
[![pkgcheck](https://github.com/gentoo/sci/workflows/pkgcheck/badge.svg)](https://github.com/gentoo/sci/actions?query=workflow%3Apkgcheck)
[![repoman](https://github.com/gentoo/sci/workflows/repoman/badge.svg)](https://github.com/gentoo/sci/actions?query=workflow%3Arepoman)
[![contributions welcome](https://img.shields.io/badge/contributions-welcome-brightgreen.svg)](https://github.com/gentoo/sci#guide)
-[![chat on freenode](https://img.shields.io/badge/chat-on%20freenode-brightgreen.svg)](https://webchat.freenode.net/#gentoo-science)
+[![chat on libera](https://img.shields.io/badge/chat-on%20libera-brightgreen.svg)](https://web.libera.chat/#gentoo-science)
<table>
<tr>
@@ -143,5 +143,5 @@ Additionally, please make sure to add the Science Project as an additional maint
## Support
-You can ask for help on [Freenode IRC](https://www.gentoo.org/get-involved/irc-channels/) in [**#gentoo-science**](http://webchat.freenode.net/?channels=gentoo-science).
+You can ask for help on [Libera IRC](https://www.gentoo.org/get-involved/irc-channels/) in [**#gentoo-science**](https://web.libera.chat/#gentoo-science).
Alternatively you can report bugs on the [GitHub issues page](https://github.com/gentoo/sci/issues).
diff --git a/app-text/zotero-bin/Manifest b/app-text/zotero-bin/Manifest
deleted file mode 100644
index 65564e616..000000000
--- a/app-text/zotero-bin/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST zotero-bin-5.0.96.tar.bz2 60474165 BLAKE2B 5330ea95360cd20cbcf9366481bf715ca0b50fe6919814bba6192cd71b6c94724bd3edb2b6cde3b894b06d2f232f867b6b52426e6ab57668150c23d487c53655 SHA512 aa755b280ac9f03031d70105ada7be9ba9da17f858bffc33e8b7598e85b53b2915854b57c78c2644d181c1368aa3fdcb87f08e6bd2a0f40592acfa7faccbb124
diff --git a/app-text/zotero-bin/metadata.xml b/app-text/zotero-bin/metadata.xml
deleted file mode 100644
index 8bf43532d..000000000
--- a/app-text/zotero-bin/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>andrewammerlaan@riseup.net</email>
- <name>Andrew Ammerlaan</name>
- </maintainer>
- <upstream>
- <remote-id type="github">zotero/zotero</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/app-text/zotero-bin/zotero-bin-5.0.96.ebuild b/app-text/zotero-bin/zotero-bin-5.0.96.ebuild
deleted file mode 100644
index 5586e8b13..000000000
--- a/app-text/zotero-bin/zotero-bin-5.0.96.ebuild
+++ /dev/null
@@ -1,53 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit desktop xdg
-
-DESCRIPTION="Helps you collect, organize, cite, and share your research sources"
-HOMEPAGE="https://www.zotero.org"
-SRC_URI="https://www.zotero.org/download/client/dl?channel=release&platform=linux-x86_64&version=${PV} -> ${P}.tar.bz2"
-
-LICENSE="GPL-3"
-SLOT="0"
-KEYWORDS="~amd64"
-
-RDEPEND="
- dev-libs/dbus-glib
- dev-libs/nss
- x11-libs/gtk+:3
- x11-libs/libXt
-"
-
-S="${WORKDIR}/Zotero_linux-x86_64"
-
-QA_PREBUILT="*"
-
-src_prepare() {
- # disable update
- sed -i -e 's/\(pref("app.update.enabled"\).*/\1, false);/' defaults/preferences/prefs.js || die
-
- # disable default oo installation questions - manual installation is still possible
- sed -i -e 's/\(pref("extensions.zoteroOpenOfficeIntegration.skipInstallation"\).*/\1, true);/' \
- extensions/zoteroOpenOfficeIntegration@zotero.org/defaults/preferences/zoteroOpenOfficeIntegration.js || die
-
- # fix desktop-file
- sed -i -e 's#^Exec=.*#Exec=zotero#' zotero.desktop
- sed -i -e 's#Icon=zotero.*#Icon=zotero#' zotero.desktop
-
- default
-}
-
-src_install() {
- dodir opt/zotero
- cp -a "${S}"/* "${ED}/opt/zotero" || die
-
- dosym ../../opt/zotero/zotero usr/bin/zotero
-
- domenu zotero.desktop
-
- for size in 16 32 48; do
- newicon -s ${size} chrome/icons/default/default${size}.png zotero.png
- done
-}
diff --git a/dev-java/netcdf/Manifest b/dev-java/netcdf/Manifest
deleted file mode 100644
index e977c681b..000000000
--- a/dev-java/netcdf/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST ncSrc-4.2.zip 59888846 BLAKE2B 08bd2ce623e081dc2c349ba64109abc39feba86c11dc3a536aaf8f18e31e6ce04983411e59807ce4720abe2c310682a82c30c4d2abd21ede7cbc951ceee7edcb SHA512 1cf22c55a43f53bbb573c6bcbc9e40b0020ed9d576c68a0d54639ca9892393735b25bfa0078fcb763c71d5d875fb1f315c6d580d6a859434d362693f6500d652
diff --git a/dev-java/netcdf/netcdf-4.2.ebuild b/dev-java/netcdf/netcdf-4.2.ebuild
deleted file mode 100644
index 0514802dc..000000000
--- a/dev-java/netcdf/netcdf-4.2.ebuild
+++ /dev/null
@@ -1,78 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-JAVA_PKG_IUSE="doc examples source test"
-
-inherit java-pkg-2 java-ant-2
-
-DESCRIPTION="Java Common Data Model (CDM) interface to to netCDF files"
-HOMEPAGE="https://www.unidata.ucar.edu/software/netcdf-java/"
-SRC_URI="ftp://ftp.unidata.ucar.edu/pub/${PN}-java/v${PV}/ncSrc-${PV}.zip"
-
-LICENSE="netCDF"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-CDEPEND="
- dev-java/commons-codec:0
- dev-java/commons-httpclient:3
- dev-java/commons-logging:0
- dev-java/ehcache:1.2
- dev-java/jcommon:1.0
- dev-java/jdom:0
- dev-java/jfreechart:1.0
- dev-java/jgoodies-forms:0
- dev-java/joda-time:0
- dev-java/junit:4
- dev-java/log4j:0
- dev-java/slf4j-api:0
- dev-java/protobuf-java:0
-"
-
-RDEPEND="${CDEPEND}
- >=virtual/jre-1.5"
-
-DEPEND="${CDEPEND}
- >=virtual/jdk-1.5
- test? (
- dev-java/ant-junit4
- dev-java/hamcrest-core
- )"
-BDEPEND="app-arch/unzip"
-
-# There is a from-source maven package in java-overlay, but it hasn't
-# been merged into the Portage trunk yet.
-
-S="${WORKDIR}"
-
-src_prepare() {
- default
- java-pkg_jar-from --into lib/external commons-codec commons-codec.jar
- java-pkg_jar-from --into lib/external commons-httpclient-3 commons-httpclient.jar
- java-pkg_jar-from --into lib/external commons-logging commons-logging.jar
- java-pkg_jar-from --into lib/external ehcache-1.2 ehcache.jar
- java-pkg_jar-from --into lib/external jcommon-1.0 jcommon.jar
- rm -f lib/external/jdom.jar || die
- java-pkg_jar-from --into lib/external jdom jdom.jar
- java-pkg_jar-from --into lib/external jfreechart-1.0 jfreechart.jar
- java-pkg_jar-from --into lib/external jgoodies-forms forms.jar jgoodies-forms.jar
- java-pkg_jar-from --into lib/external joda-time joda-time.jar
- java-pkg_jar-from --into lib/external junit-4 junit.jar
- java-pkg_jar-from --into lib/external log4j log4j.jar
- java-pkg_jar-from --into lib/external protobuf-java protobuf.jar
- java-pkg_jar-from --into lib/external slf4j-api slf4j-api.jar
-}
-
-src_compile() {
- cd "${S}"/cdm && eant
- use doc && eant javadoc
-}
-
-src_install() {
- java-pkg_newjar cdm/target/${P}.jar ${PN}.jar
- use doc && java-pkg_dojavadoc cdm/target/javadoc
- use source && java-pkg_dosrc cdm/src/main/java/*
- use examples && java-pkg_doexamples cdm/src/test/java/examples
-}
diff --git a/dev-lang/conceptual/conceptual-1.5.1b.ebuild b/dev-lang/conceptual/conceptual-1.5.1b.ebuild
index 0d3acefe7..53cfee813 100644
--- a/dev-lang/conceptual/conceptual-1.5.1b.ebuild
+++ b/dev-lang/conceptual/conceptual-1.5.1b.ebuild
@@ -3,7 +3,7 @@
EAPI=7
-PYTHON_COMPAT=( python3_7 )
+PYTHON_COMPAT=( python3_{7,8,9} )
JAVA_PKG_OPT_USE="gui"
inherit java-pkg-opt-2 python-single-r1
diff --git a/dev-libs/optix/Manifest b/dev-libs/optix/Manifest
index 99902f6d6..11e08c79f 100644
--- a/dev-libs/optix/Manifest
+++ b/dev-libs/optix/Manifest
@@ -1,3 +1,4 @@
DIST NVIDIA-OptiX-SDK-6.0.0-linux64-25650775.sh 642319364 BLAKE2B 5dc6e23d606ca9f947aff046d20592729e562c66c475d47aa0cda8d3e7361cabbe102b5b0e125744d27e25321d4ac8486a55bc145c54c96c719de6e821744ba9 SHA512 33fbb312c47174a9ddb26bd4b1a1e5089b70eaebdecd80561c91c1926fba2fb8c94ec39b4c2dc8f0ccbb5e27bbd38ad8fb08df1d605ed1ec5b3fd34ecca908b7
DIST NVIDIA-OptiX-SDK-7.0.0-linux64.sh 28930132 BLAKE2B ae09bc862ccd39c25d5cc103d97b5587e21638079905e5811528b3d59deb7fd546034f24f73696c212274c0613f5b1dca7508bff696f5fec535dda7351166d7e SHA512 349baf367af7890afac87a879c8f7360cc9c93e984cf234216062af0a3cedce8fc6f3fd74240897d4b3854622ce1976a78433cbeadf6fa89c8e84d24e26eef89
DIST NVIDIA-OptiX-SDK-7.1.0-linux64-x86_64.sh 45564234 BLAKE2B 374bdbe5045ff36b71da8200ad29189cc3afba9783a38a74515caafeb90176eec5bf7a7d5e2045e47c399aa226a61fd12e6e7dd6c034b8a0f260a5850f775e47 SHA512 808a45e2007d8081de21fe15cad4577ba9fe10fc3612486b1230e03b7f17de91902dc773d1f3fef2b89398f230448d9522a03e19d4e6fa12aa4ffd78f1a4f9dc
+DIST NVIDIA-OptiX-SDK-7.2.0-linux64-x86_64.sh 44573802 BLAKE2B 546f2f02336d7487e2aab3f348290aaf9bdac153a3fe161b48ad8a897f5d14f6126e06d3b8b4c301f8a6df5735d951dcf544795b2668bc42116bd909e032b18d SHA512 c37f36e2c0d5dbf151a03513e9dc82c21c46f1a88b123153647f44f4305367d1021e522236dda97ab9c641db006242507ae323d668cf2186cf04a83a54b5707f
diff --git a/dev-libs/optix/optix-7.2.0.ebuild b/dev-libs/optix/optix-7.2.0.ebuild
new file mode 100644
index 000000000..34dcf66c4
--- /dev/null
+++ b/dev-libs/optix/optix-7.2.0.ebuild
@@ -0,0 +1,37 @@
+# Copyright 2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="NVIDIA Ray Tracing Engine"
+HOMEPAGE="https://developer.nvidia.com/optix"
+SRC_URI="NVIDIA-OptiX-SDK-${PV}-linux64-x86_64.sh"
+S="${WORKDIR}"
+
+SLOT="0/7"
+KEYWORDS="~amd64"
+RESTRICT="fetch mirror"
+LICENSE="NVIDIA-r2"
+
+RDEPEND="
+ dev-util/nvidia-cuda-toolkit:=
+ media-libs/freeglut
+ virtual/opengl
+"
+
+pkg_nofetch() {
+ einfo "Please download ${SRC_URI} from:"
+ einfo " ${HOMEPAGE}"
+ einfo "and move it to your DISTDIR directory."
+ einfo 'DISTDIR value is available from `emerge --info`'
+}
+
+src_unpack() {
+ tail -n +223 "${DISTDIR}"/${A} | tar -zx || die
+}
+
+src_install() {
+ insinto /opt/${PN}
+ dodoc -r doc
+ doins -r include SDK
+}
diff --git a/dev-ml/lacaml/lacaml-11.0.8.ebuild b/dev-ml/lacaml/lacaml-11.0.8.ebuild
index ea091d80a..7070c04af 100644
--- a/dev-ml/lacaml/lacaml-11.0.8.ebuild
+++ b/dev-ml/lacaml/lacaml-11.0.8.ebuild
@@ -18,8 +18,10 @@ IUSE="ocamlopt"
RDEPEND="
virtual/blas
virtual/lapack
+ dev-ml/dune-configurator
"
-BDEPEND="${RDEPEND}
+DEPEND="${RDEPEND}"
+BDEPEND="
virtual/pkgconfig
"
diff --git a/dev-perl/BTLib/BTLib-0.19.ebuild b/dev-perl/BTLib/BTLib-0.19.ebuild
index 4205eca9e..6fa1072fb 100644
--- a/dev-perl/BTLib/BTLib-0.19.ebuild
+++ b/dev-perl/BTLib/BTLib-0.19.ebuild
@@ -13,4 +13,7 @@ LICENSE="|| ( Artistic GPL-1 GPL-2 GPL-3 )"
SLOT="0"
KEYWORDS="~amd64 ~x86"
+RDEPEND="
+ !app-misc/sphinx"
+
SRC_TEST="do"
diff --git a/dev-perl/BTLib/BTLib-0.20.ebuild b/dev-perl/BTLib/BTLib-0.20.ebuild
index 4205eca9e..6fa1072fb 100644
--- a/dev-perl/BTLib/BTLib-0.20.ebuild
+++ b/dev-perl/BTLib/BTLib-0.20.ebuild
@@ -13,4 +13,7 @@ LICENSE="|| ( Artistic GPL-1 GPL-2 GPL-3 )"
SLOT="0"
KEYWORDS="~amd64 ~x86"
+RDEPEND="
+ !app-misc/sphinx"
+
SRC_TEST="do"
diff --git a/dev-python/av/Manifest b/dev-python/av/Manifest
new file mode 100644
index 000000000..535dd5295
--- /dev/null
+++ b/dev-python/av/Manifest
@@ -0,0 +1 @@
+DIST av-8.0.3.tar.gz 2321046 BLAKE2B 546c79ab638ad3587d51fd8c598eb72d56455209f93163660e1e1dccbb325c86639d22a413c1b4cc6abce4c4f96e59ae0eb505d6a6604a6444895d594a652f7f SHA512 ba09286f0d786b6e697b91279d0ed8c2c241ef4579c1d74f33dcf4fd35a53e3a819dbbf9901183defd9f40921e94d261a129f1af660666bcd30868c6e4b6ec99
diff --git a/dev-python/av/av-8.0.3.ebuild b/dev-python/av/av-8.0.3.ebuild
new file mode 100644
index 000000000..57a8bbdfb
--- /dev/null
+++ b/dev-python/av/av-8.0.3.ebuild
@@ -0,0 +1,24 @@
+# Copyright 2020-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+
+inherit distutils-r1
+
+DESCRIPTION="Pythonic bindings for FFmpeg's libraries."
+HOMEPAGE="https://github.com/mikeboers/PyAV https://pypi.org/project/av/"
+SRC_URI="mirror://pypi/${P:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RESTRICT="test"
+
+DEPEND="media-video/ffmpeg"
+
+distutils_enable_tests setup.py
+# The configuration file (or one of the modules it imports) called sys.exit()
+# distutils_enable_sphinx docs
diff --git a/dev-python/av/metadata.xml b/dev-python/av/metadata.xml
new file mode 100644
index 000000000..325d9cc57
--- /dev/null
+++ b/dev-python/av/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>jpizarrocallejas@gmail.com</email>
+ <name>Jorge Pizarro Callejas</name>
+ </maintainer>
+</pkgmetadata>
diff --git a/dev-python/bokeh/Manifest b/dev-python/bokeh/Manifest
index 2077cedf4..1a38ac66c 100644
--- a/dev-python/bokeh/Manifest
+++ b/dev-python/bokeh/Manifest
@@ -3,5 +3,7 @@ DIST bokeh-2.2.2.tar.gz 8847568 BLAKE2B b279e72106ec7771fbdad6709d529e5b5e23152e
DIST bokeh-2.2.3.tar.gz 8848373 BLAKE2B 4bae1e729980bced589c256213df22cabc08b8105113698b0e5eefd37760506a625212931dcafb8c00f1a2fce1b77a48b4802ede4a3f09c73f09b8dbe39a1a81 SHA512 7d7cf6b4207644894c8a358e235f2901f65b453f3324c1b766ddca67b287e13e82df67c193ba87123d5b3b855f7ba29c01e2113fb787dd60c39bef6ba7c95aba
DIST bokeh-2.3.0.tar.gz 10617724 BLAKE2B ee20260b17a9d2fd13df0dab92d317b0c3a1709945e85bd0697f66d9d4363422fbb3efc29f0b402d5c8f7fab1e2f9d6903bc4da7951af88a7cf101ae85c1a535 SHA512 9e584810ffd1cc66b2c97ffbd527cb0fe4a7c63dd0cc9ddae29beae167db9c4333c2323928a91117ac226e401997dd2b2d6f8968c0618c3b40c70c6bac334c95
DIST bokeh-2.3.1.tar.gz 10627152 BLAKE2B 30833fb83eae60bc6b92faa3128cce8a9f2bab84179d1565acf9f08b35c39540a2a6cc2a70a5f611d2a6aeede4ce6328851ac11261fab0a491976e570456c3a8 SHA512 fd9f03ae267b4cae5cc6fdae2217ef67c27bc297c00e59971bdc8ae53389a15ea80005ed7547b4761836070e53bdbc4ec2038fc0e7624788254d8bc311b765df
+DIST bokeh-2.3.2.tar.gz 10662248 BLAKE2B c289ae8d1fddd470d838d0afe8eae46d62755c8986af79784df08af4c839129f039deca85ad5dbfedcb97163a7f630063859aeaa25e0e9a7c0c65839d2b9acee SHA512 58321d318ad69a1caee130870c5e31e59bab3c99faf070a752ee9cd506400de2007f17363930fad86af5014fb42fd80b9e9bef109c5da8d8bd83edd8d3ca3aa9
DIST conftest-bokeh-2.3.0.py 1749 BLAKE2B 60b24d84e606d06c6913ddd6cac0ddf5aecc9989b3d87c896ef554da30968e9762224e32d63cc6f5c405a279608c92153e182e4e611bd635f5d307618597469c SHA512 e352b34da8156fd9764c483a01e3979f6e44c82163cd40fef471382f23566f824e09d3ef579e7d279a546e58fc26fa169afdd6ba74a21ab79c71bb173a1c5a5b
DIST conftest-bokeh-2.3.1.py 1749 BLAKE2B 60b24d84e606d06c6913ddd6cac0ddf5aecc9989b3d87c896ef554da30968e9762224e32d63cc6f5c405a279608c92153e182e4e611bd635f5d307618597469c SHA512 e352b34da8156fd9764c483a01e3979f6e44c82163cd40fef471382f23566f824e09d3ef579e7d279a546e58fc26fa169afdd6ba74a21ab79c71bb173a1c5a5b
+DIST conftest-bokeh-2.3.2.py 1749 BLAKE2B 60b24d84e606d06c6913ddd6cac0ddf5aecc9989b3d87c896ef554da30968e9762224e32d63cc6f5c405a279608c92153e182e4e611bd635f5d307618597469c SHA512 e352b34da8156fd9764c483a01e3979f6e44c82163cd40fef471382f23566f824e09d3ef579e7d279a546e58fc26fa169afdd6ba74a21ab79c71bb173a1c5a5b
diff --git a/dev-python/bokeh/bokeh-2.3.2.ebuild b/dev-python/bokeh/bokeh-2.3.2.ebuild
new file mode 100644
index 000000000..c3f35c24c
--- /dev/null
+++ b/dev-python/bokeh/bokeh-2.3.2.ebuild
@@ -0,0 +1,85 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{6..9} )
+DISTUTILS_USE_SETUPTOOLS=rdepend
+DISTUTILS_IN_SOURCE_BUILD=1
+inherit distutils-r1 optfeature
+
+DESCRIPTION="Statistical and interactive HTML plots for Python"
+HOMEPAGE="https://bokeh.org/"
+SRC_URI="mirror://pypi/${P:0:1}/${PN}/${P}.tar.gz
+ https://raw.githubusercontent.com/bokeh/bokeh/${PV}/conftest.py -> conftest-${P}.py
+"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+# upstream authoritative dependencies
+# https://github.com/bokeh/bokeh/blob/master/conda.recipe/meta.yaml
+RDEPEND="
+ dev-python/jinja[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/packaging[${PYTHON_USEDEP}]
+ dev-python/pillow[${PYTHON_USEDEP}]
+ dev-python/pyparsing[${PYTHON_USEDEP}]
+ dev-python/python-dateutil[${PYTHON_USEDEP}]
+ dev-python/pyyaml[${PYTHON_USEDEP}]
+ dev-python/requests[${PYTHON_USEDEP}]
+ dev-python/six[${PYTHON_USEDEP}]
+ dev-python/typing-extensions[${PYTHON_USEDEP}]
+ >=www-servers/tornado-5[${PYTHON_USEDEP}]
+"
+BDEPEND="
+ test? (
+ dev-python/beautifulsoup:4[${PYTHON_USEDEP}]
+ dev-python/flaky[${PYTHON_USEDEP}]
+ dev-python/ipython_genutils[${PYTHON_USEDEP}]
+ dev-python/mock[${PYTHON_USEDEP}]
+ dev-python/networkx[${PYTHON_USEDEP}]
+ dev-python/nbconvert[${PYTHON_USEDEP}]
+ dev-python/nbformat[${PYTHON_USEDEP}]
+ dev-python/pydot[${PYTHON_USEDEP}]
+ dev-python/pytz[${PYTHON_USEDEP}]
+ dev-python/scipy[${PYTHON_USEDEP}]
+ dev-python/selenium[${PYTHON_USEDEP}]
+ )
+"
+
+distutils_enable_tests pytest
+
+python_prepare_all(){
+ cp "${DISTDIR}"/conftest-${P}.py "${S}"/conftest.py || die
+ distutils-r1_python_prepare_all
+}
+
+python_test() {
+ # disable tests having network calls
+ local SKIP_TESTS=" \
+ not (test___init__ and TestWarnings and test_filters) and \
+ not (test_json__subcommands and test_no_script) and \
+ not (test_standalone and Test_autoload_static) and \
+ not test_nodejs_compile_javascript and \
+ not test_nodejs_compile_less and \
+ not test_inline_extension and \
+ not (test_model and test_select) and \
+ not test_tornado__server and \
+ not test_client_server and \
+ not test_webdriver and \
+ not test_export and \
+ not test_server and \
+ not test_bundle and \
+ not test_ext \
+ "
+ pytest -m "not sampledata" tests/unit -k \
+ "${SKIP_TESTS}" -vv || die "unittests fail with ${EPYTHON}"
+}
+
+pkg_postinst() {
+ optfeature "integration with amazon S3" dev-python/boto
+ optfeature "pypi integration to publish packages" dev-python/twine
+ optfeature "js library usage" net-libs/nodejs
+}
diff --git a/dev-python/cadquery-pywrap/Manifest b/dev-python/cadquery-pywrap/Manifest
new file mode 100644
index 000000000..a203693d6
--- /dev/null
+++ b/dev-python/cadquery-pywrap/Manifest
@@ -0,0 +1 @@
+DIST cadquery-pywrap-7.5.2_rc20210526.tar.gz 5584220 BLAKE2B b26fd4092f94e3d3eec191c0791faf29d90da2d85f9aa9a2f1cdf128975564db9f6b6002661eed8bbecddb31988ad2076a3a00ea601a43e38ffaa47e545911ca SHA512 40aa61e0774228c70c8ae41a6078a280d63697d297234dbff51ec84982b4a9f0a09db41c74a834ae91d01881a4d5660b1ebbb701d24141307a5fedcdfb075872
diff --git a/dev-python/cadquery-pywrap/cadquery-pywrap-7.5.2_rc20210526.ebuild b/dev-python/cadquery-pywrap/cadquery-pywrap-7.5.2_rc20210526.ebuild
new file mode 100644
index 000000000..fc97f9db1
--- /dev/null
+++ b/dev-python/cadquery-pywrap/cadquery-pywrap-7.5.2_rc20210526.ebuild
@@ -0,0 +1,70 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{8..9} )
+
+inherit llvm toolchain-funcs distutils-r1
+
+DESCRIPTION="C++ binding generator based on libclang and pybind11"
+HOMEPAGE="https://github.com/CadQuery/pywrap"
+
+#FIXME: Uncomment on bumping to the next stable release.
+# MY_PN=occt
+# MY_PV=$(ver_cut 1-2)
+# MY_P="${MY_PN}${MY_PV}"
+# SRC_URI="https://github.com/CadQuery/pywrap/archive/refs/tags/${MY_P}.tar.gz"
+
+# The official pywrap 7.4.0 tarball is broken, but pywrap 7.5.2 has yet to be
+# officially released. We instead package a commit known to work as expected.
+MY_COMMIT="f8869e5a47fd3e3e1d31e7ab89b46c158f7487bf"
+SRC_URI="https://github.com/CadQuery/pywrap/archive/${MY_COMMIT}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="Apache-2.0"
+KEYWORDS="~amd64 ~x86"
+SLOT="0"
+
+# Dependencies are intentionally listed in "setup.py" order.
+RDEPEND="
+ dev-python/click[${PYTHON_USEDEP}]
+ dev-python/logzero[${PYTHON_USEDEP}]
+ dev-python/path-py[${PYTHON_USEDEP}]
+ dev-python/clang-python[${PYTHON_USEDEP}]
+ dev-python/cymbal[${PYTHON_USEDEP}]
+ dev-python/toml[${PYTHON_USEDEP}]
+ dev-python/pandas[${PYTHON_USEDEP}]
+ >=dev-python/joblib-1.0.0[${PYTHON_USEDEP}]
+ dev-python/tqdm[${PYTHON_USEDEP}]
+ dev-python/jinja[${PYTHON_USEDEP}]
+ dev-python/toposort[${PYTHON_USEDEP}]
+ dev-python/pyparsing[${PYTHON_USEDEP}]
+ dev-python/pybind11[${PYTHON_USEDEP}]
+ dev-python/schema[${PYTHON_USEDEP}]
+ sci-libs/vtk
+"
+DEPEND="${RDEPEND}"
+
+S="${WORKDIR}/pywrap-${MY_COMMIT}"
+
+src_prepare() {
+ # Relax Jinja version requirements. See also upstream pull request:
+ # https://github.com/CadQuery/pywrap/pull/34
+ sed -i -e "s~'jinja2==\\(.*\\)',~'jinja2>=\\1,<4',~" setup.py || die
+ sed -i \
+ -e 's~^\({%- macro super(cls,classes,typedefs\)\() -%}\)$~\1=[]\2~' \
+ bindgen/macros.j2 || die
+
+ #FIXME: Submit an upstream issue. This violates PEP 440 standards.
+ # Sanitize the "bindgen" version to avoid Gentoo QA notices.
+ sed -i -e 's~\(version=\)"0.1dev"~\1"'$(ver_rs 3 '')'"~' setup.py || die
+
+ # Replace conda- with Gentoo-specific prefix dirnames.
+ sed -i -e "s~\\bgetenv('CONDA_PREFIX')~'${EPREFIX}/usr'~" bindgen/*.py ||
+ die
+
+ # Reduce all hardcoded header includes to noops.
+ sed -i -e 's~rv\.append(Path(prefix).*~True~' bindgen/utils.py || die
+
+ distutils-r1_src_prepare
+}
diff --git a/dev-java/netcdf/metadata.xml b/dev-python/cadquery-pywrap/metadata.xml
index 15eb5729e..aef989a0c 100644
--- a/dev-java/netcdf/metadata.xml
+++ b/dev-python/cadquery-pywrap/metadata.xml
@@ -5,8 +5,8 @@
<email>sci@gentoo.org</email>
<name>Gentoo Science Project</name>
</maintainer>
- <longdescription lang="en">
-The NetCDF-Java Library is a Java interface to NetCDF files,
-as well as to many other types of scientific data formats.
-</longdescription>
+ <stabilize-allarches/>
+ <upstream>
+ <remote-id type="github">CadQuery/pywrap</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/dev-python/cymbal/Manifest b/dev-python/cymbal/Manifest
new file mode 100644
index 000000000..600b61b10
--- /dev/null
+++ b/dev-python/cymbal/Manifest
@@ -0,0 +1 @@
+DIST cymbal-1.0.0.tar.gz 4145 BLAKE2B b6da0ce4e32f19f0a91c7e4d917b13c64f1d0d9b37503962b5d73f6b00a37a54637c5d4ebf95d64952e32df2e7652076bde37a51dc316549775c59ea2ab50bb3 SHA512 0bd6bf5996787c5e24d9f9266654b4a501d5479dd1444d064c6a2241ce3e39ddbc12552f4cf22c03e61ba47f0492dc8a6515bb934bcc3523b5a29cb1a4530348
diff --git a/dev-python/cymbal/cymbal-1.0.0.ebuild b/dev-python/cymbal/cymbal-1.0.0.ebuild
new file mode 100644
index 000000000..a16fcd44c
--- /dev/null
+++ b/dev-python/cymbal/cymbal-1.0.0.ebuild
@@ -0,0 +1,34 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+
+inherit distutils-r1
+
+DESCRIPTION="Add functionality missing from the python libclang bindings"
+HOMEPAGE="https://pypi.org/project/cymbal"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="dev-python/clang-python[${PYTHON_USEDEP}]"
+RDEPEND="${DEPEND}"
+
+distutils_enable_tests pytest
+
+# Prevent "setup.py" from installing the "tests" package.
+src_prepare() {
+ sed -i -e 's~\(packages = \)find_packages(),~\1["cymbal"],~' \
+ setup.py || die
+
+ default_src_prepare
+}
+
+# Omit "test_class_template_arg", failing due to outdated clang assumptions.
+python_test() {
+ pytest -k 'not test_class_template_arg' || die
+}
diff --git a/dev-python/cymbal/metadata.xml b/dev-python/cymbal/metadata.xml
new file mode 100644
index 000000000..02975a0d9
--- /dev/null
+++ b/dev-python/cymbal/metadata.xml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <stabilize-allarches/>
+ <upstream>
+ <remote-id type="pypi">cymbal</remote-id>
+ <remote-id type="github">AndrewWalker/cymbal</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/dnaio/Manifest b/dev-python/dnaio/Manifest
index f217a4f43..d56f36ebe 100644
--- a/dev-python/dnaio/Manifest
+++ b/dev-python/dnaio/Manifest
@@ -1,3 +1,4 @@
DIST dnaio-0.4.2.tar.gz 125495 BLAKE2B 8034cbf2951345d7be0c0041d6ea24fc16d8e11669e04659216cd9551bc3da00b33a1c89e3b5453884e808c217b7d0ec232617da524037d834081ae3ae37f4e2 SHA512 9cd5d150fe49f6887bc3ac92975f2ec7d8f07370cfc8d8f8d556ad7b2143340c65bde87c80e02396358ea644a891dab39384641a143879e31328bfffff4c21b6
DIST dnaio-0.4.3.tar.gz 126329 BLAKE2B 03c1f0d77d1c9452ec16e2fcf50312b24ac932fbe120462d2ac8cea26a0d0ed0f6b2f65c0a1570ba116e81fd59d57469e44b9a17112a03f704d6a906802528be SHA512 79a015c3ab61b9608cace1e435ca0d749ab67bf8b6acffb1b8cafcf2614061b46254c63583e44d7995ba4548bcd19e476297a66a20aa530eb98b6cda09690e64
DIST dnaio-0.5.0.tar.gz 126321 BLAKE2B b26dc2e8f65efcc4aebe42f3ef252cc54a2c91beed65d060b51fbf4a6f3364325f884cf5d2e8269e1424d575200e4e716bc0a111c150ee403ead4cc176ed9ea6 SHA512 2e6a0dd04558b70ee08a81fd1d118525734df52701735cc27bab4c423c2030ec2fb6e83ddf02c491e1eb250c471d230b8fa72993c3a20ae844716c9542059c67
+DIST dnaio-0.5.1.tar.gz 126820 BLAKE2B d6e89ddceeb14ed50022f14e16c071e15af9bf832478dddfb4b6c086579822ea8b682f8e2c868a9f26a87637aae6959d822a8d9788ba980073740fe2e89c69fc SHA512 127e3dcc8291c21e8adce71211692e9c2284d49df336bb923c53fc5fea7dcb9d9b9f047f95642f3300240dac3d43cf6e987b3148b4ffa239d70f3b6c7ef043a5
diff --git a/dev-python/dnaio/dnaio-0.5.1.ebuild b/dev-python/dnaio/dnaio-0.5.1.ebuild
new file mode 100644
index 000000000..2a7885b90
--- /dev/null
+++ b/dev-python/dnaio/dnaio-0.5.1.ebuild
@@ -0,0 +1,22 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{7..9} )
+inherit distutils-r1
+
+DESCRIPTION="efficient reader for FASTA and FASTQ files"
+HOMEPAGE="https://pypi.python.org/pypi/xopen"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+ ${PYTHON_DEPS}
+ dev-python/xopen
+"
+
+# no tests in package
diff --git a/dev-python/gffpandas/Manifest b/dev-python/gffpandas/Manifest
new file mode 100644
index 000000000..8d84e74c6
--- /dev/null
+++ b/dev-python/gffpandas/Manifest
@@ -0,0 +1 @@
+DIST gffpandas-1.2.0.tar.gz 32040 BLAKE2B 66f53357876d417997366cdcbacd778f2b17e7df113d21f2a836b082719f549ede5e06a9a6c46e9c5bee2d86946871e68ab1f9b7af0defcaa8a55ae8ef93b274 SHA512 feb67ea93a078547103c1c6b8f32bd6bbd69ab669b93b90aa5f48bc0ebc25ea23e35130976bf1a89ff5e92fdbd054c4df98cc961278c7caaf28b48c202a662d7
diff --git a/dev-python/gffpandas/gffpandas-1.2.0.ebuild b/dev-python/gffpandas/gffpandas-1.2.0.ebuild
new file mode 100644
index 000000000..12ec9927c
--- /dev/null
+++ b/dev-python/gffpandas/gffpandas-1.2.0.ebuild
@@ -0,0 +1,29 @@
+# Copyright 2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{8..10} )
+
+inherit distutils-r1
+
+DESCRIPTION="Python library to Filter and sort GFF3 annotations"
+HOMEPAGE="https://github.com/foerstner-lab/gffpandas
+ https://gffpandas.readthedocs.io/en/latest/"
+SRC_URI="https://github.com/foerstner-lab/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="ISC"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="dev-python/pandas[${PYTHON_USEDEP}]"
+
+distutils_enable_tests pytest
+distutils_enable_sphinx docs/source dev-python/sphinx_rtd_theme
+
+python_prepare_all() {
+ # Do not depend on pytest-runner
+ sed -i -e '/pytest-runner/d' setup.py || die
+
+ distutils-r1_python_prepare_all
+}
diff --git a/sci-biology/StarORF/metadata.xml b/dev-python/gffpandas/metadata.xml
index 138cb7705..c3d31ba1d 100644
--- a/sci-biology/StarORF/metadata.xml
+++ b/dev-python/gffpandas/metadata.xml
@@ -9,4 +9,8 @@
<email>sci-biology@gentoo.org</email>
<name>Gentoo Biology Project</name>
</maintainer>
+ <upstream>
+ <remote-id type="github">foerstner-lab/gffpandas</remote-id>
+ <remote-id type="pypi">gffpandas</remote-id>
+ </upstream>
</pkgmetadata>
diff --git a/dev-python/kmapper/Manifest b/dev-python/kmapper/Manifest
index 306e9b399..61c31630b 100644
--- a/dev-python/kmapper/Manifest
+++ b/dev-python/kmapper/Manifest
@@ -1 +1,2 @@
DIST kmapper-1.4.1.tar.gz 100655 BLAKE2B 7321266be9fea509da054a481328178bd5bb5403b60f09b64ece4ef1fa54713a5f9b292553b87385464b52e82407461659575d7bd5d2b6038b69d500b934da77 SHA512 dc760c7b3c838d44f4b96ba744f03482e4495bb4341380aa4448c57a1292c6d8d95a9e7fb8bd9171a26e56677e578c1a8002fd429166fe87a60a8313fada7e4a
+DIST kmapper-2.0.1.tar.gz 6686101 BLAKE2B 8afa79a2479370c335debb4cee7375b0d47b0e79d02649ff53681d006e2a80cd6175f8aeb3c3a6fa0ac32d0cf30ba8217d348f6158b9ee1bc7c683d0a5b4290e SHA512 751f02ee3f5a55eb74b55b0a9204e54d05c9af2a816f8070082a73d4213c1fb7842e41e3e27316d69efaa2cf3e2f9b2d967870905ace8d9e9a3e67f9ea181ed2
diff --git a/dev-python/kmapper/kmapper-2.0.1.ebuild b/dev-python/kmapper/kmapper-2.0.1.ebuild
new file mode 100644
index 000000000..2099fa4db
--- /dev/null
+++ b/dev-python/kmapper/kmapper-2.0.1.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{7..9} )
+
+inherit distutils-r1
+
+DESCRIPTION="Python implementation of Mapper algorithm for Topological Data Analysis"
+HOMEPAGE="https://kepler-mapper.scikit-tda.org"
+SRC_URI="https://github.com/scikit-tda/kepler-mapper/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}"/kepler-mapper-${PV}
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="${PYTHON_DEPS}
+ dev-python/jinja[${PYTHON_USEDEP}]
+ dev-python/joblib[${PYTHON_USEDEP}]
+ dev-python/markupsafe[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/plotly[${PYTHON_USEDEP}]
+ dev-python/python-igraph[${PYTHON_USEDEP}]
+ sci-libs/scikit-learn[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+ test? (
+ dev-python/networkx[${PYTHON_USEDEP}]
+ dev-python/matplotlib[${PYTHON_USEDEP}]
+ dev-python/ipywidgets[${PYTHON_USEDEP}]
+ )
+"
+
+distutils_enable_tests pytest
+
+python_prepare_all() {
+ rm "${S}"/test/test_plotly.py || die
+ distutils-r1_python_prepare_all
+}
diff --git a/dev-python/logzero/Manifest b/dev-python/logzero/Manifest
new file mode 100644
index 000000000..73c1e0244
--- /dev/null
+++ b/dev-python/logzero/Manifest
@@ -0,0 +1 @@
+DIST logzero-1.7.0.tar.gz 577803 BLAKE2B d54c16ee55e105bf026695dcac21065f58f04bc1d6a66d0d80f4a8f2a0dddabbca8c901dd596643977010ca1aae29fddaf194ef8f2882fd6660b764ce9070d98 SHA512 6c9647e81f16479a09b11383a9b6e7fb1068e61007cf9884d59469535706850a4ef2893d7393feb68dcdeb0793dcb8c41f8f3865289792de97dd20a5d32224bb
diff --git a/dev-python/logzero/logzero-1.7.0.ebuild b/dev-python/logzero/logzero-1.7.0.ebuild
new file mode 100644
index 000000000..717426899
--- /dev/null
+++ b/dev-python/logzero/logzero-1.7.0.ebuild
@@ -0,0 +1,18 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} pypy3 )
+
+inherit distutils-r1
+
+DESCRIPTION="Robust and effective logging for Python 2 and 3"
+HOMEPAGE="https://pypi.org/project/logzero"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+distutils_enable_tests pytest
diff --git a/dev-python/logzero/metadata.xml b/dev-python/logzero/metadata.xml
new file mode 100644
index 000000000..3bdc37964
--- /dev/null
+++ b/dev-python/logzero/metadata.xml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <stabilize-allarches/>
+ <upstream>
+ <remote-id type="pypi">logzero</remote-id>
+ <remote-id type="github">metachris/logzero</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/meshio/Manifest b/dev-python/meshio/Manifest
new file mode 100644
index 000000000..191a8e4aa
--- /dev/null
+++ b/dev-python/meshio/Manifest
@@ -0,0 +1 @@
+DIST meshio-4.4.6.tar.gz 482071 BLAKE2B f8d410ad7293b5e7f9debbb1e4dc9050304731bee1091b4480aeace006a92bb8f7cec2fc442d0f5b20d492ae859bb76cbb52b6be26f06be2558bc42a27d9cd96 SHA512 624f551b017b6c4e44efc5db0fb6d08a161ceef64d1317264eaf3ba0f36202b93c3fa959ab34ce8212c01083ae570b3db25c7445eee2d51feaf84726984e2770
diff --git a/dev-python/meshio/meshio-4.4.6.ebuild b/dev-python/meshio/meshio-4.4.6.ebuild
new file mode 100644
index 000000000..ec5af300f
--- /dev/null
+++ b/dev-python/meshio/meshio-4.4.6.ebuild
@@ -0,0 +1,26 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{8..9} )
+DISTUTILS_USE_SETUPTOOLS=pyproject.toml
+
+inherit distutils-r1
+
+DESCRIPTION="Python input/output for many mesh formats"
+HOMEPAGE="https://pypi.org/project/meshio"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="MIT"
+KEYWORDS="~amd64 ~x86"
+SLOT="0"
+
+BDEPEND="
+ test? (
+ dev-python/h5py[${PYTHON_USEDEP}]
+ dev-python/netcdf4-python[${PYTHON_USEDEP}]
+ )
+"
+
+distutils_enable_tests pytest
diff --git a/dev-python/meshio/metadata.xml b/dev-python/meshio/metadata.xml
new file mode 100644
index 000000000..1bfb9f30f
--- /dev/null
+++ b/dev-python/meshio/metadata.xml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <stabilize-allarches/>
+ <upstream>
+ <remote-id type="pypi">meshio</remote-id>
+ <remote-id type="github">nschloe/meshio</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/numba/numba-0.53.1.ebuild b/dev-python/numba/numba-0.53.1.ebuild
index 7cd6dfe9c..d1ee3f0b7 100644
--- a/dev-python/numba/numba-0.53.1.ebuild
+++ b/dev-python/numba/numba-0.53.1.ebuild
@@ -18,13 +18,20 @@ SLOT="0"
KEYWORDS="~amd64 ~arm ~arm64 ~x86"
IUSE="openmp threads"
+# Minimum dependency versions derive from:
+# * For llvmlite, the "min_llvmlite_version" and "max_llvmlite_version" globals
+# in "setup.py".
+# * For NumPy, the "min_numpy_run_version" global in "setup.py".
+# * For TBB, #error pragmas in "numba/np/ufunc/tbbpool.cpp" like:
+# #error "TBB version is too old, 2019 update 5...
+# Lastly, note the "numba -s" subcommand requires "pip" at runtime.
RDEPEND="
>=dev-python/llvmlite-0.36.0[${PYTHON_USEDEP}]
<dev-python/llvmlite-0.37.0
- dev-python/numpy[${PYTHON_USEDEP}]
+ >=dev-python/numpy-1.15.0[${PYTHON_USEDEP}]
dev-python/pip[${PYTHON_USEDEP}]
dev-python/scipy[${PYTHON_USEDEP}]
- threads? ( dev-cpp/tbb )
+ threads? ( >=dev-cpp/tbb-2019.5 )
"
DEPEND="${RDEPEND}"
@@ -51,6 +58,13 @@ pkg_setup() {
fi
}
+python_compile() {
+ # FIXME: parallel python building fails. See Portage bug #614464 and
+ # gentoo/sci issue #1080.
+ export MAKEOPTS=-j1
+ distutils-r1_python_compile
+}
+
# https://numba.pydata.org/numba-doc/latest/developer/contributing.html?highlight=test#running-tests
python_test() {
distutils_install_for_testing
diff --git a/dev-python/persim/Manifest b/dev-python/persim/Manifest
index 975f7da82..44487ab15 100644
--- a/dev-python/persim/Manifest
+++ b/dev-python/persim/Manifest
@@ -1,2 +1,4 @@
DIST persim-0.1.3.tar.gz 24345 BLAKE2B df407f22226797274e64766fac98733a7c006b7577bd21432bd109f17674192b1e520744e897b5baa207aef2f9bedaa6beab6412d550090c21072860c9a9f2d1 SHA512 4d177367213353eac3bd57b1450bace3ded25480b256f700d1d5daf7f8fc63204af3bdff45f71c85d8ac4a2d3f923fac00a568d43753b321c25ab98e77010349
DIST persim-0.2.0.tar.gz 35005 BLAKE2B c3399ec13274e7fd105dccf5abdf85b973ec387196fd8659636173fa4e19bb6d8b9d8dba10d1382239d32d938a6f472b9201c7a54df7924802af3adc40d8aa8a SHA512 0bcfcc2fbf8d0449d680a8805281d01481513c060fa9ecc5f3d44ed70cda791d625bfe77fee954a186f77032f6447907f987c679a2c3bd7adc17a46eb753d083
+DIST persim-0.3.0.tar.gz 49716 BLAKE2B 8cea73e9486ecebfc5f73975341e6094d1c374d3c13b3b849988357ebec7d77ce4f59512388e7748b83c67fe32d3481dc1c9d7a74984d5faa7f8928bfcd282dd SHA512 575f21e8ae2cac7a609d8eb3691f1e7550139be2c0cbb63ff3dceefd923e42888b1ca40eef39c631e1351cdbe3c1c5a4371f4a61f0075588b13ced98ae2663a2
+DIST persim-0.3.1.tar.gz 50438 BLAKE2B 774f0adc67ec6af7e297e73a75a3c4eb6004b0ec43d685eca29e20b0b6ef214fafed638e4c1c6eb10b5dad0b836883f3396c6ed323d4530d832c2e655f5353c2 SHA512 b35884d202a98449b719527987fdf07b88b42252d403f7f0b18a2507f63db496d49e389eca5019c540ebcdc99b63b07df73f43bc7780488a6e7e6958e0017b70
diff --git a/dev-python/persim/persim-0.3.0.ebuild b/dev-python/persim/persim-0.3.0.ebuild
new file mode 100644
index 000000000..6e1d989aa
--- /dev/null
+++ b/dev-python/persim/persim-0.3.0.ebuild
@@ -0,0 +1,28 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{7..9} )
+
+inherit distutils-r1
+
+DESCRIPTION="Distances and representations of persistence diagrams"
+HOMEPAGE="https://persim.scikit-tda.org/"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="${PYTHON_DEPS}
+ dev-python/hopcroftkarp[${PYTHON_USEDEP}]
+ dev-python/matplotlib[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/plotly[${PYTHON_USEDEP}]
+ dev-python/scipy[${PYTHON_USEDEP}]
+ sci-libs/scikit-learn[${PYTHON_USEDEP}]
+"
+BDEPEND="test? ( dev-python/deprecated[${PYTHON_USEDEP}] )"
+
+distutils_enable_tests pytest
diff --git a/dev-python/persim/persim-0.3.1.ebuild b/dev-python/persim/persim-0.3.1.ebuild
new file mode 100644
index 000000000..6e1d989aa
--- /dev/null
+++ b/dev-python/persim/persim-0.3.1.ebuild
@@ -0,0 +1,28 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{7..9} )
+
+inherit distutils-r1
+
+DESCRIPTION="Distances and representations of persistence diagrams"
+HOMEPAGE="https://persim.scikit-tda.org/"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="${PYTHON_DEPS}
+ dev-python/hopcroftkarp[${PYTHON_USEDEP}]
+ dev-python/matplotlib[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/plotly[${PYTHON_USEDEP}]
+ dev-python/scipy[${PYTHON_USEDEP}]
+ sci-libs/scikit-learn[${PYTHON_USEDEP}]
+"
+BDEPEND="test? ( dev-python/deprecated[${PYTHON_USEDEP}] )"
+
+distutils_enable_tests pytest
diff --git a/dev-python/pybind11-stubgen/Manifest b/dev-python/pybind11-stubgen/Manifest
index 8a752c6dd..57271a3a5 100644
--- a/dev-python/pybind11-stubgen/Manifest
+++ b/dev-python/pybind11-stubgen/Manifest
@@ -1 +1,2 @@
DIST pybind11-stubgen-0.8.6.tar.gz 10993 BLAKE2B f3073dac1bff941cbf2470d50d11a090a99ff335a08cca3efc217d06c3a0cab266cf9769a1a7bdc5349da7cc3120e8a6b54f60df775ee27fcfbf0b5003867726 SHA512 6a8338f78d636b865bb76a3e769997f1c781acb57a0bb4f68f59ae2d6f3c60efe2b2ec7a9034f4e172b3d4bc4c74c990a4a24c6b2df242573fa7f03b97a84851
+DIST pybind11-stubgen-0.8.7.tar.gz 10993 BLAKE2B e672e955535bb7d797a3ee692f3fb13658d589bedc60c207dc094efff2e6281aec81636b0719a61567be46eb2fb27b7235e38cc06c436dea2689ae32b4b53b18 SHA512 56f3d84027d7cb06cce608ac7403a3fea902277d6e44fa3e284227656bca036ba956ef6b51a4f963a0b19e8fe30c0ddfac6670ea338905bf3ac39668748da668
diff --git a/dev-python/pybind11-stubgen/pybind11-stubgen-0.8.7.ebuild b/dev-python/pybind11-stubgen/pybind11-stubgen-0.8.7.ebuild
new file mode 100644
index 000000000..3f2b0f779
--- /dev/null
+++ b/dev-python/pybind11-stubgen/pybind11-stubgen-0.8.7.ebuild
@@ -0,0 +1,24 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{7..9} )
+DISTUTILS_USE_SETUPTOOLS=rdepend
+inherit distutils-r1
+
+DESCRIPTION="PEP 561 type stubs generator for pybind11 modules"
+HOMEPAGE="https://github.com/sizmailov/pybind11-stubgen"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="
+ ${PYTHON_DEPS}
+ dev-python/pybind11[${PYTHON_USEDEP}]
+"
+RDEPEND="${DEPEND}"
+
+# no tests in package
diff --git a/dev-python/pynndescent/Manifest b/dev-python/pynndescent/Manifest
index e7ea7da50..d3d33643f 100644
--- a/dev-python/pynndescent/Manifest
+++ b/dev-python/pynndescent/Manifest
@@ -1,3 +1 @@
-DIST pynndescent-0.4.8.tar.gz 1134120 BLAKE2B bb82bf27edee6bb5f92e7ba9c762ffadffd16854450d28c2eda416b98ff0e67127860347748c663a094ddad44027db312b935a49fa60604146a9df1620edffe1 SHA512 e85feed2cc78e9a4364a61ce3c03b029dd0db643b4d9e7efa14dfda90e6e2512ba7a4dc083b440696b070262e2111f50b6dcb41915e26fe8d8332b47837ad9fc
-DIST pynndescent-0.5.1.tar.gz 1138551 BLAKE2B 175fcc284f61f1aa4704587b8dc5fbdf356d75be79b878a7f64ec807e32f241f0c0c94bb689de64f8117e7b593f439564731cba3d2247093a98a4273a05a9e4f SHA512 15694cbed64b86d48aa70a5ccda57b21fe040fca147e367d81bf527a7c329c80b7bd0f46f09612236c470fee0d35c7f48cb42e6476f6fc022ab8612321a7cd95
DIST pynndescent-0.5.2.tar.gz 1148182 BLAKE2B 64cff5fe0d92b2d735564b7e3a1dc62c64bcaec33d8d5bfaffbcf61423ff1cef388dd2335479dff5af7f50848dbe8d9640a22add54b2b90a979cb13d0894b371 SHA512 b38bbf8aab91d4278572a6446e4750022e2b2bc82e7a8f7754b8ec74c0ae1f7795364ef4e22cd6bd39071056ebacaedeb79981620e3143d3c9060a1520c85aae
diff --git a/dev-python/pynndescent/pynndescent-0.4.8.ebuild b/dev-python/pynndescent/pynndescent-0.4.8.ebuild
deleted file mode 100644
index 49c6afa23..000000000
--- a/dev-python/pynndescent/pynndescent-0.4.8.ebuild
+++ /dev/null
@@ -1,27 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{6..8} )
-
-inherit distutils-r1
-
-DESCRIPTION="nearest neighbor descent for approximate nearest neighbors"
-HOMEPAGE="https://github.com/lmcinnes/pynndescent"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="${PYTHON_DEPS}
- dev-python/joblib[${PYTHON_USEDEP}]
- >=dev-python/numba-0.51.2[${PYTHON_USEDEP}]
- >=dev-python/llvmlite-0.34[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
- <=sci-libs/scikit-learn-0.24.0[${PYTHON_USEDEP}]
-"
-DEPEND="${RDEPEND}"
-
-distutils_enable_tests nose
diff --git a/dev-python/pynndescent/pynndescent-0.5.1.ebuild b/dev-python/pynndescent/pynndescent-0.5.1.ebuild
deleted file mode 100644
index 49c6afa23..000000000
--- a/dev-python/pynndescent/pynndescent-0.5.1.ebuild
+++ /dev/null
@@ -1,27 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{6..8} )
-
-inherit distutils-r1
-
-DESCRIPTION="nearest neighbor descent for approximate nearest neighbors"
-HOMEPAGE="https://github.com/lmcinnes/pynndescent"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="${PYTHON_DEPS}
- dev-python/joblib[${PYTHON_USEDEP}]
- >=dev-python/numba-0.51.2[${PYTHON_USEDEP}]
- >=dev-python/llvmlite-0.34[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
- <=sci-libs/scikit-learn-0.24.0[${PYTHON_USEDEP}]
-"
-DEPEND="${RDEPEND}"
-
-distutils_enable_tests nose
diff --git a/dev-python/pynndescent/pynndescent-0.5.2.ebuild b/dev-python/pynndescent/pynndescent-0.5.2.ebuild
index 894f3114f..3eeb7ae79 100644
--- a/dev-python/pynndescent/pynndescent-0.5.2.ebuild
+++ b/dev-python/pynndescent/pynndescent-0.5.2.ebuild
@@ -3,7 +3,7 @@
EAPI=7
-PYTHON_COMPAT=( python3_{6..8} )
+PYTHON_COMPAT=( python3_{8..9} )
inherit distutils-r1
@@ -19,9 +19,9 @@ RDEPEND="${PYTHON_DEPS}
dev-python/joblib[${PYTHON_USEDEP}]
>=dev-python/numba-0.51.2[${PYTHON_USEDEP}]
>=dev-python/llvmlite-0.34[${PYTHON_USEDEP}]
- dev-python/scipy[${PYTHON_USEDEP}]
- <=sci-libs/scikit-learn-0.24.0[${PYTHON_USEDEP}]
+ >=dev-python/scipy-1.0[${PYTHON_USEDEP}]
+ >=sci-libs/scikit-learn-0.18.0[${PYTHON_USEDEP}]
"
DEPEND="${RDEPEND}"
-distutils_enable_tests nose
+distutils_enable_tests pytest
diff --git a/dev-python/pyvista/Manifest b/dev-python/pyvista/Manifest
new file mode 100644
index 000000000..b4d7a9196
--- /dev/null
+++ b/dev-python/pyvista/Manifest
@@ -0,0 +1 @@
+DIST pyvista-0.31.1.tar.gz 1249426 BLAKE2B 1f52f5bf5a5bc7bee1197a8b31c8806eae9c6ca03f45b8db601625134f9ce8fd301bc8032923f31ae0e75292c1126fb65076e48a5bc11f6838d6d2b42c75fddf SHA512 f184f667759bf85801831372a91e12617c223c745c2acf778cb7b42f6a1812719714caba322ff3013cb2ed0cb32f72ddcdb279989e93b67fe8a503b85314da71
diff --git a/dev-python/pyvista/metadata.xml b/dev-python/pyvista/metadata.xml
new file mode 100644
index 000000000..0137fea97
--- /dev/null
+++ b/dev-python/pyvista/metadata.xml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <stabilize-allarches/>
+ <upstream>
+ <remote-id type="pypi">pyvista</remote-id>
+ <remote-id type="github">pyvista/pyvista</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/pyvista/pyvista-0.31.1.ebuild b/dev-python/pyvista/pyvista-0.31.1.ebuild
new file mode 100644
index 000000000..1ba6d0882
--- /dev/null
+++ b/dev-python/pyvista/pyvista-0.31.1.ebuild
@@ -0,0 +1,32 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{8..9} )
+DISTUTILS_SINGLE_IMPL=1 # because "sci-libs/vtk" inherits "python-single-r1"
+
+inherit distutils-r1
+
+DESCRIPTION="Easier Pythonic interface to VTK"
+HOMEPAGE="https://docs.pyvista.org"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="MIT"
+KEYWORDS="~amd64 ~x86"
+SLOT="0"
+
+RDEPEND="
+ sci-libs/vtk[python,imaging,rendering,views,${PYTHON_SINGLE_USEDEP}]
+ $(python_gen_cond_dep '
+ dev-python/appdirs[${PYTHON_USEDEP}]
+ dev-python/imageio[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/pillow[${PYTHON_USEDEP}]
+ !>=dev-python/meshio-5.0.0[${PYTHON_USEDEP}]
+ >=dev-python/meshio-4.0.3[${PYTHON_USEDEP}]
+ >=dev-python/scooby-0.5.1[${PYTHON_USEDEP}]
+ >=dev-python/transforms3d-0.3.1[${PYTHON_USEDEP}]
+ ')
+"
+DEPEND="${RDEPEND}"
diff --git a/dev-python/pyzotero/Manifest b/dev-python/pyzotero/Manifest
deleted file mode 100644
index 6ad97eb8e..000000000
--- a/dev-python/pyzotero/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST pyzotero-1.4.20.tar.gz 520010 BLAKE2B c2330997d454f874c91a700bfc6c15dac6a8fc760ad5b5724b32f6550b51a39a3ef2d83ee7057c1546ab01531d7fa845002bee6a2edaad61f27bb7d8f0ca5cd4 SHA512 7cd72b7d0586a601a0a57992c52bbd81f90716117d697dadd724389bfb08eab2ddd813d495f133e25563de5798c5c94ee51214304da930a37dff2a721745af5f
diff --git a/dev-python/pyzotero/metadata.xml b/dev-python/pyzotero/metadata.xml
deleted file mode 100644
index 0ed74d1c3..000000000
--- a/dev-python/pyzotero/metadata.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version='1.0' encoding='UTF-8'?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>andrewammerlaan@riseup.net</email>
- <name>Andrew Ammerlaan</name>
- </maintainer>
- <upstream>
- <remote-id type="github">urschrei/pyzotero</remote-id>
- <remote-id type="pypi">Pyzotero</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/dev-python/pyzotero/pyzotero-1.4.20.ebuild b/dev-python/pyzotero/pyzotero-1.4.20.ebuild
deleted file mode 100644
index 7d0ca2e14..000000000
--- a/dev-python/pyzotero/pyzotero-1.4.20.ebuild
+++ /dev/null
@@ -1,39 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7,8,9} )
-
-inherit distutils-r1
-
-DESCRIPTION="A Python client for the Zotero API"
-HOMEPAGE="https://github.com/urschrei/pyzotero"
-SRC_URI="https://github.com/urschrei/pyzotero/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64"
-
-RDEPEND="
- app-text/zotero-bin
- dev-python/bibtexparser[${PYTHON_USEDEP}]
- <dev-python/feedparser-6[${PYTHON_USEDEP}]
- dev-python/pathlib2[${PYTHON_USEDEP}]
- dev-python/pytz[${PYTHON_USEDEP}]
- dev-python/requests[${PYTHON_USEDEP}]
-"
-
-BDEPEND="
- dev-python/httpretty[${PYTHON_USEDEP}]
-"
-
-distutils_enable_sphinx doc --no-autodoc
-distutils_enable_tests pytest
-
-python_prepare_all() {
- # do not install tests
- sed -i "s/find_packages(),/find_packages(exclude=('test*')),/g" setup.py || die
-
- distutils-r1_python_prepare_all
-}
diff --git a/dev-python/schema/Manifest b/dev-python/schema/Manifest
new file mode 100644
index 000000000..e69b4b33b
--- /dev/null
+++ b/dev-python/schema/Manifest
@@ -0,0 +1 @@
+DIST schema-0.7.4.tar.gz 41340 BLAKE2B 3f897e7443da2a227e58e4f8655d75d2dfc9da95faca9f1737488ea7d95eefabf55c0606864164a7146d89fdb22cfb522e7e89bd648b001ac1cfe2e8e8ba4020 SHA512 6dd0ee8348fde4c6a9a39baf2b0fafff851f10ea581b16f438717d5435481f34829176bb4b82ecdd092da26332fd114fab856691b755ecf8e5648fb2233a0daf
diff --git a/dev-python/schema/metadata.xml b/dev-python/schema/metadata.xml
new file mode 100644
index 000000000..440ea4da1
--- /dev/null
+++ b/dev-python/schema/metadata.xml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <stabilize-allarches/>
+ <upstream>
+ <remote-id type="pypi">schema</remote-id>
+ <remote-id type="github">keleshev/schema</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/schema/schema-0.7.4.ebuild b/dev-python/schema/schema-0.7.4.ebuild
new file mode 100644
index 000000000..05e8712bb
--- /dev/null
+++ b/dev-python/schema/schema-0.7.4.ebuild
@@ -0,0 +1,28 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} pypy3 )
+
+inherit distutils-r1
+
+DESCRIPTION="Schema validation just got Pythonic"
+HOMEPAGE="https://pypi.org/project/schema"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+BDEPEND="test? ( dev-python/mock[${PYTHON_USEDEP}] )"
+
+distutils_enable_tests pytest
+
+src_prepare() {
+ distutils-r1_src_prepare
+
+ # Prevent schema from unconditionally requiring the last-rited contextlib2,
+ # which schema actually conditionally requires only under EOL Python 2.x.
+ sed -i -e '/\binstall_requires=/d' setup.py || die
+}
diff --git a/dev-python/scooby/Manifest b/dev-python/scooby/Manifest
new file mode 100644
index 000000000..0a16de485
--- /dev/null
+++ b/dev-python/scooby/Manifest
@@ -0,0 +1 @@
+DIST scooby-0.5.7.tar.gz 15770 BLAKE2B 08f9cf7c7e35c6c87cb80314b5287d2cbebaf46471e58e574d8f6725eb18fe95488c1043412a0abcd88040cb157713cb2076f425318c28ac02d3ad193df64b54 SHA512 4f8cc4c03c0af707115e11c11d6bbb5fb730d6221ff32598ad56e9592e1bcb2e22f56af189d05ca50fefcefd5262233594dd9b1d0dfd374d66f42700c7553d48
diff --git a/dev-python/scooby/metadata.xml b/dev-python/scooby/metadata.xml
new file mode 100644
index 000000000..c48aae2cf
--- /dev/null
+++ b/dev-python/scooby/metadata.xml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <stabilize-allarches/>
+ <upstream>
+ <remote-id type="pypi">scooby</remote-id>
+ <remote-id type="github">banesullivan/scooby</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/scooby/scooby-0.5.7.ebuild b/dev-python/scooby/scooby-0.5.7.ebuild
new file mode 100644
index 000000000..19d343eca
--- /dev/null
+++ b/dev-python/scooby/scooby-0.5.7.ebuild
@@ -0,0 +1,16 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{8..10} )
+
+inherit distutils-r1
+
+DESCRIPTION="Easily report Python package versions and hardware resources"
+HOMEPAGE="https://pypi.org/project/scooby"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="MIT"
+KEYWORDS="~amd64 ~x86"
+SLOT="0"
diff --git a/dev-python/texext/metadata.xml b/dev-python/texext/metadata.xml
index 9978dd68d..026cdb22b 100644
--- a/dev-python/texext/metadata.xml
+++ b/dev-python/texext/metadata.xml
@@ -1,8 +1,8 @@
<?xml version='1.0' encoding='UTF-8'?>
<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
<pkgmetadata>
- <maintainer type="person">
- <email>andrewammerlaan@riseup.net</email>
- <name>Andrew Ammerlaan</name>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
</maintainer>
</pkgmetadata>
diff --git a/dev-python/transforms3d/Manifest b/dev-python/transforms3d/Manifest
new file mode 100644
index 000000000..00bbff4f5
--- /dev/null
+++ b/dev-python/transforms3d/Manifest
@@ -0,0 +1 @@
+DIST transforms3d-0.3.1.tar.gz 62812 BLAKE2B 0f279bfd9cc6bac451ea311d4dc8eb779b391cbbb8a00169271838bbdbe2400a64d8d8f1a7bae91d48de36c2d49ab985f1cc87ea27d0a86b5a5760947e1b6d6d SHA512 bee42558d600f62a01b2ec08049a4680e278cff3b2c47bf9f12bc9f7d67d0b220895187d050678f347443ed02f41be0902ed1b14d976f4034bde7b849ffbc6dd
diff --git a/dev-python/transforms3d/metadata.xml b/dev-python/transforms3d/metadata.xml
new file mode 100644
index 000000000..594eae127
--- /dev/null
+++ b/dev-python/transforms3d/metadata.xml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <stabilize-allarches/>
+ <upstream>
+ <remote-id type="pypi">transforms3d</remote-id>
+ <remote-id type="github">matthew-brett/transforms3d</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/dev-python/transforms3d/transforms3d-0.3.1.ebuild b/dev-python/transforms3d/transforms3d-0.3.1.ebuild
new file mode 100644
index 000000000..ed719c6a5
--- /dev/null
+++ b/dev-python/transforms3d/transforms3d-0.3.1.ebuild
@@ -0,0 +1,23 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{8..10} )
+DISTUTILS_USE_SETUPTOOLS=no
+
+inherit distutils-r1
+
+DESCRIPTION="Functions for 3D coordinate transformations"
+HOMEPAGE="https://matthew-brett.github.io/transforms3d"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="BSD-2"
+KEYWORDS="~amd64 ~x86"
+SLOT="0"
+
+BDEPEND="test? ( dev-python/numpy[${PYTHON_USEDEP}] )"
+RDEPEND=">=dev-python/numpy-1.5.1[${PYTHON_USEDEP}]"
+DEPEND="${RDEPEND}"
+
+distutils_enable_tests nose
diff --git a/licenses/netCDF b/licenses/netCDF
deleted file mode 100644
index 780ba9ee5..000000000
--- a/licenses/netCDF
+++ /dev/null
@@ -1,31 +0,0 @@
-Copyright 1993-2012 University Corporation for Atmospheric Research/Unidata
-
-Portions of this software were developed by the Unidata Program at the
-University Corporation for Atmospheric Research.
-
-Access and use of this software shall impose the following obligations
-and understandings on the user. The user is granted the right, without
-any fee or cost, to use, copy, modify, alter, enhance and distribute
-this software, and any derivative works thereof, and its supporting
-documentation for any purpose whatsoever, provided that this entire
-notice appears in all copies of the software, derivative works and
-supporting documentation. Further, UCAR requests that the user credit
-UCAR/Unidata in any publications that result from the use of this
-software or in any product that includes this software, although this
-is not an obligation. The names UCAR and/or Unidata, however, may not
-be used in any advertising or publicity to endorse or promote any
-products or commercial entity unless specific written permission is
-obtained from UCAR/Unidata. The user also understands that
-UCAR/Unidata is not obligated to provide the user with any support,
-consulting, training or assistance of any kind with regard to the use,
-operation and performance of this software nor to provide the user
-with any updates, revisions, new versions or "bug fixes."
-
-THIS SOFTWARE IS PROVIDED BY UCAR/UNIDATA "AS IS" AND ANY EXPRESS OR
-IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
-WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
-DISCLAIMED. IN NO EVENT SHALL UCAR/UNIDATA BE LIABLE FOR ANY SPECIAL,
-INDIRECT OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING
-FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT,
-NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION
-WITH THE ACCESS, USE OR PERFORMANCE OF THIS SOFTWARE.
diff --git a/media-libs/embree-bin/Manifest b/media-libs/embree-bin/Manifest
index 18144a113..b884b5159 100644
--- a/media-libs/embree-bin/Manifest
+++ b/media-libs/embree-bin/Manifest
@@ -1,3 +1,4 @@
DIST embree-bin-3.12.0.tar.gz 95209715 BLAKE2B 74b6a9c94ff596ebab64b7f3a1e506a4b08afabf2c86823520004bb46d67d27d136e54e20e5ae238a261a9e14372139da8d5f22a8a5db3597c43a6dc78ba5140 SHA512 5cc69d9c9dacc15433a9b9a6d50893e6f4fd4146f0a0c805802504aa7c079c8960d8cacb6bbe61195d5ee61b6b688cc9b358e5c79951a7d8371ac39d5ded02c5
DIST embree-bin-3.12.1.tar.gz 95241868 BLAKE2B 6d65916a7bf95209269ee948d4dd1c2ee2218bd186f074501abd8086bdcaa5a270fa1cd8c3029763d1da746e375a29890b7c02577992edeaa8829d0b31ed0e0f SHA512 e8c8bc63e0c56360ef02c3794c18237151554d1ebcc761a50cc887bfbc4df528e56b27c4c83f7ca0fdf952b269e207b966ecc4ffbc159b75a2172541f8b5e3fe
DIST embree-bin-3.12.2.tar.gz 95365459 BLAKE2B 234aa46a6e6936591c8ad10a5bdb9f29107e1bb9a82b0f256ea23629344884fbee588dc7cf03c5bde8a8b479548cd350a645702a245452d40749b3a315357f27 SHA512 dc01aee95bef18561ec01cbc53f44c3765ffa7d25ff9289a647f86be81ab44916a6d8ba61e377de85026cac0f37eee7ccfc6c5e371cccc6d40289a8d44e4b70d
+DIST embree-bin-3.13.0.tar.gz 96162228 BLAKE2B 4cb0430beca487dba34b946e0d8f05c0f8d4cc19c373e68390b26efe5c8767282367fe13a662334da04cbb80588b36787344946954fbe4ccdf52d562c468cfc8 SHA512 f7bf28d6a50fcb5bb8ac3b87841fc8f23e78865b4be8217fc12268f2e831cdc088a97bd80f1721171ac7c7d772175a4b2bf22a48af5ad18b3835c02340435272
diff --git a/media-libs/embree-bin/embree-bin-3.13.0.ebuild b/media-libs/embree-bin/embree-bin-3.13.0.ebuild
new file mode 100644
index 000000000..a1cf40c1a
--- /dev/null
+++ b/media-libs/embree-bin/embree-bin-3.13.0.ebuild
@@ -0,0 +1,58 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="high-performance ray tracing kernels from intel"
+HOMEPAGE="https://github.com/embree/embree"
+SRC_URI="https://github.com/embree/embree/releases/download/v${PV}/embree-${PV}.x86_64.linux.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}"/embree-${PV}.x86_64.linux
+RESTRICT="mirror"
+
+LICENSE="Apache-2.0"
+KEYWORDS="~amd64"
+SLOT="0"
+RESTRICT="strip"
+
+QA_PREBUILT="
+ /opt/embree/bin/.*
+ /opt/embree/lib/.*
+"
+QA_PRESTRIPPED="${QA_PREBUILT}"
+
+RDEPEND="
+ dev-cpp/tbb
+ dev-lang/ispc
+ media-libs/glfw
+ media-libs/glu
+ virtual/jpeg:0
+ virtual/opengl
+ x11-libs/libxcb
+ x11-libs/libX11
+ x11-libs/libXau
+ x11-libs/libXdmcp
+"
+
+src_compile() {
+ true
+}
+
+src_install() {
+ dodir /opt/embree
+ cp -r "${S}"/* "${ED}"/opt/embree/ || die
+
+ doenvd "${FILESDIR}"/00embree_bin
+}
+
+pkg_postinst() {
+ elog "Embree has been installed to /opt/embree"
+ elog "you are all set to start using it as binary package"
+ elog "after you refresh your environment with"
+ elog " env-update && . /etc/profile"
+ elog "If you want to use embree as a library and wist to"
+ elog "do development using embree, you need to source"
+ elog "the appropriate shell script from either"
+ elog " . /opt/embree/embree-vars.sh"
+ elog "or if you are using csh"
+ elog " . /opt/embree/embree-vars.csh"
+}
diff --git a/media-libs/libgfx/files/1.1.0-gcc-4.3.patch b/media-libs/libgfx/files/1.1.0-gcc-4.3.patch
new file mode 100644
index 000000000..ba5eba38a
--- /dev/null
+++ b/media-libs/libgfx/files/1.1.0-gcc-4.3.patch
@@ -0,0 +1,24 @@
+cstring now contains memcpy.
+Written and tested by Lucas Mitrak.
+
+--- a/src/raster-png.cxx
++++ b/src/raster-png.cxx
+@@ -12,6 +12,7 @@
+ #include <vector>
+ #include <gfx/gfx.h>
+ #include <gfx/raster.h>
++#include <cstring>
+
+ #ifdef HAVE_LIBPNG
+
+--- a/src/raster.cxx
++++ b/src/raster.cxx
+@@ -9,7 +9,7 @@
+ #include <gfx/gfx.h>
+ #include <gfx/raster.h>
+
+-#include <string>
++#include <cstring>
+ #include <cctype>
+
+ namespace gfx
diff --git a/media-libs/libgfx/files/1.1.0-gcc4.3.patch b/media-libs/libgfx/files/1.1.0-gcc4.3.patch
deleted file mode 100644
index 811d5dbcc..000000000
--- a/media-libs/libgfx/files/1.1.0-gcc4.3.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- a/src/raster.cxx 2004-09-27 06:45:31.000000000 +0200
-+++ b/src/raster.cxx.new 2009-05-17 23:48:58.417607175 +0200
-@@ -9,7 +9,7 @@
- #include <gfx/gfx.h>
- #include <gfx/raster.h>
-
--#include <string>
-+#include <cstring>
- #include <cctype>
-
- namespace gfx
diff --git a/media-libs/libgfx/files/1.1.0-libPNG-1.2.5.patch b/media-libs/libgfx/files/1.1.0-libPNG-1.2.5.patch
new file mode 100644
index 000000000..0d648d06e
--- /dev/null
+++ b/media-libs/libgfx/files/1.1.0-libPNG-1.2.5.patch
@@ -0,0 +1,24 @@
+Changes the png buffer pointer to the new function call.
+Written and tested by Lucas Mitrak.
+https://bugs.gentoo.org/756061
+
+--- a/src/raster-png.cxx
++++ b/src/raster-png.cxx
+@@ -43,7 +43,7 @@ ByteRaster *read_png_image(const char *file_name)
+ // Because we didn't set up any error handlers, we need to be
+ // prepared to handle longjmps out of the library on error
+ // conditions.
+- if( setjmp(png_ptr->jmpbuf) )
++ if( setjmp(png_jmpbuf(png_ptr)) )
+ {
+ png_destroy_read_struct(&png_ptr, &info_ptr, NULL);
+ fclose(fp);
+@@ -133,7 +133,7 @@ bool write_png_image(const char *file_name, const ByteRaster& img)
+ return false;
+ }
+
+- if( setjmp(png_ptr->jmpbuf) )
++ if( setjmp(png_jmpbuf(png_ptr)) )
+ {
+ fclose(fp);
+ png_destroy_write_struct(&png_ptr, (png_infopp)NULL);
diff --git a/media-libs/libgfx/libgfx-1.1.0.ebuild b/media-libs/libgfx/libgfx-1.1.0.ebuild
index 7fba3d1da..01f5c7f71 100644
--- a/media-libs/libgfx/libgfx-1.1.0.ebuild
+++ b/media-libs/libgfx/libgfx-1.1.0.ebuild
@@ -12,7 +12,17 @@ SLOT="0"
KEYWORDS="~amd64 ~x86"
IUSE="static-libs"
-PATCHES=( "${FILESDIR}"/${PV}-gcc4.3.patch )
+DEPEND="
+ virtual/opengl
+ x11-libs/fltk
+"
+
+RDEPEND="${DEPEND}"
+
+PATCHES=(
+ "${FILESDIR}"/${PV}-gcc-4.3.patch
+ "${FILESDIR}"/${PV}-libPNG-1.2.5.patch
+)
src_compile() {
cd src || die
@@ -25,3 +35,9 @@ src_install() {
dodoc doc/*
}
+
+src_test() {
+ cd tests || die
+ sed -i -e 's/t-vec.cxx t-img.cxx t-gui.cxx t-glimg.cxx t-script.cxx t-glext.cxx/t-vec.cxx t-img.cxx t-script.cxx/' Makefile
+ emake
+}
diff --git a/net-misc/cernbox-client/Manifest b/net-misc/cernbox-client/Manifest
index 5976cf455..d826df9fb 100644
--- a/net-misc/cernbox-client/Manifest
+++ b/net-misc/cernbox-client/Manifest
@@ -1,3 +1,3 @@
DIST cernbox-client-2.7.1-2596.src.rpm 15434250 BLAKE2B 3ef3fcc4010b3f292aee9b6bba7b5f9a72e4fbca1236e1e85e6523cd4e38d980fe4542c5f019647a19040be64628159651630a61ee8894cb7bcf4b69d342ccd0 SHA512 e329b84fc7aa62068f934bf8a9f47432709094adc618274c1b8ddbf7331094cb71b6208d3a777150ee426141301e0279cb219d65b123335f2e198a9b87980e5d
-DIST ownCloud-2.7.5.3180.tar.xz 14154036 BLAKE2B ebee57568b917c1c7dec8f41f172caf53d0bfe4eae5e24ec5c9adbf656bf667769b0ed341a13a899ff6a04cd779d92b145736dce5a4e72055d306b2f08e0a902 SHA512 9e788341c45753eb2d2c62d252cf453259474689fd7d498147e0f4548a9038bd44bdca1539f9617d383853f8f9ca2f24c575667fb96e2a1a4ceec30195d257c2
DIST ownCloud-2.7.6.3261.tar.xz 14237692 BLAKE2B 914b069b10fa2f169677768e1578c5b8569836eb574889c72c0ea1ca3e16e6b7c65bcdd1f4a5ce4259eab6ec56110e3b45799d010921e47c7f64ccfd0ed545bf SHA512 1f647dd0b33472e31719651fa22b5864867d98fa1e2f11f9eadb6ce15382f5f97ac49d726af079716b6fac573367485a6f11a5b2e5e5c95d4d063f6caab51dcd
+DIST ownCloud-2.8.2.4246.tar.xz 15044652 BLAKE2B ee1ee412667266273a9a9722940559562c6c43213b013fe7c21328e04ac967afb16f460e6fa711f37d1d4ea7d0fc15fc398d835cf6a939f4c8dfd54cd4846fed SHA512 0ab2ef72191cc2d5c2621c97c09cb1d25472a30f511235a190465e246a8312f13a255011abb9690c481887f2f15094414c87ce594252eb8debcb39b9cbc8a178
diff --git a/net-misc/cernbox-client/cernbox-client-2.7.5.3180.ebuild b/net-misc/cernbox-client/cernbox-client-2.8.2.4246.ebuild
index 2eb01cf8e..2eb01cf8e 100644
--- a/net-misc/cernbox-client/cernbox-client-2.7.5.3180.ebuild
+++ b/net-misc/cernbox-client/cernbox-client-2.8.2.4246.ebuild
diff --git a/profiles/package.mask b/profiles/package.mask
index fb07f4d8a..d39812beb 100644
--- a/profiles/package.mask
+++ b/profiles/package.mask
@@ -29,13 +29,3 @@
## app-misc/some-package
#--- END OF EXAMPLES ---
-
-# Andrew Ammerlaan <andrewammerlaan@riseup.net> (08 May 2021)
-# netcdf(-java) is horribly outdated, it requires dev-java/ehcache which is
-# being removed. This ebuild cannot be moved into ::sci because the sources
-# are no longer available outside of the Gentoo mirror. Newer versions of
-# netcdf-java and ehcache use a maven based build system which currently does
-# not work with portage. The only real solution would be to add a netcdf-bin
-# package. If you need this software please complain on bugzilla or GitHub.
-# Masked for removal when dev-java/ehcache is removed from ::gentoo (~30 days).
-dev-java/netcdf
diff --git a/profiles/updates/2Q-2021 b/profiles/updates/2Q-2021
new file mode 100644
index 000000000..6b04562b8
--- /dev/null
+++ b/profiles/updates/2Q-2021
@@ -0,0 +1 @@
+move media-libs/libredwg media-gfx/libredwg
diff --git a/sci-biology/KING/KING-2.2.5.ebuild b/sci-biology/KING/KING-2.2.7.ebuild
index 7f8d96a89..6d01ca794 100644
--- a/sci-biology/KING/KING-2.2.5.ebuild
+++ b/sci-biology/KING/KING-2.2.7.ebuild
@@ -5,24 +5,20 @@ EAPI=7
inherit toolchain-funcs
+MY_P="KING${PV}"
DESCRIPTION="Check family relationship and infer population structure"
-HOMEPAGE="https://people.virginia.edu/~wc9c/KING
- https://people.virginia.edu/~wc9c/publications/pdf/BI26_2867.pdf"
-SRC_URI="https://people.virginia.edu/~wc9c/KING/KINGcode.tar.gz -> ${P}.tar.gz
- https://people.virginia.edu/~wc9c/KING/manual.html -> ${PN}_relationship_inference.html
- https://people.virginia.edu/~wc9c/KING/kingpopulation.html -> ${PN}.kingpopulation.html"
+HOMEPAGE="https://kingrelatedness.com"
+SRC_URI="https://www.kingrelatedness.com/executables/${MY_P}code.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}"
LICENSE="all-rights-reserved" # Our robust relationship inference algorithm is implemented in a freely available software package
SLOT="0"
KEYWORDS="~amd64 ~x86"
-S="${WORKDIR}"
-
src_compile(){
$(tc-getCXX) ${CXXFLAGS} -lm -lz -fopenmp -o king *.cpp
}
src_install(){
newbin {king,KING}
- dodoc "${DISTDIR}"/"${PN}"_relationship_inference.html "${DISTDIR}"/"${PN}".kingpopulation.html
}
diff --git a/sci-biology/KING/Manifest b/sci-biology/KING/Manifest
index c1182ffc0..5c06973e1 100644
--- a/sci-biology/KING/Manifest
+++ b/sci-biology/KING/Manifest
@@ -1,3 +1 @@
-DIST KING-2.2.5.tar.gz 515552 BLAKE2B 5242b8f8ccc14dfb723a0245fd6e452e8bf75026d0f619ba196440bc5cd09baf567fd7b4d0c7ae5b0dd77c53d716143b3acd44e1c6fb18345ffde1c63f27c0ac SHA512 9d23c88e8c143e51b4202c390878c6a51e4fc5710fba31804950375e3bd50c1fa8015fec0a4aa38b3a3a62aa5b8afc88a09fddbae6db68640b88ad421fad7670
-DIST KING.kingpopulation.html 12969 BLAKE2B ed8f47139c6b413c241d6a599c2338974678e1bd76b489a1ffb4d4f84286acb8ef05f4c6be838986c036751192076e2eaad0ae8479d3c24d2d5f6bee64a77600 SHA512 1aab7f12bf13f6e0117aa42d2e26cad86d2325fbf813efb7f0beacdffe963398a3b2766160758ec20af22969896be76b4b713a8336b9a063c327043481340f1e
-DIST KING_relationship_inference.html 38852 BLAKE2B 4a4fc501de784287f13009a06ad60a1b72b924fa421543b2de600672e8c1c19a6a819a004728824c28c2adbdcc2bcb05415eeeeacd364031ad66dc58c124ff93 SHA512 a9ebf3aacabb6e2ad65786b27e36a3d200480c427747e0c2ce6ac34ca4b953b547fd9d212374a5a1c1b2772e627b8336f30623d1ade3c719cffe973d88ba832b
+DIST KING-2.2.7.tar.gz 527147 BLAKE2B cdc294de47895088ce7917e9aae8aafce0dc293e542636c02d6356c5f42cfbb2f17986d1bf1f05b450528f27b9e9596483440134fc4cb576206742c9a8253160 SHA512 0953d4c5396395518599cc9abd31f645a804d096d19e9f33ae75362c9cf9649fbdfd3acf2d3969cc0dd17c98e7b18f1db7af4500621c55aba411b045f7b8d5de
diff --git a/sci-biology/StarORF/StarORF-9999.ebuild b/sci-biology/StarORF/StarORF-9999.ebuild
deleted file mode 100644
index eb24ff954..000000000
--- a/sci-biology/StarORF/StarORF-9999.ebuild
+++ /dev/null
@@ -1,29 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit java-pkg-2 java-ant-2 git-r3
-
-DESCRIPTION="Java-based utility to show ORFs in a sequence"
-HOMEPAGE="http://star.mit.edu/orf"
-EGIT_REPO_URI="https://github.com/starteam/starorf_java.git"
-
-LICENSE="BSD-2"
-SLOT="0"
-KEYWORDS=""
-
-DEPEND="
- >=virtual/jdk-1.5:*
- dev-java/jreleaseinfo:0"
-RDEPEND="${DEPEND}
- >=virtual/jre-1.5:*"
-
-src_prepare() {
- default
- java-pkg_jar-from --into lib jreleaseinfo
-}
-
-src_install() {
- java-pkg_dojar StarORF.jar
-}
diff --git a/sci-biology/cutadapt/Manifest b/sci-biology/cutadapt/Manifest
index 2ae274012..30063661a 100644
--- a/sci-biology/cutadapt/Manifest
+++ b/sci-biology/cutadapt/Manifest
@@ -1 +1,2 @@
DIST cutadapt-2.10.tar.gz 282198 BLAKE2B 87784fd092d3417775f3a627d68bea1d3421f6392ae90f65e9b5f231f10a4da8cfacecc8c6fc3cd8420d0255ffc44ec72188bc901d1768f18f3b78077a165314 SHA512 afefb101a25daa071e5945e442de46cd594a6f4ba5915e9d11943280039223ff5d686b358de44f11b6367f203767d97b76fc529eae70b072139e55831189e594
+DIST cutadapt-3.3.tar.gz 294579 BLAKE2B 1cf833d65a9611e50d747b6ce544dbf639ccc8eab8c5e83425d47bfe5526a0a25faab10cec7b41fad5b012ccf0552948a778b81dac3d5768674326d210dd4540 SHA512 d8895453455aff31c613a4e031559c08646ce2bf072d85ed7b195e5863700a02a1ed44bfb409b63849aadf1db7cf40dea33d0ead4f056307365dc91aa6c93234
diff --git a/sci-biology/cutadapt/cutadapt-3.3.ebuild b/sci-biology/cutadapt/cutadapt-3.3.ebuild
new file mode 100644
index 000000000..e1990f222
--- /dev/null
+++ b/sci-biology/cutadapt/cutadapt-3.3.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{7..9} )
+
+inherit distutils-r1
+
+DESCRIPTION="Remove adapter sequences from high-throughput sequencing data"
+HOMEPAGE="https://github.com/marcelm/cutadapt"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="
+ dev-python/dnaio[${PYTHON_USEDEP}]
+ dev-python/xopen[${PYTHON_USEDEP}]
+"
+RDEPEND="
+ ${PYTHON_DEPS}
+ ${DEPEND}
+"
+BDEPEND="
+ test? (
+ dev-python/cython
+ dev-python/pytest-mock
+ dev-python/pytest-timeout
+ )
+"
+
+PATCHES=( "${FILESDIR}"/${PN}-3.3-skiptest.patch )
+
+distutils_enable_tests pytest
+
+# needs call to installed cutadapt executable
+python_test() {
+ distutils_install_for_testing
+ pytest -vv || die "pytest failed with ${EPYTHON}"
+}
diff --git a/sci-biology/cutadapt/files/cutadapt-3.3-skiptest.patch b/sci-biology/cutadapt/files/cutadapt-3.3-skiptest.patch
new file mode 100644
index 000000000..c2dc2a741
--- /dev/null
+++ b/sci-biology/cutadapt/files/cutadapt-3.3-skiptest.patch
@@ -0,0 +1,13 @@
+diff --git a/tests/test_command.py b/tests/test_command.py
+index a81b04a..cf40233 100644
+--- a/tests/test_command.py
++++ b/tests/test_command.py
+@@ -76,7 +76,7 @@ def test_force_fasta_output(tmpdir, cores):
+ assert_files_equal(cutpath("small.fasta"), out_path)
+
+
+-@pytest.mark.skipif(sys.platform == "win32", reason="Maybe this can be made to work")
++@pytest.mark.skipif(reason="Maybe this can be made to work")
+ def test_non_utf8_locale():
+ subprocess.check_call(
+ [sys.executable, "-m", "cutadapt", "-o", os.devnull, datapath("small.fastq")],
diff --git a/sci-biology/dcm2niix/Manifest b/sci-biology/dcm2niix/Manifest
index 19634d154..655b0c2b9 100644
--- a/sci-biology/dcm2niix/Manifest
+++ b/sci-biology/dcm2niix/Manifest
@@ -1 +1,2 @@
DIST dcm2niix-1.0.20201102.tar.gz 382906 BLAKE2B 066b8bb33408166a301fa128d2717b1bfe4a93908e0752368a5f559cda5ed542131c330d75d6eac78b743a4e0979bd3dd7390187e65f62b1b35912606f52fd7a SHA512 9cda7f82c1424cb9476113d7ddf7965d818d95350dfdbf71536748a117d0de2c070cebb2aed980208d6142c3eb9e3d2331210cffa900209fa4320195c92fd7f1
+DIST dcm2niix-1.0.20210317.tar.gz 389930 BLAKE2B fff5c5c15765f6400dce8eb40322b91bd33181ecf9fbc9c989f2b984d7dc9835bd3314df8eeffdd34ad867f79f3b730eaadd39c59fb8dd17d670bfdff350a226 SHA512 3a702784bb4de45218ae305eb0afb0e233341b0727bf13a13d263b6e6391d04e670e5cc314d66d456fccae1a3cf36a03d8919e3d393786625e9f5a13fd039e4a
diff --git a/sci-biology/dcm2niix/dcm2niix-1.0.20201102.ebuild b/sci-biology/dcm2niix/dcm2niix-1.0.20201102.ebuild
index b7f4166f5..5ae682ea5 100644
--- a/sci-biology/dcm2niix/dcm2niix-1.0.20201102.ebuild
+++ b/sci-biology/dcm2niix/dcm2niix-1.0.20201102.ebuild
@@ -12,9 +12,29 @@ SRC_URI="https://github.com/rordenlab/dcm2niix/archive/v${PV}.tar.gz -> ${P}.tar
SLOT="0"
LICENSE="BSD"
KEYWORDS="~amd64 ~x86"
+IUSE="static system-jpeg +jpeg-ls jpeg2k"
-DEPEND=""
-RDEPEND=""
+DEPEND="
+ system-jpeg? ( media-libs/libjpeg-turbo )
+ jpeg2k? ( media-libs/openjpeg )
+"
+RDEPEND="${DEPEND}"
+BDEPEND="virtual/pkgconfig"
+
+PATCHES=(
+ "${FILESDIR}"/${PN}-disable_find_git.patch
+)
+
+src_configure() {
+ local mycmakeargs=(
+ -DUSE_STATIC_RUNTIME=$(usex static)
+ -DUSE_TURBOJPEG=$(usex system-jpeg)
+ -DUSE_JPEGLS=$(usex jpeg-ls)
+ -DUSE_OPENJPEG=$(usex jpeg2k)
+ )
+
+ cmake_src_configure
+}
pkg_postinst() {
optfeature "parallel gzip support" app-arch/pigz
diff --git a/sci-biology/dcm2niix/dcm2niix-1.0.20210317.ebuild b/sci-biology/dcm2niix/dcm2niix-1.0.20210317.ebuild
new file mode 100644
index 000000000..5ae682ea5
--- /dev/null
+++ b/sci-biology/dcm2niix/dcm2niix-1.0.20210317.ebuild
@@ -0,0 +1,41 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit cmake optfeature
+
+DESCRIPTION="DICOM to NIfTI converter"
+HOMEPAGE="https://github.com/rordenlab/dcm2niix"
+SRC_URI="https://github.com/rordenlab/dcm2niix/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+
+SLOT="0"
+LICENSE="BSD"
+KEYWORDS="~amd64 ~x86"
+IUSE="static system-jpeg +jpeg-ls jpeg2k"
+
+DEPEND="
+ system-jpeg? ( media-libs/libjpeg-turbo )
+ jpeg2k? ( media-libs/openjpeg )
+"
+RDEPEND="${DEPEND}"
+BDEPEND="virtual/pkgconfig"
+
+PATCHES=(
+ "${FILESDIR}"/${PN}-disable_find_git.patch
+)
+
+src_configure() {
+ local mycmakeargs=(
+ -DUSE_STATIC_RUNTIME=$(usex static)
+ -DUSE_TURBOJPEG=$(usex system-jpeg)
+ -DUSE_JPEGLS=$(usex jpeg-ls)
+ -DUSE_OPENJPEG=$(usex jpeg2k)
+ )
+
+ cmake_src_configure
+}
+
+pkg_postinst() {
+ optfeature "parallel gzip support" app-arch/pigz
+}
diff --git a/sci-biology/dcm2niix/files/dcm2niix-disable_find_git.patch b/sci-biology/dcm2niix/files/dcm2niix-disable_find_git.patch
new file mode 100644
index 000000000..ba51997f2
--- /dev/null
+++ b/sci-biology/dcm2niix/files/dcm2niix-disable_find_git.patch
@@ -0,0 +1,19 @@
+disable finding git because it should not be used nor needed
+Written and tested by Lucas Mitrak.
+https://bugs.gentoo.org/755746
+
+--- a/SuperBuild/SuperBuild.cmake
++++ b/SuperBuild/SuperBuild.cmake
+@@ -1,8 +1,8 @@
+ # Check if git exists
+-find_package(Git)
+-if(NOT GIT_FOUND)
+- message(FATAL_ERROR "Cannot find Git. Git is required for Superbuild")
+-endif()
++#find_package(Git)
++#if(NOT GIT_FOUND)
++# message(FATAL_ERROR "Cannot find Git. Git is required for Superbuild")
++#endif()
+
+ # Use git protocol or not
+ option(USE_GIT_PROTOCOL "If behind a firewall turn this off to use http instead." ON)
diff --git a/sci-biology/dcm2niix/metadata.xml b/sci-biology/dcm2niix/metadata.xml
index c7c32010c..9c9e19081 100644
--- a/sci-biology/dcm2niix/metadata.xml
+++ b/sci-biology/dcm2niix/metadata.xml
@@ -9,6 +9,11 @@
<email>sci@gentoo.org</email>
<name>Gentoo Science Project</name>
</maintainer>
+ <use>
+ <flag name="system-jpeg">Use the system-wide <pkg>media-libs/libjpeg-turbo</pkg>
+ instead of bundled.</flag>
+ <flag name="jpeg-ls">Supprt for converting DICOM images compressed with the JPEG-LS transfer syntaxes using the bundled CharLS library</flag>
+ </use>
<longdescription>
dcm2niix is a designed to convert neuroimaging data from the DICOM
format to the NIfTI format. ICOM provides many ways to store/compress
diff --git a/sci-biology/dipy/dipy-9999.ebuild b/sci-biology/dipy/dipy-9999.ebuild
index 2b087184f..a1b162df6 100644
--- a/sci-biology/dipy/dipy-9999.ebuild
+++ b/sci-biology/dipy/dipy-9999.ebuild
@@ -3,7 +3,7 @@
EAPI=7
-PYTHON_COMPAT=( python3_7 )
+PYTHON_COMPAT=( python3_{7..9} )
inherit distutils-r1 git-r3
diff --git a/sci-biology/fsl/Manifest b/sci-biology/fsl/Manifest
index ce2b4be84..868861b84 100644
--- a/sci-biology/fsl/Manifest
+++ b/sci-biology/fsl/Manifest
@@ -1 +1,2 @@
DIST fsl-6.0.2.tar.gz 2505331864 BLAKE2B 0fbc23c788e0960e41a895f8eddd346e8facfae448c637eca18d39b142f8aabd9531427ce4ff97c634fdc5d16a74163947c7bade219a8900722815321144b41e SHA512 fe308393076c51c50b086f9bf7ff5ddebcf8b1284128e734b9d9e501019917ceba7c0ee5cd5aa1ed44452bcd042ad72653c1a8693f94eab9b83a80fe508a56ca
+DIST fsl-6.0.4.tar.gz 2507673220 BLAKE2B 21e7437f8a3fde03ec6711b8022ee203ae159c07b5a3b998f37db768205d3335ffe9b28ad05b859e6bde4916933ea58e4e188012f147648f00fd6e6253ce1a12 SHA512 c65edcf5728920752e6dceea440dc2b528d007b7e4f56390a3d7eed91b1014457544563f699cae77f62c44cdfbdfcc5031265a5fd619fe0ecb99cad5653080d3
diff --git a/sci-biology/fsl/files/fsl-6.0.4-cuda_buildsettings.patch b/sci-biology/fsl/files/fsl-6.0.4-cuda_buildsettings.patch
new file mode 100644
index 000000000..749e80623
--- /dev/null
+++ b/sci-biology/fsl/files/fsl-6.0.4-cuda_buildsettings.patch
@@ -0,0 +1,12 @@
+diff -Naur fsl.orig/config/buildSettings.mk fsl/config/buildSettings.mk
+--- fsl.orig/config/buildSettings.mk 2020-12-02 16:22:57.999912865 -0500
++++ fsl/config/buildSettings.mk 2020-12-02 16:24:15.332915270 -0500
+@@ -144,7 +144,7 @@
+ # CUDA development environment
+ CUDAVER := $(or $(CUDAVER),9.1)
+ #$(info $$CUDAVER is [${CUDAVER}])
+-CUDA_INSTALLATION = /opt/cuda-${CUDAVER}
++CUDA_INSTALLATION = /opt/cuda
+ ifdef SINGULARITY_NAME
+ CUDA_INSTALLATION = /usr/local/cuda-${CUDAVER}
+ endif
diff --git a/sci-biology/fsl/files/fsl-6.0.4-eddy_cuda.patch b/sci-biology/fsl/files/fsl-6.0.4-eddy_cuda.patch
new file mode 100644
index 000000000..ad118c39a
--- /dev/null
+++ b/sci-biology/fsl/files/fsl-6.0.4-eddy_cuda.patch
@@ -0,0 +1,21 @@
+diff -Naur fsl.orig/src/eddy/Makefile fsl/src/eddy/Makefile
+--- fsl.orig/src/eddy/Makefile 2020-12-02 16:07:47.327884548 -0500
++++ fsl/src/eddy/Makefile 2020-12-02 16:11:21.149891196 -0500
+@@ -29,6 +29,8 @@
+ TMPCXXFLAGS_2=
+ TMPNAME_1=
+ TMPNAME_2=
++cuda=1
++cpu=1
+ TOPUP_DIR=../topup
+
+ ifndef cuda
+@@ -74,7 +75,7 @@
+ ifdef NVCC11
+ NVCC=${NVCC11}
+ endif
+-NVCCFLAGS=-c -DCOMPILE_GPU -O3 -m 64 -std=c++11
++NVCCFLAGS=-c -DCOMPILE_GPU -O3 -m 64 -std=c++11 @@GENTOO_NVCC_FLAGS@@
+ ifeq ($(CLOBBER_CLANG),1)
+ NVCCFLAGS+= -DCLOBBER_CLANG
+ endif
diff --git a/sci-biology/fsl/files/fsl-6.0.4-fdt_cuda.patch b/sci-biology/fsl/files/fsl-6.0.4-fdt_cuda.patch
new file mode 100644
index 000000000..7f322027b
--- /dev/null
+++ b/sci-biology/fsl/files/fsl-6.0.4-fdt_cuda.patch
@@ -0,0 +1,14 @@
+diff -Naur fsl.orig/src/fdt/Makefile fsl/src/fdt/Makefile
+--- fsl.orig/src/fdt/Makefile 2020-12-02 19:06:55.826218772 -0500
++++ fsl/src/fdt/Makefile 2020-12-02 19:08:02.883220858 -0500
+@@ -6,7 +6,9 @@
+ $(eval $($(PROJNAME)_MASTERBUILD))
+ endif
+
+-ifeq ($(COMPILE_GPU), 1)
++# disable CUDA support for fdt
++#ifeq ($(COMPILE_GPU), 1)
++ifeq (0, 1)
+ COMPILE_WITH_GPU=libbedpostx_cuda.so merge_parts_gpu xfibres_gpu CUDA/split_parts_gpu
+ SCRIPTS_GPU=CUDA/bedpostx_gpu CUDA/bedpostx_postproc_gpu.sh
+ endif
diff --git a/sci-biology/fsl/files/fsl-6.0.4-flameo_std.patch b/sci-biology/fsl/files/fsl-6.0.4-flameo_std.patch
new file mode 100644
index 000000000..a991f1ed3
--- /dev/null
+++ b/sci-biology/fsl/files/fsl-6.0.4-flameo_std.patch
@@ -0,0 +1,11 @@
+diff -Naur fsl.orig/src/flameo/Makefile fsl/src/flameo/Makefile
+--- fsl.orig/src/flameo/Makefile 2021-01-06 14:04:35.728274475 -0500
++++ fsl/src/flameo/Makefile 2021-01-06 14:08:18.204269285 -0500
+@@ -4,6 +4,7 @@
+
+ USRINCFLAGS = -I${INC_NEWMAT} -I${INC_PROB} -I${INC_ZLIB} -DCIFTILIB_USE_XMLPP -I${FSLEXTINC} -I${INC_XML2} -I${INC_XML++} -I${INC_XML++CONF} -I${INC_BOOST} -I${FSLDIR}/include/ciftiio
+ USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_PROB} -L${LIB_ZLIB}
++USRCXXFLAGS = -std=c++11
+
+ UNAME := $(shell uname)
+ ifeq (${UNAME},Darwin)
diff --git a/sci-biology/fsl/files/fsl-6.0.4-fsldir_redux-p1.patch b/sci-biology/fsl/files/fsl-6.0.4-fsldir_redux-p1.patch
new file mode 100644
index 000000000..ca3945442
--- /dev/null
+++ b/sci-biology/fsl/files/fsl-6.0.4-fsldir_redux-p1.patch
@@ -0,0 +1,240 @@
+From 2bc4be1f55b27a733e1e624b34bc570187ba95e1 Mon Sep 17 00:00:00 2001
+From: Fran├žois Bissey <frp.bissey@gmail.com>
+Date: Mon, 20 Jan 2020 11:40:53 +1300
+Subject: [PATCH] Making sure fsl code and executable can find other executable
+ and data in standard location.
+
+---
+ src/fast4/fast_two.cc | 8 ++++----
+ src/feat5/feat_model.cc | 8 +++-----
+ src/feat5/tsplot.cc | 7 +++----
+ src/first/first_utils.cc | 4 ++--
+ src/fnirt/fnirtfns.cpp | 11 ++++-------
+ src/fslsurface/fslsurface_first.cc | 6 ++----
+ src/fslsurface/fslsurfacemaths.cpp | 12 ------------
+ src/libvis/miscpic.h | 7 +------
+ src/melodic/meldata.cc | 4 ++--
+ src/melodic/meloptions.cc | 8 --------
+ src/melodic/meloptions.h | 1 -
+ src/melodic/melreport.cc | 12 ++++++------
+ src/melodic/melreport.h | 20 ++++++++++----------
+ src/mm/mixture_model.cc | 4 ++--
+ src/siena/siena_diff.cc | 28 +++++++++++++---------------
+ src/topup/topupfns.cpp | 3 +--
+ 16 files changed, 53 insertions(+), 90 deletions(-)
+
+diff --git a/src/fast4/fast_two.cc b/src/fast4/fast_two.cc
+index 592b5df..b525444 100644
+--- a/src/fast4/fast_two.cc
++++ b/src/fast4/fast_two.cc
+@@ -166,7 +166,7 @@ int prior_registration(string inname, string main_prior_vol, NEWIMAGE::volume<fl
+ string csfPriorName, grayPriorName, whitePriorName;
+ if(alternatePriors.unset())
+ {
+- string priorRootName=string(getenv("FSLDIR")) + "/data/standard/tissuepriors/avg152T1_";
++ string priorRootName="@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/tissuepriors/avg152T1_";
+ csfPriorName = priorRootName+"csf";
+ grayPriorName = priorRootName+"gray";
+ whitePriorName = priorRootName+"white";
+@@ -215,15 +215,15 @@ string csfPriorName, grayPriorName, whitePriorName;
+ if(bapused>0)
+ {
+ char reg[1024];
+- sprintf(reg, "%s/bin/flirt -ref %s -in %s -out %s -applyxfm -init %s", getenv("FSLDIR"), inname.c_str(), csfPriorName.c_str(), (main_prior_vol+"_csf_stdspace").c_str(), bapriori.value().c_str());
++ sprintf(reg, "flirt -ref %s -in %s -out %s -applyxfm -init %s", inname.c_str(), csfPriorName.c_str(), (main_prior_vol+"_csf_stdspace").c_str(), bapriori.value().c_str());
+ if(verbose.value())
+ cout<<reg<<endl;
+ system(reg);
+- sprintf(reg, "%s/bin/flirt -ref %s -in %s -out %s -applyxfm -init %s", getenv("FSLDIR"), inname.c_str(), grayPriorName.c_str(), (main_prior_vol+"_gm_stdspace").c_str(), bapriori.value().c_str());
++ sprintf(reg, "flirt -ref %s -in %s -out %s -applyxfm -init %s", inname.c_str(), grayPriorName.c_str(), (main_prior_vol+"_gm_stdspace").c_str(), bapriori.value().c_str());
+ if(verbose.value())
+ cout<<reg<<endl;
+ system(reg);
+- sprintf(reg, "%s/bin/flirt -ref %s -in %s -out %s -applyxfm -init %s", getenv("FSLDIR"), inname.c_str(), whitePriorName.c_str(), (main_prior_vol+"_wm_stdspace").c_str(), bapriori.value().c_str());
++ sprintf(reg, "flirt -ref %s -in %s -out %s -applyxfm -init %s", inname.c_str(), whitePriorName.c_str(), (main_prior_vol+"_wm_stdspace").c_str(), bapriori.value().c_str());
+ if(verbose.value())
+ cout << reg << endl;
+ system(reg);
+diff --git a/src/feat5/feat_model.cc b/src/feat5/feat_model.cc
+index 399a13e..e15e43c 100644
+--- a/src/feat5/feat_model.cc
++++ b/src/feat5/feat_model.cc
+@@ -744,7 +744,7 @@ int main(int argc, char **argv)
+ vector<int> G;
+ vector<string> titles;
+ float tr, mult, trmult, nltffwhm=0, maxconvwin=0;
+- char fl[10000], *FSLDIR;
++ char fl[10000];
+ string fn, filename;
+ FONT_DATA *font_data = new FONT_DATA[1];
+
+@@ -763,8 +763,6 @@ int main(int argc, char **argv)
+ if (argc==3)
+ motionparams=remmean(read_ascii_matrix(argv[2]));
+
+- FSLDIR=getenv("FSLDIR");
+-
+ fn = string(argv[1])+".fsf";
+
+ level = atoi(find_line(fn, "fmri(level)", fl));
+@@ -1510,7 +1508,7 @@ int main(int argc, char **argv)
+ writeCovarianceImage(string(argv[1])+"_cov.ppm", contrasts, F, nftests, realDesign, level, evs.eigenvals, font_data, contrasts.RE);
+ writeImagePreview(string(argv[1])+".ppm", contrasts, F, nftests, realDesign, level, evs, font_data, titles, tr, nltffwhm, nTimepoints, G);
+
+- filename=string(getenv("FSLDIR"))+"/bin/wpng -q -overwrite "+string(argv[1])+".ppm ";
++ filename="wpng -q -overwrite "+string(argv[1])+".ppm ";
+ system(filename.c_str());
+
+ return(0);
+@@ -2161,6 +2159,6 @@ char the_string[10000];
+
+ fclose(outputfile);
+
+- filename=string(getenv("FSLDIR")) + "/bin/wpng -q -overwrite " + filename;
++ filename="wpng -q -overwrite " + filename;
+ system(filename.c_str());
+ }
+diff --git a/src/feat5/tsplot.cc b/src/feat5/tsplot.cc
+index ae191fd..3a02b55 100644
+--- a/src/feat5/tsplot.cc
++++ b/src/feat5/tsplot.cc
+@@ -293,7 +293,7 @@ int main(int argc, char **argv)
+ ofstream outputFile;
+ int numEVs, npts, numContrasts=1, nftests=0, GRPHSIZE(600), PSSIZE(600);
+ vector<double> normalisedContrasts, model, triggers;
+- string fmriFileName, fslPath, featdir, vType, indexText;
++ string fmriFileName, featdir, vType, indexText;
+ ColumnVector NewimageVoxCoord(4),NiftiVoxCoord(4);
+ bool outputText(true), useCoordinate(false), prewhiten(false), useTriggers(false), customMask(false), modelFree(false), isHigherLevel(false), outputDataOnly(false);
+ bool zWeightClusters(true);
+@@ -307,7 +307,6 @@ volume<float> immask;
+ if (argc<2) usage("");
+ featdir=string(argv[1]);
+ fmriFileName=featdir+"/filtered_func_data";
+- fslPath=string(getenv("FSLDIR"));
+
+ string outputName(featdir);
+
+@@ -753,7 +752,7 @@ volume4D<float> acs;
+ cerr << "Can't open output report file " << outputName << endl;
+ exit(1);
+ }
+- outputFile << "<HTML>\n<TITLE>"<< statType << num2str(i) <<"</TITLE>\n<BODY BACKGROUND=\"file:"<< fslPath <<"/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report - "<< statType << num2str(i) <<"</H1>\n</CENTER>\n<hr><b>Full plots</b><p>\n"<< graphText;
++ outputFile << "<HTML>\n<TITLE>"<< statType << num2str(i) <<"</TITLE>\n<BODY BACKGROUND=\"file:"<< "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report - "<< statType << num2str(i) <<"</H1>\n</CENTER>\n<hr><b>Full plots</b><p>\n"<< graphText;
+ if (useTriggers) outputFile << "\n<hr><b>Peristimulus plots</b><p>\n"<< peristimulusText <<"\n<HR></BODY></HTML>\n\n";
+ else outputFile << "\n</BODY></HTML>\n\n";
+ outputFile.close();
+@@ -768,7 +767,7 @@ volume4D<float> acs;
+ cerr << "Can't open output report file " << outputName << endl;
+ exit(1);
+ }
+- outputFile << "<HTML>\n<TITLE>FEAT Time Series Report</TITLE>\n<BODY BACKGROUND=\"file:" << fslPath << "/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report</H1>\n</CENTER>\n<hr>" << indexText << "<HR></BODY></HTML>" << endl << endl;
++ outputFile << "<HTML>\n<TITLE>FEAT Time Series Report</TITLE>\n<BODY BACKGROUND=\"file:" << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">\n<hr><CENTER>\n<H1>FEAT Time Series Report</H1>\n</CENTER>\n<hr>" << indexText << "<HR></BODY></HTML>" << endl << endl;
+ outputFile.close();
+
+ /* now output same thing without start and end, for inclusion in feat report */
+diff --git a/src/first/first_utils.cc b/src/first/first_utils.cc
+index 68be44b..85960f4 100644
+--- a/src/first/first_utils.cc
++++ b/src/first/first_utils.cc
+@@ -1954,8 +1954,8 @@ void do_work_bvars(){
+ if (!surfaceVAout.value()) {
+ // do not output on the surface, instead do the new default of outputting a volume with the scalar normal dot product values (for use with randomise)
+ volume<float> refim;
+- if (useReconMNI.value()) { read_volume(refim,string(getenv("FSLDIR")) + "/data/standard/MNI152_T1_1mm"); }
+- else { read_volume(refim,string(getenv("FSLDIR")) + "/data/standard/MNI152_T1_1mm"); }
++ if (useReconMNI.value()) { read_volume(refim,"@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm"); }
++ else { read_volume(refim,"@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm"); }
+ volume<float> maskvol(refim);
+ maskvol=0.0f;
+ volume4D<float> volnormals;
+diff --git a/src/fnirt/fnirtfns.cpp b/src/fnirt/fnirtfns.cpp
+index 24e26fd..77899e7 100644
+--- a/src/fnirt/fnirtfns.cpp
++++ b/src/fnirt/fnirtfns.cpp
+@@ -1203,8 +1203,7 @@ string existing_ref_fname(const string& ref_fname)
+ return(string(ref_fname));
+ }
+ else {
+- const char *fsldir_ptr = getenv("FSLDIR");
+- string eref_fname = string(fsldir_ptr) + string("/data/standard/") + ref_fname;
++ string eref_fname = string("@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/") + ref_fname;
+ if (NEWIMAGE::FslFileExists(eref_fname)) return(eref_fname);
+ else return(string(""));
+ }
+@@ -1230,9 +1229,8 @@ string existing_ref_fname(const string& ref_fname)
+ NEWIMAGE::read_volume_hdr_only(vref,ref_fname); // Throws if file dont exist
+ eref_fname = ref_fname;
+ }
+- catch(...) { // Didn't exist in current directory, try in ${FSLDIR}/data/standard
+- const char *fsldir_ptr = getenv("FSLDIR");
+- eref_fname = string(fsldir_ptr) + string("/data/standard/") + ref_fname;
++ catch(...) { // Didn't exist in current directory, try in .../data/standard
++ eref_fname = string("@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/") + ref_fname;
+ try {
+ cout << "Could not find " << ref_fname << ", now checking " << eref_fname << endl;
+ NEWIMAGE::read_volume_hdr_only(vref,eref_fname); // Throws if file dont exist
+@@ -1267,8 +1265,7 @@ string existing_conf_file(const string& cfname)
+ if (check_exist(ecfname)) return(ecfname);
+ }
+ if (!FNIRT::path(cfname).length()) { // If no path explicitly given
+- const char *fsldir_ptr = getenv("FSLDIR");
+- ecfname = string(fsldir_ptr) + string("/etc/flirtsch/") + cfname;
++ ecfname = string("@GENTOO_PORTAGE_EPREFIX@/etc/flirtsch/") + cfname;
+ if (check_exist(ecfname)) return(ecfname);
+ else if (!FNIRT::extension(ecfname).length()) { // If no path _and_ no extension given
+ ecfname += string(".cnf");
+diff --git a/src/fslsurface/fslsurface_first.cc b/src/fslsurface/fslsurface_first.cc
+index faec642..b2ef794 100644
+--- a/src/fslsurface/fslsurface_first.cc
++++ b/src/fslsurface/fslsurface_first.cc
+@@ -500,8 +500,7 @@ namespace fslsurface_name {
+
+ volume<float>* immni = new volume<float>();
+
+- char* fsldir = getenv("FSLDIR");
+- read_volume_hdr_only(*immni, string(fsldir) + "/data/standard/MNI152_T1_1mm");
++ read_volume_hdr_only(*immni, "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm");
+
+ //read_volume_hdr_only(*immni, template_name);
+
+@@ -699,8 +698,7 @@ namespace fslsurface_name {
+
+ volume<float>* immni = new volume<float>();
+
+- char* fsldir = getenv("FSLDIR");
+- read_volume_hdr_only(*immni, string(fsldir) + "/data/standard/MNI152_T1_1mm");
++ read_volume_hdr_only(*immni, "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/data/standard/MNI152_T1_1mm");
+
+ //read_volume_hdr_only(*immni, template_name);
+
+diff --git a/src/fslsurface/fslsurfacemaths.cpp b/src/fslsurface/fslsurfacemaths.cpp
+index eaf55eb..3dc184d 100644
+--- a/src/fslsurface/fslsurfacemaths.cpp
++++ b/src/fslsurface/fslsurfacemaths.cpp
+@@ -598,12 +598,6 @@ int main (int argc, char * argv[])
+
+ }else if (command == "-reconFromBvars"){
+ cout<<"do recon "<<endl;
+- char* fsldir = getenv("FSLDIR");
+- if (fsldir == NULL)
+- {
+- cerr<<"FSLDIR has not been set. "<<endl;
+- exit(EXIT_FAILURE);
+- }
+ //file.bvars,mni_template.nii.gz
+ // string mni = string(fsldir)+"/data/standard/MNI152_T1_1mm";
+ reconSurface_from_bvars( surf, string(argv[i_arg+1]));
+@@ -612,12 +606,6 @@ int main (int argc, char * argv[])
+
+ }else if (command == "-reconAllFromBvarsAndSave"){
+ cout<<"do recon+save "<<argc<<" "<<i_arg<<endl;
+- char* fsldir = getenv("FSLDIR");
+- if (fsldir == NULL)
+- {
+- cerr<<"FSLDIR has not been set. "<<endl;
+- exit(EXIT_FAILURE);
+- }
+ //file.bvars,mni_template.nii.gz
+ // string mni = string(fsldir)+"/data/standard/MNI152_T1_1mm";
+ cout<<"recon "<< string(argv[i_arg+1])<<endl;
diff --git a/sci-biology/fsl/files/fsl-6.0.4-fsldir_redux-p2.patch b/sci-biology/fsl/files/fsl-6.0.4-fsldir_redux-p2.patch
new file mode 100644
index 000000000..af498b400
--- /dev/null
+++ b/sci-biology/fsl/files/fsl-6.0.4-fsldir_redux-p2.patch
@@ -0,0 +1,254 @@
+diff --git a/src/libvis/miscpic.h b/src/libvis/miscpic.h
+index a2f3855..5f440f2 100644
+--- a/src/libvis/miscpic.h
++++ b/src/libvis/miscpic.h
+@@ -90,12 +90,7 @@ namespace MISCPIC{
+ markRight=false;
+ trans= -10;
+ edgethresh = 0.0;
+- if(getenv("FSLDIR")!=0){
+- lutbase = string(getenv("FSLDIR")) + "/etc/luts/";
+- }
+- else{
+- lutbase = string("/");
+- }
++ lutbase = "@GENTOO_PORTAGE_EPREFIX@/etc/luts/";
+ title = string("");
+ cbartype = string("");
+ cbarptr = NULL;
+diff --git a/src/melodic/meldata.cc b/src/melodic/meldata.cc
+index 1749a45..c4ad234 100644
+--- a/src/melodic/meldata.cc
++++ b/src/melodic/meldata.cc
+@@ -992,7 +992,7 @@ namespace Melodic{
+ void MelodicData::est_smoothness()
+ {
+ if(Resels == 0){
+- string SM_path = opts.binpath + "smoothest";
++ string SM_path = "smoothest";
+ string Mask_fname = logger.appendDir("mask");
+
+ if(opts.segment.value().length()>0){
+@@ -1157,7 +1157,7 @@ namespace Melodic{
+ // set up all strings
+ string BET_outputfname = string(Mean_fname)+"_brain";
+
+- string BET_path = opts.binpath + "bet";
++ string BET_path = "bet";
+ string BET_optarg = "-m -f 0.4"; // see man bet
+ string Mask_fname = BET_outputfname+"_mask";
+
+diff --git a/src/melodic/meloptions.cc b/src/melodic/meloptions.cc
+index 08170c7..252e72b 100644
+--- a/src/melodic/meloptions.cc
++++ b/src/melodic/meloptions.cc
+@@ -93,14 +93,6 @@ MelodicOptions* MelodicOptions::gopt = NULL;
+ explicitnums = false;
+ logfname = string("log.txt");
+
+- // work out the path to the $FSLDIR/bin directory
+- if(getenv("FSLDIR")!=0){
+- binpath = (string) getenv("FSLDIR") + "/bin/";
+- } else{
+- binpath = argv[0];
+- binpath = binpath.substr(0,binpath.length()-7);
+- }
+-
+ // parse once to establish log directory name
+ for(int a = options.parse_command_line(argc, argv); a < argc; a++);
+
+diff --git a/src/melodic/meloptions.h b/src/melodic/meloptions.h
+index f546125..b964b7d 100644
+--- a/src/melodic/meloptions.h
++++ b/src/melodic/meloptions.h
+@@ -93,7 +93,6 @@ class MelodicOptions {
+ ~MelodicOptions() { delete gopt; }
+
+ string version;
+- string binpath;
+ string logfname;
+ bool filtermode;
+ bool explicitnums;
+diff --git a/src/melodic/melreport.cc b/src/melodic/melreport.cc
+index 141b6c2..2625059 100644
+--- a/src/melodic/melreport.cc
++++ b/src/melodic/melreport.cc
+@@ -84,8 +84,8 @@ namespace Melodic{
+ IChtml.setDir(report.getDir(),mmodel.get_prefix()+".html");
+
+ {//start IC page
+- IChtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
+- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl
++ IChtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:"
++ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl
+ << "<style type=\"text/css\">OBJECT { width: 100% }</style>"
+ << "<TITLE>FSL</TITLE></HEAD>" << endl
+ << "<IFRAME height=" << int(melodat.get_numfiles()/30 + 1)*50
+@@ -486,8 +486,8 @@ namespace Melodic{
+
+ {//start IC2 page
+ IChtml2.setDir(report.getDir(),mmodel.get_prefix()+"_MM.html");
+- IChtml2 << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
+- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl
++ IChtml2 << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:"
++ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl
+ << "<style type=\"text/css\">OBJECT { width: 100% }</style>"
+ << "<TITLE>FSL</TITLE></HEAD>" << endl
+ << "<IFRAME height="<< int(melodat.get_numfiles()/30 + 1)*50
+@@ -665,8 +665,8 @@ namespace Melodic{
+ IChtml << "<HTML> " << endl
+ << "<TITLE>MELODIC Component " << num2str(cnum)
+ << "</TITLE>" << endl
+- << "<BODY BACKGROUND=\"file:" << getenv("FSLDIR")
+- << "/doc/images/fsl-bg.jpg\">" << endl
++ << "<BODY BACKGROUND=\"file:"
++ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">" << endl
+ << "<hr><CENTER><H1>MELODIC Component " << num2str(cnum)
+ << "</H1>"<< endl;
+
+diff --git a/src/melodic/melreport.h b/src/melodic/melreport.h
+index 574fc4c..e444681 100644
+--- a/src/melodic/melreport.h
++++ b/src/melodic/melreport.h
+@@ -104,21 +104,21 @@ namespace Melodic{
+ const time_t tmptime = time(NULL);
+ system(("mkdir "+ logger.appendDir("report") + " 2>/dev/null").c_str());
+ report.setDir(logger.appendDir("report"),"00index.html",true,false,ios::out);
+- report << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
+- (string) getenv("FSLDIR") +"/doc/fsl.css>"
++ report << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:"
++ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>"
+ << "<TITLE>MELODIC report</TITLE></HEAD><BODY>"
+ << endl <<endl;
+ loghtml.setDir(report.getDir(),"log.html");
+- loghtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:" +
+- (string) getenv("FSLDIR") +"/doc/fsl.css>"
++ loghtml << "<HTML><HEAD><link REL=stylesheet TYPE=text/css href=file:"
++ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>"
+ << "<TITLE>MELODIC report</TITLE></HEAD><BODY>"
+ << endl <<endl;
+ navigator.setDir(report.getDir(),"nav.html");
+ head.setDir(report.getDir(),"head.html");
+- navigator << "<link REL=stylesheet TYPE=text/css href=file:"+
+- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl;
+- head << "<link REL=stylesheet TYPE=text/css href=file:"+
+- (string) getenv("FSLDIR") +"/doc/fsl.css>" << endl;
++ navigator << "<link REL=stylesheet TYPE=text/css href=file:"
++ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl;
++ head << "<link REL=stylesheet TYPE=text/css href=file:"
++ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/fsl.css>" << endl;
+ head <<"<TABLE BORDER=0><TR>" << endl
+ <<" <TD ALIGN=CENTER WIDTH=100%>"<< endl
+ <<"<TABLE BORDER=0>"<< endl
+@@ -130,8 +130,8 @@ namespace Melodic{
+ << "</tr></table>" << endl
+ << "<TD ALIGN=RIGHT>" << endl
+ << "<a href=http://www.fmrib.ox.ac.uk/fsl target=_top>" << endl
+- << "<IMG BORDER=0 SRC=file:"<< getenv("FSLDIR")
+- << "/doc/images/fsl-logo-big.jpg WIDTH=165></a>" << endl
++ << "<IMG BORDER=0 SRC=file:"
++ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-logo-big.jpg WIDTH=165></a>" << endl
+ << "</TD>"<<endl<<"</TR></TABLE> <hr>"<<endl;
+ if(opts.guireport.value()==""){
+ report <<"<OBJECT data=head.html></OBJECT>" << endl;
+diff --git a/src/mm/mixture_model.cc b/src/mm/mixture_model.cc
+index b8e6167..5f00693 100644
+--- a/src/mm/mixture_model.cc
++++ b/src/mm/mixture_model.cc
+@@ -2224,8 +2224,8 @@ namespace Mm {
+
+ htmllog << "<HTML> " << endl
+ << "<TITLE>Mixture Model fit for" << data_name << "</TITLE>" << endl
+- << "<BODY BACKGROUND=\"file:" << getenv("FSLDIR")
+- << "/doc/images/fsl-bg.jpg\">" << endl
++ << "<BODY BACKGROUND=\"file:"
++ << "@GENTOO_PORTAGE_EPREFIX@/usr/share/fsl/doc/images/fsl-bg.jpg\">" << endl
+ << "<hr><CENTER><H1>Mixture Model fit for<br>" << data_name << " </H1>"<< endl;
+
+ htmllog << "<hr><p>" << endl;
+diff -Naur fsl.orig/src/siena/siena_diff.cc fsl/src/siena/siena_diff.cc
+--- fsl.orig/src/siena/siena_diff.cc 2020-12-02 15:52:50.359856656 -0500
++++ fsl/src/siena/siena_diff.cc 2020-12-02 16:03:25.699876412 -0500
+@@ -107,7 +107,7 @@
+ {
+ // {{{ vars
+
+-char thestring[10000], segoptions[10000], fsldir[10000];
++char thestring[10000], segoptions[10000];
+ int x_size, y_size, z_size, size, x, y, z, i, count,
+ seg2=0, ignore_z=0, ignore_top_slices=0, //erode_mask=0,
+ ignore_bottom_slices=0, debug=0, flow_output=1, edge_masking=0;
+@@ -124,8 +124,6 @@
+
+ string argv1(argv[1]), argv2(argv[2]);
+
+-sprintf(fsldir,"%s",getenv("FSLDIR"));
+-
+ for (i = 3; i < argc; i++)
+ {
+ if (!strcmp(argv[i], "-i"))
+@@ -206,26 +204,26 @@
+ // }}}
+ // {{{ transform images and masks
+
+-sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
+- fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
++sprintf(thestring,"flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
++ argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
+ printf("%s\n",thestring); system(thestring);
+
+-sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
+- fsldir,argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
++sprintf(thestring,"flirt -o %s_halfwayto_%s -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s",
++ argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
+ printf("%s\n",thestring); system(thestring);
+
+-sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
+- fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
++sprintf(thestring,"flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
++ argv[1],argv[2],argv[1],argv[2],argv[1],argv[1]);
+ printf("%s\n",thestring); system(thestring);
+
+-sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
+- fsldir,argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
++sprintf(thestring,"flirt -o %s_halfwayto_%s_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_brain_mask",
++ argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
+ printf("%s\n",thestring); system(thestring);
+
+ if (edge_masking)
+ {
+- sprintf(thestring,"%s/bin/flirt -o %s_halfwayto_%s_valid_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_valid_mask_with_%s",
+- fsldir,argv[1],argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
++ sprintf(thestring,"flirt -o %s_halfwayto_%s_valid_mask -applyisoxfm 1 -paddingsize 0 -init %s_halfwayto_%s.mat -ref %s -in %s_valid_mask_with_%s",
++ argv[1],argv[2],argv[1],argv[2],argv[1],argv[1],argv[2]);
+ printf("%s\n",thestring); system(thestring);
+ }
+
+@@ -284,8 +282,8 @@
+ cout << "saving image 1 to disk prior to segmentation" << endl;
+ save_volume(in1,argv1+"_halfwayto_"+argv2+"_brain");
+ in1.destroy();
+- sprintf(thestring,"%s/bin/fast %s %s %s_halfwayto_%s_brain > %s_halfwayto_%s_brain.vol 2>&1",
+- fsldir,segtype,segoptions,argv[1],argv[2],argv[1],argv[2]);
++ sprintf(thestring,"fast %s %s %s_halfwayto_%s_brain > %s_halfwayto_%s_brain.vol 2>&1",
++ segtype,segoptions,argv[1],argv[2],argv[1],argv[2]);
+ cout << thestring << endl;
+ system(thestring);
+ }
+diff --git a/src/topup/topupfns.cpp b/src/topup/topupfns.cpp
+index 6873758..9e8b956 100644
+--- a/src/topup/topupfns.cpp
++++ b/src/topup/topupfns.cpp
+@@ -463,8 +463,7 @@ string existing_conf_file(const string& cfname)
+ if (TOPUP::check_exist(ecfname)) return(ecfname);
+ }
+ if (!TOPUP::path(cfname).length()) { // If no path explicitly given
+- const char *fsldir_ptr = getenv("FSLDIR");
+- ecfname = string(fsldir_ptr) + string("/etc/flirtsch/") + cfname;
++ ecfname = string("@GENTOO_PORTAGE_EPREFIX@/etc/flirtsch/") + cfname;
+ if (TOPUP::check_exist(ecfname)) return(ecfname);
+ else if (!TOPUP::extension(ecfname).length()) { // If no path _and_ no extension given
+ ecfname += string(".cnf");
+--
+2.24.1
+
diff --git a/sci-biology/fsl/files/fsl-6.0.4-gcc10_include.patch b/sci-biology/fsl/files/fsl-6.0.4-gcc10_include.patch
new file mode 100644
index 000000000..ae836c065
--- /dev/null
+++ b/sci-biology/fsl/files/fsl-6.0.4-gcc10_include.patch
@@ -0,0 +1,11 @@
+diff -Naur fsl.orig/src/newimage/newimageio.h fsl/src/newimage/newimageio.h
+--- fsl.orig/src/newimage/newimageio.h 2020-12-02 15:15:27.012786899 -0500
++++ fsl/src/newimage/newimageio.h 2020-12-02 15:19:51.046795110 -0500
+@@ -75,6 +75,7 @@
+ #include <iostream>
+ #include <fstream>
+ #include <sstream>
++#include <stdexcept>
+ #include "NewNifti/NewNifti.h"
+ #include "newmatio.h"
+ #include "newimage.h"
diff --git a/sci-biology/fsl/files/fsl-6.0.4-melodic_std.patch b/sci-biology/fsl/files/fsl-6.0.4-melodic_std.patch
new file mode 100644
index 000000000..83b5b9932
--- /dev/null
+++ b/sci-biology/fsl/files/fsl-6.0.4-melodic_std.patch
@@ -0,0 +1,11 @@
+diff -Naur fsl.orig/src/melodic/Makefile fsl/src/melodic/Makefile
+--- fsl.orig/src/melodic/Makefile 2021-01-06 14:04:35.743274475 -0500
++++ fsl/src/melodic/Makefile 2021-01-06 14:11:27.924264859 -0500
+@@ -9,6 +9,7 @@
+
+ USRINCFLAGS = -I${INC_NEWMAT} -I${INC_PROB} -I${INC_GD} -I${INC_GDC} -I${INC_PNG} -I${INC_ZLIB} -DCIFTILIB_USE_XMLPP -I${FSLEXTINC} -I${INC_XML2} -I${INC_XML++} -I${INC_XML++CONF} -I${INC_BOOST} -I${FSLDIR}/include/ciftiio
+ USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_PROB} -L${LIB_GD} -L${LIB_GDC} -L${LIB_PNG} -L${LIB_ZLIB}
++USRCXXFLAGS = -std=c++11
+
+ UNAME := $(shell uname)
+ ifeq (${UNAME},Darwin)
diff --git a/sci-biology/fsl/files/fsl-6.0.4-remove_fslpy_collisions-p1.patch b/sci-biology/fsl/files/fsl-6.0.4-remove_fslpy_collisions-p1.patch
new file mode 100644
index 000000000..434dc9cf6
--- /dev/null
+++ b/sci-biology/fsl/files/fsl-6.0.4-remove_fslpy_collisions-p1.patch
@@ -0,0 +1,303 @@
+diff -Naur fsl.orig/src/fslio/imln fsl/src/fslio/imln
+--- fsl.orig/src/fslio/imln 2021-02-01 15:29:34.842752994 -0500
++++ fsl/src/fslio/imln 1969-12-31 19:00:00.000000000 -0500
+@@ -1,90 +0,0 @@
+-#!/bin/sh
+-
+-# imln - make symbolic link(s) to image file(s)
+-#
+-# Stephen Smith and Mark Jenkinson, FMRIB Image Analysis Group
+-#
+-# Copyright (C) 1999-2004 University of Oxford
+-#
+-# Part of FSL - FMRIB's Software Library
+-# http://www.fmrib.ox.ac.uk/fsl
+-# fsl@fmrib.ox.ac.uk
+-#
+-# Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
+-# Imaging of the Brain), Department of Clinical Neurology, Oxford
+-# University, Oxford, UK
+-#
+-#
+-# LICENCE
+-#
+-# FMRIB Software Library, Release 6.0 (c) 2018, The University of
+-# Oxford (the "Software")
+-#
+-# The Software remains the property of the Oxford University Innovation
+-# ("the University").
+-#
+-# The Software is distributed "AS IS" under this Licence solely for
+-# non-commercial use in the hope that it will be useful, but in order
+-# that the University as a charitable foundation protects its assets for
+-# the benefit of its educational and research purposes, the University
+-# makes clear that no condition is made or to be implied, nor is any
+-# warranty given or to be implied, as to the accuracy of the Software,
+-# or that it will be suitable for any particular purpose or for use
+-# under any specific conditions. Furthermore, the University disclaims
+-# all responsibility for the use which is made of the Software. It
+-# further disclaims any liability for the outcomes arising from using
+-# the Software.
+-#
+-# The Licensee agrees to indemnify the University and hold the
+-# University harmless from and against any and all claims, damages and
+-# liabilities asserted by third parties (including claims for
+-# negligence) which arise directly or indirectly from the use of the
+-# Software or the sale of any products based on the Software.
+-#
+-# No part of the Software may be reproduced, modified, transmitted or
+-# transferred in any form or by any means, electronic or mechanical,
+-# without the express permission of the University. The permission of
+-# the University is not required if the said reproduction, modification,
+-# transmission or transference is done without financial return, the
+-# conditions of this Licence are imposed upon the receiver of the
+-# product, and all original and amended source code is included in any
+-# transmitted product. You may be held legally responsible for any
+-# copyright infringement that is caused or encouraged by your failure to
+-# abide by these terms and conditions.
+-#
+-# You are not permitted under this Licence to use this Software
+-# commercially. Use for which any financial return is received shall be
+-# defined as commercial use, and includes (1) integration of all or part
+-# of the source code or the Software into a product for sale or license
+-# by or on behalf of Licensee to third parties or (2) use of the
+-# Software or any derivative of it for research with the final aim of
+-# developing software products for sale or license to a third party or
+-# (3) use of the Software or any derivative of it for research with the
+-# final aim of developing non-software products for sale or license to a
+-# third party, or (4) use of the Software to provide any service to an
+-# external organisation for which payment is received. If you are
+-# interested in using the Software commercially, please contact Oxford
+-# University Innovation ("OUI"), the technology transfer company of the
+-# University, to negotiate a licence. Contact details are:
+-# fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.
+-export LC_ALL=C
+-
+-if [ $# -lt 2 ] ; then
+- echo "Usage: $0 <file1> <file2>"
+- echo " Makes a link (called file2) to file1"
+- echo " NB: filenames can be basenames or include an extension"
+- exit 1;
+-fi
+-
+-f1=`${FSLDIR}/bin/remove_ext $1`;
+-f2=`${FSLDIR}/bin/remove_ext $2`;
+-
+-if [ -f ${f1}.hdr ] ; then ln -fs ${f1}.hdr ${f2}.hdr ; fi
+-if [ -f ${f1}.hdr.gz ] ; then ln -fs ${f1}.hdr.gz ${f2}.hdr.gz ; fi
+-if [ -f ${f1}.img ] ; then ln -fs ${f1}.img ${f2}.img ; fi
+-if [ -f ${f1}.img.gz ] ; then ln -fs ${f1}.img.gz ${f2}.img.gz ; fi
+-if [ -f ${f1}.nii ] ; then ln -fs ${f1}.nii ${f2}.nii ; fi
+-if [ -f ${f1}.nii.gz ] ; then ln -fs ${f1}.nii.gz ${f2}.nii.gz ; fi
+-if [ -f ${f1}.mnc ] ; then ln -fs ${f1}.mnc ${f2}.mnc ; fi
+-if [ -f ${f1}.mnc.gz ] ; then ln -fs ${f1}.mnc.gz ${f2}.mnc.gz ; fi
+-
+diff -Naur fsl.orig/src/fslio/imrm fsl/src/fslio/imrm
+--- fsl.orig/src/fslio/imrm 2021-02-01 15:29:34.842752994 -0500
++++ fsl/src/fslio/imrm 1969-12-31 19:00:00.000000000 -0500
+@@ -1,83 +0,0 @@
+-#!/bin/sh
+-
+-# imrm - remove image files
+-#
+-# Stephen Smith and Mark Jenkinson, FMRIB Image Analysis Group
+-#
+-# Copyright (C) 1999-2004 University of Oxford
+-#
+-# Part of FSL - FMRIB's Software Library
+-# http://www.fmrib.ox.ac.uk/fsl
+-# fsl@fmrib.ox.ac.uk
+-#
+-# Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
+-# Imaging of the Brain), Department of Clinical Neurology, Oxford
+-# University, Oxford, UK
+-#
+-#
+-# LICENCE
+-#
+-# FMRIB Software Library, Release 6.0 (c) 2018, The University of
+-# Oxford (the "Software")
+-#
+-# The Software remains the property of the Oxford University Innovation
+-# ("the University").
+-#
+-# The Software is distributed "AS IS" under this Licence solely for
+-# non-commercial use in the hope that it will be useful, but in order
+-# that the University as a charitable foundation protects its assets for
+-# the benefit of its educational and research purposes, the University
+-# makes clear that no condition is made or to be implied, nor is any
+-# warranty given or to be implied, as to the accuracy of the Software,
+-# or that it will be suitable for any particular purpose or for use
+-# under any specific conditions. Furthermore, the University disclaims
+-# all responsibility for the use which is made of the Software. It
+-# further disclaims any liability for the outcomes arising from using
+-# the Software.
+-#
+-# The Licensee agrees to indemnify the University and hold the
+-# University harmless from and against any and all claims, damages and
+-# liabilities asserted by third parties (including claims for
+-# negligence) which arise directly or indirectly from the use of the
+-# Software or the sale of any products based on the Software.
+-#
+-# No part of the Software may be reproduced, modified, transmitted or
+-# transferred in any form or by any means, electronic or mechanical,
+-# without the express permission of the University. The permission of
+-# the University is not required if the said reproduction, modification,
+-# transmission or transference is done without financial return, the
+-# conditions of this Licence are imposed upon the receiver of the
+-# product, and all original and amended source code is included in any
+-# transmitted product. You may be held legally responsible for any
+-# copyright infringement that is caused or encouraged by your failure to
+-# abide by these terms and conditions.
+-#
+-# You are not permitted under this Licence to use this Software
+-# commercially. Use for which any financial return is received shall be
+-# defined as commercial use, and includes (1) integration of all or part
+-# of the source code or the Software into a product for sale or license
+-# by or on behalf of Licensee to third parties or (2) use of the
+-# Software or any derivative of it for research with the final aim of
+-# developing software products for sale or license to a third party or
+-# (3) use of the Software or any derivative of it for research with the
+-# final aim of developing non-software products for sale or license to a
+-# third party, or (4) use of the Software to provide any service to an
+-# external organisation for which payment is received. If you are
+-# interested in using the Software commercially, please contact Oxford
+-# University Innovation ("OUI"), the technology transfer company of the
+-# University, to negotiate a licence. Contact details are:
+-# fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.
+-export LC_ALL=C
+-
+-if [ $# -lt 1 ] ; then
+- echo "Usage: $0 <list of image names to remove>"
+- echo "NB: filenames can be basenames or not"
+- exit 1;
+-fi
+-
+-for f in $@ ; do
+- fn=`${FSLDIR}/bin/remove_ext $f`;
+- # do the rm silently
+- /bin/rm -f ${fn}.img ${fn}.hdr ${fn}.hdr.gz ${fn}.img.gz ${fn}.nii ${fn}.nii.gz ${fn}.mnc ${fn}.mnc.gz
+-done
+-
+diff -Naur fsl.orig/src/fslio/imtest fsl/src/fslio/imtest
+--- fsl.orig/src/fslio/imtest 2021-02-01 15:29:34.842752994 -0500
++++ fsl/src/fslio/imtest 1969-12-31 19:00:00.000000000 -0500
+@@ -1,118 +0,0 @@
+-#!/bin/sh
+-
+-# imtest - test to see if a valid image file exists with this name (root)
+-#
+-# Stephen Smith and Mark Jenkinson, FMRIB Image Analysis Group
+-#
+-# Copyright (C) 1999-2004 University of Oxford
+-#
+-# Part of FSL - FMRIB's Software Library
+-# http://www.fmrib.ox.ac.uk/fsl
+-# fsl@fmrib.ox.ac.uk
+-#
+-# Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
+-# Imaging of the Brain), Department of Clinical Neurology, Oxford
+-# University, Oxford, UK
+-#
+-#
+-# LICENCE
+-#
+-# FMRIB Software Library, Release 6.0 (c) 2018, The University of
+-# Oxford (the "Software")
+-#
+-# The Software remains the property of the Oxford University Innovation
+-# ("the University").
+-#
+-# The Software is distributed "AS IS" under this Licence solely for
+-# non-commercial use in the hope that it will be useful, but in order
+-# that the University as a charitable foundation protects its assets for
+-# the benefit of its educational and research purposes, the University
+-# makes clear that no condition is made or to be implied, nor is any
+-# warranty given or to be implied, as to the accuracy of the Software,
+-# or that it will be suitable for any particular purpose or for use
+-# under any specific conditions. Furthermore, the University disclaims
+-# all responsibility for the use which is made of the Software. It
+-# further disclaims any liability for the outcomes arising from using
+-# the Software.
+-#
+-# The Licensee agrees to indemnify the University and hold the
+-# University harmless from and against any and all claims, damages and
+-# liabilities asserted by third parties (including claims for
+-# negligence) which arise directly or indirectly from the use of the
+-# Software or the sale of any products based on the Software.
+-#
+-# No part of the Software may be reproduced, modified, transmitted or
+-# transferred in any form or by any means, electronic or mechanical,
+-# without the express permission of the University. The permission of
+-# the University is not required if the said reproduction, modification,
+-# transmission or transference is done without financial return, the
+-# conditions of this Licence are imposed upon the receiver of the
+-# product, and all original and amended source code is included in any
+-# transmitted product. You may be held legally responsible for any
+-# copyright infringement that is caused or encouraged by your failure to
+-# abide by these terms and conditions.
+-#
+-# You are not permitted under this Licence to use this Software
+-# commercially. Use for which any financial return is received shall be
+-# defined as commercial use, and includes (1) integration of all or part
+-# of the source code or the Software into a product for sale or license
+-# by or on behalf of Licensee to third parties or (2) use of the
+-# Software or any derivative of it for research with the final aim of
+-# developing software products for sale or license to a third party or
+-# (3) use of the Software or any derivative of it for research with the
+-# final aim of developing non-software products for sale or license to a
+-# third party, or (4) use of the Software to provide any service to an
+-# external organisation for which payment is received. If you are
+-# interested in using the Software commercially, please contact Oxford
+-# University Innovation ("OUI"), the technology transfer company of the
+-# University, to negotiate a licence. Contact details are:
+-# fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.
+-export LC_ALL=C
+-
+-# return 0 if no image exists or 1 if the image exists
+-
+-if [ $# -lt 1 ] ; then
+- echo "0";
+- exit;
+-fi
+-
+-inputfile=$1
+-
+-
+-
+-for i in 1 2 3 4 5 6 7 8 9 10 11 12
+-do
+-if [ -h $inputfile ] ; then
+-inputfile=`readlink $inputfile`;
+-fi
+-done
+-
+-filename=`${FSLDIR}/bin/remove_ext $inputfile`;
+-
+-if [ -r ${filename}.nii ] || [ -r ${filename}.nii.gz ] ; then
+- echo "1";
+- exit;
+-fi
+-
+-if [ -r ${filename}.mnc ] || [ -r ${filename}.mnc.gz ] ; then
+- echo "1";
+- exit;
+-fi
+-
+-if [ ! -r ${filename}.hdr ] && [ ! -r ${filename}.hdr.gz ] ; then
+- # return 0 here as no header exists and no single image means no image!
+- echo "0";
+- exit;
+-fi
+-
+-if [ ! -r ${filename}.img ] && [ ! -r ${filename}.img.gz ] ; then
+- # return 0 here as no img file exists and no single image means no image!
+- echo "0";
+- exit;
+-fi
+-
+-# only gets to here if there was a hdr and an img file
+-
+-echo "1";
+-exit;
+-
diff --git a/sci-biology/fsl/files/fsl-6.0.4-remove_fslpy_collisions-p2.patch b/sci-biology/fsl/files/fsl-6.0.4-remove_fslpy_collisions-p2.patch
new file mode 100644
index 000000000..ddb7cfb67
--- /dev/null
+++ b/sci-biology/fsl/files/fsl-6.0.4-remove_fslpy_collisions-p2.patch
@@ -0,0 +1,348 @@
+diff -Naur fsl.orig/src/fslio/Makefile fsl/src/fslio/Makefile
+--- fsl.orig/src/fslio/Makefile 2021-02-01 15:29:34.842752994 -0500
++++ fsl/src/fslio/Makefile 2021-02-01 15:32:19.723761859 -0500
+@@ -6,7 +6,7 @@
+
+ OBJS=fslio.o
+
+-SCRIPTS = remove_ext fsloutputtype imtest imglob imcp imln imrm immv
++SCRIPTS = fsloutputtype imglob imcp immv
+
+ all:
+
+diff -Naur fsl.orig/src/fslio/remove_ext fsl/src/fslio/remove_ext
+--- fsl.orig/src/fslio/remove_ext 2021-02-01 15:29:34.842752994 -0500
++++ fsl/src/fslio/remove_ext 1969-12-31 19:00:00.000000000 -0500
+@@ -1,87 +0,0 @@
+-#!/bin/sh
+-
+-# remove_ext - remove extension from image filename
+-#
+-# Stephen Smith and Mark Jenkinson, FMRIB Image Analysis Group
+-#
+-# Copyright (C) 1999-2004 University of Oxford
+-#
+-# Part of FSL - FMRIB's Software Library
+-# http://www.fmrib.ox.ac.uk/fsl
+-# fsl@fmrib.ox.ac.uk
+-#
+-# Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
+-# Imaging of the Brain), Department of Clinical Neurology, Oxford
+-# University, Oxford, UK
+-#
+-#
+-# LICENCE
+-#
+-# FMRIB Software Library, Release 6.0 (c) 2018, The University of
+-# Oxford (the "Software")
+-#
+-# The Software remains the property of the Oxford University Innovation
+-# ("the University").
+-#
+-# The Software is distributed "AS IS" under this Licence solely for
+-# non-commercial use in the hope that it will be useful, but in order
+-# that the University as a charitable foundation protects its assets for
+-# the benefit of its educational and research purposes, the University
+-# makes clear that no condition is made or to be implied, nor is any
+-# warranty given or to be implied, as to the accuracy of the Software,
+-# or that it will be suitable for any particular purpose or for use
+-# under any specific conditions. Furthermore, the University disclaims
+-# all responsibility for the use which is made of the Software. It
+-# further disclaims any liability for the outcomes arising from using
+-# the Software.
+-#
+-# The Licensee agrees to indemnify the University and hold the
+-# University harmless from and against any and all claims, damages and
+-# liabilities asserted by third parties (including claims for
+-# negligence) which arise directly or indirectly from the use of the
+-# Software or the sale of any products based on the Software.
+-#
+-# No part of the Software may be reproduced, modified, transmitted or
+-# transferred in any form or by any means, electronic or mechanical,
+-# without the express permission of the University. The permission of
+-# the University is not required if the said reproduction, modification,
+-# transmission or transference is done without financial return, the
+-# conditions of this Licence are imposed upon the receiver of the
+-# product, and all original and amended source code is included in any
+-# transmitted product. You may be held legally responsible for any
+-# copyright infringement that is caused or encouraged by your failure to
+-# abide by these terms and conditions.
+-#
+-# You are not permitted under this Licence to use this Software
+-# commercially. Use for which any financial return is received shall be
+-# defined as commercial use, and includes (1) integration of all or part
+-# of the source code or the Software into a product for sale or license
+-# by or on behalf of Licensee to third parties or (2) use of the
+-# Software or any derivative of it for research with the final aim of
+-# developing software products for sale or license to a third party or
+-# (3) use of the Software or any derivative of it for research with the
+-# final aim of developing non-software products for sale or license to a
+-# third party, or (4) use of the Software to provide any service to an
+-# external organisation for which payment is received. If you are
+-# interested in using the Software commercially, please contact Oxford
+-# University Innovation ("OUI"), the technology transfer company of the
+-# University, to negotiate a licence. Contact details are:
+-# fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.
+-export LC_ALL=C
+-
+-
+-if [ $# -lt 1 ] ; then
+- exit 1
+-fi
+-
+-lst="";
+-for fn in $@ ; do
+- # for the ones at the end of the line
+- f=`echo "$fn" | sed 's/\.hdr\.gz$//' | sed 's/\.img\.gz$//' | sed 's/\.hdr$//' | sed 's/\.img$//' | sed 's/\.nii.gz$//' | sed 's/\.nii$//' | sed 's/\.mnc.gz$//' | sed 's/\.mnc$//' | sed 's/\.$//'`;
+- # for the ones in the middle of the line
+- f=`echo "$f" | sed 's/\.hdr\.gz[ ]/ /g' | sed 's/\.img\.gz[ ]/ /g' | sed 's/\.hdr[ ]/ /g' | sed 's/\.img[ ]/ /g' | sed 's/\.nii\.gz[ ]/ /g' | sed 's/\.nii[ ]/ /g' | sed 's/\.mnc\.gz[ ]/ /g' | sed 's/\.mnc[ ]/ /g' |sed 's/\.[ ]/ /g'`;
+- lst="$lst $f";
+-done
+-echo $lst;
+-
+-
+diff -Naur fsl.orig/src/misc_scripts/fsl_abspath fsl/src/misc_scripts/fsl_abspath
+--- fsl.orig/src/misc_scripts/fsl_abspath 2021-02-01 15:29:34.828752994 -0500
++++ fsl/src/misc_scripts/fsl_abspath 1969-12-31 19:00:00.000000000 -0500
+@@ -1,71 +0,0 @@
+-#!/usr/bin/env fslpython
+-# fsl_abspath - return true file path
+-# Matthew Webster FMRIB Image Analysis Group
+-# Copyright (C) 2009 University of Oxford
+-# Part of FSL - FMRIB's Software Library
+-# http://www.fmrib.ox.ac.uk/fsl
+-# fsl@fmrib.ox.ac.uk
+-#
+-# Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
+-# Imaging of the Brain), Department of Clinical Neurology, Oxford
+-# University, Oxford, UK
+-#
+-#
+-# LICENCE
+-#
+-# FMRIB Software Library, Release 6.0 (c) 2018, The University of
+-# Oxford (the "Software")
+-#
+-# The Software remains the property of the Oxford University Innovation
+-# ("the University").
+-#
+-# The Software is distributed "AS IS" under this Licence solely for
+-# non-commercial use in the hope that it will be useful, but in order
+-# that the University as a charitable foundation protects its assets for
+-# the benefit of its educational and research purposes, the University
+-# makes clear that no condition is made or to be implied, nor is any
+-# warranty given or to be implied, as to the accuracy of the Software,
+-# or that it will be suitable for any particular purpose or for use
+-# under any specific conditions. Furthermore, the University disclaims
+-# all responsibility for the use which is made of the Software. It
+-# further disclaims any liability for the outcomes arising from using
+-# the Software.
+-#
+-# The Licensee agrees to indemnify the University and hold the
+-# University harmless from and against any and all claims, damages and
+-# liabilities asserted by third parties (including claims for
+-# negligence) which arise directly or indirectly from the use of the
+-# Software or the sale of any products based on the Software.
+-#
+-# No part of the Software may be reproduced, modified, transmitted or
+-# transferred in any form or by any means, electronic or mechanical,
+-# without the express permission of the University. The permission of
+-# the University is not required if the said reproduction, modification,
+-# transmission or transference is done without financial return, the
+-# conditions of this Licence are imposed upon the receiver of the
+-# product, and all original and amended source code is included in any
+-# transmitted product. You may be held legally responsible for any
+-# copyright infringement that is caused or encouraged by your failure to
+-# abide by these terms and conditions.
+-#
+-# You are not permitted under this Licence to use this Software
+-# commercially. Use for which any financial return is received shall be
+-# defined as commercial use, and includes (1) integration of all or part
+-# of the source code or the Software into a product for sale or license
+-# by or on behalf of Licensee to third parties or (2) use of the
+-# Software or any derivative of it for research with the final aim of
+-# developing software products for sale or license to a third party or
+-# (3) use of the Software or any derivative of it for research with the
+-# final aim of developing non-software products for sale or license to a
+-# third party, or (4) use of the Software to provide any service to an
+-# external organisation for which payment is received. If you are
+-# interested in using the Software commercially, please contact Oxford
+-# University Innovation ("OUI"), the technology transfer company of the
+-# University, to negotiate a licence. Contact details are:
+-# fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.
+-from __future__ import print_function
+-import sys
+-import os
+-
+-print (os.path.realpath(sys.argv[1]))
+-sys.exit(0)
+diff -Naur fsl.orig/src/misc_scripts/Makefile fsl/src/misc_scripts/Makefile
+--- fsl.orig/src/misc_scripts/Makefile 2021-02-01 15:29:34.828752994 -0500
++++ fsl/src/misc_scripts/Makefile 2021-02-01 15:32:56.027763811 -0500
+@@ -2,6 +2,6 @@
+
+ PROJNAME = misc_scripts
+
+-SCRIPTS = fslecho regscript remove_vols replace_and_average_fmrib linkbedpost ocmr_preproc correct_and_average eddy_correct Text2Vest Vest2Text AnatomicalAverage fsl_abspath fsl_anat fslFixText
++SCRIPTS = fslecho regscript remove_vols replace_and_average_fmrib linkbedpost ocmr_preproc correct_and_average eddy_correct AnatomicalAverage fsl_anat fslFixText
+
+ all:
+diff -Naur fsl.orig/src/misc_scripts/Text2Vest fsl/src/misc_scripts/Text2Vest
+--- fsl.orig/src/misc_scripts/Text2Vest 2021-02-01 15:29:34.828752994 -0500
++++ fsl/src/misc_scripts/Text2Vest 1969-12-31 19:00:00.000000000 -0500
+@@ -1,80 +0,0 @@
+-#!/bin/sh
+-# Copyright (C) 2012 University of Oxford
+-#
+-# Part of FSL - FMRIB's Software Library
+-# http://www.fmrib.ox.ac.uk/fsl
+-# fsl@fmrib.ox.ac.uk
+-#
+-# Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
+-# Imaging of the Brain), Department of Clinical Neurology, Oxford
+-# University, Oxford, UK
+-#
+-#
+-# LICENCE
+-#
+-# FMRIB Software Library, Release 6.0 (c) 2018, The University of
+-# Oxford (the "Software")
+-#
+-# The Software remains the property of the Oxford University Innovation
+-# ("the University").
+-#
+-# The Software is distributed "AS IS" under this Licence solely for
+-# non-commercial use in the hope that it will be useful, but in order
+-# that the University as a charitable foundation protects its assets for
+-# the benefit of its educational and research purposes, the University
+-# makes clear that no condition is made or to be implied, nor is any
+-# warranty given or to be implied, as to the accuracy of the Software,
+-# or that it will be suitable for any particular purpose or for use
+-# under any specific conditions. Furthermore, the University disclaims
+-# all responsibility for the use which is made of the Software. It
+-# further disclaims any liability for the outcomes arising from using
+-# the Software.
+-#
+-# The Licensee agrees to indemnify the University and hold the
+-# University harmless from and against any and all claims, damages and
+-# liabilities asserted by third parties (including claims for
+-# negligence) which arise directly or indirectly from the use of the
+-# Software or the sale of any products based on the Software.
+-#
+-# No part of the Software may be reproduced, modified, transmitted or
+-# transferred in any form or by any means, electronic or mechanical,
+-# without the express permission of the University. The permission of
+-# the University is not required if the said reproduction, modification,
+-# transmission or transference is done without financial return, the
+-# conditions of this Licence are imposed upon the receiver of the
+-# product, and all original and amended source code is included in any
+-# transmitted product. You may be held legally responsible for any
+-# copyright infringement that is caused or encouraged by your failure to
+-# abide by these terms and conditions.
+-#
+-# You are not permitted under this Licence to use this Software
+-# commercially. Use for which any financial return is received shall be
+-# defined as commercial use, and includes (1) integration of all or part
+-# of the source code or the Software into a product for sale or license
+-# by or on behalf of Licensee to third parties or (2) use of the
+-# Software or any derivative of it for research with the final aim of
+-# developing software products for sale or license to a third party or
+-# (3) use of the Software or any derivative of it for research with the
+-# final aim of developing non-software products for sale or license to a
+-# third party, or (4) use of the Software to provide any service to an
+-# external organisation for which payment is received. If you are
+-# interested in using the Software commercially, please contact Oxford
+-# University Innovation ("OUI"), the technology transfer company of the
+-# University, to negotiate a licence. Contact details are:
+-# fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.
+-export LC_ALL=C
+-if [ $# -lt 2 ] ; then
+- echo "`basename $0` <text file> <vest file>"
+- exit 0
+-fi
+-
+-NumPoints=`grep -cve '^\s*$' $1`
+-NumWaves=`wc $1 | awk '{ print $2 }'`
+-NumWaves=`expr $NumWaves / $NumPoints`
+-
+-echo /NumWaves $NumWaves > $2
+-echo /NumPoints $NumPoints >> $2
+-echo /Matrix >> $2
+-
+-cat $1 >> $2
+-
+diff -Naur fsl.orig/src/misc_scripts/Vest2Text fsl/src/misc_scripts/Vest2Text
+--- fsl.orig/src/misc_scripts/Vest2Text 2021-02-01 15:29:34.828752994 -0500
++++ fsl/src/misc_scripts/Vest2Text 1969-12-31 19:00:00.000000000 -0500
+@@ -1,71 +0,0 @@
+-#!/bin/sh
+-# Copyright (C) 2012 University of Oxford
+-#
+-# Part of FSL - FMRIB's Software Library
+-# http://www.fmrib.ox.ac.uk/fsl
+-# fsl@fmrib.ox.ac.uk
+-#
+-# Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
+-# Imaging of the Brain), Department of Clinical Neurology, Oxford
+-# University, Oxford, UK
+-#
+-#
+-# LICENCE
+-#
+-# FMRIB Software Library, Release 6.0 (c) 2018, The University of
+-# Oxford (the "Software")
+-#
+-# The Software remains the property of the Oxford University Innovation
+-# ("the University").
+-#
+-# The Software is distributed "AS IS" under this Licence solely for
+-# non-commercial use in the hope that it will be useful, but in order
+-# that the University as a charitable foundation protects its assets for
+-# the benefit of its educational and research purposes, the University
+-# makes clear that no condition is made or to be implied, nor is any
+-# warranty given or to be implied, as to the accuracy of the Software,
+-# or that it will be suitable for any particular purpose or for use
+-# under any specific conditions. Furthermore, the University disclaims
+-# all responsibility for the use which is made of the Software. It
+-# further disclaims any liability for the outcomes arising from using
+-# the Software.
+-#
+-# The Licensee agrees to indemnify the University and hold the
+-# University harmless from and against any and all claims, damages and
+-# liabilities asserted by third parties (including claims for
+-# negligence) which arise directly or indirectly from the use of the
+-# Software or the sale of any products based on the Software.
+-#
+-# No part of the Software may be reproduced, modified, transmitted or
+-# transferred in any form or by any means, electronic or mechanical,
+-# without the express permission of the University. The permission of
+-# the University is not required if the said reproduction, modification,
+-# transmission or transference is done without financial return, the
+-# conditions of this Licence are imposed upon the receiver of the
+-# product, and all original and amended source code is included in any
+-# transmitted product. You may be held legally responsible for any
+-# copyright infringement that is caused or encouraged by your failure to
+-# abide by these terms and conditions.
+-#
+-# You are not permitted under this Licence to use this Software
+-# commercially. Use for which any financial return is received shall be
+-# defined as commercial use, and includes (1) integration of all or part
+-# of the source code or the Software into a product for sale or license
+-# by or on behalf of Licensee to third parties or (2) use of the
+-# Software or any derivative of it for research with the final aim of
+-# developing software products for sale or license to a third party or
+-# (3) use of the Software or any derivative of it for research with the
+-# final aim of developing non-software products for sale or license to a
+-# third party, or (4) use of the Software to provide any service to an
+-# external organisation for which payment is received. If you are
+-# interested in using the Software commercially, please contact Oxford
+-# University Innovation ("OUI"), the technology transfer company of the
+-# University, to negotiate a licence. Contact details are:
+-# fsl@innovation.ox.ac.uk quoting Reference Project 9564, FSL.
+-export LC_ALL=C
+-if [ $# -lt 2 ] ; then
+- echo "`basename $0` <vest file> <text file>"
+- exit 0
+-fi
+-sed -e "/\//d" $1 | sed '/^$/d' > $2
+-
diff --git a/sci-biology/fsl/files/fsl-6.0.4-setup.patch b/sci-biology/fsl/files/fsl-6.0.4-setup.patch
new file mode 100644
index 000000000..061e1a22a
--- /dev/null
+++ b/sci-biology/fsl/files/fsl-6.0.4-setup.patch
@@ -0,0 +1,174 @@
+diff -Naur fsl.orig/build fsl/build
+--- fsl.orig/build 2020-12-02 15:29:12.180812558 -0500
++++ fsl/build 2020-12-02 15:34:03.854821628 -0500
+@@ -28,7 +28,6 @@
+ # The build order for MASTERLIBS is very important, and should not be modified unless you know what
+ # you are doing.
+ MASTERLIBS="
+- CiftiLib-master \
+ utils \
+ znzlib \
+ NewNifti \
+@@ -157,8 +156,8 @@
+ done #project (MASTERPROJECTS)
+ fi #full build
+
+-echo "Building projects - see build.log file for progress..."
+-./config/common/buildproj $PROJECTS > ./build.log 2>&1
++echo "Building projects"
++./config/common/buildproj $PROJECTS
+ finalStatus=$?
+ if [ $finalStatus -eq 0 ]; then
+ echo "Build completed successfully.";
+diff -Naur fsl.orig/config/buildSettings.mk fsl/config/buildSettings.mk
+--- fsl.orig/config/buildSettings.mk 2020-12-02 15:29:11.993812552 -0500
++++ fsl/config/buildSettings.mk 2020-12-02 15:39:37.269831995 -0500
+@@ -18,7 +18,7 @@
+ CHMOD = /bin/chmod
+ MKDIR = /bin/mkdir
+ INSTALL = install -p
+-TCLSH = ${FSLDIR}/bin/fsltclsh
++TCLSH = tclsh
+ DEPENDFLAGS = -MM
+ MACHDBGFLAGS = -g
+ #####################################################################
+@@ -127,19 +127,19 @@
+ #####################################################################
+ ifeq ($(SYSTYPE), Linux)
+ ############### System Vars #####################################
+-CC = gcc
+-CXX = c++
+-CXX11 = c++
++CC = @@GENTOO_CC@@
++CXX = @@GENTOO_CXX@@
++CXX11 = @@GENTOO_CXX@@
+ CSTATICFLAGS = -static
+ CXXSTATICFLAGS = -static
+-ARCHFLAGS = -m64
+-ARCHLDFLAGS = -Wl,-rpath,'$$ORIGIN/../lib'
++ARCHFLAGS =
++ARCHLDFLAGS =
+ PARALLELFLAGS = -fopenmp
+-OPTFLAGS = -g -O3 -fexpensive-optimizations ${ARCHFLAGS}
++OPTFLAGS =
+ GNU_ANSI_FLAGS = -Wall -ansi -pedantic -Wno-long-long
+ SGI_ANSI_FLAGS = -ansi -fullwarn
+ ANSI_FLAGS = ${GNU_ANSI_FLAGS}
+-RANLIB = echo
++RANLIB = @@GENTOO_RANLIB@@
+ FSLML = ${FSLDIR}/bin/fslml
+ # CUDA development environment
+ CUDAVER := $(or $(CUDAVER),9.1)
+@@ -158,8 +158,8 @@
+ NVCC = ${CUDA_INSTALLATION}/bin/nvcc
+ ############### External Libs #####################################
+ # ZLIB library
+-LIB_ZLIB = ${FSLEXTLIB}
+-INC_ZLIB = ${FSLEXTINC}
++#LIB_ZLIB = ${FSLEXTLIB}
++#INC_ZLIB = ${FSLEXTINC}
+ # QT library
+ QTDIR = /usr/lib/qt3
+ LIB_QT = ${QTDIR}/lib
+diff -Naur fsl.orig/config/common/buildproj fsl/config/common/buildproj
+--- fsl.orig/config/common/buildproj 2020-12-02 15:29:11.993812552 -0500
++++ fsl/config/common/buildproj 2020-12-02 15:41:25.579835363 -0500
+@@ -11,10 +11,10 @@
+ fi
+ PROJECTS="$@" ; export PROJECTS ;
+
+-FSLDIR=`pwd`
++#FSLDIR=`pwd`
+ FSLDEVDIR=${FSLDIR}
+ FSLCONFDIR=${FSLDIR}/config
+-FSLMACHTYPE=`${FSLDIR}/etc/fslconf/fslmachtype.sh`
++#FSLMACHTYPE=`${FSLDIR}/etc/fslconf/fslmachtype.sh`
+ FSLMASTERBUILD=1
+ export FSLDIR FSLDEVDIR FSLCONFDIR FSLMACHTYPE FSLMASTERBUILD
+
+@@ -67,7 +67,7 @@
+ if [ -x ./fslconfig ] ; then
+ . ./fslconfig ;
+ fi
+- if ${MAKE} -k ${MAKEOPTIONS} ; then
++ if ${MAKE} ${MAKEOPTIONS} ; then
+ if ${MAKE} ${MAKEOPTIONS} install ; then
+ installok=true;
+ # Clean up after ourselves
+@@ -82,6 +82,7 @@
+ if [ $installok = false ] ; then
+ echo " "
+ echo "ERROR::Could not install $projname successfully" ;
++ exit 1
+ fi
+ else
+ echo " "
+@@ -90,6 +91,7 @@
+ echo " "
+ echo " "
+ errorprojs="$errorprojs $projname" ; export errorprojs ;
++ exit 1
+ fi
+ fi
+ done
+diff -Naur fsl.orig/config/common/vars.mk fsl/config/common/vars.mk
+--- fsl.orig/config/common/vars.mk 2020-12-02 15:29:11.993812552 -0500
++++ fsl/config/common/vars.mk 2020-12-02 15:43:00.602838318 -0500
+@@ -24,15 +24,15 @@
+ USRCFLAGS =
+ USRCXXFLAGS =
+
+-LDFLAGS = ${ARCHLDFLAGS} ${USRLDFLAGS} -L. -L${DEVLIBDIR} -L${LIBDIR}
++LDFLAGS = ${ARCHLDFLAGS} ${USRLDFLAGS} -L. -L${DEVLIBDIR} -L${LIBDIR} ${USERLDFLAGS}
+
+-AccumulatedIncFlags = -I${INC_BOOST} ${USRINCFLAGS} -I. -I${DEVINCDIR} -I${INCDIR}
++AccumulatedIncFlags = ${USRINCFLAGS} -I. -I${DEVINCDIR} -I${INCDIR} ${CPPFLAGS}
+
+ CFLAGS = ${ANSI_FLAGS} ${ANSI_CFLAGS} ${DBGFLAGS} ${USEDCSTATICFLAGS} ${USRCFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \
+- ${AccumulatedIncFlags}
++ ${AccumulatedIncFlags} ${USERCFLAGS}
+
+-CXXFLAGS = ${ANSI_FLAGS} ${ANSI_CXXFLAGS} ${DBGFLAGS} ${USEDCXXSTATICFLAGS} ${USRCXXFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \
+- ${AccumulatedIncFlags}
++CXXFLAGS = ${ANSI_CXXFLAGS} ${DBGFLAGS} ${USEDCXXSTATICFLAGS} ${USRCXXFLAGS} ${ARCHFLAGS} ${OPTFLAGS} \
++ ${AccumulatedIncFlags} ${USERCXXFLAGS}
+
+ HFILES = *.h
+ AFILES = *.a
+diff -Naur fsl.orig/extras/build fsl/extras/build
+--- fsl.orig/extras/build 2020-12-02 15:29:12.404812565 -0500
++++ fsl/extras/build 2020-12-02 15:44:06.906840380 -0500
+@@ -96,16 +96,16 @@
+ BUILDICONV=1
+ fi
+ fi
+-PROJECTS="tcl tk"
++#PROJECTS="tcl tk"
+ if [ ${BUILDZLIB} -eq 1 ]; then
+ PROJECTS="${PROJECTS} zlib"
+ fi
+-PROJECTS="${PROJECTS} libpng"
++#PROJECTS="${PROJECTS} libpng"
+ if [ ${BUILDICONV} -eq 1 ]; then
+ PROJECTS="${PROJECTS} libiconv"
+ fi
+-PROJECTS="${PROJECTS} libgd libgdc libprob libcprob newmat cprob newran fftw"
+-PROJECTS="${PROJECTS} boost libxml2-2.9.2 libxmlpp libsqlite libnlopt ../include/armawrap/dummy_newmat"
++PROJECTS="${PROJECTS} libgdc libprob libcprob newmat cprob newran"
++PROJECTS="${PROJECTS} ../include/armawrap/dummy_newmat"
+ for projname in $PROJECTS; do
+ if [ -d $FSLESRCDIR/$projname ] ; then
+ buildIt $FSLESRCDIR $projname 1
+diff -Naur fsl.orig/src/mist/Makefile fsl/src/mist/Makefile
+--- fsl.orig/src/mist/Makefile 2020-12-02 15:29:12.875812580 -0500
++++ fsl/src/mist/Makefile 2020-12-02 15:45:09.805842335 -0500
+@@ -52,6 +52,8 @@
+ cp -r python/* ${DESTDIR}/python/mist
+
+ clean:
+- rm -f ${OBJS} mist/mist.o mist/mist
++ rm -f ${OBJS} mist/mist.o mist/mist || echo "CLEAN could not locate some files scheduled for deletion."
++
++
+
+ .PHONY: all clean installdata
diff --git a/sci-biology/fsl/fsl-6.0.2-r1.ebuild b/sci-biology/fsl/fsl-6.0.2-r1.ebuild
index c9162fd0e..ae12098ec 100644
--- a/sci-biology/fsl/fsl-6.0.2-r1.ebuild
+++ b/sci-biology/fsl/fsl-6.0.2-r1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -6,7 +6,7 @@ EAPI=7
inherit cuda flag-o-matic toolchain-funcs prefix
DESCRIPTION="Analysis of functional, structural, and diffusion MRI brain imaging data"
-HOMEPAGE="http://www.fmrib.ox.ac.uk/fsl"
+HOMEPAGE="https://www.fmrib.ox.ac.uk/fsl"
SRC_URI="https://fsl.fmrib.ox.ac.uk/fsldownloads/${P}-sources.tar.gz -> ${P}.tar.gz"
LICENSE="FSL BSD-2 newmat"
@@ -16,7 +16,7 @@ IUSE="cuda"
DEPEND="
dev-libs/boost
- dev-python/fslpy
+ <dev-python/fslpy-3
media-gfx/graphviz
media-libs/gd
media-libs/glu
@@ -31,8 +31,8 @@ DEPEND="
cuda? (
|| (
- ( =dev-util/nvidia-cuda-toolkit-10* =sys-devel/gcc-8* )
- ( =dev-util/nvidia-cuda-toolkit-11* =sys-devel/gcc-9* )
+ ( =dev-util/nvidia-cuda-toolkit-10* =sys-devel/gcc-8*:* )
+ ( =dev-util/nvidia-cuda-toolkit-11* =sys-devel/gcc-9*:* )
)
)
"
diff --git a/sci-biology/fsl/fsl-6.0.2.ebuild b/sci-biology/fsl/fsl-6.0.2.ebuild
index 8a7e0eebb..f490b6e7c 100644
--- a/sci-biology/fsl/fsl-6.0.2.ebuild
+++ b/sci-biology/fsl/fsl-6.0.2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -6,7 +6,7 @@ EAPI=7
inherit flag-o-matic toolchain-funcs prefix
DESCRIPTION="Analysis of functional, structural, and diffusion MRI brain imaging data"
-HOMEPAGE="http://www.fmrib.ox.ac.uk/fsl"
+HOMEPAGE="https://www.fmrib.ox.ac.uk/fsl"
SRC_URI="https://fsl.fmrib.ox.ac.uk/fsldownloads/${P}-sources.tar.gz -> ${P}.tar.gz"
LICENSE="FSL BSD-2 newmat"
@@ -16,7 +16,7 @@ IUSE=""
DEPEND="
dev-libs/boost
- dev-python/fslpy
+ <dev-python/fslpy-3
media-gfx/graphviz
media-libs/gd
media-libs/glu
diff --git a/sci-biology/fsl/fsl-6.0.4.ebuild b/sci-biology/fsl/fsl-6.0.4.ebuild
new file mode 100644
index 000000000..e0feb82d9
--- /dev/null
+++ b/sci-biology/fsl/fsl-6.0.4.ebuild
@@ -0,0 +1,217 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit cuda flag-o-matic toolchain-funcs prefix
+
+DESCRIPTION="Analysis of functional, structural, and diffusion MRI brain imaging data"
+HOMEPAGE="https://www.fmrib.ox.ac.uk/fsl"
+SRC_URI="https://fsl.fmrib.ox.ac.uk/fsldownloads/${P}-sources.tar.gz -> ${P}.tar.gz"
+
+LICENSE="FSL BSD-2 newmat"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE="cuda"
+
+DEPEND="
+ dev-libs/boost
+ >=dev-python/fslpy-3
+ media-gfx/graphviz
+ media-libs/gd
+ media-libs/glu
+ media-libs/libpng:0=
+ sci-libs/ciftilib
+ sci-libs/nlopt
+ sys-libs/zlib
+ dev-lang/tcl:0=
+ dev-lang/tk:0=
+ >=virtual/lapack-3.8
+ >=virtual/blas-3.8
+
+ cuda? (
+ || (
+ ( =dev-util/nvidia-cuda-toolkit-10* =sys-devel/gcc-8*:* )
+ ( =dev-util/nvidia-cuda-toolkit-11* =sys-devel/gcc-9*:* )
+ )
+ )
+ "
+RDEPEND="${DEPEND}"
+
+S=${WORKDIR}/${PN}
+UPSTREAM_FSLDIR="/usr/share/fsl"
+
+PATCHES=(
+ "${FILESDIR}/${P}"-gcc10_include.patch
+ "${FILESDIR}/${P}"-setup.patch
+ "${FILESDIR}/${PN}"-6.0.2-template.patch
+ "${FILESDIR}/${PN}"-6.0.2-no_xmlpp.patch
+ "${FILESDIR}/${PN}"-5.0.11-niftiio_var_fix.patch
+ "${FILESDIR}/${PN}"-5.0.11-ifstream_use.patch
+ "${FILESDIR}/${PN}"-5.0.11-fslsurface_parallel_make.patch
+ "${FILESDIR}/${PN}"-6.0.2-qstring_compat.patch
+ "${FILESDIR}/${PN}"-5.0.9-headers.patch
+ "${FILESDIR}/${P}"-fsldir_redux-p1.patch
+ "${FILESDIR}/${P}"-fsldir_redux-p2.patch
+ "${FILESDIR}/${P}"-flameo_std.patch
+ "${FILESDIR}/${P}"-melodic_std.patch
+ "${FILESDIR}/${P}"-remove_fslpy_collisions-p1.patch
+ "${FILESDIR}/${P}"-remove_fslpy_collisions-p2.patch
+ "${FILESDIR}/${P}"-fdt_cuda.patch
+)
+
+src_prepare() {
+ default
+
+ sed -i \
+ -e "s:@@GENTOO_RANLIB@@:$(tc-getRANLIB):" \
+ -e "s:@@GENTOO_CC@@:$(tc-getCC):" \
+ -e "s:@@GENTOO_CXX@@:$(tc-getCXX):" \
+ config/buildSettings.mk || die
+
+ eprefixify $(grep -rl GENTOO_PORTAGE_EPREFIX src/*) \
+ etc/js/label-div.html
+
+ # Disable mist the hard way for now.
+ rm -r src/mist || die
+
+ # Disable ptx2 for now
+ rm -r src/ptx2 || die
+
+ makefilelist=$(find src/ -name Makefile)
+
+ sed -i \
+ -e "s:-I\${INC_BOOST}::" \
+ -e "s:-I\${INC_ZLIB}::" \
+ -e "s:-I\${INC_GD}::" \
+ -e "s:-I\${INC_PNG}::" \
+ -e "s:-L\${LIB_GD}::" \
+ -e "s:-L\${LIB_PNG}::" \
+ -e "s:-L\${LIB_ZLIB}::" \
+ ${makefilelist} || die
+
+ sed -e "s:\${FSLDIR}/bin/::g" \
+ -e "s:\$FSLDIR/bin/::g" \
+ -i $(grep -rl "\${FSLDIR}/bin" src/*) \
+ -i $(grep -rl "\$FSLDIR/bin" src/*) \
+ $(grep -rl "\${FSLDIR}/bin" etc/matlab/*)\
+ $(grep -rl "\$FSLDIR/bin" etc/matlab/*) || die
+
+ sed -e "s:\$FSLDIR/data:${EPREFIX}/usr/share/fsl/data:g" \
+ -e "s:\${FSLDIR}/data:${EPREFIX}/usr/share/fsl/data:g" \
+ -i $(grep -rl "\$FSLDIR/data" src/*) \
+ $(grep -rl "\${FSLDIR}/data" src/*) || die
+
+ sed -e "s:\$FSLDIR/doc:${EPREFIX}/usr/share/fsl/doc:g" \
+ -e "s:\${FSLDIR}/doc:${EPREFIX}/usr/share/fsl/doc:g" \
+ -i $(grep -rl "\$FSLDIR/doc" src/*) \
+ $(grep -rl "\${FSLDIR}/doc" src/*) || die
+
+ sed -e "s:/usr/share/fsl/doc:${EPREFIX}/usr/share/fsl/doc:g" \
+ -i $(grep -rl "/usr/share/fsl/doc" src/*) || die
+
+ sed -e "s:\$FSLDIR/etc:${EPREFIX}/etc:g" \
+ -e "s:\${FSLDIR}/etc:${EPREFIX}/etc:g" \
+ -i $(grep -rlI "\$FSLDIR/etc" *) \
+ -i $(grep -rlI "\${FSLDIR}/etc" *) || die
+
+ # Use generic blas/lapack rather than openblas
+ sed -e "s:-lopenblas:-llapack -lblas:g" \
+ -i $(grep -rlI lopenblas *) || die
+
+ # script wanting to have access to fslversion at buildtime
+ sed -e "s:/etc/fslversion:${S}/etc/fslversion:g" \
+ -i ${makefilelist} || die
+
+ if use cuda; then
+ einfo
+
+ gcc_ver=`gcc-fullversion`
+ einfo "GCC version: ${gcc_ver}"
+
+ cuda_gcc=`cuda_gccdir`
+ cuda_NVCC_flags=`cuda_gccdir -f`
+ einfo "CUDA GCC path: ${cuda_gcc}"
+ einfo " ${cuda_NVCC_flags}"
+
+ CUDA_INSTALLATION="/opt/cuda"
+ CUDAVER=`cuda_toolkit_version`
+
+ eapply "${FILESDIR}/${P}-eddy_cuda.patch"
+ eapply "${FILESDIR}/${P}-cuda_buildsettings.patch"
+
+ sed -i \
+ -e "s:@@GENTOO_NVCC_FLAGS@@:${cuda_NVCC_flags}:" \
+ src/eddy/Makefile || die
+
+ cuda_sanitize
+ fi
+}
+
+src_compile() {
+ export FSLDIR=${WORKDIR}/${PN}
+ export FSLCONDIR=${WORKDIR}/${PN}/config
+ export FSLMACHTYPE=generic
+
+ # define the default build system to match upstream official standard
+ # -> individual projects may overwrite the '-std=' flag
+ export ANSI_CFLAGS="-std=c99"
+ export ANSI_CXXFLAGS="-std=c++98"
+
+ export USERLDFLAGS="${LDFLAGS}"
+ export USERCFLAGS="${CFLAGS}"
+ export USERCPPFLAGS="${CPPFLAGS}"
+ export USERCXXFLAGS="${CXXFLAGS}"
+
+ export CIFTICFLAGS="$($(tc-getPKG_CONFIG) --cflags CiftiLib)"
+ export CIFTILIBS="$($(tc-getPKG_CONFIG) --libs-only-l CiftiLib)"
+
+ if use cuda; then
+ einfo "CUDA_INSTALLATION: ${CUDA_INSTALLATION}"
+ einfo "CUDAVER: ${CUDAVER}"
+ fi
+
+ ./build || die
+}
+
+src_install() {
+ sed -i "s:\${FSLDIR}/tcl:/usr/libexec/fsl:g" \
+ $(grep -lI "\${FSLDIR}/tcl" bin/*) \
+ $(grep -l "\${FSLDIR}/tcl" tcl/*) || die
+ sed -i "s:\$FSLDIR/tcl:/usr/libexec/fsl:g" \
+ $(grep -l "\$FSLDIR/tcl" tcl/*) || die
+
+ dobin bin/*
+
+ insinto /usr/share/${PN}
+ doins -r data
+ dodoc -r doc/. refdoc
+
+ insinto /usr/libexec/fsl
+ doins -r tcl/*
+
+ insinto /etc/fslconf
+ doins etc/fslconf/fsl.sh
+
+ insinto /etc
+ doins etc/fslversion
+ doins -r etc/default_flobs.flobs etc/flirtsch etc/js etc/luts
+
+ #the following is needed for FSL and depending programs to be able
+ #to find its files, since FSL uses an uncommon installation path:
+ #https://github.com/gentoo-science/sci/pull/612#r60289295
+ dosym ../../../etc ${UPSTREAM_FSLDIR}/etc
+ dosym ../doc/${PF} ${UPSTREAM_FSLDIR}/doc
+ dosym ../../bin ${UPSTREAM_FSLDIR}/bin
+
+ doenvd "$(prefixify_ro "${FILESDIR}"/99fsl)"
+ mv "${ED}"/usr/bin/{,fsl_}cluster || die
+}
+
+pkg_postinst() {
+ echo
+ einfo "Please run the following commands if you"
+ einfo "intend to use fsl from an existing shell:"
+ einfo "env-update && source /etc/profile"
+ echo
+}
diff --git a/sci-biology/jellyfish/jellyfish-1.1.12.ebuild b/sci-biology/jellyfish/jellyfish-1.1.12.ebuild
index f7b7e1d29..15a2d7bca 100644
--- a/sci-biology/jellyfish/jellyfish-1.1.12.ebuild
+++ b/sci-biology/jellyfish/jellyfish-1.1.12.ebuild
@@ -18,21 +18,18 @@ SLOT="1"
KEYWORDS="~amd64 ~x86"
IUSE="cpu_flags_x86_sse"
-DEPEND=""
-DEPEND="${RDEPEND}"
BDEPEND="virtual/pkgconfig"
-src_prepare(){
+src_configure() {
# --with-sse enable SSE
# --with-half enable half float (16 bits)
# --with-int128 enable int128
local myconf
use cpu_flags_x86_sse && myconf+=( --with-sse )
econf ${myconf[@]}
- eapply_user
}
-src_install(){
+src_install() {
default
# install the binary under jellyfish1 name like Debian/Ubuntu to avoid name clash with jellyfish2 and allow simultaneous installs
mv "${ED}"/usr/bin/jellyfish "${ED}"/usr/bin/jellyfish1 || die
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild
index 40f338bc3..a8015cf70 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild
@@ -38,7 +38,7 @@ DEPEND="
<sys-devel/gcc-10:=
!sci-biology/ncbi-tools++
!sci-biology/sra_sdk
- berkdb? ( sys-libs/db:4.3[cxx] )
+ berkdb? ( sys-libs/db:=[cxx] )
boost? ( dev-libs/boost )
curl? ( net-misc/curl )
sqlite? ( dev-db/sqlite:3 )
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
index 08103e703..b17d7b00e 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild
@@ -33,7 +33,7 @@ DEPEND="
<sys-devel/gcc-10:=
!sci-biology/ncbi-tools++
!sci-biology/sra_sdk
- berkdb? ( sys-libs/db:4.3[cxx] )
+ berkdb? ( sys-libs/db:=[cxx] )
boost? ( dev-libs/boost )
curl? ( net-misc/curl )
sqlite? ( dev-db/sqlite:3 )
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
index fbd1a9d4c..58fbcd288 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild
@@ -33,7 +33,7 @@ DEPEND="
<sys-devel/gcc-10:=
!sci-biology/ncbi-tools++
!sci-biology/sra_sdk
- berkdb? ( sys-libs/db:4.3[cxx] )
+ berkdb? ( sys-libs/db:=[cxx] )
boost? ( dev-libs/boost )
curl? ( net-misc/curl )
sqlite? ( dev-db/sqlite:3 )
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
index ec3426cfb..29ba54e42 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild
@@ -34,7 +34,7 @@ DEPEND="
<sys-devel/gcc-10:=
!sci-biology/ncbi-tools++
!sci-biology/sra_sdk
- berkdb? ( sys-libs/db:4.3[cxx] )
+ berkdb? ( sys-libs/db:=[cxx] )
boost? ( dev-libs/boost )
curl? ( net-misc/curl )
sqlite? ( dev-db/sqlite:3 )
diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
index 40f338bc3..a8015cf70 100644
--- a/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
+++ b/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild
@@ -38,7 +38,7 @@ DEPEND="
<sys-devel/gcc-10:=
!sci-biology/ncbi-tools++
!sci-biology/sra_sdk
- berkdb? ( sys-libs/db:4.3[cxx] )
+ berkdb? ( sys-libs/db:=[cxx] )
boost? ( dev-libs/boost )
curl? ( net-misc/curl )
sqlite? ( dev-db/sqlite:3 )
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
index fa1caf715..41e8bdd05 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild
@@ -38,7 +38,7 @@ DEPEND="
<sys-devel/gcc-10:=
!sci-biology/sra_sdk
app-arch/cpio
- berkdb? ( sys-libs/db:4.3[cxx] )
+ berkdb? ( sys-libs/db:=[cxx] )
boost? ( dev-libs/boost[tools] )
curl? ( net-misc/curl )
sqlite? ( dev-db/sqlite:3 )
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
index 5c0b619df..55d0aa6ba 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild
@@ -41,7 +41,7 @@ DEPEND="
<sys-devel/gcc-10:=
!sci-biology/sra_sdk
app-arch/cpio
- berkdb? ( sys-libs/db:4.3[cxx] )
+ berkdb? ( sys-libs/db:=[cxx] )
boost? ( dev-libs/boost[tools] )
curl? ( net-misc/curl )
sqlite? ( dev-db/sqlite:3 )
diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild
index 004cc7086..1f34de56e 100644
--- a/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild
+++ b/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild
@@ -41,7 +41,7 @@ DEPEND="
<sys-devel/gcc-10:=
!sci-biology/sra_sdk
app-arch/cpio
- berkdb? ( sys-libs/db:4.3[cxx] )
+ berkdb? ( sys-libs/db:=[cxx] )
boost? ( dev-libs/boost[tools] )
curl? ( net-misc/curl )
sqlite? ( >=dev-db/sqlite-3.6.6:3 )
diff --git a/sci-biology/nilearn/nilearn-9999.ebuild b/sci-biology/nilearn/nilearn-9999.ebuild
index 567927a2c..7aca41bd5 100644
--- a/sci-biology/nilearn/nilearn-9999.ebuild
+++ b/sci-biology/nilearn/nilearn-9999.ebuild
@@ -3,7 +3,7 @@
EAPI=7
-PYTHON_COMPAT=( python3_7 )
+PYTHON_COMPAT=( python3_{7..9} )
inherit distutils-r1 git-r3
diff --git a/sci-chemistry/MotionCor2/MotionCor2-1.4.0.ebuild b/sci-chemistry/MotionCor2/MotionCor2-1.4.0.ebuild
index 7092e39a7..7507ca26f 100644
--- a/sci-chemistry/MotionCor2/MotionCor2-1.4.0.ebuild
+++ b/sci-chemistry/MotionCor2/MotionCor2-1.4.0.ebuild
@@ -11,12 +11,10 @@ S="${WORKDIR}"/${PN}_${PV}
LICENSE="UCSF-Motioncor2"
SLOT="0"
KEYWORDS="~amd64"
-IUSE="cuda92 +cuda102"
-REQUIRED_USE="^^ ( cuda92 cuda102 )"
+IUSE="+cuda102"
RESTRICT="fetch"
RDEPEND="
- cuda92? ( =dev-util/nvidia-cuda-toolkit-9.2* )
cuda102? ( =dev-util/nvidia-cuda-toolkit-10.2* )
media-libs/tiff
app-arch/xz-utils
@@ -38,11 +36,7 @@ src_install() {
# package also has 10.0 10.1 11.0 versions
# but these cuda versions are not in ::gentoo
local mcbin
- if use cuda92; then
- mcbin="${PN}_${PV}_Cuda92"
- elif use cuda102; then
- mcbin="${PN}_${PV}_Cuda102"
- fi
+ use cuda102 && mcbin="${PN}_${PV}_Cuda102"
dobin "${mcbin}"
dosym "${mcbin}" /usr/bin/MotionCor2
}
diff --git a/sci-chemistry/MotionCor2/metadata.xml b/sci-chemistry/MotionCor2/metadata.xml
index 5035d4d85..8571bf1df 100644
--- a/sci-chemistry/MotionCor2/metadata.xml
+++ b/sci-chemistry/MotionCor2/metadata.xml
@@ -10,7 +10,6 @@
<name>Alexey Shvetsov</name>
</maintainer>
<use>
- <flag name="cuda92">Install cuda-9.2 version</flag>
<flag name="cuda102">Install cuda-10.2 version</flag>
</use>
</pkgmetadata>
diff --git a/sci-libs/ciftilib/ciftilib-1.6.0.ebuild b/sci-libs/ciftilib/ciftilib-1.6.0.ebuild
index 062fa44ef..fffd4f9c1 100644
--- a/sci-libs/ciftilib/ciftilib-1.6.0.ebuild
+++ b/sci-libs/ciftilib/ciftilib-1.6.0.ebuild
@@ -24,6 +24,12 @@ RDEPEND="${DEPEND}"
S="${WORKDIR}/CiftiLib-${PV}"
+# fix submitted upstream
+# https://github.com/Washington-University/CiftiLib/pull/23
+PATCHES=(
+ "${FILESDIR}/${P}-version.patch"
+)
+
#TODO: Enable doc building and installation
src_prepare(){
diff --git a/sci-libs/ciftilib/files/ciftilib-1.6.0-version.patch b/sci-libs/ciftilib/files/ciftilib-1.6.0-version.patch
new file mode 100644
index 000000000..e64a55f2f
--- /dev/null
+++ b/sci-libs/ciftilib/files/ciftilib-1.6.0-version.patch
@@ -0,0 +1,27 @@
+--- a/CMakeLists.txt
++++ b/CMakeLists.txt
+@@ -83,18 +83,18 @@ ENDIF (NOT QT_FOUND)
+ INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIRS})
+ SET(LIBS ${LIBS} ${Boost_LIBRARIES})
+ #boost quirks
+-IF (Boost_VERSION LESS 104400)
++IF (Boost_VERSION VERSION_LESS 1.44.00)
+ #absolute() was added in 1.44.0, with filesystem v3
+ ADD_DEFINITIONS(-DCIFTILIB_BOOST_NO_FSV3)
+-ENDIF (Boost_VERSION LESS 104400)
+-IF (Boost_VERSION LESS 104800)
++ENDIF (Boost_VERSION VERSION_LESS 1.44.00)
++IF (Boost_VERSION VERSION_LESS 1.48.00)
+ #canonical() was added in 1.48.0
+ ADD_DEFINITIONS(-DCIFTILIB_BOOST_NO_CANONICAL)
+-ENDIF (Boost_VERSION LESS 104800)
+-IF (Boost_VERSION LESS 105600)
++ENDIF (Boost_VERSION VERSION_LESS 1.48.00)
++IF (Boost_VERSION VERSION_LESS 1.56.00)
+ #try_lexical_cast was added in 1.56.0
+ ADD_DEFINITIONS(-DCIFTILIB_BOOST_NO_TRY_LEXICAL)
+-ENDIF (Boost_VERSION LESS 105600)
++ENDIF (Boost_VERSION VERSION_LESS 1.56.00)
+
+ #zlib, useful for volume reading
+ FIND_PACKAGE(ZLIB)
diff --git a/sci-libs/ensmallen/Manifest b/sci-libs/ensmallen/Manifest
index 901f5f942..d74da89b9 100644
--- a/sci-libs/ensmallen/Manifest
+++ b/sci-libs/ensmallen/Manifest
@@ -2,3 +2,4 @@ DIST ensmallen-2.14.2.tar.gz 1262697 BLAKE2B c3ecd10271a476cdb03de0a74dd1e7d2502
DIST ensmallen-2.15.0.tar.gz 1266409 BLAKE2B 379ea897d3b29440e89d65cb60c65dca3c34a530dd8a4cee321349d177455b020d4aa19ee1e701b46a325a8f56028c236ab80b0383bee84018952034106f7161 SHA512 7e8ea0d64788287e58ee14e922c81c18e1804a23dba3d144fe6e66de8a81dfd3755c9f36a1e8a480aa6e15f0f7b1ff886e0aeecde0be35993db0ba69ca7e12e0
DIST ensmallen-2.15.1.tar.gz 1266496 BLAKE2B 7ff803207c59be03fa47e7fddafb49176d307fbea89f5688bd591898fb36d7d8ee018dec933b59a06063dc6c2a7117d3ec0d330cd37d475e4f387528f2d86f6a SHA512 4f0cda1ad0d02e823042fb6af03635677e3d5cac28f7f13fab20fc7f4b3d7fbe1b182777c573187a403eff5e5fd7e1e577e290a4b624a9c2a71cbfd347e14afa
DIST ensmallen-2.16.0.tar.gz 1264948 BLAKE2B a58de7e7d8aa88988b08d76c2a5746daf9074ccc39bc8df9d21b61d745741d6521922b578e01b60e0d1657f84f377f411172a01d50bbcd30cca7142da0baeb7b SHA512 39afc19936710d5595218292f5d6a055b4f644ca157f9fc2329fb18b71318b9f613dc26169921e1fda3dd949d06847dee4f09f13c1902a92e38826e122c1adc5
+DIST ensmallen-2.16.2.tar.gz 1294240 BLAKE2B b388f2c99f289dd20f6d94b5b185d872abc553637c6081ea3a80a3c82ce9ac8b1327496bf3eae6dc5cbf5f4ae12a9fd1e8ccf9c296007f9af9cbfc7560cd0301 SHA512 290932f8e423be7c57d8ba38783a29798df52a7505ded7683f969fa30391398edcca584daca1b1c42977f06180a802d4c3640a9ec24cd787a3914723e4eb6f8d
diff --git a/sci-libs/ensmallen/ensmallen-2.16.2.ebuild b/sci-libs/ensmallen/ensmallen-2.16.2.ebuild
new file mode 100644
index 000000000..bd1c0530b
--- /dev/null
+++ b/sci-libs/ensmallen/ensmallen-2.16.2.ebuild
@@ -0,0 +1,28 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit cmake
+
+DESCRIPTION="header only C++ library for numerical optimization"
+HOMEPAGE="https://ensmallen.org"
+SRC_URI="https://github.com/mlpack/ensmallen/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+KEYWORDS="~amd64"
+
+LICENSE="BSD"
+SLOT="0"
+IUSE="openmp test"
+RESTRICT="!test? ( test )"
+
+RDEPEND="sci-libs/armadillo[lapack]"
+DEPEND="${RDEPEND}"
+
+src_configure() {
+ local mycmakeargs=(
+ -DUSE_OPENMP=$(usex openmp)
+ -DBUILD_TESTS=$(usex test)
+ )
+ cmake_src_configure
+}
diff --git a/sci-libs/fox/fox-4.1.2-r2.ebuild b/sci-libs/fox/fox-4.1.2-r2.ebuild
index 42283ca9e..a8900c153 100644
--- a/sci-libs/fox/fox-4.1.2-r2.ebuild
+++ b/sci-libs/fox/fox-4.1.2-r2.ebuild
@@ -3,6 +3,8 @@
EAPI=7
+inherit fortran-2
+
MY_PN="FoX"
MY_P="${MY_PN}-${PV}"
diff --git a/sci-libs/mlpack/mlpack-3.4.1.ebuild b/sci-libs/mlpack/mlpack-3.4.1.ebuild
index 359060d13..bc5f8d642 100644
--- a/sci-libs/mlpack/mlpack-3.4.1.ebuild
+++ b/sci-libs/mlpack/mlpack-3.4.1.ebuild
@@ -22,7 +22,7 @@ CDEPEND="
${PYTHON_DEPS}
julia? ( || (
dev-lang/julia
- dev-lang/julia-bin
+ dev-lang/julia-bin:*
)
)
go? ( dev-lang/go )
diff --git a/sci-libs/mlpack/mlpack-3.4.2.ebuild b/sci-libs/mlpack/mlpack-3.4.2.ebuild
index 359060d13..bc5f8d642 100644
--- a/sci-libs/mlpack/mlpack-3.4.2.ebuild
+++ b/sci-libs/mlpack/mlpack-3.4.2.ebuild
@@ -22,7 +22,7 @@ CDEPEND="
${PYTHON_DEPS}
julia? ( || (
dev-lang/julia
- dev-lang/julia-bin
+ dev-lang/julia-bin:*
)
)
go? ( dev-lang/go )
diff --git a/sci-libs/nipy/nipy-9999.ebuild b/sci-libs/nipy/nipy-9999.ebuild
index 9878397aa..7e0f61d2d 100644
--- a/sci-libs/nipy/nipy-9999.ebuild
+++ b/sci-libs/nipy/nipy-9999.ebuild
@@ -3,7 +3,7 @@
EAPI=7
-PYTHON_COMPAT=( python3_7 )
+PYTHON_COMPAT=( python3_{7..9} )
inherit distutils-r1 eutils multilib flag-o-matic git-r3
diff --git a/sci-libs/pytorch/Manifest b/sci-libs/pytorch/Manifest
index feaaba61d..65e5fc7a8 100644
--- a/sci-libs/pytorch/Manifest
+++ b/sci-libs/pytorch/Manifest
@@ -1,58 +1,81 @@
DIST FP16-4dfe081c.tar.gz 71301 BLAKE2B f6a2115a82ca9acd7ccb1bf94c59f68e6ffea4b0e20aa5152349a10119b45d8ba45f5673899b6f18ee044289a51141944e41d7b0972889afc1d93db88d88ed7c SHA512 e79a1f6f8d4aeca85982158d5b070923d31d4f2062ed84cfa6f26c47a34f2e8ac49e0f330b7d49f5732d5e1eec6e7afccdac43645070060fb7827e2ce261dd3e
DIST FP16-4dfe081cf.tar.gz 71301 BLAKE2B f6a2115a82ca9acd7ccb1bf94c59f68e6ffea4b0e20aa5152349a10119b45d8ba45f5673899b6f18ee044289a51141944e41d7b0972889afc1d93db88d88ed7c SHA512 e79a1f6f8d4aeca85982158d5b070923d31d4f2062ed84cfa6f26c47a34f2e8ac49e0f330b7d49f5732d5e1eec6e7afccdac43645070060fb7827e2ce261dd3e
+DIST FP16-4dfe081cf6bcd15db339cf2680b9281b8451eeb3.tar.gz 71301 BLAKE2B f6a2115a82ca9acd7ccb1bf94c59f68e6ffea4b0e20aa5152349a10119b45d8ba45f5673899b6f18ee044289a51141944e41d7b0972889afc1d93db88d88ed7c SHA512 e79a1f6f8d4aeca85982158d5b070923d31d4f2062ed84cfa6f26c47a34f2e8ac49e0f330b7d49f5732d5e1eec6e7afccdac43645070060fb7827e2ce261dd3e
DIST FXdiv-b408327a.tar.gz 9652 BLAKE2B ce2082f9e0ec55ab43cfee57e29cfc8f1957bdde70c1bbeadc599ac34ed8ade9d1334e68583a0fb14b4405357cc1039579b09fff4b39a5190bdae304c4ea3de3 SHA512 d46d7c1437eccf8dc5ab5e51b0641d190839451ab059c8a24a220a9cf05a84a66b5d08c3ff730622efe491152a8378a2c726fd9abad19a3df98db40d6a13e4b9
DIST FXdiv-b408327ac.tar.gz 9652 BLAKE2B ce2082f9e0ec55ab43cfee57e29cfc8f1957bdde70c1bbeadc599ac34ed8ade9d1334e68583a0fb14b4405357cc1039579b09fff4b39a5190bdae304c4ea3de3 SHA512 d46d7c1437eccf8dc5ab5e51b0641d190839451ab059c8a24a220a9cf05a84a66b5d08c3ff730622efe491152a8378a2c726fd9abad19a3df98db40d6a13e4b9
+DIST FXdiv-b408327ac2a15ec3e43352421954f5b1967701d1.tar.gz 9652 BLAKE2B ce2082f9e0ec55ab43cfee57e29cfc8f1957bdde70c1bbeadc599ac34ed8ade9d1334e68583a0fb14b4405357cc1039579b09fff4b39a5190bdae304c4ea3de3 SHA512 d46d7c1437eccf8dc5ab5e51b0641d190839451ab059c8a24a220a9cf05a84a66b5d08c3ff730622efe491152a8378a2c726fd9abad19a3df98db40d6a13e4b9
DIST NNPACK-24b55303.tar.gz 219131 BLAKE2B 7fbc786d59352270d7b3664c46ab9401a0199aa8973cdbe8385840354f576eb945faa93be7070dafc9e453a415af227f5f64ffc21a33fd28e4c7a9ec94ca00b3 SHA512 43d6c69f19f9604809a2cc9cd9f8f027ff1f3dc2bac106429df1a0cf65f3f8b8fc3ec4c6b76a29decf3584440ad4c83f800ae2f8bfdc9b73df903a076cd97a18
DIST NNPACK-24b55303f.tar.gz 219131 BLAKE2B 7fbc786d59352270d7b3664c46ab9401a0199aa8973cdbe8385840354f576eb945faa93be7070dafc9e453a415af227f5f64ffc21a33fd28e4c7a9ec94ca00b3 SHA512 43d6c69f19f9604809a2cc9cd9f8f027ff1f3dc2bac106429df1a0cf65f3f8b8fc3ec4c6b76a29decf3584440ad4c83f800ae2f8bfdc9b73df903a076cd97a18
+DIST NNPACK-c07e3a0400713d546e0dea2d5466dd22ea389c73.tar.gz 219318 BLAKE2B 6b6619c8a706ef9630f20fda1e276314b2ef7f6c9aed26836a48bdaa0ae198a86383e68b04c651f37c07d34e400bc54b5daa75b06fc18cdb0a9c55e2cb33bbe1 SHA512 f0b261e8698b412d12dd739e5d0cf71c284965ae28da735ae22814a004358ba3ecaea6cd26fa17b594c0245966b7dd2561c1e05c6cbf0592fd7b85ea0f21eb37
DIST PeachPy-07d8fde8.tar.gz 401648 BLAKE2B c563cd77a9e2eda34bbec6a34f94111a6db9500b7cda9a18e791984b789c29dde7199ed21696f10cdfb088b05e18163b02a8ca8c9e48a91b9e4a757020f096b0 SHA512 8d6cc91c8c4d56b86ef93f0acd6768a1830ecd078524b21d1a3b9ecb015f06607070148de3e634d9c5ce63ed523a8e34aa388d490e7eee061200098f39126afa
DIST PeachPy-07d8fde8a.tar.gz 401648 BLAKE2B c563cd77a9e2eda34bbec6a34f94111a6db9500b7cda9a18e791984b789c29dde7199ed21696f10cdfb088b05e18163b02a8ca8c9e48a91b9e4a757020f096b0 SHA512 8d6cc91c8c4d56b86ef93f0acd6768a1830ecd078524b21d1a3b9ecb015f06607070148de3e634d9c5ce63ed523a8e34aa388d490e7eee061200098f39126afa
+DIST PeachPy-07d8fde8ac45d7705129475c0f94ed8925b93473.tar.gz 401648 BLAKE2B c563cd77a9e2eda34bbec6a34f94111a6db9500b7cda9a18e791984b789c29dde7199ed21696f10cdfb088b05e18163b02a8ca8c9e48a91b9e4a757020f096b0 SHA512 8d6cc91c8c4d56b86ef93f0acd6768a1830ecd078524b21d1a3b9ecb015f06607070148de3e634d9c5ce63ed523a8e34aa388d490e7eee061200098f39126afa
DIST QNNPACK-7d2a4e99.tar.gz 205600 BLAKE2B f174051cba9e3307633f0b12326a37d8fde23562d47e09d3c078350146439094ca6cb2f032cf3aa4af40e5968ee16b8847241f787f7c84ea501124e0528fb82d SHA512 437a835acfedae851a9a8572fa6eea9854dcb8bcca499bc4a2582314e44f5f199778e857932da4aecf943bea7cb2eb5b1c41d4b4ca6075bddbe0f18b2c7b9127
DIST QNNPACK-7d2a4e993.tar.gz 205600 BLAKE2B f174051cba9e3307633f0b12326a37d8fde23562d47e09d3c078350146439094ca6cb2f032cf3aa4af40e5968ee16b8847241f787f7c84ea501124e0528fb82d SHA512 437a835acfedae851a9a8572fa6eea9854dcb8bcca499bc4a2582314e44f5f199778e857932da4aecf943bea7cb2eb5b1c41d4b4ca6075bddbe0f18b2c7b9127
+DIST QNNPACK-7d2a4e9931a82adc3814275b6219a03e24e36b4c.tar.gz 205600 BLAKE2B f174051cba9e3307633f0b12326a37d8fde23562d47e09d3c078350146439094ca6cb2f032cf3aa4af40e5968ee16b8847241f787f7c84ea501124e0528fb82d SHA512 437a835acfedae851a9a8572fa6eea9854dcb8bcca499bc4a2582314e44f5f199778e857932da4aecf943bea7cb2eb5b1c41d4b4ca6075bddbe0f18b2c7b9127
DIST XNNPACK-1b354636.tar.gz 1353346 BLAKE2B ce286e1a1f14aa195baffa48ef8c21c4ae0ec85ae89169a429fc06077e34f28302930e081cf464dbe78252bb065a247b65b61d8aa3872375043176d150f97651 SHA512 9e7528334a8e3df18a54fce44a122fb6d989a946bb456b01f81772f160bd6532fad460e787c976bbdd76ebaa78cd1c64329ffeb498c5d27e1cd53195bb8a9db4
DIST XNNPACK-1b354636b.tar.gz 1353346 BLAKE2B ce286e1a1f14aa195baffa48ef8c21c4ae0ec85ae89169a429fc06077e34f28302930e081cf464dbe78252bb065a247b65b61d8aa3872375043176d150f97651 SHA512 9e7528334a8e3df18a54fce44a122fb6d989a946bb456b01f81772f160bd6532fad460e787c976bbdd76ebaa78cd1c64329ffeb498c5d27e1cd53195bb8a9db4
+DIST XNNPACK-79cd5f9e18ad0925ac9a050b00ea5a36230072db.tar.gz 3955905 BLAKE2B d787d4a965c53c8d65887f3b111da950f3b5558cd28ce468764c5bf8efbaddeea567803cfcd89a1aab4a0bc781816871dcca2901e762257aaf96a1d8f868ffd2 SHA512 72c3e53b00d77cfd94db93c60276ca7fd419554dadddf74286e85e0500dbdad0bf65694e451e832de89ea17e7731a9ec9e9f1d831b03c1b81946e0dacb96197d
DIST asmjit-9057aa30.tar.gz 534633 BLAKE2B faec98981c67110294e4135a9cb7f47b038d44a02483728a4c79c7094da62b8a6a1c805eba69f1258a99b24b699823f02516c50d166a96eb5ff65227406f402e SHA512 678e5ce4a8d96961be4c10aac67d43aa8949ff022dce855a92cf6d626738be8667668c48953d43b6ef21ad7c5f913d07f7f692ad719870700aa97deb80662baf
DIST benchmark-505be96a.tar.gz 129647 BLAKE2B d9f435f464fa1db18b86258947b8c5077b8b20b9c26ca00aeeca79da604f299f776673c374b7d0db10a5d40cbc84774642b29e756a83f02cda5d085280387346 SHA512 2ec79b66c31d4741b214c04f7865cf0139b4c0b14a8fb2a70bf332cf90e73821282b510719689bc2fe59542ee51c87e9f9b49a47b6a67cad897f7f906f0b05e9
DIST benchmark-505be96ab.tar.gz 129647 BLAKE2B d9f435f464fa1db18b86258947b8c5077b8b20b9c26ca00aeeca79da604f299f776673c374b7d0db10a5d40cbc84774642b29e756a83f02cda5d085280387346 SHA512 2ec79b66c31d4741b214c04f7865cf0139b4c0b14a8fb2a70bf332cf90e73821282b510719689bc2fe59542ee51c87e9f9b49a47b6a67cad897f7f906f0b05e9
DIST benchmark-5b7683f4.tar.gz 102332 BLAKE2B a7210a2c7a173a9df8bf03b83fc9712d5b52ded13c932e4d13a93004b93ad816895b722acc941b1d94c6b403e4ccb846141f5a38f42baafc5fb3cb108c039559 SHA512 a4e69ee8ec824e418abd713cb3597175cd40ecee9bc539e2d3592f9ec0f8ee54e7466984874f410b78beee82b4c396a7f2824880f808c4217704cf9970411ebf
DIST benchmark-e776aa02.tar.gz 126890 BLAKE2B 389a4fc0bfedc20227de31d4b1447b8370300a8e3cbea8a8d4b1c82ee90757c2a035ea0324e762217f5a6279a4277f431b7e511d8a9a3bcf226fe31c0022b83c SHA512 d9f70c617af75683dfcf5a0d7ff14b3374258bcf869e3b69b23e85c980366cc4f9859fef3d3dd84a2a92933729053eb02663eaf4bbe0a020a2e001f42b85230d
+DIST benchmark-e991355c02b93fe17713efe04cbc2e278e00fdbd.tar.gz 176771 BLAKE2B 22280c0777635d57574852e6e3ad276683d582eed9b17ef93f09f6a5560dc3d06bbabdead9cfc72f5059570436515855a841118c47f23c3793e1b83e368cc75b SHA512 aa4455fa0f8546ec5762f14065e0be6667b5874e6991ca6dd21dc7b29e38c7c74cfddb2c99c7a1ed2f7636aa7bdec8fc0fc1523967b179f5642c2dc2e968089c
+DIST cpuinfo-5916273f79a21551890fd3d56fc5375a78d1598d.tar.gz 3496223 BLAKE2B 4da452faf12138fbc1abd266d8ae6e0a0192f48a84faccb55fd05c3ac85d0bea2ecbd80b5eda69bb51c6704a223f90dd83d1f0fc79d56d35dd21cae5c5b8fab5 SHA512 50e537b61d991e8579577fb1ecf8d9ceb2171dbad96dfe159a062eadfdc0b2372b94988fc6f223c20e327453c7f55042ee06779f5b5fe0922f4470f746c9686b
DIST cpuinfo-63b25457.tar.gz 3495405 BLAKE2B bb7cefa2bfe6e44134c52b8ba8048a84f0063623e566e89dd92ed6ff5e383a150c554a45b66ee5c4ba6d1544de948ac978ab6e53101399d4768bace20110b4e6 SHA512 44f4a55eea9c0d707818dedfec26f007c2bc2271c7bf9375e6e30171384fb0fa2e1d5731cb946570c717e6d88e6b1496d498e6e55dbf37d66174a4c675a3a006
DIST cpuinfo-63b254577.tar.gz 3495405 BLAKE2B bb7cefa2bfe6e44134c52b8ba8048a84f0063623e566e89dd92ed6ff5e383a150c554a45b66ee5c4ba6d1544de948ac978ab6e53101399d4768bace20110b4e6 SHA512 44f4a55eea9c0d707818dedfec26f007c2bc2271c7bf9375e6e30171384fb0fa2e1d5731cb946570c717e6d88e6b1496d498e6e55dbf37d66174a4c675a3a006
DIST cpuinfo-d5e37adf.tar.gz 3489028 BLAKE2B aa6b7719eb9871b6cc71318cb4a9c2e2397e665662b7978daecd9e8380304691a78b95118eba5cbbb738c4b490352a847f6ce6b5c4ae29de0543b95ecc557cbb SHA512 ecd2115340fa82a67db7889ce286c3070d5ab9c30b02372b08aac893e90ccebc65c6b3e66aa02a9ae9c57892d2d8c3b77cb836e5fc3b88df2c75d33e574d90d2
DIST cub-d106ddb9.tar.gz 398104 BLAKE2B 287f020189be877c7a9e667bdfb591da14046199b7336074040c3301d69110c8408d89a72cdcd74d8519deb200ec61823a6d2160d4ecbd00002338651dbf312e SHA512 8d65c0407448125378495190ee2a2c0e3b27a3577efbd6bb5aa8ad76f5bf2bf17becdc6ef931672a4d16b033fd7c0a199bb60e62b0b2b311e5f59c4136f55835
DIST cub-d106ddb99.tar.gz 398104 BLAKE2B 287f020189be877c7a9e667bdfb591da14046199b7336074040c3301d69110c8408d89a72cdcd74d8519deb200ec61823a6d2160d4ecbd00002338651dbf312e SHA512 8d65c0407448125378495190ee2a2c0e3b27a3577efbd6bb5aa8ad76f5bf2bf17becdc6ef931672a4d16b033fd7c0a199bb60e62b0b2b311e5f59c4136f55835
+DIST cub-d106ddb991a56c3df1b6d51b2409e36ba8181ce4.tar.gz 398104 BLAKE2B 287f020189be877c7a9e667bdfb591da14046199b7336074040c3301d69110c8408d89a72cdcd74d8519deb200ec61823a6d2160d4ecbd00002338651dbf312e SHA512 8d65c0407448125378495190ee2a2c0e3b27a3577efbd6bb5aa8ad76f5bf2bf17becdc6ef931672a4d16b033fd7c0a199bb60e62b0b2b311e5f59c4136f55835
DIST fbgemm-1d710393.tar.gz 259645 BLAKE2B 7b159c67ee66679985758f59b001aea02f141e2a36af2dd12731bd260ba5a5834a2a5eefd9b8b43454a0d4c75df929fa302e7ba0e5210ee67c150b405d3b4cac SHA512 19bbc9ed274bced7b8453d9ec4f43bb998725764aeeee72782abff36fc77e9ef918396f5c462da7b448e9a3bb7a834f143cfdf6777ef0cdddada63bc2bf98761
+DIST fbgemm-7495417ad31c38a06b1b13db66b355b6f23cd96d.tar.gz 444575 BLAKE2B 97c0672119eee2e0a770445fbc7d3fad8d91d86d7a860f75e20b0a9b8dabae555b324f12d63092463eb1882ccb9d587e73cbb34013acaa3a76f015f093792e9f SHA512 b4cb8964e84dbe4065d7b9292c5877305a43b7dc21e896e3d20d3082c208eca2afe2348face8ce2236256e436c611d6adf9c9f729ef07b2ae9f939e25ec21e00
DIST fbgemm-87c378172.tar.gz 244850 BLAKE2B 322d892cc34921c9ffd7b9faf67804f3cfc3a427281e12afeeca4af3df37a8aa47198695e28e33feb836605d29925f566a4a290206ce6209478af87883561564 SHA512 42e678560dc774694ed6e2eb7d62a0284532be9c206aa1e056810e00bb7c06d557541e0ce56446735e163d480b504854e45cce9d7f23368974c500ecfe6e9961
DIST fmt-9bdd1596c.tar.gz 733867 BLAKE2B b5c62ea43bfd99268dd120d5a09eb5f80bc29411268367e63bdf7034aeb98c9aed00da019ad6e259922adbb849b4484353142e9d3449a256909e72f4a50ddee4 SHA512 3639b4984a88fc5495c6cb1a0a09bb0a13f5dc05286f5a2b15e60dfda780bcc1fe213497006cc27247c3c358be27d8af4dd995db2b3de0f6a5a1288dc1058585
DIST fmt-cd4af11e.tar.gz 740467 BLAKE2B da998415363b8205cb3be5c677ff8c3ea4aa5636741a5cfe45d7b6e54c1f6d0a36696158e2e21f37978323a11150e01efb2793de6a42af4ed19aac52381e0afc SHA512 24b42288be97849533dc82282fc08833d74642ad2afeb511e65c6389d88c709cf25345dec5b550c18af3705f4c0847fa0d4066308b51cd41ccfdda1a2c3babd0
+DIST fmt-cd4af11efc9c622896a3e4cb599fa28668ca3d05.tar.gz 740467 BLAKE2B da998415363b8205cb3be5c677ff8c3ea4aa5636741a5cfe45d7b6e54c1f6d0a36696158e2e21f37978323a11150e01efb2793de6a42af4ed19aac52381e0afc SHA512 24b42288be97849533dc82282fc08833d74642ad2afeb511e65c6389d88c709cf25345dec5b550c18af3705f4c0847fa0d4066308b51cd41ccfdda1a2c3babd0
DIST foxi-4aba696e.tar.gz 28740 BLAKE2B 54b2eb9610f402b89ed64b0f487326a58c8ecf9a195d0081329e4b55cc531bca45065f10176ba29ff7cc18b29c89ba7f0aa5046c35a78c562986e8dab40451e8 SHA512 6aec53e9489f87fab6ef70ddef20854f551ccc54368800f7c465c73858f13fd6db8f031fb6db43c9e26c1fd13d65389501d1db97148afc518277f4f95a5367d6
DIST foxi-8015abb72.tar.gz 28571 BLAKE2B d64b00bb81e43a9b1f55f640ab6e6845d33e01520daf7e1b56cd6ef3f82b38c5c8d6cb5c54d55302524f46a6ca2fbc43ef1aa3ee0fba563a8de502a8c4720175 SHA512 94c8c25d90273941161e04bedee521d3f7bbb296c125083e1d3c1421210b18758917d95c95bbd213c8eb19ad36f4e088c943816505e7fc462aecf12e00ebd2f6
+DIST foxi-c278588e34e535f0bb8f00df3880d26928038cad.tar.gz 28960 BLAKE2B 06c960f829b090eec4fe9e8c981e119578f358724e0b63991173bb7e318d23654261b901d1e15efeb6240bba75cc05fd45ab32fb30bbdf48369e139cf152f398 SHA512 ad42cfd70e40ba0f0a9187b34ae9e3bd361c8c0038669f4c1591c4f7421d12ad93f76f42b33c2575eea1a3ddb3ff781da2895cdc636df5b60422598f450203c7
DIST gemmlowp-3fb5c176.tar.gz 826382 BLAKE2B c5e68cb78429fe8ce96c752270e747382287937d0a0c1af26b444eda495a78438193c54900cd7906b34b369e170d582c5599f541d23d1280e38f972d6daea1ea SHA512 1c97bba41931c7fddf0e7c01312892cfa3d87abe2a4cdaf4cd20d846a102c5ad3d85329ccdb386f7047f2f037e92639cbcf91b317c2bf38bee11c12e71584afc
DIST gemmlowp-3fb5c176c.tar.gz 826382 BLAKE2B c5e68cb78429fe8ce96c752270e747382287937d0a0c1af26b444eda495a78438193c54900cd7906b34b369e170d582c5599f541d23d1280e38f972d6daea1ea SHA512 1c97bba41931c7fddf0e7c01312892cfa3d87abe2a4cdaf4cd20d846a102c5ad3d85329ccdb386f7047f2f037e92639cbcf91b317c2bf38bee11c12e71584afc
DIST gloo-3d08580f9.tar.gz 227739 BLAKE2B 3b011cc8ae08da36a917860dd58b87bc5b08c7189926b2f5bfaf839a9d53c5e7dee881e836f659e90269149eba6d80807e3a8e450b31f71220ba442ab59a389a SHA512 3dee533b350862cabce410f054fd943b4524b60394da1e92b9c73830e143b9abd30e5a493fe0c064d6fee8c15bd09b12620f0b528122170df329548c57116bd1
DIST gloo-3dc0328f.tar.gz 231048 BLAKE2B aa06ea3ca8c522652a405c0b56662bc5bd0eba5ef38770aaa2a078a8fd19fd1eeaa2e1007e537e584c5b07a84abe991c810f2a9c73e5b8df820dacde703bb81a SHA512 a6401f4b5e91130a7880a6742c075fdeb94026c3a04a57ce59b6dabc78b44d2f5e93803b3a7289e0c116bde4366536bb55f6dfd91a9a0d8af9640a81e3e4fe7b
+DIST gloo-c22a5cfba94edf8ea4f53a174d38aa0c629d070f.tar.gz 247789 BLAKE2B a8b72ee81c47d6b52559a5a7dc7a74dec56747c2fa46437fc9b3be9535b2ac577031a235c1a2cc7029c840a1ad28e58d2e91d7db820af3c0ce474e2a3ebea8a8 SHA512 1aa7bd5511a55ecb7a318cafa6ae1bde94d7cbc4d1483727e3b07c86a4c6e32864aa740d5a58a452d7cb7f37d84a928fa740f1fdb73e3309061d88b018083c56
DIST googletest-0fc5466d.tar.gz 993626 BLAKE2B f80e5d7e92c665a964add6370b6420ac00b0309768d21d52ce74e87b548293e05271456c63d171eb36389c601febc3514ea81d991145b1921e27f38e5fc0e084 SHA512 ac57b52454c027d4c14b0ca339ff4b5d36b66da38c7420164c44c11c214b617c79cf690b74b6f2f233b5df5dff200d97afa40c9b814f8b6117cd3d9e382a20c5
DIST googletest-2fe3bd99.tar.gz 993527 BLAKE2B fa631eadc310607dbe19cec6d66d8fb1c5e99e2dfc5031fff26f8c12c951d7798ad2062edf21589020cafc821bfe4b5e89310ee4e85f45d7d7fcd435ddd5eef9 SHA512 130182d2c1067bcd263fb27999c164d240f5d06d837475e71e7cadbf65c7211de00154dc1e15deae0b6ec2963799e55c0c21ee971e1c588064c5063e69a2bf1e
DIST googletest-2fe3bd994.tar.gz 993527 BLAKE2B fa631eadc310607dbe19cec6d66d8fb1c5e99e2dfc5031fff26f8c12c951d7798ad2062edf21589020cafc821bfe4b5e89310ee4e85f45d7d7fcd435ddd5eef9 SHA512 130182d2c1067bcd263fb27999c164d240f5d06d837475e71e7cadbf65c7211de00154dc1e15deae0b6ec2963799e55c0c21ee971e1c588064c5063e69a2bf1e
DIST googletest-5ec7f0c4.tar.gz 961649 BLAKE2B 2c518a4006e7a9decff3d4b81c30a910c01f6bf2a71593da25f6e74d5117cbf56de486078a3caf6be255df473fc1c2a04de5317cf882396114be0625d67d041b SHA512 623b077b3334958fafcbc34aa85891883277994af33be530efd903f47738a3e3562001cbf3b6da1a5e7d03803c5bd51bcc1fab81490db85d5a4f2b15e7de1495
+DIST googletest-e2239ee6043f73722e7aa812a459f54a28552929.tar.gz 887296 BLAKE2B 8f29b7028a6dd8190a113cd93398705b23b61d88bee38beaf9dcc0dfc8a463aed7fcd3719f6f1b131d4363aa57231629aaeffa108f6558efb58416cfface6d6e SHA512 cf9e7f3fd3e31ce6677eac355fb8bfe19c5b56a8ec3af8b9417d0904cdf5da92f99f7411a08131cc9fa4fc7d38e6a71fcfac993648e47b269a74a27de7607f7a
DIST ideep-938cc6889.tar.gz 27315 BLAKE2B 967bff56175d6f6b6e9895ef8e7ecf22f2bcbc4aa33074654b8c527165beb280e70c1b39da37ae2cd432eaa8d0ec600b83282d86faac05e17319dbd647f22107 SHA512 24a3f0b35756e3892af99658f7de7d17dff369601ffa7d39a6e2c3609c9c667f341cc66b6664fb69c4d938a1f7b3454e7106b8e27ec9995be5ad2d541927e2e1
+DIST ideep-9ca27bbfd88fa1469cbf0467bd6f14cd1738fa40.tar.gz 30949 BLAKE2B 07028f6544e5e088c01b111e89defd02eed022663536c4b1fe582e3b8da65a383aeb75e191f433e4cf497236630dcc531fa16a2758cd9be6db504c6b04f2a9b0 SHA512 0b51c41124ed033fd608b1ae7a6de3ebbb5c8b96c53cea594966178b5e0bd38d8b1b2773c4ba5e8f7b2f4af6d6ce1aef8fcb84bbe05780822976644d0e79b20f
DIST ideep-ba885200.tar.gz 27307 BLAKE2B 710dde31a8784315c88df9869e50c3940416263958ab653bce9876d60786906565b12f36c2d716a8a1f6009bc9e532e06733ddfac0d4079dba13ea153b8acbd9 SHA512 0c1bca04adbe797e5767f8b86fb3b247a2a287ffa2b3b19a918f976312175b459a6488166d12cf55e68c9aced84038fcda0d1d1c51a5034c83f844f51d462727
+DIST kineto-dbfa0ead96612f7ca265c63a35fdf0488395179b.tar.gz 7245955 BLAKE2B 09e6b1b1e15c485bbcc20713d07dab42fcc1b075557b6f202089696944b379d9fb3a860f68c16946b6f3eb76b12cf52a7fbc99a14af1baa40fb09b3f6d295c4e SHA512 6c479c3a14887c0703843416a961b6c92169caada029683a1d6d8463b4001a5bf8606dcd480df509c0f1fe53206001ab7428c9352fa638acc581523f55687e2b
DIST libnop-aa95422e.tar.gz 124202 BLAKE2B 5a74ecbf473dba09db1a11172a4aa432d81b14adb3826bef9aa8bae1bf1e2d0d5a7bf775fd4343fa9d7b235b17cafe949e47c903e92fd5eae9cc0717a552ea45 SHA512 62b21be874d2117294925c2497394d166da43d534776764c9c124699b5799d99790a2c6420804f8e143e1a18a536106852082f3a9d0052a726abc624fc19f937
DIST libuv-02a9e1be.tar.gz 1250418 BLAKE2B 49d7c6161614218bf856f7e23cd3e483bf1ac682bdc78b9624b9b5b52edde31aae005638bbc01e89f01421097e0bd4e07893db464326741ca6d1abaf45e633fe SHA512 de6d5d014b61804884a3945f2992f4aecf642fdd330927aa9a3bc17b76c29c51f6615d3d04542b24bb9ccdfd5207155e282f2fcd3aac14233d5bde4b1bc30284
DIST mkl-dnn-5ef631a0.tar.gz 5799312 BLAKE2B ea2aafcf45adadb0546781b00b44a0e9712c28e4937ef4daeef8b910e76bbb152e5434e45bec2aae0f6cb86fd7b5098e61842d7e99258db6fa846a79996d2e23 SHA512 66df9ea574010616df46d85ef25d23bd9ed31f9719cdbec4c727de58728fe095cd412d7663c2d456dba2f26848e45c1d67e34bffe4e25beeef9c1d40f187e8d6
DIST nccl-033d7995.tar.gz 146624 BLAKE2B b6f15d5d4690a5cbcf882c10826def400a14c58ff5f5af276b5b9a615a567de36ca907120cc681cdf2f2eb207f22bc87ee87d145a365097a64fb3d9de82432fb SHA512 3b3e087cb729b10e3251dfef52196bddd33e3e777df289c5fc537e99473e78f8720255fbd3e14ae2d2a6126d1e9d59aa6d57d7c7958d919e65834fef92c1c835
DIST nccl-5949d96f3.tar.gz 147548 BLAKE2B f3d3dd222ae90ac9ac1457a9695f112a21f5652a5b40e10ac049da910f07707b1c3910f59734fbe5e2c6523c1e83f3801f809efa77d122a57e859828c74ba8c2 SHA512 d9ea83caf7940fb47134293236fcb7478c0d4e40365d3b0a29427758e2e2dbb980c5e8c05fc9fc3956ed5e21a82ec0efaa31d973fe9c73fa3f50465f76756131
+DIST onnx-29e7aa7048809784465d06e897f043a4600642b2.tar.gz 9332964 BLAKE2B 20858ed93a7e2064624f13bb345ad7ad699ddc8c5e9ce9af27ae49d14bd7db9a0d9ff463919dd0c840595916ac7a720344608c586e87b522d5e2b78fde42eb6a SHA512 bcc1edbc4ce29b1c3c9f1ac4854f13d547d9efa6b712ddb5afb3d84637687aba1dbb2224ac4278a2b2e677ee485397c432554e7f02d51333c57a1ed7e0909d32
DIST onnx-765f5ee8.tar.gz 2379139 BLAKE2B 3e3299e2f3c1184937820b137d5fb492abe216ae3a054f4a17c6cb037168f4a77d8c90db0ba657ba9c9f7af2099f71ae0b8658a573c9f2f6d29fbc9d5f0f1b8a SHA512 7e10717546d1ed0bab780768e907f957294bfda47748b4c7576b75a761f5e006fdd21f0b014ce6d761a0ac6ae59dd8bc71592785b67167a6b3692d1a56dbbda9
DIST onnx-a82c6a70.tar.gz 4874549 BLAKE2B 055f89d63c03304264b7dd64d5eb6c892a4a280693001ca932f0d352379630870d96dadd6e734b1ec1044cfd92856cd9bb362021a6424ef79e6a408a9c17bc3c SHA512 1ead6644cd28198a428ebcd0f127343c6cbcfdbf39a0832c62ee5ee320a06c655448f508406637702e2da33057c92f76da12302b403ac339a5cad8ea4b5ebab2
DIST onnx-a82c6a701.tar.gz 4874549 BLAKE2B 055f89d63c03304264b7dd64d5eb6c892a4a280693001ca932f0d352379630870d96dadd6e734b1ec1044cfd92856cd9bb362021a6424ef79e6a408a9c17bc3c SHA512 1ead6644cd28198a428ebcd0f127343c6cbcfdbf39a0832c62ee5ee320a06c655448f508406637702e2da33057c92f76da12302b403ac339a5cad8ea4b5ebab2
DIST onnx-tensorrt-c1532114.tar.gz 72464 BLAKE2B 45301706ca5c91c39e24db84e1dc4e968a8540b760d7b16df08f3a76c407dfceb38962520d822b84618be088fc3d69431f738a8bc7b0f578c84f35234061e99a SHA512 9e814b5dfc3a65ddba229bbddada4c686afab233463329a02cea176b6b1994643f9835ce44a84a9ac1a49e12a7fe2325fd6cd9d2d99a422284089df0202a69a5
DIST onnx-tensorrt-c15321141.tar.gz 72464 BLAKE2B 45301706ca5c91c39e24db84e1dc4e968a8540b760d7b16df08f3a76c407dfceb38962520d822b84618be088fc3d69431f738a8bc7b0f578c84f35234061e99a SHA512 9e814b5dfc3a65ddba229bbddada4c686afab233463329a02cea176b6b1994643f9835ce44a84a9ac1a49e12a7fe2325fd6cd9d2d99a422284089df0202a69a5
+DIST onnx-tensorrt-c153211418a7c57ce071d9ce2a41f8d1c85a878f.tar.gz 72464 BLAKE2B 45301706ca5c91c39e24db84e1dc4e968a8540b760d7b16df08f3a76c407dfceb38962520d822b84618be088fc3d69431f738a8bc7b0f578c84f35234061e99a SHA512 9e814b5dfc3a65ddba229bbddada4c686afab233463329a02cea176b6b1994643f9835ce44a84a9ac1a49e12a7fe2325fd6cd9d2d99a422284089df0202a69a5
DIST psimd-072586a7.tar.gz 6825 BLAKE2B db255d2a62ffa320b1e190a7a9ac923d812e918a72ce8ecfeeb926709ece92d05497430196b0fc833d910b9d24bf0140d20bcce1de695e1c39211158440608db SHA512 a18faea093423dd9fe19ece8b228e011dccce0a2a22222f777ea19b023a13173966d4a8aea01147e8fc58de5d39cffcedeb2221a1572ae52bd5aba1295f86a94
DIST psimd-072586a71.tar.gz 6825 BLAKE2B db255d2a62ffa320b1e190a7a9ac923d812e918a72ce8ecfeeb926709ece92d05497430196b0fc833d910b9d24bf0140d20bcce1de695e1c39211158440608db SHA512 a18faea093423dd9fe19ece8b228e011dccce0a2a22222f777ea19b023a13173966d4a8aea01147e8fc58de5d39cffcedeb2221a1572ae52bd5aba1295f86a94
+DIST psimd-072586a71b55b7f8c584153d223e95687148a90.tar.gz 6825 BLAKE2B db255d2a62ffa320b1e190a7a9ac923d812e918a72ce8ecfeeb926709ece92d05497430196b0fc833d910b9d24bf0140d20bcce1de695e1c39211158440608db SHA512 a18faea093423dd9fe19ece8b228e011dccce0a2a22222f777ea19b023a13173966d4a8aea01147e8fc58de5d39cffcedeb2221a1572ae52bd5aba1295f86a94
DIST pthreadpool-029c8862.tar.gz 45970 BLAKE2B 09bd7d258f45fbe703238826b7435d8a5d013700cd734282b646420ba0854c0a386712f6bc3ed44e7496d51471b1e0a965f01ebdb09786e2020d979ecddb767a SHA512 b51099fa9d62065883cc43dcd5f9717a17be5ee2e87fc861667172a09acb3a62929c8bbc8a5c0c00885a638af0ec2ae4149adde2ba85bf3c80834f9b973c2d5b
DIST pthreadpool-029c88620.tar.gz 45970 BLAKE2B 09bd7d258f45fbe703238826b7435d8a5d013700cd734282b646420ba0854c0a386712f6bc3ed44e7496d51471b1e0a965f01ebdb09786e2020d979ecddb767a SHA512 b51099fa9d62065883cc43dcd5f9717a17be5ee2e87fc861667172a09acb3a62929c8bbc8a5c0c00885a638af0ec2ae4149adde2ba85bf3c80834f9b973c2d5b
+DIST pthreadpool-a134dd5d4cee80cce15db81a72e7f929d71dd413.tar.gz 49011 BLAKE2B 7bfbca81321243e64aa53c668dfe380ce4f7b88477a1c794a4dea9062c9b0969ca745dbfe0abbb95fffbf44080763506609c387ed085d89f6c612be6804b5cc2 SHA512 5f5a1275bbcef13cea88e381010bf2654c9646d30c5fb061f1d6e9e9a0ae6398e137c5e4f7da69f7d8d8b58fb5a7e79f7a4c0c1c3bbaad8f3d0c896d21bc7691
DIST pytorch-1.6.0.tar.gz 11376568 BLAKE2B 30aac34e14837ed6942ef7577aea77752cd9c809cb751fa837693b2b60eeda9a371421c4b4678fe94763a47e434b65ea60afc56aec7863887ba12bf362b96f0a SHA512 117ff1588ed1ebd0df15fbed066c65ea026893fe9a40d14aa1f73d848fab114b1b11bd7ed083815030f7fdf13a824480521cb40865f48a24c7028f4d195f2127
DIST pytorch-1.7.1.tar.gz 13012087 BLAKE2B ff498814178281ca59ae80bfe51dde3ffb0cde1eaa762bd9b36c2ff7f07d4b5ae4d68e10c76158e5e9e4250fcb01265a3755575b761495e20cf677e9a9825454 SHA512 359e271093e7afd374202f48e40356d195f644f78377a0b88f38627ad7aeabb9201a18c12ff35fb4aaf0d731168e511504445d8b4c08e92eed50264e23d81bae
+DIST pytorch-1.9.0.tar.gz 16772380 BLAKE2B 16f369cf2752082ab07fa0e497aaff7b90daf94cf39cce533c4a8b06a9237710089af0c137e29fbc79b4cf72d8d47681408e9ada1692431b573d90a07c373f1e SHA512 389ff114367a4337ab6e68178184f04751e4641fac685923afa019093951fa3a446f5265f6661f3aaad99c733c0107391431896c6e876796b8837f5ae75edd99
DIST sleef-7f523de6.tar.gz 1174007 BLAKE2B 58ebdddea912c841a4d917111d81051860631e93abbed43fb9899eff9370181f9227419e87872799a650e6a50cf174d0bf3b90c699a0e0763e903976baf95c9c SHA512 d83b24c34e83b36314344d5b31f1c3b673e38b44bc2d2bbbfdaf2019c3f0e73a83f2d13c6d745ca99d1532c1a3e0fcb4a71bd212e423bec03d610af5dd49e3f3
DIST sleef-7f523de65.tar.gz 1174007 BLAKE2B 58ebdddea912c841a4d917111d81051860631e93abbed43fb9899eff9370181f9227419e87872799a650e6a50cf174d0bf3b90c699a0e0763e903976baf95c9c SHA512 d83b24c34e83b36314344d5b31f1c3b673e38b44bc2d2bbbfdaf2019c3f0e73a83f2d13c6d745ca99d1532c1a3e0fcb4a71bd212e423bec03d610af5dd49e3f3
+DIST sleef-e0a003ee838b75d11763aa9c3ef17bf71a725bff.tar.gz 1642070 BLAKE2B 366fa96e35f429199e8462c63bc9cfbd1888aa65170d3203a5b0391fb855c29241eb225f847e416650e6ed5544f17a745c5a43a622a2847416ad7bd207572840 SHA512 13ea28745e796f8b77a40c99f679e0955e213128fb05d17b61cdcef102b7a758cbda04def3544767a81ddf170b7800f168d25fb1b55093614c7126456765cbea
DIST tensorpipe-3b8089c9c.tar.gz 141980 BLAKE2B 6c2a1e630412e9f8e039d5c44aaed4623f51516d59ee4237b9ec95d5b30970dbf4961aca0d84f1fee621ab8b8f668f0e8dbfbe558614d5651a00d9be21259a88 SHA512 1e9473532b11c23ec7dd9fdb148c0440263ae41f42a7826a4f7e098ed2a7e0c99d5e9df344b310e17098c3d70749a38d20d8af992c4820bebdbd5078d1a20dcc
DIST tensorpipe-95ff9319.tar.gz 155511 BLAKE2B bc074efe7501fd29fbff177c2782d4be1d514c8f2f5c9fe0fcdcbd0ca3a33bb91cab8fc95e8e5dac1bc4f65d904d0beef3d30f001eab9884b0506edbbee774fd SHA512 5ef38f10c65c49b3feea964c45564196005ebf47b365ed0cf60916215bac4fa04525ec9de007342fe520206b8e8663c0264fd838e89073a752d308418a2b1dd6
+DIST tensorpipe-c0e7623adb05f36311c7cde6dac8fc4c290419d9.tar.gz 253518 BLAKE2B fcef24208f97c1a96a3b0d30a76c3956de4383823c908982bcf1ef7fdacd14f6ada6fa3b797d3b6c9bd3dea3d1dd4bfc6f7b2136057a385ab42b2909cd1beee3 SHA512 734e919df485b590ff3bc022b53bbe8aeda1c2178ab8c6938e9fb6d977b48d4fa9a395f65f3727f602d0b25d0a7d419ad9ea96566b644b83073291ae40c54856
diff --git a/sci-libs/pytorch/pytorch-1.9.0.ebuild b/sci-libs/pytorch/pytorch-1.9.0.ebuild
new file mode 100644
index 000000000..c997f8da8
--- /dev/null
+++ b/sci-libs/pytorch/pytorch-1.9.0.ebuild
@@ -0,0 +1,321 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{7,8,9} )
+
+inherit cmake cuda distutils-r1 prefix
+
+DESCRIPTION="Tensors and Dynamic neural networks in Python with strong GPU acceleration"
+HOMEPAGE="https://pytorch.org/"
+SRC_URI="https://github.com/pytorch/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz
+https://github.com/google/benchmark/archive/e991355c02b93fe17713efe04cbc2e278e00fdbd.tar.gz -> benchmark-e991355c02b93fe17713efe04cbc2e278e00fdbd.tar.gz
+https://github.com/pytorch/cpuinfo/archive/63b25457.tar.gz -> cpuinfo-63b25457.tar.gz
+https://github.com/NVlabs/cub/archive/d106ddb991a56c3df1b6d51b2409e36ba8181ce4.tar.gz -> cub-d106ddb991a56c3df1b6d51b2409e36ba8181ce4.tar.gz
+https://github.com/pytorch/fbgemm/archive/7495417ad31c38a06b1b13db66b355b6f23cd96d.tar.gz -> fbgemm-7495417ad31c38a06b1b13db66b355b6f23cd96d.tar.gz
+https://github.com/asmjit/asmjit/archive/9057aa30.tar.gz -> asmjit-9057aa30.tar.gz
+https://github.com/pytorch/cpuinfo/archive/5916273f79a21551890fd3d56fc5375a78d1598d.tar.gz -> cpuinfo-5916273f79a21551890fd3d56fc5375a78d1598d.tar.gz
+https://github.com/google/googletest/archive/0fc5466d.tar.gz -> googletest-0fc5466d.tar.gz
+https://github.com/fmtlib/fmt/archive/cd4af11efc9c622896a3e4cb599fa28668ca3d05.tar.gz -> fmt-cd4af11efc9c622896a3e4cb599fa28668ca3d05.tar.gz
+https://github.com/houseroad/foxi/archive/c278588e34e535f0bb8f00df3880d26928038cad.tar.gz -> foxi-c278588e34e535f0bb8f00df3880d26928038cad.tar.gz
+https://github.com/Maratyszcza/FP16/archive/4dfe081cf6bcd15db339cf2680b9281b8451eeb3.tar.gz -> FP16-4dfe081cf6bcd15db339cf2680b9281b8451eeb3.tar.gz
+https://github.com/Maratyszcza/FXdiv/archive/b408327ac2a15ec3e43352421954f5b1967701d1.tar.gz -> FXdiv-b408327ac2a15ec3e43352421954f5b1967701d1.tar.gz
+https://github.com/google/gemmlowp/archive/3fb5c176.tar.gz -> gemmlowp-3fb5c176.tar.gz
+https://github.com/facebookincubator/gloo/archive/c22a5cfba94edf8ea4f53a174d38aa0c629d070f.tar.gz -> gloo-c22a5cfba94edf8ea4f53a174d38aa0c629d070f.tar.gz
+https://github.com/google/googletest/archive/e2239ee6043f73722e7aa812a459f54a28552929.tar.gz -> googletest-e2239ee6043f73722e7aa812a459f54a28552929.tar.gz
+https://github.com/intel/ideep/archive/9ca27bbfd88fa1469cbf0467bd6f14cd1738fa40.tar.gz -> ideep-9ca27bbfd88fa1469cbf0467bd6f14cd1738fa40.tar.gz
+https://github.com/intel/mkl-dnn/archive/5ef631a0.tar.gz -> mkl-dnn-5ef631a0.tar.gz
+cuda? ( https://github.com/NVIDIA/nccl/archive/033d7995.tar.gz -> nccl-033d7995.tar.gz )
+https://github.com/Maratyszcza/NNPACK/archive/c07e3a0400713d546e0dea2d5466dd22ea389c73.tar.gz -> NNPACK-c07e3a0400713d546e0dea2d5466dd22ea389c73.tar.gz
+https://github.com/onnx/onnx/archive/a82c6a70.tar.gz -> onnx-a82c6a70.tar.gz
+https://github.com/onnx/onnx-tensorrt/archive/c153211418a7c57ce071d9ce2a41f8d1c85a878f.tar.gz -> onnx-tensorrt-c153211418a7c57ce071d9ce2a41f8d1c85a878f.tar.gz
+https://github.com/onnx/onnx/archive/29e7aa7048809784465d06e897f043a4600642b2.tar.gz -> onnx-29e7aa7048809784465d06e897f043a4600642b2.tar.gz
+https://github.com/google/benchmark/archive/e776aa02.tar.gz -> benchmark-e776aa02.tar.gz
+https://github.com/google/benchmark/archive/5b7683f4.tar.gz -> benchmark-5b7683f4.tar.gz
+https://github.com/google/googletest/archive/5ec7f0c4.tar.gz -> googletest-5ec7f0c4.tar.gz
+https://github.com/Maratyszcza/psimd/archive/072586a71b55b7f8c584153d223e95687148a90.tar.gz -> psimd-072586a71b55b7f8c584153d223e95687148a90.tar.gz
+https://github.com/Maratyszcza/pthreadpool/archive/a134dd5d4cee80cce15db81a72e7f929d71dd413.tar.gz -> pthreadpool-a134dd5d4cee80cce15db81a72e7f929d71dd413.tar.gz
+https://github.com/Maratyszcza/PeachPy/archive/07d8fde8ac45d7705129475c0f94ed8925b93473.tar.gz -> PeachPy-07d8fde8ac45d7705129475c0f94ed8925b93473.tar.gz
+https://github.com/pytorch/QNNPACK/archive/7d2a4e9931a82adc3814275b6219a03e24e36b4c.tar.gz -> QNNPACK-7d2a4e9931a82adc3814275b6219a03e24e36b4c.tar.gz
+https://github.com/shibatch/sleef/archive/e0a003ee838b75d11763aa9c3ef17bf71a725bff.tar.gz -> sleef-e0a003ee838b75d11763aa9c3ef17bf71a725bff.tar.gz
+https://github.com/pytorch/tensorpipe/archive/c0e7623adb05f36311c7cde6dac8fc4c290419d9.tar.gz -> tensorpipe-c0e7623adb05f36311c7cde6dac8fc4c290419d9.tar.gz
+https://github.com/google/googletest/archive/2fe3bd99.tar.gz -> googletest-2fe3bd99.tar.gz
+https://github.com/google/libnop/archive/aa95422e.tar.gz -> libnop-aa95422e.tar.gz
+https://github.com/libuv/libuv/archive/02a9e1be.tar.gz -> libuv-02a9e1be.tar.gz
+https://github.com/google/XNNPACK/archive/79cd5f9e18ad0925ac9a050b00ea5a36230072db.tar.gz -> XNNPACK-79cd5f9e18ad0925ac9a050b00ea5a36230072db.tar.gz
+https://github.com/pytorch/kineto/archive/dbfa0ead96612f7ca265c63a35fdf0488395179b.tar.gz -> kineto-dbfa0ead96612f7ca265c63a35fdf0488395179b.tar.gz
+"
+
+# git clone git@github.com:pytorch/pytorch.git && cd pytorch
+# git submodules update --init --recursive
+# ${FILESDIR}/get_third_paries
+# cat SRC_URI src_prepare
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS=""
+
+IUSE="asan blas cuda +fbgemm ffmpeg gflags glog +gloo leveldb lmdb mkldnn mpi namedtensor +nnpack numa +observers opencl opencv +openmp +python +qnnpack redis rocm static test tools zeromq"
+RESTRICT="!test? ( test )"
+REQUIRED_USE="
+ ?? ( cuda rocm )
+"
+
+RDEPEND="
+ dev-python/pyyaml[${PYTHON_USEDEP}]
+ blas? ( virtual/blas )
+ cuda? ( dev-libs/cudnn
+ dev-cpp/eigen[cuda] )
+ rocm? ( >=dev-util/hip-4.0.0-r1
+ >=dev-libs/rccl-4
+ >=sci-libs/rocThrust-4
+ >=sci-libs/hipCUB-4
+ >=sci-libs/rocPRIM-4
+ >=sci-libs/miopen-4
+ >=sci-libs/rocBLAS-4
+ >=sci-libs/rocRAND-4
+ >=sci-libs/hipSPARSE-4
+ >=sci-libs/rocFFT-4
+ >=dev-util/roctracer-4 )
+ ffmpeg? ( media-video/ffmpeg )
+ gflags? ( dev-cpp/gflags )
+ glog? ( dev-cpp/glog )
+ leveldb? ( dev-libs/leveldb )
+ lmdb? ( dev-db/lmdb )
+ mpi? ( virtual/mpi )
+ opencl? ( dev-libs/clhpp virtual/opencl )
+ opencv? ( media-libs/opencv )
+ python? ( ${PYTHON_DEPS}
+ dev-python/pybind11[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/protobuf-python:0/22
+ )
+ redis? ( dev-db/redis )
+ zeromq? ( net-libs/zeromq )
+ dev-cpp/eigen
+ dev-libs/protobuf:0/22
+ dev-libs/libuv
+"
+
+#ATen code generation
+BDEPEND="dev-python/pyyaml"
+
+DEPEND="${RDEPEND}
+ test? ( dev-python/pytest[${PYTHON_USEDEP}] )
+ dev-cpp/tbb
+ app-arch/zstd
+ dev-python/pybind11[${PYTHON_USEDEP}]
+ dev-python/typing-extensions[${PYTHON_USEDEP}]
+ sys-fabric/libibverbs
+ sys-process/numactl
+"
+
+PATCHES=(
+ "${FILESDIR}"/${PN}-1.6.0-skip-tests.patch
+ "${FILESDIR}"/${PN}-1.6.0-global-dlopen.patch
+ "${FILESDIR}"/0002-Don-t-build-libtorch-again-for-PyTorch-1.7.1.patch
+ "${FILESDIR}"/${PN}-1.7.1-no-rpath.patch
+ "${FILESDIR}"/${PN}-1.7.1-torch_shm_manager.patch
+)
+
+src_prepare() {
+ cmake_src_prepare
+ eprefixify torch/__init__.py
+
+ rmdir third_party/benchmark || die
+ ln -sv "${WORKDIR}"/benchmark-e991355c02b93fe17713efe04cbc2e278e00fdbd third_party/benchmark || die
+ rmdir third_party/cpuinfo || die
+ ln -sv "${WORKDIR}"/cpuinfo-5916273f79a21551890fd3d56fc5375a78d1598d third_party/cpuinfo || die
+ rmdir third_party/cub || die
+ ln -sv "${WORKDIR}"/cub-d106ddb991a56c3df1b6d51b2409e36ba8181ce4 third_party/cub || die
+ rmdir third_party/fbgemm || die
+ ln -sv "${WORKDIR}"/FBGEMM-7495417ad31c38a06b1b13db66b355b6f23cd96d third_party/fbgemm || die
+ rmdir third_party/fbgemm/third_party/asmjit || die
+ ln -sv "${WORKDIR}"/asmjit-9057aa30b620f0662ff51e2230c126a345063064 third_party/fbgemm/third_party/asmjit || die
+ rmdir third_party/fbgemm/third_party/cpuinfo || die
+ ln -sv "${WORKDIR}"/cpuinfo-d5e37adf1406cf899d7d9ec1d317c47506ccb970 third_party/fbgemm/third_party/cpuinfo || die
+ rmdir third_party/fbgemm/third_party/googletest || die
+ ln -sv "${WORKDIR}"/googletest-0fc5466dbb9e623029b1ada539717d10bd45e99e third_party/fbgemm/third_party/googletest || die
+ rmdir third_party/fmt || die
+ ln -sv "${WORKDIR}"/fmt-cd4af11efc9c622896a3e4cb599fa28668ca3d05 third_party/fmt || die
+ rmdir third_party/foxi || die
+ ln -sv "${WORKDIR}"/foxi-c278588e34e535f0bb8f00df3880d26928038cad third_party/foxi || die
+ rmdir third_party/FP16 || die
+ ln -sv "${WORKDIR}"/FP16-4dfe081cf6bcd15db339cf2680b9281b8451eeb3 third_party/FP16 || die
+ rmdir third_party/FXdiv
+ ln -sv "${WORKDIR}"/FXdiv-b408327ac2a15ec3e43352421954f5b1967701d1 third_party/FXdiv || die
+ rmdir third_party/gemmlowp/gemmlowp || die
+ ln -sv "${WORKDIR}"/gemmlowp-3fb5c176c17c765a3492cd2f0321b0dab712f350 third_party/gemmlowp/gemmlowp || die
+ rmdir third_party/gloo || die
+ ln -sv "${WORKDIR}"/gloo-c22a5cfba94edf8ea4f53a174d38aa0c629d070f third_party/gloo || die
+ rmdir third_party/googletest || die
+ ln -sv "${WORKDIR}"/googletest-e2239ee6043f73722e7aa812a459f54a28552929 third_party/googletest || die
+ rmdir third_party/ideep || die
+ ln -sv "${WORKDIR}"/ideep-9ca27bbfd88fa1469cbf0467bd6f14cd1738fa40 third_party/ideep || die
+ rmdir third_party/ideep/mkl-dnn || die
+ ln -sv "${WORKDIR}"/mkl-dnn-5ef631a030a6f73131c77892041042805a06064f third_party/ideep/mkl-dnn || die
+ rmdir third_party/nccl/nccl || die
+ ln -sv "${WORKDIR}"/nccl-033d799524fb97629af5ac2f609de367472b2696 third_party/nccl/nccl || die
+ rmdir third_party/NNPACK || die
+ ln -sv "${WORKDIR}"/NNPACK-c07e3a0400713d546e0dea2d5466dd22ea389c73 third_party/NNPACK || die
+ rmdir third_party/onnx || die
+ ln -sv "${WORKDIR}"/onnx-29e7aa7048809784465d06e897f043a4600642b2 third_party/onnx || die
+ rmdir third_party/onnx-tensorrt || die
+ ln -sv "${WORKDIR}"/onnx-tensorrt-c153211418a7c57ce071d9ce2a41f8d1c85a878f third_party/onnx-tensorrt || die
+ rmdir third_party/onnx-tensorrt/third_party/onnx || die
+ ln -sv "${WORKDIR}"/onnx-765f5ee823a67a866f4bd28a9860e81f3c811ce8 third_party/onnx-tensorrt/third_party/onnx || die
+ rmdir third_party/onnx/third_party/benchmark || die
+ ln -sv "${WORKDIR}"/benchmark-e776aa0275e293707b6a0901e0e8d8a8a3679508 third_party/onnx/third_party/benchmark || die
+ rmdir third_party/psimd || die
+ ln -sv "${WORKDIR}"/psimd-072586a71b55b7f8c584153d223e95687148a900 third_party/psimd || die
+ rmdir third_party/pthreadpool || die
+ ln -sv "${WORKDIR}"/pthreadpool-a134dd5d4cee80cce15db81a72e7f929d71dd413 third_party/pthreadpool || die
+ rmdir third_party/python-peachpy || die
+ ln -sv "${WORKDIR}"/PeachPy-07d8fde8ac45d7705129475c0f94ed8925b93473 third_party/python-peachpy || die
+ rmdir third_party/QNNPACK || die
+ ln -sv "${WORKDIR}"/QNNPACK-7d2a4e9931a82adc3814275b6219a03e24e36b4c third_party/QNNPACK || die
+ rmdir third_party/sleef || die
+ ln -sv "${WORKDIR}"/sleef-e0a003ee838b75d11763aa9c3ef17bf71a725bff third_party/sleef || die
+ rmdir third_party/tensorpipe || die
+ ln -sv "${WORKDIR}"/tensorpipe-c0e7623adb05f36311c7cde6dac8fc4c290419d9 third_party/tensorpipe || die
+ rmdir third_party/tensorpipe/third_party/googletest || die
+ ln -sv "${WORKDIR}"/googletest-2fe3bd994b3189899d93f1d5a881e725e046fdc2 third_party/tensorpipe/third_party/googletest || die
+ rmdir third_party/tensorpipe/third_party/libnop || die
+ ln -sv "${WORKDIR}"/libnop-aa95422ea8c409e3f078d2ee7708a5f59a8b9fa2 third_party/tensorpipe/third_party/libnop || die
+ rmdir third_party/tensorpipe/third_party/libuv || die
+ ln -sv "${WORKDIR}"/libuv-02a9e1be252b623ee032a3137c0b0c94afbe6809 third_party/tensorpipe/third_party/libuv || die
+ rmdir third_party/XNNPACK || die
+ ln -sv "${WORKDIR}"/XNNPACK-79cd5f9e18ad0925ac9a050b00ea5a36230072db third_party/XNNPACK || die
+ rmdir third_party/kineto || die
+ ln -sv "${WORKDIR}"/kineto-dbfa0ead96612f7ca265c63a35fdf0488395179b third_party/kineto || die
+
+ if use cuda; then
+ cd third_party/nccl/nccl || die
+ eapply "${FILESDIR}"/${PN}-1.6.0-nccl-nvccflags.patch
+
+# addpredict /dev/nvidiactl
+ cuda_src_prepare
+ export CUDAHOSTCXX=$(cuda_gccdir)/g++
+ fi
+
+ if use rocm; then
+ #Allow escaping sandbox
+ addread /dev/kfd
+ addread /dev/dri
+ addwrite /dev/kfd
+ addwrite /dev/dri
+
+ ebegin "HIPifying cuda sources"
+ tools/amd_build/build_amd.py
+ eend $?
+
+ export PYTORCH_ROCM_ARCH=$(rocminfo | egrep -o "gfx[0-9]+" | uniq | awk -vORS=';' "{print $1}" | sed 's/;$/\n/') || die
+ sed -e "/set(roctracer_INCLUDE_DIRS/s,\${ROCTRACER_PATH}/include,${EPREFIX}/usr/include/roctracer," \
+ -i cmake/public/LoadHIP.cmake || die
+ fi
+}
+
+src_configure() {
+ local mycmakeargs=(
+ -DTORCH_BUILD_VERSION=${PV}
+ -DTORCH_INSTALL_LIB_DIR=$(get_libdir)
+ -DBUILD_BINARY=$(usex tools ON OFF)
+ -DBUILD_CUSTOM_PROTOBUF=OFF
+ -DBUILD_PYTHON=$(usex python ON OFF)
+ -DBUILD_SHARED_LIBS=$(usex static OFF ON)
+ -DBUILD_TEST=$(usex test ON OFF)
+ -DUSE_ASAN=$(usex asan ON OFF)
+ -DUSE_CUDA=$(usex cuda ON OFF)
+ -DUSE_NCCL=$(usex cuda ON OFF)
+ -DUSE_SYSTEM_NCCL=OFF
+ -DUSE_ROCM=$(usex rocm ON OFF)
+ -DUSE_FBGEMM=$(usex fbgemm ON OFF)
+ -DUSE_FFMPEG=$(usex ffmpeg ON OFF)
+ -DUSE_GFLAGS=$(usex gflags ON OFF)
+ -DUSE_GLOG=$(usex glog ON OFF)
+ -DUSE_LEVELDB=$(usex leveldb ON OFF)
+ -DUSE_LITE_PROTO=OFF
+ -DUSE_LMDB=$(usex lmdb ON OFF)
+ -DUSE_MKLDNN=$(usex mkldnn ON OFF)
+ -DUSE_MKLDNN_CBLAS=OFF
+ -DUSE_NNPACK=$(usex nnpack ON OFF)
+ -DUSE_NUMPY=$(usex python ON OFF)
+ -DUSE_NUMA=$(usex numa ON OFF)
+ -DUSE_OBSERVERS=$(usex observers ON OFF)
+ -DUSE_OPENCL=$(usex opencl ON OFF)
+ -DUSE_OPENCV=$(usex opencv ON OFF)
+ -DUSE_OPENMP=$(usex openmp ON OFF)
+ -DUSE_TBB=OFF
+ -DUSE_PROF=OFF
+ -DUSE_QNNPACK=$(usex qnnpack ON OFF)
+ -DUSE_REDIS=$(usex redis ON OFF)
+ -DUSE_ROCKSDB=OFF
+ -DUSE_ZMQ=$(usex zeromq ON OFF)
+ -DUSE_MPI=$(usex mpi ON OFF)
+ -DUSE_GLOO=$(usex gloo ON OFF)
+ -DUSE_SYSTEM_EIGEN_INSTALL=ON
+ -DBUILD_NAMEDTENSOR=$(usex namedtensor ON OFF)
+ -DBLAS=$(usex blas Generic Eigen)
+ -DTP_BUILD_LIBUV=OFF
+ -Wno-dev
+ )
+
+ cmake_src_configure
+
+ if use python; then
+ CMAKE_BUILD_DIR="${BUILD_DIR}" distutils-r1_src_configure
+ fi
+
+ # do not rerun cmake and the build process in src_install
+ sed '/RERUN/,+1d' -i "${BUILD_DIR}"/build.ninja || die
+}
+
+src_compile() {
+ cmake_src_compile
+
+ if use python; then
+ CMAKE_BUILD_DIR=${BUILD_DIR} distutils-r1_src_compile
+ fi
+}
+
+src_install() {
+ cmake_src_install
+
+ local LIB=$(get_libdir)
+ if [[ ${LIB} != lib ]]; then
+ mv -fv "${ED}"/usr/lib/*.so "${ED}"/usr/${LIB}/ || die
+ fi
+
+ rm -rfv "${ED}/torch"
+ rm -rfv "${ED}/var"
+ rm -rfv "${ED}/usr/lib"
+
+ rm -fv "${ED}/usr/include/*.{h,hpp}"
+ rm -rfv "${ED}/usr/include/asmjit"
+ rm -rfv "${ED}/usr/include/c10d"
+ rm -rfv "${ED}/usr/include/fbgemm"
+ rm -rfv "${ED}/usr/include/fp16"
+ rm -rfv "${ED}/usr/include/gloo"
+ rm -rfv "${ED}/usr/include/include"
+ rm -rfv "${ED}/usr/include/var"
+
+ cp -rv "${WORKDIR}/${P}/third_party/pybind11/include/pybind11" "${ED}/usr/include/"
+
+ rm -fv "${ED}/usr/${LIB}/libtbb.so"
+ rm -rfv "${ED}/usr/${LIB}/cmake"
+
+ if use python; then
+ scanelf -r --fix "${BUILD_DIR}/caffe2/python"
+ CMAKE_BUILD_DIR=${BUILD_DIR} distutils-r1_src_install
+
+ python_foreach_impl python_optimize
+ fi
+
+ find "${ED}/usr/${LIB}" -name "*.a" -exec rm -fv {} \;
+
+ use test && rm -rfv "${ED}/usr/test" "${ED}"/usr/bin/test_{api,jit}
+
+ # Remove the empty directories by CMake Python:
+ find "${ED}" -type d -empty -delete || die
+}
diff --git a/sci-mathematics/gap/gap-4.11.0.ebuild b/sci-mathematics/gap/gap-4.11.0.ebuild
index db0da0967..d94a02143 100644
--- a/sci-mathematics/gap/gap-4.11.0.ebuild
+++ b/sci-mathematics/gap/gap-4.11.0.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
@@ -16,7 +16,7 @@ SLOT="0"
LICENSE="GPL-2"
KEYWORDS="~amd64"
# broken HPC and boehm
-IUSE="-boehm debug -hpc julia julia-gc memcheck valgrind"
+IUSE="boehm debug hpc julia julia-gc memcheck valgrind"
REQUIRED_USE="valgrind? ( memcheck ) julia-gc? ( julia ) hpc? ( boehm )"
RDEPEND+="
@@ -27,7 +27,7 @@ RDEPEND+="
sys-libs/zlib
julia? ( || (
dev-lang/julia
- dev-lang/julia-bin
+ dev-lang/julia-bin:*
) )
valgrind? ( dev-util/valgrind )
"
diff --git a/sci-mathematics/gappa/Manifest b/sci-mathematics/gappa/Manifest
index c250c9090..132e4af1c 100644
--- a/sci-mathematics/gappa/Manifest
+++ b/sci-mathematics/gappa/Manifest
@@ -1 +1,2 @@
DIST gappa-1.3.5.tar.gz 412527 BLAKE2B cf3dc69e9ef538cda7eee42c81dfa5cdfb765967745f68dabd5937cb00ea075f6c6b1614afefe10e7dfe69377ec5ba7f5fed5e4d45b45efd4362090a0bb136cb SHA512 60b5719e3a321df43e33045fa8f4511fc02a4218d1ae7e476e7c6ebcf90ae208832881f6eea5b99a3296dfcc3a18c7e1f4ea9dbea446fc502e14306b6975f6e6
+DIST gappa-1.4.0.tar.gz 387988 BLAKE2B f1c4666b3e3048686753a2cee12b64e7d8c4b2007723c364541458e127b0575836d0b831e2a837cb833b0b7d9a609ab708595ac9498d166a8ae67a566347a0f1 SHA512 fe8ee10b74a257b3df8d7c3fdb9095a10a7d5ee5af41b031d5bb9b981db00832a025bc1d6fce92f97f294fc9f3ab846531a864548e57e9fe191c79b828eb6475
diff --git a/sci-mathematics/gappa/gappa-1.3.5.ebuild b/sci-mathematics/gappa/gappa-1.3.5.ebuild
index 26461a439..58ce7ffe7 100644
--- a/sci-mathematics/gappa/gappa-1.3.5.ebuild
+++ b/sci-mathematics/gappa/gappa-1.3.5.ebuild
@@ -3,6 +3,8 @@
EAPI=7
+inherit multiprocessing
+
DESCRIPTION="Verifying and proving properties on floating-point or fixed-point arithmetic"
HOMEPAGE="http://gappa.gforge.inria.fr/"
SRC_URI="https://gforge.inria.fr/frs/download.php/file/38044/${P}.tar.gz"
@@ -28,7 +30,8 @@ src_prepare() {
}
src_compile() {
- ./remake -d ${MAKEOPTS} || die "emake failed"
+ # Only accept number of parrellel jobs because remake does not understand --load-average
+ ./remake -d -j$(makeopts_jobs) || die "emake failed"
if use doc; then
./remake doc/html/index.html
fi
diff --git a/sci-mathematics/gappa/gappa-1.4.0.ebuild b/sci-mathematics/gappa/gappa-1.4.0.ebuild
new file mode 100644
index 000000000..7395c8ea3
--- /dev/null
+++ b/sci-mathematics/gappa/gappa-1.4.0.ebuild
@@ -0,0 +1,42 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DOCS_BUILDER="doxygen"
+DOCS_DIR="doc/doxygen"
+
+inherit docs multiprocessing
+
+DESCRIPTION="Verifying and proving properties on floating-point or fixed-point arithmetic"
+HOMEPAGE="https://gappa.gitlabpages.inria.fr/"
+SRC_URI="https://gforge.inria.fr/frs/download.php/file/38436/${P}.tar.gz"
+
+LICENSE="|| ( CeCILL-2 GPL-2 )"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+ dev-libs/gmp:0=
+ dev-libs/mpfr:0=
+ dev-libs/boost
+"
+DEPEND="${RDEPEND}"
+
+src_prepare() {
+ default
+ sed -i Remakefile.in \
+ -e "s:mkdir -p @bindir@:mkdir -p \${DESTDIR}@bindir@:g" \
+ -e "s:cp src/gappa @bindir@:cp src/gappa \${DESTDIR}@bindir@:g" || die
+}
+
+src_compile() {
+ # Only accept number of parrellel jobs because remake does not understand --load-average
+ ./remake -d -j$(makeopts_jobs) || die "emake failed"
+ docs_compile
+}
+
+src_install() {
+ DESTDIR="${D}" ./remake install
+ einstalldocs
+}
diff --git a/sci-visualization/forge/Manifest b/sci-visualization/forge/Manifest
index 3ae78eef0..4af43c3f5 100644
--- a/sci-visualization/forge/Manifest
+++ b/sci-visualization/forge/Manifest
@@ -1 +1,2 @@
DIST forge-1.0.5.tar.gz 1076708 BLAKE2B 9615e9b6d684ce9dab3600350f66654fa65d987ebd921d304c1106e2fe6111ff9efabac89b06a046cf060f13ee4bd1776ac91459afc25172d93483399a04b068 SHA512 01dc17f202bc79734bb997065c8cbc8d950204a47f979afddd8df14e40774dc712ecb7c34b11f0e312b1598fcbc9d25dd0bb089956d86508aac5b10fe1789fc3
+DIST forge-1.0.7.tar.gz 6146823 BLAKE2B 50ab2425f44216dd9e67e513b6e5a27d0a12729c2622b8139ba783668cb09ac23bdce2b1ce5313c21c669349cece47cc1e28972a1582bf043d37a7aa8a702baa SHA512 d341d5c6bdccf7d2f085162d1d8209b0b28d73b8a9f3173546b26f06bf8e422b3fdf1cfbaa7d122ea75cee5cf5f6bb6dbd2bffc10d8e0c336b5b8695c39f7b54
diff --git a/sci-visualization/forge/forge-1.0.7.ebuild b/sci-visualization/forge/forge-1.0.7.ebuild
new file mode 100644
index 000000000..ab5fa17bb
--- /dev/null
+++ b/sci-visualization/forge/forge-1.0.7.ebuild
@@ -0,0 +1,54 @@
+# Copyright 2019-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+inherit cmake multilib
+
+DESCRIPTION="High Performance Visualizations for ArrayFire"
+HOMEPAGE="http://www.arrayfire.com/"
+
+if [[ ${PV} == 9999 ]]; then
+ inherit git-r3
+ EGIT_REPO_URI="https://github.com/arrayfire/forge"
+else
+ SRC_URI="https://github.com/arrayfire/forge/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+ KEYWORDS="~amd64"
+fi
+
+LICENSE="BSD"
+SLOT="0"
+IUSE="doc examples"
+
+RDEPEND="
+ dev-libs/boost
+ media-libs/glfw
+ media-libs/fontconfig:1.0
+ media-libs/freeimage
+ media-libs/freetype:2
+ media-libs/glbinding
+ media-libs/glm
+ virtual/opengl
+ "
+DEPEND="${RDEPEND}"
+BDEPEND="
+ doc? (
+ app-doc/doxygen
+ dev-python/breathe
+ dev-python/recommonmark
+ dev-python/sphinx
+ )
+"
+
+src_configure() {
+ local mycmakeargs=(
+ -DBUILD_SHARED_LIBS=ON
+ -DFG_USE_STATIC_CPPFLAGS=OFF
+ -DFG_BUILD_DOCS=$(usex doc ON OFF)
+ -DFG_BUILD_EXAMPLES=$(usex examples ON OFF)
+ -DFG_WITH_FREEIMAGE=ON
+ -DFG_USE_STATIC_FREEIMAGE=OFF
+ -DFG_INSTALL_CMAKE_DIR=/usr/$(get_libdir)/cmake/Forge
+ )
+ cmake_src_configure
+}
diff --git a/sci-visualization/scidavis/Manifest b/sci-visualization/scidavis/Manifest
deleted file mode 100644
index c31dbb3e5..000000000
--- a/sci-visualization/scidavis/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST scidavis-2.3.0.tar.gz 9821439 BLAKE2B df542f570c4aa0ac93b8565dbd96937e6d3afe74d907d3f5145abd68cd44eff67f7d8892c70c21d9e9b308db119635050630efab9ca6ecffe70df38415711b86 SHA512 2ede70bcf5b910fc61e5a23ba36129bde11fd10b14470d4e8c9509eecb245c73242a3a1eec174b4f9a22abd21880e6ecbd9f0d1e492af87ff781163ad05e20cf
diff --git a/sci-visualization/scidavis/files/scidavis-build.patch b/sci-visualization/scidavis/files/scidavis-build.patch
deleted file mode 100644
index cb1e2600c..000000000
--- a/sci-visualization/scidavis/files/scidavis-build.patch
+++ /dev/null
@@ -1,39 +0,0 @@
-diff --git a/config.pri b/config.pri
-index 2b8d943..6034b6a 100644
---- a/config.pri
-+++ b/config.pri
-@@ -278,30 +278,13 @@ osx_dist {
-
- contains(PRESET, linux_package) {
- ### dynamically link against Qwt(3D) installed system-wide
--
-- exists(/usr/include/qt5/qwt5-qt5) {INCLUDEPATH+=/usr/include/qt5/qwt5-qt5}
-- exists(/usr/include/qt5/qwtplot3d-qt5) {INCLUDEPATH+=/usr/include/qt5/qwtplot3d-qt5}
-- exists(/usr/include/qwt5-qt5) {INCLUDEPATH+=/usr/include/qwt5-qt5}
-- exists(/usr/include/qwtplot3d) {INCLUDEPATH+=/usr/include/qwtplot3d}
--
-- system (ls /usr/lib*/libqwt5-qt5.so) {LIBS+=-lqwt5-qt5}
-- system (ls /usr/lib*/*/libqwt5-qt5.so) {LIBS+=-lqwt5-qt5}
-- system (ls /usr/lib*/libqwt-qt5.so) {LIBS+=-lqwt-qt5}
-- system (ls /usr/lib*/libqwtplot3d-qt5.so) {LIBS+=-lqwtplot3d-qt5}
-- system (ls /usr/lib*/*/libqwtplot3d-qt5.so) {LIBS+=-lqwtplot3d-qt5}
--
--
-+ INCLUDEPATH +=/usr/include/qwt5
-+ INCLUDEPATH +=/usr/include/qwtplot3d
-+ LIBS +=-lqwt5-qt5
-+ LIBS +=-lqwtplot3d
- LIBS += -lz -lGLU
--
-- INCLUDEPATH += /usr/include/muParser
- LIBS += -lgsl -lgslcblas
- LIBS += -lmuparser
--
-- # enable user installed packages
-- INCLUDEPATH = "$(HOME)/usr/include" $$INCLUDEPATH
-- QMAKE_LIBDIR = "$(HOME)/usr/lib" $$QMAKE_LIBDIR
--
--
- }
-
- contains(PRESET, self_contained) {
diff --git a/sci-visualization/scidavis/files/scidavis-tests.patch b/sci-visualization/scidavis/files/scidavis-tests.patch
deleted file mode 100644
index 2c9fa0095..000000000
--- a/sci-visualization/scidavis/files/scidavis-tests.patch
+++ /dev/null
@@ -1,10 +0,0 @@
-diff --git a/test/testPaintDevice.cpp b/test/testPaintDevice.cpp
-index 8657307..89693b0 100644
---- a/test/testPaintDevice.cpp
-+++ b/test/testPaintDevice.cpp
-@@ -1,4 +1,5 @@
- #include "testPaintDevice.h"
-+#include <QPainterPath>
- using namespace std;
-
- namespace
diff --git a/sci-visualization/scidavis/metadata.xml b/sci-visualization/scidavis/metadata.xml
deleted file mode 100644
index 089e4b033..000000000
--- a/sci-visualization/scidavis/metadata.xml
+++ /dev/null
@@ -1,24 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>andrewammerlaan@riseup.net</email>
- <name>Andrew Ammerlaan</name>
- </maintainer>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
- <longdescription lang="en">
- SciDAVis is a user-friendly data analysis and visualization program primarily aimed at high-quality plotting of scientific data.
- It strives to combine an intuitive, easy-to-use graphical user interface with powerful features such as Python scriptability.
- </longdescription>
- <use>
- <flag name="assistant">Compile with QAssistant (documentation broweser) support from <pkg>dev-qt/assistant</pkg>.</flag>
- <flag name="origin">Add support for reading OriginLab OPJ project files through <pkg>sci-libs/liborigin</pkg>.</flag>
- <flag name="python">Build support for python scripting.</flag>
- </use>
- <upstream>
- <remote-id type="sourceforge">SciDAVis</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/sci-visualization/scidavis/scidavis-2.3.0.ebuild b/sci-visualization/scidavis/scidavis-2.3.0.ebuild
deleted file mode 100644
index 9676cfaac..000000000
--- a/sci-visualization/scidavis/scidavis-2.3.0.ebuild
+++ /dev/null
@@ -1,93 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7,8,9} )
-
-inherit python-single-r1 qmake-utils xdg
-
-DESCRIPTION="Application for Scientific Data Analysis and Visualization"
-HOMEPAGE="http://scidavis.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/SciDAVis/$(ver_cut 1)/$(ver_cut 1-2)/${P}.tar.gz"
-
-LICENSE="GPL-2"
-KEYWORDS="~amd64 ~x86"
-SLOT="0"
-
-IUSE="assistant doc origin python test"
-REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )"
-RESTRICT="!test? ( test )"
-
-RDEPEND="
- dev-cpp/muParser
- dev-qt/qtgui:5
- dev-qt/qtopengl:5
- sci-libs/gsl
- sys-libs/zlib[minizip]
- x11-libs/qwt:5
- x11-libs/qwtplot3d
- assistant? ( dev-qt/assistant )
- origin? ( sci-libs/liborigin )
- python? (
- ${PYTHON_DEPS}
- $(python_gen_cond_dep '
- dev-python/PyQt5[${PYTHON_USEDEP}]
- dev-python/PyQt5-sip[${PYTHON_USEDEP}]
- dev-python/sip[${PYTHON_USEDEP}]
- ')
- )
-"
-BDEPEND="
- doc? ( app-doc/doxygen )
- test? ( dev-libs/unittest++ )
-"
-
-PATCHES=(
- "${FILESDIR}/${PN}-build.patch"
- "${FILESDIR}/${PN}-tests.patch"
-)
-
-src_prepare() {
- default
-
- # OF has been renamed in Gentoo https://bugs.gentoo.org/383179
- # Note this is *not* packaged in sys-libs/zlib[minizip] because
- # this file resides in the test directory in upstream zlib
- sed -i -r 's:\<(O[FN])\>:_Z_\1:g' 3rdparty/minigzip/minigzip.c || die
-
- # fix paths
- cat >> config.pri <<-EOF
- # install docs to ${PF} instead of ${PN}
- documentation.path = "\$\$INSTALLBASE/share/doc/${PF}"
-
- # install python files in Gentoo specific directories
- pythonconfig.path = "$(python_get_scriptdir)"
- pythonutils.path = "$(python_get_scriptdir)"
-
- # /usr/share/appdata is deprecated
- appdata.path = "\$\$INSTALLBASE/share/metainfo"
- EOF
-}
-
-src_configure() {
- INSTALLBASE="${EPREFIX}/usr" eqmake5 \
- $(usex assistant " " " CONFIG+=noassistant ") \
- $(usex origin " CONFIG+=liborigin " " ") \
- $(usex python " CONFIG+=python " " ") \
- $(usex test " CONFIG+=test " " ")
-}
-
-src_compile() {
- default
- if use doc ; then
- doxygen Doxyfile || die "doxygen failed"
- HTML_DOCS="API/html"
- fi
-}
-
-src_install () {
- emake INSTALL_ROOT="${D}" install
- einstalldocs
- use python && python_optimize
-}
diff --git a/scripts/check-duplicates.sh b/scripts/check-duplicates.sh
index 3f1c38329..56c5bf1dd 100755
--- a/scripts/check-duplicates.sh
+++ b/scripts/check-duplicates.sh
@@ -1,5 +1,5 @@
#! /usr/bin/env bash
-# Maintainer: Andrew Ammerlaan <andrewammerlaan@riseup.net>
+# Maintainer: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
# Maintainer: Theo Anderson <telans@posteo.de>
#
# This checks for potential and exact package matches within an overlay & ::gentoo
diff --git a/scripts/setup-and-run-repoman.sh b/scripts/setup-and-run-repoman.sh
index f6607549d..e2e10c78e 100755
--- a/scripts/setup-and-run-repoman.sh
+++ b/scripts/setup-and-run-repoman.sh
@@ -1,5 +1,5 @@
#! /usr/bin/env bash
-# Maintainer: Andrew Ammerlaan <andrewammerlaan@riseup.net>
+# Maintainer: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
#
# This sets up repoman and runs the latest version
#
@@ -16,7 +16,7 @@ git clone https://github.com/gentoo/portage.git
cd portage
# Get all versions, and read into array
-mapfile -t RM_VERSIONS < <( git tag | grep repoman | sort -u )
+mapfile -t RM_VERSIONS < <( git tag | grep portage | sort -uV )
# Select latests version (last element in array)
RM_VERS="${RM_VERSIONS[-1]}"
diff --git a/scripts/setup-master-gentoo.sh b/scripts/setup-master-gentoo.sh
index a2939721a..1a19d18df 100755
--- a/scripts/setup-master-gentoo.sh
+++ b/scripts/setup-master-gentoo.sh
@@ -1,5 +1,5 @@
#! /usr/bin/env bash
-# Maintainer: Andrew Ammerlaan <andrewammerlaan@riseup.net>
+# Maintainer: Andrew Ammerlaan <andrewammerlaan@gentoo.org>
#
# Fetch and setup the latest ::gentoo
diff --git a/sys-kernel/dkms/Manifest b/sys-kernel/dkms/Manifest
deleted file mode 100644
index c688e13d0..000000000
--- a/sys-kernel/dkms/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST dkms-2.8.4.tar.gz 104625 BLAKE2B 0bd9c47d2a4bf313426832ec88bbda9bd58a482c691de145ff87ce05d47d473132f2a300e8d0e6e0609b6dcdd47f8f9e521a104ae19cfa8b1ba453fc6de7a412 SHA512 1b8b987b239db8cf00f367ee4f5faf13dc41b450f09fb046dc719e51d6a762d6b700bf41156d8011c3ea7e139064119d6717b60c1bf7fa0a75ea1fc63887baa5
diff --git a/sys-kernel/dkms/dkms-2.8.4.ebuild b/sys-kernel/dkms/dkms-2.8.4.ebuild
deleted file mode 100644
index 895780135..000000000
--- a/sys-kernel/dkms/dkms-2.8.4.ebuild
+++ /dev/null
@@ -1,41 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit linux-info
-
-DESCRIPTION="Dynamic Kernel Module Support"
-HOMEPAGE="https://github.com/dell/dkms"
-SRC_URI="https://github.com/dell/dkms/archive/v${PV}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="GPL-2"
-KEYWORDS="~amd64 ~x86"
-SLOT="0"
-
-IUSE="doc"
-
-CONFIG_CHECK="~MODULES"
-
-RDEPEND="sys-apps/kmod"
-
-src_prepare() {
- # Install uncompressed version of man files
- sed -i \
- -e '\_gzip -c -9 dkms.8 > $(MAN)/dkms.8.gz_d' \
- -e '\_chmod 0644 $(MAN)/dkms.8.gz_d' \
- -e 's/dkms.8.gz/dkms.8/g' \
- Makefile || die
- default
-}
-
-src_compile() {
- # Nothing to do here
- return
-}
-
-src_install() {
- emake install DESTDIR="${D}" LIBDIR="${D}"/usr/$(get_libdir)/
- use doc && emake install-doc DOCDIR="${D}/usr/share/doc/${PF}"
- einstalldocs
-}
diff --git a/sys-kernel/dkms/metadata.xml b/sys-kernel/dkms/metadata.xml
deleted file mode 100644
index d46f906b8..000000000
--- a/sys-kernel/dkms/metadata.xml
+++ /dev/null
@@ -1,22 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>andrewammerlaan@riseup.net</email>
- <name>Andrew Ammerlaan</name>
- </maintainer>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
- <upstream>
- <remote-id type="github">dell/dkms</remote-id>
- </upstream>
- <longdescription lang="en">
- Dynamic Kernel Module Support (DKMS) is a program/framework that enables generating Linux kernel modules whose sources generally reside outside the kernel source tree. The concept is to have DKMS modules automatically rebuilt when a new kernel is installed.
- An essential feature of DKMS is that it automatically recompiles all DKMS modules if a new kernel version is installed. This allows drivers and devices outside of the mainline kernel to continue working after a Linux kernel upgrade.
- Another benefit of DKMS is that it allows the installation of a new driver on an existing system, running an arbitrary kernel version, without any need for manual compilation or precompiled packages provided by the vendor.
- DKMS was written by the Linux Engineering Team at Dell in 2003. It is included in many distributions, such as Ubuntu, Debian, Fedora, SUSE, and Arch. DKMS is free software released under the terms of the GNU General Public License (GPL) v2 or later.
- DKMS supports both the rpm and deb package formats out-of-the-box.
- </longdescription>
-</pkgmetadata>
diff --git a/x11-libs/qwt/Manifest b/x11-libs/qwt/Manifest
deleted file mode 100644
index 9b777a64e..000000000
--- a/x11-libs/qwt/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST qwt-5.2.3_p20200902.tar.gz 2317623 BLAKE2B 5ac4333b01eac3a0b8b2f291804408679b8173ff624932d94e85a6789ad7f966417f80acba8c8d993465703e256c9ac7c675971cffac40d5f3b2becf0e7e7460 SHA512 1980f7e21684dba36c192a08e1a3bce719dcd7b1e700ce5f8a27821af83a65fe518d078888d6ad3733d3cde1c2af40cd694537ce0193d622d7f0b3bcee1ed55e
diff --git a/x11-libs/qwt/metadata.xml b/x11-libs/qwt/metadata.xml
deleted file mode 100644
index f793a4b23..000000000
--- a/x11-libs/qwt/metadata.xml
+++ /dev/null
@@ -1,18 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
- <longdescription lang="en">
- The Qwt library contains GUI Components and utility classes which are
- primarily useful for programs with a technical background.
- Besides a 2D plot widget it provides scales, sliders, dials,
- compasses, thermometers, wheels and knobs to control or display
- values, arrays or ranges of type double.
-</longdescription>
- <upstream>
- <remote-id type="sourceforge">qwt</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/x11-libs/qwt/qwt-5.2.3_p20200902.ebuild b/x11-libs/qwt/qwt-5.2.3_p20200902.ebuild
deleted file mode 100644
index f945bc877..000000000
--- a/x11-libs/qwt/qwt-5.2.3_p20200902.ebuild
+++ /dev/null
@@ -1,88 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit qmake-utils
-
-COMMIT="0052f96fdd6d5f021f20a1cfc4d2fcfc605941da"
-
-DESCRIPTION="2D plotting library for Qt5"
-HOMEPAGE="https://qwt.sourceforge.io/ https://github.com/gbm19/qwt5-qt5"
-SRC_URI="https://github.com/gbm19/qwt5-qt5/archive/${COMMIT}.tar.gz -> ${P}.tar.gz"
-
-LICENSE="qwt"
-KEYWORDS="~amd64 ~arm ~ppc ~ppc64 ~x86"
-SLOT="5"
-IUSE="doc examples svg"
-
-RDEPEND="
- dev-qt/designer:5
- dev-qt/qtgui:5
- svg? ( dev-qt/qtsvg:5 )
-"
-BDEPEND="doc? ( app-doc/doxygen )"
-
-DOCS=( CHANGES README )
-
-S="${WORKDIR}/${PN}5-qt5-${COMMIT}"
-
-src_prepare() {
- default
- sed -e "/QwtVersion/s:5.2.2.:${PV}:g" -i ${PN}.prf || die
-
- cat > qwtconfig.pri <<-EOF
- target.path = "${EPREFIX}/usr/$(get_libdir)"
- headers.path = "${EPREFIX}/usr/include/qwt5"
- doc.path = "${EPREFIX}/usr/share/doc/${PF}"
- CONFIG += qt warn_on thread release
- CONFIG += QwtDll QwtPlot QwtWidgets QwtDesigner
- VERSION = ${PV}
- QWT_VERSION = ${PV/_*}
- QWT_INSTALL_PLUGINS = "${EPREFIX}/usr/$(get_libdir)/qt5/plugins/designer"
- QWT_INSTALL_FEATURES = "${EPREFIX}/usr/share/qt5/mkspecs/features"
- EOF
- sed -i -e 's/headers doc/headers/' src/src.pro || die
- use svg && echo >> qwtconfig.pri "CONFIG += QwtSVGItem"
-}
-
-src_configure() {
- eqmake5
-}
-
-src_compile() {
- default
- if use doc ; then
- cd doc || die
- doxygen Doxyfile || die "doxygen failed"
- HTML_DOCS="doc/html"
- fi
-}
-
-src_install () {
- emake INSTALL_ROOT="${D}" install
- einstalldocs
- doman doc/man/*/*
-
- if use examples; then
- # don't build examples - fix the qt files to build once installed
- cat > examples/examples.pri <<-EOF
- include( qwtconfig.pri )
- TEMPLATE = app
- MOC_DIR = moc
- INCLUDEPATH += "${EPREFIX}/usr/include/qwt5"
- DEPENDPATH += "${EPREFIX}/usr/include/qwt5"
- LIBS += -lqwt
- EOF
- sed -i -e 's:../qwtconfig:qwtconfig:' examples/examples.pro || die
- cp *.pri examples/ || die
- insinto /usr/share/${PN}5
- doins -r examples
- fi
-
- # avoid file conflict with qwt:6
- # https://github.com/gbm19/qwt5-qt5/issues/2
- pushd "${ED}/usr/share/man/man3/"
- for f in *; do mv ${f} ${f//.3/.5qt5.3}; done
- popd
-}
diff --git a/x11-libs/qwtplot3d/Manifest b/x11-libs/qwtplot3d/Manifest
deleted file mode 100644
index c241a80ab..000000000
--- a/x11-libs/qwtplot3d/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST qwtplot3d-0.2.7.tgz 183836 BLAKE2B f34fafdea591b2a1440321756872eb8f5580ccf8d5785eeeb6b32e1a4ee515b48ce2cf6e97462f69c2c82b83eebd90226b73d160e1e7027695024f590c4c1c6f SHA512 88e6d270695931775f3c1c0e718118e31118dbfe9f5f582834de09ab515fdf9e8a0f90d424f276653fdf1cf0b39e2060282385701a4ab48843420fe55a1dcf0c
diff --git a/x11-libs/qwtplot3d/files/qwtplot3d-doxygen.patch b/x11-libs/qwtplot3d/files/qwtplot3d-doxygen.patch
deleted file mode 100644
index b0632a380..000000000
--- a/x11-libs/qwtplot3d/files/qwtplot3d-doxygen.patch
+++ /dev/null
@@ -1,28 +0,0 @@
---- qwtplot3d/doc/Doxyfile.doxygen.orig 2007-11-26 22:30:57.000000000 +0000
-+++ qwtplot3d/doc/Doxyfile.doxygen 2007-11-26 22:30:03.000000000 +0000
-@@ -116,7 +116,7 @@
- HTML_ALIGN_MEMBERS = YES
- GENERATE_HTMLHELP = NO
- CHM_FILE = qwtplot3d.chm
--HHC_LOCATION = "c:\Programme\HTML Help Workshop\hhc.exe"
-+#HHC_LOCATION = "c:\Programme\HTML Help Workshop\hhc.exe"
- GENERATE_CHI = NO
- BINARY_TOC = YES
- TOC_EXPAND = YES
-@@ -181,7 +181,7 @@
- MACRO_EXPANSION = NO
- EXPAND_ONLY_PREDEF = NO
- SEARCH_INCLUDES = YES
--INCLUDE_PATH = V:/cvs/qwtplot3d/include/
-+INCLUDE_PATH = ../include
- INCLUDE_FILE_PATTERNS = *.h
- PREDEFINED = QWT3D_NOT_FOR_DOXYGEN \
- QT_VERSION=0x040000
-@@ -212,7 +212,6 @@
- GRAPHICAL_HIERARCHY = YES
- DIRECTORY_GRAPH = YES
- DOT_IMAGE_FORMAT = png
--DOT_PATH = V:/graphviz/Graphviz/bin/
- DOTFILE_DIRS =
- MAX_DOT_GRAPH_WIDTH = 974
- MAX_DOT_GRAPH_HEIGHT = 10000
diff --git a/x11-libs/qwtplot3d/files/qwtplot3d-examples.patch b/x11-libs/qwtplot3d/files/qwtplot3d-examples.patch
deleted file mode 100644
index f142c3379..000000000
--- a/x11-libs/qwtplot3d/files/qwtplot3d-examples.patch
+++ /dev/null
@@ -1,125 +0,0 @@
-diff -Nur qwtplot3d.orig/examples/axes/src/axesmainwindow.cpp qwtplot3d/examples/axes/src/axesmainwindow.cpp
---- qwtplot3d.orig/examples/axes/src/axesmainwindow.cpp 2007-11-26 22:16:54.000000000 +0000
-+++ qwtplot3d/examples/axes/src/axesmainwindow.cpp 2007-11-26 22:21:56.000000000 +0000
-@@ -9,7 +9,7 @@
-
- #include "axes.h"
- #include "axesmainwindow.h"
--#include "../../../include/qwt3d_function.h"
-+#include <qwt3d_function.h>
-
- using namespace std;
- using namespace Qwt3D;
-diff -Nur qwtplot3d.orig/examples/common.pro qwtplot3d/examples/common.pro
---- qwtplot3d.orig/examples/common.pro 2007-11-26 22:16:54.000000000 +0000
-+++ qwtplot3d/examples/common.pro 2007-11-26 23:43:33.000000000 +0000
-@@ -1,13 +1,13 @@
- TEMPLATE = app
--CONFIG += qt warn_on thread debug
-+CONFIG += qt warn_on thread
- UI_DIR = tmp
- MOC_DIR = tmp
- OBJECTS_DIR = tmp
--INCLUDEPATH += ../../include
-+INCLUDEPATH += /usr/include/qwtplot3d
- DEPENDPATH = $$INCLUDEPATH
- DESTDIR = ../bin
-
--unix:LIBS += -lqwtplot3d -L../../lib
-+unix:LIBS += -lqwtplot3d
- linux-g++:QMAKE_CXXFLAGS += -fno-exceptions
-
- win32{
-@@ -25,7 +25,7 @@
- ISQT4 = $$find(MYVERSION, ^[2-9])
-
- !isEmpty( ISQT4 ) {
--RESOURCES = ../images.qrc
-+#RESOURCES = ../images.qrc
- QT += opengl
- }
-
-diff -Nur qwtplot3d.orig/examples/enrichments/src/enrichmentmainwindow.cpp qwtplot3d/examples/enrichments/src/enrichmentmainwindow.cpp
---- qwtplot3d.orig/examples/enrichments/src/enrichmentmainwindow.cpp 2007-11-26 22:16:54.000000000 +0000
-+++ qwtplot3d/examples/enrichments/src/enrichmentmainwindow.cpp 2007-11-26 22:22:48.000000000 +0000
-@@ -6,7 +6,7 @@
-
- #include "enrichmentmainwindow.h"
- #include "enrichments.h"
--#include "../../../include/qwt3d_function.h"
-+#include <qwt3d_function.h>
-
- using namespace Qwt3D;
-
-diff -Nur qwtplot3d.orig/examples/mesh2/src/colormapreader.h qwtplot3d/examples/mesh2/src/colormapreader.h
---- qwtplot3d.orig/examples/mesh2/src/colormapreader.h 2007-11-26 22:16:54.000000000 +0000
-+++ qwtplot3d/examples/mesh2/src/colormapreader.h 2007-11-26 22:23:19.000000000 +0000
-@@ -5,7 +5,7 @@
- #include <qframe.h>
- #include <qpixmap.h>
-
--#include "../../../include/qwt3d_types.h"
-+#include <qwt3d_types.h>
-
- #if QT_VERSION < 0x040000
-
-diff -Nur qwtplot3d.orig/examples/mesh2/src/functions.h qwtplot3d/examples/mesh2/src/functions.h
---- qwtplot3d.orig/examples/mesh2/src/functions.h 2007-11-26 22:16:54.000000000 +0000
-+++ qwtplot3d/examples/mesh2/src/functions.h 2007-11-26 22:23:47.000000000 +0000
-@@ -2,8 +2,8 @@
- #define __EXAMPLE_H__
-
- #include <math.h>
--#include "../../../include/qwt3d_parametricsurface.h"
--#include "../../../include/qwt3d_function.h"
-+#include <qwt3d_parametricsurface.h>
-+#include <qwt3d_function.h>
-
- using namespace Qwt3D;
-
-diff -Nur qwtplot3d.orig/examples/mesh2/src/lightingdlg.h qwtplot3d/examples/mesh2/src/lightingdlg.h
---- qwtplot3d.orig/examples/mesh2/src/lightingdlg.h 2007-11-26 22:16:54.000000000 +0000
-+++ qwtplot3d/examples/mesh2/src/lightingdlg.h 2007-11-26 22:24:41.000000000 +0000
-@@ -3,10 +3,10 @@
-
- #include <math.h>
- #include <qapplication.h>
--#include "../../../include/qwt3d_parametricsurface.h"
--#include "../../../include/qwt3d_surfaceplot.h"
--#include "../../../include/qwt3d_enrichment.h"
--#include "../../../include/qwt3d_color.h"
-+#include <qwt3d_parametricsurface.h>
-+#include <qwt3d_surfaceplot.h>
-+#include <qwt3d_enrichment.h>
-+#include <qwt3d_color.h>
-
- #if QT_VERSION < 0x040000
- #include "lightingdlgbase.h"
-diff -Nur qwtplot3d.orig/examples/mesh2/src/mesh2mainwindow.cpp qwtplot3d/examples/mesh2/src/mesh2mainwindow.cpp
---- qwtplot3d.orig/examples/mesh2/src/mesh2mainwindow.cpp 2007-11-26 22:16:54.000000000 +0000
-+++ qwtplot3d/examples/mesh2/src/mesh2mainwindow.cpp 2007-11-26 22:25:33.000000000 +0000
-@@ -33,9 +33,9 @@
- #include "colormapreader.h"
- #include "lightingdlg.h"
- #include "femreader.h"
--#include "../../../include/qwt3d_io.h"
--#include "../../../include/qwt3d_io_gl2ps.h"
--#include "../../../include/qwt3d_io_reader.h"
-+#include <qwt3d_io.h>
-+#include <qwt3d_io_gl2ps.h>
-+#include <qwt3d_io_reader.h>
-
- using namespace Qwt3D;
- using namespace std;
-diff -Nur qwtplot3d.orig/examples/mesh2/src/mesh2mainwindow.h qwtplot3d/examples/mesh2/src/mesh2mainwindow.h
---- qwtplot3d.orig/examples/mesh2/src/mesh2mainwindow.h 2007-11-26 22:16:54.000000000 +0000
-+++ qwtplot3d/examples/mesh2/src/mesh2mainwindow.h 2007-11-26 22:26:09.000000000 +0000
-@@ -1,7 +1,7 @@
- #ifndef mesh2mainwindow_h__2004_03_07_13_38_begin_guarded_code
- #define mesh2mainwindow_h__2004_03_07_13_38_begin_guarded_code
-
--#include "../../../include/qwt3d_surfaceplot.h"
-+#include <qwt3d_surfaceplot.h>
-
-
- #if QT_VERSION < 0x040000
diff --git a/x11-libs/qwtplot3d/files/qwtplot3d-gcc44.patch b/x11-libs/qwtplot3d/files/qwtplot3d-gcc44.patch
deleted file mode 100644
index a76fe831a..000000000
--- a/x11-libs/qwtplot3d/files/qwtplot3d-gcc44.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff -ur qwtplot3d-orig/include/qwt3d_function.h qwtplot3d/include/qwt3d_function.h
---- qwtplot3d-orig/include/qwt3d_function.h 2009-07-25 18:18:58.000000000 -0400
-+++ qwtplot3d/include/qwt3d_function.h 2009-07-25 18:19:19.000000000 -0400
-@@ -2,6 +2,7 @@
- #define qwt3d_function_h__2004_03_05_13_51_begin_guarded_code
-
- #include "qwt3d_gridmapping.h"
-+#include <cstdio>
-
- namespace Qwt3D
- {
-Only in qwtplot3d/tmp: qwt3d_function.o
diff --git a/x11-libs/qwtplot3d/files/qwtplot3d-profile.patch b/x11-libs/qwtplot3d/files/qwtplot3d-profile.patch
deleted file mode 100644
index 831ad558d..000000000
--- a/x11-libs/qwtplot3d/files/qwtplot3d-profile.patch
+++ /dev/null
@@ -1,27 +0,0 @@
---- qwtplot3d.orig/qwtplot3d.pro 2007-11-26 22:16:54.000000000 +0000
-+++ qwtplot3d/qwtplot3d.pro 2007-11-26 23:45:18.000000000 +0000
-@@ -3,7 +3,7 @@
-
- TARGET = qwtplot3d
- TEMPLATE = lib
--CONFIG += qt warn_on opengl thread zlib debug
-+CONFIG += qt warn_on opengl thread zlib
- MOC_DIR = tmp
- OBJECTS_DIR = tmp
- INCLUDEPATH = include
-@@ -21,7 +21,7 @@
- win32:CONFIG -= zlib
-
- linux-g++:TMAKE_CXXFLAGS += -fno-exceptions
--unix:VERSION = 0.2.6
-+unix:VERSION = 0.2.7
-
- # Input
- SOURCES += src/qwt3d_axis.cpp \
-@@ -92,4 +92,4 @@
- DEFINES += GL2PS_HAVE_ZLIB
- win32:LIBS += zlib.lib
- unix:LIBS += -lz
--}
-\ No newline at end of file
-+}
diff --git a/x11-libs/qwtplot3d/files/qwtplot3d-qt-4.8.0.patch b/x11-libs/qwtplot3d/files/qwtplot3d-qt-4.8.0.patch
deleted file mode 100644
index ae10f48f0..000000000
--- a/x11-libs/qwtplot3d/files/qwtplot3d-qt-4.8.0.patch
+++ /dev/null
@@ -1,34 +0,0 @@
-diff -urbN qwtplot3d/include/qwt3d_io_gl2ps.h qwtplot3d.patched/include/qwt3d_io_gl2ps.h
---- qwtplot3d/include/qwt3d_io_gl2ps.h 2005-07-10 16:54:52.000000000 +0300
-+++ qwtplot3d.patched/include/qwt3d_io_gl2ps.h 2012-01-21 22:15:20.000000000 +0200
-@@ -2,12 +2,7 @@
- #define qwt3d_io_gl2ps_h__2004_05_07_01_16_begin_guarded_code
-
- #include <time.h>
--
--#if QT_VERSION < 0x040000
--#include <qgl.h>
--#else
--#include <QtOpenGL/qgl.h>
--#endif
-+#include <QtOpenGL>
-
- #include "qwt3d_types.h"
- #include "qwt3d_io.h"
-diff -urbN qwtplot3d/include/qwt3d_openglhelper.h qwtplot3d.patched/include/qwt3d_openglhelper.h
---- qwtplot3d/include/qwt3d_openglhelper.h 2005-07-19 17:40:28.000000000 +0300
-+++ qwtplot3d.patched/include/qwt3d_openglhelper.h 2012-01-21 22:29:56.000000000 +0200
-@@ -2,11 +2,8 @@
- #define __openglhelper_2003_06_06_15_49__
-
- #include "qglobal.h"
--#if QT_VERSION < 0x040000
--#include <qgl.h>
--#else
--#include <QtOpenGL/qgl.h>
--#endif
-+#include <QtOpenGL>
-+#include <GL/glu.h>
-
- namespace Qwt3D
- {
diff --git a/x11-libs/qwtplot3d/files/qwtplot3d-sys-gl2ps.patch b/x11-libs/qwtplot3d/files/qwtplot3d-sys-gl2ps.patch
deleted file mode 100644
index 81a77e132..000000000
--- a/x11-libs/qwtplot3d/files/qwtplot3d-sys-gl2ps.patch
+++ /dev/null
@@ -1,31 +0,0 @@
---- qwtplot3d.pro.orig 2009-04-07 19:45:29.985645378 +0100
-+++ qwtplot3d.pro 2009-04-07 19:46:50.095747068 +0100
-@@ -80,13 +80,11 @@
- include/qwt3d_graphplot.h \
- include/qwt3d_multiplot.h
-
--# gl2ps support
--HEADERS+=3rdparty/gl2ps/gl2ps.h \
-- include/qwt3d_io_gl2ps.h
-+# gl2ps support taken from system libs
-+HEADERS+=include/qwt3d_io_gl2ps.h
-
--SOURCES+=src/qwt3d_io_gl2ps.cpp \
-- 3rdparty/gl2ps/gl2ps.c
--
-+SOURCES+=src/qwt3d_io_gl2ps.cpp
-+unix:LIBS += -lgl2ps
- # zlib support for gl2ps
- zlib {
- DEFINES += GL2PS_HAVE_ZLIB
---- src/qwt3d_io_gl2ps.cpp.orig 2009-04-07 19:44:38.536418391 +0100
-+++ src/qwt3d_io_gl2ps.cpp 2009-04-07 19:45:03.685133854 +0100
-@@ -4,7 +4,7 @@
-
- #include <time.h>
- #include "qwt3d_openglhelper.h"
--#include "../3rdparty/gl2ps/gl2ps.h"
-+#include <gl2ps.h>
- #include "qwt3d_io_gl2ps.h"
- #include "qwt3d_plot.h"
-
diff --git a/x11-libs/qwtplot3d/metadata.xml b/x11-libs/qwtplot3d/metadata.xml
deleted file mode 100644
index bfd320fe9..000000000
--- a/x11-libs/qwtplot3d/metadata.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="project">
- <email>sci@gentoo.org</email>
- <name>Gentoo Science Project</name>
- </maintainer>
- <longdescription lang="en">
- QwtPlot3D is a graphics extension to the Qt GUI application framework.
- It provides a 3D plotting widget for scientific data and mathematical expressions.
- It compares to the existing Qwt Project.
- </longdescription>
- <upstream>
- <remote-id type="sourceforge">qwtplot3d</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/x11-libs/qwtplot3d/qwtplot3d-0.2.7.ebuild b/x11-libs/qwtplot3d/qwtplot3d-0.2.7.ebuild
deleted file mode 100644
index 954735573..000000000
--- a/x11-libs/qwtplot3d/qwtplot3d-0.2.7.ebuild
+++ /dev/null
@@ -1,66 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-inherit qmake-utils
-
-DESCRIPTION="3D plotting library for Qt5"
-HOMEPAGE="http://qwtplot3d.sourceforge.net/"
-SRC_URI="mirror://sourceforge/${PN}/${P}.tgz"
-
-LICENSE="ZLIB"
-KEYWORDS="~amd64 ~x86"
-SLOT="0"
-
-IUSE="doc examples"
-
-RDEPEND="
- dev-qt/qtgui:5
- dev-qt/qtopengl:5
- x11-libs/gl2ps
-"
-BDEPEND="doc? ( app-doc/doxygen )"
-
-S="${WORKDIR}/${PN}"
-
-PATCHES=(
- "${FILESDIR}/${PN}-profile.patch"
- "${FILESDIR}/${PN}-examples.patch"
- "${FILESDIR}/${PN}-doxygen.patch"
- "${FILESDIR}/${PN}-gcc44.patch"
- "${FILESDIR}/${PN}-qt-4.8.0.patch"
-)
-
-src_prepare() {
- default
- eapply -p0 "${FILESDIR}/${PN}-sys-gl2ps.patch"
- cat >> ${PN}.pro <<-EOF
- target.path = "${EPREFIX}/usr/$(get_libdir)"
- headers.path = "${EPREFIX}/usr/include/${PN}"
- headers.files = \$\$HEADERS
- INSTALLS = target headers
- EOF
-}
-
-src_configure() {
- eqmake5
-}
-
-src_compile() {
- default
- if use doc ; then
- cd doc || die
- doxygen Doxyfile.doxygen || die "doxygen failed"
- HTML_DOCS="doc/web/doxygen/"
- fi
-}
-
-src_install () {
- emake INSTALL_ROOT="${D}" install
- einstalldocs
- if use examples; then
- insinto /usr/share/${PN}
- doins -r examples
- fi
-}