diff options
1514 files changed, 21409 insertions, 28713 deletions
@@ -17,6 +17,7 @@ ### Contents 1. [Installation](#install) + - [Eselect](#install-eselect) - [Manual](#install-manual) - [Layman](#install-layman) 2. [Usage](#usage) @@ -28,25 +29,35 @@ ## Installation <a name="install"></a> -### Eselect-repository install <a name="install-eselect"></a> +As per the current [Portage specification](https://dev.gentoo.org/~zmedico/portage/doc/man/portage.5.html), ebuild repositories (a.k.a. overlays) can be managed via file collections under `/etc/portage/repos.conf/`, via the new [plug-in sync system](https://wiki.gentoo.org/wiki/Project:Portage/Sync). + +### Eselect-repository Install <a name="install-eselect"></a> + +The overlay can be enabled via the `repository` extension of the Gentoo `eselect` utility. -The easiest way to enable the overlay is to: ```console -emerge --noreplace eselect-repository && eselect repository enable science && emerge --sync +emerge --ask --noreplace --verbose eselect-repository +eselect repository enable science ``` -and emerge the package as usual. -### Manual Install <a name="install-manual"></a> +### Eselect-repository Uninstall + +To disable and remove the overlay, run: -As per the current [Portage specifications](https://dev.gentoo.org/~zmedico/portage/doc/man/portage.5.html), ebuild repositories (a.k.a. overlays) can be managed via file collections under `/etc/portage/repos.conf/`, via the new [plug-in sync system](https://wiki.gentoo.org/wiki/Project:Portage/Sync). +```console +eselect repository disable science +eselect repository remove science +``` + +### Manual Install <a name="install-manual"></a> -To enable the overlay without the need for additional software, you first need to have `git` installed: +To enable the overlay without the need for dedicated repository software, you need to have `git` installed: ```console -emerge --ask --verbose dev-vcs/git +emerge --ask --noreplace --verbose dev-vcs/git ```` -Then you need to add the science repository configuration by downloading the [science.conf](metadata/science.conf) file: +Then you can simply download the science repository configuration file, [science.conf](metadata/science.conf): ```console wget https://gitweb.gentoo.org/proj/sci.git/plain/metadata/science.conf \ @@ -55,7 +66,7 @@ wget https://gitweb.gentoo.org/proj/sci.git/plain/metadata/science.conf \ ### Manual Uninstall -To uninstall the overlay, simply run: +To disable and remove the overlay, run: ```console rm /etc/portage/repos.conf/science @@ -67,7 +78,7 @@ rm /var/db/repos/science -rf You can also install the overlay via the [layman](https://wiki.gentoo.org/wiki/Layman) overlay manager. ```console -emerge --ask --verbose app-portage/layman +emerge --ask --noreplace --verbose app-portage/layman layman --add science ``` diff --git a/app-arch/libdeflate/Manifest b/app-arch/libdeflate/Manifest deleted file mode 100644 index f26d506d5..000000000 --- a/app-arch/libdeflate/Manifest +++ /dev/null @@ -1,6 +0,0 @@ -DIST libdeflate-1.11.tar.gz 162862 BLAKE2B 70ee15bdbe697083f84eef4bfce069b3bff8499a8daf53037a52fd247a47cd04867c1d93265e1b88232da52919ad15333e90d787dff05f7d8e5abe7a9613a07a SHA512 71badc0d934dde5fa79c0d8661b3a38a45d7189fba6f1c77986b2fb6baa03233b8474f0a83f004242410421c2063d2f98f02ca4f8a7a7a14cc7bcd3a9be4fbbc -DIST libdeflate-1.2.tar.gz 133494 BLAKE2B cd43b691bda16134ee1d2cdeeea8e5bab7bd8b841dec41fcf93ca0b3383f9c465e095fc7c97b743dc34c2bd6a1d340f8bfda4f4448af832cfec0240965957ffa SHA512 181b53ee9aea96b2520e287824573d111eeacaeae2011e093ca4d4fdd77e4e09bd261d741fac567302cf031058779ccc775dce1f603a05810b0c3b7d96b26fdb -DIST libdeflate-1.6.tar.gz 139031 BLAKE2B c9390408322dc71f27d86fb69e0dd47996a725a3f4ddbe1d395e07dcd1b1f2b6fde1a9decfa8d7a0bd841defff67a659b1f2efd2609db7d79626e038cb44e020 SHA512 b7225c7defb3e9b1177c434aa0de80e525de06160894282e9d3e736d6c17d2ee107e321042104a67dfa3649d982a022ee30fe30380259b8aa65ac75d1d02e334 -DIST libdeflate-1.7.tar.gz 144143 BLAKE2B 6aa947a4e2489f5a3e5681d56c2272b0a694981ed2607fa4112d90a8b4565ba1066364ffcac2fe8836bacbbad0346bce5efea54b4abae55022a33ee7d983e570 SHA512 82b297af2d3128a244e561893cce1d3664de410469ba6745c3f68fc3a1962c62467c427f3857bb679578e0f704cd0eba1a64b13c30505addd310ff9af1883068 -DIST libdeflate-1.8.tar.gz 145823 BLAKE2B 3597e41cbcae17b5b6b5bbb196af6ea52ac55b279f42e1ca3b12ba45638602e8a3f7520d84d7be637675c04fd82e096cb03d15f5fd742a31db5ba22cbd6e71f4 SHA512 b40caecdf783487488a5bd8213304175348b9db9bc1efdf6d5222fb912f61698b5e196522195a3640d7ff61ba953a93c0c8f75e07f548ac8b9d9c5dd5a787544 -DIST libdeflate-1.9.tar.gz 157565 BLAKE2B a8762bb1c2e73d9f7bf26121ac194362be61fd14a8e2a2a0ca72ffc7c512f5c96b19f3f0c563495e25e849342de26f89260af5e67aa5ec2b37b30da596ec3cdf SHA512 aecfa2414a4d22f5233cbe58385e1637b5cbe252e1d4dc55e20e7769908158190a22af11af175e5dfb376f3b4a90fcee58e25468ccb47a5d5b02ae2b248c58f3 diff --git a/app-arch/libdeflate/files/libdeflate-1.2-respect_EPREFIX.patch b/app-arch/libdeflate/files/libdeflate-1.2-respect_EPREFIX.patch deleted file mode 100644 index 790aa6de9..000000000 --- a/app-arch/libdeflate/files/libdeflate-1.2-respect_EPREFIX.patch +++ /dev/null @@ -1,54 +0,0 @@ ---- libdeflate-1.2/Makefile 2019-01-15 06:37:48.000000000 +0100 -+++ libdeflate-1.2/Makefile 2019-01-22 14:06:13.427054892 +0100 -@@ -21,7 +21,7 @@ - 1>&2 2>/dev/null; then echo $(1); fi) - - override CFLAGS := \ -- $(CFLAGS) -O2 -fomit-frame-pointer -std=c99 -I. -Icommon \ -+ $(CFLAGS) -fomit-frame-pointer -std=c99 -I. -Icommon \ - -Wall -Wundef \ - $(call cc-option,-Wpedantic) \ - $(call cc-option,-Wdeclaration-after-statement) \ -@@ -34,6 +34,9 @@ - ############################################################################## - - PREFIX ?= /usr -+BINDIR ?= $(PREFIX)/bin -+INCDIR ?= $(PREFIX)/include -+LIBDIR ?= $(PREFIX)/lib - - SOVERSION := 0 - STATIC_LIB_SUFFIX := .a -@@ -240,20 +243,20 @@ - all:$(DEFAULT_TARGETS) - - install:all -- install -Dm644 -t $(DESTDIR)$(PREFIX)/lib $(STATIC_LIB) -- install -Dm755 -t $(DESTDIR)$(PREFIX)/lib $(SHARED_LIB) -- ln -sf $(SHARED_LIB) $(DESTDIR)$(PREFIX)/lib/libdeflate.so -- install -Dm644 -t $(DESTDIR)$(PREFIX)/include libdeflate.h -- install -Dm755 gzip $(DESTDIR)$(PREFIX)/bin/libdeflate-gzip -- ln -f $(DESTDIR)$(PREFIX)/bin/libdeflate-gzip $(DESTDIR)$(PREFIX)/bin/libdeflate-gunzip -+ install -Dm644 -t $(DESTDIR)$(LIBDIR) $(STATIC_LIB) -+ install -Dm755 -t $(DESTDIR)$(LIBDIR) $(SHARED_LIB) -+ ln -sf $(SHARED_LIB) $(DESTDIR)$(LIBDIR)/libdeflate.so -+ install -Dm644 -t $(DESTDIR)$(INCDIR) libdeflate.h -+ install -Dm755 gzip $(DESTDIR)$(BINDIR)/libdeflate-gzip -+ ln -f $(DESTDIR)$(BINDIR)/libdeflate-gzip $(DESTDIR)$(BINDIR)/libdeflate-gunzip - - uninstall: -- rm -f $(DESTDIR)$(PREFIX)/lib/$(STATIC_LIB) \ -- $(DESTDIR)$(PREFIX)/lib/$(SHARED_LIB) \ -- $(DESTDIR)$(PREFIX)/lib/libdeflate.so \ -- $(DESTDIR)$(PREFIX)/include/libdeflate.h \ -- $(DESTDIR)$(PREFIX)/bin/libdeflate-gzip \ -- $(DESTDIR)$(PREFIX)/bin/libdeflate-gunzip -+ rm -f $(DESTDIR)$(LIBDIR)/$(STATIC_LIB) \ -+ $(DESTDIR)$(LIBDIR)/$(SHARED_LIB) \ -+ $(DESTDIR)$(LIBDIR)/libdeflate.so \ -+ $(DESTDIR)$(INCDIR)/libdeflate.h \ -+ $(DESTDIR)$(BINDIR)/libdeflate-gzip \ -+ $(DESTDIR)$(BINDIR)/libdeflate-gunzip - - test_programs:$(TEST_PROGRAMS) - diff --git a/app-arch/libdeflate/libdeflate-1.11.ebuild b/app-arch/libdeflate/libdeflate-1.11.ebuild deleted file mode 100644 index 9e7344b22..000000000 --- a/app-arch/libdeflate/libdeflate-1.11.ebuild +++ /dev/null @@ -1,28 +0,0 @@ -# Copyright 2019-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -DESCRIPTION="Heavily optimized DEFLATE/zlib/gzip (de)compression" -HOMEPAGE="https://github.com/ebiggers/libdeflate" - -if [[ ${PV} == *9999 ]]; then - inherit git-r3 - EGIT_REPO_URI="https://github.com/ebiggers/libdeflate" -else - SRC_URI="https://github.com/ebiggers/libdeflate/archive/v${PV}.tar.gz -> ${P}.tar.gz" - KEYWORDS="~amd64 ~x86" -fi - -LICENSE="MIT" -SLOT="0" -IUSE="static-libs test" -RESTRICT="!test? ( test )" - -src_install() { - emake DESTDIR="${ED}" PREFIX=/usr LIBDIR="/usr/$(get_libdir)" install - if ! use static-libs; then - find "${ED}" -name '*.a' -delete || die - fi - dodoc NEWS.md README.md -} diff --git a/app-arch/libdeflate/libdeflate-1.2.ebuild b/app-arch/libdeflate/libdeflate-1.2.ebuild deleted file mode 100644 index c5924c064..000000000 --- a/app-arch/libdeflate/libdeflate-1.2.ebuild +++ /dev/null @@ -1,27 +0,0 @@ -# Copyright 2019-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DESCRIPTION="Heavily optimized DEFLATE/zlib/gzip (de)compression" -HOMEPAGE="https://github.com/ebiggers/libdeflate" -SRC_URI="https://github.com/ebiggers/libdeflate/archive/v1.2.tar.gz -> ${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="static-libs" - -DEPEND="" -RDEPEND="${DEPEND}" -BDEPEND="" - -PATCHES=( "${FILESDIR}"/libdeflate-1.2-respect_EPREFIX.patch ) - -src_install() { - if ! use static-libs; then - find "${ED}" -name '*.a' -delete || die - fi - emake install DESTDIR="${ED}" LIBDIR=/usr/"$(get_libdir)" - dodoc NEWS README.md -} diff --git a/app-arch/libdeflate/libdeflate-1.6.ebuild b/app-arch/libdeflate/libdeflate-1.6.ebuild deleted file mode 100644 index 666506943..000000000 --- a/app-arch/libdeflate/libdeflate-1.6.ebuild +++ /dev/null @@ -1,21 +0,0 @@ -# Copyright 2019-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DESCRIPTION="Heavily optimized DEFLATE/zlib/gzip (de)compression" -HOMEPAGE="https://github.com/ebiggers/libdeflate" -SRC_URI="https://github.com/ebiggers/libdeflate/archive/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="static-libs" - -src_install() { - if ! use static-libs; then - find "${ED}" -name '*.a' -delete || die - fi - emake install DESTDIR="${ED}" PREFIX=/usr LIBDIR=/usr/"$(get_libdir)" - dodoc NEWS README.md -} diff --git a/app-arch/libdeflate/libdeflate-1.7.ebuild b/app-arch/libdeflate/libdeflate-1.7.ebuild deleted file mode 100644 index bfafcfecd..000000000 --- a/app-arch/libdeflate/libdeflate-1.7.ebuild +++ /dev/null @@ -1,28 +0,0 @@ -# Copyright 2019-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DESCRIPTION="Heavily optimized DEFLATE/zlib/gzip (de)compression" -HOMEPAGE="https://github.com/ebiggers/libdeflate" - -if [[ ${PV} == *9999 ]]; then - inherit git-r3 - EGIT_REPO_URI="https://github.com/ebiggers/libdeflate" -else - SRC_URI="https://github.com/ebiggers/libdeflate/archive/v${PV}.tar.gz -> ${P}.tar.gz" - KEYWORDS="~amd64 ~x86" -fi - -LICENSE="MIT" -SLOT="0" -IUSE="static-libs test" -RESTRICT="!test? ( test )" - -src_install() { - emake DESTDIR="${ED}" PREFIX=/usr LIBDIR="/usr/$(get_libdir)" install - if ! use static-libs; then - find "${ED}" -name '*.a' -delete || die - fi - dodoc NEWS README.md -} diff --git a/app-arch/libdeflate/libdeflate-1.8.ebuild b/app-arch/libdeflate/libdeflate-1.8.ebuild deleted file mode 100644 index bfafcfecd..000000000 --- a/app-arch/libdeflate/libdeflate-1.8.ebuild +++ /dev/null @@ -1,28 +0,0 @@ -# Copyright 2019-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DESCRIPTION="Heavily optimized DEFLATE/zlib/gzip (de)compression" -HOMEPAGE="https://github.com/ebiggers/libdeflate" - -if [[ ${PV} == *9999 ]]; then - inherit git-r3 - EGIT_REPO_URI="https://github.com/ebiggers/libdeflate" -else - SRC_URI="https://github.com/ebiggers/libdeflate/archive/v${PV}.tar.gz -> ${P}.tar.gz" - KEYWORDS="~amd64 ~x86" -fi - -LICENSE="MIT" -SLOT="0" -IUSE="static-libs test" -RESTRICT="!test? ( test )" - -src_install() { - emake DESTDIR="${ED}" PREFIX=/usr LIBDIR="/usr/$(get_libdir)" install - if ! use static-libs; then - find "${ED}" -name '*.a' -delete || die - fi - dodoc NEWS README.md -} diff --git a/app-arch/libdeflate/libdeflate-1.9.ebuild b/app-arch/libdeflate/libdeflate-1.9.ebuild deleted file mode 100644 index ef7ead774..000000000 --- a/app-arch/libdeflate/libdeflate-1.9.ebuild +++ /dev/null @@ -1,28 +0,0 @@ -# Copyright 2019-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DESCRIPTION="Heavily optimized DEFLATE/zlib/gzip (de)compression" -HOMEPAGE="https://github.com/ebiggers/libdeflate" - -if [[ ${PV} == *9999 ]]; then - inherit git-r3 - EGIT_REPO_URI="https://github.com/ebiggers/libdeflate" -else - SRC_URI="https://github.com/ebiggers/libdeflate/archive/v${PV}.tar.gz -> ${P}.tar.gz" - KEYWORDS="~amd64 ~x86" -fi - -LICENSE="MIT" -SLOT="0" -IUSE="static-libs test" -RESTRICT="!test? ( test )" - -src_install() { - emake DESTDIR="${ED}" PREFIX=/usr LIBDIR="/usr/$(get_libdir)" install - if ! use static-libs; then - find "${ED}" -name '*.a' -delete || die - fi - dodoc NEWS,d README.md -} diff --git a/app-arch/libdeflate/libdeflate-9999.ebuild b/app-arch/libdeflate/libdeflate-9999.ebuild deleted file mode 100644 index 35aff28c3..000000000 --- a/app-arch/libdeflate/libdeflate-9999.ebuild +++ /dev/null @@ -1,28 +0,0 @@ -# Copyright 2019-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -DESCRIPTION="Heavily optimized DEFLATE/zlib/gzip (de)compression" -HOMEPAGE="https://github.com/ebiggers/libdeflate" - -if [[ ${PV} == *9999 ]]; then - inherit git-r3 - EGIT_REPO_URI="https://github.com/ebiggers/libdeflate" -else - SRC_URI="https://github.com/ebiggers/libdeflate/archive/v${PV}.tar.gz -> ${P}.tar.gz" - KEYWORDS="~amd64 ~x86" -fi - -LICENSE="MIT" -SLOT="0" -IUSE="static-libs test" -RESTRICT="!test? ( test )" - -src_install() { - emake DESTDIR="${ED}" PREFIX=/usr LIBDIR="/usr/$(get_libdir)" install - if ! use static-libs; then - find "${ED}" -name '*.a' -delete || die - fi - dodoc NEWS.md README.md -} diff --git a/app-arch/libdeflate/metadata.xml b/app-arch/libdeflate/metadata.xml deleted file mode 100644 index 6e347494a..000000000 --- a/app-arch/libdeflate/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="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="person"> - <email>gentoo@aisha.cc</email> - <name>Aisha Tammy</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/app-office/visidata/Manifest b/app-office/visidata/Manifest index 125ed2aa0..841bc773a 100644 --- a/app-office/visidata/Manifest +++ b/app-office/visidata/Manifest @@ -1 +1,4 @@ -DIST visidata-2.8.tar.gz 1791958 BLAKE2B f7a7dec514bcca37b4ee6ee9c16eb07a625b83e601a5bcf1ca5589a462e50086cbd9997238230ac464b4dc77e9deb421d3ff0bcf0fa39b32f1c1ce0308d2cb7b SHA512 da9bce4e59054ea518024639a1f60d6f19886cd061a52aa49189d7478ea27950e6e97e0d1730456b65815f9298d0225bfcebe4bba5452e1a9a87f5f56aa11dc3 +DIST visidata-2.11.1.gh.tar.gz 1928973 BLAKE2B bb9c40121175db262d4e0256b4e5b71313228590b9517e42589158d1a6279add0c1eacf1fe0ae5d38bd013b53c3ccad92ba0c4e39d40e27605c1502c84c40a5d SHA512 01905795ae6216e3cf662b43732394c68b43ffc8a4dc40da8552ebefaba4535fa3937aec1825cb108267dd83ab1b6a1072d1e698d416eae883dba915ca40b332 +DIST visidata-2.11.gh.tar.gz 1927455 BLAKE2B 95f868028fabb488f550b2ba15b60104a2d54dff972946ac38996d2906464e306e396adbf8dee32107aaf19a48d0e5d087aeeec82909e1d09b1d84b1e61138b7 SHA512 01512d47da329ba95aa7ceb5678a652fba5e06f6ff7ef0216b6271bf5b63a10712d425a2a1668ef6399b74f9fa9cb8d2d0f7bfa9316488ef5d64285ddcdde31a +DIST visidata-2.11_p20230217.gh.tar.gz 2062327 BLAKE2B c7cd07ac816a31c2294d431c6426fc44f8a2cf015e7994d8b918c9e60cce2e7700ac77919c5a9e5c3ad5ccf41cb5b04e34fc84016a0c6faa8bd4e8e470275d0a SHA512 eaf2060c6fe6d1fed713cb0318d12233f279151a1a97b11ae3a7ccf07a065d716cf81872b76aa71a15dda3bfd85c09e7e03f9be2fae857f8edbded86e06b597f +DIST visidata-2.8.gh.tar.gz 1791958 BLAKE2B f7a7dec514bcca37b4ee6ee9c16eb07a625b83e601a5bcf1ca5589a462e50086cbd9997238230ac464b4dc77e9deb421d3ff0bcf0fa39b32f1c1ce0308d2cb7b SHA512 da9bce4e59054ea518024639a1f60d6f19886cd061a52aa49189d7478ea27950e6e97e0d1730456b65815f9298d0225bfcebe4bba5452e1a9a87f5f56aa11dc3 diff --git a/app-office/visidata/visidata-2.11-r1.ebuild b/app-office/visidata/visidata-2.11-r1.ebuild new file mode 100644 index 000000000..208587336 --- /dev/null +++ b/app-office/visidata/visidata-2.11-r1.ebuild @@ -0,0 +1,90 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) + +inherit distutils-r1 optfeature + +DESCRIPTION="Terminal spreadsheet multitool for discovering and arranging data" +HOMEPAGE="http://visidata.org" +SRC_URI="https://github.com/saulpw/${PN}/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86" +# Tests fail on recent Python: +# https://github.com/saulpw/visidata/issues/1905 +RESTRICT="test" + +RDEPEND=" + >=dev-python/importlib-metadata-3.6[${PYTHON_USEDEP}] + dev-python/python-dateutil[${PYTHON_USEDEP}] +" +BDEPEND=" + test? ( + dev-python/h5py[${PYTHON_USEDEP}] + dev-python/odfpy[${PYTHON_USEDEP}] + dev-python/openpyxl[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + dev-python/pytest[${PYTHON_USEDEP}] + dev-python/requests[${PYTHON_USEDEP}] + dev-vcs/git + $(python_gen_impl_dep sqlite) + ) +" + +#distutils_enable_sphinx docs \ +# dev-python/recommonmark \ +# dev-python/sphinx-argparse +# dev-python/sphinx-markdown-tables + +distutils_enable_tests pytest + +python_prepare_all() { + rm tests/load-http.vd || die "Could not remove network-dependent test." + rm tests/graph-cursor-nosave.vd || die "Could not remove network-dependent test." + rm tests/messenger-nosave.vd || die "Could not remove network-dependent test." + rm tests/save-benchmarks.vd || die "Could not benchmarks test" + rm tests/graphpr-nosave.vd || die "Could not benchmarks test" + rm tests/describe-error.vd || die "Could not remove network-dependent test" + rm tests/describe.vd || die "Could not remove network-dependent test" + rm tests/edit-type.vd || die "Could not remove network-dependent test" + + distutils-r1_python_prepare_all +} + +python_test() { + git init || die "Git init failed." + git add tests/golden/ || die "Git add failed." + # this test script eventually calls pytest under the hood + dev/test.sh || die "Tests failed." + rm .git -rf || die "Could not clean up git test directory." +} + +pkg_postinst() { + optfeature "integration with yaml" >=dev-python/pyyaml-5.1 + optfeature "integration with pcap" dev-python/dnslib #dpkt pypcapkit + optfeature "integration with png" dev-python/pypng + optfeature "integration with http" dev-python/requests + optfeature "integration with postgres" dev-python/psycopg-binary + optfeature "integration with xlsx" dev-python/openpyxl + optfeature "integration with xls" dev-python/xlrd + optfeature "integration with hdf5" dev-python/h5py + optfeature "integration with ttf/otf" dev-python/fonttools + optfeature "integration with xml/htm/html" dev-python/lxml + optfeature "integration with dta (Stata)" dev-python/pandas + optfeature "integration with shapefiles" sci-libs/pyshp + optfeature "integration with namestand" dev-python/graphviz + optfeature "integration with pdfminer.six" dev-python/pdfminer-six # in guru + optfeature "integration with vobject" dev-python/vobject + optfeature "integration with tabulate" dev-python/tabulate + optfeature "integration with tabulate (with unicode)" dev-python/wcwidth + # optfeature "pdf tables" tabula # no package presently + #optfeature "integration with mbtiles" mapbox-vector-tile + #optfeature "integration with xpt (SAS)" xport + #optfeature "integration with sas7bdat (SAS)" sas7bdat + #optfeature "integration with sav (SPSS)" savReaderWriter +} diff --git a/app-office/visidata/visidata-2.11.1.ebuild b/app-office/visidata/visidata-2.11.1.ebuild new file mode 100644 index 000000000..3a5c510b4 --- /dev/null +++ b/app-office/visidata/visidata-2.11.1.ebuild @@ -0,0 +1,88 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_11 ) + +inherit distutils-r1 optfeature + +DESCRIPTION="Terminal spreadsheet multitool for discovering and arranging data" +HOMEPAGE="https://www.visidata.org/" +SRC_URI="https://github.com/saulpw/visidata/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +RDEPEND=" + >=dev-python/importlib-metadata-3.6[${PYTHON_USEDEP}] + dev-python/python-dateutil[${PYTHON_USEDEP}] +" +DEPEND="${RDEPEND}" +BDEPEND=" + test? ( + dev-python/h5py[${PYTHON_USEDEP}] + dev-python/odfpy[${PYTHON_USEDEP}] + dev-python/openpyxl[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + dev-python/pytest[${PYTHON_USEDEP}] + dev-python/requests[${PYTHON_USEDEP}] + dev-vcs/git + $(python_gen_impl_dep sqlite) + ) +" + +#distutils_enable_sphinx docs \ +# dev-python/recommonmark \ +# dev-python/sphinx-argparse +# dev-python/sphinx-markdown-tables + +distutils_enable_tests pytest + +python_prepare_all() { + rm tests/load-http.vd || die "Could not remove network-dependent test." + rm tests/graph-cursor-nosave.vd || die "Could not remove network-dependent test." + rm tests/messenger-nosave.vd || die "Could not remove network-dependent test." + rm tests/save-benchmarks.vd || die "Could not benchmarks test" + rm tests/graphpr-nosave.vd || die "Could not benchmarks test" + rm tests/describe-error.vd || die "Could not remove network-dependent test" + rm tests/describe.vd || die "Could not remove network-dependent test" + rm tests/edit-type.vd || die "Could not remove network-dependent test" + + distutils-r1_python_prepare_all +} + +python_test() { + git init || die "Git init failed." + git add tests/golden/ || die "Git add failed." + # this test script eventually calls pytest under the hood + dev/test.sh || die "Tests failed." + rm .git -rf || die "Could not clean up git test directory." +} + +pkg_postinst() { + optfeature "integration with yaml" >=dev-python/pyyaml-5.1 + optfeature "integration with pcap" dev-python/dnslib #dpkt pypcapkit + optfeature "integration with png" dev-python/pypng + optfeature "integration with http" dev-python/requests + optfeature "integration with postgres" dev-python/psycopg-binary + optfeature "integration with xlsx" dev-python/openpyxl + optfeature "integration with xls" dev-python/xlrd + optfeature "integration with hdf5" dev-python/h5py + optfeature "integration with ttf/otf" dev-python/fonttools + optfeature "integration with xml/htm/html" dev-python/lxml + optfeature "integration with dta (Stata)" dev-python/pandas + optfeature "integration with shapefiles" sci-libs/pyshp + optfeature "integration with namestand" dev-python/graphviz + optfeature "integration with pdfminer.six" dev-python/pdfminer-six # in guru + optfeature "integration with vobject" dev-python/vobject + optfeature "integration with tabulate" dev-python/tabulate + optfeature "integration with tabulate (with unicode)" dev-python/wcwidth + # optfeature "pdf tables" tabula # no package presently + #optfeature "integration with mbtiles" mapbox-vector-tile + #optfeature "integration with xpt (SAS)" xport + #optfeature "integration with sas7bdat (SAS)" sas7bdat + #optfeature "integration with sav (SPSS)" savReaderWriter +} diff --git a/app-office/visidata/visidata-2.11_p20230217-r1.ebuild b/app-office/visidata/visidata-2.11_p20230217-r1.ebuild new file mode 100644 index 000000000..5edfdcb23 --- /dev/null +++ b/app-office/visidata/visidata-2.11_p20230217-r1.ebuild @@ -0,0 +1,90 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{11..11} ) + +inherit distutils-r1 optfeature + +MY_HASH="5ff7883563eeac32fe192c5b2d4290a4e1e91cc2" +DESCRIPTION="Terminal spreadsheet multitool for discovering and arranging data" +HOMEPAGE="http://visidata.org" +SRC_URI="https://github.com/saulpw/visidata/archive/${MY_HASH}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +RDEPEND=" + >=dev-python/importlib-metadata-3.6[${PYTHON_USEDEP}] + dev-python/python-dateutil[${PYTHON_USEDEP}] +" +BDEPEND=" + test? ( + dev-python/h5py[${PYTHON_USEDEP}] + dev-python/odfpy[${PYTHON_USEDEP}] + dev-python/openpyxl[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + dev-python/pytest[${PYTHON_USEDEP}] + dev-python/requests[${PYTHON_USEDEP}] + dev-vcs/git + $(python_gen_impl_dep sqlite) + ) +" + +S="${WORKDIR}/${PN}-${MY_HASH}" + +#distutils_enable_sphinx docs \ +# dev-python/recommonmark \ +# dev-python/sphinx-argparse +# dev-python/sphinx-markdown-tables + +distutils_enable_tests pytest + +python_prepare_all() { + rm tests/load-http.vd || die "Could not remove network-dependent test." + rm tests/graph-cursor-nosave.vd || die "Could not remove network-dependent test." + rm tests/messenger-nosave.vd || die "Could not remove network-dependent test." + rm tests/save-benchmarks.vd || die "Could not benchmarks test" + rm tests/graphpr-nosave.vd || die "Could not benchmarks test" + rm tests/describe-error.vd || die "Could not remove network-dependent test" + rm tests/describe.vd || die "Could not remove network-dependent test" + rm tests/edit-type.vd || die "Could not remove network-dependent test" + + distutils-r1_python_prepare_all +} + +python_test() { + git init || die "Git init failed." + git add tests/golden/ || die "Git add failed." + # this test script eventually calls pytest under the hood + dev/test.sh || die "Tests failed." + rm .git -rf || die "Could not clean up git test directory." +} + +pkg_postinst() { + optfeature "integration with yaml" >=dev-python/pyyaml-5.1 + optfeature "integration with pcap" dev-python/dnslib #dpkt pypcapkit + optfeature "integration with png" dev-python/pypng + optfeature "integration with http" dev-python/requests + optfeature "integration with postgres" dev-python/psycopg-binary + optfeature "integration with xlsx" dev-python/openpyxl + optfeature "integration with xls" dev-python/xlrd + optfeature "integration with hdf5" dev-python/h5py + optfeature "integration with ttf/otf" dev-python/fonttools + optfeature "integration with xml/htm/html" dev-python/lxml + optfeature "integration with dta (Stata)" dev-python/pandas + optfeature "integration with shapefiles" sci-libs/pyshp + optfeature "integration with namestand" dev-python/graphviz + optfeature "integration with pdfminer.six" dev-python/pdfminer-six # in guru + optfeature "integration with vobject" dev-python/vobject + optfeature "integration with tabulate" dev-python/tabulate + optfeature "integration with tabulate (with unicode)" dev-python/wcwidth + # optfeature "pdf tables" tabula # no package presently + #optfeature "integration with mbtiles" mapbox-vector-tile + #optfeature "integration with xpt (SAS)" xport + #optfeature "integration with sas7bdat (SAS)" sas7bdat + #optfeature "integration with sav (SPSS)" savReaderWriter +} diff --git a/app-office/visidata/visidata-2.8.ebuild b/app-office/visidata/visidata-2.8.ebuild index bb35b1c03..11c164d7e 100644 --- a/app-office/visidata/visidata-2.8.ebuild +++ b/app-office/visidata/visidata-2.8.ebuild @@ -1,20 +1,23 @@ -# Copyright 1999-2022 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 -PYTHON_COMPAT=( python3_{8..9} ) -DISTUTILS_USE_SETUPTOOLS=rdepend +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) inherit distutils-r1 optfeature DESCRIPTION="Terminal spreadsheet multitool for discovering and arranging data" HOMEPAGE="http://visidata.org" -SRC_URI="https://github.com/saulpw/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz" +SRC_URI="https://github.com/saulpw/${PN}/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz" LICENSE="GPL-3" SLOT="0" KEYWORDS="~amd64 ~x86" +# Tests fail on recent Python: +# https://github.com/saulpw/visidata/issues/1905 +RESTRICT="test" RDEPEND="dev-python/python-dateutil[${PYTHON_USEDEP}]" BDEPEND=" diff --git a/dev-cpp/Fastor/metadata.xml b/dev-cpp/Fastor/metadata.xml index e97c4322a..9937ac435 100644 --- a/dev-cpp/Fastor/metadata.xml +++ b/dev-cpp/Fastor/metadata.xml @@ -9,4 +9,7 @@ <email>sci@gentoo.org</email> <name>Gentoo Science Project</name> </maintainer> + <upstream> + <remote-id type="github">romeric/Fastor</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-cpp/blitz/blitz-1.0.3_pre20200524.ebuild b/dev-cpp/blitz/blitz-1.0.3_pre20200524.ebuild index 389e5430d..e331bc6c9 100644 --- a/dev-cpp/blitz/blitz-1.0.3_pre20200524.ebuild +++ b/dev-cpp/blitz/blitz-1.0.3_pre20200524.ebuild @@ -1,14 +1,12 @@ # Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 - -PYTHON_COMPAT=( python3_{7..9} ) +EAPI=8 +PYTHON_COMPAT=( python3_{10..11} ) inherit cmake python-any-r1 COMMIT="39f885951a9b8b11f931f917935a16066a945056" - DESCRIPTION="Multi-dimensional array library for C++" HOMEPAGE="https://github.com/blitzpp/blitz" SRC_URI="https://github.com/blitzpp/blitz/archive/${COMMIT}.tar.gz -> ${P}.tar.gz" @@ -22,7 +20,7 @@ RESTRICT="!test? ( test )" BDEPEND=" ${PYTHON_DEPS} - doc? ( app-doc/doxygen[dot] ) + doc? ( app-text/doxygen[dot] ) " DEPEND=" boost? ( dev-libs/boost:= ) diff --git a/dev-cpp/castxml/Manifest b/dev-cpp/castxml/Manifest deleted file mode 100644 index a7d756e8b..000000000 --- a/dev-cpp/castxml/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST castxml-0.3.6.tar.gz 95844 BLAKE2B c0ab3c7ba29b2abb4755320d97c36ee850135fff6fd5bb7a9436d68f50e9c6a80108ac95958fe9b51afaf6b4ebdde7db825a9cdf047c5e8f47f4f57fba77dcc1 SHA512 c850ce9ce0ef716cf64139d4311955deb8373db691e3cb7348932bbd3945056366838187603e5850a088911a8be6b0e5b53e2c700c0b5c8fed71008de7ab2350 -DIST castxml-0.4.3.tar.gz 103188 BLAKE2B ceaeaa0e228865847fc9627e93366c9dc2d33f89c97621af25ce84746ffe79b0db7cf52a93aed3ac297ce116e1f63f4bcc636dc21419aabf3ba737f545b240c1 SHA512 af2c03e148d42615a9ad0366a224ebeb06ca0348c0b5fcc0a93cba4871710dd8901874e5e30968532cdb1254e63a7ab596403bf2f3c836eed57be287203ddbed diff --git a/dev-cpp/castxml/castxml-0.3.6.ebuild b/dev-cpp/castxml/castxml-0.3.6.ebuild deleted file mode 100644 index 6fb7ac720..000000000 --- a/dev-cpp/castxml/castxml-0.3.6.ebuild +++ /dev/null @@ -1,35 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit cmake llvm - -MY_PN="CastXML" - -DESCRIPTION="CastXML is a C-family abstract syntax tree XML output tool." -HOMEPAGE="https://github.com/CastXML/CastXML" -if [[ ${PV} == 9999 ]]; then - inherit git-r3 - EGIT_REPO_URI="https://github.com/CastXML/CastXML" -else - SRC_URI="https://github.com/CastXML/CastXML/archive/v${PV}.tar.gz -> ${P}.tar.gz" - KEYWORDS="~amd64 ~x86" -fi - -LICENSE="Apache-2.0" -SLOT="0" -IUSE="test" -RESTRICT="!test? ( test )" - -DEPEND="${RDEPEND}" -RDEPEND=" - dev-libs/glib:2 - dev-libs/libxml2 - sys-devel/llvm:= - sys-devel/clang:= -" - -S="${WORKDIR}/${MY_PN}-${PV}" - -PATCHES=( "${FILESDIR}"/${PN}-0.3.6-install-paths.patch ) diff --git a/dev-cpp/castxml/castxml-0.4.3.ebuild b/dev-cpp/castxml/castxml-0.4.3.ebuild deleted file mode 100644 index 6fb7ac720..000000000 --- a/dev-cpp/castxml/castxml-0.4.3.ebuild +++ /dev/null @@ -1,35 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit cmake llvm - -MY_PN="CastXML" - -DESCRIPTION="CastXML is a C-family abstract syntax tree XML output tool." -HOMEPAGE="https://github.com/CastXML/CastXML" -if [[ ${PV} == 9999 ]]; then - inherit git-r3 - EGIT_REPO_URI="https://github.com/CastXML/CastXML" -else - SRC_URI="https://github.com/CastXML/CastXML/archive/v${PV}.tar.gz -> ${P}.tar.gz" - KEYWORDS="~amd64 ~x86" -fi - -LICENSE="Apache-2.0" -SLOT="0" -IUSE="test" -RESTRICT="!test? ( test )" - -DEPEND="${RDEPEND}" -RDEPEND=" - dev-libs/glib:2 - dev-libs/libxml2 - sys-devel/llvm:= - sys-devel/clang:= -" - -S="${WORKDIR}/${MY_PN}-${PV}" - -PATCHES=( "${FILESDIR}"/${PN}-0.3.6-install-paths.patch ) diff --git a/dev-cpp/castxml/castxml-9999.ebuild b/dev-cpp/castxml/castxml-9999.ebuild deleted file mode 100644 index dbf7fff49..000000000 --- a/dev-cpp/castxml/castxml-9999.ebuild +++ /dev/null @@ -1,33 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit cmake llvm - -MY_PN="CastXML" - -DESCRIPTION="CastXML is a C-family abstract syntax tree XML output tool." -HOMEPAGE="https://github.com/CastXML/CastXML" -if [[ ${PV} == 9999 ]]; then - inherit git-r3 - EGIT_REPO_URI="https://github.com/CastXML/CastXML" -else - SRC_URI="https://github.com/CastXML/CastXML/archive/v${PV}.tar.gz -> ${P}.tar.gz" - KEYWORDS="~amd64 ~x86" -fi - -LICENSE="Apache-2.0" -SLOT="0" -IUSE="test" -RESTRICT="!test? ( test )" - -DEPEND="${RDEPEND}" -RDEPEND=" - dev-libs/glib:2 - dev-libs/libxml2 - sys-devel/llvm:= - sys-devel/clang:= -" - -PATCHES=( "${FILESDIR}"/${PN}-0.3.6-install-paths.patch ) diff --git a/dev-cpp/castxml/files/castxml-0.3.6-install-paths.patch b/dev-cpp/castxml/files/castxml-0.3.6-install-paths.patch deleted file mode 100644 index 0b72085b4..000000000 --- a/dev-cpp/castxml/files/castxml-0.3.6-install-paths.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff --git a/CMakeLists.txt b/CMakeLists.txt -index 90feea4..4b058a8 100644 ---- a/CMakeLists.txt -+++ b/CMakeLists.txt -@@ -194,5 +194,5 @@ install(DIRECTORY share/castxml/ DESTINATION "${CastXML_INSTALL_DATA_DIR}") - install(FILES - "LICENSE" - "NOTICE" -- DESTINATION "${CastXML_INSTALL_DOC_DIR}" -+ DESTINATION "${CastXML_INSTALL_DATA_DIR}" - ) - diff --git a/dev-cpp/castxml/metadata.xml b/dev-cpp/castxml/metadata.xml deleted file mode 100644 index 3cef409d1..000000000 --- a/dev-cpp/castxml/metadata.xml +++ /dev/null @@ -1,15 +0,0 @@ -<?xml version='1.0' encoding='UTF-8'?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>gw.fossdev@gmail.com</email> - </maintainer> - <maintainer type="person"> - <email>gentoo@chymera.eu</email> - <name>Horea Christian</name> - </maintainer> - <maintainer type="project"> - <email>sci@gentoo.org</email> - <name>Gentoo Science Project</name> - </maintainer> -</pkgmetadata> diff --git a/dev-cpp/highwayhash/highwayhash-20200922.ebuild b/dev-cpp/highwayhash/highwayhash-20200922.ebuild index 8483be41f..2eb0ccaa2 100644 --- a/dev-cpp/highwayhash/highwayhash-20200922.ebuild +++ b/dev-cpp/highwayhash/highwayhash-20200922.ebuild @@ -25,6 +25,6 @@ src_install() { LIBDIR="/usr/$(get_libdir)" \ install use static-libs || \ - rm "${ED}"/${EPREFIX}/usr/$(get_libdir)/lib*.a || die + rm "${ED}/usr/$(get_libdir)"/lib*.a || die einstalldocs } diff --git a/dev-cpp/highwayhash/metadata.xml b/dev-cpp/highwayhash/metadata.xml index ef6b5dcd5..ce99f4b00 100644 --- a/dev-cpp/highwayhash/metadata.xml +++ b/dev-cpp/highwayhash/metadata.xml @@ -5,4 +5,7 @@ <email>junghans@gentoo.org</email> <name>Christoph Junghans</name> </maintainer> + <upstream> + <remote-id type="github">google/highwayhash</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-cpp/xor_singleheader/metadata.xml b/dev-cpp/xor_singleheader/metadata.xml index e97c4322a..cebb00f2c 100644 --- a/dev-cpp/xor_singleheader/metadata.xml +++ b/dev-cpp/xor_singleheader/metadata.xml @@ -9,4 +9,7 @@ <email>sci@gentoo.org</email> <name>Gentoo Science Project</name> </maintainer> + <upstream> + <remote-id type="github">FastFilter/xor_singleheader</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-java/jama/Manifest b/dev-java/jama/Manifest new file mode 100644 index 000000000..47e1c0f12 --- /dev/null +++ b/dev-java/jama/Manifest @@ -0,0 +1 @@ +DIST jama-1.0.3-sources.tar.gz 82188 BLAKE2B 35de815f770b192cd1b86a56ddf1919e12675d898ec4473489d3ce2c3899185f9d96eda39b6f7520fc67edfd17fe58b585f788f6a6967220150fc9a334b219ea SHA512 9bedf8f35ea1d400194b5a3b49914ebd04b5a31247959886f1967d062ceffae30993d34cd2f15d3942285a45c6930e2d4518f4ed0cc013ce853cc26aca021b0d diff --git a/dev-java/jama/jama-1.0.3.ebuild b/dev-java/jama/jama-1.0.3.ebuild new file mode 100644 index 000000000..9a88f35c4 --- /dev/null +++ b/dev-java/jama/jama-1.0.3.ebuild @@ -0,0 +1,32 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +MY_PN="Jama" + +JAVA_PKG_IUSE="doc source test" + +inherit java-pkg-2 java-pkg-simple + +DESCRIPTION="JAMA is a basic linear algebra package for Java. " +HOMEPAGE="https://math.nist.gov/javanumerics/jama/" + +SRC_URI="https://math.nist.gov/javanumerics/jama/${MY_PN}-${PV}.tar.gz -> ${P}-sources.tar.gz" +S="${WORKDIR}/${MY_PN}" +KEYWORDS="~amd64" + +LICENSE="public-domain" +SLOT="0" + +BDEPEND=">=virtual/jdk-1.8:*" + +RDEPEND=">=virtual/jre-1.8:*" + +JAVA_SRC_DIR=( + "./" + "util" +) +JAVA_MAIN_CLASS="gov.math.nist.Main" + +JAVA_TEST_SRC_DIR="test" diff --git a/dev-java/jama/metadata.xml b/dev-java/jama/metadata.xml new file mode 100644 index 000000000..f3dd4314e --- /dev/null +++ b/dev-java/jama/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <longdescription> + JAMA is a basic linear algebra package for Java. It provides user-level classes for constructing and manipulating real, dense matrices. It is meant to provide sufficient functionality for routine problems, packaged in a way that is natural and understandable to non-experts. + </longdescription> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> +</pkgmetadata> diff --git a/dev-java/jeuclid-core/Manifest b/dev-java/jeuclid-core/Manifest deleted file mode 100644 index 6df1751b1..000000000 --- a/dev-java/jeuclid-core/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST jeuclid-core-3.1.14.tar.gz 7244186 BLAKE2B 9cada848e516aba942ef87e7b746296f9565d5271a1ce6635e80e6559edcedac3245c4bde28e8d1053cacc5774e6a015079b0281802559e86366a75223b8ea2c SHA512 7b52491d7fac40a13f41176a49f36411681c957aba95c23bb6396f4e1248f5463afcd5394b0bb8e3dfbdd498d3290ac5f787e876636f5f282b703a72799eff4e diff --git a/dev-java/jeuclid-core/files/jeuclid-core-no-freehep.patch b/dev-java/jeuclid-core/files/jeuclid-core-no-freehep.patch deleted file mode 100644 index daf123c92..000000000 --- a/dev-java/jeuclid-core/files/jeuclid-core-no-freehep.patch +++ /dev/null @@ -1,10 +0,0 @@ ---- a/build.xml 2010-01-22 17:46:35.000000000 +0000 -+++ b/build.xml 2010-01-22 17:49:07.000000000 +0000 -@@ -113,6 +113,7 @@ - <src> - <pathelement location="src/main/java"/> - </src> -+ <exclude name="**/FreeHep*" /> - <classpath refid="libs-build-classpath"/> - </javac> - <copy todir="${build.output}"> diff --git a/dev-java/jeuclid-core/jeuclid-core-3.1.14.ebuild b/dev-java/jeuclid-core/jeuclid-core-3.1.14.ebuild deleted file mode 100644 index a64ebcd74..000000000 --- a/dev-java/jeuclid-core/jeuclid-core-3.1.14.ebuild +++ /dev/null @@ -1,55 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 -JAVA_PKG_IUSE="source" - -inherit java-pkg-2 java-ant-2 - -DESCRIPTION="Core module of MathML rendering solution" -HOMEPAGE="https://github.com/rototor/jeuclid" -SRC_URI="https://github.com/rototor/jeuclid/archive/jeuclid-parent-${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="Apache-2.0" -SLOT="0" -KEYWORDS="~amd64" - -COMMON_DEPEND=" - dev-java/ant-core:0 - dev-java/batik:1.9 - dev-java/commons-logging:0 - dev-java/jcip-annotations:0 - dev-java/jsr305:0 - dev-java/xml-commons-external:1.3 - dev-java/xmlgraphics-commons:2 -" - -RDEPEND=">=virtual/jre-1.7 - ${COMMON_DEPEND}" - -DEPEND=">=virtual/jdk-1.7 - ${COMMON_DEPEND}" - -S="${WORKDIR}/jeuclid-jeuclid-parent-${PV}/${PN}" - -PATCHES=( - "${FILESDIR}"/${PN}-no-freehep.patch -) - -src_prepare() { - default - - # create directory for dependencies - mkdir lib && cd lib || die - - # add dependencies into the lib dir - java-pkg_jar-from ant-core ant.jar - java-pkg_jar-from batik-1.9 batik-all.jar - java-pkg_jar-from commons-logging,jcip-annotations,xml-commons-external-1.3 - java-pkg_jar-from xml-commons-external-1.3,xmlgraphics-commons-2 - java-pkg_jar-from jsr305 -} - -src_install() { - java-pkg_dojar target/${PN}.jar -} diff --git a/dev-java/jeuclid-core/metadata.xml b/dev-java/jeuclid-core/metadata.xml deleted file mode 100644 index 8b5c039f5..000000000 --- a/dev-java/jeuclid-core/metadata.xml +++ /dev/null @@ -1,21 +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"> -JEuclid is a complete MathML rendering solution, consisting of: -* A MathViewer application -* Command line converters from MathML to other formats -* An ant task for automated conversion -* Display components for AWT and Swing -* A component for Apache Cocoon -This package contains the basic JEuclid rendering and document -handling classes. -</longdescription> - <upstream> - <remote-id type="sourceforge">jeuclid</remote-id> - </upstream> -</pkgmetadata> diff --git a/dev-java/parsington/Manifest b/dev-java/parsington/Manifest new file mode 100644 index 000000000..970430d78 --- /dev/null +++ b/dev-java/parsington/Manifest @@ -0,0 +1 @@ +DIST parsington-3.1.0-sources.tar.gz 45883 BLAKE2B 39d37c772ba12f845fc6a53762e474f534dbb4920bc7178e885d560550a60c4e3949406d94a604b2b8740b9d337a504783111ccf28d480da10454db55abe853c SHA512 d1596e67b691148838116a02a88b2c520f0887952d254939cec0c77f225601be5f7d19f44c6b310126c7d210c726ec3399d77f8d91d590c377a2cd22814a68a7 diff --git a/dev-java/parsington/metadata.xml b/dev-java/parsington/metadata.xml new file mode 100644 index 000000000..3c4854834 --- /dev/null +++ b/dev-java/parsington/metadata.xml @@ -0,0 +1,14 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <longdescription> + Parsington is an infix-to-postfix and infix-to-syntax-tree expression parser for mathematical expressions written in Java. It is simple yet fancy, handling (customizable) operators, functions, variables and constants in a similar way to what the Java language itself supports. + </longdescription> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <upstream> + <remote-id type="github">scijava/parsington</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-java/parsington/parsington-3.1.0.ebuild b/dev-java/parsington/parsington-3.1.0.ebuild new file mode 100644 index 000000000..c583c89e9 --- /dev/null +++ b/dev-java/parsington/parsington-3.1.0.ebuild @@ -0,0 +1,48 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +JAVA_PKG_IUSE="doc source test" +JAVA_TESTING_FRAMEWORKS="junit-jupiter" + +inherit java-pkg-2 java-pkg-simple + +DESCRIPTION="A mathematical expression parser for infix expression strings" +HOMEPAGE="https://github.com/scijava/parsington" + +if [[ ${PV} == 9999 ]]; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/scijava/parsington.git" + S="${WORKDIR}/${P}" + MAVEN_ID="org.scijava:parsington:9999" +else + SRC_URI=" + https://github.com/scijava/${PN}/archive/refs/tags/${P}.tar.gz -> ${P}-sources.tar.gz + " + S="${WORKDIR}/${PN}-${P}" + MAVEN_ID="org.scijava:parsington:3.1.0" + KEYWORDS="~amd64" +fi + +LICENSE="BSD-2" +SLOT="0" + +CDEPEND=">=dev-java/junit-5.9.1:5" + +BDEPEND=" + >=virtual/jdk-1.8:* + test? ( + "${CDEPEND}" + ) +" + +DEPEND="${CDEPEND}" + +RDEPEND=">=virtual/jre-1.8:*" + +JAVA_SRC_DIR="src/main/java" +JAVA_MAIN_CLASS="org.scijava.parsington.Main" + +JAVA_TEST_GENTOO_CLASSPATH="junit-5" +JAVA_TEST_SRC_DIR="src/test/java" diff --git a/dev-java/parsington/parsington-9999.ebuild b/dev-java/parsington/parsington-9999.ebuild new file mode 100644 index 000000000..c583c89e9 --- /dev/null +++ b/dev-java/parsington/parsington-9999.ebuild @@ -0,0 +1,48 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +JAVA_PKG_IUSE="doc source test" +JAVA_TESTING_FRAMEWORKS="junit-jupiter" + +inherit java-pkg-2 java-pkg-simple + +DESCRIPTION="A mathematical expression parser for infix expression strings" +HOMEPAGE="https://github.com/scijava/parsington" + +if [[ ${PV} == 9999 ]]; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/scijava/parsington.git" + S="${WORKDIR}/${P}" + MAVEN_ID="org.scijava:parsington:9999" +else + SRC_URI=" + https://github.com/scijava/${PN}/archive/refs/tags/${P}.tar.gz -> ${P}-sources.tar.gz + " + S="${WORKDIR}/${PN}-${P}" + MAVEN_ID="org.scijava:parsington:3.1.0" + KEYWORDS="~amd64" +fi + +LICENSE="BSD-2" +SLOT="0" + +CDEPEND=">=dev-java/junit-5.9.1:5" + +BDEPEND=" + >=virtual/jdk-1.8:* + test? ( + "${CDEPEND}" + ) +" + +DEPEND="${CDEPEND}" + +RDEPEND=">=virtual/jre-1.8:*" + +JAVA_SRC_DIR="src/main/java" +JAVA_MAIN_CLASS="org.scijava.parsington.Main" + +JAVA_TEST_GENTOO_CLASSPATH="junit-5" +JAVA_TEST_SRC_DIR="src/test/java" diff --git a/dev-java/scijava-common/Manifest b/dev-java/scijava-common/Manifest new file mode 100644 index 000000000..51c68561b --- /dev/null +++ b/dev-java/scijava-common/Manifest @@ -0,0 +1 @@ +DIST scijava-common-2.97.1-sources.tar.gz 559336 BLAKE2B 4511202aaa7947a57a8fff6420397c05d5768571045519b9d02aa67a5b3ecefd738418d8412f447678d5133e089fa73bd335543979a58ae55b0e31e53eedc8ae SHA512 cf8e47097f608480c59b24d7487dbf1e138c16a63660aa3b5f5de4c600913e509b64e2d9360f7fdb6e5558a1320fb7d6f09bd3184e5e99da2c5265a91050002b diff --git a/dev-java/scijava-common/metadata.xml b/dev-java/scijava-common/metadata.xml new file mode 100644 index 000000000..374f9940a --- /dev/null +++ b/dev-java/scijava-common/metadata.xml @@ -0,0 +1,14 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <longdescription> + SciJava Common is a common library for SciJava software. It provides a plugin framework, with an extensible mechanism for service discovery, backed by its own annotation processor, so that plugins can be loaded dynamically. It is used by both ImageJ2 and SCIFIO. + </longdescription> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <upstream> + <remote-id type="github">scijava/scijava-common</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-java/scijava-common/scijava-common-2.97.1.ebuild b/dev-java/scijava-common/scijava-common-2.97.1.ebuild new file mode 100644 index 000000000..37a9bca8d --- /dev/null +++ b/dev-java/scijava-common/scijava-common-2.97.1.ebuild @@ -0,0 +1,67 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +JAVA_PKG_IUSE="doc source test" + +JAVA_TESTING_FRAMEWORKS="junit-4" + +inherit java-pkg-2 java-pkg-simple + +DESCRIPTION="SciJava Common is a shared library for SciJava software." +HOMEPAGE=" + https://imagej.net/libs/scijava#scijava-common + https://github.com/scijava/scijava-common + " + +if [[ ${PV} == 9999 ]]; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/scijava/scijava-common.git" + S="${WORKDIR}/${P}" + MAVEN_ID="org.scijava:scijava-common:9999" +else + SRC_URI=" + https://github.com/scijava/${PN}/archive/refs/tags/${P}.tar.gz -> ${P}-sources.tar.gz + " + S="${WORKDIR}/${PN}-${P}" + MAVEN_ID="org.scijava:scijava-common:2.97.1" + KEYWORDS="~amd64" +fi + +LICENSE="BSD-2" +SLOT="0" + +CDEPEND=" + dev-java/parsington:0 + dev-java/jaxws-api:0 + dev-java/jaxb-api:2 +" + +BDEPEND="${CDEPEND} + >=virtual/jdk-1.8:* +" + +DEPEND="${CDEPEND} + test? ( + >=dev-java/junit-4.13.2 + >=dev-java/mockito-4.11.0:4 + ) +" + +RDEPEND="${CDEPEND} + >=virtual/jre-1.8:* +" + +JAVA_GENTOO_CLASSPATH="parsington,jaxws-api,jaxb-api-2" +JAVA_SRC_DIR="src/main/java" +JAVA_MAIN_CLASS="" +JAVA_RESOURCE_DIRS=( + "src/main/resources" +) + +JAVA_TEST_GENTOO_CLASSPATH="junit-4,mockito-4" +JAVA_TEST_SRC_DIR="src/test/java" +JAVA_TEST_RESOURCE_DIRS=( + "src/test/resources" +) diff --git a/dev-java/scijava-common/scijava-common-9999.ebuild b/dev-java/scijava-common/scijava-common-9999.ebuild new file mode 100644 index 000000000..37a9bca8d --- /dev/null +++ b/dev-java/scijava-common/scijava-common-9999.ebuild @@ -0,0 +1,67 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +JAVA_PKG_IUSE="doc source test" + +JAVA_TESTING_FRAMEWORKS="junit-4" + +inherit java-pkg-2 java-pkg-simple + +DESCRIPTION="SciJava Common is a shared library for SciJava software." +HOMEPAGE=" + https://imagej.net/libs/scijava#scijava-common + https://github.com/scijava/scijava-common + " + +if [[ ${PV} == 9999 ]]; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/scijava/scijava-common.git" + S="${WORKDIR}/${P}" + MAVEN_ID="org.scijava:scijava-common:9999" +else + SRC_URI=" + https://github.com/scijava/${PN}/archive/refs/tags/${P}.tar.gz -> ${P}-sources.tar.gz + " + S="${WORKDIR}/${PN}-${P}" + MAVEN_ID="org.scijava:scijava-common:2.97.1" + KEYWORDS="~amd64" +fi + +LICENSE="BSD-2" +SLOT="0" + +CDEPEND=" + dev-java/parsington:0 + dev-java/jaxws-api:0 + dev-java/jaxb-api:2 +" + +BDEPEND="${CDEPEND} + >=virtual/jdk-1.8:* +" + +DEPEND="${CDEPEND} + test? ( + >=dev-java/junit-4.13.2 + >=dev-java/mockito-4.11.0:4 + ) +" + +RDEPEND="${CDEPEND} + >=virtual/jre-1.8:* +" + +JAVA_GENTOO_CLASSPATH="parsington,jaxws-api,jaxb-api-2" +JAVA_SRC_DIR="src/main/java" +JAVA_MAIN_CLASS="" +JAVA_RESOURCE_DIRS=( + "src/main/resources" +) + +JAVA_TEST_GENTOO_CLASSPATH="junit-4,mockito-4" +JAVA_TEST_SRC_DIR="src/test/java" +JAVA_TEST_RESOURCE_DIRS=( + "src/test/resources" +) diff --git a/dev-java/scijava-optional/Manifest b/dev-java/scijava-optional/Manifest new file mode 100644 index 000000000..eb3283b48 --- /dev/null +++ b/dev-java/scijava-optional/Manifest @@ -0,0 +1 @@ +DIST scijava-optional-1.0.1-sources.tar.gz 7659 BLAKE2B c5a99b5ffcd5c8a09cc40d360d31796002993352b581509bbb78d4464f0119313b743bdf94b22532bd5bcc3a8baf614273378031154588245805cc6bccf39de5 SHA512 e083586fb6015354bc7520bed04d4c7c745445e01ffb6ba86bb91505f65ba06dfb50cbcecf3971fcb9161c16a2e112af31e247edffae973bf310e13bded99e89 diff --git a/dev-java/scijava-optional/metadata.xml b/dev-java/scijava-optional/metadata.xml new file mode 100644 index 000000000..e7e56ccca --- /dev/null +++ b/dev-java/scijava-optional/metadata.xml @@ -0,0 +1,11 @@ +<?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> + <upstream> + <remote-id type="github">scijava/scijava-optional</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-java/scijava-optional/scijava-optional-1.0.1.ebuild b/dev-java/scijava-optional/scijava-optional-1.0.1.ebuild new file mode 100644 index 000000000..54010f802 --- /dev/null +++ b/dev-java/scijava-optional/scijava-optional-1.0.1.ebuild @@ -0,0 +1,44 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +JAVA_PKG_IUSE="doc source test" +JAVA_TESTING_FRAMEWORKS="junit-4" + +inherit java-pkg-2 java-pkg-simple + +DESCRIPTION="Helpers for emulating named and default arguments" +HOMEPAGE="https://github.com/scijava/scijava-optional" + +if [[ ${PV} == 9999 ]]; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/scijava/scijava-optional.git" + S="${WORKDIR}/${P}" + MAVEN_ID="org.scijava:scijava-optional:9999" +else + SRC_URI=" + https://github.com/scijava/${PN}/archive/refs/tags/${P}.tar.gz -> ${P}-sources.tar.gz + " + S="${WORKDIR}/${PN}-${P}" + MAVEN_ID="org.scijava:scijava-optional:1.0.2" + KEYWORDS="~amd64" +fi + +LICENSE="BSD-2" +SLOT="0" + +BDEPEND=" + >=virtual/jdk-1.8:* + test? ( + >=dev-java/junit-4.13.2:4 + ) +" + +RDEPEND=">=virtual/jre-1.8:*" + +JAVA_SRC_DIR="src/main/java" +JAVA_MAIN_CLASS="" + +JAVA_TEST_GENTOO_CLASSPATH="junit-4" +JAVA_TEST_SRC_DIR="src/test/java" diff --git a/dev-java/scijava-optional/scijava-optional-9999.ebuild b/dev-java/scijava-optional/scijava-optional-9999.ebuild new file mode 100644 index 000000000..54010f802 --- /dev/null +++ b/dev-java/scijava-optional/scijava-optional-9999.ebuild @@ -0,0 +1,44 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +JAVA_PKG_IUSE="doc source test" +JAVA_TESTING_FRAMEWORKS="junit-4" + +inherit java-pkg-2 java-pkg-simple + +DESCRIPTION="Helpers for emulating named and default arguments" +HOMEPAGE="https://github.com/scijava/scijava-optional" + +if [[ ${PV} == 9999 ]]; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/scijava/scijava-optional.git" + S="${WORKDIR}/${P}" + MAVEN_ID="org.scijava:scijava-optional:9999" +else + SRC_URI=" + https://github.com/scijava/${PN}/archive/refs/tags/${P}.tar.gz -> ${P}-sources.tar.gz + " + S="${WORKDIR}/${PN}-${P}" + MAVEN_ID="org.scijava:scijava-optional:1.0.2" + KEYWORDS="~amd64" +fi + +LICENSE="BSD-2" +SLOT="0" + +BDEPEND=" + >=virtual/jdk-1.8:* + test? ( + >=dev-java/junit-4.13.2:4 + ) +" + +RDEPEND=">=virtual/jre-1.8:*" + +JAVA_SRC_DIR="src/main/java" +JAVA_MAIN_CLASS="" + +JAVA_TEST_GENTOO_CLASSPATH="junit-4" +JAVA_TEST_SRC_DIR="src/test/java" diff --git a/dev-java/scijava-table/Manifest b/dev-java/scijava-table/Manifest new file mode 100644 index 000000000..ba3cb11b6 --- /dev/null +++ b/dev-java/scijava-table/Manifest @@ -0,0 +1 @@ +DIST scijava-table-1.0.2-sources.tar.gz 37037 BLAKE2B 61a6b2da5cb355e00feb49895ae1a9a978ba50ee75e60c4f74d1490d1c167ca3a19452621ba25afccc975f4fbf3636ae09c0d25019e04980c4247fc18d859951 SHA512 17bbb1f798f7ee718fd2fbd9f9c81419cb5054b40d82cac9fa3b9f882e9ba46b410979038d8031d6f6dea53902f0865e68d59e55e1b02ab717da40aed5726b70 diff --git a/dev-java/scijava-table/metadata.xml b/dev-java/scijava-table/metadata.xml new file mode 100644 index 000000000..d86e34de2 --- /dev/null +++ b/dev-java/scijava-table/metadata.xml @@ -0,0 +1,11 @@ +<?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> + <upstream> + <remote-id type="github">scijava/scijava-table</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-java/scijava-table/scijava-table-1.0.2.ebuild b/dev-java/scijava-table/scijava-table-1.0.2.ebuild new file mode 100644 index 000000000..c2e06ac37 --- /dev/null +++ b/dev-java/scijava-table/scijava-table-1.0.2.ebuild @@ -0,0 +1,54 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +JAVA_PKG_IUSE="doc source test" +JAVA_TESTING_FRAMEWORKS="junit-4" + +inherit java-pkg-2 java-pkg-simple + +DESCRIPTION="Table structures for SciJava." +HOMEPAGE="https://github.com/scijava/scijava-table" + +if [[ ${PV} == 9999 ]]; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/scijava/scijava-table.git" + S="${WORKDIR}/${P}" + MAVEN_ID="org.scijava:scijava-table:9999" +else + SRC_URI=" + https://github.com/scijava/${PN}/archive/refs/tags/${P}.tar.gz -> ${P}-sources.tar.gz + " + S="${WORKDIR}/${PN}-${P}" + MAVEN_ID="org.scijava:scijava-table:1.0.3" + KEYWORDS="~amd64" +fi + +LICENSE="BSD-2" +SLOT="0" + +CDEPEND=" + >=dev-java/scijava-common-2.89.0:0 + >=dev-java/scijava-optional-1.0.1:0 +" + +BDEPEND=" + >=virtual/jdk-1.8:* + ${CDEPEND} + test? ( >=dev-java/junit-4.13.2:4 ) +" + +DEPEND="${CDEPEND}" + +RDEPEND=" + >=virtual/jre-1.8:* + ${CDEPEND} +" + +JAVA_GENTOO_CLASSPATH="scijava-common,scijava-optional" +JAVA_SRC_DIR="src/main/java" +JAVA_MAIN_CLASS="" + +JAVA_TEST_GENTOO_CLASSPATH="junit-4" +JAVA_TEST_SRC_DIR="src/test/java" diff --git a/dev-java/scijava-table/scijava-table-9999.ebuild b/dev-java/scijava-table/scijava-table-9999.ebuild new file mode 100644 index 000000000..c2e06ac37 --- /dev/null +++ b/dev-java/scijava-table/scijava-table-9999.ebuild @@ -0,0 +1,54 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +JAVA_PKG_IUSE="doc source test" +JAVA_TESTING_FRAMEWORKS="junit-4" + +inherit java-pkg-2 java-pkg-simple + +DESCRIPTION="Table structures for SciJava." +HOMEPAGE="https://github.com/scijava/scijava-table" + +if [[ ${PV} == 9999 ]]; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/scijava/scijava-table.git" + S="${WORKDIR}/${P}" + MAVEN_ID="org.scijava:scijava-table:9999" +else + SRC_URI=" + https://github.com/scijava/${PN}/archive/refs/tags/${P}.tar.gz -> ${P}-sources.tar.gz + " + S="${WORKDIR}/${PN}-${P}" + MAVEN_ID="org.scijava:scijava-table:1.0.3" + KEYWORDS="~amd64" +fi + +LICENSE="BSD-2" +SLOT="0" + +CDEPEND=" + >=dev-java/scijava-common-2.89.0:0 + >=dev-java/scijava-optional-1.0.1:0 +" + +BDEPEND=" + >=virtual/jdk-1.8:* + ${CDEPEND} + test? ( >=dev-java/junit-4.13.2:4 ) +" + +DEPEND="${CDEPEND}" + +RDEPEND=" + >=virtual/jre-1.8:* + ${CDEPEND} +" + +JAVA_GENTOO_CLASSPATH="scijava-common,scijava-optional" +JAVA_SRC_DIR="src/main/java" +JAVA_MAIN_CLASS="" + +JAVA_TEST_GENTOO_CLASSPATH="junit-4" +JAVA_TEST_SRC_DIR="src/test/java" diff --git a/dev-lang/conceptual/Manifest b/dev-lang/conceptual/Manifest deleted file mode 100644 index e981b3cd2..000000000 --- a/dev-lang/conceptual/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST conceptual-1.5.1b.tar.gz 5416709 BLAKE2B 9ac64c9e509613b3dcafa80a05d295845644b58b09797a4c9ee046b26969b7222648c93d9950e906e586195f2b5eecc7392be7b69ffd3e28d624c79ca0f2099e SHA512 08aab08cbbc56be54ef0ffbaf6acbe5013c312e62451e97faf3278f1a63a015a9b5f20d21899c9d125522331731e60fb17208c446640cc5d2bae622ea714d82d diff --git a/dev-lang/conceptual/conceptual-1.5.1b.ebuild b/dev-lang/conceptual/conceptual-1.5.1b.ebuild deleted file mode 100644 index 53cfee813..000000000 --- a/dev-lang/conceptual/conceptual-1.5.1b.ebuild +++ /dev/null @@ -1,43 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7,8,9} ) -JAVA_PKG_OPT_USE="gui" - -inherit java-pkg-opt-2 python-single-r1 - -DESCRIPTION="A Network Correctness and Performance Testing Language" -HOMEPAGE="http://conceptual.sourceforge.net/" -SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz" - -SLOT="0" -LICENSE="BSD-2" -IUSE="gui" -KEYWORDS="~amd64" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND=" - virtual/mpi - ${PYTHON_DEPS} - gui? ( - virtual/jdk:* - dev-java/jython - )" -DEPEND="${RDEPEND}" - -src_compile() { - default - use gui && emake gui -} - -src_install () { - default - if use gui; then - java-pkg_newjar gui/ncptlGUI-1.5.1b.jar ${PN}.jar - java-pkg_dolauncher - fi - python_optimize -} diff --git a/dev-lang/conceptual/metadata.xml b/dev-lang/conceptual/metadata.xml deleted file mode 100644 index c73b3a9fa..000000000 --- a/dev-lang/conceptual/metadata.xml +++ /dev/null @@ -1,14 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>ottxor@gentoo.org</email> - <name>Christoph Junghans</name> - </maintainer> - <use> - <flag name="gui">Build the Java base graphical interface</flag> - </use> - <upstream> - <remote-id type="sourceforge">conceptual</remote-id> - </upstream> -</pkgmetadata> diff --git a/dev-lang/icc/Manifest b/dev-lang/icc/Manifest deleted file mode 100644 index 0007a0681..000000000 --- a/dev-lang/icc/Manifest +++ /dev/null @@ -1,3 +0,0 @@ -DIST parallel_studio_xe_2018_update2_professional_edition.tgz 3877755304 BLAKE2B c8852df23abf080f482002a37af7781b3fbae3ecec448914ea5a237fa2b925073d1a3dc2dd94ba64002ff0f6c7e9b18b25fa7ada811a83b10344eb9b92cb37ff SHA512 a9b644b0305d83a9d0daa14d146cb3ce79949db55a410afe48d62259414e6256d9ef533a04bb50807103511db2016c4abcbbf769146854a25638f402a6d0f2be -DIST parallel_studio_xe_2019_update4_professional_edition.tgz 2629662464 BLAKE2B a5619f33535063ccd7310378504ca960aa8512527cef7e0884fae5570633c1823e50ff7135adbbc571b4d47e0b6fcc01afe8639e09feb50a7f289eeec3f61ca0 SHA512 d8f6780a3671f30a1bad5d3a9792062c73b31188dc31fbd38212e98abc593f1c8f64bb970a8a4fce9ce237afef18ed38adf8fd81aa73b63ec964224590d4a34d -DIST parallel_studio_xe_2020_update1_professional_edition.tgz 2783012958 BLAKE2B 975103ec4551a0e3bd84034ce771a5fc459d5de47f4247b5915b54d9c827e50e913f9054a103424b764f730190675d42b52a97e68551b34df6b3d8d9b922517a SHA512 00a3334bcdb8b30216ecb40fcfc709b27d043697606a53f522c90b05cf8598e1e60311d629ec17b6fe1016a7d2a27f4b428abddc9eba39badebfd8a9b53de404 diff --git a/dev-lang/icc/icc-18.0.2.199-r1.ebuild b/dev-lang/icc/icc-18.0.2.199-r1.ebuild deleted file mode 100644 index 84641de62..000000000 --- a/dev-lang/icc/icc-18.0.2.199-r1.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 - -INTEL_DIST_SKU=3235 -INTEL_DIST_PV=2018_update2_professional_edition - -inherit intel-sdp-r1 - -DESCRIPTION="Intel C/C++ Compiler" -HOMEPAGE="http://software.intel.com/en-us/articles/intel-composer-xe/" - -IUSE="doc" -KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux" - -# avoid file collision with ifc #476330 -RDEPEND="~dev-libs/intel-common-${PV}[compiler]" - -CHECKREQS_DISK_BUILD=500M - -INTEL_DIST_DAT_RPMS=( - "icc-common-18.0.2-199-18.0.2-199.noarch.rpm" - "icc-common-ps-18.0.2-199-18.0.2-199.noarch.rpm" - "icc-common-ps-ss-bec-18.0.2-199-18.0.2-199.noarch.rpm") -INTEL_DIST_AMD64_RPMS=( - "icc-18.0.2-199-18.0.2-199.x86_64.rpm" - "icc-ps-18.0.2-199-18.0.2-199.x86_64.rpm" - "icc-ps-ss-18.0.2-199-18.0.2-199.x86_64.rpm" - "icc-ps-ss-bec-18.0.2-199-18.0.2-199.x86_64.rpm") -INTEL_DIST_X86_RPMS=( - "icc-32bit-18.0.2-199-18.0.2-199.x86_64.rpm" - "icc-ps-ss-bec-32bit-18.0.2-199-18.0.2-199.x86_64.rpm") - -pkg_setup() { - if use doc; then - INTEL_DIST_DAT_RPMS+=( - "icc-doc-18.0-18.0.2-199.noarch.rpm" - "icc-doc-ps-18.0-18.0.2-199.noarch.rpm") - fi -} diff --git a/dev-lang/icc/icc-19.0.4.243.ebuild b/dev-lang/icc/icc-19.0.4.243.ebuild deleted file mode 100644 index 9a166f221..000000000 --- a/dev-lang/icc/icc-19.0.4.243.ebuild +++ /dev/null @@ -1,40 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -INTEL_DIST_PV=2019_update4_professional_edition - -inherit intel-sdp-r1 - -DESCRIPTION="Intel C/C++ Compiler" -HOMEPAGE="http://software.intel.com/en-us/articles/intel-composer-xe/" - -IUSE="doc" -KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux" - -# avoid file collision with ifc #476330 -RDEPEND="~dev-libs/intel-common-${PV}[compiler]" - -CHECKREQS_DISK_BUILD=500M - -INTEL_DIST_DAT_RPMS=( - "icc-common-19.0.4-243-19.0.4-243.noarch.rpm" - "icc-common-ps-19.0.4-243-19.0.4-243.noarch.rpm" - "icc-common-ps-ss-bec-19.0.4-243-19.0.4-243.noarch.rpm") -INTEL_DIST_AMD64_RPMS=( - "icc-19.0.4-243-19.0.4-243.x86_64.rpm" - "icc-ps-19.0.4-243-19.0.4-243.x86_64.rpm" - "icc-ps-ss-bec-19.0.4-243-19.0.4-243.x86_64.rpm") - -INTEL_DIST_X86_RPMS=( - "icc-32bit-19.0.4-243-19.0.4-243.x86_64.rpm" - "icc-ps-ss-bec-32bit-19.0.4-243-19.0.4-243.x86_64.rpm") - -pkg_setup() { - if use doc; then - INTEL_DIST_DAT_RPMS+=( - "icc-doc-19.0-19.0.4-243.noarch.rpm" - "icc-doc-ps-19.0-19.0.4-243.noarch.rpm") - fi -} diff --git a/dev-lang/icc/icc-19.1.1.217.ebuild b/dev-lang/icc/icc-19.1.1.217.ebuild deleted file mode 100644 index 226b9c784..000000000 --- a/dev-lang/icc/icc-19.1.1.217.ebuild +++ /dev/null @@ -1,41 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -INTEL_DIST_PV=2020_update1_professional_edition - -inherit intel-sdp-r1 - -DESCRIPTION="Intel C/C++ Compiler" -HOMEPAGE="http://software.intel.com/en-us/articles/intel-composer-xe/" - -IUSE="doc" -KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux" - -RDEPEND="~dev-libs/intel-common-${PV}[compiler]" - -CHECKREQS_DISK_BUILD=500M - -MY_PV="$(ver_rs 3 '-')" # 20.1.0-607630 - -QA_PREBUILT="*" - -INTEL_DIST_DAT_RPMS=( - "icc-common-${MY_PV}-${MY_PV}.noarch.rpm" - "icc-common-ps-${MY_PV}-${MY_PV}.noarch.rpm" - "idesupport-icc-common-ps-19.1-${MY_PV}.noarch.rpm") -INTEL_DIST_AMD64_RPMS=( - "icc-${MY_PV}-${MY_PV}.x86_64.rpm" - "icc-ps-${MY_PV}-${MY_PV}.x86_64.rpm" - "icc-ps-ss-bec-${MY_PV}-${MY_PV}.x86_64.rpm") - -INTEL_DIST_X86_RPMS=( - "icc-32bit-${MY_PV}-${MY_PV}.x86_64.rpm" - "icc-ps-ss-bec-32bit-${MY_PV}-${MY_PV}.x86_64.rpm") - -pkg_setup() { - if use doc; then - INTEL_DIST_DAT_RPMS+=( "icc-doc-19.1-${MY_PV}.noarch.rpm" ) - fi -} diff --git a/dev-lang/icc/metadata.xml b/dev-lang/icc/metadata.xml deleted file mode 100644 index 7c4d1a96d..000000000 --- a/dev-lang/icc/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"> -The Intel® C++ Compiler is a full featured C/C++ compiler for Intel -based architectures. The compiler supports multi-threading, automatic -processor dispatch, vectorization, auto-parallelization, OpenMP, data -prefetching, loop unrolling. The package comes with extensive -documentation. The product can be installed as a non-commercial as -well. License, terms of qualifications can be found on the web site. -</longdescription> -</pkgmetadata> diff --git a/dev-lang/ifc/Manifest b/dev-lang/ifc/Manifest deleted file mode 100644 index 0007a0681..000000000 --- a/dev-lang/ifc/Manifest +++ /dev/null @@ -1,3 +0,0 @@ -DIST parallel_studio_xe_2018_update2_professional_edition.tgz 3877755304 BLAKE2B c8852df23abf080f482002a37af7781b3fbae3ecec448914ea5a237fa2b925073d1a3dc2dd94ba64002ff0f6c7e9b18b25fa7ada811a83b10344eb9b92cb37ff SHA512 a9b644b0305d83a9d0daa14d146cb3ce79949db55a410afe48d62259414e6256d9ef533a04bb50807103511db2016c4abcbbf769146854a25638f402a6d0f2be -DIST parallel_studio_xe_2019_update4_professional_edition.tgz 2629662464 BLAKE2B a5619f33535063ccd7310378504ca960aa8512527cef7e0884fae5570633c1823e50ff7135adbbc571b4d47e0b6fcc01afe8639e09feb50a7f289eeec3f61ca0 SHA512 d8f6780a3671f30a1bad5d3a9792062c73b31188dc31fbd38212e98abc593f1c8f64bb970a8a4fce9ce237afef18ed38adf8fd81aa73b63ec964224590d4a34d -DIST parallel_studio_xe_2020_update1_professional_edition.tgz 2783012958 BLAKE2B 975103ec4551a0e3bd84034ce771a5fc459d5de47f4247b5915b54d9c827e50e913f9054a103424b764f730190675d42b52a97e68551b34df6b3d8d9b922517a SHA512 00a3334bcdb8b30216ecb40fcfc709b27d043697606a53f522c90b05cf8598e1e60311d629ec17b6fe1016a7d2a27f4b428abddc9eba39badebfd8a9b53de404 diff --git a/dev-lang/ifc/ifc-18.0.2.199-r1.ebuild b/dev-lang/ifc/ifc-18.0.2.199-r1.ebuild deleted file mode 100644 index f37dd5491..000000000 --- a/dev-lang/ifc/ifc-18.0.2.199-r1.ebuild +++ /dev/null @@ -1,40 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -INTEL_DIST_SKU=3235 -INTEL_DIST_PV=2018_update2_professional_edition - -inherit intel-sdp-r1 - -DESCRIPTION="Intel FORTRAN Compiler" -HOMEPAGE="http://software.intel.com/en-us/articles/intel-composer-xe/" - -IUSE="doc" -KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux" - -RDEPEND="~dev-libs/intel-common-${PV}[compiler]" - -CHECKREQS_DISK_BUILD=400M - -INTEL_DIST_DAT_RPMS=( "ifort-common-18.0.2-199-18.0.2-199.noarch.rpm" ) -INTEL_DIST_X86_RPMS=( "ifort-32bit-18.0.2-199-18.0.2-199.x86_64.rpm" ) -INTEL_DIST_AMD64_RPMS=( "ifort-18.0.2-199-18.0.2-199.x86_64.rpm" ) - -pkg_setup() { - if use doc; then - INTEL_DIST_DAT_RPMS+=( "ifort-doc-18.0-18.0.2-199.noarch.rpm" ) - fi -} - -src_install() { - # already provided in dev-libs/intel-common - rm \ - "${WORKDIR}"/opt/intel/compilers_and_libraries_2018.2.199/linux/compiler/include/omp_lib.f90 \ - "${WORKDIR}"/opt/intel/compilers_and_libraries_2018.2.199/linux/compiler/include/intel64/omp_lib.mod \ - "${WORKDIR}"/opt/intel/compilers_and_libraries_2018.2.199/linux/compiler/include/intel64/omp_lib_kinds.mod \ - || die "rm failed" - - intel-sdp-r1_src_install -} diff --git a/dev-lang/ifc/ifc-19.0.4.243.ebuild b/dev-lang/ifc/ifc-19.0.4.243.ebuild deleted file mode 100644 index a45765a2f..000000000 --- a/dev-lang/ifc/ifc-19.0.4.243.ebuild +++ /dev/null @@ -1,39 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -INTEL_DIST_PV=2019_update4_professional_edition - -inherit intel-sdp-r1 - -DESCRIPTION="Intel FORTRAN Compiler" -HOMEPAGE="http://software.intel.com/en-us/articles/intel-composer-xe/" - -IUSE="doc" -KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux" - -RDEPEND="~dev-libs/intel-common-${PV}[compiler]" - -CHECKREQS_DISK_BUILD=400M - -INTEL_DIST_DAT_RPMS=( "ifort-common-19.0.4-243-19.0.4-243.noarch.rpm" ) -INTEL_DIST_AMD64_RPMS=( "ifort-19.0.4-243-19.0.4-243.x86_64.rpm" ) -INTEL_DIST_X86_RPMS=( "ifort-32bit-19.0.4-243-19.0.4-243.x86_64.rpm" ) - -pkg_setup() { - if use doc; then - INTEL_DIST_DAT_RPMS+=( "ifort-doc-19.0-19.0.4-243.noarch.rpm" ) - fi -} - -src_install() { - # already provided in dev-libs/intel-common - rm \ - "${WORKDIR}"/opt/intel/compilers_and_libraries_2019.4.243/linux/compiler/include/omp_lib.f90 \ - "${WORKDIR}"/opt/intel/compilers_and_libraries_2019.4.243/linux/compiler/include/intel64/omp_lib.mod \ - "${WORKDIR}"/opt/intel/compilers_and_libraries_2019.4.243/linux/compiler/include/intel64/omp_lib_kinds.mod \ - || die "rm failed" - - intel-sdp-r1_src_install -} diff --git a/dev-lang/ifc/ifc-19.1.1.217.ebuild b/dev-lang/ifc/ifc-19.1.1.217.ebuild deleted file mode 100644 index 4157a3eec..000000000 --- a/dev-lang/ifc/ifc-19.1.1.217.ebuild +++ /dev/null @@ -1,43 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -INTEL_DIST_PV=2020_update1_professional_edition - -inherit intel-sdp-r1 - -DESCRIPTION="Intel FORTRAN Compiler" -HOMEPAGE="http://software.intel.com/en-us/articles/intel-composer-xe/" - -IUSE="doc" -KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux" - -RDEPEND="~dev-libs/intel-common-${PV}[compiler]" - -MY_PV="$(ver_rs 3 '-')" # 20.1.0-607630 - -QA_PREBUILT="*" - -CHECKREQS_DISK_BUILD=400M - -INTEL_DIST_DAT_RPMS=( "ifort-common-${MY_PV}-${MY_PV}.noarch.rpm" ) -INTEL_DIST_AMD64_RPMS=( "ifort-${MY_PV}-${MY_PV}.x86_64.rpm" ) -INTEL_DIST_X86_RPMS=( "ifort-32bit-${MY_PV}-${MY_PV}.x86_64.rpm" ) - -pkg_setup() { - if use doc; then - INTEL_DIST_DAT_RPMS+=( "ifort-doc-19.1-${MY_PV}.noarch.rpm" ) - fi -} - -src_install() { - # already provided in dev-libs/intel-common - rm \ - "${WORKDIR}"/opt/intel/compilers_and_libraries_2020.1.217/linux/compiler/include/omp_lib.f90 \ - "${WORKDIR}"/opt/intel/compilers_and_libraries_2020.1.217/linux/compiler/include/intel64/omp_lib.mod \ - "${WORKDIR}"/opt/intel/compilers_and_libraries_2020.1.217/linux/compiler/include/intel64/omp_lib_kinds.mod \ - || die "rm failed" - - intel-sdp-r1_src_install -} diff --git a/dev-lang/ifc/metadata.xml b/dev-lang/ifc/metadata.xml deleted file mode 100644 index 0cc12d890..000000000 --- a/dev-lang/ifc/metadata.xml +++ /dev/null @@ -1,17 +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 Intel® Fortran Compiler is a full featured FORTRAN 77/95 and -substantial FORTRAN 2003 compiler for Intel based architectures. The -compiler supports multi-threading with automatic processor dispatch, -vectorization, auto-parallelization, OpenMP, data prefetching, loop -unrolling. The package comes with extensive documentation. -The product can be installed as a non-commercial as well. License, -terms of qualifications can be found on the web site. -</longdescription> -</pkgmetadata> diff --git a/dev-lang/pgi/Manifest b/dev-lang/pgi/Manifest deleted file mode 100644 index 27c00897e..000000000 --- a/dev-lang/pgi/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST pgilinux-2013-135.tar.gz 949594228 SHA256 94dc015b5758486905643a729f7ece5c68038667385cbd08406b8799fcf9a22c SHA512 1bbd26f14c6757677c30fc2f4598f2b26072d34f0fe90a8914b55b0e52472adc1d342398372581ee9eef43480b5207d7998322f9621d0993f0a82d9055b7a5c6 WHIRLPOOL ad299eb206748f921ab826093a2a728ea100b0b51f2eca30562a956ed5885791c1b6465d3877586e626bb3ba6d397e6cd0d13e8bc736f2ccbf64e2e5601e7d8f diff --git a/dev-lang/pgi/files/pgi-13.5-glibc.patch b/dev-lang/pgi/files/pgi-13.5-glibc.patch deleted file mode 100644 index 434f12cb5..000000000 --- a/dev-lang/pgi/files/pgi-13.5-glibc.patch +++ /dev/null @@ -1,31 +0,0 @@ -diff -ru opt/pgi/linux86/13.5/include/bits/types.h opt/pgi-b/linux86/13.5/include/bits/types.h ---- opt/pgi/linux86/13.5/include/bits/types.h 2013-05-07 21:45:39.000000000 +0200 -+++ opt/pgi-b/linux86/13.5/include/bits/types.h 2013-06-02 01:24:19.000000000 +0200 -@@ -136,6 +136,7 @@ - #include <bits/typesizes.h> /* Defines __*_T_TYPE macros. */ - - -+__STD_TYPE __SQUAD_TYPE __syscall_slong_t; - __STD_TYPE __DEV_T_TYPE __dev_t; /* Type of device numbers. */ - __STD_TYPE __UID_T_TYPE __uid_t; /* Type of user identifications. */ - __STD_TYPE __GID_T_TYPE __gid_t; /* Type of group identifications. */ -diff -ru opt/pgi/linux86-64/13.5/include/bits/types.h opt/pgi-b/linux86-64/13.5/include/bits/types.h ---- opt/pgi/linux86-64/13.5/include/bits/types.h 2013-05-07 21:45:39.000000000 +0200 -+++ opt/pgi-b/linux86-64/13.5/include/bits/types.h 2013-06-02 01:23:51.000000000 +0200 -@@ -135,7 +135,7 @@ - #endif - #include <bits/typesizes.h> /* Defines __*_T_TYPE macros. */ - -- -+__STD_TYPE __SQUAD_TYPE __syscall_slong_t; - __STD_TYPE __DEV_T_TYPE __dev_t; /* Type of device numbers. */ - __STD_TYPE __UID_T_TYPE __uid_t; /* Type of user identifications. */ - __STD_TYPE __GID_T_TYPE __gid_t; /* Type of group identifications. */ -@@ -156,7 +156,6 @@ - __STD_TYPE __SUSECONDS_T_TYPE __suseconds_t; /* Signed count of microseconds. */ - - __STD_TYPE __DADDR_T_TYPE __daddr_t; /* The type of a disk address. */ --__STD_TYPE __SWBLK_T_TYPE __swblk_t; /* Type of a swap block maybe? */ - __STD_TYPE __KEY_T_TYPE __key_t; /* Type of an IPC key. */ - - /* Clock ID used in clock and timer functions. */ diff --git a/dev-lang/pgi/files/pgi-13.5-terminal.patch b/dev-lang/pgi/files/pgi-13.5-terminal.patch deleted file mode 100644 index 9b5b67474..000000000 --- a/dev-lang/pgi/files/pgi-13.5-terminal.patch +++ /dev/null @@ -1,39 +0,0 @@ -diff -ru pgi-a/install pgi/install ---- pgi-a/install 2013-06-01 01:24:11.522714654 +0200 -+++ pgi/install 2013-06-01 01:27:36.372713265 +0200 -@@ -83,7 +83,7 @@ - else - licensefile=$SRC/common/BETA_LICENSE - fi --more $licensefile -+#more $licensefile - echo - echo -n 'Do you accept these terms? (accept,decline) ' - read x -@@ -296,7 +296,7 @@ - echo - echo 'In order to install the ACML software, please read and accept the' - echo 'following license.' -- more $SRC/common/LICENSE_ACML.txt -+ #more $SRC/common/LICENSE_ACML.txt - echo - echo -n 'Do you accept these terms? (accept,decline) ' - read x -@@ -342,7 +342,7 @@ - echo - echo 'In order to install the CUDA software, please read and accept the' - echo 'following license.' -- more $SRC/common/LICENSE_NVIDIA_CUDA.txt -+ #more $SRC/common/LICENSE_NVIDIA_CUDA.txt - echo - echo -n 'Do you accept these terms? (accept,decline) ' - read x -@@ -398,7 +398,7 @@ - echo - echo 'In order to install the JAVA software, please read and accept the' - echo 'following license.' -- more $SRC/common/LICENSE_JRE_6U21.txt -+ #more $SRC/common/LICENSE_JRE_6U21.txt - echo - echo -n 'Do you accept these terms? (accept,decline) ' - read x diff --git a/dev-lang/pgi/metadata.xml b/dev-lang/pgi/metadata.xml deleted file mode 100644 index b9e493f21..000000000 --- a/dev-lang/pgi/metadata.xml +++ /dev/null @@ -1,15 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>gentryx@gmx.de</email> - </maintainer> - <maintainer type="project"> - <email>cluster@gentoo.org</email> - <name>Gentoo Cluster Project</name> - </maintainer> - <use> - <flag name="java">Install a PGI-tuned JRE.</flag> - <flag name="cuda">Install PGI's CUDA components (e.g. for OpenACC)</flag> - </use> -</pkgmetadata> diff --git a/dev-lang/pgi/pgi-13.5.ebuild b/dev-lang/pgi/pgi-13.5.ebuild deleted file mode 100644 index 19ec7445b..000000000 --- a/dev-lang/pgi/pgi-13.5.ebuild +++ /dev/null @@ -1,105 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DESCRIPTION="PGI compiler suite" -HOMEPAGE="https://www.pgroup.com" -SRC_URI="pgilinux-2013-135.tar.gz" - -LICENSE="PGI" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="cuda java" - -RDEPEND="net-misc/curl" - -RESTRICT="mirror strip fetch" - -QA_PREBUILT=" - opt/pgi/linux86/2013/cuda/4.2/lib/lib*.so.* - opt/pgi/linux86-64/13.5/bin/* - opt/pgi/linux86-64/13.5/lib/lib* - opt/pgi/linux86-64/13.5/lib/*.o - opt/pgi/linux86-64/13.5/libso/lib* - opt/pgi/linux86-64/13.5/libso/*.o - opt/pgi/linux86-64/13.5/cray/lib* - opt/pgi/linux86-64/13.5/etc/pgi_license_tool/curl - opt/pgi/linux86-64/13.5/REDIST/lib*.so - opt/pgi/linux86-64/2013/cuda/5.0/nvvm/cicc - opt/pgi/linux86-64/2013/cuda/4.2/nvvm/cicc - opt/pgi/linux86-64/2013/acml/5.3.0/lib/lib* - opt/pgi/linux86-64/2013/acml/5.3.0/libso/lib*.so - opt/pgi/linux86/13.5/etc/pgi_license_tool/curl - opt/pgi/linux86/13.5/bin/* - opt/pgi/linux86/13.5/lib/lib* - opt/pgi/linux86/13.5/lib/*.o - opt/pgi/linux86/13.5/libso/lib* - opt/pgi/linux86/13.5/cray/lib* - opt/pgi/linux86/2013/cuda/5.0/nvvm/cicc - opt/pgi/linux86/2013/cuda/4.2/nvvm/cicc - opt/pgi/linux86/2013/acml/4.4.0/lib/lib* - opt/pgi/linux86/2013/acml/4.4.0/libso/lib*.so -" - -S="${WORKDIR}" - -PATCHES=( "${FILESDIR}"/${P}-terminal.patch ) - -pkg_nofetch() { - einfo "PGI doesn't provide direct download links. Please download" - einfo "${ARCHIVE} from ${HOMEPAGE}" -} - -src_install() { - dodir /opt/pgi - - command="accept -1 -${ED}/opt/pgi" - - command="${command} -n" - - if use cuda; then - command="${command} -y -accept" - else - command="${command} -n" - fi - - if use java; then - command="${command} - -accept" - else - command="${command} -no" - fi - - command="${command} -y -n -n -y -" - ./install <<EOF -${command} -EOF - # fix problems with PGI's C++ compiler and current glibc: - cd "${ED}" - epatch "${FILESDIR}/${P}-glibc.patch" - - # java symlink might be broken if useflag is disabled: - if ! use java; then - rm opt/pgi/linux86-64/13.5/jre || die - fi - - # replace PGI's curl with the stock version: - dodir /opt/pgi/linux86-64/13.5/etc/pgi_license_tool - dosym ../../../../../../usr/bin/curl /opt/pgi/linux86-64/13.5/etc/pgi_license_tool/curl - dodir /opt/pgi/linux86/13.5/etc/pgi_license_tool - dosym ../../../../../../usr/bin/curl /opt/pgi/linux86/13.5/etc/pgi_license_tool/curl -} diff --git a/dev-lang/vtune/Manifest b/dev-lang/vtune/Manifest deleted file mode 100644 index 0007a0681..000000000 --- a/dev-lang/vtune/Manifest +++ /dev/null @@ -1,3 +0,0 @@ -DIST parallel_studio_xe_2018_update2_professional_edition.tgz 3877755304 BLAKE2B c8852df23abf080f482002a37af7781b3fbae3ecec448914ea5a237fa2b925073d1a3dc2dd94ba64002ff0f6c7e9b18b25fa7ada811a83b10344eb9b92cb37ff SHA512 a9b644b0305d83a9d0daa14d146cb3ce79949db55a410afe48d62259414e6256d9ef533a04bb50807103511db2016c4abcbbf769146854a25638f402a6d0f2be -DIST parallel_studio_xe_2019_update4_professional_edition.tgz 2629662464 BLAKE2B a5619f33535063ccd7310378504ca960aa8512527cef7e0884fae5570633c1823e50ff7135adbbc571b4d47e0b6fcc01afe8639e09feb50a7f289eeec3f61ca0 SHA512 d8f6780a3671f30a1bad5d3a9792062c73b31188dc31fbd38212e98abc593f1c8f64bb970a8a4fce9ce237afef18ed38adf8fd81aa73b63ec964224590d4a34d -DIST parallel_studio_xe_2020_update1_professional_edition.tgz 2783012958 BLAKE2B 975103ec4551a0e3bd84034ce771a5fc459d5de47f4247b5915b54d9c827e50e913f9054a103424b764f730190675d42b52a97e68551b34df6b3d8d9b922517a SHA512 00a3334bcdb8b30216ecb40fcfc709b27d043697606a53f522c90b05cf8598e1e60311d629ec17b6fe1016a7d2a27f4b428abddc9eba39badebfd8a9b53de404 diff --git a/dev-lang/vtune/metadata.xml b/dev-lang/vtune/metadata.xml deleted file mode 100644 index 718cc299c..000000000 --- a/dev-lang/vtune/metadata.xml +++ /dev/null @@ -1,15 +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 Intel® VTuneâ„¢ Profiler collects key profiling data and presents -it with a powerful interface that simplifies its analysis and -interpretation. The package comes with extensive documentation. The -product can be installed as a non-commercial as well. License, terms -of qualifications can be found on the web site. -</longdescription> -</pkgmetadata> diff --git a/dev-lang/vtune/vtune-18.0.2.0.551022.ebuild b/dev-lang/vtune/vtune-18.0.2.0.551022.ebuild deleted file mode 100644 index 9ec0beef6..000000000 --- a/dev-lang/vtune/vtune-18.0.2.0.551022.ebuild +++ /dev/null @@ -1,49 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -INTEL_DIST_SKU=3235 -INTEL_DIST_PV=2018_update2_professional_edition -INTEL_SUBDIR=vtune_amplifier - -inherit intel-sdp-r1 - -DESCRIPTION="Intel VTune Amplifier XE" -HOMEPAGE="http://software.intel.com/en-us/articles/intel-vtune-amplifier-xe/" - -IUSE="doc" -KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux" - -RDEPEND="~dev-libs/intel-common-18.0.2.199[compiler]" - -INTEL_DIST_DAT_RPMS=( - "vtune-amplifier-2018-cli-common-2018.2-551022.noarch.rpm" - "vtune-amplifier-2018-common-2018.2-551022.noarch.rpm" - "vtune-amplifier-2018-common-pset-2018.2-551022.noarch.rpm" - "vtune-amplifier-2018-gui-common-2018.2-551022.noarch.rpm" - "vtune-amplifier-2018-sep-2018.2-551022.noarch.rpm" - "vtune-amplifier-2018-target-2018.2-551022.noarch.rpm") -INTEL_DIST_AMD64_RPMS=( - "vtune-amplifier-2018-cli-2018.2-551022.x86_64.rpm" - "vtune-amplifier-2018-collector-64linux-2018.2-551022.x86_64.rpm" - "vtune-amplifier-2018-gui-2018.2-551022.x86_64.rpm") -INTEL_DIST_X86_RPMS=( - "vtune-amplifier-2018-cli-32bit-2018.2-551022.i486.rpm" - "vtune-amplifier-2018-collector-32linux-2018.2-551022.i486.rpm") - -pkg_setup() { - if use doc; then - INTEL_DIST_DAT_RPMS+=( "vtune-amplifier-2018-doc-2018.2-551022.noarch.rpm" ) - fi -} - -src_install() { - intel-sdp-r1_src_install - - local path="PATH=" - use abi_x86_64 && path+=":$(isdp_get-sdp-edir)/bin64" - use abi_x86_32 && path+=":$(isdp_get-sdp-edir)/bin32" - echo "${path}" > "${T}"/35vtune || die - doenvd "${T}"/35vtune -} diff --git a/dev-lang/vtune/vtune-19.0.4.0.597835.ebuild b/dev-lang/vtune/vtune-19.0.4.0.597835.ebuild deleted file mode 100644 index e090c10b7..000000000 --- a/dev-lang/vtune/vtune-19.0.4.0.597835.ebuild +++ /dev/null @@ -1,48 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -INTEL_DIST_PV=2019_update4_professional_edition -INTEL_SUBDIR=vtune_amplifier - -inherit intel-sdp-r1 - -DESCRIPTION="Intel VTune Amplifier XE" -HOMEPAGE="http://software.intel.com/en-us/articles/intel-vtune-amplifier-xe/" - -IUSE="doc" -KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux" - -RDEPEND="~dev-libs/intel-common-19.0.4.243[compiler]" - -INTEL_DIST_DAT_RPMS=( - "vtune-amplifier-2019-cli-common-2019.4-597835.noarch.rpm" - "vtune-amplifier-2019-common-2019.4-597835.noarch.rpm" - "vtune-amplifier-2019-common-pset-2019.4-597835.noarch.rpm" - "vtune-amplifier-2019-gui-common-2019.4-597835.noarch.rpm" - "vtune-amplifier-2019-sep-2019.4-597835.noarch.rpm" - "vtune-amplifier-2019-target-2019.4-597835.noarch.rpm") -INTEL_DIST_AMD64_RPMS=( - "vtune-amplifier-2019-cli-2019.4-597835.x86_64.rpm" - "vtune-amplifier-2019-collector-64linux-2019.4-597835.x86_64.rpm" - "vtune-amplifier-2019-gui-2019.4-597835.x86_64.rpm") -INTEL_DIST_X86_RPMS=( - "vtune-amplifier-2019-cli-32bit-2019.4-597835.i486.rpm" - "vtune-amplifier-2019-collector-32linux-2019.4-597835.i486.rpm") - -pkg_setup() { - if use doc; then - INTEL_DIST_DAT_RPMS+=( "vtune-amplifier-2019-doc-2019.4-597835.noarch.rpm" ) - fi -} - -src_install() { - intel-sdp-r1_src_install - - local path="PATH=" - use abi_x86_64 && path+=":$(isdp_get-sdp-edir)/bin64" - use abi_x86_32 && path+=":$(isdp_get-sdp-edir)/bin32" - echo "${path}" > "${T}"/35vtune || die - doenvd "${T}"/35vtune -} diff --git a/dev-lang/vtune/vtune-2020.1.0.607630.ebuild b/dev-lang/vtune/vtune-2020.1.0.607630.ebuild deleted file mode 100644 index e1ec58882..000000000 --- a/dev-lang/vtune/vtune-2020.1.0.607630.ebuild +++ /dev/null @@ -1,52 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -INTEL_DIST_PV=2020_update1_professional_edition -INTEL_SUBDIR=vtune_profiler - -inherit intel-sdp-r1 - -DESCRIPTION="Intel VTune Profiler" -HOMEPAGE="https://software.intel.com/en-us/vtune" - -IUSE="doc" -KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux" - -RDEPEND="~dev-libs/intel-common-19.1.1.217[compiler]" - -MY_PV="$(ver_rs 3 '-')" # 20.1.0-607630 - -QA_PREBUILT="*" - -INTEL_DIST_DAT_RPMS=( - "vtune-profiler-2020-cli-common-${MY_PV}.noarch.rpm" - "vtune-profiler-2020-common-${MY_PV}.noarch.rpm" - "vtune-profiler-2020-common-pset-${MY_PV}.noarch.rpm" - "vtune-profiler-2020-sep-${MY_PV}.noarch.rpm" - "vtune-profiler-2020-target-${MY_PV}.noarch.rpm") -INTEL_DIST_AMD64_RPMS=( - "vtune-profiler-2020-cli-${MY_PV}.x86_64.rpm" - "vtune-profiler-2020-collector-64linux-${MY_PV}.x86_64.rpm" - "vtune-profiler-2020-gui-${MY_PV}.x86_64.rpm" - "vtune-profiler-2020-vpp-server-${MY_PV}.x86_64.rpm") -INTEL_DIST_X86_RPMS=( - "vtune-profiler-2020-cli-32bit-${MY_PV}.i486.rpm" - "vtune-profiler-2020-collector-32linux-${MY_PV}.i486.rpm") - -pkg_setup() { - if use doc; then - INTEL_DIST_DAT_RPMS+=( "vtune-profiler-2020-doc-${MY_PV}.noarch.rpm" ) - fi -} - -src_install() { - intel-sdp-r1_src_install - - local path="PATH=" - use abi_x86_64 && path+=":$(isdp_get-sdp-edir)/bin64" - use abi_x86_32 && path+=":$(isdp_get-sdp-edir)/bin32" - echo "${path}" > "${T}"/35vtune || die - doenvd "${T}"/35vtune -} diff --git a/dev-lang/yaggo/metadata.xml b/dev-lang/yaggo/metadata.xml index 138cb7705..61d3a34e2 100644 --- a/dev-lang/yaggo/metadata.xml +++ b/dev-lang/yaggo/metadata.xml @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">gmarcais/yaggo</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-libs/intel-common/Manifest b/dev-libs/intel-common/Manifest deleted file mode 100644 index 21dea448d..000000000 --- a/dev-libs/intel-common/Manifest +++ /dev/null @@ -1,4 +0,0 @@ -DIST parallel_studio_xe_2018_update2_professional_edition.tgz 3877755304 BLAKE2B c8852df23abf080f482002a37af7781b3fbae3ecec448914ea5a237fa2b925073d1a3dc2dd94ba64002ff0f6c7e9b18b25fa7ada811a83b10344eb9b92cb37ff SHA512 a9b644b0305d83a9d0daa14d146cb3ce79949db55a410afe48d62259414e6256d9ef533a04bb50807103511db2016c4abcbbf769146854a25638f402a6d0f2be -DIST parallel_studio_xe_2019_update3_professional_edition.tgz 4777019188 BLAKE2B 1ebbc23d1370bb396b452dc73d4a79b4ea7be0e304e3d38b3cba77372df6af097ea1109535d166b56a6c50e28e3330a1ed49c6a9270411b14ccf48f32a9eaedd SHA512 622b1a8877f06247a0a93cb98d2cc6d5b359aa2c9cf7ff6f45a8e1dca34fecea10d603d632a7b3454d809d6e38cb860b40ae3f782e250279768937af6ceb015d -DIST parallel_studio_xe_2019_update4_professional_edition.tgz 2629662464 BLAKE2B a5619f33535063ccd7310378504ca960aa8512527cef7e0884fae5570633c1823e50ff7135adbbc571b4d47e0b6fcc01afe8639e09feb50a7f289eeec3f61ca0 SHA512 d8f6780a3671f30a1bad5d3a9792062c73b31188dc31fbd38212e98abc593f1c8f64bb970a8a4fce9ce237afef18ed38adf8fd81aa73b63ec964224590d4a34d -DIST parallel_studio_xe_2020_update1_professional_edition.tgz 2783012958 BLAKE2B 975103ec4551a0e3bd84034ce771a5fc459d5de47f4247b5915b54d9c827e50e913f9054a103424b764f730190675d42b52a97e68551b34df6b3d8d9b922517a SHA512 00a3334bcdb8b30216ecb40fcfc709b27d043697606a53f522c90b05cf8598e1e60311d629ec17b6fe1016a7d2a27f4b428abddc9eba39badebfd8a9b53de404 diff --git a/dev-libs/intel-common/intel-common-18.0.2.199-r1.ebuild b/dev-libs/intel-common/intel-common-18.0.2.199-r1.ebuild deleted file mode 100644 index 5397d76b6..000000000 --- a/dev-libs/intel-common/intel-common-18.0.2.199-r1.ebuild +++ /dev/null @@ -1,95 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -INTEL_DIST_SKU=3235 -INTEL_DIST_PV=2018_update2_professional_edition - -inherit intel-sdp-r1 - -DESCRIPTION="Common libraries and utilities needed for Intel compilers and libraries" -HOMEPAGE="http://software.intel.com/en-us/articles/intel-compilers/" - -IUSE="+compiler doc +mpi +openmp" -KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux" - -CHECKREQS_DISK_BUILD=750M - -INTEL_DIST_BIN_RPMS=() -INTEL_DIST_DAT_RPMS=( - "c-comp-common-18.0.2-199-18.0.2-199.noarch.rpm" - "comp-l-all-common-18.0.2-199-18.0.2-199.noarch.rpm" - "comp-l-all-vars-18.0.2-199-18.0.2-199.noarch.rpm" - "comp-nomcu-vars-18.0.2-199-18.0.2-199.noarch.rpm") -INTEL_DIST_X86_RPMS=( - "comp-32bit-18.0.2-199-18.0.2-199.x86_64.rpm" - "comp-ps-32bit-18.0.2-199-18.0.2-199.x86_64.rpm" - "comp-ps-ss-bec-32bit-18.0.2-199-18.0.2-199.x86_64.rpm") -INTEL_DIST_AMD64_RPMS=( - "comp-18.0.2-199-18.0.2-199.x86_64.rpm" - "comp-ps-18.0.2-199-18.0.2-199.x86_64.rpm" - "comp-ps-ss-18.0.2-199-18.0.2-199.x86_64.rpm" - "comp-ps-ss-bec-18.0.2-199-18.0.2-199.x86_64.rpm") - -pkg_setup() { - if use doc; then - INTEL_DIST_DAT_RPMS+=( "comp-doc-18.0-18.0.2-199.noarch.rpm" ) - fi - - if use mpi; then - INTEL_DIST_AMD64_RPMS+=( "mpi-rt-2018.2-199-2018.2-199.x86_64.rpm" ) - - if use doc; then - INTEL_DIST_DAT_RPMS+=( "mpi-doc-2018-2018.2-199.x86_64.rpm" ) - fi - fi - - if use openmp; then - INTEL_DIST_DAT_RPMS+=( "openmp-common-18.0.2-199-18.0.2-199.noarch.rpm" ) - INTEL_DIST_AMD64_RPMS+=( "openmp-18.0.2-199-18.0.2-199.x86_64.rpm" ) - INTEL_DIST_X86_RPMS+=( "openmp-32bit-18.0.2-199-18.0.2-199.x86_64.rpm" ) - - if use compiler; then - INTEL_DIST_DAT_RPMS+=( - "openmp-common-icc-18.0.2-199-18.0.2-199.noarch.rpm" - "openmp-common-ifort-18.0.2-199-18.0.2-199.noarch.rpm") - INTEL_DIST_AMD64_RPMS+=( - "openmp-ifort-18.0.2-199-18.0.2-199.x86_64.rpm") - INTEL_DIST_X86_RPMS+=( - "openmp-ifort-32bit-18.0.2-199-18.0.2-199.x86_64.rpm") - fi - fi -} - -src_install() { - intel-sdp-r1_src_install - local path rootpath ldpath arch fenv=35intelsdp - cat > ${fenv} <<-EOF - NLSPATH=$(isdp_get-sdp-edir)/linux/compiler/lib/$(isdp_get-native-abi-arch)/locale/en_US/%N - INTEL_LICENSE_FILE=${EPREFIX}/opt/intel/licenses:$(isdp_get-sdp-edir)/licenses - EOF - for arch in $(isdp_get-sdp-installed-arches); do - path="${path}:$(isdp_get-sdp-edir)/linux/bin/${arch}" - rootpath="${rootpath}:$(isdp_get-sdp-edir)/linux/bin/${arch}" - ldpath="${ldpath}:$(isdp_get-sdp-edir)/linux/compiler/lib/${arch}" - done - if use mpi && use amd64; then - path="${path}:$(isdp_get-sdp-edir)/linux/mpi/intel64/bin/" - rootpath="${rootpath}:$(isdp_get-sdp-edir)/linux/mpi/intel64/bin/" - ldpath="${ldpath}:$(isdp_get-sdp-edir)/linux/mpi/intel64/lib/" - fi - cat >> ${fenv} <<-EOF - PATH=${path#:} - ROOTPATH=${rootpath#:} - LDPATH=${ldpath#:} - EOF - - doenvd ${fenv} - - cat >> "${T}"/40-${PN} <<- EOF - SEARCH_DIRS_MASK=$(isdp_get-sdp-edir) - EOF - insinto /etc/revdep-rebuild/ - doins "${T}"/40-${PN} -} diff --git a/dev-libs/intel-common/intel-common-19.0.3.199-r1.ebuild b/dev-libs/intel-common/intel-common-19.0.3.199-r1.ebuild deleted file mode 100644 index dc06e4551..000000000 --- a/dev-libs/intel-common/intel-common-19.0.3.199-r1.ebuild +++ /dev/null @@ -1,101 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -INTEL_DIST_PV=2019_update3_professional_edition - -inherit intel-sdp-r1 - -DESCRIPTION="Common libraries and utilities needed for Intel compilers and libraries" -HOMEPAGE="http://software.intel.com/en-us/articles/intel-compilers/" - -IUSE="+compiler doc +mpi +openmp" -KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux" - -SLOT="0" - -MY_PV=$(ver_rs 3 '-') # 19.0.3-199 -MY_PV2=$(ver_cut 1-2) # 19.0 -MY_PV3='20'$(ver_cut 1) # 2019 -MY_PV4="${MY_PV3}."$(ver_cut 3)'-'$(ver_cut 4) # 2019.3-199 - -CHECKREQS_DISK_BUILD=750M - -INTEL_DIST_BIN_RPMS=() -INTEL_DIST_DAT_RPMS=( - "c-comp-common-${MY_PV}-${MY_PV}.noarch.rpm" - "comp-l-all-common-${MY_PV}-${MY_PV}.noarch.rpm" - "comp-l-all-vars-${MY_PV}-${MY_PV}.noarch.rpm" - "comp-nomcu-vars-${MY_PV}-${MY_PV}.noarch.rpm") -INTEL_DIST_X86_RPMS=( - "comp-32bit-${MY_PV}-${MY_PV}.x86_64.rpm" - "comp-ps-32bit-${MY_PV}-${MY_PV}.x86_64.rpm" - "comp-ps-ss-bec-32bit-${MY_PV}-${MY_PV}.x86_64.rpm") -INTEL_DIST_AMD64_RPMS=( - "comp-${MY_PV}-${MY_PV}.x86_64.rpm" - "comp-ps-${MY_PV}-${MY_PV}.x86_64.rpm" - "comp-ps-ss-${MY_PV}-${MY_PV}.x86_64.rpm" - "comp-ps-ss-bec-${MY_PV}-${MY_PV}.x86_64.rpm") - -pkg_setup() { - if use doc; then - INTEL_DIST_DAT_RPMS+=( "comp-doc-${MY_PV2}-${MY_PV}.noarch.rpm" ) - fi - - if use mpi; then - INTEL_DIST_AMD64_RPMS+=( "mpi-rt-${MY_PV4}-${MY_PV4}.x86_64.rpm" ) - - if use doc; then - INTEL_DIST_DAT_RPMS+=( "mpi-doc-${MY_PV3}-${MY_PV4}.x86_64.rpm" ) - fi - fi - - if use openmp; then - INTEL_DIST_DAT_RPMS+=( "openmp-common-${MY_PV}-${MY_PV}.noarch.rpm" ) - INTEL_DIST_AMD64_RPMS+=( "openmp-${MY_PV}-${MY_PV}.x86_64.rpm" ) - INTEL_DIST_X86_RPMS+=( "openmp-32bit-${MY_PV}-${MY_PV}.x86_64.rpm" ) - - if use compiler; then - INTEL_DIST_DAT_RPMS+=( - "openmp-common-icc-${MY_PV}-${MY_PV}.noarch.rpm" - "openmp-common-ifort-${MY_PV}-${MY_PV}.noarch.rpm") - INTEL_DIST_AMD64_RPMS+=( - "openmp-ifort-${MY_PV}-${MY_PV}.x86_64.rpm") - INTEL_DIST_X86_RPMS+=( - "openmp-ifort-32bit-${MY_PV}-${MY_PV}.x86_64.rpm") - fi - fi -} - -src_install() { - intel-sdp-r1_src_install - local path rootpath ldpath arch fenv=35intelsdp - cat > ${fenv} <<-EOF - NLSPATH=$(isdp_get-sdp-edir)/linux/compiler/lib/$(isdp_get-native-abi-arch)/locale/en_US/%N - INTEL_LICENSE_FILE=${EPREFIX}/opt/intel/licenses:$(isdp_get-sdp-edir)/licenses - EOF - for arch in $(isdp_get-sdp-installed-arches); do - path="${path}:$(isdp_get-sdp-edir)/linux/bin/${arch}" - rootpath="${rootpath}:$(isdp_get-sdp-edir)/linux/bin/${arch}" - ldpath="${ldpath}:$(isdp_get-sdp-edir)/linux/compiler/lib/${arch}" - done - if use mpi && use amd64; then - path="${path}:$(isdp_get-sdp-edir)/linux/mpi/intel64/bin/" - rootpath="${rootpath}:$(isdp_get-sdp-edir)/linux/mpi/intel64/bin/" - ldpath="${ldpath}:$(isdp_get-sdp-edir)/linux/mpi/intel64/lib/" - fi - cat >> ${fenv} <<-EOF - PATH=${path#:} - ROOTPATH=${rootpath#:} - LDPATH=${ldpath#:} - EOF - - doenvd ${fenv} - - cat >> "${T}"/40-${PN} <<- EOF - SEARCH_DIRS_MASK=$(isdp_get-sdp-edir) - EOF - insinto /etc/revdep-rebuild/ - doins "${T}"/40-${PN} -} diff --git a/dev-libs/intel-common/intel-common-19.0.4.243.ebuild b/dev-libs/intel-common/intel-common-19.0.4.243.ebuild deleted file mode 100644 index df8f5574c..000000000 --- a/dev-libs/intel-common/intel-common-19.0.4.243.ebuild +++ /dev/null @@ -1,101 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -INTEL_DIST_PV=2019_update4_professional_edition - -inherit intel-sdp-r1 - -DESCRIPTION="Common libraries and utilities needed for Intel compilers and libraries" -HOMEPAGE="http://software.intel.com/en-us/articles/intel-compilers/" - -IUSE="+compiler doc +mpi +openmp" -KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux" - -SLOT="0" - -MY_PV=$(ver_rs 3 '-') # 19.0.3-199 -MY_PV2=$(ver_cut 1-2) # 19.0 -MY_PV3='20'$(ver_cut 1) # 2019 -MY_PV4="${MY_PV3}."$(ver_cut 3)'-'$(ver_cut 4) # 2019.3-199 - -CHECKREQS_DISK_BUILD=750M - -INTEL_DIST_BIN_RPMS=() -INTEL_DIST_DAT_RPMS=( - "c-comp-common-${MY_PV}-${MY_PV}.noarch.rpm" - "comp-l-all-common-${MY_PV}-${MY_PV}.noarch.rpm" - "comp-l-all-vars-${MY_PV}-${MY_PV}.noarch.rpm" - "comp-nomcu-vars-${MY_PV}-${MY_PV}.noarch.rpm") -INTEL_DIST_X86_RPMS=( - "comp-32bit-${MY_PV}-${MY_PV}.x86_64.rpm" - "comp-ps-32bit-${MY_PV}-${MY_PV}.x86_64.rpm" - "comp-ps-ss-bec-32bit-${MY_PV}-${MY_PV}.x86_64.rpm") -INTEL_DIST_AMD64_RPMS=( - "comp-${MY_PV}-${MY_PV}.x86_64.rpm" - "comp-ps-${MY_PV}-${MY_PV}.x86_64.rpm" - "comp-ps-ss-${MY_PV}-${MY_PV}.x86_64.rpm" - "comp-ps-ss-bec-${MY_PV}-${MY_PV}.x86_64.rpm") - -pkg_setup() { - if use doc; then - INTEL_DIST_DAT_RPMS+=( "comp-doc-${MY_PV2}-${MY_PV}.noarch.rpm" ) - fi - - if use mpi; then - INTEL_DIST_AMD64_RPMS+=( "mpi-rt-${MY_PV4}-${MY_PV4}.x86_64.rpm" ) - - if use doc; then - INTEL_DIST_DAT_RPMS+=( "mpi-doc-${MY_PV3}-${MY_PV4}.x86_64.rpm" ) - fi - fi - - if use openmp; then - INTEL_DIST_DAT_RPMS+=( "openmp-common-${MY_PV}-${MY_PV}.noarch.rpm" ) - INTEL_DIST_AMD64_RPMS+=( "openmp-${MY_PV}-${MY_PV}.x86_64.rpm" ) - INTEL_DIST_X86_RPMS+=( "openmp-32bit-${MY_PV}-${MY_PV}.x86_64.rpm" ) - - if use compiler; then - INTEL_DIST_DAT_RPMS+=( - "openmp-common-icc-${MY_PV}-${MY_PV}.noarch.rpm" - "openmp-common-ifort-${MY_PV}-${MY_PV}.noarch.rpm") - INTEL_DIST_AMD64_RPMS+=( - "openmp-ifort-${MY_PV}-${MY_PV}.x86_64.rpm") - INTEL_DIST_X86_RPMS+=( - "openmp-ifort-32bit-${MY_PV}-${MY_PV}.x86_64.rpm") - fi - fi -} - -src_install() { - intel-sdp-r1_src_install - local path rootpath ldpath arch fenv=35intelsdp - cat > ${fenv} <<-EOF - NLSPATH=$(isdp_get-sdp-edir)/linux/compiler/lib/$(isdp_get-native-abi-arch)/locale/en_US/%N - INTEL_LICENSE_FILE=${EPREFIX}/opt/intel/licenses:$(isdp_get-sdp-edir)/licenses - EOF - for arch in $(isdp_get-sdp-installed-arches); do - path="${path}:$(isdp_get-sdp-edir)/linux/bin/${arch}" - rootpath="${rootpath}:$(isdp_get-sdp-edir)/linux/bin/${arch}" - ldpath="${ldpath}:$(isdp_get-sdp-edir)/linux/compiler/lib/${arch}" - done - if use mpi && use amd64; then - path="${path}:$(isdp_get-sdp-edir)/linux/mpi/intel64/bin/" - rootpath="${rootpath}:$(isdp_get-sdp-edir)/linux/mpi/intel64/bin/" - ldpath="${ldpath}:$(isdp_get-sdp-edir)/linux/mpi/intel64/lib/" - fi - cat >> ${fenv} <<-EOF - PATH=${path#:} - ROOTPATH=${rootpath#:} - LDPATH=${ldpath#:} - EOF - - doenvd ${fenv} - - cat >> "${T}"/40-${PN} <<- EOF - SEARCH_DIRS_MASK=$(isdp_get-sdp-edir) - EOF - insinto /etc/revdep-rebuild/ - doins "${T}"/40-${PN} -} diff --git a/dev-libs/intel-common/intel-common-19.1.1.217.ebuild b/dev-libs/intel-common/intel-common-19.1.1.217.ebuild deleted file mode 100644 index 4ba98edad..000000000 --- a/dev-libs/intel-common/intel-common-19.1.1.217.ebuild +++ /dev/null @@ -1,102 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -INTEL_DIST_PV=2020_update1_professional_edition - -inherit intel-sdp-r1 - -DESCRIPTION="Common libraries and utilities needed for Intel compilers and libraries" -HOMEPAGE="http://software.intel.com/en-us/articles/intel-compilers/" - -IUSE="+compiler doc +mpi +openmp" -KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux" - -SLOT="0" - -MY_PV="$(ver_rs 3 '-')" # 19.1.1-217 -MY_PV2="$(ver_cut 1-2)" # 19.1 -MY_PV3="2019" # 2019 -MY_PV4="${MY_PV3}.7-$(ver_cut 4)" # 2019.7-217 sic! - -CHECKREQS_DISK_BUILD=750M - -QA_PREBUILT="*" - -INTEL_DIST_BIN_RPMS=() -INTEL_DIST_DAT_RPMS=( - "c-comp-common-${MY_PV}-${MY_PV}.noarch.rpm" - "comp-l-all-common-${MY_PV}-${MY_PV}.noarch.rpm" - "comp-l-all-vars-${MY_PV}-${MY_PV}.noarch.rpm" - "comp-nomcu-vars-${MY_PV}-${MY_PV}.noarch.rpm") -INTEL_DIST_X86_RPMS=( - "comp-32bit-${MY_PV}-${MY_PV}.x86_64.rpm" - "comp-ps-32bit-${MY_PV}-${MY_PV}.x86_64.rpm" - "comp-ps-ss-bec-32bit-${MY_PV}-${MY_PV}.x86_64.rpm") -INTEL_DIST_AMD64_RPMS=( - "comp-${MY_PV}-${MY_PV}.x86_64.rpm" - "comp-ps-${MY_PV}-${MY_PV}.x86_64.rpm" - "comp-ps-ss-bec-${MY_PV}-${MY_PV}.x86_64.rpm") - -pkg_setup() { - if use doc; then - INTEL_DIST_DAT_RPMS+=( "comp-doc-${MY_PV2}-${MY_PV}.noarch.rpm" ) - fi - - if use mpi; then - INTEL_DIST_AMD64_RPMS+=( "mpi-rt-${MY_PV4}-${MY_PV4}.x86_64.rpm" ) - - if use doc; then - INTEL_DIST_DAT_RPMS+=( "mpi-doc-${MY_PV3}-${MY_PV4}.x86_64.rpm" ) - fi - fi - - if use openmp; then - INTEL_DIST_DAT_RPMS+=( "openmp-common-${MY_PV}-${MY_PV}.noarch.rpm" ) - INTEL_DIST_AMD64_RPMS+=( "openmp-${MY_PV}-${MY_PV}.x86_64.rpm" ) - INTEL_DIST_X86_RPMS+=( "openmp-32bit-${MY_PV}-${MY_PV}.x86_64.rpm" ) - - if use compiler; then - INTEL_DIST_DAT_RPMS+=( - "openmp-common-icc-${MY_PV}-${MY_PV}.noarch.rpm" - "openmp-common-ifort-${MY_PV}-${MY_PV}.noarch.rpm") - INTEL_DIST_AMD64_RPMS+=( - "openmp-ifort-${MY_PV}-${MY_PV}.x86_64.rpm") - INTEL_DIST_X86_RPMS+=( - "openmp-ifort-32bit-${MY_PV}-${MY_PV}.x86_64.rpm") - fi - fi -} - -src_install() { - intel-sdp-r1_src_install - local path rootpath ldpath arch fenv=35intelsdp - cat > ${fenv} <<-EOF - NLSPATH=$(isdp_get-sdp-edir)/linux/compiler/lib/$(isdp_get-native-abi-arch)/locale/en_US/%N - INTEL_LICENSE_FILE=${EPREFIX}/opt/intel/licenses:$(isdp_get-sdp-edir)/licenses - EOF - for arch in $(isdp_get-sdp-installed-arches); do - path="${path}:$(isdp_get-sdp-edir)/linux/bin/${arch}" - rootpath="${rootpath}:$(isdp_get-sdp-edir)/linux/bin/${arch}" - ldpath="${ldpath}:$(isdp_get-sdp-edir)/linux/compiler/lib/${arch}" - done - if use mpi && use amd64; then - path="${path}:$(isdp_get-sdp-edir)/linux/mpi/intel64/bin/" - rootpath="${rootpath}:$(isdp_get-sdp-edir)/linux/mpi/intel64/bin/" - ldpath="${ldpath}:$(isdp_get-sdp-edir)/linux/mpi/intel64/lib/" - fi - cat >> ${fenv} <<-EOF - PATH=${path#:} - ROOTPATH=${rootpath#:} - LDPATH=${ldpath#:} - EOF - - doenvd ${fenv} - - cat >> "${T}"/40-${PN} <<- EOF - SEARCH_DIRS_MASK=$(isdp_get-sdp-edir) - EOF - insinto /etc/revdep-rebuild/ - doins "${T}"/40-${PN} -} diff --git a/dev-libs/intel-common/metadata.xml b/dev-libs/intel-common/metadata.xml deleted file mode 100644 index 026b5a33d..000000000 --- a/dev-libs/intel-common/metadata.xml +++ /dev/null @@ -1,15 +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"> -This package contains the core files to be installed for the Intel -compilers and libraries. Probably useless if installed standalone. -</longdescription> - <use> - <flag name="compiler">Install the libraries needed for the icc and ifort compilers</flag> - </use> -</pkgmetadata> diff --git a/dev-libs/lief/lief-0.11.5.ebuild b/dev-libs/lief/lief-0.11.5.ebuild index 519729525..c2c38e5ba 100644 --- a/dev-libs/lief/lief-0.11.5.ebuild +++ b/dev-libs/lief/lief-0.11.5.ebuild @@ -4,7 +4,7 @@ EAPI=7 CMAKE_ECLASS=cmake -PYTHON_COMPAT=( python3_{8..10} pypy3 ) +PYTHON_COMPAT=( python3_10 pypy3 ) # Upstream has two alternate approaches to building its Python API: # 1. A working "CMakeList.txt" only supporting a single Python target. diff --git a/dev-libs/oneCCL/Manifest b/dev-libs/oneCCL/Manifest new file mode 100644 index 000000000..2eb21d0f6 --- /dev/null +++ b/dev-libs/oneCCL/Manifest @@ -0,0 +1,3 @@ +DIST oneCCL-2021.10.tar.gz 37777252 BLAKE2B fb8d4429cbd7366efdd6e392d8132631c4dbc770962781a49b5b2df6e0c0a9b9b6c97043997066879b22ea85bf76e507bdcc27a78e40beffa7520d2a420b35ef SHA512 3ff845bf28e18c195411f5ed4542f172648feeb385fc456b6222d527018f48625c9be7e96a0f9b973f8af7ad1cc122a83ac8e169eeb59d5a35ed901910fdbace +DIST oneCCL-2021.7.1.tar.gz 35807233 BLAKE2B 0608b548f42c28983453a1e693c922aff0f6c77ffbf35f92b69113ba9fb02263bf8e1efa94ba47330559bb97b81493923cac10ce2c68c5fb50181677152fcc28 SHA512 e77d836afdcccbc2a1d2f9903916f17698a0d5ad795cd76dbb19a835375e89d0ecfa4695d87758e1ca6078bc23e30416d0a228ad3060816409b91851ad0b0790 +DIST oneCCL-2021.8.tar.gz 36868388 BLAKE2B b27f04efaddf2c31befd70388f0aa84b9cb5266b5d4e4a300064e0dc98e4d7eee3590288dc0b8cc1640fe0a9b928a0dfdf16a2ea45db9bd1517a8ca2dd00bdfe SHA512 879d1b73e594d5ff2c5a5aee08dfb4aded11c4974a9efcc199e7c2ee87b00c2441edb1dcb073bb4ed2587d752efcafe338072959b7b0f89fc1692dc377f748c2 diff --git a/dev-libs/oneCCL/files/oneCCL-2021.7.1-use-system-libs.patch b/dev-libs/oneCCL/files/oneCCL-2021.7.1-use-system-libs.patch new file mode 100644 index 000000000..e92608f4a --- /dev/null +++ b/dev-libs/oneCCL/files/oneCCL-2021.7.1-use-system-libs.patch @@ -0,0 +1,104 @@ +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 74c4fc0..92c4d16 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -87,15 +87,13 @@ add_definitions(-DCCL_CXX_COMPILER="${CMAKE_CXX_COMPILER_ID} ${CMAKE_CXX_COMPILE + SET(CCL_ENABLE_ZE OFF CACHE BOOL "Enable Level Zero support") + + set(CCL_COMMON_INSTALL_PREFIX "intel64") +-set(CMAKE_INSTALL_LIBDIR "lib") + set(CCL_INSTALL_LIB "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBDIR}") + set(CCL_INSTALL_INCLUDE "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_INCLUDEDIR}") + set(CCL_INSTALL_DOC "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_DOCDIR}") + set(CCL_INSTALL_BIN "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_BINDIR}") +-set(CCL_INSTALL_ENV "${CMAKE_INSTALL_PREFIX}/env") +-set(CCL_INSTALL_ETC "${CMAKE_INSTALL_PREFIX}/etc") +-set(CCL_INSTALL_LICENSE "${CMAKE_INSTALL_PREFIX}/licensing") +-set(CCL_INSTALL_MODULE "${CMAKE_INSTALL_PREFIX}/modulefiles") ++set(CCL_INSTALL_ENV "${CMAKE_INSTALL_FULL_SYSCONFDIR}/env") ++set(CCL_INSTALL_ETC "${CMAKE_INSTALL_FULL_SYSCONFDIR}") ++set(CCL_INSTALL_MODULE "${CMAKE_INSTALL_FULL_SYSCONFDIR}/modulefiles") + set(CCL_INSTALL_EXAMPLES "${CMAKE_INSTALL_PREFIX}/examples") + set(CCL_INSTALL_TESTS "${CMAKE_INSTALL_PREFIX}/tests") + set(CCL_INSTALL_KERNELS "${CMAKE_INSTALL_PREFIX}/lib/kernels") +@@ -103,23 +101,23 @@ set(CCL_INSTALL_KERNELS "${CMAKE_INSTALL_PREFIX}/lib/kernels") + # setup dependency directories + set(DEPS_DIR "${PROJECT_SOURCE_DIR}/deps") + +-set(MPI_INCLUDE_DIR "${DEPS_DIR}/mpi/include/") +-set(MPI_LIB_DIR "${DEPS_DIR}/mpi/lib/") ++set(MPI_INCLUDE_DIR "/usr/include/") ++set(MPI_LIB_DIR "/usr/lib64/") + message(STATUS "MPI_INCLUDE_DIR: ${MPI_INCLUDE_DIR}") + message(STATUS "MPI_LIB_DIR: ${MPI_LIB_DIR}") + + if ("${LIBFABRIC_DIR}" STREQUAL "") +- set(LIBFABRIC_INCLUDE_DIR "${DEPS_DIR}/ofi/include") +- set(LIBFABRIC_LIB_DIR "${DEPS_DIR}/ofi/lib/") ++ set(LIBFABRIC_INCLUDE_DIR "${DEPS_DIR}/ofi/include/") ++ set(LIBFABRIC_LIB_DIR "${DEPS_DIR}/ofi/lib64/") + else() + set(LIBFABRIC_INCLUDE_DIR "${LIBFABRIC_DIR}/include/") +- set(LIBFABRIC_LIB_DIR "${LIBFABRIC_DIR}/lib") ++ set(LIBFABRIC_LIB_DIR "${LIBFABRIC_DIR}/lib64/") + endif() + message(STATUS "LIBFABRIC_LIB_DIR: ${LIBFABRIC_LIB_DIR}") + message(STATUS "LIBFABRIC_INCLUDE_DIR: ${LIBFABRIC_INCLUDE_DIR}") + +-set(HWLOC_INCLUDE_DIR "${DEPS_DIR}/hwloc/include/") +-set(HWLOC_LIB_DIR "${DEPS_DIR}/hwloc/lib/") ++set(HWLOC_INCLUDE_DIR "/usr/include/") ++set(HWLOC_LIB_DIR "/usr/lib64/") + message(STATUS "HWLOC_INCLUDE_DIR: ${HWLOC_INCLUDE_DIR}") + message(STATUS "HWLOC_LIB_DIR: ${HWLOC_LIB_DIR}") + +@@ -128,7 +126,7 @@ set(ITT_LIB_DIR "${DEPS_DIR}/itt/lib64") + message(STATUS "ITT_INCLUDE_DIR: ${ITT_INCLUDE_DIR}") + message(STATUS "ITT_LIB_DIR: ${ITT_LIB_DIR}") + +-set(LEVEL_ZERO_INCLUDE_DIR "${DEPS_DIR}/level_zero/include/") ++set(LEVEL_ZERO_INCLUDE_DIR "/usr/include/level_zero") + message(STATUS "LEVEL_ZERO_INCLUDE_DIR: ${LEVEL_ZERO_INCLUDE_DIR}") + + set(CMAKE_SKIP_INSTALL_RPATH TRUE) +@@ -241,8 +239,6 @@ configure_file(third-party-programs.txt ${CMAKE_CURRENT_BINARY_DIR}/third-party- + install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/vars.sh DESTINATION ${CCL_INSTALL_ENV}) + install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/setvars.sh DESTINATION ${CCL_INSTALL_ENV}) + install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/ccl DESTINATION ${CCL_INSTALL_MODULE}) +-install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/third-party-programs.txt DESTINATION ${CCL_INSTALL_LICENSE}) +-install(PROGRAMS ${PROJECT_SOURCE_DIR}/LICENSE DESTINATION ${CCL_INSTALL_LICENSE}) + + # copy kernels + if (COMPUTE_BACKEND AND EXISTS "${PROJECT_SOURCE_DIR}/src/kernels") +diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt +index 7b4cff9..e8296a0 100644 +--- a/src/CMakeLists.txt ++++ b/src/CMakeLists.txt +@@ -263,8 +263,8 @@ list(APPEND SRC_LINK_LIBS + pthread + ${EXTERNAL_LIBS} + fabric +- ${HWLOC_LIB_DIR}/libhwloc.a +- ${ITT_LIB_DIR}/libittnotify.a) ++ libhwloc.so ++ libittnotify.so) + + if (ENABLE_MPI) + set(SRC_C_FLAGS "${SRC_C_FLAGS} -DCCL_ENABLE_MPI") +@@ -335,16 +335,3 @@ if ("${LIBFABRIC_DIR}" STREQUAL "") + install(DIRECTORY ${DEPS_DIR}/ofi/lib/ + DESTINATION ${CCL_INSTALL_LIB}) + endif() +- +-if (ENABLE_MPI) +- file(GLOB mpi_bins "${DEPS_DIR}/mpi/bin/*") +- install(PROGRAMS ${mpi_bins} DESTINATION ${CCL_INSTALL_BIN}) +- install(DIRECTORY ${DEPS_DIR}/mpi/include/ +- DESTINATION ${CCL_INSTALL_INCLUDE}) +- install(DIRECTORY ${DEPS_DIR}/mpi/lib/ +- DESTINATION ${CCL_INSTALL_LIB}) +- install(DIRECTORY ${DEPS_DIR}/mpi/etc/ +- DESTINATION ${CCL_INSTALL_ETC}) +- install(DIRECTORY ${DEPS_DIR}/mpi/licensing/ +- DESTINATION ${CCL_INSTALL_LICENSE}/mpi/) +-endif() diff --git a/dev-libs/oneCCL/files/oneCCL-2021.8-use-system-libs.patch b/dev-libs/oneCCL/files/oneCCL-2021.8-use-system-libs.patch new file mode 100644 index 000000000..dbb3a9e5f --- /dev/null +++ b/dev-libs/oneCCL/files/oneCCL-2021.8-use-system-libs.patch @@ -0,0 +1,104 @@ +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 1e65ce9..cabbff9 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -109,15 +109,13 @@ add_definitions(-DCCL_CXX_COMPILER="${CMAKE_CXX_COMPILER_ID} ${CMAKE_CXX_COMPILE + SET(CCL_ENABLE_ZE OFF CACHE BOOL "Enable Level Zero support") + + set(CCL_COMMON_INSTALL_PREFIX "intel64") +-set(CMAKE_INSTALL_LIBDIR "lib") + set(CCL_INSTALL_LIB "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBDIR}") + set(CCL_INSTALL_INCLUDE "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_INCLUDEDIR}") + set(CCL_INSTALL_DOC "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_DOCDIR}") + set(CCL_INSTALL_BIN "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_BINDIR}") +-set(CCL_INSTALL_ENV "${CMAKE_INSTALL_PREFIX}/env") +-set(CCL_INSTALL_ETC "${CMAKE_INSTALL_PREFIX}/etc") +-set(CCL_INSTALL_LICENSE "${CMAKE_INSTALL_PREFIX}/licensing") +-set(CCL_INSTALL_MODULE "${CMAKE_INSTALL_PREFIX}/modulefiles") ++set(CCL_INSTALL_ENV "${CMAKE_INSTALL_FULL_SYSCONFDIR}/env") ++set(CCL_INSTALL_ETC "${CMAKE_INSTALL_FULL_SYSCONFDIR}") ++set(CCL_INSTALL_MODULE "${CMAKE_INSTALL_FULL_SYSCONFDIR}/modulefiles") + set(CCL_INSTALL_EXAMPLES "${CMAKE_INSTALL_PREFIX}/examples") + set(CCL_INSTALL_TESTS "${CMAKE_INSTALL_PREFIX}/tests") + set(CCL_INSTALL_KERNELS "${CMAKE_INSTALL_PREFIX}/lib/kernels") +@@ -125,23 +123,23 @@ set(CCL_INSTALL_KERNELS "${CMAKE_INSTALL_PREFIX}/lib/kernels") + # setup dependency directories + set(DEPS_DIR "${PROJECT_SOURCE_DIR}/deps") + +-set(MPI_INCLUDE_DIR "${DEPS_DIR}/mpi/include/") +-set(MPI_LIB_DIR "${DEPS_DIR}/mpi/lib/") ++set(MPI_INCLUDE_DIR "/usr/include/") ++set(MPI_LIB_DIR "/usr/lib64/") + message(STATUS "MPI_INCLUDE_DIR: ${MPI_INCLUDE_DIR}") + message(STATUS "MPI_LIB_DIR: ${MPI_LIB_DIR}") + + if ("${LIBFABRIC_DIR}" STREQUAL "") +- set(LIBFABRIC_INCLUDE_DIR "${DEPS_DIR}/ofi/include") +- set(LIBFABRIC_LIB_DIR "${DEPS_DIR}/ofi/lib/") ++ set(LIBFABRIC_INCLUDE_DIR "${DEPS_DIR}/ofi/include/") ++ set(LIBFABRIC_LIB_DIR "${DEPS_DIR}/ofi/lib64/") + else() + set(LIBFABRIC_INCLUDE_DIR "${LIBFABRIC_DIR}/include/") +- set(LIBFABRIC_LIB_DIR "${LIBFABRIC_DIR}/lib") ++ set(LIBFABRIC_LIB_DIR "${LIBFABRIC_DIR}/lib64/") + endif() + message(STATUS "LIBFABRIC_LIB_DIR: ${LIBFABRIC_LIB_DIR}") + message(STATUS "LIBFABRIC_INCLUDE_DIR: ${LIBFABRIC_INCLUDE_DIR}") + +-set(HWLOC_INCLUDE_DIR "${DEPS_DIR}/hwloc/include/") +-set(HWLOC_LIB_DIR "${DEPS_DIR}/hwloc/lib/") ++set(HWLOC_INCLUDE_DIR "/usr/include/") ++set(HWLOC_LIB_DIR "/usr/lib64/") + message(STATUS "HWLOC_INCLUDE_DIR: ${HWLOC_INCLUDE_DIR}") + message(STATUS "HWLOC_LIB_DIR: ${HWLOC_LIB_DIR}") + +@@ -150,7 +148,7 @@ set(ITT_LIB_DIR "${DEPS_DIR}/itt/lib64") + message(STATUS "ITT_INCLUDE_DIR: ${ITT_INCLUDE_DIR}") + message(STATUS "ITT_LIB_DIR: ${ITT_LIB_DIR}") + +-set(LEVEL_ZERO_INCLUDE_DIR "${DEPS_DIR}/level_zero/include/") ++set(LEVEL_ZERO_INCLUDE_DIR "/usr/include/level_zero") + message(STATUS "LEVEL_ZERO_INCLUDE_DIR: ${LEVEL_ZERO_INCLUDE_DIR}") + + message(STATUS "DRM_INCLUDE_DIR: ${DRM_INCLUDE_DIR}") +@@ -290,8 +288,6 @@ configure_file(third-party-programs.txt ${CMAKE_CURRENT_BINARY_DIR}/third-party- + install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/vars.sh DESTINATION ${CCL_INSTALL_ENV}) + install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/setvars.sh DESTINATION ${CCL_INSTALL_ENV}) + install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/ccl DESTINATION ${CCL_INSTALL_MODULE}) +-install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/third-party-programs.txt DESTINATION ${CCL_INSTALL_LICENSE}) +-install(PROGRAMS ${PROJECT_SOURCE_DIR}/LICENSE DESTINATION ${CCL_INSTALL_LICENSE}) + + # copy kernels + if (COMPUTE_BACKEND AND EXISTS "${PROJECT_SOURCE_DIR}/src/kernels") +diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt +index 3948373..168a690 100644 +--- a/src/CMakeLists.txt ++++ b/src/CMakeLists.txt +@@ -279,8 +279,8 @@ list(APPEND SRC_LINK_LIBS + dl + pthread + ${EXTERNAL_LIBS} +- ${HWLOC_LIB_DIR}/libhwloc.a +- ${ITT_LIB_DIR}/libittnotify.a) ++ libhwloc.so ++ libittnotify.so) + + if (ENABLE_MPI) + set(SRC_C_FLAGS "${SRC_C_FLAGS} -DCCL_ENABLE_MPI") +@@ -350,16 +350,3 @@ if ("${LIBFABRIC_DIR}" STREQUAL "") + install(DIRECTORY ${DEPS_DIR}/ofi/lib/ + DESTINATION ${CCL_INSTALL_LIB}) + endif() +- +-if (ENABLE_MPI) +- file(GLOB mpi_bins "${DEPS_DIR}/mpi/bin/*") +- install(PROGRAMS ${mpi_bins} DESTINATION ${CCL_INSTALL_BIN}) +- install(DIRECTORY ${DEPS_DIR}/mpi/include/ +- DESTINATION ${CCL_INSTALL_INCLUDE}) +- install(DIRECTORY ${DEPS_DIR}/mpi/lib/ +- DESTINATION ${CCL_INSTALL_LIB}) +- install(DIRECTORY ${DEPS_DIR}/mpi/etc/ +- DESTINATION ${CCL_INSTALL_ETC}) +- install(DIRECTORY ${DEPS_DIR}/mpi/licensing/ +- DESTINATION ${CCL_INSTALL_LICENSE}/mpi/) +-endif() diff --git a/dev-libs/oneCCL/metadata.xml b/dev-libs/oneCCL/metadata.xml new file mode 100644 index 000000000..cbb320b12 --- /dev/null +++ b/dev-libs/oneCCL/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <upstream> + <remote-id type="github">oneapi-src/oneCCL</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-libs/oneCCL/oneCCL-2021.10.ebuild b/dev-libs/oneCCL/oneCCL-2021.10.ebuild new file mode 100644 index 000000000..a67659f4a --- /dev/null +++ b/dev-libs/oneCCL/oneCCL-2021.10.ebuild @@ -0,0 +1,62 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit cmake + +DESCRIPTION="oneAPI Collective Communications Library" +HOMEPAGE="https://github.com/oneapi-src/oneCCL" +SRC_URI="https://github.com/oneapi-src/oneCCL/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="~amd64" + +IUSE="mpi" + +BDEPEND="sys-devel/DPC++" + +DEPEND=" + dev-libs/level-zero:= + sys-apps/hwloc:= + sys-block/libfabric:= + sys-devel/ittapi + sys-cluster/pmix + mpi? ( virtual/mpi ) +" +RDEPEND="${DEPEND}" + +PATCHES=( + "${FILESDIR}/${PN}-2021.8-use-system-libs.patch" +) + +src_prepare() { + # No -Werror + find . -name "CMakeLists.txt" -exec sed -i "s/-Werror//g" {} + || die + + # Use system libs instead + rm -r deps/* || die + + # DPC++ compiler required for full functionality + export CC="${ESYSROOT}/usr/lib/llvm/intel/bin/clang" + export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++" + + cmake_src_prepare +} + +src_configure() { + local mycmakeargs=( + -DBUILD_EXAMPLES=OFF + # BUILD_CONFIG causes sandbox violation + -DBUILD_CONFIG=OFF + -DCCL_ENABLE_ZE=ON + # TODO: Find out how to execute the tests + -DBUILD_FT=OFF + -DENABLE_MPI_TESTS=OFF + -DENABLE_MPI="$(usex mpi)" + # Use system fabric + -DLIBFABRIC_DIR="${ESYSROOT}/usr" + ) + cmake_src_configure +} diff --git a/dev-libs/oneCCL/oneCCL-2021.7.1-r1.ebuild b/dev-libs/oneCCL/oneCCL-2021.7.1-r1.ebuild new file mode 100644 index 000000000..76ab29af2 --- /dev/null +++ b/dev-libs/oneCCL/oneCCL-2021.7.1-r1.ebuild @@ -0,0 +1,61 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit cmake + +DESCRIPTION="oneAPI Collective Communications Library" +HOMEPAGE="https://github.com/oneapi-src/oneCCL" +SRC_URI="https://github.com/oneapi-src/oneCCL/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="~amd64" + +IUSE="mpi" + +BDEPEND="sys-devel/DPC++" + +DEPEND=" + dev-libs/level-zero:= + sys-apps/hwloc:= + sys-block/libfabric:= + sys-devel/ittapi + mpi? ( virtual/mpi ) +" +RDEPEND="${DEPEND}" + +PATCHES=( + "${FILESDIR}/${PN}-2021.7.1-use-system-libs.patch" +) + +src_prepare() { + # No -Werror + find . -name "CMakeLists.txt" -exec sed -i "s/-Werror//g" {} + || die + + # Use system libs instead + rm -r deps/* || die + + # DPC++ compiler required for full functionality + export CC="${ESYSROOT}/usr/lib/llvm/intel/bin/clang" + export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++" + + cmake_src_prepare +} + +src_configure() { + local mycmakeargs=( + -DBUILD_EXAMPLES=OFF + # BUILD_CONFIG causes sandbox violation + -DBUILD_CONFIG=OFF + -DCCL_ENABLE_ZE=ON + # TODO: Find out how to execute the tests + -DBUILD_FT=OFF + -DENABLE_MPI_TESTS=OFF + -DENABLE_MPI="$(usex mpi)" + # Use system fabric + -DLIBFABRIC_DIR="${ESYSROOT}/usr" + ) + cmake_src_configure +} diff --git a/dev-libs/oneCCL/oneCCL-2021.8.ebuild b/dev-libs/oneCCL/oneCCL-2021.8.ebuild new file mode 100644 index 000000000..a67659f4a --- /dev/null +++ b/dev-libs/oneCCL/oneCCL-2021.8.ebuild @@ -0,0 +1,62 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit cmake + +DESCRIPTION="oneAPI Collective Communications Library" +HOMEPAGE="https://github.com/oneapi-src/oneCCL" +SRC_URI="https://github.com/oneapi-src/oneCCL/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="~amd64" + +IUSE="mpi" + +BDEPEND="sys-devel/DPC++" + +DEPEND=" + dev-libs/level-zero:= + sys-apps/hwloc:= + sys-block/libfabric:= + sys-devel/ittapi + sys-cluster/pmix + mpi? ( virtual/mpi ) +" +RDEPEND="${DEPEND}" + +PATCHES=( + "${FILESDIR}/${PN}-2021.8-use-system-libs.patch" +) + +src_prepare() { + # No -Werror + find . -name "CMakeLists.txt" -exec sed -i "s/-Werror//g" {} + || die + + # Use system libs instead + rm -r deps/* || die + + # DPC++ compiler required for full functionality + export CC="${ESYSROOT}/usr/lib/llvm/intel/bin/clang" + export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++" + + cmake_src_prepare +} + +src_configure() { + local mycmakeargs=( + -DBUILD_EXAMPLES=OFF + # BUILD_CONFIG causes sandbox violation + -DBUILD_CONFIG=OFF + -DCCL_ENABLE_ZE=ON + # TODO: Find out how to execute the tests + -DBUILD_FT=OFF + -DENABLE_MPI_TESTS=OFF + -DENABLE_MPI="$(usex mpi)" + # Use system fabric + -DLIBFABRIC_DIR="${ESYSROOT}/usr" + ) + cmake_src_configure +} diff --git a/dev-libs/optix/Manifest b/dev-libs/optix/Manifest deleted file mode 100644 index 0a6859644..000000000 --- a/dev-libs/optix/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST NVIDIA-OptiX-SDK-7.4.0-linux64-x86_64.sh 57923655 BLAKE2B c3e159106ec6c8c446090ebd182fd3b0a75ec48b62e6984ae6559578688fd9a6cb29ea6065cb89aecdeb02247acbf3fb3bb0cbf69b10c29c222eb9fcbb0c6d90 SHA512 04f50c49d08c5e4e9be73ee322c4bff4f10a5e30445bc431e213c879a35cc5e36e0ceb8c864313f417628575a3c71593e65467ea13dd111b432fdf1db9383ae0 diff --git a/dev-libs/optix/metadata.xml b/dev-libs/optix/metadata.xml deleted file mode 100644 index 43be4e4e4..000000000 --- a/dev-libs/optix/metadata.xml +++ /dev/null @@ -1,10 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>heroxbd@gentoo.org</email> - </maintainer> - <maintainer type="person"> - <email>rich@warfaresdl.com</email> - </maintainer> -</pkgmetadata> diff --git a/dev-libs/optix/optix-7.4.0.ebuild b/dev-libs/optix/optix-7.4.0.ebuild deleted file mode 100644 index a3f61205e..000000000 --- a/dev-libs/optix/optix-7.4.0.ebuild +++ /dev/null @@ -1,37 +0,0 @@ -# Copyright 2021-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -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-libs/simclist/metadata.xml b/dev-libs/simclist/metadata.xml index 8426fdb21..62c13e1e4 100644 --- a/dev-libs/simclist/metadata.xml +++ b/dev-libs/simclist/metadata.xml @@ -15,4 +15,7 @@ <flag name="dump">Disable building of dump and restore functionalities</flag> <flag name="hash">Allow list_hash() to work exclusively on memory locations</flag> </use> + <upstream> + <remote-id type="github">mij/simclist</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-libs/simclist/simclist-1.6_p1.ebuild b/dev-libs/simclist/simclist-1.6_p1.ebuild index 2b7eb84f1..41c9151c5 100644 --- a/dev-libs/simclist/simclist-1.6_p1.ebuild +++ b/dev-libs/simclist/simclist-1.6_p1.ebuild @@ -16,7 +16,7 @@ SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="debug doc dump hash threads" -BDEPEND="doc? ( app-doc/doxygen )" +BDEPEND="doc? ( app-text/doxygen )" CMAKE_IN_SOURCE_BUILD=1 diff --git a/dev-libs/tut/Manifest b/dev-libs/tut/Manifest deleted file mode 100644 index 30c2a9334..000000000 --- a/dev-libs/tut/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST tut-0_p20200320.tar.gz 262793 BLAKE2B fb8d16a7ca099dda88d300fb2521affb59fc7c84d52ba3a278cbd573621f1b922a3330097bd756844841582d6d0b5d76d8c90529e6f18a3020cd4ae0655e4591 SHA512 54b34519c90d8ab5e8264572c43245122d8c0f9d41a8acf86ad29f2cd4f35bf481b00f3aaedd922febd79b6da148fd90bb9d1521a148e7a7d6d01204805df1fb diff --git a/dev-libs/tut/metadata.xml b/dev-libs/tut/metadata.xml deleted file mode 100644 index 026cdb22b..000000000 --- a/dev-libs/tut/metadata.xml +++ /dev/null @@ -1,8 +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> -</pkgmetadata> diff --git a/dev-libs/tut/tut-0_p20200320.ebuild b/dev-libs/tut/tut-0_p20200320.ebuild deleted file mode 100644 index f4f13064e..000000000 --- a/dev-libs/tut/tut-0_p20200320.ebuild +++ /dev/null @@ -1,48 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DOCS_BUILDER="doxygen" -DOCS_DIR="doc/webgen" -DOCS_DEPEND="media-gfx/graphviz" - -inherit docs - -COMMIT="a8e49ef56dc8be5256b5305ec6702d50c5b36c09" - -DESCRIPTION="C++ Template Unit Test Framework" -HOMEPAGE="https://mrzechonek.github.io/tut-framework/" -SRC_URI="https://github.com/mrzechonek/tut-framework/archive/${COMMIT}.tar.gz -> ${P}.tar.gz" - -LICENSE="BSD-2" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -IUSE="examples" - -S="${WORKDIR}/${PN}-framework-${COMMIT}" - -BDEPEND="dev-util/waf" - -src_configure() { - waf configure || die "waf configure failed" -} - -src_compile() { - waf build || die "waf compile failed" - docs_compile -} - -src_install() { - default - # install function does not work for some reason - #waf install || die "waf install failed" - cp -r build/* . || die - - doheader -r include/* - - if use examples ; then - dodoc -r example - fi -} diff --git a/dev-ml/lacaml/metadata.xml b/dev-ml/lacaml/metadata.xml index 1094bf3da..24157e1f0 100644 --- a/dev-ml/lacaml/metadata.xml +++ b/dev-ml/lacaml/metadata.xml @@ -15,5 +15,6 @@ </longdescription> <upstream> <remote-id type="bitbucket">mmottl/lacaml</remote-id> + <remote-id type="github">mmottl/lacaml</remote-id> </upstream> </pkgmetadata> diff --git a/dev-python/Forthon/Forthon-0.8.49.ebuild b/dev-python/Forthon/Forthon-0.8.49.ebuild deleted file mode 100644 index f24277001..000000000 --- a/dev-python/Forthon/Forthon-0.8.49.ebuild +++ /dev/null @@ -1,23 +0,0 @@ -# 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 interface generator for Fortran based codes" -HOMEPAGE="https://github.com/dpgrote/Forthon" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -# no tests in package - -python_install_all() { - dodoc -r example simpleexample docs - - distutils-r1_python_install_all -} diff --git a/dev-python/Forthon/Forthon-0.9.4.ebuild b/dev-python/Forthon/Forthon-0.9.4.ebuild deleted file mode 100644 index fa6e3fde3..000000000 --- a/dev-python/Forthon/Forthon-0.9.4.ebuild +++ /dev/null @@ -1,17 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 -PYTHON_COMPAT=( python3_{7..9} ) - -inherit distutils-r1 - -DESCRIPTION="Python interface generator for Fortran based codes" -HOMEPAGE="https://github.com/dpgrote/Forthon" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -# no tests in package diff --git a/dev-python/Forthon/Manifest b/dev-python/Forthon/Manifest deleted file mode 100644 index fc38dbbbb..000000000 --- a/dev-python/Forthon/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST Forthon-0.8.49.tar.gz 83622 BLAKE2B 0c9d6af9a68cb05bf75fc638f3bb080aab25a5f575d2fb92c97ff3d1ae7f6925680d15fad8ae8e67c23b12c2b230ddd5bf0ef8e5900f5f379e4a3b843a449888 SHA512 50b8f2af32af061e0349a97076c50c54b22581c2b2c857a5529eca7714f2ad22ace25d792072397ba64b267ec9a24b1a670f454667ee9e3aae97331311870035 -DIST Forthon-0.9.4.tar.gz 86694 BLAKE2B 962e732543a0d5197a26b0d2036952fc056f0d23f771fd286fae874b33386422d2bf15ba51b31d596348c2291ef6490830d80d709e0cbe420179603956ce6567 SHA512 1e48bcd5610e1431474d9f9721ea375650a36ddffb796fd3ff8b710c53fe6814d7ae6b12d054451ac2c44febff126500c1ea6e66acdeda65c3a1818295dbbf50 diff --git a/dev-python/Forthon/metadata.xml b/dev-python/Forthon/metadata.xml deleted file mode 100644 index 8ddc1aa0d..000000000 --- a/dev-python/Forthon/metadata.xml +++ /dev/null @@ -1,23 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>gentoo@aisha.cc</email> - <name>Aisha Tammy</name> - </maintainer> - <maintainer type="project"> - <email>sci@gentoo.org</email> - <name>Gentoo Science Project</name> - </maintainer> - <longdescription> - Forthon generates links between Fortran95 and Python. Python is a high - level, object oriented, interactive and scripting language that allows - a flexible and versatile interface to computational tools. The Forthon - package generates the necessary wrapping code which allows access to - the Fortran database and to the Fortran subroutines and - functions. This provides a development package where the - computationally intensive parts of a code can be written in efficient - Fortran, and the high level controlling code can be written in the - much more versatile Python language. - </longdescription> -</pkgmetadata> diff --git a/dev-python/MagnetoResistance-tool/MagnetoResistance-tool-0.0.2.ebuild b/dev-python/MagnetoResistance-tool/MagnetoResistance-tool-0.0.2.ebuild new file mode 100644 index 000000000..23e03adcf --- /dev/null +++ b/dev-python/MagnetoResistance-tool/MagnetoResistance-tool-0.0.2.ebuild @@ -0,0 +1,22 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..12} ) +DISTUTILS_USE_PEP517=setuptools +PYPI_NO_NORMALIZE=1 +inherit distutils-r1 pypi + +DESCRIPTION="Create calibration matrix to correct for magneto-resistance in resistive sensors" +HOMEPAGE="https://gitlab.science.ru.nl/hfml/MRcalib" + +LICENSE="GPL-3+" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + dev-python/matplotlib[${PYTHON_USEDEP}] +" diff --git a/dev-python/MagnetoResistance-tool/Manifest b/dev-python/MagnetoResistance-tool/Manifest new file mode 100644 index 000000000..b8d0afd21 --- /dev/null +++ b/dev-python/MagnetoResistance-tool/Manifest @@ -0,0 +1 @@ +DIST MagnetoResistance-tool-0.0.2.tar.gz 21657 BLAKE2B 5d1a2f497f742df04aac5db6afe83373e6e3e3cea3891585c22d1585186665f0d597b3dccd5f2adfef4e58bc41f680b974974cb12c56e3ef29f69122407cfff5 SHA512 4866197feb96912edc19691ba7ea54303ed168d8ab72c534ad910a3a77ce6e8ccf0f19744eca5044936c29bde131d4c352abbd57547f1c30b3ae59d4aac36986 diff --git a/dev-python/MagnetoResistance-tool/metadata.xml b/dev-python/MagnetoResistance-tool/metadata.xml new file mode 100644 index 000000000..aed122741 --- /dev/null +++ b/dev-python/MagnetoResistance-tool/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>andrewammerlaan@gentoo.org</email> + <name>Andrew Ammerlaan</name> + </maintainer> + <upstream> + <remote-id type="pypi">MagnetoResistance-tool</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/POT/Manifest b/dev-python/POT/Manifest deleted file mode 100644 index 9db8bb97b..000000000 --- a/dev-python/POT/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST POT-0.7.0.tar.gz 189869 BLAKE2B 40f651d70e3177cc1d778b635e8609057cebe1685c36ed65d1d5ec26ae3c5665fb872b7efcd98d90012ed3e2a0251ddd8fafcae551254ee68697788cfd9e984e SHA512 a52f748ebee128732cd17281aace1f95bf638cbc8e1610774aef947b27b5172bcbf434c9e6a36ef4d2920940331d6ced1ff5315ca1b7705fda14489c34e5b6ff diff --git a/dev-python/POT/POT-0.7.0.ebuild b/dev-python/POT/POT-0.7.0.ebuild deleted file mode 100644 index e25d01017..000000000 --- a/dev-python/POT/POT-0.7.0.ebuild +++ /dev/null @@ -1,29 +0,0 @@ -# Copyright 1999-2020 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 Optimal Transport Library" -HOMEPAGE="https://github.com/PythonOT/POT" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -RDEPEND="${PYTHON_DEPS} - dev-python/cython[${PYTHON_USEDEP}] - dev-python/scipy[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] -" -DEPEND="${RDEPEND}" - -distutils_enable_tests pytest - -python_test() { - pytest -c /dev/null -vv || die "tests failed for ${EPYTHON}" -} diff --git a/dev-python/POT/metadata.xml b/dev-python/POT/metadata.xml deleted file mode 100644 index 2f2c0b51c..000000000 --- a/dev-python/POT/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>gentoo@aisha.cc</email> - <name>Aisha Tammy</name> - </maintainer> - <maintainer type="project"> - <email>sci@gentoo.org</email> - <name>Gentoo Science Project</name> - </maintainer> -</pkgmetadata> diff --git a/dev-python/PeakUtils/Manifest b/dev-python/PeakUtils/Manifest deleted file mode 100644 index 8b9972e10..000000000 --- a/dev-python/PeakUtils/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST PeakUtils-1.3.3.tar.gz 118684 BLAKE2B 978128ca36150487b54d491845b2eb4d28718760a43e5e71eb8a11142dd6dca3ffbb60e7a9c2e604c4b9868180f5fbe1a13c89a8390ecac34dce50f5e1b83548 SHA512 c6bc49907221b11ca4af204f55b24e8ca2b8267e989d9971523d33077519027ffc140883c8dca5988f04a4adf2e02d5c15b595d5474b2be410cc8ca87840cf4a diff --git a/dev-python/PeakUtils/PeakUtils-1.3.3.ebuild b/dev-python/PeakUtils/PeakUtils-1.3.3.ebuild deleted file mode 100644 index 983d2c645..000000000 --- a/dev-python/PeakUtils/PeakUtils-1.3.3.ebuild +++ /dev/null @@ -1,28 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 -PYTHON_COMPAT=( python3_{7..9} ) - -inherit distutils-r1 - -DESCRIPTION="Peak detection utilities for 1D data" -HOMEPAGE="https://bitbucket.org/lucashnegri/peakutils" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64" - -RDEPEND=" - >=dev-python/numpy-1.8.0[${PYTHON_USEDEP}] - dev-python/scipy[${PYTHON_USEDEP}] - " -DEPEND="${RDEPEND}" -BDEPEND=" - test? ( - dev-python/pandas - ) -" - -distutils_enable_tests pytest diff --git a/dev-python/PeakUtils/metadata.xml b/dev-python/PeakUtils/metadata.xml deleted file mode 100644 index ba9535089..000000000 --- a/dev-python/PeakUtils/metadata.xml +++ /dev/null @@ -1,19 +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> -As the name implies, this package provides utilities related to the -detection of peaks on 1D data. Includes functions to perform -baseline estimation, to find the indexes of the peaks in the data -and performing Gaussian fitting or centroid computation to further -increase the resolution of the peak detection. -</longdescription> - <upstream> - <remote-id type="bitbucket">lucashnegri/peakutils</remote-id> - <remote-id type="pypi">PeakUtils</remote-id> - </upstream> -</pkgmetadata> diff --git a/dev-python/affine/affine-2.3.0.ebuild b/dev-python/affine/affine-2.3.0.ebuild index a298cec26..7cc363d92 100644 --- a/dev-python/affine/affine-2.3.0.ebuild +++ b/dev-python/affine/affine-2.3.0.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) DISTUTILS_USE_PEP517="setuptools" inherit distutils-r1 diff --git a/dev-python/amply/Manifest b/dev-python/amply/Manifest deleted file mode 100644 index 09b9588e7..000000000 --- a/dev-python/amply/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST amply-0.1.4.tar.gz 28182 BLAKE2B 78ae51f18355968c7713351267fe8a60adc797c9e0e37092f538935026898b51413f346a0faecc748a290f3fd3e4c313cfab6d0ddacfe34f76ecdb4ecd562ffb SHA512 cb9140a157059edd69f634499946b1e006993037eed44c6eb844e211454d975455e00cc5da8771a09b4345d77c30515b7c106420b15dae8ca54ac599399fb3ed diff --git a/dev-python/amply/amply-0.1.4.ebuild b/dev-python/amply/amply-0.1.4.ebuild deleted file mode 100644 index db2b71b73..000000000 --- a/dev-python/amply/amply-0.1.4.ebuild +++ /dev/null @@ -1,25 +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 distutils-r1 - -DESCRIPTION="Allows you to load and manipulate AMPL/GLPK data as Python data structures" -HOMEPAGE="https://github.com/willu47/amply/" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="EPL-1.0" -KEYWORDS="~amd64 ~x86" -SLOT="0" - -BDEPEND="dev-python/setuptools_scm[${PYTHON_USEDEP}]" - -RDEPEND=" - dev-python/docutils[${PYTHON_USEDEP}] - dev-python/pyparsing[${PYTHON_USEDEP}] -" - -distutils_enable_tests pytest diff --git a/dev-python/amply/metadata.xml b/dev-python/amply/metadata.xml deleted file mode 100644 index 3d5e87252..000000000 --- a/dev-python/amply/metadata.xml +++ /dev/null @@ -1,11 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci@gentoo.org</email> - <name>Gentoo Science Project</name> - </maintainer> - <upstream> - <remote-id type="pypi">amply</remote-id> - </upstream> -</pkgmetadata> diff --git a/dev-python/annexremote/annexremote-1.5.0.ebuild b/dev-python/annexremote/annexremote-1.5.0.ebuild index b35e3c274..a6dacd5c9 100644 --- a/dev-python/annexremote/annexremote-1.5.0.ebuild +++ b/dev-python/annexremote/annexremote-1.5.0.ebuild @@ -3,27 +3,20 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) -inherit distutils-r1 +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) +inherit distutils-r1 pypi DESCRIPTION="Helper module to easily develop git-annex remotes" HOMEPAGE="https://github.com/Lykos153/AnnexRemote" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" LICENSE="GPL-3" SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="examples" - -COMMON_DEPEND="dev-python/future[${PYTHON_USEDEP}]" -RDEPEND=" - ${COMMON_DEPEND} -" -DEPEND=" - ${COMMON_DEPEND} -" - -distutils_enable_tests nose +# Tests require nose, reported upstream: +# https://github.com/Lykos153/AnnexRemote/issues/61 +RESTRICT="test" python_install_all() { distutils-r1_python_install_all diff --git a/dev-python/annexremote/annexremote-1.6.0.ebuild b/dev-python/annexremote/annexremote-1.6.0.ebuild index b35e3c274..a6dacd5c9 100644 --- a/dev-python/annexremote/annexremote-1.6.0.ebuild +++ b/dev-python/annexremote/annexremote-1.6.0.ebuild @@ -3,27 +3,20 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) -inherit distutils-r1 +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) +inherit distutils-r1 pypi DESCRIPTION="Helper module to easily develop git-annex remotes" HOMEPAGE="https://github.com/Lykos153/AnnexRemote" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" LICENSE="GPL-3" SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="examples" - -COMMON_DEPEND="dev-python/future[${PYTHON_USEDEP}]" -RDEPEND=" - ${COMMON_DEPEND} -" -DEPEND=" - ${COMMON_DEPEND} -" - -distutils_enable_tests nose +# Tests require nose, reported upstream: +# https://github.com/Lykos153/AnnexRemote/issues/61 +RESTRICT="test" python_install_all() { distutils-r1_python_install_all diff --git a/dev-python/anys/Manifest b/dev-python/anys/Manifest index d5c7418ba..bb3dbee15 100644 --- a/dev-python/anys/Manifest +++ b/dev-python/anys/Manifest @@ -1,2 +1 @@ -DIST anys-0.2.0.tar.gz 17799 BLAKE2B d481c43df1a3161f75a32b6fc7a38d3e18dc996f05dd08abb3891ca9570a2a841b159547f1c6889b73d2476a141404baba4ad3e10c318bc2e230c9d136b02ff6 SHA512 72bdc9df4cd805604f5497418a90738fccbc0ffd2dddf81324fe50d0d8ab13e036ff829e284dea8473427af396f02ceb01a191ad7d6946427478a12c04ca2ffd DIST anys-0.2.1.tar.gz 17850 BLAKE2B c7eda2e245108f9a0a0263af45589d7b0df78767517e9b56768626e43badc5100f01a844d17b10e34a19c0a0fbfa951ba97a374cb8951e7a5560e11867b12d78 SHA512 5a46d9e8aa97401f11dcc7a26a3d8dc759c59b5485222cb6ba1df3d4b2d8d67455102943f044850d289cd3e32bcaf6413ed4a4dfbee26c049a6ef32dfa5cd87e diff --git a/dev-python/anys/anys-0.2.0.ebuild b/dev-python/anys/anys-0.2.0.ebuild deleted file mode 100644 index 0d2fec35f..000000000 --- a/dev-python/anys/anys-0.2.0.ebuild +++ /dev/null @@ -1,28 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{8..9} ) -DISTUTILS_USE_SETUPTOOLS=pyproject.toml -inherit distutils-r1 - -DESCRIPTION="Matchers for pytest" -HOMEPAGE="https://github.com/jwodder/anys" -SRC_URI="https://github.com/jwodder/anys/releases/download/v${PV}/${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="test" -RESTRICT="!test? ( test )" - -RDEPEND=" - dev-python/wheel[${PYTHON_USEDEP}] -" - -PATCHES=( - "${FILESDIR}/${PN}-0.2.0-coverage.patch" -) - -distutils_enable_tests pytest diff --git a/dev-python/anys/anys-0.2.1.ebuild b/dev-python/anys/anys-0.2.1.ebuild index 783fc75ce..88e61a12e 100644 --- a/dev-python/anys/anys-0.2.1.ebuild +++ b/dev-python/anys/anys-0.2.1.ebuild @@ -1,10 +1,10 @@ -# Copyright 1999-2022 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) -DISTUTILS_USE_SETUPTOOLS=pyproject.toml +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools inherit distutils-r1 DESCRIPTION="Matchers for pytest" @@ -18,6 +18,7 @@ IUSE="test" RESTRICT="!test? ( test )" RDEPEND=" + dev-python/deprecated[${PYTHON_USEDEP}] dev-python/wheel[${PYTHON_USEDEP}] " diff --git a/dev-python/archspec/Manifest b/dev-python/archspec/Manifest new file mode 100644 index 000000000..8ad1830fc --- /dev/null +++ b/dev-python/archspec/Manifest @@ -0,0 +1,2 @@ +DIST archspec-0.1.4.tar.gz 35184 BLAKE2B fe05cab539163d986e639e7e9cf57db208f9cce7ee447d2d3207af0bad68f2d5410e720e5f73376f950b9672602885fe34942fb885d7acbb8ad7e31b7f139ee0 SHA512 28da79ba1469db38ab1424be49feba87378c252ead5ad07fca8ae752dc3503d281f2f3f30391fe6209b118800f357b5219593c2d0d11608d683e56c95ca8f286 +DIST archspec-0.2.2.tar.gz 38306 BLAKE2B c8f8011e122d31a603120231b5f4f034316e06412d64e0bb0fe38886508470d264f7a20da5ef79634fa5ba2f3d3b176b08151f9b5d72d64dbc5c90ce9bd6ff42 SHA512 e2310ca041064109358c918abbdfb581a1494d51d4c0f41e6172fdb9defcefd60f1b80ae2187c8143e37569c815fdc29508d52c048fe88c8c198e85997cef34d diff --git a/dev-python/archspec/archspec-0.1.4.ebuild b/dev-python/archspec/archspec-0.1.4.ebuild new file mode 100644 index 000000000..35500e00d --- /dev/null +++ b/dev-python/archspec/archspec-0.1.4.ebuild @@ -0,0 +1,19 @@ +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=poetry +inherit distutils-r1 pypi + +DESCRIPTION="labels for various aspects of a system architecture like CPU, etc." +HOMEPAGE="https://archspec.readthedocs.io/en/latest/index.html" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + >=dev-python/six-1.16.0[${PYTHON_USEDEP}] + <=dev-python/six-2.0.0[${PYTHON_USEDEP}] + >=dev-python/click-7.1.2[${PYTHON_USEDEP}] +" +DEPEND="${RDEPEND}" diff --git a/dev-python/archspec/archspec-0.2.2.ebuild b/dev-python/archspec/archspec-0.2.2.ebuild new file mode 100644 index 000000000..a7287fc72 --- /dev/null +++ b/dev-python/archspec/archspec-0.2.2.ebuild @@ -0,0 +1,13 @@ +EAPI=8 + +PYTHON_COMPAT=( python3_{10..12} ) +DISTUTILS_USE_PEP517=poetry +inherit distutils-r1 pypi + +DESCRIPTION="Labels for various aspects of a system architecture like CPU, etc." +HOMEPAGE="https://archspec.readthedocs.io/en/latest/index.html" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" + diff --git a/dev-python/archspec/metadata.xml b/dev-python/archspec/metadata.xml new file mode 100644 index 000000000..3688592b1 --- /dev/null +++ b/dev-python/archspec/metadata.xml @@ -0,0 +1,20 @@ +<?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> + <maintainer type="person"> + <email>alexander@neuwirth-informatik.de</email> + <name>Alexander Puck Neuwirth</name> + </maintainer> + <longdescription lang="en"> + Archspec aims at providing a standard set of human-understandable labels for various aspects of a system architecture like CPU, network fabrics, etc. and APIs to detect, query and compare them. + </longdescription> + <upstream> + <remote-id type="pypi">archspec</remote-id> + <remote-id type="github">archspec/archspec</remote-id> + <bugs-to>https://github.com/archspec/archspec/issues</bugs-to> + </upstream> +</pkgmetadata> diff --git a/dev-python/arrayfire-python/Manifest b/dev-python/arrayfire-python/Manifest deleted file mode 100644 index 6d077c449..000000000 --- a/dev-python/arrayfire-python/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST arrayfire-python-3.6.20181017.tar.gz 115659 BLAKE2B a58f8a3e929b9b04a7ce4339624833a9bcf513c790e6bf66edabaaeb01b590d651d6a89584ccf04387e9844dc506b1d21ea3392a2b6361802404820c1ff9d91a SHA512 8ae9d0c3e4b27ff237c47a55358ab6421eef4a3d251583e8d64b48ff40a8b9e6773e6fc27473c228141a5c9be86ba096bacd8ee1716d2f82f5dd97440b87bec4 -DIST arrayfire-python-3.6.20181017_p1.tar.gz 126376 BLAKE2B 33699c33a12a9231baac11a462502dbda2eb0e743256b7d4bff0b9b0925652efa9504ed5dc123b86493b7751bed85cd4050807297da087fe765dbc44ba985520 SHA512 2977365f7817528cf0c73fe0c21704efba9c5b30b902a5b3449ed6b4487492ed1baa2a60c03b42087232d8a119f5a0b0af9aa16cf8d83a05092c0eb78fa8e147 diff --git a/dev-python/arrayfire-python/arrayfire-python-3.6.20181017.ebuild b/dev-python/arrayfire-python/arrayfire-python-3.6.20181017.ebuild deleted file mode 100644 index 443642962..000000000 --- a/dev-python/arrayfire-python/arrayfire-python-3.6.20181017.ebuild +++ /dev/null @@ -1,35 +0,0 @@ -# Copyright 1999-2020 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 bindings for ArrayFire" -HOMEPAGE="http://www.arrayfire.com" - -if [[ ${PV} == 9999 ]]; then - inherit git-r3 - EGIT_REPO_URI="https://github.com/arrayfire/arrayfire-python" -else - SRC_URI="https://github.com/arrayfire/arrayfire-python/archive/${PV}.tar.gz -> ${P}.tar.gz" - KEYWORDS="~amd64" -fi - -LICENSE="BSD" -SLOT="0" -IUSE="test" -RESTRICT="!test? ( test )" - -RDEPEND=" - sci-libs/arrayfire -" -DEPEND="${RDEPEND}" - -DISTUTILS_IN_SOURCE_BUILD=1 - -python_test() { - ${EPYTHON} -m arrayfire.tests || \ - die "tests failed with ${EPYTHON}" -} diff --git a/dev-python/arrayfire-python/arrayfire-python-3.6.20181017_p1.ebuild b/dev-python/arrayfire-python/arrayfire-python-3.6.20181017_p1.ebuild deleted file mode 100644 index 7907a4e33..000000000 --- a/dev-python/arrayfire-python/arrayfire-python-3.6.20181017_p1.ebuild +++ /dev/null @@ -1,39 +0,0 @@ -# Copyright 1999-2020 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 bindings for ArrayFire" -HOMEPAGE="http://www.arrayfire.com" - -if [[ ${PV} == 9999 ]]; then - inherit git-r3 - EGIT_REPO_URI="https://github.com/arrayfire/arrayfire-python" -else - COMMIT=534b8c2ab4db5b08347f4d3d2f86a58ba8fcfdb6 - SRC_URI="https://github.com/arrayfire/arrayfire-python/archive/${COMMIT}.tar.gz -> ${P}.tar.gz" - S="${WORKDIR}"/${PN}-${COMMIT} - KEYWORDS="~amd64" -fi - -LICENSE="BSD" -SLOT="0" -IUSE="test" -RESTRICT="!test? ( test )" - -RDEPEND=" - sci-libs/arrayfire -" -DEPEND="${RDEPEND}" - -DISTUTILS_IN_SOURCE_BUILD=1 - -PATCHES=( "${FILESDIR}"/${P}-skip_tests.patch ) - -python_test() { - ${EPYTHON} -m tests || \ - die "tests failed with ${EPYTHON}" -} diff --git a/dev-python/arrayfire-python/files/arrayfire-python-3.6.20181017_p1-skip_tests.patch b/dev-python/arrayfire-python/files/arrayfire-python-3.6.20181017_p1-skip_tests.patch deleted file mode 100644 index eb4eb54cf..000000000 --- a/dev-python/arrayfire-python/files/arrayfire-python-3.6.20181017_p1-skip_tests.patch +++ /dev/null @@ -1,20 +0,0 @@ -diff --git a/tests/simple/__init__.py b/tests/simple/__init__.py -index 4950136..41c9cf2 100644 ---- a/tests/simple/__init__.py -+++ b/tests/simple/__init__.py -@@ -11,7 +11,6 @@ - - from ._util import tests - from .algorithm import simple_algorithm --from .arith import simple_arith - from .array_test import simple_array - from .blas import simple_blas - from .data import simple_data -@@ -28,7 +27,6 @@ from .statistics import simple_statistics - __all__ = [ - "tests", - "simple_algorithm", -- "simple_arith", - "simple_array", - "simple_blas", - "simple_data", diff --git a/dev-python/arrayfire-python/metadata.xml b/dev-python/arrayfire-python/metadata.xml deleted file mode 100644 index 8cbbb986a..000000000 --- a/dev-python/arrayfire-python/metadata.xml +++ /dev/null @@ -1,21 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>gentoo@aisha.cc</email> - <name>Aisha Tammy</name> - </maintainer> - <maintainer type="project"> - <email>sci@gentoo.org</email> - <name>Gentoo Science Project</name> - </maintainer> - <longdescription> - ArrayFire is a high performance library for parallel computing - wih an easy-to-use API. This package project Python bindings - for the ArrayFire library. - </longdescription> - <upstream> - <remote-id type="github">arrayfire/arrayfire-python</remote-id> - <remote-id type="pypi">arrayfire</remote-id> - </upstream> -</pkgmetadata> diff --git a/dev-python/asciitree/asciitree-0.3.3.ebuild b/dev-python/asciitree/asciitree-0.3.3.ebuild index 0ced423c8..29d5ecf87 100644 --- a/dev-python/asciitree/asciitree-0.3.3.ebuild +++ b/dev-python/asciitree/asciitree-0.3.3.ebuild @@ -1,14 +1,14 @@ -# Copyright 1999-2022 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_{10..11} ) inherit distutils-r1 DESCRIPTION="ASCII trees in python" HOMEPAGE="https://github.com/mbr/asciitree" -SRC_URI="https://github.com/mbr/asciitree/archive/refs/tags/0.3.3.tar.gz -> ${P}.tar.gz" +SRC_URI="https://github.com/mbr/asciitree/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz" LICENSE="MIT" SLOT="0" diff --git a/dev-python/asciitree/metadata.xml b/dev-python/asciitree/metadata.xml index f6f63a810..8b000b491 100644 --- a/dev-python/asciitree/metadata.xml +++ b/dev-python/asciitree/metadata.xml @@ -1,4 +1,4 @@ -<?xml version='1.0' encoding='UTF-8'?> +<?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -9,4 +9,7 @@ <email>sci@gentoo.org</email> <name>Gentoo Science Project</name> </maintainer> + <upstream> + <remote-id type="github">mbr/asciitree</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/asdf/Manifest b/dev-python/asdf/Manifest index 3b2cf6ef8..ac7f18004 100644 --- a/dev-python/asdf/Manifest +++ b/dev-python/asdf/Manifest @@ -1 +1 @@ -DIST asdf-2.8.3.tar.gz 513853 BLAKE2B 73afb6f5799a13689bd2be73b8d9b45d5bb4a1f093654e3d8a0796a6342f03deabe64c6de4d33213ba762e3b2508541a25b24cccc490f0685714180af6790c43 SHA512 c3b72ed7fefd33958413c962d81213d2d141072473e08c767059a3ff46ba03f0135c9435a7893eb0eb43b199e2c701d62f263a487872a120465979dfec8988df +DIST asdf-2.14.3.tar.gz 489097 BLAKE2B 26e3da88f4b0ada5a995ff77fdb55a26aa9af1b53c4e90723b36080526ee218581d09295b169bddd998a4055d1b9818e793bfdafdc786a27f5ea87021e9f85e7 SHA512 125015a1d3a26034c8d483bebf609af02489d0710973828e443dea5cfa46cb33826078714b9ccbd385fcc92fd6b2d92253e80c32ca90565a48f45e4ff47b8655 diff --git a/dev-python/asdf/asdf-2.14.3.ebuild b/dev-python/asdf/asdf-2.14.3.ebuild new file mode 100644 index 000000000..2c935c1fb --- /dev/null +++ b/dev-python/asdf/asdf-2.14.3.ebuild @@ -0,0 +1,46 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools + +inherit distutils-r1 pypi + +DESCRIPTION="Python library for the Advanced Scientific Data Format" +HOMEPAGE="https://asdf.readthedocs.io/en/latest/" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" +# Reported upstream: +# https://github.com/asdf-format/asdf/issues/1319 +RESTRICT="test" + +BDEPEND="dev-python/setuptools-scm[${PYTHON_USEDEP}] + test? ( + dev-python/astropy[${PYTHON_USEDEP}] + dev-python/pytest-doctestplus[${PYTHON_USEDEP}] + dev-python/psutil[${PYTHON_USEDEP}] + dev-python/gwcs[${PYTHON_USEDEP}] + ) + doc? ( media-gfx/graphviz ) +" + +RDEPEND=" + >=dev-python/jmespath-0.6.2[${PYTHON_USEDEP}] + >=dev-python/jsonschema-3.0.2[${PYTHON_USEDEP}] + >=dev-python/numpy-1.10[${PYTHON_USEDEP}] + >=dev-python/pyyaml-3.10[${PYTHON_USEDEP}] + >=dev-python/semantic-version-2.8[${PYTHON_USEDEP}] +" + +distutils_enable_tests pytest +distutils_enable_sphinx docs dev-python/astropy dev-python/sphinx-astropy dev-python/matplotlib dev-python/docutils + +python_test() { + # discovers things in docs dir if we do not + # explicitly set it to run on the tests dir + epytest asdf/tests +} diff --git a/dev-python/asdf/asdf-2.8.3.ebuild b/dev-python/asdf/asdf-2.8.3.ebuild deleted file mode 100644 index 96663e49a..000000000 --- a/dev-python/asdf/asdf-2.8.3.ebuild +++ /dev/null @@ -1,44 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{8..9} ) -DISTUTILS_USE_SETUPTOOLS=rdepend - -inherit distutils-r1 - -DESCRIPTION="Python library for the Advanced Scientific Data Format" -HOMEPAGE="https://asdf.readthedocs.io/en/latest/" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -BDEPEND="dev-python/setuptools_scm[${PYTHON_USEDEP}] - test? ( - dev-python/astropy[${PYTHON_USEDEP}] - dev-python/pytest-doctestplus[${PYTHON_USEDEP}] - dev-python/psutil[${PYTHON_USEDEP}] - dev-python/gwcs[${PYTHON_USEDEP}] - ) - doc? ( media-gfx/graphviz ) -" - -RDEPEND=" - >=dev-python/jmespath-0.6.2[${PYTHON_USEDEP}] - >=dev-python/jsonschema-3.0.2[${PYTHON_USEDEP}] - >=dev-python/numpy-1.10[${PYTHON_USEDEP}] - >=dev-python/pyyaml-3.10[${PYTHON_USEDEP}] - >=dev-python/semantic_version-2.8[${PYTHON_USEDEP}] -" - -distutils_enable_tests pytest -distutils_enable_sphinx docs dev-python/astropy dev-python/sphinx-astropy dev-python/matplotlib dev-python/docutils - -python_test() { - # discovers things in docs dir if we do not - # explicitly set it to run on the tests dir - epytest asdf/tests -} diff --git a/dev-python/asdf/metadata.xml b/dev-python/asdf/metadata.xml index 4f4367037..332ed9dd0 100644 --- a/dev-python/asdf/metadata.xml +++ b/dev-python/asdf/metadata.xml @@ -5,4 +5,7 @@ <email>sci-astronomy@gentoo.org</email> <name>Gentoo Astronomy Project</name> </maintainer> + <upstream> + <remote-id type="pypi">asdf</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/astropy-healpix/Manifest b/dev-python/astropy-healpix/Manifest index 0845b8ed4..ee0baaaa9 100644 --- a/dev-python/astropy-healpix/Manifest +++ b/dev-python/astropy-healpix/Manifest @@ -1 +1 @@ -DIST astropy_healpix-0.6.tar.gz 104224 BLAKE2B a06474de29f2848d18dedb45202ea63ba5893d6993ef39ebb91e02b55c0f5e100522c267198a233c8771f3920c620f7eddb83f08c82c3cb4151432e1815b00d8 SHA512 c54a41e50c7eaa51126b20abc88e5fc8f7c02521baeb4a69a5a8eac42f59350273e8f30c17926daf628c7866550eec141980ce0349028ff72a4ac2786275f428 +DIST astropy_healpix-0.7.tar.gz 107330 BLAKE2B c1daed6475b63d59debd19ad97fc3547917df93b9b6998aef51f38a7e4014a543f25f6823dac12e93745fa8cd6c17b418035730b4d37f85b7df250e8d4fd6026 SHA512 33e23a616a0a36880066d96a50b949b1a96b4a1cecc1ebe8584c817a10587d26eb58879fb175c3fd675c3fbc98d4be1cfa9b19aa9ad4ac7a1528a8e6d32f7436 diff --git a/dev-python/astropy-healpix/astropy-healpix-0.6.ebuild b/dev-python/astropy-healpix/astropy-healpix-0.6.ebuild deleted file mode 100644 index ce6ec0cd3..000000000 --- a/dev-python/astropy-healpix/astropy-healpix-0.6.ebuild +++ /dev/null @@ -1,36 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{8..10} ) - -inherit distutils-r1 - -DESCRIPTION="HEALPix for Astropy" -HOMEPAGE="https://github.com/astropy/astropy-healpix" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P/-/_}.tar.gz" -S="${WORKDIR}/${P/-/_}" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -#TODO: Package all these pytest deps: -# pytest-doctestplus>=0.2.0 -# pytest-remotedata>=0.3.1 -# pytest-openfiles>=0.3.1 -# pytest-astropy-header>=0.1.2 -# pytest-arraydiff>=0.1 -# pytest-filter-subpackage>=0.1 -RESTRICT="test" - -BDEPEND="dev-python/setuptools_scm[${PYTHON_USEDEP}]" - -RDEPEND=" - >=dev-python/astropy-3.2[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] -" - -distutils_enable_sphinx docs dev-python/sphinx-astropy dev-python/matplotlib -distutils_enable_tests --install pytest diff --git a/dev-python/astropy-healpix/astropy-healpix-0.7.ebuild b/dev-python/astropy-healpix/astropy-healpix-0.7.ebuild new file mode 100644 index 000000000..9bf99f7e2 --- /dev/null +++ b/dev-python/astropy-healpix/astropy-healpix-0.7.ebuild @@ -0,0 +1,35 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 pypi + +DESCRIPTION="HEALPix for Astropy" +HOMEPAGE="https://github.com/astropy/astropy-healpix" +S="${WORKDIR}/${P/-/_}" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +#TODO: Package all these pytest deps: +# pytest-doctestplus>=0.2.0 +# pytest-remotedata>=0.3.1 +# pytest-openfiles>=0.3.1 +# pytest-astropy-header>=0.1.2 +# pytest-arraydiff>=0.1 +# pytest-filter-subpackage>=0.1 +RESTRICT="test" + +BDEPEND="dev-python/setuptools-scm[${PYTHON_USEDEP}]" + +RDEPEND=" + >=dev-python/astropy-3.2[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] +" + +distutils_enable_sphinx docs dev-python/sphinx-astropy dev-python/matplotlib +distutils_enable_tests pytest diff --git a/dev-python/astropy-healpix/metadata.xml b/dev-python/astropy-healpix/metadata.xml index 4f4367037..2d40d7328 100644 --- a/dev-python/astropy-healpix/metadata.xml +++ b/dev-python/astropy-healpix/metadata.xml @@ -5,4 +5,8 @@ <email>sci-astronomy@gentoo.org</email> <name>Gentoo Astronomy Project</name> </maintainer> + <upstream> + <remote-id type="github">astropy/astropy-healpix</remote-id> + <remote-id type="pypi">astropy-healpix</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/astropy-helpers/astropy-helpers-4.0.1-r1.ebuild b/dev-python/astropy-helpers/astropy-helpers-4.0.1-r1.ebuild new file mode 100644 index 000000000..be72affc7 --- /dev/null +++ b/dev-python/astropy-helpers/astropy-helpers-4.0.1-r1.ebuild @@ -0,0 +1,29 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools +PYPI_NO_NORMALIZE=1 +inherit distutils-r1 pypi xdg-utils + +MYPV=${PV/_/} +S=${WORKDIR}/${PN}-${MYPV} + +DESCRIPTION="Helpers for Astropy and Affiliated packages" +HOMEPAGE="https://github.com/astropy/astropy-helpers" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +python_prepare_all() { + sed -e '/import ah_bootstrap/d' \ + -i setup.py || die "Removing ah_bootstrap failed" + xdg_environment_reset + distutils-r1_python_prepare_all +} + +# master file /var/tmp/portage/dev-python/astropy-helpers-4.0.1/work/astropy-helpers-4.0.1/astropy_helpers/sphinx/index.rst not found +#distutils_enable_sphinx astropy_helpers/sphinx dev-python/sphinx-astropy diff --git a/dev-python/astropy-helpers/astropy-helpers-4.0.1.ebuild b/dev-python/astropy-helpers/astropy-helpers-4.0.1.ebuild deleted file mode 100644 index 393066583..000000000 --- a/dev-python/astropy-helpers/astropy-helpers-4.0.1.ebuild +++ /dev/null @@ -1,29 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{8..10} ) - -inherit distutils-r1 xdg-utils - -MYPV=${PV/_/} -S=${WORKDIR}/${PN}-${MYPV} - -DESCRIPTION="Helpers for Astropy and Affiliated packages" -HOMEPAGE="https://github.com/astropy/astropy-helpers" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${PN}-${MYPV}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -python_prepare_all() { - sed -e '/import ah_bootstrap/d' \ - -i setup.py || die "Removing ah_bootstrap failed" - xdg_environment_reset - distutils-r1_python_prepare_all -} - -# master file /var/tmp/portage/dev-python/astropy-helpers-4.0.1/work/astropy-helpers-4.0.1/astropy_helpers/sphinx/index.rst not found -#distutils_enable_sphinx astropy_helpers/sphinx dev-python/sphinx-astropy diff --git a/dev-python/astropy-helpers/metadata.xml b/dev-python/astropy-helpers/metadata.xml index 8bc35edb7..8bd2cb74a 100644 --- a/dev-python/astropy-helpers/metadata.xml +++ b/dev-python/astropy-helpers/metadata.xml @@ -15,5 +15,6 @@ </maintainer> <upstream> <remote-id type="github">astropy/astropy-helpers</remote-id> + <remote-id type="pypi">astropy-helpers</remote-id> </upstream> </pkgmetadata> diff --git a/dev-python/astropy-sphinx-theme/astropy-sphinx-theme-1.1-r1.ebuild b/dev-python/astropy-sphinx-theme/astropy-sphinx-theme-1.1-r1.ebuild new file mode 100644 index 000000000..5b63931b8 --- /dev/null +++ b/dev-python/astropy-sphinx-theme/astropy-sphinx-theme-1.1-r1.ebuild @@ -0,0 +1,19 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools +PYPI_NO_NORMALIZE=1 + +inherit distutils-r1 pypi + +DESCRIPTION="The sphinx theme for Astropy and affiliated packages" +HOMEPAGE="https://github.com/astropy/astropy-sphinx-theme" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +distutils_enable_tests pytest diff --git a/dev-python/astropy-sphinx-theme/astropy-sphinx-theme-1.1.ebuild b/dev-python/astropy-sphinx-theme/astropy-sphinx-theme-1.1.ebuild deleted file mode 100644 index 844b614bd..000000000 --- a/dev-python/astropy-sphinx-theme/astropy-sphinx-theme-1.1.ebuild +++ /dev/null @@ -1,19 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{8..10} ) -DISTUTILS_USE_SETUPTOOLS=rdepend - -inherit distutils-r1 - -DESCRIPTION="The sphinx theme for Astropy and affiliated packages" -HOMEPAGE="https://github.com/astropy/astropy-sphinx-theme" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -distutils_enable_tests pytest diff --git a/dev-python/astropy-sphinx-theme/metadata.xml b/dev-python/astropy-sphinx-theme/metadata.xml index 4f4367037..7db317173 100644 --- a/dev-python/astropy-sphinx-theme/metadata.xml +++ b/dev-python/astropy-sphinx-theme/metadata.xml @@ -5,4 +5,8 @@ <email>sci-astronomy@gentoo.org</email> <name>Gentoo Astronomy Project</name> </maintainer> + <upstream> + <remote-id type="github">astropy/astropy-sphinx-theme</remote-id> + <remote-id type="pypi">astropy-sphinx-theme</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/astropy/Manifest b/dev-python/astropy/Manifest index c8278e21a..3d86b9bab 100644 --- a/dev-python/astropy/Manifest +++ b/dev-python/astropy/Manifest @@ -1 +1 @@ -DIST astropy-5.0.tar.gz 7823746 BLAKE2B e769f9ea26e156a2342dc75b307c16c2c38108adf0dfd931812b2eb3234941055c013378a492306f2247c16b4804fe569ba1cbfd8427df1aac2b808976082cf9 SHA512 3c0b0cdef434f27ee399fbfc3d55b95ce8395624caf8e73a205dba7742c39d8a2bcea9bf61c2c20235da7388d40c657c5474bfc7e3dc3c9e5911e39bab47cdb9 +DIST astropy-5.2.1.tar.gz 8284422 BLAKE2B ded3556d6b16fe7abbbd019c23c0297f4690b13f054a1b98ab6aaeb20b92debefbc6e7c6c5eff8c65dfaa271826885027d6ba4a92f94218632162501a30b025b SHA512 46da7b065e119fa36233ced928abab31d6022fd116d2ed6825cb88b456ab57130772eea1de8cff7b5b7f30aadf46b933ad56a47cf6d2d68c0fa7593f322a6ea0 diff --git a/dev-python/astropy/astropy-5.0.ebuild b/dev-python/astropy/astropy-5.0.ebuild deleted file mode 100644 index c650533d6..000000000 --- a/dev-python/astropy/astropy-5.0.ebuild +++ /dev/null @@ -1,59 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{8..10} ) - -inherit distutils-r1 - -DESCRIPTION="Core functionality for performing astrophysics with Python" -HOMEPAGE="https://astropy.org/" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -#TODO: Package all these pytest deps: -# pytest-remotedata>=0.3.1 -# pytest-openfiles>=0.3.1 -# pytest-astropy-header>=0.1.2 -# pytest-arraydiff>=0.1 -# pytest-filter-subpackage>=0.1 -RESTRICT="test" - -RDEPEND=" - dev-libs/expat:0= - >=dev-python/numpy-1.18[${PYTHON_USEDEP}] - >=dev-python/pyerfa-2.0[${PYTHON_USEDEP}] - >=dev-python/pyyaml-3.13[${PYTHON_USEDEP}] - >=dev-python/packaging-19.0[${PYTHON_USEDEP}] - sci-astronomy/wcslib:0= - >=sci-libs/cfitsio-3.350:0= - sys-libs/zlib:0= -" -BDEPEND="${RDEPEND} - dev-python/astropy-helpers[${PYTHON_USEDEP}] - dev-python/extension-helpers[${PYTHON_USEDEP}] - dev-python/cython[${PYTHON_USEDEP}] - dev-python/setuptools_scm[${PYTHON_USEDEP}] - test? ( - dev-libs/libxml2 - dev-python/h5py[${PYTHON_USEDEP}] - dev-python/ipython[${PYTHON_USEDEP}] - dev-python/matplotlib[${PYTHON_USEDEP}] - dev-python/objgraph[${PYTHON_USEDEP}] - dev-python/pytest-xdist[${PYTHON_USEDEP}] - dev-python/scipy[${PYTHON_USEDEP}] - )" - -distutils_enable_tests pytest -# TODO: Fix this -# NameError: name 'disabled_intersphinx_mapping' is not defined -#distutils_enable_sphinx docs \ -# dev-python/matplotlib \ -# dev-python/graphviz \ -# dev-python/sphinx-astropy \ -# dev-python/pyyaml \ -# dev-python/scipy diff --git a/dev-python/astropy/astropy-5.2.1.ebuild b/dev-python/astropy/astropy-5.2.1.ebuild new file mode 100644 index 000000000..b52d1e6f5 --- /dev/null +++ b/dev-python/astropy/astropy-5.2.1.ebuild @@ -0,0 +1,60 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools + +inherit distutils-r1 pypi + +DESCRIPTION="Core functionality for performing astrophysics with Python" +HOMEPAGE="https://www.astropy.org/" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +#TODO: Package all these pytest deps: +# pytest-remotedata>=0.3.1 +# pytest-openfiles>=0.3.1 +# pytest-astropy-header>=0.1.2 +# pytest-arraydiff>=0.1 +# pytest-filter-subpackage>=0.1 +RESTRICT="test" + +RDEPEND=" + dev-libs/expat:0= + >=dev-python/numpy-1.18[${PYTHON_USEDEP}] + >=dev-python/pyerfa-2.0[${PYTHON_USEDEP}] + >=dev-python/pyyaml-3.13[${PYTHON_USEDEP}] + >=dev-python/packaging-19.0[${PYTHON_USEDEP}] + sci-astronomy/wcslib:0= + >=sci-libs/cfitsio-3.350:0= + sys-libs/zlib:0= +" +DEPEND="${RDEPEND}" +BDEPEND=" + dev-python/astropy-helpers[${PYTHON_USEDEP}] + dev-python/extension-helpers[${PYTHON_USEDEP}] + dev-python/cython[${PYTHON_USEDEP}] + dev-python/setuptools-scm[${PYTHON_USEDEP}] + test? ( + dev-libs/libxml2 + dev-python/h5py[${PYTHON_USEDEP}] + dev-python/ipython[${PYTHON_USEDEP}] + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/objgraph[${PYTHON_USEDEP}] + dev-python/pytest-xdist[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + )" + +distutils_enable_tests pytest +# TODO: Fix this +# NameError: name 'disabled_intersphinx_mapping' is not defined +#distutils_enable_sphinx docs \ +# dev-python/matplotlib \ +# dev-python/graphviz \ +# dev-python/sphinx-astropy \ +# dev-python/pyyaml \ +# dev-python/scipy diff --git a/dev-python/astropy/metadata.xml b/dev-python/astropy/metadata.xml index 3d1dc456d..3891d8cc8 100644 --- a/dev-python/astropy/metadata.xml +++ b/dev-python/astropy/metadata.xml @@ -9,4 +9,7 @@ <email>sci-astronomy@gentoo.org</email> <name>Gentoo Astronomy Project</name> </maintainer> + <upstream> + <remote-id type="pypi">astropy</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/astroquery/Manifest b/dev-python/astroquery/Manifest index 5d34a7193..2472dec6d 100644 --- a/dev-python/astroquery/Manifest +++ b/dev-python/astroquery/Manifest @@ -1 +1 @@ -DIST astroquery-0.4.1.tar.gz 6525892 BLAKE2B 9ee1d57f265e0370df4f302b6422955701c5fd8deb27c4dd76b5746f3c307e5b4d09b29a8746ff0f6b406065b0d339b3afa59e974806e47d9d9ee6fef3e18e09 SHA512 71e160c9495532c0bf0060574996187d7801feeecac526b50b3aebd0ce147ae3877a2a235ab5c49690733d5833050bd3f8365be7ba6f97f2db8a416766f12c15 +DIST astroquery-0.4.6.tar.gz 6070636 BLAKE2B 9ea912661e3d0ad59ca42087527eeee5657062c39c389a2635e699a5cb683eb6f4324b9c546e227f26e57b645057ad6bde0b2dad7f71cf5f7b090792ca9f4afc SHA512 4ec5e2fbd9754ae0be614011a0020218fbdd7d7cf4511836b40cefcf99fa0feb88cc247c2c83e556aa11ff10930b9e4d7784d175039f9581a4551bb4667a3529 diff --git a/dev-python/astroquery/astroquery-0.4.1.ebuild b/dev-python/astroquery/astroquery-0.4.1.ebuild deleted file mode 100644 index a7884eb1d..000000000 --- a/dev-python/astroquery/astroquery-0.4.1.ebuild +++ /dev/null @@ -1,45 +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 collection of packages to access online astronomical resources" -HOMEPAGE="https://www.astropy.org/astroquery/" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -#TODO: Package all these pytest deps: -# pytest-doctestplus>=0.2.0 -# pytest-remotedata>=0.3.1 -# pytest-openfiles>=0.3.1 -# pytest-astropy-header>=0.1.2 -# pytest-arraydiff>=0.1 -# pytest-filter-subpackage>=0.1 -RESTRICT="test" - -RDEPEND=" - >=dev-python/astropy-0.2[${PYTHON_USEDEP}] - dev-python/beautifulsoup4[${PYTHON_USEDEP}] - dev-python/html5lib[${PYTHON_USEDEP}] - dev-python/keyring[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/requests[${PYTHON_USEDEP}] - dev-python/six[${PYTHON_USEDEP}] -" - -BDEPEND="test? ( - dev-python/photutils[${PYTHON_USEDEP}] - dev-python/scipy[${PYTHON_USEDEP}] -)" - -# TODO: Fix this -# NameError: name 'disabled_intersphinx_mapping' is not defined -#distutils_enable_sphinx docs dev-python/sphinx-astropy -distutils_enable_tests pytest diff --git a/dev-python/astroquery/astroquery-0.4.6.ebuild b/dev-python/astroquery/astroquery-0.4.6.ebuild new file mode 100644 index 000000000..3e140280c --- /dev/null +++ b/dev-python/astroquery/astroquery-0.4.6.ebuild @@ -0,0 +1,45 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools + +inherit distutils-r1 pypi + +DESCRIPTION="A collection of packages to access online astronomical resources" +HOMEPAGE="https://astroquery.readthedocs.io/" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +#TODO: Package all these pytest deps: +# pytest-doctestplus>=0.2.0 +# pytest-remotedata>=0.3.1 +# pytest-openfiles>=0.3.1 +# pytest-astropy-header>=0.1.2 +# pytest-arraydiff>=0.1 +# pytest-filter-subpackage>=0.1 +RESTRICT="test" + +RDEPEND=" + >=dev-python/astropy-0.2[${PYTHON_USEDEP}] + dev-python/beautifulsoup4[${PYTHON_USEDEP}] + dev-python/html5lib[${PYTHON_USEDEP}] + dev-python/keyring[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/requests[${PYTHON_USEDEP}] + dev-python/six[${PYTHON_USEDEP}] +" + +BDEPEND="test? ( + dev-python/photutils[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] +)" + +# TODO: Fix this +# NameError: name 'disabled_intersphinx_mapping' is not defined +#distutils_enable_sphinx docs dev-python/sphinx-astropy +distutils_enable_tests pytest diff --git a/dev-python/astroquery/metadata.xml b/dev-python/astroquery/metadata.xml index bb6a20b51..b70564de2 100644 --- a/dev-python/astroquery/metadata.xml +++ b/dev-python/astroquery/metadata.xml @@ -12,5 +12,6 @@ to support many services with a uniform API. </longdescription> <upstream> <remote-id type="github">astropy/astroquery</remote-id> + <remote-id type="pypi">astroquery</remote-id> </upstream> </pkgmetadata> diff --git a/dev-python/astroscrappy/astroscrappy-1.1.0-r1.ebuild b/dev-python/astroscrappy/astroscrappy-1.1.0-r1.ebuild new file mode 100644 index 000000000..cd34136af --- /dev/null +++ b/dev-python/astroscrappy/astroscrappy-1.1.0-r1.ebuild @@ -0,0 +1,29 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools + +inherit distutils-r1 pypi + +DESCRIPTION="Speedy Cosmic Ray Annihilation Package in Python" +HOMEPAGE="https://github.com/astropy/astroscrappy" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +#TODO: Fix this +RESTRICT="test" + +RDEPEND=" + >=dev-python/astropy-2.0[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] +" +BDEPEND="dev-python/cython[${PYTHON_USEDEP}]" + +# Requires self to already be installed +#distutils_enable_sphinx docs dev-python/sphinx-astropy +distutils_enable_tests pytest diff --git a/dev-python/astroscrappy/astroscrappy-1.1.0.ebuild b/dev-python/astroscrappy/astroscrappy-1.1.0.ebuild deleted file mode 100644 index f4ef741da..000000000 --- a/dev-python/astroscrappy/astroscrappy-1.1.0.ebuild +++ /dev/null @@ -1,31 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{8..10} ) - -inherit distutils-r1 - -DESCRIPTION="Speedy Cosmic Ray Annihilation Package in Python" -HOMEPAGE="https://github.com/astropy/astroscrappy" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -#TODO: Fix this -# ModuleNotFoundError: No module named 'astroscrappy.astroscrappy' -# happens even with --install argument -RESTRICT="test" - -RDEPEND=" - >=dev-python/astropy-2.0[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] -" -BDEPEND="dev-python/cython[${PYTHON_USEDEP}]" - -# Requires self to already be installed -#distutils_enable_sphinx docs dev-python/sphinx-astropy -distutils_enable_tests --install pytest diff --git a/dev-python/astroscrappy/metadata.xml b/dev-python/astroscrappy/metadata.xml index 4f4367037..b308f644b 100644 --- a/dev-python/astroscrappy/metadata.xml +++ b/dev-python/astroscrappy/metadata.xml @@ -5,4 +5,8 @@ <email>sci-astronomy@gentoo.org</email> <name>Gentoo Astronomy Project</name> </maintainer> + <upstream> + <remote-id type="github">astropy/astroscrappy</remote-id> + <remote-id type="pypi">astroscrappy</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/av/av-8.0.3.ebuild b/dev-python/av/av-8.0.3.ebuild index 57a8bbdfb..75236266d 100644 --- a/dev-python/av/av-8.0.3.ebuild +++ b/dev-python/av/av-8.0.3.ebuild @@ -3,13 +3,11 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) - -inherit distutils-r1 +PYTHON_COMPAT=( python3_10 ) +inherit distutils-r1 pypi DESCRIPTION="Pythonic bindings for FFmpeg's libraries." -HOMEPAGE="https://github.com/mikeboers/PyAV https://pypi.org/project/av/" -SRC_URI="mirror://pypi/${P:0:1}/${PN}/${P}.tar.gz" +HOMEPAGE="https://github.com/PyAV-Org/PyAV https://pypi.org/project/av/" LICENSE="BSD" SLOT="0" diff --git a/dev-python/av/metadata.xml b/dev-python/av/metadata.xml index 325d9cc57..2231a73ae 100644 --- a/dev-python/av/metadata.xml +++ b/dev-python/av/metadata.xml @@ -5,4 +5,8 @@ <email>jpizarrocallejas@gmail.com</email> <name>Jorge Pizarro Callejas</name> </maintainer> + <upstream> + <remote-id type="github">mikeboers/PyAV</remote-id> + <remote-id type="pypi">av</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/awkward-cpp/Manifest b/dev-python/awkward-cpp/Manifest new file mode 100644 index 000000000..8d27c5f19 --- /dev/null +++ b/dev-python/awkward-cpp/Manifest @@ -0,0 +1 @@ +DIST awkward-cpp-28.tar.gz 1422514 BLAKE2B ec87c37a37e3aceb0a35b580122a8c632070dc9fd284e34de66db2611cf1024dbd7ec8a355f52349783258cdaa91e0f966156689c82427f72574230c8b6ae6e1 SHA512 bbe0df527a7863b192c3c85a90c1295d2eb788eb7670a04a001838294dcdd434b49bdc2b4c3f71e34f5f160b4b9cafdea1cf290206fdcb14c0555005797a666d diff --git a/dev-python/awkward-cpp/awkward-cpp-28.ebuild b/dev-python/awkward-cpp/awkward-cpp-28.ebuild new file mode 100644 index 000000000..57634d120 --- /dev/null +++ b/dev-python/awkward-cpp/awkward-cpp-28.ebuild @@ -0,0 +1,26 @@ +EAPI=8 + +PYTHON_COMPAT=( python3_{10..12} ) + +CMAKE_MAKEFILE_GENERATOR="emake" +DISTUTILS_USE_PEP517=scikit-build-core +PYPI_NO_NORMALIZE=1 + +inherit pypi distutils-r1 + +DESCRIPTION="awkward-cpp bindings for Python" +HOMEPAGE="https://github.com/scikit-hep/awkward/" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" + +DEPEND=" + >=dev-python/numpy-1.18.0[${PYTHON_USEDEP}] +" +RDEPEND="${DEPEND}" +BDEPEND=" + >=dev-python/scikit-build-core-0.2.0[${PYTHON_USEDEP}] +" + +distutils_enable_tests pytest diff --git a/dev-python/awkward-cpp/metadata.xml b/dev-python/awkward-cpp/metadata.xml new file mode 100644 index 000000000..a94e99f4b --- /dev/null +++ b/dev-python/awkward-cpp/metadata.xml @@ -0,0 +1,19 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <maintainer type="person"> + <email>alexander@neuwirth-informatik.de</email> + <name>Alexander Puck Neuwirth</name> + </maintainer> + <longdescription lang="en"> + awkward-cpp provides precompiled routines for the awkward package. It is not useful on its own, only as a dependency for awkward . + </longdescription> + <upstream> + <remote-id type="pypi">awkward</remote-id> + <remote-id type="github">scikit-hep/awkward</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/awkward/Manifest b/dev-python/awkward/Manifest new file mode 100644 index 000000000..d3422fc99 --- /dev/null +++ b/dev-python/awkward/Manifest @@ -0,0 +1 @@ +DIST awkward-2.5.2.tar.gz 5561040 BLAKE2B 4799eeb25fa7433b4889328f9f147b435024c3f507ce66b5cbfcfc5b9c50e63f77131a43b8acd3d9f22d20915eaeb129162e26ffa83fd2071b9a393fbc441e7e SHA512 b6f4f2841e642bfc17aaf40779030d125e9737ef0ded20cc8a898c4b8c15c2932f12c8a0bda3e8c48bb8d13729cf97e181866f15913317bd2dba13b0dad6b929 diff --git a/dev-python/awkward/awkward-2.5.2.ebuild b/dev-python/awkward/awkward-2.5.2.ebuild new file mode 100644 index 000000000..c11095214 --- /dev/null +++ b/dev-python/awkward/awkward-2.5.2.ebuild @@ -0,0 +1,38 @@ +EAPI=8 + +PYTHON_COMPAT=( python3_{10..12} ) +DISTUTILS_USE_PEP517=hatchling +export SETUPTOOLS_SCM_PRETEND_VERSION=${PV} +inherit distutils-r1 pypi + +DESCRIPTION="Manipulate JSON-like data with NumPy-like idioms." +HOMEPAGE="https://github.com/scikit-hep/awkward" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + >=dev-python/numpy-1.18.0[${PYTHON_USEDEP}] + ~dev-python/awkward-cpp-28[${PYTHON_USEDEP}] +" +DEPEND="${RDEPEND}" +BDEPEND=" + dev-python/packaging[${PYTHON_USEDEP}] + dev-python/hatch-vcs[${PYTHON_USEDEP}] + dev-python/hatch-fancy-pypi-readme[${PYTHON_USEDEP}] + test? ( + dev-libs/apache-arrow[zstd] + dev-python/pyarrow[${PYTHON_USEDEP}] + dev-python/fsspec[${PYTHON_USEDEP}] + dev-python/numexpr[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + ) +" + +EPYTEST_IGNORE=( + tests-cuda/ + tests-cuda-kernels/ +) + +distutils_enable_tests pytest diff --git a/dev-python/awkward/metadata.xml b/dev-python/awkward/metadata.xml new file mode 100644 index 000000000..b3ac679d3 --- /dev/null +++ b/dev-python/awkward/metadata.xml @@ -0,0 +1,19 @@ +<?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> + <maintainer type="person"> + <email>alexander@neuwirth-informatik.de</email> + <name>Alexander Puck Neuwirth</name> + </maintainer> + <longdescription lang="en"> + Awkward Array is a library for nested, variable-sized data, including arbitrary-length lists, records, mixed types, and missing data, using NumPy-like idioms. + </longdescription> + <upstream> + <remote-id type="pypi">awkward</remote-id> + <remote-id type="github">scikit-hep/awkward</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/bcbio-gff/Manifest b/dev-python/bcbio-gff/Manifest deleted file mode 100644 index a4a0d0677..000000000 --- a/dev-python/bcbio-gff/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST bcbio-gff-0.6.6.tar.gz 19099 BLAKE2B d86840ecb3b3073ddb4810fad976fa306e9b7cd13bb3779f4b0832deef01388ed39a529fde75b2dbae1078132889007bf4cef728c0fb41ddc7f363209382914a SHA512 b8880181b8308cd729936cda9102c0ea4793aeb551d75d639fe23712245fd0c4c1a72de7d96e0739d92260503c2b45d22bf73ddfe6f260629b29409097050da5 diff --git a/dev-python/bcbio-gff/bcbio-gff-0.6.6.ebuild b/dev-python/bcbio-gff/bcbio-gff-0.6.6.ebuild deleted file mode 100644 index 73f412971..000000000 --- a/dev-python/bcbio-gff/bcbio-gff-0.6.6.ebuild +++ /dev/null @@ -1,18 +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="Read and write Generic Feature Format (GFF) with Biopython" -HOMEPAGE="https://pypi.python.org/pypi/bcbio-gff" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="HPND" # same as biopython -SLOT="0" -KEYWORDS="~amd64 ~x86" - -RDEPEND="dev-python/six[${PYTHON_USEDEP}]" diff --git a/dev-python/bcbio-gff/metadata.xml b/dev-python/bcbio-gff/metadata.xml deleted file mode 100644 index 138cb7705..000000000 --- a/dev-python/bcbio-gff/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>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/dev-python/bokeh/bokeh-2.4.2.ebuild b/dev-python/bokeh/bokeh-2.4.2.ebuild index d6dfa1901..7347e5110 100644 --- a/dev-python/bokeh/bokeh-2.4.2.ebuild +++ b/dev-python/bokeh/bokeh-2.4.2.ebuild @@ -3,14 +3,13 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) -DISTUTILS_USE_SETUPTOOLS=rdepend -DISTUTILS_IN_SOURCE_BUILD=1 -inherit distutils-r1 optfeature +PYTHON_COMPAT=( python3_{10..12} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 optfeature pypi DESCRIPTION="Statistical and interactive HTML plots for Python" HOMEPAGE="https://bokeh.org/" -SRC_URI="mirror://pypi/${P:0:1}/${PN}/${P}.tar.gz +SRC_URI+=" https://raw.githubusercontent.com/bokeh/bokeh/${PV}/conftest.py -> conftest-${P}.py " @@ -25,7 +24,7 @@ RDEPEND=" >=dev-python/pillow-7.1.0[${PYTHON_USEDEP}] >=dev-python/pyyaml-3.10[${PYTHON_USEDEP}] >=dev-python/typing-extensions-3.10.0[${PYTHON_USEDEP}] - >=www-servers/tornado-5.1[${PYTHON_USEDEP}] + >=dev-python/tornado-5.1[${PYTHON_USEDEP}] " BDEPEND=" test? ( diff --git a/dev-python/boost-histogram/Manifest b/dev-python/boost-histogram/Manifest new file mode 100644 index 000000000..1fb711744 --- /dev/null +++ b/dev-python/boost-histogram/Manifest @@ -0,0 +1 @@ +DIST boost_histogram-1.4.0.tar.gz 1329002 BLAKE2B 1636ed04c5df2f6c156468ffc0fed7b82469bb903c316b1b9fd209b7072ebb5b0de9969f4f8b50da69db7ee40009df534959db7734f1161da2c6216bddce858b SHA512 e7f61cc2d013a0664646d9edf1f713eb5f06f000ad2105e90229ef9b01b25a08c8e717a2ac241ed990fa2c082a1bb84af18e17b238640de5679d0ab76ff08af6 diff --git a/dev-python/boost-histogram/boost-histogram-1.4.0.ebuild b/dev-python/boost-histogram/boost-histogram-1.4.0.ebuild new file mode 100644 index 000000000..96950ebe5 --- /dev/null +++ b/dev-python/boost-histogram/boost-histogram-1.4.0.ebuild @@ -0,0 +1,39 @@ +EAPI=8 + +PYTHON_COMPAT=( python3_{10..12} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 pypi + +DESCRIPTION="Python bindings for the C++14 Boost::Histogram library" +HOMEPAGE="https://github.com/scikit-hep/boost-histogram" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + dev-libs/boost:=[python,${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] +" +DEPEND="${RDEPEND}" +BDEPEND=" + test? ( + dev-python/cloudpickle[${PYTHON_USEDEP}] + dev-python/hypothesis[${PYTHON_USEDEP}] + ) +" + +src_prepare() { + default + sed -i 's/"pytest-benchmark"//g' pyproject.toml || die +} + +distutils_enable_tests pytest + +EPYTEST_IGNORE=( + tests/test_benchmark_1d.py + tests/test_benchmark_2d.py + tests/test_benchmark_category_axis.py + tests/test_pickle.py + tests/test_threaded_fill.py +) diff --git a/dev-python/boost-histogram/metadata.xml b/dev-python/boost-histogram/metadata.xml new file mode 100644 index 000000000..345502cba --- /dev/null +++ b/dev-python/boost-histogram/metadata.xml @@ -0,0 +1,19 @@ +<?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> + <maintainer type="person"> + <email>alexander@neuwirth-informatik.de</email> + <name>Alexander Puck Neuwirth</name> + </maintainer> + <longdescription lang="en"> + Python bindings for Boost::Histogram (source), a C++14 library. This is one of the fastest libraries for histogramming, while still providing the power of a full histogram object. See what's new. + </longdescription> + <upstream> + <remote-id type="pypi">boost-histogram</remote-id> + <remote-id type="github">scikit-hep/boost-histogram</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/bz2file/Manifest b/dev-python/bz2file/Manifest deleted file mode 100644 index f8c6f14de..000000000 --- a/dev-python/bz2file/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST bz2file-0.98.tar.gz 11333 BLAKE2B 4ec4687f609521a637c20a512b544cd99d7c334f7cffaeff71d2a893eefe131a10bd548b9f1e829c899cdcf181f5e877e092cf08d709bb3f1ba9901d3386b3e6 SHA512 2d28e71fe71b5fea4008d65a1fa91d5c6fafcacc09f891c5deaaa985661576bd97f2e33fe9f8c5943841f09c153f2079a2511329c066e57c775fb0b089b30b20 diff --git a/dev-python/bz2file/bz2file-0.98.ebuild b/dev-python/bz2file/bz2file-0.98.ebuild deleted file mode 100644 index 0324854a1..000000000 --- a/dev-python/bz2file/bz2file-0.98.ebuild +++ /dev/null @@ -1,23 +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 distutils-r1 - -DESCRIPTION="Read and write bzip2-compressed files" -HOMEPAGE="https://github.com/nvawda/bz2file" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="Apache-2.0" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -PATCHES=( "${FILESDIR}"/${P}-always-threading.patch ) - -python_test() { - distutils_install_for_testing - ${EPYTHON} test_bz2file.py || die "tests failed for ${EPYTHON}" -} diff --git a/dev-python/bz2file/files/bz2file-0.98-always-threading.patch b/dev-python/bz2file/files/bz2file-0.98-always-threading.patch deleted file mode 100644 index ec11bce25..000000000 --- a/dev-python/bz2file/files/bz2file-0.98-always-threading.patch +++ /dev/null @@ -1,22 +0,0 @@ -threading is always available in newer pythons - -https://github.com/nvawda/bz2file/issues/7 - ---- a/test_bz2file.py -+++ b/test_bz2file.py -@@ -496,15 +496,6 @@ class BZ2FileTest(BaseTest): - for t in threads: - t.join() - -- def testWithoutThreading(self): -- if not hasattr(support, "import_fresh_module"): -- return -- module = support.import_fresh_module("bz2file", blocked=("threading",)) -- with module.BZ2File(self.filename, "wb") as f: -- f.write(b"abc") -- with module.BZ2File(self.filename, "rb") as f: -- self.assertEqual(f.read(), b"abc") -- - def testMixedIterationAndReads(self): - self.createTempFile() - linelen = len(self.TEXT_LINES[0]) diff --git a/dev-python/bz2file/metadata.xml b/dev-python/bz2file/metadata.xml deleted file mode 100644 index bb126c586..000000000 --- a/dev-python/bz2file/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="project"> - <email>sci@gentoo.org</email> - <name>Gentoo Science Project</name> - </maintainer> - <upstream> - <remote-id type="pypi">bz2file</remote-id> - </upstream> -</pkgmetadata> diff --git a/dev-python/cadquery-ocp/Manifest b/dev-python/cadquery-ocp/Manifest deleted file mode 100644 index 4818fac84..000000000 --- a/dev-python/cadquery-ocp/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST cadquery-ocp-7.5.2_beta.tar.gz 5571554 BLAKE2B 552e44b301b69f1b1b4f6c26c46638bcf94a5f753d4d35e2cbbd6e1d963a23c685d6c05ead56c970c6532a3adbbf7b1f2bd572e72fb482ccd2dac04585764910 SHA512 041d12632678b96f23528f289516e31457a4e0d3251db6f01e3fc2bb2ccc41d2df8b825c94db0cebd7419cf82070c75d20852f25d91f05377502d75adf493fd8 -DIST cadquery-ocp-7.5.3.0.tar.gz 5571719 BLAKE2B ba31d7ae2f54e2f4c17f0914cab1299b91254a3fab7d07f18b2d698ce6e47e9ea174e449e18971197b39f08fa755c4d16d8cba24f894372f5bd515ec6686935e SHA512 b89dc91f224ee87e288bd7e3a10cb3b2c6559e2b36c24aac2f675fb05ecda755b723721122a7e58d87ba4253024892795369b1e747fb77684c739d01d516d1a2 diff --git a/dev-python/cadquery-ocp/cadquery-ocp-7.5.2_beta.ebuild b/dev-python/cadquery-ocp/cadquery-ocp-7.5.2_beta.ebuild deleted file mode 100644 index ec0b8526d..000000000 --- a/dev-python/cadquery-ocp/cadquery-ocp-7.5.2_beta.ebuild +++ /dev/null @@ -1,195 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{8..9} ) - -# OCP uses "python-single-r1" only because VTK uses "python-single-r1". -inherit check-reqs cmake llvm multiprocessing python-single-r1 toolchain-funcs - -MY_PN=OCP -MY_PV="${PV//_/-}" -MY_P="${MY_PN}-${MY_PV}" -OCCT_PV=$(ver_cut 1-3) - -DESCRIPTION="Python wrapper for OCCT generated using pywrap" -HOMEPAGE="https://github.com/CadQuery/OCP" -SRC_URI="https://github.com/CadQuery/OCP/archive/refs/tags/${MY_PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="Apache-2.0" -KEYWORDS="~amd64 ~x86" -SLOT="0" -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -# CMake and VTK requirements derive from the "OCP/CMakeLists.txt" file -# generated by the src_prepare() phase. OCP currently requires opencascade -# (OCCT) to be built with "-DUSE_GLES2=OFF" and thus "-gles2". See also: -# https://github.com/CadQuery/OCP/issues/46#issuecomment-808920994 -BDEPEND=" - >=dev-libs/lief-0.11.5[python,${PYTHON_SINGLE_USEDEP}] - >=dev-util/cmake-3.16 -" -RDEPEND=" - ${PYTHON_DEPS} - sci-libs/opencascade:0/7.5[json,tbb,vtk] - >=sci-libs/vtk-9.0.0[python,${PYTHON_SINGLE_USEDEP}] -" -DEPEND="${RDEPEND} - $(python_gen_cond_dep ' - >=dev-python/cadquery-pywrap-'${OCCT_PV}'_rc0[${PYTHON_USEDEP}]') -" - -S="${WORKDIR}/${MY_P}" - -# The source "OCP/CMakeLists.txt" file is output by "bindgen" in src_prepare(). -CMAKE_IN_SOURCE_BUILD=True - -# Ensure the path returned by get_llvm_prefix() contains clang. -llvm_check_deps() { - has_version -r "sys-devel/clang:${LLVM_SLOT}" -} - -cadquery-ocp_check_reqs() { - CHECKREQS_DISK_BUILD=1300M check-reqs_pkg_${EBUILD_PHASE} -} - -pkg_pretend() { - cadquery-ocp_check_reqs -} - -pkg_setup() { - cadquery-ocp_check_reqs - llvm_pkg_setup - python-single-r1_pkg_setup -} - -# OCP currently requires manual configuration, compilation, and installation -# loosely inspired by the conda-specific "build-bindings-job.yml" file. -# -# Note that the cmake_src_prepare() function called below handles user patches. -src_prepare() { - # Most recently installed version of Clang. - local _CLANG_VERSION="$(CPP=clang clang-fullversion)" - - # Most recently installed version (excluding trailing patch) of VTK. - local _VTK_VERSION="$(best_version -r sci-libs/vtk)" - _VTK_VERSION="$(ver_cut 1-2 "${_VTK_VERSION##sci-libs/vtk}")" - - # Absolute dirname of the most recently installed Clang include directory, - # mimicing similar logic in the "dev-python/shiboken2" ebuild. See also: - # https://bugs.gentoo.org/619490 - local _CLANG_INCLUDE_DIR="${EPREFIX}/usr/lib/clang/${_CLANG_VERSION}/include" - - # Absolute filename of the most recently installed Clang shared library. - local _CLANG_LIB_FILE="$(get_llvm_prefix)/lib64/libclang.so" - - # Absolute dirname of OCCT's include and shared library directories. - local _OCCT_INCLUDE_DIR="${EPREFIX}/usr/include/opencascade-${OCCT_PV}" - local _OCCT_LIB_DIR="${EPREFIX}/usr/lib64/opencascade-${OCCT_PV}" - - # Absolute dirname of a temporary directory to store symbol tables for this - # OCCT version dumped below by the "dump_symbols.py" script. - local _OCCT_DUMP_SYMBOLS_ROOT_DIR="${T}/dump_symbols" - local _OCCT_DUMP_SYMBOLS_DIR="${_OCCT_DUMP_SYMBOLS_ROOT_DIR}/lib_linux" - - # Absolute dirname of VTK's include directory, - local _VTK_INCLUDE_DIR="${EPREFIX}/usr/include/vtk-${_VTK_VERSION}" - - # Ensure the above paths exist as a crude sanity test. - test -d "${_CLANG_INCLUDE_DIR}" || die "${_CLANG_INCLUDE_DIR} not found." - test -f "${_CLANG_LIB_FILE}" || die "${_CLANG_LIB_FILE} not found." - test -d "${_OCCT_INCLUDE_DIR}" || die "${_OCCT_INCLUDE_DIR} not found." - test -d "${_OCCT_LIB_DIR}" || die "${_OCCT_LIB_DIR} not found." - test -d "${_VTK_INCLUDE_DIR}" || die "${_VTK_INCLUDE_DIR} not found." - - # "dev-python/clang-python" atom targeting this Clang version. - local _CLANG_PYTHON_ATOM="dev-python/clang-python-${_CLANG_VERSION}" - - # Ensure "dev-python/clang-python" targets this Clang version. - has_version -r "=${_CLANG_PYTHON_ATOM}" || - die "${_CLANG_PYTHON_ATOM} not installed." - - # Remove all vendored paths. - rm -r conda opencascade pywrap *.dat || die - - # Inject a symlink to OCCT's include directory. - ln -s "${_OCCT_INCLUDE_DIR}" opencascade || die - - # Inject a symlink from OCCT's shared library directory into this temporary - # directory as required by the "dump_symbols.py" script. - mkdir -p "${_OCCT_DUMP_SYMBOLS_DIR}" || die - ln -s "${_OCCT_LIB_DIR}" "${_OCCT_DUMP_SYMBOLS_DIR}"/. || die - - # Update all hardcoded OCCT shared library versions in "dump_symbols.py". - sed -i -e 's~\(\.so\.\)[0-9]\+.[0-9]\+.[0-9]\+~\1'${OCCT_PV}'~' \ - dump_symbols.py || die - - # Dump (i.e., generate) symbol tables for this OCCT version. - einfo 'Dumping OCCT symbol tables...' - ${EPYTHON} dump_symbols.py "${_OCCT_DUMP_SYMBOLS_ROOT_DIR}" || die - - # Generate OCCT bindings in the "OCP/" subdirectory. - einfo 'Building OCP CMake binary tree...' - ${EPYTHON} -m bindgen \ - --verbose \ - --njobs $(makeopts_jobs) \ - --libclang "${_CLANG_LIB_FILE}" \ - --include "${_CLANG_INCLUDE_DIR}" \ - --include "${_VTK_INCLUDE_DIR}" \ - all ocp.toml || die - - # Remove the source "FindOpenCascade.cmake" after generating bindings, - # which copied that file to the target "OCP/FindOpenCascade.cmake". - rm FindOpenCascade.cmake || die - - #FIXME: Submit an issue recommending upstream replace their - #non-working "OCP/FindOpenCascade.cmake" file with a standard top-level - #"CMakeLists.txt" file that finds dependency paths: e.g., via @waebbl - # find_package(vtk 9 CONFIG REQUIRED) - # if(TARGET VTK::VTK) - # get_target_property(VTK_INCLUDE_DIRS VTK::VTK INTERFACE_INCLUDE_DIRECTORIES) - # endif() - - # Replace all hardcoded paths in "OCP/FindOpenCascade.cmake" with - # standard OCCT paths derived above. That file is both fundamentally - # broken and useless, as the ${CASROOT} environment variable and - # "/usr/lib64/cmake/opencascade-${PV}/OpenCASCADEConfig.cmake" file - # already reliably identify all requisite OpenCASCADE paths. Failure to - # patch this file results in src_configure() failures resembling: - # -- Could NOT find OPENCASCADE (missing: OPENCASCADE_LIBRARIES) - sed -i \ - -e 's~$ENV{CONDA_PREFIX}/include/opencascade\b~'${_OCCT_INCLUDE_DIR}'~' \ - -e 's~$ENV{CONDA_PREFIX}/lib\b~'${_OCCT_LIB_DIR}'~' \ - -e 's~$ENV{CONDA_PREFIX}/Library/\(lib\|include/opencascade\)~~' \ - OCP/FindOpenCascade.cmake || die - - # Patch the "OCP/CMakeLists.txt" file generated by "bindgen" above, passed - # as an absolute path both here and below to minimize eclass issues. - CMAKE_USE_DIR="${S}/OCP" cmake_src_prepare -} - -src_configure() { - local mycmakeargs=( - -B "${S}/OCP.build" - -DPYTHON_EXECUTABLE="${PYTHON}" - -Wno-dev - ) - - CMAKE_USE_DIR="${S}/OCP" cmake_src_configure -} - -src_compile() { - CMAKE_USE_DIR="${S}/OCP.build" cmake_src_compile -} - -# OCP currently ships no test suite, so we synthesize a crude import unit test. -src_test() { - PYTHONPATH="${S}/OCP.build" ${EPYTHON} -c \ - 'from OCP.gp import gp_Vec, gp_Ax1, gp_Ax3, gp_Pnt, gp_Dir, gp_Trsf, gp_GTrsf, gp, gp_XYZ' -} - -src_install() { - python_moduleinto . - python_domodule "${S}/OCP.build/"OCP*.so -} diff --git a/dev-python/cadquery-ocp/cadquery-ocp-7.5.3.0.ebuild b/dev-python/cadquery-ocp/cadquery-ocp-7.5.3.0.ebuild deleted file mode 100644 index 064952018..000000000 --- a/dev-python/cadquery-ocp/cadquery-ocp-7.5.3.0.ebuild +++ /dev/null @@ -1,195 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{8..10} ) - -# OCP uses "python-single-r1" only because VTK uses "python-single-r1". -inherit check-reqs cmake llvm multiprocessing python-single-r1 toolchain-funcs - -MY_PN=OCP -MY_PV="${PV//_/-}" -MY_P="${MY_PN}-${MY_PV}" -OCCT_PV=$(ver_cut 1-3) - -DESCRIPTION="Python wrapper for OCCT generated using pywrap" -HOMEPAGE="https://github.com/CadQuery/OCP" -SRC_URI="https://github.com/CadQuery/OCP/archive/refs/tags/${MY_PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="Apache-2.0" -KEYWORDS="~amd64 ~x86" -SLOT="0" -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -# CMake and VTK requirements derive from the "OCP/CMakeLists.txt" file -# generated by the src_prepare() phase. OCP currently requires opencascade -# (OCCT) to be built with "-DUSE_GLES2=OFF" and thus "-gles2". See also: -# https://github.com/CadQuery/OCP/issues/46#issuecomment-808920994 -BDEPEND=" - >=dev-libs/lief-0.11.5[python,${PYTHON_SINGLE_USEDEP}] - >=dev-util/cmake-3.16 -" -RDEPEND=" - ${PYTHON_DEPS} - sci-libs/opencascade:0/7.5[json,tbb,vtk] - >=sci-libs/vtk-9.0.0[python,${PYTHON_SINGLE_USEDEP}] -" -DEPEND="${RDEPEND} - $(python_gen_cond_dep ' - >=dev-python/cadquery-pywrap-'${OCCT_PV}'_rc0[${PYTHON_USEDEP}]') -" - -S="${WORKDIR}/${MY_P}" - -# The source "OCP/CMakeLists.txt" file is output by "bindgen" in src_prepare(). -CMAKE_IN_SOURCE_BUILD=True - -# Ensure the path returned by get_llvm_prefix() contains clang. -llvm_check_deps() { - has_version -r "sys-devel/clang:${LLVM_SLOT}" -} - -cadquery-ocp_check_reqs() { - CHECKREQS_DISK_BUILD=1300M check-reqs_pkg_${EBUILD_PHASE} -} - -pkg_pretend() { - cadquery-ocp_check_reqs -} - -pkg_setup() { - cadquery-ocp_check_reqs - llvm_pkg_setup - python-single-r1_pkg_setup -} - -# OCP currently requires manual configuration, compilation, and installation -# loosely inspired by the conda-specific "build-bindings-job.yml" file. -# -# Note that the cmake_src_prepare() function called below handles user patches. -src_prepare() { - # Most recently installed version of Clang. - local _CLANG_VERSION="$(CPP=clang clang-fullversion)" - - # Most recently installed version (excluding trailing patch) of VTK. - local _VTK_VERSION="$(best_version -r sci-libs/vtk)" - _VTK_VERSION="$(ver_cut 1-2 "${_VTK_VERSION##sci-libs/vtk}")" - - # Absolute dirname of the most recently installed Clang include directory, - # mimicing similar logic in the "dev-python/shiboken2" ebuild. See also: - # https://bugs.gentoo.org/619490 - local _CLANG_INCLUDE_DIR="${EPREFIX}/usr/lib/clang/${_CLANG_VERSION}/include" - - # Absolute filename of the most recently installed Clang shared library. - local _CLANG_LIB_FILE="$(get_llvm_prefix)/lib64/libclang.so" - - # Absolute dirname of OCCT's include and shared library directories. - local _OCCT_INCLUDE_DIR="${EPREFIX}/usr/include/opencascade" - local _OCCT_LIB_DIR="${EPREFIX}/usr/lib64/opencascade" - - # Absolute dirname of a temporary directory to store symbol tables for this - # OCCT version dumped below by the "dump_symbols.py" script. - local _OCCT_DUMP_SYMBOLS_ROOT_DIR="${T}/dump_symbols" - local _OCCT_DUMP_SYMBOLS_DIR="${_OCCT_DUMP_SYMBOLS_ROOT_DIR}/lib_linux" - - # Absolute dirname of VTK's include directory, - local _VTK_INCLUDE_DIR="${EPREFIX}/usr/include/vtk-${_VTK_VERSION}" - - # Ensure the above paths exist as a crude sanity test. - test -d "${_CLANG_INCLUDE_DIR}" || die "${_CLANG_INCLUDE_DIR} not found." - test -f "${_CLANG_LIB_FILE}" || die "${_CLANG_LIB_FILE} not found." - test -d "${_OCCT_INCLUDE_DIR}" || die "${_OCCT_INCLUDE_DIR} not found." - test -d "${_OCCT_LIB_DIR}" || die "${_OCCT_LIB_DIR} not found." - test -d "${_VTK_INCLUDE_DIR}" || die "${_VTK_INCLUDE_DIR} not found." - - # "dev-python/clang-python" atom targeting this Clang version. - local _CLANG_PYTHON_ATOM="dev-python/clang-python-${_CLANG_VERSION}" - - # Ensure "dev-python/clang-python" targets this Clang version. - has_version -r "=${_CLANG_PYTHON_ATOM}" || - die "${_CLANG_PYTHON_ATOM} not installed." - - # Remove all vendored paths. - rm -r conda opencascade pywrap *.dat || die - - # Inject a symlink to OCCT's include directory. - ln -s "${_OCCT_INCLUDE_DIR}" opencascade || die - - # Inject a symlink from OCCT's shared library directory into this temporary - # directory as required by the "dump_symbols.py" script. - mkdir -p "${_OCCT_DUMP_SYMBOLS_DIR}" || die - ln -s "${_OCCT_LIB_DIR}" "${_OCCT_DUMP_SYMBOLS_DIR}"/. || die - - # Update all hardcoded OCCT shared library versions in "dump_symbols.py". - sed -i -e 's~\(\.so\.\)[0-9]\+.[0-9]\+.[0-9]\+~\1'${OCCT_PV}'~' \ - dump_symbols.py || die - - # Dump (i.e., generate) symbol tables for this OCCT version. - einfo 'Dumping OCCT symbol tables...' - ${EPYTHON} dump_symbols.py "${_OCCT_DUMP_SYMBOLS_ROOT_DIR}" || die - - # Generate OCCT bindings in the "OCP/" subdirectory. - einfo 'Building OCP CMake binary tree...' - ${EPYTHON} -m bindgen \ - --verbose \ - --njobs $(makeopts_jobs) \ - --libclang "${_CLANG_LIB_FILE}" \ - --include "${_CLANG_INCLUDE_DIR}" \ - --include "${_VTK_INCLUDE_DIR}" \ - all ocp.toml || die - - # Remove the source "FindOpenCascade.cmake" after generating bindings, - # which copied that file to the target "OCP/FindOpenCascade.cmake". - rm FindOpenCascade.cmake || die - - #FIXME: Submit an issue recommending upstream replace their - #non-working "OCP/FindOpenCascade.cmake" file with a standard top-level - #"CMakeLists.txt" file that finds dependency paths: e.g., via @waebbl - # find_package(vtk 9 CONFIG REQUIRED) - # if(TARGET VTK::VTK) - # get_target_property(VTK_INCLUDE_DIRS VTK::VTK INTERFACE_INCLUDE_DIRECTORIES) - # endif() - - # Replace all hardcoded paths in "OCP/FindOpenCascade.cmake" with - # standard OCCT paths derived above. That file is both fundamentally - # broken and useless, as the ${CASROOT} environment variable and - # "/usr/lib64/cmake/opencascade-${PV}/OpenCASCADEConfig.cmake" file - # already reliably identify all requisite OpenCASCADE paths. Failure to - # patch this file results in src_configure() failures resembling: - # -- Could NOT find OPENCASCADE (missing: OPENCASCADE_LIBRARIES) - sed -i \ - -e 's~$ENV{CONDA_PREFIX}/include/opencascade\b~'${_OCCT_INCLUDE_DIR}'~' \ - -e 's~$ENV{CONDA_PREFIX}/lib\b~'${_OCCT_LIB_DIR}'~' \ - -e 's~$ENV{CONDA_PREFIX}/Library/\(lib\|include/opencascade\)~~' \ - OCP/FindOpenCascade.cmake || die - - # Patch the "OCP/CMakeLists.txt" file generated by "bindgen" above, passed - # as an absolute path both here and below to minimize eclass issues. - CMAKE_USE_DIR="${S}/OCP" cmake_src_prepare -} - -src_configure() { - local mycmakeargs=( - -B "${S}/OCP.build" - -DPYTHON_EXECUTABLE="${PYTHON}" - -Wno-dev - ) - - CMAKE_USE_DIR="${S}/OCP" cmake_src_configure -} - -src_compile() { - CMAKE_USE_DIR="${S}/OCP.build" cmake_src_compile -} - -# OCP currently ships no test suite, so we synthesize a crude import unit test. -src_test() { - PYTHONPATH="${S}/OCP.build" ${EPYTHON} -c \ - 'from OCP.gp import gp_Vec, gp_Ax1, gp_Ax3, gp_Pnt, gp_Dir, gp_Trsf, gp_GTrsf, gp, gp_XYZ' -} - -src_install() { - python_moduleinto . - python_domodule "${S}/OCP.build/"OCP*.so -} diff --git a/dev-python/cadquery-ocp/metadata.xml b/dev-python/cadquery-ocp/metadata.xml deleted file mode 100644 index a8bf5ee04..000000000 --- a/dev-python/cadquery-ocp/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="project"> - <email>sci@gentoo.org</email> - <name>Gentoo Science Project</name> - </maintainer> - <upstream> - <remote-id type="github">CadQuery/OCP</remote-id> - </upstream> -</pkgmetadata> diff --git a/dev-python/cadquery-pywrap/Manifest b/dev-python/cadquery-pywrap/Manifest deleted file mode 100644 index e5aef7ccf..000000000 --- a/dev-python/cadquery-pywrap/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST cadquery-pywrap-7.5.2_rc20210526.tar.gz 5584220 BLAKE2B b26fd4092f94e3d3eec191c0791faf29d90da2d85f9aa9a2f1cdf128975564db9f6b6002661eed8bbecddb31988ad2076a3a00ea601a43e38ffaa47e545911ca SHA512 40aa61e0774228c70c8ae41a6078a280d63697d297234dbff51ec84982b4a9f0a09db41c74a834ae91d01881a4d5660b1ebbb701d24141307a5fedcdfb075872 -DIST cadquery-pywrap-7.5.3_rc20220113.tar.gz 5584755 BLAKE2B d6585d33eddc34c719f9694322d209969698d6e5c67288a95ad841efbc2347d2cb162d8f3443a4e3373d70b97423485d1535c60713e4cb8ace413d114b852083 SHA512 f0d984b6fa6df3151d9cb612560a5266f98d286b9ab283c4647095dda3da1c54fb102babee4d2db574b695604332bc7576740406907995940eb60635afb614b8 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 deleted file mode 100644 index 19494930c..000000000 --- a/dev-python/cadquery-pywrap/cadquery-pywrap-7.5.2_rc20210526.ebuild +++ /dev/null @@ -1,70 +0,0 @@ -# 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 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-python/cadquery-pywrap/cadquery-pywrap-7.5.3_rc20220113.ebuild b/dev-python/cadquery-pywrap/cadquery-pywrap-7.5.3_rc20220113.ebuild deleted file mode 100644 index b2213cef7..000000000 --- a/dev-python/cadquery-pywrap/cadquery-pywrap-7.5.3_rc20220113.ebuild +++ /dev/null @@ -1,63 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{8..10} ) - -inherit llvm 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 7.5.3 has yet to be -# officially released. We instead package a commit known to work as expected. -MY_COMMIT="66e7376d3a27444393fc99acbdbef40bbc7031ae" -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() { - #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-python/cadquery-pywrap/metadata.xml b/dev-python/cadquery-pywrap/metadata.xml deleted file mode 100644 index aef989a0c..000000000 --- a/dev-python/cadquery-pywrap/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="project"> - <email>sci@gentoo.org</email> - <name>Gentoo Science Project</name> - </maintainer> - <stabilize-allarches/> - <upstream> - <remote-id type="github">CadQuery/pywrap</remote-id> - </upstream> -</pkgmetadata> diff --git a/dev-python/cadquery/Manifest b/dev-python/cadquery/Manifest deleted file mode 100644 index 380c3e6ae..000000000 --- a/dev-python/cadquery/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST cadquery-2.2_rc20210804.tar.gz 2832275 BLAKE2B b1b25130a9eb73e4913c6e9fc8d1fafd689bc9d216adee6d7fcc6fd80805b9351e87839fae3d6bf7e0a1ccf147e5b4a9afe8f6afc0e01c1b3a287e2671870c8d SHA512 0c5b16da24deba2267b204e5f51f707fffab9a238b27af84a500b8a98aa190be24be75d7bc2d1e282c04aea7116eb404ed4520515d53ae5a64aebafc647aa4a3 -DIST cadquery-2.2_rc20220506.tar.gz 2872821 BLAKE2B a48b4279a6e24166842c3f7c43e0ff3552f22f8821fa203fce30b76110423c375019228b1a458b0020ebfd23a052545ae0d90e3246619a2e53dbe8f411449f3d SHA512 65bd62268f920d1fa170921033c4e4f451e1bdf7e4d1cef457bf34c4466a076de57f40d38ed7fb1d8f207b45447d6763a52880d9d49426372b06fefd536e7c17 diff --git a/dev-python/cadquery/cadquery-2.2_rc20210804.ebuild b/dev-python/cadquery/cadquery-2.2_rc20210804.ebuild deleted file mode 100644 index 3eafde559..000000000 --- a/dev-python/cadquery/cadquery-2.2_rc20210804.ebuild +++ /dev/null @@ -1,56 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -DISTUTILS_SINGLE_IMPL=1 -PYTHON_COMPAT=( python3_{8..9} ) - -inherit distutils-r1 - -DESCRIPTION="Python parametric CAD scripting framework based on OCCT" -HOMEPAGE="https://cadquery.readthedocs.io" - -# The official CadQuery 2.1 tarball requires the obsolete OCCT 7.4.0, but -# CadQuery 2.2 has yet to be officially released. We instead package a commit -# known to work as expected with OCCT 7.5.2. -MY_COMMIT="9b657093c30147293034068dd9d58ec2b728e61a" - -#FIXME: Uncomment on bumping to the next stable release. -# SRC_URI="https://github.com/CadQuery/cadquery/archive/refs/tags/${PV}.tar.gz" -SRC_URI="https://github.com/CadQuery/cadquery/archive/${MY_COMMIT}.tar.gz -> ${P}.tar.gz" - -LICENSE="Apache-2.0" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -# Dependencies are intentionally listed in "conda/meta.yml" order. Due to its -# Anaconda focus, "setup.py" currently fails to list dependencies. -BDEPEND=" - test? ( - $(python_gen_cond_dep ' - dev-python/pytest[${PYTHON_USEDEP}] - dev-python/docutils[${PYTHON_USEDEP}] - dev-python/path-py[${PYTHON_USEDEP}] - ') - ) -" -RDEPEND=" - >=dev-python/cadquery-ocp-7.5.0[${PYTHON_SINGLE_USEDEP}] - $(python_gen_cond_dep ' - >=dev-python/pyparsing-2.0.0[${PYTHON_USEDEP}] - dev-python/ezdxf[${PYTHON_USEDEP}] - dev-python/ipython[${PYTHON_USEDEP}] - dev-python/typing-extensions[${PYTHON_USEDEP}] - dev-python/nptyping[${PYTHON_USEDEP}] - sci-libs/nlopt[python,${PYTHON_USEDEP}] - ') -" -DEPEND="${RDEPEND}" - -S="${WORKDIR}/${PN}-${MY_COMMIT}" - -distutils_enable_tests pytest - -#FIXME: Uncomment after packaging "dev-python/sphinx-autodoc-typehints". -# distutils_enable_sphinx docs dev-python/sphinx_rtd_theme dev-python/sphinx-autodoc-typehints diff --git a/dev-python/cadquery/cadquery-2.2_rc20220506.ebuild b/dev-python/cadquery/cadquery-2.2_rc20220506.ebuild deleted file mode 100644 index 26aa07b6d..000000000 --- a/dev-python/cadquery/cadquery-2.2_rc20220506.ebuild +++ /dev/null @@ -1,58 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -DISTUTILS_USE_PEP517=setuptools -DISTUTILS_SINGLE_IMPL=1 -PYTHON_COMPAT=( python3_{8..10} ) - -inherit distutils-r1 - -DESCRIPTION="Python parametric CAD scripting framework based on OCCT" -HOMEPAGE="https://cadquery.readthedocs.io" - -# The official CadQuery 2.1 tarball requires the obsolete OCCT 7.4.0, but -# CadQuery 2.2 has yet to be officially released. We instead package a commit -# known to work as expected with OCCT 7.5.2. -MY_COMMIT="803a05e78c233fdb537a8604c3f2b56a52179bbe" - -#FIXME: Uncomment on bumping to the next stable release. -# SRC_URI="https://github.com/CadQuery/cadquery/archive/refs/tags/${PV}.tar.gz" -SRC_URI="https://github.com/CadQuery/cadquery/archive/${MY_COMMIT}.tar.gz -> ${P}.tar.gz" - -LICENSE="Apache-2.0" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -# Dependencies are intentionally listed in "conda/meta.yml" order. Due to its -# Anaconda focus, "setup.py" currently fails to list dependencies. -BDEPEND=" - test? ( - $(python_gen_cond_dep ' - dev-python/docutils[${PYTHON_USEDEP}] - dev-python/path-py[${PYTHON_USEDEP}] - ') - ) -" -RDEPEND=" - >=dev-python/cadquery-ocp-7.5.0[${PYTHON_SINGLE_USEDEP}] - $(python_gen_cond_dep ' - >=dev-python/pyparsing-2.0.0[${PYTHON_USEDEP}] - dev-python/ezdxf[${PYTHON_USEDEP}] - dev-python/ipython[${PYTHON_USEDEP}] - dev-python/typing-extensions[${PYTHON_USEDEP}] - dev-python/nptyping[${PYTHON_USEDEP}] - sci-libs/nlopt[python,${PYTHON_USEDEP}] - dev-python/multimethod[${PYTHON_USEDEP}] - dev-python/typish[${PYTHON_USEDEP}] - ') -" -DEPEND="${RDEPEND}" - -S="${WORKDIR}/${PN}-${MY_COMMIT}" - -distutils_enable_tests pytest - -#FIXME: Uncomment after packaging "dev-python/sphinx-autodoc-typehints". -# distutils_enable_sphinx docs dev-python/sphinx_rtd_theme dev-python/sphinx-autodoc-typehints diff --git a/dev-python/cadquery/metadata.xml b/dev-python/cadquery/metadata.xml deleted file mode 100644 index 86166e277..000000000 --- a/dev-python/cadquery/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci@gentoo.org</email> - <name>Gentoo Science Project</name> - </maintainer> - <stabilize-allarches/> - <upstream> - <remote-id type="github">CadQuery/cadquery</remote-id> - </upstream> -</pkgmetadata> diff --git a/dev-python/ccdproc/ccdproc-2.3.0.ebuild b/dev-python/ccdproc/ccdproc-2.3.0.ebuild index 015dd2910..cdbe1c92c 100644 --- a/dev-python/ccdproc/ccdproc-2.3.0.ebuild +++ b/dev-python/ccdproc/ccdproc-2.3.0.ebuild @@ -1,15 +1,13 @@ -# Copyright 1999-2022 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) - -inherit distutils-r1 +PYTHON_COMPAT=( python3_10 ) +inherit distutils-r1 pypi DESCRIPTION="Astropy affiliated package for reducing optical/IR CCD data" HOMEPAGE="https://github.com/astropy/ccdproc" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" LICENSE="BSD" SLOT="0" @@ -24,13 +22,13 @@ KEYWORDS="~amd64 ~x86" # pytest-filter-subpackage>=0.1 RESTRICT="test" -BDEPEND="dev-python/setuptools_scm[${PYTHON_USEDEP}]" +BDEPEND="dev-python/setuptools-scm[${PYTHON_USEDEP}]" RDEPEND=" >=dev-python/astropy-4.0.6[${PYTHON_USEDEP}] >=dev-python/astroscrappy-1.0.8[${PYTHON_USEDEP}] >=dev-python/reproject-0.7[${PYTHON_USEDEP}] - sci-libs/scikit-image[${PYTHON_USEDEP}] + dev-python/scikit-image[${PYTHON_USEDEP}] dev-python/scipy[${PYTHON_USEDEP}] " diff --git a/dev-python/ccdproc/metadata.xml b/dev-python/ccdproc/metadata.xml index 387ed8dcd..72370beb3 100644 --- a/dev-python/ccdproc/metadata.xml +++ b/dev-python/ccdproc/metadata.xml @@ -12,5 +12,6 @@ and bad pixel tracking through the reduction steps. </longdescription> <upstream> <remote-id type="github">astropy/ccdproc</remote-id> + <remote-id type="pypi">ccdproc</remote-id> </upstream> </pkgmetadata> diff --git a/dev-python/click-didyoumean/Manifest b/dev-python/click-didyoumean/Manifest deleted file mode 100644 index 5c8198fe3..000000000 --- a/dev-python/click-didyoumean/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST click-didyoumean-0.2.0.tar.gz 309305 BLAKE2B 498571996758c57e015dd2f5de8966ace78defb2b1f9faa5a99c6020fb143bafa03e240f183f46a962dc9a3d39e1e9a7a49855f6f6e2dfd5452c546f015b17ce SHA512 690438809d103d2f2b54fc1dabb912b359f5355ba242bb37ef420cd8fcc3ed226911d7216acdcb3574bb0e93231c3a3ca7b00e9e99365955387cfeddeed449ae -DIST click-didyoumean-0.3.0.tar.gz 309301 BLAKE2B 2b667b5e94dd690e5b7a2e96b83197f52e201b002a32fff4a8dbb4bd5497d5b816b40d9da98729821e1d17a795a3776c1553a746aa4c4144cf7fe6540768e1ca SHA512 4927ee392f27950c3f7ef5e0f1d5a5e2421172f3e9d34ec76986c9c7ea698cfa1981678a06fb8682577d6ed04c242c42bdd1d796d7623a1c99dfdbdb61c80fca diff --git a/dev-python/click-didyoumean/click-didyoumean-0.2.0.ebuild b/dev-python/click-didyoumean/click-didyoumean-0.2.0.ebuild deleted file mode 100644 index b9a65c5d8..000000000 --- a/dev-python/click-didyoumean/click-didyoumean-0.2.0.ebuild +++ /dev/null @@ -1,24 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( pypy3 python3_{8..10} ) -inherit distutils-r1 - -DESCRIPTION="Enable git-like did-you-mean feature in click" -HOMEPAGE="https://github.com/click-contrib/click-didyoumean" -SRC_URI="https://github.com/click-contrib/click-didyoumean/archive/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" -RESTRICT="test" -# Tests actually pass, but not included in archive: -# https://github.com/click-contrib/click-didyoumean/issues/11 -DEPEND=" - dev-python/click -" -RDEPEND="${DEPEND}" - -distutils_enable_tests pytest diff --git a/dev-python/click-didyoumean/click-didyoumean-0.3.0.ebuild b/dev-python/click-didyoumean/click-didyoumean-0.3.0.ebuild deleted file mode 100644 index 9fe4373c8..000000000 --- a/dev-python/click-didyoumean/click-didyoumean-0.3.0.ebuild +++ /dev/null @@ -1,22 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -DISTUTILS_USE_SETUPTOOLS=pyproject.toml -PYTHON_COMPAT=( pypy3 python3_{8..10} ) -inherit distutils-r1 - -DESCRIPTION="Enable git-like did-you-mean feature in click" -HOMEPAGE="https://github.com/click-contrib/click-didyoumean" -SRC_URI="https://github.com/click-contrib/click-didyoumean/archive/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" -DEPEND=" - dev-python/click -" -RDEPEND="${DEPEND}" - -distutils_enable_tests pytest diff --git a/dev-python/click-didyoumean/metadata.xml b/dev-python/click-didyoumean/metadata.xml deleted file mode 100644 index d206a1b1c..000000000 --- a/dev-python/click-didyoumean/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="person"> - <email>gentoo@chymera.eu</email> - <name>Horea Christian</name> - </maintainer> - <maintainer type="project"> - <email>sci@gentoo.org</email> - <name>Gentoo Science Project</name> - </maintainer> - <upstream> - <remote-id type="github">click-contrib/click-didyoumean</remote-id> - <remote-id type="pypi">click-didyoumean</remote-id> - </upstream> -</pkgmetadata> diff --git a/dev-python/cligj/cligj-0.7.2.ebuild b/dev-python/cligj/cligj-0.7.2.ebuild index c90584b75..28e7f5510 100644 --- a/dev-python/cligj/cligj-0.7.2.ebuild +++ b/dev-python/cligj/cligj-0.7.2.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_{10..11} ) DISTUTILS_USE_PEP517="setuptools" inherit distutils-r1 diff --git a/dev-python/colorcet/Manifest b/dev-python/colorcet/Manifest index 0bb308038..a743f1d71 100644 --- a/dev-python/colorcet/Manifest +++ b/dev-python/colorcet/Manifest @@ -1 +1 @@ -DIST colorcet-2.0.6.tar.gz 2924576 BLAKE2B 7354047b9cad133d7376d9ad19a6c09f6aa0c70e5cf0b5df6405064fdea2013df97e3beda7bba2d2483134ce3c3d63287dd911d2c2c9ed52b932eb0069dfb3a0 SHA512 b447e21a8922f0df94fd73791b8794467cc1a6a576367f073693450121fe936837da558e9ce79b930db64bcbc910f0528d84dd90eaf8ffe68b5546ac81a37813 +DIST colorcet-3.0.1.tar.gz 3036207 BLAKE2B fabdd32dafc1828d50236ec93aa78e46aa125fe3564e732c2ece203cb71578d2d23303ccb2d069c938f513bd7df6a35f692b74b0c692546544f9e04fc28e9cae SHA512 92ede4947ef3af8b8cc3a4822c0e738cc8f0730fafb9f58a4a2c9bd3cda9c1e6ed254b9eec92f0306de95643eccd644b8ad955bc079ad20c00ee62e5f611431e diff --git a/dev-python/colorcet/colorcet-2.0.6.ebuild b/dev-python/colorcet/colorcet-2.0.6.ebuild deleted file mode 100644 index c8024aa51..000000000 --- a/dev-python/colorcet/colorcet-2.0.6.ebuild +++ /dev/null @@ -1,27 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -# Portage incorrectly claims "DISTUTILS_USE_SETUPTOOLS value is probably -# incorrect" for this package. It isn't. This package imports from neither -# "distutils", "packaging", "pkg_resources", nor "setuptools" at runtime. -PYTHON_COMPAT=( python3_{7..9} pypy3 ) - -inherit distutils-r1 - -DESCRIPTION="Collection of perceptually uniform colormaps" -HOMEPAGE="https://holoviz.org" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -DEPEND=" - >=dev-python/param-1.7.0[${PYTHON_USEDEP}] - >=dev-python/pyct-0.4.4[${PYTHON_USEDEP}] -" -RDEPEND="${DEPEND}" - -distutils_enable_tests pytest diff --git a/dev-python/colorcet/colorcet-3.0.1.ebuild b/dev-python/colorcet/colorcet-3.0.1.ebuild new file mode 100644 index 000000000..08ea7d55a --- /dev/null +++ b/dev-python/colorcet/colorcet-3.0.1.ebuild @@ -0,0 +1,27 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +# Portage incorrectly claims "DISTUTILS_USE_SETUPTOOLS value is probably +# incorrect" for this package. It isn't. This package imports from neither +# "distutils", "packaging", "pkg_resources", nor "setuptools" at runtime. +PYTHON_COMPAT=( python3_{10..11} pypy3 ) +DISTUTILS_USE_PEP517=setuptools + +inherit distutils-r1 pypi + +DESCRIPTION="Collection of perceptually uniform colormaps" +HOMEPAGE="https://holoviz.org" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +DEPEND=" + >=dev-python/param-1.7.0[${PYTHON_USEDEP}] + >=dev-python/pyct-0.4.4[${PYTHON_USEDEP}] +" +RDEPEND="${DEPEND}" + +distutils_enable_tests pytest diff --git a/dev-python/colorlover/Manifest b/dev-python/colorlover/Manifest deleted file mode 100644 index 0df2f3e30..000000000 --- a/dev-python/colorlover/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST colorlover-0.3.0.tar.gz 9060 BLAKE2B 33d060d7b324f47b785964e53473b4c2e70a130cfa9cf933222fe65dc6cbe93e7dd7054f6a38ab9ca79ac82e119e8b973266a06f4892bbb3b954cfcea4cb45b0 SHA512 4c39176c3375894202ecee86f3b4c45cd814720b4ce990e4d0605530a4fe2d71e28caa01aba143a86fc824c266cdf6f350cf84de6e1b01bfa2bdfae92a48bb2b diff --git a/dev-python/colorlover/colorlover-0.3.0.ebuild b/dev-python/colorlover/colorlover-0.3.0.ebuild deleted file mode 100644 index abf84b9b9..000000000 --- a/dev-python/colorlover/colorlover-0.3.0.ebuild +++ /dev/null @@ -1,18 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7..9} ) - -inherit distutils-r1 - -DESCRIPTION="color scales in python for humans" -HOMEPAGE="https://github.com/plotly/colorlover" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -# no tests in package diff --git a/dev-python/colorlover/metadata.xml b/dev-python/colorlover/metadata.xml deleted file mode 100644 index 2f2c0b51c..000000000 --- a/dev-python/colorlover/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>gentoo@aisha.cc</email> - <name>Aisha Tammy</name> - </maintainer> - <maintainer type="project"> - <email>sci@gentoo.org</email> - <name>Gentoo Science Project</name> - </maintainer> -</pkgmetadata> diff --git a/dev-python/colormath/Manifest b/dev-python/colormath/Manifest new file mode 100644 index 000000000..82abf9e32 --- /dev/null +++ b/dev-python/colormath/Manifest @@ -0,0 +1 @@ +DIST colormath-3.0.0.tar.gz 39761 BLAKE2B 3c7cdd08336a3ab35618a79ad31717433c08b23d8ee4fc5484da7305395fce61fa442fc9ff979ff107808c56e809deca9d176677f17106651047be14edc27e9e SHA512 12d1ab931000dadb087fdf7e56280690ff51a299e976347026703eac83373edcacd3310255fd52e05d842aab54d4f7d3ed19deda8db4b78574a7273f1c8cc058 diff --git a/dev-python/colormath/colormath-3.0.0.ebuild b/dev-python/colormath/colormath-3.0.0.ebuild new file mode 100644 index 000000000..8bd5a2b02 --- /dev/null +++ b/dev-python/colormath/colormath-3.0.0.ebuild @@ -0,0 +1,23 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..12} ) + +inherit pypi distutils-r1 + +DESCRIPTION="Easy color scales and color conversion for Python" +HOMEPAGE="https://pypi.org/project/colormath/" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~amd64-linux" + +RDEPEND="dev-python/networkx[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}]" + +# Nose test no longer supported +RESTRICT="test" +#distutils_enable_tests nose diff --git a/dev-python/colormath/metadata.xml b/dev-python/colormath/metadata.xml new file mode 100644 index 000000000..a633acfa0 --- /dev/null +++ b/dev-python/colormath/metadata.xml @@ -0,0 +1,12 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>mschu.dev@gmail.com</email> + <name>Michael Schubert</name> + </maintainer> + <upstream> + <remote-id type="github">gtaylor/python-colormath</remote-id> + <remote-id type="pypi">colormath</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/connection_pool/Manifest b/dev-python/connection_pool/Manifest new file mode 100644 index 000000000..3e0ede4f4 --- /dev/null +++ b/dev-python/connection_pool/Manifest @@ -0,0 +1 @@ +DIST connection_pool-0.0.3.tar.gz 3795 BLAKE2B 6a391b739f2727c69abad3ad95635aef7fa542f86b0f4c8a440ae28dee1af80d3af022733685f8e671ed3be479db291b2f763424b746c0918faf991c4b830981 SHA512 a628608f4b57156b2f3f036ccbc620d9ba457f5958d907fa8749dd8df83a167654efd04f411e20436cf1958d9cf6b3f49bf0a11703bfc8d85332d5fc93b13183 diff --git a/dev-python/connection_pool/connection_pool-0.0.3.ebuild b/dev-python/connection_pool/connection_pool-0.0.3.ebuild new file mode 100644 index 000000000..96d3c1f62 --- /dev/null +++ b/dev-python/connection_pool/connection_pool-0.0.3.ebuild @@ -0,0 +1,16 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools + +inherit distutils-r1 pypi + +DESCRIPTION="Thread safe connection pool" +HOMEPAGE="https://github.com/zhouyl/ConnectionPool" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" diff --git a/dev-python/connection_pool/metadata.xml b/dev-python/connection_pool/metadata.xml new file mode 100644 index 000000000..efc2a5c9e --- /dev/null +++ b/dev-python/connection_pool/metadata.xml @@ -0,0 +1,12 @@ +<?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> + <upstream> + <remote-id type="github">zhouyl/ConnectionPool</remote-id> + <remote-id type="pypi">connection_pool</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/cymbal/cymbal-1.0.0.ebuild b/dev-python/cymbal/cymbal-1.0.0.ebuild index a16fcd44c..c5d9eec8e 100644 --- a/dev-python/cymbal/cymbal-1.0.0.ebuild +++ b/dev-python/cymbal/cymbal-1.0.0.ebuild @@ -3,13 +3,11 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) - -inherit distutils-r1 +PYTHON_COMPAT=( python3_10 ) +inherit distutils-r1 pypi 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" +HOMEPAGE="https://pypi.org/project/cymbal/" LICENSE="MIT" SLOT="0" diff --git a/dev-python/dandi-schema/Manifest b/dev-python/dandi-schema/Manifest index cb098f9b4..acdfa9d63 100644 --- a/dev-python/dandi-schema/Manifest +++ b/dev-python/dandi-schema/Manifest @@ -1,4 +1 @@ -DIST dandi-schema-0.4.3.tar.gz 51831 BLAKE2B 177a0ec148c1e823abdaa2b7e60d971c17a7f49bc72b69b16989e32ed014cf6df6378530be7fa142ca49662134a169b21903e9c49d9849ee944dfa9462fe6c3a SHA512 3d6c8f8cf86c933a04017f34a3832d642cf4ee27fd3edf6cf57ceab2e0ad6a1b82c245e4e27283913db941f86877996256604d345c1ee798acca2981ee046b5e -DIST dandi-schema-0.5.1.tar.gz 55945 BLAKE2B b9af1b34c7e4ce07b2fdac1d74dd746684f9e5e4667890931bbf2cb2421a01690eaed5114f2d077c46304f1298475739acef5a256430cac470ceb9fc1884e182 SHA512 699e9fb6626dd87576f29b908cd259748a6ebbd94391d8c5ba821273496323a3b4b9e88ee337809abc65c9aaeadca8aee4d986c173b055914c4ca67ddfd88804 -DIST dandi-schema-0.5.3.tar.gz 56222 BLAKE2B 3b23c93330f621a5a050c9e5b597fd8b9046a66465c16f26b5216d443547a0c8d07a491213cde90c411f5cda6f6c6b2a23d1c0f4b2d7a1e7336c55e5768d3338 SHA512 bf0d434ac6d8e5584ba9f31dd179e5402c13c89257bc87c2d34b03483e9ab85d9b616391a40c64ad853e6774f950ecc58d3f3fde29305586d5faa387dc5b3e80 -DIST dandi-schema-0.6.0.tar.gz 57102 BLAKE2B eb4ef024ef87e234c4c9e741fa2e70920aa13e0ab661aa179553b81ae8d28853274102b49532fc542368ebb43be9779a96434134e35b7c3380609511bed5ce8c SHA512 e2846e3e573264b83e95d92e7d2f2e4177721f32228beb63c701280312611bc668d1042248f4c65ed8f07b8c80991c398a4d29969513f235b4d37369cae0ddcd +DIST dandi-schema-0.9.1.gh.tar.gz 61794 BLAKE2B f18dda919dad9a685793d075e54c798fd9a0d68926b776f1f5617d414554fed7609684dab3311d35056f385443037f03ab16f7edfb7b57c33f9da1aed9c8016c SHA512 c6ed9763a5a77b8741063ef5f311a889e7e0ba2ef02ab97e2912e1a129da503453d9ccb1b9ed13726f071594af42e564986ef9298b21c07cff6ef48eb3f58fc1 diff --git a/dev-python/dandi-schema/dandi-schema-0.4.3.ebuild b/dev-python/dandi-schema/dandi-schema-0.4.3.ebuild deleted file mode 100644 index cf3c8a34f..000000000 --- a/dev-python/dandi-schema/dandi-schema-0.4.3.ebuild +++ /dev/null @@ -1,46 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{8..10} ) -inherit distutils-r1 - -DESCRIPTION="Schemata for DANDI archive project" -HOMEPAGE="https://github.com/dandi/dandi-schema" -SRC_URI="https://github.com/dandi/dandi-schema/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="Apache-2.0" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="test" -RESTRICT="!test? ( test )" - -RDEPEND=" - dev-python/wheel[${PYTHON_USEDEP}] - dev-python/jsonschema[${PYTHON_USEDEP}] - dev-python/pydantic[${PYTHON_USEDEP}] - dev-python/python-email-validator[${PYTHON_USEDEP}] - dev-python/requests[${PYTHON_USEDEP}] -" -DEPEND=" - dev-python/setuptools[${PYTHON_USEDEP}] -" - -PATCHES=( - "${FILESDIR}/${PN}-0.3.4-coverage.patch" - "${FILESDIR}/${PN}-0.3.4-versioningit.patch" -) - -src_configure() { - echo "__version__ = '${PV}'" >> dandischema/_version.py -} - -distutils_enable_tests pytest - -python_test() { - export DANDI_TESTS_NONETWORK=1 - pushd dandischema || die - epytest tests - popd -} diff --git a/dev-python/dandi-schema/dandi-schema-0.5.1.ebuild b/dev-python/dandi-schema/dandi-schema-0.5.1.ebuild deleted file mode 100644 index 19a906634..000000000 --- a/dev-python/dandi-schema/dandi-schema-0.5.1.ebuild +++ /dev/null @@ -1,42 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -DISTUTILS_USE_PEP517=setuptools -PYTHON_COMPAT=( python3_{8..10} ) - -inherit distutils-r1 - -DESCRIPTION="Schemata for DANDI archive project" -HOMEPAGE="https://github.com/dandi/dandi-schema" -SRC_URI="https://github.com/dandi/dandi-schema/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="Apache-2.0" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -RDEPEND=" - dev-python/wheel[${PYTHON_USEDEP}] - dev-python/jsonschema[${PYTHON_USEDEP}] - dev-python/pydantic[${PYTHON_USEDEP}] - dev-python/python-email-validator[${PYTHON_USEDEP}] - dev-python/requests[${PYTHON_USEDEP}] -" - -PATCHES=( - "${FILESDIR}/${PN}-0.3.4-coverage.patch" -) - -src_configure() { - echo "__version__ = '${PV}'" >> dandischema/_version.py -} - -distutils_enable_tests pytest - -python_test() { - export DANDI_TESTS_NONETWORK=1 - pushd dandischema || die - epytest tests - popd -} diff --git a/dev-python/dandi-schema/dandi-schema-0.5.3.ebuild b/dev-python/dandi-schema/dandi-schema-0.5.3.ebuild deleted file mode 100644 index 19a906634..000000000 --- a/dev-python/dandi-schema/dandi-schema-0.5.3.ebuild +++ /dev/null @@ -1,42 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -DISTUTILS_USE_PEP517=setuptools -PYTHON_COMPAT=( python3_{8..10} ) - -inherit distutils-r1 - -DESCRIPTION="Schemata for DANDI archive project" -HOMEPAGE="https://github.com/dandi/dandi-schema" -SRC_URI="https://github.com/dandi/dandi-schema/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="Apache-2.0" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -RDEPEND=" - dev-python/wheel[${PYTHON_USEDEP}] - dev-python/jsonschema[${PYTHON_USEDEP}] - dev-python/pydantic[${PYTHON_USEDEP}] - dev-python/python-email-validator[${PYTHON_USEDEP}] - dev-python/requests[${PYTHON_USEDEP}] -" - -PATCHES=( - "${FILESDIR}/${PN}-0.3.4-coverage.patch" -) - -src_configure() { - echo "__version__ = '${PV}'" >> dandischema/_version.py -} - -distutils_enable_tests pytest - -python_test() { - export DANDI_TESTS_NONETWORK=1 - pushd dandischema || die - epytest tests - popd -} diff --git a/dev-python/dandi-schema/dandi-schema-0.6.0.ebuild b/dev-python/dandi-schema/dandi-schema-0.6.0.ebuild deleted file mode 100644 index 19a906634..000000000 --- a/dev-python/dandi-schema/dandi-schema-0.6.0.ebuild +++ /dev/null @@ -1,42 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -DISTUTILS_USE_PEP517=setuptools -PYTHON_COMPAT=( python3_{8..10} ) - -inherit distutils-r1 - -DESCRIPTION="Schemata for DANDI archive project" -HOMEPAGE="https://github.com/dandi/dandi-schema" -SRC_URI="https://github.com/dandi/dandi-schema/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="Apache-2.0" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -RDEPEND=" - dev-python/wheel[${PYTHON_USEDEP}] - dev-python/jsonschema[${PYTHON_USEDEP}] - dev-python/pydantic[${PYTHON_USEDEP}] - dev-python/python-email-validator[${PYTHON_USEDEP}] - dev-python/requests[${PYTHON_USEDEP}] -" - -PATCHES=( - "${FILESDIR}/${PN}-0.3.4-coverage.patch" -) - -src_configure() { - echo "__version__ = '${PV}'" >> dandischema/_version.py -} - -distutils_enable_tests pytest - -python_test() { - export DANDI_TESTS_NONETWORK=1 - pushd dandischema || die - epytest tests - popd -} diff --git a/dev-python/dandi-schema/dandi-schema-0.9.1.ebuild b/dev-python/dandi-schema/dandi-schema-0.9.1.ebuild new file mode 100644 index 000000000..0e7986806 --- /dev/null +++ b/dev-python/dandi-schema/dandi-schema-0.9.1.ebuild @@ -0,0 +1,49 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..12} ) + +inherit distutils-r1 + +DESCRIPTION="Schemata for DANDI archive project" +HOMEPAGE="https://github.com/dandi/dandi-schema" +SRC_URI="https://github.com/dandi/dandi-schema/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +# Package has pydantic version restriction (2.4*), which, however, breaks the test suite: +# https://github.com/dandi/dandi-schema/issues/228 +# Commented failing tests with upstream version restriction listed below. +RDEPEND=" + dev-python/wheel[${PYTHON_USEDEP}] + dev-python/jsonschema[${PYTHON_USEDEP}] + >=dev-python/pydantic-2.5[${PYTHON_USEDEP}] + dev-python/email-validator[${PYTHON_USEDEP}] + dev-python/requests[${PYTHON_USEDEP}] +" + +PATCHES=( + "${FILESDIR}/${P}-coverage.patch" +) + +src_configure() { + echo "__version__ = '${PV}'" >> dandischema/_version.py +} + +#EPYTEST_DESELECT=( +# "dandischema/tests/test_metadata.py::test_asset" +# "dandischema/tests/test_metadata.py::test_aggregate[files1-summary1]" +# "dandischema/tests/test_metadata.py::test_aggregate[files2-summary2]" +#) + +distutils_enable_tests pytest + +python_test() { + export DANDI_TESTS_NONETWORK=1 + epytest dandischema +} diff --git a/dev-python/dandi-schema/files/dandi-schema-0.3.4-versioningit.patch b/dev-python/dandi-schema/files/dandi-schema-0.3.4-versioningit.patch deleted file mode 100644 index 589091756..000000000 --- a/dev-python/dandi-schema/files/dandi-schema-0.3.4-versioningit.patch +++ /dev/null @@ -1,10 +0,0 @@ ---- a/setup.py 2021-09-22 19:31:20.533576086 -0400 -+++ b/setup.py 2021-09-23 07:42:02.856983656 -0400 -@@ -21,7 +21,7 @@ - - # Give setuptools a hint to complain if it's too old a version - # Should match pyproject.toml --SETUP_REQUIRES = ["setuptools >= 42.0.0", "versioningit ~= 0.1.0"] -+SETUP_REQUIRES = ["setuptools >= 42.0.0"] - # This enables setuptools to install wheel on-the-fly - SETUP_REQUIRES += ["wheel"] if "bdist_wheel" in sys.argv else [] diff --git a/dev-python/dandi-schema/files/dandi-schema-0.9.1-coverage.patch b/dev-python/dandi-schema/files/dandi-schema-0.9.1-coverage.patch new file mode 100644 index 000000000..7f9b7dba0 --- /dev/null +++ b/dev-python/dandi-schema/files/dandi-schema-0.9.1-coverage.patch @@ -0,0 +1,13 @@ +diff --git a/tox.ini b/tox.ini +index c32f3b9..d552c6c 100644 +--- a/tox.ini ++++ b/tox.ini +@@ -30,7 +30,7 @@ commands = + mypy dandischema + + [pytest] +-addopts = --cov=dandischema --tb=short --durations=10 ++addopts = --tb=short --durations=10 + filterwarnings = + error + # <https://github.com/dateutil/dateutil/issues/1284> diff --git a/dev-python/datrie/datrie-0.8.2-r1.ebuild b/dev-python/datrie/datrie-0.8.2-r1.ebuild new file mode 100644 index 000000000..e8f9f9336 --- /dev/null +++ b/dev-python/datrie/datrie-0.8.2-r1.ebuild @@ -0,0 +1,32 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +# Fails to compile with pep517 +#DISTUTILS_USE_PEP517=setuptools + +inherit distutils-r1 pypi + +DESCRIPTION="Implements a topological sort algorithm" +HOMEPAGE="https://github.com/pytries/datrie" + +LICENSE="LGPL-2+" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +BDEPEND=" + dev-python/cython[${PYTHON_USEDEP}] + test? ( + dev-python/hypothesis[${PYTHON_USEDEP}] + ) +" + +distutils_enable_tests pytest + +python_prepare_all() { + # do not depend on pytest-runner + sed -i "/pytest-runner/d" setup.py || die + distutils-r1_python_prepare_all +} diff --git a/dev-python/datrie/datrie-0.8.2.ebuild b/dev-python/datrie/datrie-0.8.2.ebuild deleted file mode 100644 index d3046bf8d..000000000 --- a/dev-python/datrie/datrie-0.8.2.ebuild +++ /dev/null @@ -1,31 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7,8,9} ) - -inherit distutils-r1 - -DESCRIPTION="Implements a topological sort algorithm" -HOMEPAGE="https://github.com/pytries/datrie" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="LGPL-2+" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -BDEPEND=" - dev-python/cython[${PYTHON_USEDEP}] - test? ( - dev-python/hypothesis[${PYTHON_USEDEP}] - ) -" - -distutils_enable_tests pytest - -python_prepare_all() { - # do not depend on pytest-runner - sed -i "/pytest-runner/d" setup.py || die - distutils-r1_python_prepare_all -} diff --git a/dev-python/delegator/delegator-0.1.1.ebuild b/dev-python/delegator/delegator-0.1.1.ebuild index f56de2340..0a22057ef 100644 --- a/dev-python/delegator/delegator-0.1.1.ebuild +++ b/dev-python/delegator/delegator-0.1.1.ebuild @@ -1,15 +1,15 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7..9} ) - -inherit distutils-r1 +PYTHON_COMPAT=( python3_{10..11} ) +PYPI_NO_NORMALIZE=1 +PYPI_PN=delegator.py +inherit distutils-r1 pypi DESCRIPTION="Subprocesses for Humans 2.0." HOMEPAGE="https://github.com/amitt001/delegator.py" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}.py/${PN}.py-${PV}.tar.gz" LICENSE="MIT" SLOT="0" diff --git a/dev-python/delegator/metadata.xml b/dev-python/delegator/metadata.xml index aaa27d18e..57368da50 100644 --- a/dev-python/delegator/metadata.xml +++ b/dev-python/delegator/metadata.xml @@ -9,13 +9,8 @@ <email>sci@gentoo.org</email> <name>Gentoo Science Project</name> </maintainer> - <longdescription lang="en"> - The num2words library converts numbers like 42 to words like forty-two. - It supports multiple languages (see the list below for full list of - languages) and can even generate ordinal numbers like forty-second - (although this last feature is a bit buggy for some languages at the moment). - </longdescription> <upstream> - <remote-id type="github">savoirefairelinux/num2words</remote-id> + <remote-id type="github">amitt001/delegator.py</remote-id> + <remote-id type="pypi">delegator.py</remote-id> </upstream> </pkgmetadata> diff --git a/dev-python/dijitso/Manifest b/dev-python/dijitso/Manifest deleted file mode 100644 index d822cce7e..000000000 --- a/dev-python/dijitso/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST dijitso-2017.1.0.tar.gz 51223 BLAKE2B dd36d97ae3051779a4a21f277fddd02460f3572029b70a1fa5a799a54749cbd807bf9e12a41f2138cc917dfa3ea43368a96bb079dc2e99b6be6900f735e425ce SHA512 994c3d88ca207b3d3065f9376546580492a06eda51a340fc16bbd768248dc26a2984af064e9d970657509b003e403db329aea9ca9cca2f428764b7ec0a367040 diff --git a/dev-python/dijitso/dijitso-2017.1.0.ebuild b/dev-python/dijitso/dijitso-2017.1.0.ebuild deleted file mode 100644 index cef1e1eb7..000000000 --- a/dev-python/dijitso/dijitso-2017.1.0.ebuild +++ /dev/null @@ -1,26 +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} ) -DISTUTILS_USE_SETUPTOOLS=rdepend - -inherit distutils-r1 - -DESCRIPTION="Python module for distributed just-in-time shared library building" -HOMEPAGE="https://bitbucket.org/fenics-project/dijitso/" -SRC_URI="https://bitbucket.org/fenics-project/dijitso/downloads/${P}.tar.gz" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -RDEPEND=" - dev-python/mpi4py[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/six[${PYTHON_USEDEP}] -" -# TODO: fix this, seems to require self -#distutils_enable_sphinx doc/sphinx/source -distutils_enable_tests --install pytest diff --git a/dev-python/dijitso/metadata.xml b/dev-python/dijitso/metadata.xml deleted file mode 100644 index 483c5a2ef..000000000 --- a/dev-python/dijitso/metadata.xml +++ /dev/null @@ -1,17 +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"> -This module was written to improve a core component of the FEniCS -framework, namely the just in time compilation of C++ code that is -generated from Python modules, but is only called from within a C++ -library, and thus do not need wrapping in a nice Python interface. -</longdescription> - <upstream> - <remote-id type="bitbucket">fenics-project/dijitso</remote-id> - </upstream> -</pkgmetadata> diff --git a/dev-python/distinctipy/.tridesclous-1.6.6.ebuild.swp b/dev-python/distinctipy/.tridesclous-1.6.6.ebuild.swp Binary files differnew file mode 100644 index 000000000..d281f7480 --- /dev/null +++ b/dev-python/distinctipy/.tridesclous-1.6.6.ebuild.swp diff --git a/dev-python/distinctipy/Manifest b/dev-python/distinctipy/Manifest new file mode 100644 index 000000000..b6e69e178 --- /dev/null +++ b/dev-python/distinctipy/Manifest @@ -0,0 +1 @@ +DIST distinctipy-1.2.2.gh.tar.gz 8215214 BLAKE2B c25f34f1b0000751fe22e73845922f31bc3cb1a03a673df608cfb8dda9493765c3694bc151a7318d6702f4ed6d151d9336e75828599ee0cb568d3eaf808786ab SHA512 52ec8189a699fe4dd10e3e3d43f50551ce8825835c4605a7f674db022b766a4a9f1714e6ba312bec8f2f0ce87a4d9d038b784f68c0aae603e2011908529010ec diff --git a/dev-python/distinctipy/distinctipy-1.2.2.ebuild b/dev-python/distinctipy/distinctipy-1.2.2.ebuild new file mode 100644 index 000000000..cd4c407d8 --- /dev/null +++ b/dev-python/distinctipy/distinctipy-1.2.2.ebuild @@ -0,0 +1,34 @@ +# Copyright 2021-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 + +DESCRIPTION="Lightweight package for generating visually distinct colours" +HOMEPAGE=" + https://distinctipy.readthedocs.io/en/latest/ + https://github.com/alan-turing-institute/distinctipy +" +# PyPI archive does not include tests: +# https://github.com/alan-turing-institute/distinctipy/issues/29 +SRC_URI="https://github.com/alan-turing-institute/distinctipy/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" +IUSE="test" + +RDEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] +" + +distutils_enable_tests pytest + +# Requires networking: +EPYTEST_DESELECT=( + tests/test_examples.py::test_compare_clusters + tests/test_examples.py::test_simulate_clusters +) diff --git a/dev-python/distinctipy/metadata.xml b/dev-python/distinctipy/metadata.xml new file mode 100644 index 000000000..eb8a425e8 --- /dev/null +++ b/dev-python/distinctipy/metadata.xml @@ -0,0 +1,16 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>gentoo@chymera.eu</email> + <name>Horea Christian</name> + </maintainer> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <upstream> + <remote-id type="github">alan-turing-institute/distinctipy</remote-id> + <remote-id type="pypi">distinctipy</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/dnaio/Manifest b/dev-python/dnaio/Manifest deleted file mode 100644 index d56f36ebe..000000000 --- a/dev-python/dnaio/Manifest +++ /dev/null @@ -1,4 +0,0 @@ -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-0.4.2.ebuild b/dev-python/dnaio/dnaio-0.4.2.ebuild deleted file mode 100644 index d5c738db4..000000000 --- a/dev-python/dnaio/dnaio-0.4.2.ebuild +++ /dev/null @@ -1,22 +0,0 @@ -# Copyright 1999-2020 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=" - ${PYTHON_DEPS} - dev-python/xopen -" - -# no tests in package diff --git a/dev-python/dnaio/dnaio-0.4.3.ebuild b/dev-python/dnaio/dnaio-0.4.3.ebuild deleted file mode 100644 index d5c738db4..000000000 --- a/dev-python/dnaio/dnaio-0.4.3.ebuild +++ /dev/null @@ -1,22 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7..9} ) -inherit distutils-r1 - -DESCRIPTION="efficient reader for FASTA and FASTQ files" -HOMEPAGE="https://pypi.python.org/pypi/xopen" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -RDEPEND=" - ${PYTHON_DEPS} - dev-python/xopen -" - -# no tests in package diff --git a/dev-python/dnaio/dnaio-0.5.0.ebuild b/dev-python/dnaio/dnaio-0.5.0.ebuild deleted file mode 100644 index d5c738db4..000000000 --- a/dev-python/dnaio/dnaio-0.5.0.ebuild +++ /dev/null @@ -1,22 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7..9} ) -inherit distutils-r1 - -DESCRIPTION="efficient reader for FASTA and FASTQ files" -HOMEPAGE="https://pypi.python.org/pypi/xopen" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -RDEPEND=" - ${PYTHON_DEPS} - dev-python/xopen -" - -# no tests in package diff --git a/dev-python/dnaio/dnaio-0.5.1.ebuild b/dev-python/dnaio/dnaio-0.5.1.ebuild deleted file mode 100644 index 2a7885b90..000000000 --- a/dev-python/dnaio/dnaio-0.5.1.ebuild +++ /dev/null @@ -1,22 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7..9} ) -inherit distutils-r1 - -DESCRIPTION="efficient reader for FASTA and FASTQ files" -HOMEPAGE="https://pypi.python.org/pypi/xopen" -SRC_URI="mirror://pypi/${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/dnaio/metadata.xml b/dev-python/dnaio/metadata.xml deleted file mode 100644 index e97c4322a..000000000 --- a/dev-python/dnaio/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>gentoo@aisha.cc</email> - <name>Aisha Tammy</name> - </maintainer> - <maintainer type="project"> - <email>sci@gentoo.org</email> - <name>Gentoo Science Project</name> - </maintainer> -</pkgmetadata> diff --git a/dev-python/docstring-parser/Manifest b/dev-python/docstring-parser/Manifest new file mode 100644 index 000000000..9f508a4f7 --- /dev/null +++ b/dev-python/docstring-parser/Manifest @@ -0,0 +1 @@ +DIST docstring_parser-0.16.tar.gz 26565 BLAKE2B 3785bc9176bc06624a43c50a147c3143e344b8093b9c2db90ab49baed807d598a3538344f79a3da7515c16fc2afc90813e26a3a8f3aa5deb6bc2bf1554303d2e SHA512 6bda195f0e60173c9e78f300a05f8ab2d51ec37848c6f3eddccf889f01abc7dd00b1987028bc59058056e2ab4a50e4631d4d0ec10e54180178372001d65c431f diff --git a/dev-python/docstring-parser/docstring-parser-0.16.ebuild b/dev-python/docstring-parser/docstring-parser-0.16.ebuild new file mode 100644 index 000000000..1d82de77c --- /dev/null +++ b/dev-python/docstring-parser/docstring-parser-0.16.ebuild @@ -0,0 +1,18 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=poetry +PYTHON_COMPAT=( python3_{10..12} ) + +inherit distutils-r1 pypi + +DESCRIPTION="Parse Python docstrings in various flavors" +HOMEPAGE="https://github.com/rr-/docstring_parser" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +distutils_enable_tests pytest diff --git a/dev-python/docstring-parser/metadata.xml b/dev-python/docstring-parser/metadata.xml new file mode 100644 index 000000000..140ee785a --- /dev/null +++ b/dev-python/docstring-parser/metadata.xml @@ -0,0 +1,16 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>gentoo@chymera.eu</email> + <name>Horea Christian</name> + </maintainer> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <upstream> + <remote-id type="pypi">docstring-parser</remote-id> + <remote-id type="github">rr-/docstring_parser</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/dpath/Manifest b/dev-python/dpath/Manifest new file mode 100644 index 000000000..81aa6ca1c --- /dev/null +++ b/dev-python/dpath/Manifest @@ -0,0 +1 @@ +DIST dpath-2.1.6.tar.gz 28142 BLAKE2B 78cb4a8eb7278cd0c1818ffba9d77a917d89f3454a047a82d9031028b34ea2969fe98ed7086d26f6697a166b81cd50439b7b3bd545ab7e6cadcd0606c24be61e SHA512 2f2dac39b6e1ad2effd8d61ac4acf6619205423389ecebc54061aa10ec11ce3236ea666b632a7dca349e9b7a6579815c97e01c930eaa1a99d965e37b9825b82c diff --git a/dev-python/dpath/dpath-2.1.6.ebuild b/dev-python/dpath/dpath-2.1.6.ebuild new file mode 100644 index 000000000..55da56b96 --- /dev/null +++ b/dev-python/dpath/dpath-2.1.6.ebuild @@ -0,0 +1,18 @@ +# Copyright 1999-2018 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..12} ) + +inherit pypi distutils-r1 + +DESCRIPTION="Accessing and searching dictionaries via /slashed/paths" +HOMEPAGE="https://pypi.org/project/dpath/" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" + +distutils_enable_tests pytest diff --git a/dev-python/dpath/metadata.xml b/dev-python/dpath/metadata.xml new file mode 100644 index 000000000..347155fb7 --- /dev/null +++ b/dev-python/dpath/metadata.xml @@ -0,0 +1,16 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>mschu.dev@gmail.com</email> + <name>Michael Schubert</name> + </maintainer> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <upstream> + <remote-id type="github">dpath-maintainers/dpath-python</remote-id> + <remote-id type="pypi">dpath</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/dpctl/Manifest b/dev-python/dpctl/Manifest new file mode 100644 index 000000000..d402c3e9e --- /dev/null +++ b/dev-python/dpctl/Manifest @@ -0,0 +1,2 @@ +DIST dpctl-0.14.1_rc2.gh.tar.gz 409028 BLAKE2B 481be08bb6a7b1a439580d600b0e14036f10793e568314f9373ffa46daad7d3e43d33fc66c3c48ec7e3de71e9d0a7256cdfdd984c38fa7f1694dcc0227dae93f SHA512 91ab20a51893e3afc9e140ab9dfd1aa19b24e58227a001faefb9ceba6ffc4aa235214663c7456e977acf556796be097eabacc9b01b94eb42e8c70677a2f2dd9d +DIST dpctl-0.14.5.gh.tar.gz 552066 BLAKE2B f668ceea99125dad1e0a6989db5bd59df087840d09b1a1538c38cddd0f482f4fc4053ef400e86ddedee4b1906575a441fb97d2caaf3c3718d8aac503d942c0b5 SHA512 6df39eec93da38b86df4cdfdf90350ff11f95d4884bb762289af9b0a6e240d45ed7cc7243677ca7403b042f8938f8acfa42a974d6cff673cd846c0b0f22d0803 diff --git a/dev-python/dpctl/dpctl-0.14.1_rc2.ebuild b/dev-python/dpctl/dpctl-0.14.1_rc2.ebuild new file mode 100644 index 000000000..4ef429b97 --- /dev/null +++ b/dev-python/dpctl/dpctl-0.14.1_rc2.ebuild @@ -0,0 +1,69 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..12} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 + +DESCRIPTION="Data Parallel Control " +HOMEPAGE="https://github.com/IntelPython/dpctl" +SRC_URI="https://github.com/IntelPython/dpctl/archive/refs/tags/${PV//_rc/dev}.tar.gz -> ${P}.gh.tar.gz" +S="${WORKDIR}/${PN}-${PV//_rc/dev}" + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="~amd64" + +BDEPEND=" + dev-python/cython[${PYTHON_USEDEP}] + dev-python/scikit-build[${PYTHON_USEDEP}] + dev-python/pybind11[${PYTHON_USEDEP}] + dev-python/versioneer[${PYTHON_USEDEP}] + dev-build/cmake + dev-vcs/git + sys-devel/DPC++ +" + +DEPEND=" + dev-libs/level-zero + dev-libs/opencl-icd-loader + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/wheel[${PYTHON_USEDEP}] + sci-libs/oneDAL + sys-devel/DPC++:0/6 +" +RDEPEND="${DEPEND}" + +PATCHES=( + "${FILESDIR}/${PN}-0.14.0-find-opencl.patch" + "${FILESDIR}/${PN}-0.14.1_rc2-dont-fetch-level-zero.patch" + "${FILESDIR}/${PN}-0.14.1_rc2-dont-fetch-pybind.patch" + #"${FILESDIR}/${PN}-0.14.1_rc2-include-tuple.patch" +) + +distutils_enable_tests pytest + +python_prepare_all() { + # DPC++ compiler required for full functionality + export CC="${ESYSROOT}/usr/lib/llvm/intel/bin/clang" + export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++" + export DPCPPROOT="${ESYSROOT}/usr/lib/llvm/intel" + + # Build system reads version from git tag + git init -q || die + git config --global user.email "larry@gentoo.org" || die + git config --global user.name "Larry the Cow" || die + git add . || die + git commit -qm "init" || die + git tag -a "${PV}" -m "${PN} version ${PV}" || die + + distutils-r1_python_prepare_all +} + +python_test() { + export PYTHONPATH="${BUILD_DIR}/install/usr/lib/${EPYTHON}/site-packages" + # We don't use epytest because it overwrites our PYTHONPATH + pytest -vv || die +} diff --git a/dev-python/dpctl/dpctl-0.14.5.ebuild b/dev-python/dpctl/dpctl-0.14.5.ebuild new file mode 100644 index 000000000..4ef429b97 --- /dev/null +++ b/dev-python/dpctl/dpctl-0.14.5.ebuild @@ -0,0 +1,69 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..12} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 + +DESCRIPTION="Data Parallel Control " +HOMEPAGE="https://github.com/IntelPython/dpctl" +SRC_URI="https://github.com/IntelPython/dpctl/archive/refs/tags/${PV//_rc/dev}.tar.gz -> ${P}.gh.tar.gz" +S="${WORKDIR}/${PN}-${PV//_rc/dev}" + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="~amd64" + +BDEPEND=" + dev-python/cython[${PYTHON_USEDEP}] + dev-python/scikit-build[${PYTHON_USEDEP}] + dev-python/pybind11[${PYTHON_USEDEP}] + dev-python/versioneer[${PYTHON_USEDEP}] + dev-build/cmake + dev-vcs/git + sys-devel/DPC++ +" + +DEPEND=" + dev-libs/level-zero + dev-libs/opencl-icd-loader + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/wheel[${PYTHON_USEDEP}] + sci-libs/oneDAL + sys-devel/DPC++:0/6 +" +RDEPEND="${DEPEND}" + +PATCHES=( + "${FILESDIR}/${PN}-0.14.0-find-opencl.patch" + "${FILESDIR}/${PN}-0.14.1_rc2-dont-fetch-level-zero.patch" + "${FILESDIR}/${PN}-0.14.1_rc2-dont-fetch-pybind.patch" + #"${FILESDIR}/${PN}-0.14.1_rc2-include-tuple.patch" +) + +distutils_enable_tests pytest + +python_prepare_all() { + # DPC++ compiler required for full functionality + export CC="${ESYSROOT}/usr/lib/llvm/intel/bin/clang" + export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++" + export DPCPPROOT="${ESYSROOT}/usr/lib/llvm/intel" + + # Build system reads version from git tag + git init -q || die + git config --global user.email "larry@gentoo.org" || die + git config --global user.name "Larry the Cow" || die + git add . || die + git commit -qm "init" || die + git tag -a "${PV}" -m "${PN} version ${PV}" || die + + distutils-r1_python_prepare_all +} + +python_test() { + export PYTHONPATH="${BUILD_DIR}/install/usr/lib/${EPYTHON}/site-packages" + # We don't use epytest because it overwrites our PYTHONPATH + pytest -vv || die +} diff --git a/dev-python/dpctl/files/dpctl-0.14.0-find-opencl.patch b/dev-python/dpctl/files/dpctl-0.14.0-find-opencl.patch new file mode 100644 index 000000000..3841816ee --- /dev/null +++ b/dev-python/dpctl/files/dpctl-0.14.0-find-opencl.patch @@ -0,0 +1,13 @@ +diff --git a/libsyclinterface/cmake/modules/FindIntelSycl.cmake b/libsyclinterface/cmake/modules/FindIntelSycl.cmake +index 84e8946..ccc2591 100644 +--- a/libsyclinterface/cmake/modules/FindIntelSycl.cmake ++++ b/libsyclinterface/cmake/modules/FindIntelSycl.cmake +@@ -134,7 +134,7 @@ if(${clangxx_result} MATCHES "0") + find_file( + IntelSycl_OPENCL_LIBRARY + NAMES "libOpenCL.so" +- PATHS ${IntelSycl_LIBRARY_DIR} ++ PATHS /usr/lib64 + ) + endif() + diff --git a/dev-python/dpctl/files/dpctl-0.14.1_rc2-dont-fetch-level-zero.patch b/dev-python/dpctl/files/dpctl-0.14.1_rc2-dont-fetch-level-zero.patch new file mode 100644 index 000000000..a7a4adf8b --- /dev/null +++ b/dev-python/dpctl/files/dpctl-0.14.1_rc2-dont-fetch-level-zero.patch @@ -0,0 +1,82 @@ +diff --git a/libsyclinterface/cmake/modules/GetLevelZeroHeaders.cmake b/libsyclinterface/cmake/modules/GetLevelZeroHeaders.cmake +index fe109fc..55595e9 100644 +--- a/libsyclinterface/cmake/modules/GetLevelZeroHeaders.cmake ++++ b/libsyclinterface/cmake/modules/GetLevelZeroHeaders.cmake +@@ -26,76 +26,10 @@ + + function(get_level_zero_headers) + +- if(EXISTS level-zero) +- # Update the checkout +- execute_process( +- COMMAND ${GIT_EXECUTABLE} fetch +- RESULT_VARIABLE result +- ERROR_VARIABLE error +- WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/level-zero +- OUTPUT_STRIP_TRAILING_WHITESPACE +- ERROR_STRIP_TRAILING_WHITESPACE +- ) +- +- if(NOT result EQUAL 0) +- message(FATAL_ERROR +- "Could not update Level Zero sources. Return code: ${result}" +- ) +- endif() +- else() +- # Clone the Level Zero git repo +- execute_process( +- COMMAND ${GIT_EXECUTABLE} clone https://github.com/oneapi-src/level-zero.git +- RESULT_VARIABLE result +- ERROR_VARIABLE error +- OUTPUT_STRIP_TRAILING_WHITESPACE +- ERROR_STRIP_TRAILING_WHITESPACE +- ) +- +- if(NOT result EQUAL 0) +- message(FATAL_ERROR +- "Could not clone Level Zero sources from github.com/oneapi-src/level-zero. Return code: ${result}" +- ) +- endif() +- endif() +- +- # Use git describe to get latest tag name +- execute_process( +- COMMAND ${GIT_EXECUTABLE} describe --tags --abbrev=0 +- RESULT_VARIABLE result +- OUTPUT_VARIABLE latest_tag +- ERROR_VARIABLE error +- WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/level-zero +- OUTPUT_STRIP_TRAILING_WHITESPACE +- ERROR_STRIP_TRAILING_WHITESPACE +- ) +- +- if(NOT result EQUAL 0) +- message(FATAL_ERROR +- "Could not get the name for the latest release. Return code: ${result}" +- ) +- endif() +- +- # Use git describe to get latest tag name +- execute_process( +- COMMAND ${GIT_EXECUTABLE} checkout ${latest_tag} +- RESULT_VARIABLE result +- ERROR_VARIABLE error +- WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/level-zero +- OUTPUT_STRIP_TRAILING_WHITESPACE +- ERROR_STRIP_TRAILING_WHITESPACE +- ) +- +- if(NOT result EQUAL 0) +- message(FATAL_ERROR +- "Could not checkout the latest release. Return code: ${result}" +- ) +- endif() +- + # Populate the path to the headers + find_path(LEVEL_ZERO_INCLUDE_DIR + NAMES zet_api.h +- PATHS ${CMAKE_BINARY_DIR}/level-zero/include ++ PATHS /usr/include/level_zero + NO_DEFAULT_PATH + NO_CMAKE_ENVIRONMENT_PATH + NO_CMAKE_PATH diff --git a/dev-python/dpctl/files/dpctl-0.14.1_rc2-dont-fetch-pybind.patch b/dev-python/dpctl/files/dpctl-0.14.1_rc2-dont-fetch-pybind.patch new file mode 100644 index 000000000..d56dc27b3 --- /dev/null +++ b/dev-python/dpctl/files/dpctl-0.14.1_rc2-dont-fetch-pybind.patch @@ -0,0 +1,21 @@ +diff --git a/CMakeLists.txt b/CMakeLists.txt +index d97ca9a..3914bd9 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -32,15 +32,7 @@ install(FILES ${_dpctl_capi_headers} + # Define CMAKE_INSTALL_xxx: LIBDIR, INCLUDEDIR + include(GNUInstallDirs) + +-# Fetch pybind11 +-include(FetchContent) +- +-FetchContent_Declare( +- pybind11 +- URL https://github.com/pybind/pybind11/archive/refs/tags/v2.10.2.tar.gz +- URL_HASH SHA256=93bd1e625e43e03028a3ea7389bba5d3f9f2596abc074b068e70f4ef9b1314ae +-) +-FetchContent_MakeAvailable(pybind11) ++include(/usr/share/cmake/pybind11/pybind11Config.cmake) + + add_subdirectory(dpctl) + diff --git a/dev-python/dpctl/metadata.xml b/dev-python/dpctl/metadata.xml new file mode 100644 index 000000000..06d339ee1 --- /dev/null +++ b/dev-python/dpctl/metadata.xml @@ -0,0 +1,12 @@ +<?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> + <upstream> + <remote-id type="github">IntelPython/dpctl</remote-id> + <remote-id type="pypi">dpctl</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/dpnp/Manifest b/dev-python/dpnp/Manifest new file mode 100644 index 000000000..0286f1b8e --- /dev/null +++ b/dev-python/dpnp/Manifest @@ -0,0 +1 @@ +DIST dpnp-0.11.1_rc1.gh.tar.gz 495726 BLAKE2B 13e9696195abd21f41b1a8e6f235f840cd22a4eb1b67f7bbedfdc775f0cb7832157af51309b1d8a5f2d1cde78250c70730a2794f11b01f8bd572e7a1e29f2b47 SHA512 ef58591aaed330123b78268c7b0b04222efc8e688e1bfe2426e13836fe23ae84572f3337d7084525a6dd5e5fcf91dd68c501643b922ebebc7f0fb94115f92749 diff --git a/dev-python/dpnp/dpnp-0.11.1_rc1.ebuild b/dev-python/dpnp/dpnp-0.11.1_rc1.ebuild new file mode 100644 index 000000000..5d25d62d1 --- /dev/null +++ b/dev-python/dpnp/dpnp-0.11.1_rc1.ebuild @@ -0,0 +1,65 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..12} ) +# Breaks library installation +#DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 + +DESCRIPTION="Data Parallel Extension for NumPy" +HOMEPAGE="https://github.com/IntelPython/dpnp" +SRC_URI="https://github.com/IntelPython/dpnp/archive/refs/tags/${PV//_rc/dev}.tar.gz -> ${P}.gh.tar.gz" +S="${WORKDIR}/${PN}-${PV//_rc/dev}" + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="~amd64" + +BDEPEND=" + dev-python/cython[${PYTHON_USEDEP}] + dev-build/cmake + sys-devel/DPC++ +" + +RDEPEND=" + dev-cpp/tbb + dev-python/dpctl[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + sci-libs/mkl + sys-devel/DPC++:= +" +DEPEND="${RDEPEND} + sys-devel/oneDPL +" + +PATCHES=( + "${FILESDIR}/${P}-fix-compile.patch" +) + +distutils_enable_tests pytest + +python_prepare_all() { + # DPC++ compiler required for full functionality + export CC="${ESYSROOT}/usr/lib/llvm/intel/bin/clang" + export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++" + export DPCPPROOT="${ESYSROOT}/usr/lib/llvm/intel" + export DPL_ROOT="${ESYSROOT}/usr/include/include/oneapi/dpl" + # Parallel build broken + export MAKEOPTS="-j1" + + distutils-r1_python_prepare_all +} + +python_compile() { + export BUILD_DIR_LIBS="${BUILD_DIR}/lib/dpnp" + distutils-r1_python_compile +} + +python_test() { + export PYTHONPATH="${BUILD_DIR}/lib" + elog $PYTHONPATH + # We don't use epytest because it overwrites our PYTHONPATH + pytest -vv || die +} diff --git a/dev-python/dpnp/files/dpnp-0.11.1_rc1-fix-compile.patch b/dev-python/dpnp/files/dpnp-0.11.1_rc1-fix-compile.patch new file mode 100644 index 000000000..25c0d3484 --- /dev/null +++ b/dev-python/dpnp/files/dpnp-0.11.1_rc1-fix-compile.patch @@ -0,0 +1,71 @@ +diff --git a/dpnp/backend/CMakeLists.txt b/dpnp/backend/CMakeLists.txt +index baee709..3202662 100644 +--- a/dpnp/backend/CMakeLists.txt ++++ b/dpnp/backend/CMakeLists.txt +@@ -99,30 +99,6 @@ string(CONCAT COMMON_LINK_FLAGS + "-fsycl " + "-fsycl-device-code-split=per_kernel " + ) +-if(UNIX) +- set(CMAKE_CXX_COMPILER "icpx") +- # add_compile_options(-fPIC) +-elseif(WIN32) +- set(CMAKE_CXX_COMPILER "icx") +- # set(CMAKE_SHARED_LINKER_FLAGS_INIT "-fuse-ld=lld-link") +- # set(CMAKE_LINKER "lld-link") +- # include (Platform/Windows-Clang) +- # set(CMAKE_LINKER "dpcpp") +- # set(CMAKE_AR "llvm-ar") +- # set(CMAKE_RANLIB "llvm-ranlib") +- # set(CMAKE_CXX_FLAGS "/EHsc") +- +- string(APPEND COMMON_COMPILE_FLAGS +- "/EHsc " +-# "/Ox " +-# "/W3 " +-# "/GL " +-# "/DNDEBUG " +-# "/MD " +- ) +-else() +- message(FATAL_ERROR "Unsupported system ${CMAKE_SYSTEM} in compiler selection case") +-endif() + + # set language version + set(CMAKE_CXX_STANDARD 17) +@@ -334,6 +310,7 @@ endif() + # set_target_properties(dpnp_backend_c PROPERTIES VERSION ${DPNP_VERSION} SOVERSION ${DPNP_API_VERSION}) + + install(TARGETS dpnp_backend_c ++ DESTINATION ${DPNP_INSTALL_PREFIX} + PERMISSIONS OWNER_WRITE OWNER_READ OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE + ) + +diff --git a/utils/command_build_clib.py b/utils/command_build_clib.py +index d16bab3..7fd2afa 100644 +--- a/utils/command_build_clib.py ++++ b/utils/command_build_clib.py +@@ -61,8 +61,8 @@ else: + Set compiler for the project + """ + # default variables (for Linux) +-_project_compiler = "icpx" +-_project_linker = "icpx" ++_project_compiler = os.environ.get("CXX") ++_project_linker = os.environ.get("CXX") + _project_cmplr_flag_sycl_devel = ["-fsycl-device-code-split=per_kernel", "-fno-approx-func", "-fno-finite-math-only"] + _project_cmplr_flag_sycl = ["-fsycl"] + _project_cmplr_flag_stdcpp_static = [] # This brakes TBB ["-static-libstdc++", "-static-libgcc"] +diff --git a/utils/command_build_cmake_clib.py b/utils/command_build_cmake_clib.py +index 0ef0e24..84f2469 100644 +--- a/utils/command_build_cmake_clib.py ++++ b/utils/command_build_cmake_clib.py +@@ -112,7 +112,7 @@ class custom_build_cmake_clib(build_clib.build_clib): + "-S" + backend_directory, + "-B" + abs_build_temp_path, + "-DCMAKE_BUILD_TYPE=" + config, +- "-DDPNP_INSTALL_PREFIX=" + install_directory.replace(os.sep, "/"), # adjust to cmake requirenments ++ "-DDPNP_INSTALL_PREFIX=" + os.environ.get('BUILD_DIR_LIBS'), # adjust to cmake requirenments + "-DDPNP_INSTALL_STRUCTURED=OFF", + # "-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=" + install_directory, + "-DDPNP_SYCL_QUEUE_MGR_ENABLE:BOOL=" + _dpctrl_exists, diff --git a/dev-python/dpnp/metadata.xml b/dev-python/dpnp/metadata.xml new file mode 100644 index 000000000..868959c89 --- /dev/null +++ b/dev-python/dpnp/metadata.xml @@ -0,0 +1,12 @@ +<?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> + <upstream> + <remote-id type="github">IntelPython/dpnp</remote-id> + <remote-id type="pypi">dpnp</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/extension-helpers/Manifest b/dev-python/extension-helpers/Manifest index b80cb117c..33d56a849 100644 --- a/dev-python/extension-helpers/Manifest +++ b/dev-python/extension-helpers/Manifest @@ -1 +1 @@ -DIST extension-helpers-0.1.tar.gz 24306 BLAKE2B 8fa5134bd26f4c5b9a66694d1c057c969607bfe9a05d5c470cdccda87bbff329174916bccc390ff80fdce72af5b764d0b3a7c34b632c01e33e3c84f913c6527b SHA512 d8394f5f0de28dfa2c204b918a39b5f3b990057bfdb7a21907b0b9ae3bacd5b95c5f25b32a08a50606fbae35b93629dcfe1fee512c6aa4f4e7c08c22bcfd3fbb +DIST extension-helpers-1.0.0.tar.gz 23463 BLAKE2B 0b1edffabc112120ac85c6445255986145143da9552221390a0827516a20e2877cad47e5968f6c7d293550db566574f86c877758d6233e51ca0762c3ff2e9327 SHA512 30234591100e5e8b7bda4392d72421911773a3aabb40c003367e8b335edcea3285f79fd962edd3d09b96ed7b4b936a97086376dfff50b18df85b55c612d61f8d diff --git a/dev-python/extension-helpers/extension-helpers-0.1.ebuild b/dev-python/extension-helpers/extension-helpers-0.1.ebuild deleted file mode 100644 index 8119b0206..000000000 --- a/dev-python/extension-helpers/extension-helpers-0.1.ebuild +++ /dev/null @@ -1,28 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{8..10} ) - -inherit distutils-r1 - -DESCRIPTION="Utilities for building and installing packages in the Astropy ecosystem" -HOMEPAGE="https://github.com/astropy/astropy-helpers" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -#TODO: Package all these pytest deps: -# pytest-doctestplus>=0.2.0 -# pytest-remotedata>=0.3.1 -# pytest-openfiles>=0.3.1 -# pytest-astropy-header>=0.1.2 -# pytest-arraydiff>=0.1 -# pytest-filter-subpackage>=0.1 -RESTRICT="test" - -distutils_enable_tests pytest -distutils_enable_sphinx docs dev-python/sphinx-astropy diff --git a/dev-python/extension-helpers/extension-helpers-1.0.0.ebuild b/dev-python/extension-helpers/extension-helpers-1.0.0.ebuild new file mode 100644 index 000000000..4532642fa --- /dev/null +++ b/dev-python/extension-helpers/extension-helpers-1.0.0.ebuild @@ -0,0 +1,29 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools +PYPI_NO_NORMALIZE=1 + +inherit distutils-r1 pypi + +DESCRIPTION="Utilities for building and installing packages in the Astropy ecosystem" +HOMEPAGE="https://github.com/astropy/astropy-helpers" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +#TODO: Package all these pytest deps: +# pytest-doctestplus>=0.2.0 +# pytest-remotedata>=0.3.1 +# pytest-openfiles>=0.3.1 +# pytest-astropy-header>=0.1.2 +# pytest-arraydiff>=0.1 +# pytest-filter-subpackage>=0.1 +RESTRICT="test" + +distutils_enable_tests pytest +distutils_enable_sphinx docs dev-python/sphinx-astropy diff --git a/dev-python/extension-helpers/metadata.xml b/dev-python/extension-helpers/metadata.xml index 4f4367037..9f1bfe0c4 100644 --- a/dev-python/extension-helpers/metadata.xml +++ b/dev-python/extension-helpers/metadata.xml @@ -5,4 +5,8 @@ <email>sci-astronomy@gentoo.org</email> <name>Gentoo Astronomy Project</name> </maintainer> + <upstream> + <remote-id type="github">astropy/astropy-helpers</remote-id> + <remote-id type="pypi">extension-helpers</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/ezdxf/ezdxf-0.16.5.ebuild b/dev-python/ezdxf/ezdxf-0.16.5.ebuild index 43bf7c371..b3a0148f7 100644 --- a/dev-python/ezdxf/ezdxf-0.16.5.ebuild +++ b/dev-python/ezdxf/ezdxf-0.16.5.ebuild @@ -4,13 +4,12 @@ EAPI=8 #FIXME: Upstream explicitly supports "pypy3", but Gentoo dependencies do not. -PYTHON_COMPAT=( python3_{8..10} ) - -inherit distutils-r1 +PYTHON_COMPAT=( python3_10 ) +inherit distutils-r1 pypi DESCRIPTION="Python interface to DXF" -HOMEPAGE="https://pypi.org/project/ezdxf" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.zip" +HOMEPAGE="https://pypi.org/project/ezdxf/" +SRC_URI="$(pypi_sdist_url ${PN} ${PV} .zip)" LICENSE="MIT" SLOT="0" diff --git a/dev-python/ffc/Manifest b/dev-python/ffc/Manifest deleted file mode 100644 index 266151bd7..000000000 --- a/dev-python/ffc/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST ffc-2019.1.0.tar.gz 1365806 BLAKE2B a9c2e03f3cc178d279fea89eb95090a8417351ccde61f1a357e14610d952dd20870617bf32daf1bf79d2535997d4ce7e1a8971d9b03a0ee2636d4e18d208bd17 SHA512 c7deaeb5a0deadd998ba7809b7725e2d28a84bf82706427b5273310292d50380d132088ca04bc9a3945b543709226b7c2c2cbb28dde63fc06033f9d1f123433e diff --git a/dev-python/ffc/ffc-2019.1.0.ebuild b/dev-python/ffc/ffc-2019.1.0.ebuild deleted file mode 100644 index a164e1356..000000000 --- a/dev-python/ffc/ffc-2019.1.0.ebuild +++ /dev/null @@ -1,23 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7,8,9} ) - -inherit distutils-r1 - -DESCRIPTION="Compiler for multilinear forms by generating C or C++ code" -HOMEPAGE="https://bitbucket.org/fenics-project/ffc/" -SRC_URI="https://bitbucket.org/fenics-project/ffc/downloads/${P}.tar.gz" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -RDEPEND=" - ~dev-python/ufl-${PV}[${PYTHON_USEDEP}] - ~dev-python/fiat-${PV}[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - " diff --git a/dev-python/ffc/metadata.xml b/dev-python/ffc/metadata.xml deleted file mode 100644 index 744ca900c..000000000 --- a/dev-python/ffc/metadata.xml +++ /dev/null @@ -1,19 +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"> -FFC works as a compiler for multilinear forms by generating code (C or -C++) for the evaluation of a multilinear form given in mathematical -notation. This new approach to form evaluation makes it possible to -combine generality with efficiency; the form can be given in -mathematical notation and the generated code is as efficient as -hand-optimized code. -</longdescription> - <upstream> - <remote-id type="bitbucket">fenics-project/ffc</remote-id> - </upstream> -</pkgmetadata> diff --git a/dev-python/fiat/Manifest b/dev-python/fiat/Manifest deleted file mode 100644 index 17a7b25c7..000000000 --- a/dev-python/fiat/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST fiat-2019.1.0.tar.gz 108440 BLAKE2B ebf4f9e342e063be3be51daf28d433274a3238f6dda7515e350d374427157490d86dfbfd4faba13fef1def58623ff38ed3df445815b5cbe2e1f6afd4b0dfa374 SHA512 15de17b2a28ba5071c0dd9ecc05ec36eeae76de3aa9f068577d43b7526778116e2ded412fa8c26189e7c505881dd2b68b2c45704c8446d9ef9d9d3797c3592e6 diff --git a/dev-python/fiat/fiat-2019.1.0.ebuild b/dev-python/fiat/fiat-2019.1.0.ebuild deleted file mode 100644 index b50646eb3..000000000 --- a/dev-python/fiat/fiat-2019.1.0.ebuild +++ /dev/null @@ -1,19 +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="FInite element Automatic Tabulator" -HOMEPAGE="https://github.com/FEniCS/fiat" -SRC_URI="https://github.com/FEniCS/fiat/archive/2019.1.0.tar.gz -> ${P}.tar.gz" - -LICENSE="LGPL-3" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]" -DEPEND="${RDEPEND}" diff --git a/dev-python/fiat/metadata.xml b/dev-python/fiat/metadata.xml deleted file mode 100644 index d08e0d509..000000000 --- a/dev-python/fiat/metadata.xml +++ /dev/null @@ -1,21 +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 FInite element Automatic Tabulator FIAT supports generation of -arbitrary order instances of the Lagrange elements on lines, triangles, -and tetrahedra. It is also capable of generating arbitrary order -instances of Jacobi-type quadrature rules on the same element shapes. -Further, H(div) and H(curl) conforming finite element spaces such as the -families of Raviart-Thomas, Brezzi-Douglas-Marini and Nedelec are -supported on triangles and tetrahedra. Upcoming versions will also -support Hermite and nonconforming elements. -</longdescription> - <upstream> - <remote-id type="bitbucket">fenics-project/fiat</remote-id> - </upstream> -</pkgmetadata> diff --git a/dev-python/fiona/Manifest b/dev-python/fiona/Manifest index 2140ef1a5..bed2fa4ce 100644 --- a/dev-python/fiona/Manifest +++ b/dev-python/fiona/Manifest @@ -1,2 +1 @@ -DIST fiona-1.8.21.tar.gz 270166 BLAKE2B 752957f3cc3ed6a35713536e90cdbc542d73de9718e878a449f71c9b9a2150b4ead90ff5d9ce254a6adcfcf7deb61b4483e7cf5bfee12997e581fd0a3ffc767e SHA512 c77cedae67fb7e2b6b6a84aeef39ce5424ccb38b13774f7c2e9bd5934836a6abe6759eeea1d4a8cfc83c5111442f2028d18dd79af209e11618789de2149e7885 - +DIST fiona-1.9.0.gh.tar.gz 290797 BLAKE2B 1cd2a4a26d23d057433889937b4fecefb1e1585dc6b507e297ef3bab8cf72f734bc080bab8487d58c636312bca1330960f78fc2916d27c9a7247df087818c9b3 SHA512 f59d148cfc4f1cab6d89660146522920fab8b6fb1120ad8f3d3e8349d5fa823860984f8fd331e2fc3183a4a186a165508db8dcbcbdf4b943a7dad82d8d51d866 diff --git a/dev-python/fiona/fiona-1.8.21.ebuild b/dev-python/fiona/fiona-1.8.21.ebuild deleted file mode 100644 index 51ded0d37..000000000 --- a/dev-python/fiona/fiona-1.8.21.ebuild +++ /dev/null @@ -1,78 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{8..10} ) -DISTUTILS_USE_PEP517="setuptools" -inherit distutils-r1 - -DESCRIPTION="API for reading/writing vector geospatial data" -HOMEPAGE="https://github.com/Toblerity/fiona" -SRC_URI="https://github.com/Toblerity/${PN}/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -RDEPEND=" - sci-libs/gdal[geos,sqlite] - dev-python/attrs[${PYTHON_USEDEP}] - dev-python/click-plugins[${PYTHON_USEDEP}] - dev-python/cligj[${PYTHON_USEDEP}] - dev-python/munch[${PYTHON_USEDEP}] - dev-python/six[${PYTHON_USEDEP}] - dev-python/certifi[${PYTHON_USEDEP}] -" - -BDEPEND=" - dev-python/cython[${PYTHON_USEDEP}] - test? ( - dev-python/boto3[${PYTHON_USEDEP}] - sci-libs/gdal[geos,sqlite] - ) -" - -S="${WORKDIR}/Fiona-${PV}" - -distutils_enable_tests pytest - -python_test() { - local deselect=( - # disable tests due to networking blocked - tests/test_vfs.py::test_open_http - tests/test_vfs.py::test_open_zip_https - tests/test_collection.py::test_collection_http - tests/test_collection.py::test_collection_zip_http - - # disable tests failing due to deprecated GDAL features - tests/test_data_paths.py::test_gdal_data_wheel - tests/test_data_paths.py::test_proj_data_wheel - tests/test_data_paths.py::test_env_gdal_data_wheel - tests/test_data_paths.py::test_env_proj_data_wheel - tests/test_datetime.py::test_datefield[GPSTrackMaker-datetime] - tests/test_datetime.py::test_datefield_null[GPSTrackMaker-datetime] - tests/test_drvsupport.py::test_write_or_driver_error[GPSTrackMaker] - tests/test_drvsupport.py::test_no_append_driver_cannot_append[GPSTrackMaker] - tests/test_drvsupport.py::test_no_append_driver_cannot_append[PCIDSK] - tests/test_drvsupport.py::test_write_or_driver_error[DGN] - - # failure in flatgeobuf impl - tests/test_drvsupport.py::test_no_append_driver_cannot_append[FlatGeobuf] - - # geos - #tests/test_collection.py::test_mask_polygon_triangle - #tests/test_collection.py::test_mask_polygon_triangle - #tests/test_collection.py::test_mask_polygon_triangle - - # sqlite - #tests/test_schema.py::test_geometry_only_schema_write[GPKG] - #tests/test_schema.py::test_geometry_only_schema_update[GPKG] - #tests/test_schema.py::test_property_only_schema_write[GPKG] - #tests/test_schema.py::test_property_only_schema_update[GPKG] - ) - - mv fiona{,.bak} || die # Avoid non-working local import - epytest ${deselect[@]/#/--deselect } - mv fiona{.bak,} || die -} diff --git a/dev-python/fiona/fiona-1.9.0.ebuild b/dev-python/fiona/fiona-1.9.0.ebuild new file mode 100644 index 000000000..7bc415b14 --- /dev/null +++ b/dev-python/fiona/fiona-1.9.0.ebuild @@ -0,0 +1,76 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517="setuptools" +inherit distutils-r1 + +DESCRIPTION="API for reading/writing vector geospatial data" +HOMEPAGE="https://github.com/Toblerity/fiona" +SRC_URI="https://github.com/Toblerity/${PN}/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz" +S="${WORKDIR}/Fiona-${PV}" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +RDEPEND=" + sci-libs/gdal[geos,sqlite] + dev-python/attrs[${PYTHON_USEDEP}] + dev-python/click-plugins[${PYTHON_USEDEP}] + dev-python/cligj[${PYTHON_USEDEP}] + dev-python/munch[${PYTHON_USEDEP}] + dev-python/certifi[${PYTHON_USEDEP}] +" + +BDEPEND=" + dev-python/cython[${PYTHON_USEDEP}] + test? ( + dev-python/boto3[${PYTHON_USEDEP}] + sci-libs/gdal[geos,sqlite] + ) +" + +distutils_enable_tests pytest + +python_test() { + local deselect=( + # disable tests due to networking blocked + tests/test_vfs.py::test_open_http + tests/test_vfs.py::test_open_zip_https + tests/test_collection.py::test_collection_http + tests/test_collection.py::test_collection_zip_http + + # disable tests failing due to deprecated GDAL features + tests/test_data_paths.py::test_gdal_data_wheel + tests/test_data_paths.py::test_proj_data_wheel + tests/test_data_paths.py::test_env_gdal_data_wheel + tests/test_data_paths.py::test_env_proj_data_wheel + tests/test_datetime.py::test_datefield[GPSTrackMaker-datetime] + tests/test_datetime.py::test_datefield_null[GPSTrackMaker-datetime] + tests/test_drvsupport.py::test_write_or_driver_error[GPSTrackMaker] + tests/test_drvsupport.py::test_no_append_driver_cannot_append[GPSTrackMaker] + tests/test_drvsupport.py::test_no_append_driver_cannot_append[PCIDSK] + tests/test_drvsupport.py::test_write_or_driver_error[DGN] + + # failure in flatgeobuf impl + tests/test_drvsupport.py::test_no_append_driver_cannot_append[FlatGeobuf] + + # geos + #tests/test_collection.py::test_mask_polygon_triangle + #tests/test_collection.py::test_mask_polygon_triangle + #tests/test_collection.py::test_mask_polygon_triangle + + # sqlite + #tests/test_schema.py::test_geometry_only_schema_write[GPKG] + #tests/test_schema.py::test_geometry_only_schema_update[GPKG] + #tests/test_schema.py::test_property_only_schema_write[GPKG] + #tests/test_schema.py::test_property_only_schema_update[GPKG] + ) + + mv fiona{,.bak} || die # Avoid non-working local import + epytest ${deselect[@]/#/--deselect } + mv fiona{.bak,} || die +} diff --git a/dev-python/fscacher/Manifest b/dev-python/fscacher/Manifest index 67c5c736e..779c470e4 100644 --- a/dev-python/fscacher/Manifest +++ b/dev-python/fscacher/Manifest @@ -1,2 +1,2 @@ -DIST fscacher-0.1.4.tar.gz 35097 BLAKE2B 32cd904d9d3bd36b4b14a55a4d618a99f73afda2807a1f655931b8b26e8ce0b1126773c5b242af824e2014cf634200a17f95d547c75ec4f6a3dd959ee5c37e23 SHA512 e3e85cee4c446552215b6d7092bdc72c31709e05dee7efb52fc6fc985992a3ece338c5a0dee54ed7e6aec797d4b7e2bd77b00f634112134c61f402b604103b5c -DIST fscacher-0.2.0.tar.gz 37693 BLAKE2B 4e6493d5ec1bb56b53ab72842b6861fbfb916698b80021bbb5c8a8c89be9d90661c78bef9f5b09d3f681b40e45fa52b06dc93231df2228e3a00ee13f913544d8 SHA512 eca32e84f2b317b57aca749644fb76e6c7a0e65384903def29ff70d23740cf2cac8c29e78985dc516f2e01544a0173846fe700e3abb1543fd47c17e9a44ceb9e +DIST fscacher-0.1.4.gh.tar.gz 35097 BLAKE2B 32cd904d9d3bd36b4b14a55a4d618a99f73afda2807a1f655931b8b26e8ce0b1126773c5b242af824e2014cf634200a17f95d547c75ec4f6a3dd959ee5c37e23 SHA512 e3e85cee4c446552215b6d7092bdc72c31709e05dee7efb52fc6fc985992a3ece338c5a0dee54ed7e6aec797d4b7e2bd77b00f634112134c61f402b604103b5c +DIST fscacher-0.2.0.gh.tar.gz 37693 BLAKE2B 4e6493d5ec1bb56b53ab72842b6861fbfb916698b80021bbb5c8a8c89be9d90661c78bef9f5b09d3f681b40e45fa52b06dc93231df2228e3a00ee13f913544d8 SHA512 eca32e84f2b317b57aca749644fb76e6c7a0e65384903def29ff70d23740cf2cac8c29e78985dc516f2e01544a0173846fe700e3abb1543fd47c17e9a44ceb9e diff --git a/dev-python/fscacher/fscacher-0.1.4.ebuild b/dev-python/fscacher/fscacher-0.1.4.ebuild index 3f55c8604..50dcd6914 100644 --- a/dev-python/fscacher/fscacher-0.1.4.ebuild +++ b/dev-python/fscacher/fscacher-0.1.4.ebuild @@ -1,14 +1,14 @@ -# Copyright 1999-2022 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_{10..11} ) inherit distutils-r1 DESCRIPTION="Cache results of operations on heavy file trees" HOMEPAGE="https://github.com/con/fscacher" -SRC_URI="https://github.com/con/fscacher/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz" +SRC_URI="https://github.com/con/fscacher/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz" SLOT="0" LICENSE="MIT" diff --git a/dev-python/fscacher/fscacher-0.2.0.ebuild b/dev-python/fscacher/fscacher-0.2.0.ebuild index bb632800e..f466d0675 100644 --- a/dev-python/fscacher/fscacher-0.2.0.ebuild +++ b/dev-python/fscacher/fscacher-0.2.0.ebuild @@ -1,14 +1,14 @@ -# Copyright 1999-2022 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_{10..11} ) inherit distutils-r1 DESCRIPTION="Cache results of operations on heavy file trees" HOMEPAGE="https://github.com/con/fscacher" -SRC_URI="https://github.com/con/fscacher/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz" +SRC_URI="https://github.com/con/fscacher/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz" SLOT="0" LICENSE="MIT" diff --git a/dev-python/fslpy/Manifest b/dev-python/fslpy/Manifest index 196e885ac..f2c52a88e 100644 --- a/dev-python/fslpy/Manifest +++ b/dev-python/fslpy/Manifest @@ -1 +1 @@ -DIST fslpy-3.8.1.tar.gz 4698603 BLAKE2B 33740081a065b6684b864eaf50910a38e26ce7aa10d18bf8faaeaf34ee87dfa22e8f2ee3cebc5681f2356cfb519a59ba07232a3cfb81526258ef92f3ced893ea SHA512 1b5d945f6aae6557e892e5700f228170bab8a235c77d06b162fc2afc16663f3bdbe18e54e4e20dad46ac873ccbf0cdc2649e5ac1c53e17b0d78c45e91e8a1896 +DIST fslpy-3.10.0.tar.gz 4695461 BLAKE2B 9ce74ed6175fb84fe0f123375273a9450c03b659c977b48e3fb874509d5b3f728c75aff850931e1af4fd398fb5eda80a6eef90b2a582e8db3f2135704b4124ed SHA512 b9b12350308d2aee5d10c16582abd96f17b56893287fc32ab3942e8edce8add1f96e1f5c83cca761707be9b2442262e28d961879d5d02e1001006805a74e1cda diff --git a/dev-python/fslpy/files/fslpy-2.7.0-coverage.patch b/dev-python/fslpy/files/fslpy-2.7.0-coverage.patch deleted file mode 100644 index 3de6d92f1..000000000 --- a/dev-python/fslpy/files/fslpy-2.7.0-coverage.patch +++ /dev/null @@ -1,16 +0,0 @@ -diff --git a/setup.cfg b/setup.cfg -index 9ea1ddb..00eb59b 100644 ---- a/setup.cfg -+++ b/setup.cfg -@@ -18,8 +18,8 @@ markers = - - - testpaths = tests --addopts = -v --niters=50 --cov=fsl -m "not longtest" -+addopts = -v --niters=50 -m "not longtest" - - - [flake8] --ignore = E127,E201,E203,E221,E222,E241,E271,E272,E301,E302,E303,E701,W504 -\ No newline at end of file -+ignore = E127,E201,E203,E221,E222,E241,E271,E272,E301,E302,E303,E701,W504 diff --git a/dev-python/fslpy/fslpy-3.10.0.ebuild b/dev-python/fslpy/fslpy-3.10.0.ebuild new file mode 100644 index 000000000..3f6262707 --- /dev/null +++ b/dev-python/fslpy/fslpy-3.10.0.ebuild @@ -0,0 +1,47 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 virtualx + +DESCRIPTION="The FSL Python Library" +HOMEPAGE="https://git.fmrib.ox.ac.uk/fsl/fslpy" +SRC_URI="https://git.fmrib.ox.ac.uk/fsl/${PN}/-/archive/${PV}/${P}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +RDEPEND=" + dev-python/dill[${PYTHON_USEDEP}] + >=dev-python/h5py-2.9[${PYTHON_USEDEP}] + >=dev-python/indexed-gzip-0.7.0[${PYTHON_USEDEP}] + >=dev-python/numpy-1[${PYTHON_USEDEP}] + >=dev-python/pillow-3.2.0[${PYTHON_USEDEP}] + >=dev-python/trimesh-2.37.29[${PYTHON_USEDEP}] + =dev-python/wxpython-4*[${PYTHON_USEDEP}] + >=sci-libs/rtree-0.8.3[${PYTHON_USEDEP}] + >=sci-libs/nibabel-2.4[${PYTHON_USEDEP}] + >=dev-python/scipy-0.18[${PYTHON_USEDEP}] +" + +distutils_enable_tests pytest +distutils_enable_sphinx doc dev-python/sphinx-rtd-theme + +python_prepare_all() { + # Do not depend on coverage + sed -i -e 's/--cov=fsl//g' setup.cfg || die + + distutils-r1_python_prepare_all +} + +src_test() { + virtx distutils-r1_src_test +} + +python_test() { + epytest -m "not (dicomtest or longtest or fsltest)" || die "Tests failed with ${EPYTHON}" +} diff --git a/dev-python/fslpy/fslpy-3.8.1.ebuild b/dev-python/fslpy/fslpy-3.8.1.ebuild deleted file mode 100644 index 5bff5ed60..000000000 --- a/dev-python/fslpy/fslpy-3.8.1.ebuild +++ /dev/null @@ -1,39 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{8..9} ) - -inherit distutils-r1 virtualx - -DESCRIPTION="The FSL Python Library" -HOMEPAGE="https://git.fmrib.ox.ac.uk/fsl/fslpy" -SRC_URI="https://git.fmrib.ox.ac.uk/fsl/${PN}/-/archive/${PV}/${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -RDEPEND=" - >=dev-python/h5py-2.9[${PYTHON_USEDEP}] - >=dev-python/indexed_gzip-0.7.0[${PYTHON_USEDEP}] - >=dev-python/numpy-1[${PYTHON_USEDEP}] - >=dev-python/pillow-3.2.0[${PYTHON_USEDEP}] - >=dev-python/trimesh-2.37.29[${PYTHON_USEDEP}] - =dev-python/wxpython-4*[${PYTHON_USEDEP}] - >=sci-libs/rtree-0.8.3[${PYTHON_USEDEP}] - >=sci-libs/nibabel-2.4[${PYTHON_USEDEP}] - >=dev-python/scipy-0.18[${PYTHON_USEDEP}] -" - -PATCHES=( - "${FILESDIR}/fslpy-2.7.0-coverage.patch" -) - -distutils_enable_tests pytest -distutils_enable_sphinx doc dev-python/sphinx_rtd_theme - -python_test() { - virtx epytest --niters=50 -m "not (dicomtest or longtest or fsltest)" -} diff --git a/dev-python/gammapy/Manifest b/dev-python/gammapy/Manifest index 4645ef4fd..6cd1ed25d 100644 --- a/dev-python/gammapy/Manifest +++ b/dev-python/gammapy/Manifest @@ -1 +1 @@ -DIST gammapy-0.18.2.tar.gz 2077004 BLAKE2B 1dd22566d92d73bb9ef5f0cca455096caa014353a570dfa111c22db174dd52ebe93752347fc37d086a6f16b567227a45a18f2212f5078639793593c0fa77ec39 SHA512 b500756a90eb29fd3c275166b6d980249b2db48fd007f25a43a53d5d63a9e1e53fb16e4a4707313616ece2abdfa3e8d339e99f8f4c2f0bb9b3bd9287c86ce958 +DIST gammapy-1.0.tar.gz 3548471 BLAKE2B c6f66a5fe3158d42fefbae3e14a659d2d637b935cede97e0dfefad32d0aa39a3d5ece23b19e95436deb1299e60b472c7ed01bd5c9c4c1e009618d8dead8b1951 SHA512 acf8f7940b910cdd1277a876e14fde9e962c40d7742610dd8c37b7769b132485bb0aa6fadbd0f68af37858c110985d34679e6f3f4fe52c28a11bd4d56dcf3699 diff --git a/dev-python/gammapy/gammapy-0.18.2.ebuild b/dev-python/gammapy/gammapy-0.18.2.ebuild deleted file mode 100644 index c26732aed..000000000 --- a/dev-python/gammapy/gammapy-0.18.2.ebuild +++ /dev/null @@ -1,59 +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} ) -DISTUTILS_USE_SETUPTOOLS=rdepend - -inherit distutils-r1 optfeature - -DESCRIPTION="A Python package for gamma-ray astronomy" -HOMEPAGE="https://github.com/gammapy/gammapy" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -#TODO: Package all these pytest deps: -# pytest-doctestplus>=0.2.0 -# pytest-remotedata>=0.3.1 -# pytest-openfiles>=0.3.1 -# pytest-astropy-header>=0.1.2 -# pytest-arraydiff>=0.1 -# pytest-filter-subpackage>=0.1 -RESTRICT="test" - -RDEPEND=" - dev-python/click[${PYTHON_USEDEP}] - >=dev-python/astropy-0.4[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/pydantic[${PYTHON_USEDEP}] - dev-python/pyyaml[${PYTHON_USEDEP}] - dev-python/regions[${PYTHON_USEDEP}] - dev-python/scipy[${PYTHON_USEDEP}] -" - -# TODO: fix this -# There is a programmable error in your configuration file: -# KeyError: 'build_docs' -#distutils_enable_sphinx docs dev-python/sphinx-astropy -distutils_enable_tests pytest - -pkg_postinst() { - elog "To get additional features, a number of optional runtime" - elog "dependencies may be installed:" - elog "" - optfeature "Plotting" dev-python/matplotlib - optfeature "Plotting Astronomical Images" dev-python/aplpy - optfeature "Read/write CVS files" dev-python/pandas - optfeature "Image Processing" sci-libs/scikit-image - optfeature "Conversion helper functions" dev-python/rootpy - - # In science overlay: - optfeature "Image photometry" dev-python/photutils - optfeature "Image Utility Functions" dev-python/imageutils - - # Not packaged: Gammalib, ctools, sherpa, imfun, uncertainties, reproject -} diff --git a/dev-python/gammapy/gammapy-1.0.ebuild b/dev-python/gammapy/gammapy-1.0.ebuild new file mode 100644 index 000000000..6357014ed --- /dev/null +++ b/dev-python/gammapy/gammapy-1.0.ebuild @@ -0,0 +1,58 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools + +inherit distutils-r1 pypi optfeature + +DESCRIPTION="A Python package for gamma-ray astronomy" +HOMEPAGE="https://github.com/gammapy/gammapy" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +#TODO: Package all these pytest deps: +# pytest-doctestplus>=0.2.0 +# pytest-remotedata>=0.3.1 +# pytest-openfiles>=0.3.1 +# pytest-astropy-header>=0.1.2 +# pytest-arraydiff>=0.1 +# pytest-filter-subpackage>=0.1 +RESTRICT="test" + +RDEPEND=" + dev-python/click[${PYTHON_USEDEP}] + >=dev-python/astropy-0.4[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/pydantic[${PYTHON_USEDEP}] + dev-python/pyyaml[${PYTHON_USEDEP}] + dev-python/regions[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] +" + +# TODO: fix this +# There is a programmable error in your configuration file: +# KeyError: 'build_docs' +#distutils_enable_sphinx docs dev-python/sphinx-astropy +distutils_enable_tests pytest + +pkg_postinst() { + elog "To get additional features, a number of optional runtime" + elog "dependencies may be installed:" + elog "" + optfeature "Plotting" dev-python/matplotlib + optfeature "Plotting Astronomical Images" dev-python/aplpy + optfeature "Read/write CVS files" dev-python/pandas + optfeature "Image Processing" dev-python/scikit-image + optfeature "Conversion helper functions" dev-python/rootpy + + # In science overlay: + optfeature "Image photometry" dev-python/photutils + optfeature "Image Utility Functions" dev-python/imageutils + + # Not packaged: Gammalib, ctools, sherpa, imfun, uncertainties, reproject +} diff --git a/dev-python/gammapy/metadata.xml b/dev-python/gammapy/metadata.xml index a9f88e7d8..f4a01e639 100644 --- a/dev-python/gammapy/metadata.xml +++ b/dev-python/gammapy/metadata.xml @@ -12,5 +12,6 @@ H.E.S.S, and CTA in primarily Galactic plane survey studies. </longdescription> <upstream> <remote-id type="github">gammapy/gammapy</remote-id> + <remote-id type="pypi">gammapy</remote-id> </upstream> </pkgmetadata> diff --git a/dev-python/geopandas/Manifest b/dev-python/geopandas/Manifest index c541ed559..037a125d3 100644 --- a/dev-python/geopandas/Manifest +++ b/dev-python/geopandas/Manifest @@ -1 +1 @@ -DIST geopandas-0.10.2.tar.gz 6317604 BLAKE2B 5eb0d84c11eda99b43bc15b179a971c5e56fb36d40c771b523161dd6ddac4faee4bac483ccd1bdb9f10f73dfd2adf6d72703cc180359cd68383bfba9410f4f5b SHA512 339660c423955b9f110eb390c3d1dc88eeb1ed74fa300870ae277d312e9b2e6733463bc45b445c73a9f8b6dee82d82f203c7b75c0a4aad7e36e43e5c7ec78f42 +DIST geopandas-0.13.2.gh.tar.gz 6388249 BLAKE2B 910f32ea7d798bbdeee77be190c57daf7bdc719901a2183b5328ec13619ff9b4145d1717afed8fc71da154d84f388ce2bc30c541478f95ed121c7d8681c691ae SHA512 4dff4bfeca2490081c02c41edf92037fa8a8f4b030b6f6a0cdc231b3119f829604af39277125db9535c66aac0698d2d4dcfac2bb58b92d31bea83f0ee296e21a diff --git a/dev-python/geopandas/geopandas-0.10.2.ebuild b/dev-python/geopandas/geopandas-0.10.2.ebuild deleted file mode 100644 index e63aaa1bc..000000000 --- a/dev-python/geopandas/geopandas-0.10.2.ebuild +++ /dev/null @@ -1,34 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{8..10} ) -DISTUTILS_USE_PEP517="setuptools" -inherit distutils-r1 - -DESCRIPTION="Python tools for geographic data" -HOMEPAGE="https://github.com/geopandas/geopandas" -SRC_URI="https://github.com/geopandas/${PN}/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -RDEPEND=" - dev-python/pandas[${PYTHON_USEDEP}] - dev-python/shapely[${PYTHON_USEDEP}] - dev-python/fiona[${PYTHON_USEDEP}] - dev-python/pyproj[${PYTHON_USEDEP}]" - -distutils_enable_tests pytest - -python_test() { - local deselect=( - # disable tests due to networking being blocked - geopandas/io/tests/test_file.py::test_read_file_remote_zipfile_url - geopandas/io/tests/test_file.py::test_read_file_remote_geojson_url - ) - - epytest ${deselect[@]/#/--deselect } -} diff --git a/dev-python/geopandas/geopandas-0.13.2.ebuild b/dev-python/geopandas/geopandas-0.13.2.ebuild new file mode 100644 index 000000000..921c13417 --- /dev/null +++ b/dev-python/geopandas/geopandas-0.13.2.ebuild @@ -0,0 +1,42 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 optfeature + +DESCRIPTION="Python tools for geographic data" +HOMEPAGE="https://github.com/geopandas/geopandas https://pypi.org/project/geopandas/" +SRC_URI="https://github.com/geopandas/${PN}/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +RDEPEND=" + dev-python/pandas[${PYTHON_USEDEP}] + dev-python/shapely[${PYTHON_USEDEP}] + dev-python/fiona[${PYTHON_USEDEP}] + dev-python/pyproj[${PYTHON_USEDEP}]" + +distutils_enable_tests pytest + +python_test() { + local deselect=( + # needs network access + geopandas/io/tests/test_file.py::test_read_file_url + # fails with RuntimeError thrown by matplotlib + geopandas/tests/test_plotting.py::TestGeoplotAccessor::test_pandas_kind + ) + + epytest ${deselect[@]/#/--deselect } +} + +pkg_postinst() { + optfeature "plotting" dev-python/matplotlib + optfeature "spatial indexes and spatial joins" sci-libs/rtree + optfeature "geocoding" sci-geosciences/geopy + optfeature "geodatabase access" dev-python/psycopg dev-python/sqlalchemy +} diff --git a/dev-python/geopandas/metadata.xml b/dev-python/geopandas/metadata.xml index a9b62a0d8..a102c7148 100644 --- a/dev-python/geopandas/metadata.xml +++ b/dev-python/geopandas/metadata.xml @@ -1,19 +1,19 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="project"> - <email>sci@gentoo.org</email> - <name>Gentoo Science Project</name> - </maintainer> - <longdescription lang="en"> - GeoPandas is a project to add support for geographic data to pandas - objects. It currently implements GeoSeries and GeoDataFrame types - which are subclasses of pandas.Series and pandas.DataFrame - respectively. GeoPandas objects can act on shapely geometry objects - and perform geometric operations. -</longdescription> - <upstream> - <remote-id type="github">geopandas/geopandas</remote-id> - <remote-id type="pypi">geopandas</remote-id> - </upstream> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + GeoPandas is a project to add support for geographic data to pandas + objects. It currently implements GeoSeries and GeoDataFrame types + which are subclasses of pandas.Series and pandas.DataFrame + respectively. GeoPandas objects can act on shapely geometry objects + and perform geometric operations. + </longdescription> + <upstream> + <remote-id type="github">geopandas/geopandas</remote-id> + <remote-id type="pypi">geopandas</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/gffpandas/Manifest b/dev-python/gffpandas/Manifest index 8d84e74c6..1a3ae3b5f 100644 --- a/dev-python/gffpandas/Manifest +++ b/dev-python/gffpandas/Manifest @@ -1 +1 @@ -DIST gffpandas-1.2.0.tar.gz 32040 BLAKE2B 66f53357876d417997366cdcbacd778f2b17e7df113d21f2a836b082719f549ede5e06a9a6c46e9c5bee2d86946871e68ab1f9b7af0defcaa8a55ae8ef93b274 SHA512 feb67ea93a078547103c1c6b8f32bd6bbd69ab669b93b90aa5f48bc0ebc25ea23e35130976bf1a89ff5e92fdbd054c4df98cc961278c7caaf28b48c202a662d7 +DIST gffpandas-1.2.0.gh.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 index 12ec9927c..e0fe2f621 100644 --- a/dev-python/gffpandas/gffpandas-1.2.0.ebuild +++ b/dev-python/gffpandas/gffpandas-1.2.0.ebuild @@ -1,16 +1,16 @@ -# Copyright 2021 Gentoo Authors +# Copyright 2021-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_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 -> ${P}.tar.gz" +SRC_URI="https://github.com/foerstner-lab/${PN}/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz" LICENSE="ISC" SLOT="0" @@ -19,7 +19,7 @@ KEYWORDS="~amd64 ~x86" RDEPEND="dev-python/pandas[${PYTHON_USEDEP}]" distutils_enable_tests pytest -distutils_enable_sphinx docs/source dev-python/sphinx_rtd_theme +distutils_enable_sphinx docs/source dev-python/sphinx-rtd-theme python_prepare_all() { # Do not depend on pytest-runner diff --git a/dev-python/gmsh_interop/gmsh_interop-2021.1.1.ebuild b/dev-python/gmsh_interop/gmsh_interop-2021.1.1.ebuild index 785646336..3185102ba 100644 --- a/dev-python/gmsh_interop/gmsh_interop-2021.1.1.ebuild +++ b/dev-python/gmsh_interop/gmsh_interop-2021.1.1.ebuild @@ -3,13 +3,11 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) - -inherit distutils-r1 +PYTHON_COMPAT=( python3_10 ) +inherit distutils-r1 pypi DESCRIPTION="Interoperability with Gmsh for Python" HOMEPAGE="https://github.com/inducer/gmsh_interop/" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" LICENSE="MIT" SLOT="0" diff --git a/dev-python/gmsh_interop/metadata.xml b/dev-python/gmsh_interop/metadata.xml index 2f2c0b51c..ed015f298 100644 --- a/dev-python/gmsh_interop/metadata.xml +++ b/dev-python/gmsh_interop/metadata.xml @@ -9,4 +9,8 @@ <email>sci@gentoo.org</email> <name>Gentoo Science Project</name> </maintainer> + <upstream> + <remote-id type="pypi">gmsh_interop</remote-id> + <remote-id type="github">inducer/gmsh_interop</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/google-cloud-storage/Manifest b/dev-python/google-cloud-storage/Manifest new file mode 100644 index 000000000..6bd5af5b0 --- /dev/null +++ b/dev-python/google-cloud-storage/Manifest @@ -0,0 +1 @@ +DIST google-cloud-storage-2.7.0.tar.gz 5490914 BLAKE2B 582fcf9a84bedcff41de2b26558ccae96474cbbe91c86bbe6bf53ff6a2fe38d7eb8dbe396fccd36ad252f171ed7eda45974ca9e7867e3ee9542c85570a951aef SHA512 89c4208781735bb0e8b0978202877af324154d5233d7abafd1b2b14b4bb381c18572cfdc791e42577ad929f3c4ded0857d9bd9f4eb52a93ed74e8884d797b365 diff --git a/dev-python/google-cloud-storage/google-cloud-storage-2.7.0.ebuild b/dev-python/google-cloud-storage/google-cloud-storage-2.7.0.ebuild new file mode 100644 index 000000000..403f75dee --- /dev/null +++ b/dev-python/google-cloud-storage/google-cloud-storage-2.7.0.ebuild @@ -0,0 +1,25 @@ +# Copyright 2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools +PYPI_NO_NORMALIZE=1 + +inherit distutils-r1 pypi + +DESCRIPTION="Google Cloud Storage API client library" +HOMEPAGE="https://github.com/googleapis/python-storage" + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + dev-python/google-auth[${PYTHON_USEDEP}] + dev-python/google-api-core[${PYTHON_USEDEP}] + dev-python/requests[${PYTHON_USEDEP}] +" + +distutils_enable_tests pytest diff --git a/dev-python/google-cloud-storage/metadata.xml b/dev-python/google-cloud-storage/metadata.xml new file mode 100644 index 000000000..d67c6b09f --- /dev/null +++ b/dev-python/google-cloud-storage/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <upstream> + <remote-id type="github">googleapis/python-storage</remote-id> + <remote-id type="pypi">google-cloud-storage</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/grabbit/grabbit-0.2.6.ebuild b/dev-python/grabbit/grabbit-0.2.6.ebuild index 045f26d06..722048089 100644 --- a/dev-python/grabbit/grabbit-0.2.6.ebuild +++ b/dev-python/grabbit/grabbit-0.2.6.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2020 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7..9} ) +PYTHON_COMPAT=( python3_{10..11} ) inherit distutils-r1 diff --git a/dev-python/gwcs/Manifest b/dev-python/gwcs/Manifest index 4c4dc60c1..4e040149b 100644 --- a/dev-python/gwcs/Manifest +++ b/dev-python/gwcs/Manifest @@ -1 +1 @@ -DIST gwcs-0.16.1.tar.gz 171068 BLAKE2B 0406a7b8545b56d7811b8326c148f0d413dd6ae38f90c9e50d984fd9a35d2f130d61821a237acc2bec2746e012d199f4ed08231299520de46ffa1554fe4d860b SHA512 2414f1c40be632e7b7cdb6657f54869a2aa8aefce6074ff0e6c5c277fd6c125d72c42b76e9344f100367f810bfcd5dc49b4e6ec6318b08a975799a918debb9cc +DIST gwcs-0.18.3.tar.gz 184361 BLAKE2B a4afcf3d6281f65f1ff6733bb83f82ba089fc56d2a21c2d6f5fd8370ef518b97376ebe718a9e4f9fa34ae80fc66baecf9e32835bb18f1737bf3f47e972e31118 SHA512 51aac4dd1f3b835b274f265cf26d4f9cf757435bb8355d43a31b7eba665991c233b46f9e0a87d22985c04fdabc0455958b99f37aeb55a04a9c0b4901d5069891 diff --git a/dev-python/gwcs/gwcs-0.16.1.ebuild b/dev-python/gwcs/gwcs-0.16.1.ebuild deleted file mode 100644 index 373410501..000000000 --- a/dev-python/gwcs/gwcs-0.16.1.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="Generalized World Coordinate System" -HOMEPAGE="https://gwcs.readthedocs.io/en/latest/" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -BDEPEND="dev-python/setuptools_scm[${PYTHON_USEDEP}] - test? ( - dev-python/pytest-doctestplus[${PYTHON_USEDEP}] - ) -" - -RDEPEND=" - dev-python/asdf[${PYTHON_USEDEP}] - >=dev-python/astropy-4.1[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/scipy[${PYTHON_USEDEP}] -" - -# TODO: package stsci-rtd-theme -#distutils_enable_sphinx docs dev-python/sphinx-astropy dev-python/sphinx-automodapi dev-python/sphinx_rtd_theme -distutils_enable_tests pytest - -python_test() { - # discovers things in docs dir if we do not - # explicitly set it to run on the tests dir - pytest -vv gwcs/tests || die " Tests failed with ${EPYTHON}" -} diff --git a/dev-python/gwcs/gwcs-0.18.3-r1.ebuild b/dev-python/gwcs/gwcs-0.18.3-r1.ebuild new file mode 100644 index 000000000..eef5aeb36 --- /dev/null +++ b/dev-python/gwcs/gwcs-0.18.3-r1.ebuild @@ -0,0 +1,42 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools + +inherit distutils-r1 pypi + +DESCRIPTION="Generalized World Coordinate System" +HOMEPAGE="https://gwcs.readthedocs.io/en/latest/" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" +# Tests do not pass, reported upstream: +# https://github.com/spacetelescope/gwcs/issues/437 +RESTRICT=test + +BDEPEND="dev-python/setuptools-scm[${PYTHON_USEDEP}] + test? ( + dev-python/pytest-doctestplus[${PYTHON_USEDEP}] + ) +" + +RDEPEND=" + dev-python/asdf[${PYTHON_USEDEP}] + >=dev-python/astropy-4.1[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] +" + +# TODO: package stsci-rtd-theme +#distutils_enable_sphinx docs dev-python/sphinx-astropy dev-python/sphinx-automodapi dev-python/sphinx_rtd_theme +distutils_enable_tests pytest + +python_test() { + # discovers things in docs dir if we do not + # explicitly set it to run on the tests dir + epytest gwcs/tests +} diff --git a/dev-python/gwcs/metadata.xml b/dev-python/gwcs/metadata.xml index 4f4367037..d7b713ef5 100644 --- a/dev-python/gwcs/metadata.xml +++ b/dev-python/gwcs/metadata.xml @@ -5,4 +5,7 @@ <email>sci-astronomy@gentoo.org</email> <name>Gentoo Astronomy Project</name> </maintainer> + <upstream> + <remote-id type="pypi">gwcs</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/hdbscan/Manifest b/dev-python/hdbscan/Manifest new file mode 100644 index 000000000..7ffc42c8b --- /dev/null +++ b/dev-python/hdbscan/Manifest @@ -0,0 +1 @@ +DIST hdbscan-0.8.29.tar.gz 11666106 BLAKE2B de324386d7d2178f74ea958fa75e5eccb9dcdeba3d85cecce1150930e2d687caecbc79469de6ad62806c5bd860962bba57f27323c69f3abc6b0d4694a553656d SHA512 fd349c1c6c09f0288a9a2501eb7794fb03139c11261a835d90f1c9cd80955a4d8d075ff3864ddb9cfcbc204a3d0662011074bdb29b66b72d5469f76bc4f7ecca diff --git a/dev-python/hdbscan/hdbscan-0.8.29.ebuild b/dev-python/hdbscan/hdbscan-0.8.29.ebuild new file mode 100644 index 000000000..33947fd22 --- /dev/null +++ b/dev-python/hdbscan/hdbscan-0.8.29.ebuild @@ -0,0 +1,32 @@ +# Copyright 2021-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 pypi + +DESCRIPTION="A high performance implementation of HDBSCAN clustering." +HOMEPAGE="https://github.com/scikit-learn-contrib/hdbscan" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="test" +# Reported upstream: +# https://github.com/scikit-learn-contrib/hdbscan/issues/501 +RESTRICT="test" + +DEPEND="" +RDEPEND=" + dev-python/cython[${PYTHON_USEDEP}] + dev-python/joblib[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + dev-python/six[${PYTHON_USEDEP}] + sci-libs/scikit-learn[${PYTHON_USEDEP}] +" +BDEPEND="" + +distutils_enable_tests pytest diff --git a/dev-python/hdbscan/metadata.xml b/dev-python/hdbscan/metadata.xml new file mode 100644 index 000000000..3e9aab1c5 --- /dev/null +++ b/dev-python/hdbscan/metadata.xml @@ -0,0 +1,29 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>gentoo@chymera.eu</email> + <name>Horea Christian</name> + </maintainer> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + HDBSCAN - Hierarchical Density-Based Spatial Clustering of Applications with + Noise. Performs DBSCAN over varying epsilon values and integrates the result + to find a clustering that gives the best stability over epsilon. This allows + HDBSCAN to find clusters of varying densities (unlike DBSCAN), and be more + robust to parameter selection. + + In practice this means that HDBSCAN returns a good clustering straight away + with little or no parameter tuning -- and the primary parameter, minimum + cluster size, is intuitive and easy to select. HDBSCAN is ideal for + exploratory data analysis; it's a fast and robust algorithm that you can + trust to return meaningful clusters (if there are any). + </longdescription> + <upstream> + <remote-id type="github">scikit-learn-contrib/hdbscan</remote-id> + <remote-id type="pypi">hdbscan</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/hdf5storage/Manifest b/dev-python/hdf5storage/Manifest index b9aa0d469..caea5df39 100644 --- a/dev-python/hdf5storage/Manifest +++ b/dev-python/hdf5storage/Manifest @@ -1 +1 @@ -DIST hdf5storage-0.1.15_p1.tar.gz 117372 BLAKE2B 56839673864fbb41ea96b535293dc35cff99635f2d8f37b4b57c184a62a4a957a12f99387f43f53061ce5b49c8dcbc6816db6eaa43d0f98ac7f54d530675b487 SHA512 38b71b5e061da3ea259decefeb0f0dd4812f92839dd06b24b6cdf11a225b8dd7446e37972987f9be914448fd05ca780ca0239d0275464e64775a867420c3c819 +DIST hdf5storage-0.1.19.tar.gz 92294 BLAKE2B b4379e9c6b69af1c205072d0d8b29f6322c3271cc1f5e56ab81a4ec3c09db9f9ac107b912e4d74772253ade269db589ed4ac140cde6cfd95346de7fcdc6dc752 SHA512 0ea4068be1af2521bba3fba3b0b020c0faff64be487644c46350ef19f4f3997593af90438db5b0d9b80ac303ff99755a0f59504ad34cfa27f1bc8c7881f024ce diff --git a/dev-python/hdf5storage/hdf5storage-0.1.15_p1.ebuild b/dev-python/hdf5storage/hdf5storage-0.1.15_p1.ebuild deleted file mode 100644 index 8a7b76420..000000000 --- a/dev-python/hdf5storage/hdf5storage-0.1.15_p1.ebuild +++ /dev/null @@ -1,31 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 -PYTHON_COMPAT=( python3_{7..9} ) - -inherit distutils-r1 - -DESCRIPTION="Read/write Python types to/from HDF5 files, including MATLAB v7.3 MAT files" -HOMEPAGE="https://github.com/frejanordsiek/hdf5storage" - -if [[ ${PV} == 9999 ]]; then - inherit git-r3 - EGIT_REPO_URI="https://github.com/frejanordsiek/hdf5storage" -else - COMMIT=09dfc5fb3a6a3f9c32c2479a896c7f14d3c8d830 - SRC_URI="https://github.com/frejanordsiek/hdf5storage/archive/${COMMIT}.tar.gz -> ${P}.tar.gz" - S="${WORKDIR}"/${PN}-${COMMIT} - KEYWORDS="~amd64" -fi - -LICENSE="BSD" -SLOT="0" - -RDEPEND=" - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/h5py[${PYTHON_USEDEP}] -" -DEPEND="${RDEPEND}" - -distutils_enable_tests nose diff --git a/dev-python/hdf5storage/hdf5storage-0.1.19.ebuild b/dev-python/hdf5storage/hdf5storage-0.1.19.ebuild new file mode 100644 index 000000000..ab64fefbc --- /dev/null +++ b/dev-python/hdf5storage/hdf5storage-0.1.19.ebuild @@ -0,0 +1,25 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools + +inherit distutils-r1 + +DESCRIPTION="Read/write Python types to/from HDF5 files, including MATLAB v7.3 MAT files" +HOMEPAGE="https://github.com/frejanordsiek/hdf5storage" + +SRC_URI="https://github.com/frejanordsiek/hdf5storage/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz" +KEYWORDS="~amd64 ~x86" + +LICENSE="BSD" +SLOT="0" + +RDEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/h5py[${PYTHON_USEDEP}] +" +DEPEND="${RDEPEND}" + +distutils_enable_tests pytest diff --git a/dev-python/hdf5storage/hdf5storage-9999.ebuild b/dev-python/hdf5storage/hdf5storage-9999.ebuild index 8a7b76420..1bcf35a57 100644 --- a/dev-python/hdf5storage/hdf5storage-9999.ebuild +++ b/dev-python/hdf5storage/hdf5storage-9999.ebuild @@ -1,8 +1,9 @@ -# Copyright 1999-2020 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 -PYTHON_COMPAT=( python3_{7..9} ) +EAPI=8 +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools inherit distutils-r1 @@ -28,4 +29,4 @@ RDEPEND=" " DEPEND="${RDEPEND}" -distutils_enable_tests nose +distutils_enable_tests pytest diff --git a/dev-python/hdmf-zarr/Manifest b/dev-python/hdmf-zarr/Manifest new file mode 100644 index 000000000..6b7d2418b --- /dev/null +++ b/dev-python/hdmf-zarr/Manifest @@ -0,0 +1 @@ +DIST hdmf_zarr-0.5.0.tar.gz 3095566 BLAKE2B f824b480bb99ffbf495b18505d561a3511af60f654df66f89c2c5c081ba49889512e29cb31b6eb617ef7abac58472fa4b6d9f23cd9c33be436a77ceb2d54130a SHA512 205dd5b2de1a403fc7098e7ba26e4bbba1949b8f50641173ea614011e821a77a461ab255f19afefddcd5fa019ed0e7c047fd7c940a2d09a1f63c5de5f1ac50cb diff --git a/dev-python/hdmf-zarr/files/hdmf-zarr-0.5.0-coverage.patch b/dev-python/hdmf-zarr/files/hdmf-zarr-0.5.0-coverage.patch new file mode 100644 index 000000000..d82c30960 --- /dev/null +++ b/dev-python/hdmf-zarr/files/hdmf-zarr-0.5.0-coverage.patch @@ -0,0 +1,28 @@ +diff --git a/pyproject.toml b/pyproject.toml +index 4008b3b..40e281a 100644 +--- a/pyproject.toml ++++ b/pyproject.toml +@@ -62,9 +62,6 @@ exclude = [".git_archival.txt"] + [tool.hatch.build.targets.wheel] + packages = ["src/hdmf_zarr"] + +-[tool.pytest.ini_options] +-addopts = "--cov --cov-report html" +- + [tool.codespell] + skip = "htmlcov,.git,.mypy_cache,.pytest_cache,.coverage,*.pdf,*.svg,venvs,.tox,./docs/_build/*,*.ipynb" + ignore-words-list = "datas" +diff --git a/tox.ini b/tox.ini +index 720a97f..66d0df3 100644 +--- a/tox.ini ++++ b/tox.ini +@@ -28,8 +28,7 @@ commands = + [testenv:localcoverage] + basepython = python3.11 + commands = +- pytest --cov=hdmf_zarr +- coverage html -d tests/coverage/htmlcov ++ pytest + + # Test with python 3.11; pinned dev and optional reqs + [testenv:py311-optional] diff --git a/dev-python/hdmf-zarr/hdmf-zarr-0.5.0.ebuild b/dev-python/hdmf-zarr/hdmf-zarr-0.5.0.ebuild new file mode 100644 index 000000000..692197867 --- /dev/null +++ b/dev-python/hdmf-zarr/hdmf-zarr-0.5.0.ebuild @@ -0,0 +1,32 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=hatchling + +inherit distutils-r1 pypi + +DESCRIPTION="Zarr I/O backend for HDMF" +HOMEPAGE="https://github.com/hdmf-dev/hdmf-zarr" +#SRC_URI="https://github.com/hdmf-dev/hdmf-zarr/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz" +KEYWORDS="~amd64 ~x86" + +LICENSE="BSD" +SLOT="0" + +RDEPEND=" + dev-python/hdmf[${PYTHON_USEDEP}] + dev-python/numcodecs[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/pynwb[${PYTHON_USEDEP}] + dev-python/threadpoolctl[${PYTHON_USEDEP}] + dev-python/zarr[${PYTHON_USEDEP}] +" +DEPEND="${RDEPEND}" + +PATCHES=( + "${FILESDIR}/${P}-coverage.patch" +) + +distutils_enable_tests pytest diff --git a/dev-python/hdmf-zarr/metadata.xml b/dev-python/hdmf-zarr/metadata.xml new file mode 100644 index 000000000..1ced471a1 --- /dev/null +++ b/dev-python/hdmf-zarr/metadata.xml @@ -0,0 +1,16 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>gentoo@chymera.eu</email> + <name>Horea Christian</name> + </maintainer> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <upstream> + <remote-id type="github">hdmf-dev/hdmf-zarr</remote-id> + <remote-id type="pypi">hdmf-zarr</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/hdmf/Manifest b/dev-python/hdmf/Manifest index 67e1f4b6c..204753b4e 100644 --- a/dev-python/hdmf/Manifest +++ b/dev-python/hdmf/Manifest @@ -1 +1 @@ -DIST hdmf-3.1.1.tar.gz 292419 BLAKE2B eed1b1c282f022f7e1bd3af63c3078563a74895bf177244841ee0cabd3ab391e2d7a48c9a111a909f5982bf1a1c9b44f1b82fd710f9729681bcada396d3c3d7b SHA512 41776932b1150126a162e9f87072d6626a28bb3f0e05f75337e4f6529c27005ca9db932fdff0c45bb16cbebf68388c7cbf575bbd17950c29c300702a37afacf0 +DIST hdmf-3.13.0.tar.gz 15855926 BLAKE2B 8eb386540768a83954745c02f7142d2a0b466ef670baaf13a1dfee0ce02261f0f89a9b173dfb8d2673d1f538c35e800117f6f0fe2ca77e5ca6a94b01e9908917 SHA512 5d6f97abb28b46136b3a62f915f8c14cc48e49c1ec3d44e3d863b1c3e7aebb1cfea428b77311ca51dbf5ef9a1e529e73cdb477d863e3d0cd6641fbf79a043f20 diff --git a/dev-python/hdmf/files/hdmf-3.1.1-versions.patch b/dev-python/hdmf/files/hdmf-3.1.1-versions.patch deleted file mode 100644 index 58822989d..000000000 --- a/dev-python/hdmf/files/hdmf-3.1.1-versions.patch +++ /dev/null @@ -1,21 +0,0 @@ ---- a/setup.py 2022-01-31 02:48:24.645837186 -0500 -+++ b/setup.py 2022-01-31 02:49:55.066949247 -0500 -@@ -12,12 +12,12 @@ - schema_dir = 'common/hdmf-common-schema/common' - - reqs = [ -- 'h5py>=2.10,<4', -- 'numpy>=1.16,<1.22', -- 'scipy>=1.1,<2', -- 'pandas>=1.0.5,<2', -- 'ruamel.yaml>=0.16,<1', -- 'jsonschema>=2.6.0,<4', -+ 'h5py', -+ 'numpy', -+ 'scipy', -+ 'pandas', -+ 'ruamel.yaml', -+ 'jsonschema', - 'setuptools', - ] - diff --git a/dev-python/hdmf/files/hdmf-3.11.0-no_test_coverage.patch b/dev-python/hdmf/files/hdmf-3.11.0-no_test_coverage.patch new file mode 100644 index 000000000..e44a68902 --- /dev/null +++ b/dev-python/hdmf/files/hdmf-3.11.0-no_test_coverage.patch @@ -0,0 +1,10 @@ +--- a/pyproject.toml 2020-02-01 19:00:00.000000000 -0500 ++++ b/pyproject.toml 2023-12-11 12:00:19.368474488 -0500 +@@ -76,7 +76,6 @@ + # verbose = 1 + + [tool.pytest.ini_options] +-addopts = "--cov --cov-report html" + norecursedirs = "tests/unit/helpers" + + [tool.codespell] diff --git a/dev-python/hdmf/hdmf-3.1.1-r1.ebuild b/dev-python/hdmf/hdmf-3.1.1-r1.ebuild deleted file mode 100644 index 76d40c95f..000000000 --- a/dev-python/hdmf/hdmf-3.1.1-r1.ebuild +++ /dev/null @@ -1,32 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{8..10} ) -DISTUTILS_USE_SETUPTOOLS=rdepend -inherit distutils-r1 - -DESCRIPTION="The Hierarchical Data Modeling Framework" -HOMEPAGE="https://github.com/hdmf-dev/hdmf" -SRC_URI="https://github.com/hdmf-dev/hdmf/releases/download/${PV}/${P}.tar.gz" - -SLOT="0" -LICENSE="BSD" -KEYWORDS="~amd64 ~x86" - -RDEPEND=" - dev-python/h5py[${PYTHON_USEDEP}] - dev-python/jsonschema[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/pandas[${PYTHON_USEDEP}] - dev-python/ruamel-yaml[${PYTHON_USEDEP}] - dev-python/scipy[${PYTHON_USEDEP}] - " -BDEPEND="" - -distutils_enable_tests pytest - -PATCHES=( - "${FILESDIR}/${PN}-3.1.1-versions.patch" -) diff --git a/dev-python/hdmf/hdmf-3.13.0.ebuild b/dev-python/hdmf/hdmf-3.13.0.ebuild new file mode 100644 index 000000000..7068afb01 --- /dev/null +++ b/dev-python/hdmf/hdmf-3.13.0.ebuild @@ -0,0 +1,31 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=hatchling +PYTHON_COMPAT=( python3_{10..12} ) +inherit distutils-r1 pypi + +DESCRIPTION="The Hierarchical Data Modeling Framework" +HOMEPAGE="https://github.com/hdmf-dev/hdmf" +SRC_URI="$(pypi_sdist_url hdmf)" + +SLOT="0" +LICENSE="BSD" +KEYWORDS="~amd64 ~x86" + +RDEPEND=" + dev-python/h5py[${PYTHON_USEDEP}] + dev-python/jsonschema[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + dev-python/ruamel-yaml[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + " + +PATCHES=( + "${FILESDIR}/${PN}-3.11.0-no_test_coverage.patch" + ) + +distutils_enable_tests pytest diff --git a/dev-python/hdmf/metadata.xml b/dev-python/hdmf/metadata.xml index 82da7c426..ac3f7a6cb 100644 --- a/dev-python/hdmf/metadata.xml +++ b/dev-python/hdmf/metadata.xml @@ -15,4 +15,8 @@ data models, reading and writing data to different storage backends, and representing data with Python object. </longdescription> + <upstream> + <remote-id type="github">hdmf-dev/hdmf</remote-id> + <remote-id type="pypi">hdmf</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/heudiconv/Manifest b/dev-python/heudiconv/Manifest new file mode 100644 index 000000000..fe38a3307 --- /dev/null +++ b/dev-python/heudiconv/Manifest @@ -0,0 +1,2 @@ +DIST heudiconv-0.13.0.tar.gz 9158053 BLAKE2B 9f87fbcd5ea8ccca39cc029f1bdd84906412a22e5d18e2afe280d19737f0dda4c03248ba93f58c06aae4b15366477e8a5d1c41d09d1b1d3a10ff673aaa050e26 SHA512 b867ee0a60ad98099a3802e290ebb24b858befbd45e93772fafe437a87ea867c5076680ea3ed7856272397267c740ef2eade9f64ffc0d4216d4a37be39add158 +DIST heudiconv-1.0.0.tar.gz 9158631 BLAKE2B af5b3dee2448a025a231fad0ac9692b13d431288ea0ca19b4919d9ae83c86a7c72cf11f9bd3a0ec6b18259d2f8e8cecf9372a0fae605ecb5e9cac0bd4975693a SHA512 165bd814e3c7f25b51ed8884bddde45b82dc226ee93af5984b822aa53ad5e7504aae57088cd1f777c62835669e8816d95dbf84de7fb379038308dca7871d8739 diff --git a/dev-python/heudiconv/heudiconv-0.13.0.ebuild b/dev-python/heudiconv/heudiconv-0.13.0.ebuild new file mode 100644 index 000000000..7f7db0b0e --- /dev/null +++ b/dev-python/heudiconv/heudiconv-0.13.0.ebuild @@ -0,0 +1,42 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) +inherit distutils-r1 pypi + +DESCRIPTION="Flexible DICOM conversion to structured directory layouts" +HOMEPAGE=" + https://github.com/nipy/heudiconv + https://heudiconv.readthedocs.io/en/latest/ +" + +SLOT="0" +LICENSE="Apache-2.0" +KEYWORDS="~amd64 ~x86" + +RDEPEND=" + dev-python/filelock[${PYTHON_USEDEP}] + dev-python/versioningit[${PYTHON_USEDEP}] + sci-biology/dcm2niix + sci-biology/dcmstack[${PYTHON_USEDEP}] + sci-libs/nibabel[${PYTHON_USEDEP}] + sci-libs/nipype[${PYTHON_USEDEP}] + sci-libs/pydicom[${PYTHON_USEDEP}] + " +BDEPEND=" + test? ( + dev-python/mock[${PYTHON_USEDEP}] + dev-python/six[${PYTHON_USEDEP}] + ) +" + +# Reported upstream: +# https://github.com/nipy/heudiconv/issues/679 +EPYTEST_DESELECT=( + heudiconv/tests/test_main.py::test_prepare_for_datalad +) + +distutils_enable_tests pytest diff --git a/dev-python/heudiconv/heudiconv-1.0.0.ebuild b/dev-python/heudiconv/heudiconv-1.0.0.ebuild new file mode 100644 index 000000000..7f7db0b0e --- /dev/null +++ b/dev-python/heudiconv/heudiconv-1.0.0.ebuild @@ -0,0 +1,42 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) +inherit distutils-r1 pypi + +DESCRIPTION="Flexible DICOM conversion to structured directory layouts" +HOMEPAGE=" + https://github.com/nipy/heudiconv + https://heudiconv.readthedocs.io/en/latest/ +" + +SLOT="0" +LICENSE="Apache-2.0" +KEYWORDS="~amd64 ~x86" + +RDEPEND=" + dev-python/filelock[${PYTHON_USEDEP}] + dev-python/versioningit[${PYTHON_USEDEP}] + sci-biology/dcm2niix + sci-biology/dcmstack[${PYTHON_USEDEP}] + sci-libs/nibabel[${PYTHON_USEDEP}] + sci-libs/nipype[${PYTHON_USEDEP}] + sci-libs/pydicom[${PYTHON_USEDEP}] + " +BDEPEND=" + test? ( + dev-python/mock[${PYTHON_USEDEP}] + dev-python/six[${PYTHON_USEDEP}] + ) +" + +# Reported upstream: +# https://github.com/nipy/heudiconv/issues/679 +EPYTEST_DESELECT=( + heudiconv/tests/test_main.py::test_prepare_for_datalad +) + +distutils_enable_tests pytest diff --git a/dev-python/heudiconv/metadata.xml b/dev-python/heudiconv/metadata.xml new file mode 100644 index 000000000..a98cbf459 --- /dev/null +++ b/dev-python/heudiconv/metadata.xml @@ -0,0 +1,16 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>gentoo@chymera.eu</email> + <name>Horea Christian</name> + </maintainer> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <upstream> + <remote-id type="pypi">heudiconv</remote-id> + <remote-id type="github">nipy/heudiconv</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/holoviews/Manifest b/dev-python/holoviews/Manifest index 94e17efc1..ec3bb1815 100644 --- a/dev-python/holoviews/Manifest +++ b/dev-python/holoviews/Manifest @@ -1 +1 @@ -DIST holoviews-1.14.2.tar.gz 6929549 BLAKE2B 72746a846ea7628b45e61b892ea940df4b2d7886efda054eedb859caac5dc3b66ed1c0aa9a4df8766905e35a973f6ee9226558cf6fb68394d17fe7c2f77982b2 SHA512 473a344f36c6ab1abc0847df46f4dc015fe225b9285a86152a78e13402770d5e7fdbd51aef21ff5cc53fbab89898237a260bea86dadef91ccb30bbce9344daf0 +DIST holoviews-1.15.3.tar.gz 6905214 BLAKE2B 60bb7008dd5af474295245eb0dbce240cfb4dcaf4122bc6073561e829c506b670201ac7d2b7ae1eea640929eb0993148c22c1a3e8d8ccb8e00582a2fbd3e696b SHA512 b1d4b64503511c61ede67d6d45472acde1afb854e19f7a30acb35d7fab2400ffe1e43db7b6e85eefe542b8353982af9cb41d505412bb0674cb20926c24f76494 diff --git a/dev-python/holoviews/holoviews-1.14.2.ebuild b/dev-python/holoviews/holoviews-1.14.2.ebuild deleted file mode 100644 index 505133d78..000000000 --- a/dev-python/holoviews/holoviews-1.14.2.ebuild +++ /dev/null @@ -1,31 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7..9} ) - -# HoloViews imports from "distutils" at runtime. -DISTUTILS_USE_SETUPTOOLS=rdepend - -inherit distutils-r1 - -DESCRIPTION="Make data analysis and visualization seamless and simple" -HOMEPAGE="https://holoviews.org" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -DEPEND=" - >=dev-python/param-1.9.3[${PYTHON_USEDEP}] - >=dev-python/pyct-0.4.4[${PYTHON_USEDEP}] -" -RDEPEND="${DEPEND} - dev-python/colorcet[${PYTHON_USEDEP}] - dev-python/pandas[${PYTHON_USEDEP}] - >=dev-python/numpy-1.0.0[${PYTHON_USEDEP}] - >=dev-python/panel-0.8.0[${PYTHON_USEDEP}] - >=dev-python/pyviz_comms-0.7.4[${PYTHON_USEDEP}] -" diff --git a/dev-python/holoviews/holoviews-1.15.3.ebuild b/dev-python/holoviews/holoviews-1.15.3.ebuild new file mode 100644 index 000000000..154b7195d --- /dev/null +++ b/dev-python/holoviews/holoviews-1.15.3.ebuild @@ -0,0 +1,45 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) + +# HoloViews imports from "distutils" at runtime. +DISTUTILS_USE_SETUPTOOLS=rdepend + +inherit distutils-r1 pypi + +DESCRIPTION="Make data analysis and visualization seamless and simple" +HOMEPAGE="https://holoviews.org" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" +# Reported upstream: +# https://github.com/holoviz/holoviews/issues/5592 +RESTRICT="test" + +DEPEND=" + >=dev-python/param-1.9.3[${PYTHON_USEDEP}] + >=dev-python/pyct-0.4.4[${PYTHON_USEDEP}] +" +BDEPEND=" + test? ( + dev-python/bokeh[${PYTHON_USEDEP}] + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/nbconvert[${PYTHON_USEDEP}] + dev-python/pillow[${PYTHON_USEDEP}] + dev-python/plotly[${PYTHON_USEDEP}] + sci-visualization/dash[${PYTHON_USEDEP}] + ) +" +RDEPEND="${DEPEND} + dev-python/colorcet[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + >=dev-python/numpy-1.0.0[${PYTHON_USEDEP}] + >=dev-python/panel-0.8.0[${PYTHON_USEDEP}] + >=dev-python/pyviz_comms-0.7.4[${PYTHON_USEDEP}] +" + +distutils_enable_tests pytest diff --git a/dev-python/hopcroftkarp/hopcroftkarp-1.2.5_p1-r1.ebuild b/dev-python/hopcroftkarp/hopcroftkarp-1.2.5_p1-r1.ebuild new file mode 100644 index 000000000..29c57f90a --- /dev/null +++ b/dev-python/hopcroftkarp/hopcroftkarp-1.2.5_p1-r1.ebuild @@ -0,0 +1,23 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools + +inherit distutils-r1 + +DESCRIPTION="python frontend for the fast ripser tda tool" +HOMEPAGE="https://ripser.scikit-tda.org/ https://github.com/sofiatolaosebikan/hopcroftkarp" +COMMIT="2846e1dd3265d95d2bddb0cf4190b830cbb4efe6" +SRC_URI="https://github.com/sofiatolaosebikan/hopcroftkarp/archive/${COMMIT}.tar.gz -> ${P}.tar.gz" +S="${WORKDIR}"/${PN}-${COMMIT} + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +PATCHES=( "${FILESDIR}"/${P}-setup_py.patch ) + +distutils_enable_tests pytest diff --git a/dev-python/hopcroftkarp/hopcroftkarp-1.2.5_p1.ebuild b/dev-python/hopcroftkarp/hopcroftkarp-1.2.5_p1.ebuild deleted file mode 100644 index 5dfb4bc6b..000000000 --- a/dev-python/hopcroftkarp/hopcroftkarp-1.2.5_p1.ebuild +++ /dev/null @@ -1,22 +0,0 @@ -# Copyright 1999-2020 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 frontend for the fast ripser tda tool" -HOMEPAGE="https://ripser.scikit-tda.org/" -COMMIT="2846e1dd3265d95d2bddb0cf4190b830cbb4efe6" -SRC_URI="https://github.com/sofiatolaosebikan/hopcroftkarp/archive/${COMMIT}.tar.gz -> ${P}.tar.gz" -S="${WORKDIR}"/${PN}-${COMMIT} - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -PATCHES=( "${FILESDIR}"/${P}-setup_py.patch ) - -distutils_enable_tests pytest diff --git a/dev-python/hopcroftkarp/metadata.xml b/dev-python/hopcroftkarp/metadata.xml index 2f2c0b51c..6959005e7 100644 --- a/dev-python/hopcroftkarp/metadata.xml +++ b/dev-python/hopcroftkarp/metadata.xml @@ -1,12 +1,15 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="person"> - <email>gentoo@aisha.cc</email> - <name>Aisha Tammy</name> - </maintainer> - <maintainer type="project"> - <email>sci@gentoo.org</email> - <name>Gentoo Science Project</name> - </maintainer> + <maintainer type="person"> + <email>gentoo@aisha.cc</email> + <name>Aisha Tammy</name> + </maintainer> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <upstream> + <remote-id type="github">sofiatolaosebikan/hopcroftkarp</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/imageutils/Manifest b/dev-python/imageutils/Manifest deleted file mode 100644 index ccb3920ff..000000000 --- a/dev-python/imageutils/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST imageutils-0.3.8.tar.gz 3531 BLAKE2B 58b8248faa79f36cb24451c5d174fba421cc4c8664d9093047dfd4460f0c80941912859fe6507d2f2a0814f00d6a64631617ad6731e1dddb7525e6ed087ad825 SHA512 5399fe0586929b5fa4e3d70177179f3c050527115f32ac84d16c0ace1d650c789555329cc86a533fa38778cce5bcb0b6c12886195876e7103535b74b508998f6 diff --git a/dev-python/imageutils/imageutils-0.3.8.ebuild b/dev-python/imageutils/imageutils-0.3.8.ebuild deleted file mode 100644 index 09db367f1..000000000 --- a/dev-python/imageutils/imageutils-0.3.8.ebuild +++ /dev/null @@ -1,16 +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="Various utilities for working with images" -HOMEPAGE="https://pypi.org/project/imageutils/" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="public-domain" -SLOT="0" -KEYWORDS="~amd64 ~x86" diff --git a/dev-python/imageutils/metadata.xml b/dev-python/imageutils/metadata.xml deleted file mode 100644 index b75b1ab3a..000000000 --- a/dev-python/imageutils/metadata.xml +++ /dev/null @@ -1,16 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-astronomy@gentoo.org</email> - <name>Gentoo Astronomy Project</name> - </maintainer> - <longdescription lang="en"> -imageutils is a collection of image processing utilities that are generally -useful to astronomers. These will likely become part of the core AstroPy -package before the 1.0 release. -</longdescription> - <upstream> - <remote-id type="github">astropy/imageutils</remote-id> - </upstream> -</pkgmetadata> diff --git a/dev-python/interleave/interleave-0.2.0.ebuild b/dev-python/interleave/interleave-0.2.0.ebuild index c8a9c9ca1..4434b8fdd 100644 --- a/dev-python/interleave/interleave-0.2.0.ebuild +++ b/dev-python/interleave/interleave-0.2.0.ebuild @@ -1,16 +1,15 @@ -# Copyright 1999-2022 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 DISTUTILS_USE_PEP517=setuptools -PYTHON_COMPAT=( python3_{8..10}) +PYTHON_COMPAT=( python3_{10..11} ) -inherit distutils-r1 +inherit distutils-r1 pypi DESCRIPTION="Yield from multiple iterators as values become available" HOMEPAGE="https://github.com/jwodder/interleave" -SRC_URI="mirror://pypi/${P:0:1}/${PN}/${P}.tar.gz" LICENSE="MIT" SLOT="0" diff --git a/dev-python/jacobi/Manifest b/dev-python/jacobi/Manifest new file mode 100644 index 000000000..be04d75f2 --- /dev/null +++ b/dev-python/jacobi/Manifest @@ -0,0 +1,2 @@ +DIST jacobi-0.8.1.tar.gz 997020 BLAKE2B ba54654e8a202976242674afa79de06d486d03c6d78b5566711df7df4ddcf5bbaa0e536eb9feeb0b0d6aaa9a444f677dfbbfa9928e38431aa9377c97132d4a26 SHA512 4a9a280cfae81926563c9736bf1805a3fe379809fe51421bdd0659651008d07d9f772df5006a1b796959311956822839791289eacb03af39823dd5a671b3845a +DIST jacobi-0.9.2.tar.gz 998268 BLAKE2B 93ed0a03e8984143229929d04dd7b166c71bf10e98b98d396c58a5cea556b2b8da7977538a419cfbff26a5f681885df2f952a7aef98822dea885b408e12033a7 SHA512 ef91d8aceab8823913820c46e33db43a3daba90bfacf640167987cd92006c4b253ec17166fc1750902afec69385d35559fede17a8ed227dab582f1490711bff1 diff --git a/dev-python/jacobi/jacobi-0.8.1.ebuild b/dev-python/jacobi/jacobi-0.8.1.ebuild new file mode 100644 index 000000000..93afcbf16 --- /dev/null +++ b/dev-python/jacobi/jacobi-0.8.1.ebuild @@ -0,0 +1,24 @@ +EAPI=8 + +PYTHON_COMPAT=( python3_{10..12} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 pypi + +DESCRIPTION="Numerical derivatives for analytic functions with arbitrary precision." +HOMEPAGE="https://github.com/HDembinski/jacobi" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + >=dev-python/numpy-1.10[${PYTHON_USEDEP}] +" +DEPEND="${RDEPEND}" + +distutils_enable_tests pytest + +EPYTEST_IGNORE=( + tests/bench.py +) + diff --git a/dev-python/jacobi/jacobi-0.9.2.ebuild b/dev-python/jacobi/jacobi-0.9.2.ebuild new file mode 100644 index 000000000..806967a38 --- /dev/null +++ b/dev-python/jacobi/jacobi-0.9.2.ebuild @@ -0,0 +1,26 @@ +EAPI=8 + +PYTHON_COMPAT=( python3_{11..12} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 pypi + +DESCRIPTION="Numerical derivatives for analytic functions with arbitrary precision." +HOMEPAGE="https://github.com/HDembinski/jacobi" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + >=dev-python/numpy-1.10[${PYTHON_USEDEP}] +" +DEPEND="${RDEPEND}" + +distutils_enable_tests pytest + +python_test() { + local EPYTEST_IGNORE=( + tests/bench.py + ) + epytest +} diff --git a/dev-python/jacobi/metadata.xml b/dev-python/jacobi/metadata.xml new file mode 100644 index 000000000..ebbabb06c --- /dev/null +++ b/dev-python/jacobi/metadata.xml @@ -0,0 +1,21 @@ +<?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> + <maintainer type="person"> + <email>alexander@neuwirth-informatik.de</email> + <name>Alexander Puck Neuwirth</name> + </maintainer> + <longdescription lang="en"> + Robustly compute the generalised Jacobi matrix for an arbitrary real analytic mapping â„⿠→ â„â±Â¹ × ... × â„â±â¿ + Returns error estimates for derivatives + Perform statistical error propagation based on numerically computed jacobian + </longdescription> + <upstream> + <remote-id type="pypi">jacobi</remote-id> + <remote-id type="github">HDembinski/jacobi</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/json_tricks/Manifest b/dev-python/json_tricks/Manifest deleted file mode 100644 index 24618b3f4..000000000 --- a/dev-python/json_tricks/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST json_tricks-3.15.5.tar.gz 41517 BLAKE2B beca160278281161ad480848da7971b4bcd0c3624ada8e1092edaf5c56abedf3fb4f5bc96c4efbd714cbdc07c3ba5d63fa4e97efcd040f1f6bc5406d6a841580 SHA512 e43ead9ffd3966f5c548f70bacd58baa275d63e3a55fbd49d84d477fc0bea30cbeaeac46c308b6251bc141efb949c2e73444432c14608d9a8fc5dfc6c7c246d6 diff --git a/dev-python/json_tricks/json_tricks-3.15.5.ebuild b/dev-python/json_tricks/json_tricks-3.15.5.ebuild deleted file mode 100644 index f659a2a18..000000000 --- a/dev-python/json_tricks/json_tricks-3.15.5.ebuild +++ /dev/null @@ -1,21 +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="Extra features for Python's JSON" -HOMEPAGE="https://github.com/mverleg/pyjson_tricks" -SRC_URI="https://github.com/mverleg/pyjson_tricks/archive/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -S="${WORKDIR}/py${PN}-${PV}" - -distutils_enable_tests pytest -distutils_enable_sphinx docs diff --git a/dev-python/json_tricks/metadata.xml b/dev-python/json_tricks/metadata.xml deleted file mode 100644 index f5804b4b0..000000000 --- a/dev-python/json_tricks/metadata.xml +++ /dev/null @@ -1,26 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>gentoo@chymera.eu</email> - <name>Horea Christian</name> - </maintainer> - <maintainer type="project"> - <email>sci@gentoo.org</email> - <name>Gentoo Science Project</name> - </maintainer> - <longdescription lang="en"> - The json-tricks package brings several pieces of functionality to - Python handling of json files: (1) Store and load numpy arrays in - human-readable format; (2) Store and load class instances both - generic and customized; (3) Store and load date/times as a - dictionary (including timezone); (4) Preserve map order {} using - OrderedDict; (5) Allow for comments in json files by starting lines - with #; (6) Sets, complex numbers, Decimal, Fraction, enums, - compression, duplicate keys, pathlib Paths ... - </longdescription> - <upstream> - <remote-id type="pypi">json-tricks</remote-id> - </upstream> -</pkgmetadata> - diff --git a/dev-python/jupyterlab_launcher/Manifest b/dev-python/jupyterlab_launcher/Manifest deleted file mode 100644 index c1d49b101..000000000 --- a/dev-python/jupyterlab_launcher/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST jupyterlab_launcher-0.13.1.tar.gz 20418 BLAKE2B 1cfe0e357da0926468a7dfb8b6b2d6eb870593b6bb9ac5c798a90f876c76b82c07cca7948bbdfdc0f4e49cefb67c0ba56edc0d7334e969a76cec2407353afd63 SHA512 f7b4267379fd21e80688e565f788277b92aad748971c077e694246ae01c7f56b5a6a50d4fa9d3bfecc561b723d6bcbbb988f019268d2752076ec6293f9960406 diff --git a/dev-python/jupyterlab_launcher/jupyterlab_launcher-0.13.1.ebuild b/dev-python/jupyterlab_launcher/jupyterlab_launcher-0.13.1.ebuild deleted file mode 100644 index 80abd3be5..000000000 --- a/dev-python/jupyterlab_launcher/jupyterlab_launcher-0.13.1.ebuild +++ /dev/null @@ -1,26 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{8..9} ) - -inherit distutils-r1 - -DESCRIPTION="Jupyter Launcher" -HOMEPAGE="https://jupyter.org/" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64" - -# TODO: fix this -RESTRICT="test" - -RDEPEND=" - >=dev-python/jsonschema-2.6.0[${PYTHON_USEDEP}] - >=dev-python/notebook-4.2.0[${PYTHON_USEDEP}] -" - -distutils_enable_tests pytest diff --git a/dev-python/keyrings_alt/Manifest b/dev-python/keyrings_alt/Manifest deleted file mode 100644 index ec1eff845..000000000 --- a/dev-python/keyrings_alt/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST keyrings.alt-4.1.0.tar.gz 28581 BLAKE2B bb4c8c5faa130c4cfb377985ee8692bcce802f0e03d1121281a8d73ac1c4ced4c6f913e6ab9ff39b1b7d37ff41b37905910d3a02e91fa4160fbe109aa16c2ae0 SHA512 6c2a7637bc73971081b95851898dcc2fafe5fd155333cee7032983b16f668d8db941c972747c7c4a2e20b4d6a5fe52d8ad96448f8ae7d372cd1c32e2a0d344f9 diff --git a/dev-python/keyrings_alt/files/keyrings_alt-4.1.0-pycryptodome.patch b/dev-python/keyrings_alt/files/keyrings_alt-4.1.0-pycryptodome.patch deleted file mode 100644 index e0ca3a012..000000000 --- a/dev-python/keyrings_alt/files/keyrings_alt-4.1.0-pycryptodome.patch +++ /dev/null @@ -1,90 +0,0 @@ -diff --git a/keyrings/alt/file.py b/keyrings/alt/file.py -index 37c837f..866e8d0 100644 ---- a/keyrings/alt/file.py -+++ b/keyrings/alt/file.py -@@ -44,8 +44,12 @@ class Encrypted: - """ - Create the cipher object to encrypt or decrypt a payload. - """ -- from Cryptodome.Protocol.KDF import PBKDF2 -- from Cryptodome.Cipher import AES -+ try: -+ from Cryptodome.Protocol.KDF import PBKDF2 -+ from Cryptodome.Cipher import AES -+ except ImportError: -+ from Crypto.Protocol.KDF import PBKDF2 -+ from Crypto.Cipher import AES - - pw = PBKDF2(password, salt, dkLen=self.block_size) - return AES.new(pw[: self.block_size], AES.MODE_CFB, IV) -@@ -79,7 +83,12 @@ class EncryptedKeyring(Encrypted, Keyring): - __import__('Cryptodome.Protocol.KDF') - __import__('Cryptodome.Random') - except ImportError: # pragma: no cover -- raise RuntimeError("pycryptodomex required") -+ try: -+ __import__('Crypto.Cipher.AES') -+ __import__('Crypto.Protocol.KDF') -+ __import__('Crypto.Random') -+ except ImportError: -+ raise RuntimeError("pycryptodomex or pycryptodome required") - if not json: # pragma: no cover - raise RuntimeError("JSON implementation such as simplejson required.") - return 0.6 -@@ -190,10 +199,16 @@ class EncryptedKeyring(Encrypted, Keyring): - - def encrypt(self, password, assoc=None): - # encrypt password, ignore associated data -- from Cryptodome.Random import get_random_bytes -+ try: -+ from Cryptodome.Random import get_random_bytes -+ except ImportError: -+ from Crypto.Random import get_random_bytes - - salt = get_random_bytes(self.block_size) -- from Cryptodome.Cipher import AES -+ try: -+ from Cryptodome.Cipher import AES -+ except ImportError: -+ from Crypto.Cipher import AES - - IV = get_random_bytes(AES.block_size) - cipher = self._create_cipher(self.keyring_key, salt, IV) -diff --git a/tests/test_crypto.py b/tests/test_crypto.py -index cfc782a..7396023 100644 ---- a/tests/test_crypto.py -+++ b/tests/test_crypto.py -@@ -14,7 +14,12 @@ def is_crypto_supported(): - __import__('Cryptodome.Protocol.KDF') - __import__('Cryptodome.Random') - except ImportError: -- return False -+ try: -+ __import__('Crypto.Cipher.AES') -+ __import__('Crypto.Protocol.KDF') -+ __import__('Crypto.Random') -+ except ImportError: -+ return False - return True - - -diff --git a/tests/test_file.py b/tests/test_file.py -index 62192da..3f813f0 100644 ---- a/tests/test_file.py -+++ b/tests/test_file.py -@@ -157,7 +157,14 @@ class FileKeyringTests(BackendBasicTests): - class TestEncryptedFileKeyring(FileKeyringTests): - @pytest.fixture(autouse=True) - def crypt_fixture(self, monkeypatch): -- pytest.importorskip('Cryptodome') -+ try: -+ import Cryptodome -+ except ImportError: -+ try: -+ import Crypto -+ except ImportError: -+ pytest.skip("Neither pycryptodome nor pycryptodomex are available", -+ allow_module_level=True) - fake_getpass = mock.Mock(return_value='abcdef') - monkeypatch.setattr(getpass, 'getpass', fake_getpass) - diff --git a/dev-python/keyrings_alt/keyrings_alt-4.1.0-r1.ebuild b/dev-python/keyrings_alt/keyrings_alt-4.1.0-r1.ebuild deleted file mode 100644 index 290c2f434..000000000 --- a/dev-python/keyrings_alt/keyrings_alt-4.1.0-r1.ebuild +++ /dev/null @@ -1,31 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -DISTUTILS_USE_PEP517=setuptools -PYTHON_COMPAT=( pypy3 python3_{8..10} ) - -inherit distutils-r1 - -MY_PN="keyrings.alt" -MY_P="${MY_PN}-${PV}" - -DESCRIPTION="Alternate keyring backend implementations used with dev-python/keyring" -HOMEPAGE="https://github.com/jaraco/keyrings.alt/" -SRC_URI="mirror://pypi/${MY_P:0:1}/${MY_PN}/${MY_P}.tar.gz" - -SLOT="0" -LICENSE="MIT" -KEYWORDS="~alpha ~amd64 ~arm ~arm64 ~x86" - -DEPEND="" - -S="${WORKDIR}/${MY_P}" - -# Patch sumbitted upstream: -# https://github.com/jaraco/keyrings.alt/pull/46 -PATCHES=( "${FILESDIR}/${P}-pycryptodome.patch" ) - -distutils_enable_tests pytest -distutils_enable_sphinx docs diff --git a/dev-python/keyrings_alt/metadata.xml b/dev-python/keyrings_alt/metadata.xml deleted file mode 100644 index 59728c331..000000000 --- a/dev-python/keyrings_alt/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>gentoo@chymera.eu</email> - <name>Horea Christian</name> - </maintainer> - <maintainer type="project"> - <email>sci@gentoo.org</email> - <name>Gentoo Science Project</name> - </maintainer> - <longdescription lang="en"> - This package distributes backends extracted from the main Python keyring - project to make them available for those who wish to employ them, but - are discouraged for general production use. Include this module and use - its backends at your own risk. - For example, the PlaintextKeyring stores passwords in plain text on the - file system, defeating the intended purpose of this library to encourage - best practices for security. - </longdescription> - <upstream> - <remote-id type="github">jaraco/keyrings.alt</remote-id> - </upstream> -</pkgmetadata> diff --git a/dev-python/kmapper/Manifest b/dev-python/kmapper/Manifest index 61c31630b..0eeec60f6 100644 --- a/dev-python/kmapper/Manifest +++ b/dev-python/kmapper/Manifest @@ -1,2 +1 @@ -DIST kmapper-1.4.1.tar.gz 100655 BLAKE2B 7321266be9fea509da054a481328178bd5bb5403b60f09b64ece4ef1fa54713a5f9b292553b87385464b52e82407461659575d7bd5d2b6038b69d500b934da77 SHA512 dc760c7b3c838d44f4b96ba744f03482e4495bb4341380aa4448c57a1292c6d8d95a9e7fb8bd9171a26e56677e578c1a8002fd429166fe87a60a8313fada7e4a -DIST kmapper-2.0.1.tar.gz 6686101 BLAKE2B 8afa79a2479370c335debb4cee7375b0d47b0e79d02649ff53681d006e2a80cd6175f8aeb3c3a6fa0ac32d0cf30ba8217d348f6158b9ee1bc7c683d0a5b4290e SHA512 751f02ee3f5a55eb74b55b0a9204e54d05c9af2a816f8070082a73d4213c1fb7842e41e3e27316d69efaa2cf3e2f9b2d967870905ace8d9e9a3e67f9ea181ed2 +DIST kmapper-2.0.1.gh.tar.gz 6686101 BLAKE2B 8afa79a2479370c335debb4cee7375b0d47b0e79d02649ff53681d006e2a80cd6175f8aeb3c3a6fa0ac32d0cf30ba8217d348f6158b9ee1bc7c683d0a5b4290e SHA512 751f02ee3f5a55eb74b55b0a9204e54d05c9af2a816f8070082a73d4213c1fb7842e41e3e27316d69efaa2cf3e2f9b2d967870905ace8d9e9a3e67f9ea181ed2 diff --git a/dev-python/kmapper/kmapper-1.4.1.ebuild b/dev-python/kmapper/kmapper-1.4.1.ebuild deleted file mode 100644 index 763a962de..000000000 --- a/dev-python/kmapper/kmapper-1.4.1.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 - -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="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -RDEPEND="${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/kmapper/kmapper-2.0.1-r1.ebuild b/dev-python/kmapper/kmapper-2.0.1-r1.ebuild new file mode 100644 index 000000000..22f35fbda --- /dev/null +++ b/dev-python/kmapper/kmapper-2.0.1-r1.ebuild @@ -0,0 +1,43 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools + +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 -> ${P}.gh.tar.gz" +S="${WORKDIR}"/kepler-mapper-${PV} + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND="${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/kmapper/kmapper-2.0.1.ebuild b/dev-python/kmapper/kmapper-2.0.1.ebuild deleted file mode 100644 index 2099fa4db..000000000 --- a/dev-python/kmapper/kmapper-2.0.1.ebuild +++ /dev/null @@ -1,42 +0,0 @@ -# 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/kmapper/metadata.xml b/dev-python/kmapper/metadata.xml index e97c4322a..4dee7702f 100644 --- a/dev-python/kmapper/metadata.xml +++ b/dev-python/kmapper/metadata.xml @@ -9,4 +9,8 @@ <email>sci@gentoo.org</email> <name>Gentoo Science Project</name> </maintainer> + <upstream> + <remote-id type="github">scikit-tda/kepler-mapper</remote-id> + <remote-id type="pypi">kmapper</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/latexify_py/Manifest b/dev-python/latexify_py/Manifest new file mode 100644 index 000000000..7a500fe7d --- /dev/null +++ b/dev-python/latexify_py/Manifest @@ -0,0 +1 @@ +DIST latexify_py-0.2.0.tar.gz 30995 BLAKE2B 2b55c83ea073b221096b4e44fad362d421f5d526bdff79a825b67a5fb419ff6185cd9f18a49727b988409f257318845a90f78223cf6eb9dd264ce6d1c0b71b82 SHA512 17250784d7a009705854d3f6118b3c854c4e86e007a45740c2b6d314ff25503b3561327b610b17e49652fa59ff6612bae8e74ea4caedeaa4f6a0b1e446fe086c diff --git a/dev-python/latexify_py/latexify_py-0.2.0.ebuild b/dev-python/latexify_py/latexify_py-0.2.0.ebuild new file mode 100644 index 000000000..bd42c3cf3 --- /dev/null +++ b/dev-python/latexify_py/latexify_py-0.2.0.ebuild @@ -0,0 +1,34 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=hatchling + +inherit distutils-r1 + +DESCRIPTION="Generate LaTeX expression from Python code" +HOMEPAGE="https://github.com/google/latexify_py" +SRC_URI="https://github.com/google/${PN}/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + dev-python/dill[${PYTHON_USEDEP}] +" + +BDEPEND="test? ( + dev-python/notebook[${PYTHON_USEDEP}] + dev-python/twine[${PYTHON_USEDEP}] +)" + +distutils_enable_tests pytest + +DOCS=( README.md docs ) + +python_test() { + PYTHONPATH="${S}/src" epytest +} diff --git a/dev-python/jupyterlab_launcher/metadata.xml b/dev-python/latexify_py/metadata.xml index ae9640ffb..ae9640ffb 100644 --- a/dev-python/jupyterlab_launcher/metadata.xml +++ b/dev-python/latexify_py/metadata.xml diff --git a/dev-python/lazy_ops/Manifest b/dev-python/lazy_ops/Manifest new file mode 100644 index 000000000..b5b4cce5e --- /dev/null +++ b/dev-python/lazy_ops/Manifest @@ -0,0 +1 @@ +DIST lazy_ops-0.2.0.tar.gz 5284 BLAKE2B ba8747ba9028103fad7e0cab5eb53ebfefca5e886dcd39a499c8c8c6c8c466dcdb85438fc012f32cff7b98e486fe8154ef4e3c08241c3c9c738f0a399a6f91af SHA512 b0c7e49d37553f56f491d7e7aaeee8e6e18d44f6f34f7148ed98a596573dc26523e9cbc7bb6dce04bae99dbe59cecd35759173985fc203d7e59dfa61592e6955 diff --git a/dev-python/lazy_ops/lazy_ops-0.2.0.ebuild b/dev-python/lazy_ops/lazy_ops-0.2.0.ebuild new file mode 100644 index 000000000..d624fb2aa --- /dev/null +++ b/dev-python/lazy_ops/lazy_ops-0.2.0.ebuild @@ -0,0 +1,26 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 pypi + +DESCRIPTION="Lazy transposing and slicing of h5py and Zarr data" +HOMEPAGE="https://github.com/catalystneuro/lazy_ops" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="test" +# There are no source archive with tests available: +# https://github.com/catalystneuro/lazy_ops/issues/29 +RESTRICT="test" + +RDEPEND=" + dev-python/h5py[${PYTHON_USEDEP}] + dev-python/zarr[${PYTHON_USEDEP}] +" + +distutils_enable_tests pytest diff --git a/dev-python/lazy_ops/metadata.xml b/dev-python/lazy_ops/metadata.xml new file mode 100644 index 000000000..d5101128a --- /dev/null +++ b/dev-python/lazy_ops/metadata.xml @@ -0,0 +1,16 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>gentoo@chymera.eu</email> + <name>Horea Christian</name> + </maintainer> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <upstream> + <remote-id type="github">catalystneuro/lazy_ops</remote-id> + <remote-id type="pypi">lazy_ops</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/llvmlite/Manifest b/dev-python/llvmlite/Manifest deleted file mode 100644 index ea7fa3ead..000000000 --- a/dev-python/llvmlite/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST llvmlite-0.37.0.gh.tar.gz 223602 BLAKE2B 74f975d5ac1782528f60f1c0d5c6230a02953e0d494d8323e4caa6651f642ad791ad51df44f6593da41edc5c34bd883f144e95b16f9b8962393d16de013fdbc5 SHA512 665f486fd38c9cc4ee91b15fc75f33451ada6391fc9f1b371091ece844693e0cd8e23766400bf76d9879e8f10f53f4e21f8bb19f3ff1e01c4a95ce9004b0884a -DIST llvmlite-0.38.0.gh.tar.gz 230044 BLAKE2B b027f34a6ba4c6d8a4fe8963501a49b1f87cc86976c131c94c597383ab47aef1faf6bb05f27f148f03b2d6673e12b04fdfbdab20658de32b18c257bb1cd16fee SHA512 014e2ba08a451ff8bb76ea4b25d2d6605bc048cae560ad367a3bb3afd13421aaf151862116e73e7606d800638d2a2df713cc0e187a6acc483b80df1290c81743 diff --git a/dev-python/llvmlite/files/llvmlite-0.37.0-llvm12.patch b/dev-python/llvmlite/files/llvmlite-0.37.0-llvm12.patch deleted file mode 100644 index ed104ab99..000000000 --- a/dev-python/llvmlite/files/llvmlite-0.37.0-llvm12.patch +++ /dev/null @@ -1,91 +0,0 @@ -From 1d928ebcd59b23b5050234a2bf71f9be7f5f6bd1 Mon Sep 17 00:00:00 2001 -From: Richard Barnes <rbarnes@umn.edu> -Date: Wed, 1 Dec 2021 10:29:08 -0700 -Subject: [PATCH] Enable LLVM-12 and LLVM-13 - ---- - ffi/build.py | 5 ++--- - ffi/targets.cpp | 2 ++ - llvmlite/tests/test_binding.py | 19 ++++++++++++++++--- - 3 files changed, 20 insertions(+), 6 deletions(-) - -diff --git a/ffi/build.py b/ffi/build.py -index 6408bf5f..95e33c64 100755 ---- a/ffi/build.py -+++ b/ffi/build.py -@@ -162,9 +162,8 @@ def main_posix(kind, library_ext): - print(msg) - print(warning + '\n') - else: -- -- if not out.startswith('11'): -- msg = ("Building llvmlite requires LLVM 11.x.x, got " -+ if not (out.startswith('11') or out.startswith('12') or out.startswith('13')): -+ msg = ("Building llvmlite requires LLVM 11-13.x.x, got " - "{!r}. Be sure to set LLVM_CONFIG to the right executable " - "path.\nRead the documentation at " - "http://llvmlite.pydata.org/ for more information about " -diff --git a/ffi/targets.cpp b/ffi/targets.cpp -index 1ce472c2..4ba33e79 100644 ---- a/ffi/targets.cpp -+++ b/ffi/targets.cpp -@@ -233,6 +233,8 @@ LLVMPY_CreateTargetMachine(LLVMTargetRef T, - rm = Reloc::DynamicNoPIC; - - TargetOptions opt; -+#if LLVM_VERSION_MAJOR < 12 - opt.PrintMachineCode = PrintMC; -+#endif - - bool jit = JIT; -diff --git a/llvmlite/tests/test_binding.py b/llvmlite/tests/test_binding.py -index 80495787..fee2372a 100644 ---- a/llvmlite/tests/test_binding.py -+++ b/llvmlite/tests/test_binding.py -@@ -18,6 +18,16 @@ - from llvmlite.tests import TestCase - - -+def clean_string_whitespace(x: str) -> str: -+ # Remove trailing whitespace from the end of each line -+ x = re.sub(r"\s+$", "", x, flags=re.MULTILINE) -+ # Remove intermediate blank lines -+ x = re.sub(r"\n\s*\n", r"\n", x, flags=re.MULTILINE) -+ # Remove extraneous whitespace from the beginning and end of the string -+ x = x.strip() -+ return x -+ -+ - # arvm7l needs extra ABI symbols to link successfully - if platform.machine() == 'armv7l': - llvm.load_library_permanently('libgcc_s.so.1') -@@ -158,7 +168,7 @@ def no_de_locale(): - target triple = "unknown-unknown-unknown" - target datalayout = "" - --define i32 @"foo"() -+define i32 @"foo"() - { - "<>!*''#": - ret i32 12345 -@@ -424,7 +434,10 @@ def test_nonalphanum_block_name(self): - bd = ir.IRBuilder(fn.append_basic_block(name="<>!*''#")) - bd.ret(ir.Constant(ir.IntType(32), 12345)) - asm = str(mod) -- self.assertEqual(asm, asm_nonalphanum_blocklabel) -+ self.assertEqual( -+ clean_string_whitespace(asm), -+ clean_string_whitespace(asm_nonalphanum_blocklabel) -+ ) - - def test_global_context(self): - gcontext1 = llvm.context.get_global_context() -@@ -509,7 +522,7 @@ def test_set_option(self): - def test_version(self): - major, minor, patch = llvm.llvm_version_info - # one of these can be valid -- valid = [(11,)] -+ valid = [(11,), (12,), (13,)] - self.assertIn((major,), valid) - self.assertIn(patch, range(10)) - diff --git a/dev-python/llvmlite/files/llvmlite-0.38.0-llvm12.patch b/dev-python/llvmlite/files/llvmlite-0.38.0-llvm12.patch deleted file mode 100644 index 6630652c2..000000000 --- a/dev-python/llvmlite/files/llvmlite-0.38.0-llvm12.patch +++ /dev/null @@ -1,92 +0,0 @@ -From 1d928ebcd59b23b5050234a2bf71f9be7f5f6bd1 Mon Sep 17 00:00:00 2001 -From: Richard Barnes <rbarnes@umn.edu> -Date: Wed, 1 Dec 2021 10:29:08 -0700 -Subject: [PATCH] Enable LLVM-12 and LLVM-13 - ---- - ffi/build.py | 5 ++--- - ffi/targets.cpp | 2 ++ - llvmlite/tests/test_binding.py | 19 ++++++++++++++++--- - 3 files changed, 20 insertions(+), 6 deletions(-) - -diff --git a/ffi/build.py b/ffi/build.py -index 6408bf5f..95e33c64 100755 ---- a/ffi/build.py -+++ b/ffi/build.py -@@ -162,9 +162,8 @@ def main_posix(kind, library_ext): - print(msg) - print(warning + '\n') - else: -- -- if not out.startswith('11'): -- msg = ("Building llvmlite requires LLVM 11.x.x, got " -+ if not (out.startswith('11') or out.startswith('12') or out.startswith('13')): -+ msg = ("Building llvmlite requires LLVM 11-13.x.x, got " - "{!r}. Be sure to set LLVM_CONFIG to the right executable " - "path.\nRead the documentation at " - "http://llvmlite.pydata.org/ for more information about " -diff --git a/ffi/targets.cpp b/ffi/targets.cpp -index 1ce472c2..4ba33e79 100644 ---- a/ffi/targets.cpp -+++ b/ffi/targets.cpp -@@ -233,7 +233,9 @@ LLVMPY_CreateTargetMachine(LLVMTargetRef T, - rm = Reloc::DynamicNoPIC; - - TargetOptions opt; -+#if LLVM_VERSION_MAJOR < 12 - opt.PrintMachineCode = PrintMC; -+#endif - opt.MCOptions.ABIName = ABIName; - - bool jit = JIT; -diff --git a/llvmlite/tests/test_binding.py b/llvmlite/tests/test_binding.py -index 80495787..fee2372a 100644 ---- a/llvmlite/tests/test_binding.py -+++ b/llvmlite/tests/test_binding.py -@@ -18,6 +18,16 @@ - from llvmlite.tests import TestCase - - -+def clean_string_whitespace(x: str) -> str: -+ # Remove trailing whitespace from the end of each line -+ x = re.sub(r"\s+$", "", x, flags=re.MULTILINE) -+ # Remove intermediate blank lines -+ x = re.sub(r"\n\s*\n", r"\n", x, flags=re.MULTILINE) -+ # Remove extraneous whitespace from the beginning and end of the string -+ x = x.strip() -+ return x -+ -+ - # arvm7l needs extra ABI symbols to link successfully - if platform.machine() == 'armv7l': - llvm.load_library_permanently('libgcc_s.so.1') -@@ -158,7 +168,7 @@ def no_de_locale(): - target triple = "unknown-unknown-unknown" - target datalayout = "" - --define i32 @"foo"() -+define i32 @"foo"() - { - "<>!*''#": - ret i32 12345 -@@ -424,7 +434,10 @@ def test_nonalphanum_block_name(self): - bd = ir.IRBuilder(fn.append_basic_block(name="<>!*''#")) - bd.ret(ir.Constant(ir.IntType(32), 12345)) - asm = str(mod) -- self.assertEqual(asm, asm_nonalphanum_blocklabel) -+ self.assertEqual( -+ clean_string_whitespace(asm), -+ clean_string_whitespace(asm_nonalphanum_blocklabel) -+ ) - - def test_global_context(self): - gcontext1 = llvm.context.get_global_context() -@@ -509,7 +522,7 @@ def test_set_option(self): - def test_version(self): - major, minor, patch = llvm.llvm_version_info - # one of these can be valid -- valid = [(11,)] -+ valid = [(11,), (12,), (13,)] - self.assertIn((major,), valid) - self.assertIn(patch, range(10)) - diff --git a/dev-python/llvmlite/llvmlite-0.37.0-r1.ebuild b/dev-python/llvmlite/llvmlite-0.37.0-r1.ebuild deleted file mode 100644 index 607c1bb0b..000000000 --- a/dev-python/llvmlite/llvmlite-0.37.0-r1.ebuild +++ /dev/null @@ -1,62 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{8..10} ) -inherit distutils-r1 llvm - -DESCRIPTION="Python wrapper around the llvm C++ library" -HOMEPAGE="https://llvmlite.pydata.org/" -SRC_URI="https://github.com/numba/llvmlite/archive/v${PV/_/}.tar.gz -> ${P/_/}.gh.tar.gz" -S="${WORKDIR}/${P/_/}" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~arm ~arm64 ~x86" -IUSE="examples" - -LLVM_MAX_SLOT=12 - -RDEPEND=" - sys-devel/llvm:${LLVM_MAX_SLOT} - sys-libs/zlib:0= -" -DEPEND="${RDEPEND}" - -PATCHES=( "${FILESDIR}/${P}-llvm12.patch" ) - -src_prepare() { - sed -i -e '/max_python/s:3\.10:3.11:' setup.py || die - distutils-r1_src_prepare -} - -python_configure_all() { - # upstream's build system is just horrible, and they ignored the PR - # fixing it, so let's build the shared lib properly using implicit - # make rules - - export LDLIBS=$(llvm-config --libs all) - export CXXFLAGS="$(llvm-config --cxxflags) -fPIC ${CXXFLAGS}" - export LDFLAGS="$(llvm-config --ldflags) ${LDFLAGS}" - - local files=( ffi/*.cpp ) - emake -f - <<EOF -ffi/libllvmlite.so: ${files[*]/.cpp/.o} - \$(CXX) -shared \$(CXXFLAGS) \$(LDFLAGS) -o \$@ \$^ \$(LDLIBS) -EOF - - export LLVMLITE_SKIP_LLVM_VERSION_CHECK=1 -} - -python_test() { - "${EPYTHON}" runtests.py -v || die "Tests failed under ${EPYTHON}" -} - -python_install_all() { - distutils-r1_python_install_all - if use examples; then - dodoc -r examples - docompress -x /usr/share/doc/${PF}/examples - fi -} diff --git a/dev-python/llvmlite/llvmlite-0.38.0-r1.ebuild b/dev-python/llvmlite/llvmlite-0.38.0-r1.ebuild deleted file mode 100644 index 607c1bb0b..000000000 --- a/dev-python/llvmlite/llvmlite-0.38.0-r1.ebuild +++ /dev/null @@ -1,62 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{8..10} ) -inherit distutils-r1 llvm - -DESCRIPTION="Python wrapper around the llvm C++ library" -HOMEPAGE="https://llvmlite.pydata.org/" -SRC_URI="https://github.com/numba/llvmlite/archive/v${PV/_/}.tar.gz -> ${P/_/}.gh.tar.gz" -S="${WORKDIR}/${P/_/}" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~arm ~arm64 ~x86" -IUSE="examples" - -LLVM_MAX_SLOT=12 - -RDEPEND=" - sys-devel/llvm:${LLVM_MAX_SLOT} - sys-libs/zlib:0= -" -DEPEND="${RDEPEND}" - -PATCHES=( "${FILESDIR}/${P}-llvm12.patch" ) - -src_prepare() { - sed -i -e '/max_python/s:3\.10:3.11:' setup.py || die - distutils-r1_src_prepare -} - -python_configure_all() { - # upstream's build system is just horrible, and they ignored the PR - # fixing it, so let's build the shared lib properly using implicit - # make rules - - export LDLIBS=$(llvm-config --libs all) - export CXXFLAGS="$(llvm-config --cxxflags) -fPIC ${CXXFLAGS}" - export LDFLAGS="$(llvm-config --ldflags) ${LDFLAGS}" - - local files=( ffi/*.cpp ) - emake -f - <<EOF -ffi/libllvmlite.so: ${files[*]/.cpp/.o} - \$(CXX) -shared \$(CXXFLAGS) \$(LDFLAGS) -o \$@ \$^ \$(LDLIBS) -EOF - - export LLVMLITE_SKIP_LLVM_VERSION_CHECK=1 -} - -python_test() { - "${EPYTHON}" runtests.py -v || die "Tests failed under ${EPYTHON}" -} - -python_install_all() { - distutils-r1_python_install_all - if use examples; then - dodoc -r examples - docompress -x /usr/share/doc/${PF}/examples - fi -} diff --git a/dev-python/llvmlite/metadata.xml b/dev-python/llvmlite/metadata.xml deleted file mode 100644 index 0983f7a41..000000000 --- a/dev-python/llvmlite/metadata.xml +++ /dev/null @@ -1,18 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci@gentoo.org</email> - <name>Gentoo Science Project</name> - </maintainer> - <longdescription> - llvmlite uses the LLVM library for JIT (just-in-time) compilation of - Python code into native machine instructions during runtime. Instead - of exposing large parts of the LLVM C++ API for direct calls into the - LLVM library, llvmlite follows a lightweight multi-layered approach. - </longdescription> - <upstream> - <remote-id type="pypi">llvmlite</remote-id> - <remote-id type="github">numba/llvmlite</remote-id> - </upstream> -</pkgmetadata> diff --git a/dev-python/logzero/logzero-1.7.0.ebuild b/dev-python/logzero/logzero-1.7.0.ebuild index 717426899..2c3f44eb1 100644 --- a/dev-python/logzero/logzero-1.7.0.ebuild +++ b/dev-python/logzero/logzero-1.7.0.ebuild @@ -3,13 +3,11 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} pypy3 ) - -inherit distutils-r1 +PYTHON_COMPAT=( python3_10 pypy3 ) +inherit distutils-r1 pypi 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" diff --git a/dev-python/lzstring/Manifest b/dev-python/lzstring/Manifest new file mode 100644 index 000000000..f44e5e773 --- /dev/null +++ b/dev-python/lzstring/Manifest @@ -0,0 +1 @@ +DIST lzstring-1.0.4.tar.gz 4256 BLAKE2B e1a205f980de050635114e26a86d7251e0822a4459c44042291e80d55129d815f0753ff2b45a179fb468e9020a0a6255748566bc4e62fc98e7e041b07ae073f3 SHA512 0d61fe04402aaa5325d3ab555b9b83132048124a2ff11ae3a947a188d5507f1043b0522fcb7024009d75cf3efd3afbb64d24c238c4c2181346a823c77cb4ea02 diff --git a/dev-python/lzstring/lzstring-1.0.4.ebuild b/dev-python/lzstring/lzstring-1.0.4.ebuild new file mode 100644 index 000000000..bfdb76a67 --- /dev/null +++ b/dev-python/lzstring/lzstring-1.0.4.ebuild @@ -0,0 +1,16 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) + +inherit pypi distutils-r1 + +DESCRIPTION="String encoding/decoding of binary data" +HOMEPAGE="https://pypi.org/project/lzstring/" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~amd64-linux" diff --git a/dev-python/lzstring/metadata.xml b/dev-python/lzstring/metadata.xml new file mode 100644 index 000000000..4dde9fdd9 --- /dev/null +++ b/dev-python/lzstring/metadata.xml @@ -0,0 +1,12 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>mschu.dev@gmail.com</email> + <name>Michael Schubert</name> + </maintainer> + <upstream> + <remote-id type="github">gkovacs/lz-string-python</remote-id> + <remote-id type="pypi">lzstring</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/matlabengine/Manifest b/dev-python/matlabengine/Manifest new file mode 100644 index 000000000..8704c974e --- /dev/null +++ b/dev-python/matlabengine/Manifest @@ -0,0 +1 @@ +DIST matlabengine-9.13.7.tar.gz 18796 BLAKE2B ccc5dae8fb9bc7a7cf240021f6066d4779d86d266b76cad3a610ed1fb455e1eefbef00cc5b1fe425f1f4f033dcb7721c2d1d3856c026fba13d2155604bfbf81f SHA512 b8d5d4d99f657fd24226f2accab676340a34739464fd289f1ca1c2db28a22f4b1288dfe160e8e193926e5db3e4fda0fcbbbf67b67f9a509910429e023b9cc3fb diff --git a/dev-python/matlabengine/matlabengine-9.13.7.ebuild b/dev-python/matlabengine/matlabengine-9.13.7.ebuild new file mode 100644 index 000000000..d65b1c0e5 --- /dev/null +++ b/dev-python/matlabengine/matlabengine-9.13.7.ebuild @@ -0,0 +1,17 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_10 ) # No 3.11 according to setup.py +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 pypi + +DESCRIPTION="A module to call MATLAB from Python" +HOMEPAGE="https://github.com/mathworks/matlab-engine-for-python" + +LICENSE="MathWorks" +SLOT="0" +KEYWORDS="-* ~amd64" + +RESTRICT="bindist mirror" diff --git a/dev-python/matlabengine/metadata.xml b/dev-python/matlabengine/metadata.xml new file mode 100644 index 000000000..83a61da06 --- /dev/null +++ b/dev-python/matlabengine/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <upstream> + <remote-id type="pypi">matlabengine</remote-id> + <remote-id type="github">mathworks/matlab-engine-for-python</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/matrix2latex/Manifest b/dev-python/matrix2latex/Manifest deleted file mode 100644 index 996d52a66..000000000 --- a/dev-python/matrix2latex/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST matrix2latex-1.10.tar.gz 594004 BLAKE2B 0950af176071470781f45a37955ce4222299c0cae276ea7b0b767d372b3c5fc1eff4f67c26d3702dd0bc2a06c8eca5569e8fbb67b247c0bba698df2bdf8a762a SHA512 61570aa8dbb396b1c33fd327acae67b1c5b7c1655a60ad73da0ed01627c569f88f318aec92cbef1df25fc2da6e68ecf38fb1a94d26777bd50caffa694f587efe diff --git a/dev-python/matrix2latex/matrix2latex-1.10.ebuild b/dev-python/matrix2latex/matrix2latex-1.10.ebuild deleted file mode 100644 index 0d84ff9e9..000000000 --- a/dev-python/matrix2latex/matrix2latex-1.10.ebuild +++ /dev/null @@ -1,28 +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 tool to create LaTeX tables from python lists and arrays" -HOMEPAGE="https://github.com/TheChymera/matrix2latex" -SRC_URI="https://github.com/TheChymera/matrix2latex/archive/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -S="${WORKDIR}/${PN}-${COMMIT}" - -distutils_enable_sphinx doc_sphinx -distutils_enable_tests pytest - -python_prepare_all() { - # this has been renamed in newer versions of sphinx - sed -i -e 's/sphinx.ext.pngmath/sphinx.ext.imgmath/g' doc_sphinx/conf.py - - distutils-r1_python_prepare_all -} diff --git a/dev-python/matrix2latex/metadata.xml b/dev-python/matrix2latex/metadata.xml deleted file mode 100644 index 744e5412e..000000000 --- a/dev-python/matrix2latex/metadata.xml +++ /dev/null @@ -1,19 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>gentoo@chymera.eu</email> - <name>Horea Christian</name> - </maintainer> - <maintainer type="project"> - <email>sci@gentoo.org</email> - <name>Gentoo Science Project</name> - </maintainer> - <longdescription lang="en"> - A tool for converting Python or MATLAB matrices to LaTeX tables, that - can optionally create self-sustained LATeX documents and compile them. - </longdescription> - <upstream> - <remote-id type="github">TheChymera/matrix2latex</remote-id> - </upstream> -</pkgmetadata> diff --git a/dev-python/meshpy/meshpy-2020.1.ebuild b/dev-python/meshpy/meshpy-2020.1.ebuild index 191589690..78ee45fbc 100644 --- a/dev-python/meshpy/meshpy-2020.1.ebuild +++ b/dev-python/meshpy/meshpy-2020.1.ebuild @@ -4,7 +4,7 @@ EAPI=8 DISTUTILS_IN_SOURCE_BUILD=1 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) inherit distutils-r1 diff --git a/dev-python/meshpy/metadata.xml b/dev-python/meshpy/metadata.xml index fff86775c..77991f7a8 100644 --- a/dev-python/meshpy/metadata.xml +++ b/dev-python/meshpy/metadata.xml @@ -15,5 +15,6 @@ Hang Si. Both are included in the package in slightly modified versions. </longdescription> <upstream> <remote-id type="pypi">MeshPy</remote-id> + <remote-id type="github">inducer/meshpy</remote-id> </upstream> </pkgmetadata> diff --git a/dev-python/mkl-service/Manifest b/dev-python/mkl-service/Manifest new file mode 100644 index 000000000..f0b775c11 --- /dev/null +++ b/dev-python/mkl-service/Manifest @@ -0,0 +1 @@ +DIST mkl-service-2.4.0.gh.tar.gz 18705 BLAKE2B 12896adba1c001a581ff10a18cf11b3b87344687807307ae7ee002583281ac8072730b9496ce94c48d8d9ded5ae815c432e1944715091043c222bd93e2728ed8 SHA512 fc33b0a3670fcac5564c020ee870a800b113b93f344eddf63874303347c7151b7f00052adf5a9544ff7557892aefb6088ee9c53cce043536f4456bd9903dc232 diff --git a/dev-python/mkl-service/metadata.xml b/dev-python/mkl-service/metadata.xml new file mode 100644 index 000000000..813808eb0 --- /dev/null +++ b/dev-python/mkl-service/metadata.xml @@ -0,0 +1,12 @@ +<?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> + <upstream> + <remote-id type="github">IntelPython/mkl-service</remote-id> + <remote-id type="pypi">mkl-service</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/mkl-service/mkl-service-2.4.0.ebuild b/dev-python/mkl-service/mkl-service-2.4.0.ebuild new file mode 100644 index 000000000..decfc57bb --- /dev/null +++ b/dev-python/mkl-service/mkl-service-2.4.0.ebuild @@ -0,0 +1,38 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 + +DESCRIPTION="Python hooks for Intel Math Kernel Library runtime control settings" +HOMEPAGE="https://github.com/IntelPython/mkl-service" +SRC_URI="https://github.com/IntelPython/mkl-service/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" + +BDEPEND=" + dev-python/cython[${PYTHON_USEDEP}] + sys-devel/DPC++ +" + +RDEPEND=" + sci-libs/mkl +" +DEPEND="${RDEPEND}" + +distutils_enable_tests pytest + +python_prepare_all() { + # DPC++ compiler required for full functionality + export CC="${ESYSROOT}/usr/lib/llvm/intel/bin/clang" + export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++" + export DPCPPROOT="${ESYSROOT}/usr/lib/llvm/intel" + export MKLROOT="${ESYSROOT}/opt/intel/oneapi/mkl/latest" + + distutils-r1_python_prepare_all +} diff --git a/dev-python/mkl_fft/Manifest b/dev-python/mkl_fft/Manifest new file mode 100644 index 000000000..24960cd58 --- /dev/null +++ b/dev-python/mkl_fft/Manifest @@ -0,0 +1 @@ +DIST mkl_fft-1.3.1.gh.tar.gz 41796 BLAKE2B 880c5fef47e8f489c51c7ae69516ca073fe49583a1a11c16289d5313161190d0f4fe2be43defe51b26c6d1f5a4df8c40da8fe65c10911f40483e0400d177f859 SHA512 5d9bb76a5d5dfcf93a05fe6e1ebc267ba7011370ef40e84d6e017e90db301cedb1fb202b1f0851133537fa8bf09260bc9b3f5eb497efc049d6153a4de088854f diff --git a/dev-python/mkl_fft/metadata.xml b/dev-python/mkl_fft/metadata.xml new file mode 100644 index 000000000..95348817f --- /dev/null +++ b/dev-python/mkl_fft/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <upstream> + <remote-id type="github">IntelPython/mkl_fft</remote-id> + <remote-id type="pypi">mkl-fft</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/mkl_fft/mkl_fft-1.3.1.ebuild b/dev-python/mkl_fft/mkl_fft-1.3.1.ebuild new file mode 100644 index 000000000..9b9c72d41 --- /dev/null +++ b/dev-python/mkl_fft/mkl_fft-1.3.1.ebuild @@ -0,0 +1,39 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 + +DESCRIPTION="NumPy-based Python interface to Intel MKL FFT functionality" +HOMEPAGE="https://github.com/IntelPython/mkl_fft" +SRC_URI="https://github.com/IntelPython/mkl_fft/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" + +BDEPEND=" + dev-python/cython[${PYTHON_USEDEP}] + sys-devel/DPC++ +" + +RDEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + sci-libs/mkl +" +DEPEND="${RDEPEND}" + +distutils_enable_tests pytest + +python_prepare_all() { + # DPC++ compiler required for full functionality + export CC="${ESYSROOT}/usr/lib/llvm/intel/bin/clang" + export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++" + export DPCPPROOT="${ESYSROOT}/usr/lib/llvm/intel" + export MKLROOT="${ESYSROOT}/opt/intel/oneapi/mkl/latest" + + distutils-r1_python_prepare_all +} diff --git a/dev-python/mkl_random/Manifest b/dev-python/mkl_random/Manifest new file mode 100644 index 000000000..a826880d4 --- /dev/null +++ b/dev-python/mkl_random/Manifest @@ -0,0 +1 @@ +DIST mkl_random-1.2.2.gh.tar.gz 80274 BLAKE2B f59091c2bdb4b0136e218e3a1341d1852aa9fcec097dc435330f9b175a71aefc1d7fe7fb56411f562f4f56bbff52fa46dec3506a36f73fecd91646b7b1ac56d4 SHA512 dd691fb9873cf54e4f488a20de9c85993536bbeaedb7fbd731e9c021e3b40992f45a01268f3166ce08e766b9374745ac2ee81e99eb013c7406d40d365241cb31 diff --git a/dev-python/mkl_random/metadata.xml b/dev-python/mkl_random/metadata.xml new file mode 100644 index 000000000..394347ca5 --- /dev/null +++ b/dev-python/mkl_random/metadata.xml @@ -0,0 +1,12 @@ +<?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> + <upstream> + <remote-id type="github">IntelPython/mkl_random</remote-id> + <remote-id type="pypi">mkl-random</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/mkl_random/mkl_random-1.2.2.ebuild b/dev-python/mkl_random/mkl_random-1.2.2.ebuild new file mode 100644 index 000000000..7bd845de9 --- /dev/null +++ b/dev-python/mkl_random/mkl_random-1.2.2.ebuild @@ -0,0 +1,41 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 + +DESCRIPTION="Python interface to Intel Math Kernel Library's random number generation" +HOMEPAGE="https://github.com/IntelPython/mkl_random" +SRC_URI="https://github.com/IntelPython/mkl_random/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" + +BDEPEND=" + dev-python/cython[${PYTHON_USEDEP}] + sys-devel/DPC++ +" + +RDEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + sci-libs/mkl +" +DEPEND="${RDEPEND}" + +distutils_enable_tests pytest + +python_prepare_all() { + # DPC++ compiler required for full functionality + export CC="${ESYSROOT}/usr/lib/llvm/intel/bin/clang" + export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++" + export DPCPPROOT="${ESYSROOT}/usr/lib/llvm/intel" + export MKLROOT="${ESYSROOT}/opt/intel/oneapi/mkl/latest" + export C_INCLUDE_PATH="${ESYSROOT}/opt/intel/oneapi/mkl/latest/include/" + export CPLUS_INCLUDE_PATH="${ESYSROOT}/opt/intel/oneapi/mkl/latest/include/" + + distutils-r1_python_prepare_all +} diff --git a/dev-python/mkl_umath/Manifest b/dev-python/mkl_umath/Manifest new file mode 100644 index 000000000..6e1df7796 --- /dev/null +++ b/dev-python/mkl_umath/Manifest @@ -0,0 +1 @@ +DIST mkl_umath-0.1.1.gh.tar.gz 47263 BLAKE2B cb336ad38853298152ebef56e20dac5c6154352a1e443097db27c21ef3099b1ce93ba14a8a9d93ec163aecd0bef2ad8bbff436ae3f4f35ff1029ac6c34a808f5 SHA512 7e545c294d879ca602d2527945b9bb6782cf4e01c44cbde617c3ffcf8d639e428fecc3c9427b4089d70dbc8ae723630a8148917df18109b9c1727a25ad651775 diff --git a/dev-python/mkl_umath/metadata.xml b/dev-python/mkl_umath/metadata.xml new file mode 100644 index 000000000..f23ce9644 --- /dev/null +++ b/dev-python/mkl_umath/metadata.xml @@ -0,0 +1,12 @@ +<?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> + <upstream> + <remote-id type="github">IntelPython/mkl_umath</remote-id> + <remote-id type="pypi">mkl-umath</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/mkl_umath/mkl_umath-0.1.1.ebuild b/dev-python/mkl_umath/mkl_umath-0.1.1.ebuild new file mode 100644 index 000000000..1210fdfd8 --- /dev/null +++ b/dev-python/mkl_umath/mkl_umath-0.1.1.ebuild @@ -0,0 +1,37 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 + +DESCRIPTION="Package implementing NumPy's UFuncs based on SVML and MKL VML" +HOMEPAGE="https://github.com/IntelPython/mkl_umath" +SRC_URI="https://github.com/IntelPython/mkl_umath/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" + +BDEPEND=" + dev-python/cython[${PYTHON_USEDEP}] + sys-devel/DPC++ +" + +RDEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + sci-libs/mkl +" +DEPEND="${RDEPEND}" + +python_prepare_all() { + # DPC++ compiler required for full functionality + export CC="${ESYSROOT}/usr/lib/llvm/intel/bin/clang" + export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++" + export DPCPPROOT="${ESYSROOT}/usr/lib/llvm/intel" + export MKLROOT="${ESYSROOT}/opt/intel/oneapi/mkl/latest" + + distutils-r1_python_prepare_all +} diff --git a/dev-python/multimethod/multimethod-1.8.ebuild b/dev-python/multimethod/multimethod-1.8.ebuild index 4d3c7837c..595a728a4 100644 --- a/dev-python/multimethod/multimethod-1.8.ebuild +++ b/dev-python/multimethod/multimethod-1.8.ebuild @@ -4,7 +4,7 @@ EAPI=8 DISTUTILS_USE_PEP517=setuptools -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) inherit distutils-r1 diff --git a/dev-python/neo/Manifest b/dev-python/neo/Manifest new file mode 100644 index 000000000..346e022b8 --- /dev/null +++ b/dev-python/neo/Manifest @@ -0,0 +1,3 @@ +DIST neo-0.11.0.tar.gz 9411608 BLAKE2B 9257fd8ff9eea8ec80b0a4eb701b63a9db10d51e6f145b704eb5e9a394dd13a5c6e567cb3469fa4d86f538637f80e9c660823d358bb7ddfd651291dc5df73450 SHA512 dab4832317c8dc6a794ffc9fb118124734fa2428c0527eb9c86bc3d35195a34bdb162bc0a44a3604cb8067fff7263ab5b106c0f9871007a093e7185df5ba9993 +DIST neo-0.11.1.tar.gz 3906151 BLAKE2B 26b60c715d6f3ec017cdb909c1f54b1509db4862f0630ab6d60b4b07153d5cb8512fbf16dd9039d1998b08e0f9e828bb271d4f482cc2d34a5d17a010ef4d203b SHA512 1f93a9eea020ee40f792f038bef76e053ff4f6e05951f78afa70bf4009bac3da8222be57c2cee88ae5e7539c5c8978cf50bf52cce787dbacafe6d5450d5e1aa7 +DIST neo-0.12.0.tar.gz 28377158 BLAKE2B efc6ae96d8cf8325355367af482d4e6dcc0dc3e3c5f3d449076a1c3ef32f530f777a2b125c946360b05a070cd75ae3f04b31a9e63d9bee7fecf437c3a19fc284 SHA512 1849c5074afb71cba7e90a78fa51b9967b27cb3f0b6242cfbadc3c29faf7a4a13da0a15a1c43cf43df810a5c0ed0b45cf60b42f3ed83520689acc27d3bde07b9 diff --git a/dev-python/neo/metadata.xml b/dev-python/neo/metadata.xml new file mode 100644 index 000000000..5a50da2a7 --- /dev/null +++ b/dev-python/neo/metadata.xml @@ -0,0 +1,23 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>gentoo@chymera.eu</email> + <name>Horea Christian</name> + </maintainer> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <longdescription lang="en"> + Neo is a Python package for working with electrophysiology data in Python, + together with support for reading a wide range of neurophysiology file + formats, including Spike2, NeuroExplorer, AlphaOmega, Axon, Blackrock, + Plexon, Tdt, and support for writing to a subset of these formats plus + non-proprietary formats including HDF5. + </longdescription> + <upstream> + <remote-id type="github">NeuralEnsemble/python-neo</remote-id> + <remote-id type="pypi">neo</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/neo/neo-0.11.0.ebuild b/dev-python/neo/neo-0.11.0.ebuild new file mode 100644 index 000000000..dedbcea6e --- /dev/null +++ b/dev-python/neo/neo-0.11.0.ebuild @@ -0,0 +1,61 @@ +# Copyright 2021-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 pypi + +MY_PN="python-neo" + +DESCRIPTION="Read and represent a wide range of neurophysiology file formats in Python" +HOMEPAGE="https://github.com/NeuralEnsemble/python-neo" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" +IUSE="test" + +RDEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/quantities[${PYTHON_USEDEP}] +" +BDEPEND=" + test? ( + ${RDEPEND} + dev-python/scipy[${PYTHON_USEDEP}] + dev-python/h5py[${PYTHON_USEDEP}] + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/pillow[${PYTHON_USEDEP}] + dev-python/probeinterface[${PYTHON_USEDEP}] + dev-python/pynwb[${PYTHON_USEDEP}] + dev-python/tqdm[${PYTHON_USEDEP}] + dev-vcs/datalad[${PYTHON_USEDEP}] + ) +" +# Testing deps also need: +# igor +# pyedflib https://github.com/holgern/pyedflib +# klusta +# nixio +# sonpy +# ipython + +S="${WORKDIR}/${MY_PN}-${PV}" + +distutils_enable_tests pytest + +EPYTEST_DESELECT=( + neo/test/utils/test_datasets.py::TestDownloadDataset::test_download_dataset +) + +# Reported upstream +# https://github.com/NeuralEnsemble/python-neo/issues/1037 +python_test() { + local EPYTEST_IGNORE=( + neo/test/iotest/* + neo/test/rawiotest/* + ) + epytest +} diff --git a/dev-python/neo/neo-0.11.1.ebuild b/dev-python/neo/neo-0.11.1.ebuild new file mode 100644 index 000000000..6f43494f8 --- /dev/null +++ b/dev-python/neo/neo-0.11.1.ebuild @@ -0,0 +1,53 @@ +# Copyright 2021-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 pypi + +DESCRIPTION="Read and represent a wide range of neurophysiology file formats in Python" +HOMEPAGE="https://github.com/NeuralEnsemble/python-neo" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" +IUSE="test" + +RDEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/quantities[${PYTHON_USEDEP}] +" +BDEPEND=" + test? ( + ${RDEPEND} + dev-python/scipy[${PYTHON_USEDEP}] + dev-python/h5py[${PYTHON_USEDEP}] + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/pillow[${PYTHON_USEDEP}] + dev-python/probeinterface[${PYTHON_USEDEP}] + dev-python/pynwb[${PYTHON_USEDEP}] + dev-python/tqdm[${PYTHON_USEDEP}] + dev-vcs/datalad[${PYTHON_USEDEP}] + ) +" +# Testing deps also need: +# igor +# pyedflib https://github.com/holgern/pyedflib +# klusta +# nixio +# sonpy +# ipython + +distutils_enable_tests pytest + +# Reported upstream +# https://github.com/NeuralEnsemble/python-neo/issues/1037 +python_test() { + local EPYTEST_IGNORE=( + neo/test/iotest/* + neo/test/rawiotest/* + ) + epytest +} diff --git a/dev-python/neo/neo-0.12.0.ebuild b/dev-python/neo/neo-0.12.0.ebuild new file mode 100644 index 000000000..6e058728e --- /dev/null +++ b/dev-python/neo/neo-0.12.0.ebuild @@ -0,0 +1,57 @@ +# Copyright 2021-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 pypi + +DESCRIPTION="Read and represent a wide range of neurophysiology file formats in Python" +HOMEPAGE="https://github.com/NeuralEnsemble/python-neo" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" +IUSE="test" + +RDEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/quantities[${PYTHON_USEDEP}] +" +BDEPEND=" + test? ( + ${RDEPEND} + dev-python/scipy[${PYTHON_USEDEP}] + dev-python/h5py[${PYTHON_USEDEP}] + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/pillow[${PYTHON_USEDEP}] + dev-python/probeinterface[${PYTHON_USEDEP}] + dev-python/pynwb[${PYTHON_USEDEP}] + dev-python/tqdm[${PYTHON_USEDEP}] + dev-vcs/datalad[${PYTHON_USEDEP}] + ) +" +# Testing deps also need: +# igor +# pyedflib https://github.com/holgern/pyedflib +# klusta +# nixio +# sonpy +# ipython + +distutils_enable_tests pytest + +python_test() { + # Reported upstream + # https://github.com/NeuralEnsemble/python-neo/issues/1037 + local EPYTEST_IGNORE=( + neo/test/iotest/* + neo/test/rawiotest/* + ) + # Requires dynamic data download + local EPYTEST_DESELECT=( + neo/test/utils/test_datasets.py::TestDownloadDataset::test_download_dataset + ) + epytest +} diff --git a/dev-python/nptyping/Manifest b/dev-python/nptyping/Manifest new file mode 100644 index 000000000..8a541f60d --- /dev/null +++ b/dev-python/nptyping/Manifest @@ -0,0 +1 @@ +DIST nptyping-2.5.0.gh.tar.gz 72870 BLAKE2B 16c6cb90c36bbf0b97da5ff74cee7030c641ef76d055cc5691b9d83adab2714d6e3515fd4e8616fece74606e109e6b115348964614b408df06b4f5c3cbccce37 SHA512 2cde9c5f7694d4f916b85c93b86df7f72709a70b2ffa91b7bbc98c5884236f5b36bb545a89c37e8c02a9b460065c97151d77c64f8d93b92fd93bcff406f039d9 diff --git a/dev-python/nptyping/metadata.xml b/dev-python/nptyping/metadata.xml new file mode 100644 index 000000000..45345f0dc --- /dev/null +++ b/dev-python/nptyping/metadata.xml @@ -0,0 +1,16 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <maintainer type="person"> + <email>gentoo@chymera.eu</email> + <name>Horea Christian</name> + </maintainer> + <upstream> + <remote-id type="pypi">nptyping</remote-id> + <remote-id type="github">ramonhagenaars/nptyping</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/nptyping/nptyping-2.5.0.ebuild b/dev-python/nptyping/nptyping-2.5.0.ebuild new file mode 100644 index 000000000..f6e8864df --- /dev/null +++ b/dev-python/nptyping/nptyping-2.5.0.ebuild @@ -0,0 +1,66 @@ +# Copyright 2022-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{9..11} ) + +inherit distutils-r1 + +DESCRIPTION="Type hints for Numpy" +HOMEPAGE=" + https://pypi.org/project/nptyping/ + https://github.com/ramonhagenaars/nptyping/ +" +SRC_URI=" + https://github.com/ramonhagenaars/nptyping/archive/v${PV}.tar.gz + -> ${P}.gh.tar.gz +" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] +" +BDEPEND=" + test? ( + dev-python/mypy[${PYTHON_USEDEP}] + dev-python/pandas-stubs[${PYTHON_USEDEP}] + dev-python/typeguard[${PYTHON_USEDEP}] + dev-python/beartype[${PYTHON_USEDEP}] + ) +" + +EPYTEST_IGNORE=( + # requires pyright, which is not yet packaged + tests/test_pyright.py + # requires Internet + feedparser, meaningless for users + tests/test_package_info.py + # relying on Internet access to fetch packages for pip + tests/test_wheel.py + tests/pandas_/test_fork_sync.py +) + +EPYTEST_DESELECT=( + # Reported upstream: + # https://github.com/ramonhagenaars/nptyping/issues/113 + tests/test_mypy.py::MyPyTest::test_mypy_accepts_ndarray_with_any + tests/test_mypy.py::MyPyTest::test_mypy_accepts_ndarray_with_shape + tests/test_mypy.py::MyPyTest::test_mypy_accepts_ndarray_with_structure + tests/test_mypy.py::MyPyTest::test_mypy_accepts_ndarrays_as_function_arguments + tests/test_mypy.py::MyPyTest::test_mypy_accepts_ndarrays_as_variable_hints + tests/test_mypy.py::MyPyTest::test_mypy_accepts_nptyping_types + tests/test_mypy.py::MyPyTest::test_mypy_accepts_numpy_types + tests/test_mypy.py::MyPyTest::test_mypy_accepts_recarray_with_structure + tests/test_mypy.py::MyPyTest::test_mypy_disapproves_ndarray_with_wrong_function_arguments + tests/test_mypy.py::MyPyTest::test_mypy_knows_of_ndarray_methods + tests/test_typeguard.py::TypeguardTest::test_success + tests/pandas_/test_mypy_dataframe.py::MyPyDataFrameTest::test_mypy_accepts_dataframe + tests/pandas_/test_mypy_dataframe.py::MyPyDataFrameTest::test_mypy_disapproves_dataframe_with_wrong_function_arguments + tests/pandas_/test_mypy_dataframe.py::MyPyDataFrameTest::test_mypy_knows_of_dataframe_methods +) + +distutils_enable_tests pytest diff --git a/dev-python/num2words/metadata.xml b/dev-python/num2words/metadata.xml index aaa27d18e..f3e4e8fcd 100644 --- a/dev-python/num2words/metadata.xml +++ b/dev-python/num2words/metadata.xml @@ -16,6 +16,7 @@ (although this last feature is a bit buggy for some languages at the moment). </longdescription> <upstream> - <remote-id type="github">savoirefairelinux/num2words</remote-id> + <remote-id type="github">savoirfairelinux/num2words</remote-id> + <remote-id type="pypi">num2words</remote-id> </upstream> </pkgmetadata> diff --git a/dev-python/num2words/num2words-0.5.10.ebuild b/dev-python/num2words/num2words-0.5.10.ebuild index 7e62a328d..f57281b6e 100644 --- a/dev-python/num2words/num2words-0.5.10.ebuild +++ b/dev-python/num2words/num2words-0.5.10.ebuild @@ -1,15 +1,13 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7..9} ) - -inherit distutils-r1 +PYTHON_COMPAT=( python3_{10..11} ) +inherit distutils-r1 pypi DESCRIPTION="Modules to convert numbers to words." HOMEPAGE="https://github.com/savoirfairelinux/num2words" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" LICENSE="MIT" SLOT="0" diff --git a/dev-python/numba/Manifest b/dev-python/numba/Manifest deleted file mode 100644 index a4d39c09c..000000000 --- a/dev-python/numba/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST numba-0.54.0.tar.gz 2263302 BLAKE2B 24747fcf23f686460fdd8df4784a3bccd6c41f07ff7e657f797a2959066254c079b05ec4460a7cbafef9482f463aa000ee28f8f09339cd7568a0c85b52bc4437 SHA512 ad1142e8c772660b7cbbd17566b9dc96784057467b5cc546f88e2215c9428905e1f6da05ffe104f4ad526f5131fedfa9057745d5458c3293a8cd8e01a49d0fad -DIST numba-0.55.0.tar.gz 2335687 BLAKE2B 439206cb94149226f54eb988bcc9cefb815f734b0bfa01888f7ba16525ae2cbab39ee929a655086a47a3c3bc540e8589bdbf119cc084e876d9b61da1017bdfe9 SHA512 3651d1d06c5f325459ab73c07f501c12b3081d97d0f92d0120c8cfb312092658bbebc91f8340786f7b10cd43a95e278085cbba6d199cb3d0b5f71987ee7e5776 diff --git a/dev-python/numba/files/numba-0.51.2-skip_tests.patch b/dev-python/numba/files/numba-0.51.2-skip_tests.patch deleted file mode 100644 index 327271a04..000000000 --- a/dev-python/numba/files/numba-0.51.2-skip_tests.patch +++ /dev/null @@ -1,46 +0,0 @@ -diff --git a/numba/tests/test_jitclasses.py b/numba/tests/test_jitclasses.py -index 87f1165..c1c5f35 100644 ---- a/numba/tests/test_jitclasses.py -+++ b/numba/tests/test_jitclasses.py -@@ -909,6 +909,7 @@ class TestJitClass(TestCase, MemoryLeakMixin): - self.assertEqual(t[2:2:1], 2) - self.assertEqual(t[6:6:1], 3) - -+ @unittest.skip("Gentoo has not reverted the LLVM 'truncate longlabel' patch") - def test_jitclass_longlabel_not_truncated(self): - # See issue #3872, llvm 7 introduced a max label length of 1024 chars - # Numba ships patched llvm 7.1 (ppc64le) and patched llvm 8 to undo this -diff --git a/numba/tests/test_np_functions.py b/numba/tests/test_np_functions.py -index 01c15fd..3d9e228 100644 ---- a/numba/tests/test_np_functions.py -+++ b/numba/tests/test_np_functions.py -@@ -2028,6 +2028,7 @@ class TestNPFunctions(MemoryLeakMixin, TestCase): - params = {'ary': ary, 'to_begin': a, 'to_end': b} - _check(params) - -+ @unittest.skip("unhandled type error") - def test_ediff1d_edge_cases(self): - # NOTE: NumPy 1.16 has a variety of behaviours for type conversion, see - # https://github.com/numpy/numpy/issues/13103, as this is not resolved -diff --git a/numba/tests/test_record_dtype.py b/numba/tests/test_record_dtype.py -index 6d479c4..2357206 100644 ---- a/numba/tests/test_record_dtype.py -+++ b/numba/tests/test_record_dtype.py -@@ -796,7 +796,7 @@ class TestRecordDtype(unittest.TestCase): - # len(transformed) is generally 10, but could be longer if a large - # number of typecodes are in use. Checking <20 should provide enough - # tolerance. -- self.assertLess(len(transformed), 20) -+ self.assertLessEqual(len(transformed), 20) - - struct_arr = types.Array(rec, 1, 'C') - transformed = mangle_type(struct_arr) -@@ -804,7 +804,7 @@ class TestRecordDtype(unittest.TestCase): - self.assertNotIn('first', transformed) - self.assertNotIn('second', transformed) - # Length is usually 50 - 5 chars tolerance as above. -- self.assertLess(len(transformed), 50) -+ self.assertLessEqual(len(transformed), 50) - - def test_record_two_arrays(self): - """ diff --git a/dev-python/numba/files/numba-0.52.0-skip_tests.patch b/dev-python/numba/files/numba-0.52.0-skip_tests.patch deleted file mode 100644 index f31af4bfb..000000000 --- a/dev-python/numba/files/numba-0.52.0-skip_tests.patch +++ /dev/null @@ -1,34 +0,0 @@ -Index: numba-0.52.0/numba/tests/test_jitclasses.py -=================================================================== ---- numba-0.52.0.orig/numba/tests/test_jitclasses.py -+++ numba-0.52.0/numba/tests/test_jitclasses.py -@@ -929,6 +929,7 @@ class TestJitClass(TestCase, MemoryLeakM - self.assertEqual(t[2:2:1], 2) - self.assertEqual(t[6:6:1], 3) - -+ @unittest.skip("Gentoo has not reverted the LLVM 'truncate longlabel' patch") - def test_jitclass_longlabel_not_truncated(self): - # See issue #3872, llvm 7 introduced a max label length of 1024 chars - # Numba ships patched llvm 7.1 (ppc64le) and patched llvm 8 to undo this -Index: numba-0.52.0/numba/tests/test_record_dtype.py -=================================================================== ---- numba-0.52.0.orig/numba/tests/test_record_dtype.py -+++ numba-0.52.0/numba/tests/test_record_dtype.py -@@ -796,7 +796,7 @@ class TestRecordDtype(unittest.TestCase) - # len(transformed) is generally 10, but could be longer if a large - # number of typecodes are in use. Checking <20 should provide enough - # tolerance. -- self.assertLess(len(transformed), 20) -+ self.assertLessEqual(len(transformed), 20) - - struct_arr = types.Array(rec, 1, 'C') - transformed = mangle_type(struct_arr) -@@ -804,7 +804,7 @@ class TestRecordDtype(unittest.TestCase) - self.assertNotIn('first', transformed) - self.assertNotIn('second', transformed) - # Length is usually 50 - 5 chars tolerance as above. -- self.assertLess(len(transformed), 50) -+ self.assertLessEqual(len(transformed), 50) - - def test_record_two_arrays(self): - """ diff --git a/dev-python/numba/metadata.xml b/dev-python/numba/metadata.xml deleted file mode 100644 index e97c4322a..000000000 --- a/dev-python/numba/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>gentoo@aisha.cc</email> - <name>Aisha Tammy</name> - </maintainer> - <maintainer type="project"> - <email>sci@gentoo.org</email> - <name>Gentoo Science Project</name> - </maintainer> -</pkgmetadata> diff --git a/dev-python/numba/numba-0.54.0.ebuild b/dev-python/numba/numba-0.54.0.ebuild deleted file mode 100644 index 125b20daf..000000000 --- a/dev-python/numba/numba-0.54.0.ebuild +++ /dev/null @@ -1,84 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{8..9} ) - -DISTUTILS_USE_SETUPTOOLS=rdepend -inherit optfeature multiprocessing distutils-r1 - -DESCRIPTION="NumPy aware dynamic Python compiler using LLVM" -HOMEPAGE="https://numba.pydata.org/ - https://github.com/numba" -SRC_URI="https://github.com/numba/numba/archive/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~arm ~arm64 ~x86" -IUSE="openmp threads" - -RDEPEND=" - >=dev-python/llvmlite-0.37.0[${PYTHON_USEDEP}] - <dev-python/llvmlite-0.38.0 - >=dev-python/numpy-1.17.0[${PYTHON_USEDEP}] - threads? ( >=dev-cpp/tbb-2019.5 ) -" -BDEPEND=" - dev-python/pip[${PYTHON_USEDEP}] - dev-python/versioneer[${PYTHON_USEDEP}] -" - -DISTUTILS_IN_SOURCE_BUILD=1 -distutils_enable_tests unittest -distutils_enable_sphinx docs/source dev-python/numpydoc dev-python/sphinx_rtd_theme - -PATCHES=( - "${FILESDIR}/${PN}-0.52.0-skip_tests.patch" -) - -pkg_setup() { - if ! use openmp; then - export NUMBA_DISABLE_OPENMP=1 || die - else - unset NUMBA_DISABLE_OPENMP || die - fi - if ! use threads; then - export NUMBA_DISABLE_TBB=1 || die - else - unset NUMBA_DISABLE_TBB || die - export TBBROOT="${EPREFIX}/usr" || die - fi -} - -python_prepare_all() { - # This conf.py only works in a git repo - if use doc; then - git init -q || die - git config user.email "larry@gentoo.org" || die - git config user.name "Larry the Cow" || die - git add . || die - git commit -m "init" || die - fi - distutils-r1_python_prepare_all -} - -python_compile() { - # FIXME: parallel python building fails. See Portage bug #614464 and - # gentoo/sci issue #1080. - export MAKEOPTS=-j1 || die - distutils-r1_python_compile -} - -# https://numba.pydata.org/numba-doc/latest/developer/contributing.html?highlight=test#running-tests -python_test() { - distutils_install_for_testing - ${EPYTHON} setup.py build_ext --inplace || die \ - "${EPYTHON} failed to build_ext" - ${EPYTHON} runtests.py -m $(makeopts_jobs) || die \ - "${EPYTHON} failed unittests" -} - -pkg_postinst() { - optfeature "compile cuda code" dev-util/nvidia-cuda-sdk -} diff --git a/dev-python/numba/numba-0.55.0.ebuild b/dev-python/numba/numba-0.55.0.ebuild deleted file mode 100644 index 342c3894f..000000000 --- a/dev-python/numba/numba-0.55.0.ebuild +++ /dev/null @@ -1,85 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{8..10} ) - -DISTUTILS_USE_SETUPTOOLS=rdepend -inherit optfeature multiprocessing distutils-r1 - -DESCRIPTION="NumPy aware dynamic Python compiler using LLVM" -HOMEPAGE="https://numba.pydata.org/ - https://github.com/numba" -SRC_URI="https://github.com/numba/numba/archive/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~arm ~arm64 ~x86" -IUSE="openmp threads" - -RDEPEND=" - >=dev-python/llvmlite-0.38.0[${PYTHON_USEDEP}] - <=dev-python/llvmlite-0.39.0 - >=dev-python/numpy-1.18.0[${PYTHON_USEDEP}] - <dev-python/numpy-1.22[${PYTHON_USEDEP}] - threads? ( >=dev-cpp/tbb-2021.1 ) -" -BDEPEND=" - dev-python/pip[${PYTHON_USEDEP}] - dev-python/versioneer[${PYTHON_USEDEP}] -" - -DISTUTILS_IN_SOURCE_BUILD=1 -distutils_enable_tests unittest -distutils_enable_sphinx docs/source dev-python/numpydoc dev-python/sphinx_rtd_theme - -PATCHES=( - "${FILESDIR}/${PN}-0.52.0-skip_tests.patch" -) - -pkg_setup() { - if ! use openmp; then - export NUMBA_DISABLE_OPENMP=1 || die - else - unset NUMBA_DISABLE_OPENMP || die - fi - if ! use threads; then - export NUMBA_DISABLE_TBB=1 || die - else - unset NUMBA_DISABLE_TBB || die - export TBBROOT="${EPREFIX}/usr" || die - fi -} - -python_prepare_all() { - # This conf.py only works in a git repo - if use doc; then - git init -q || die - git config user.email "larry@gentoo.org" || die - git config user.name "Larry the Cow" || die - git add . || die - git commit -m "init" || die - fi - distutils-r1_python_prepare_all -} - -python_compile() { - # FIXME: parallel python building fails. See Portage bug #614464 and - # gentoo/sci issue #1080. - export MAKEOPTS=-j1 || die - distutils-r1_python_compile -} - -# https://numba.pydata.org/numba-doc/latest/developer/contributing.html?highlight=test#running-tests -python_test() { - distutils_install_for_testing - ${EPYTHON} setup.py build_ext --inplace || die \ - "${EPYTHON} failed to build_ext" - ${EPYTHON} runtests.py -m $(makeopts_jobs) || die \ - "${EPYTHON} failed unittests" -} - -pkg_postinst() { - optfeature "compile cuda code" dev-util/nvidia-cuda-sdk -} diff --git a/dev-python/numcodecs/Manifest b/dev-python/numcodecs/Manifest index 761068546..b14e3311b 100644 --- a/dev-python/numcodecs/Manifest +++ b/dev-python/numcodecs/Manifest @@ -1,2 +1,2 @@ -DIST numcodecs-0.9.0.tar.gz 4514267 BLAKE2B d7042ff0296a8246f063f55f31d790fcfbd59de07c08ff0d57e1bd4c7094c6f375ef55714866061f449dcca87d39abd36c56218d23aca0fd6bcfae491fb10097 SHA512 1525e5a7f7a7427752d3ccfbbb82b7afbfc90fcbc2c9e886e31d286c64478d85747de7e6bf16a8e980af96cf952d1202a15affa02cf6a22b4aac3725a0c8a65f -DIST numcodecs-0.9.1.tar.gz 4514374 BLAKE2B b418ee0fd27cb5f7bf8def3b124f31af7c0e2e2610dca55351c105933f7471e2465f24fa24e53ee607abcf26d690ba2b368e77618c703a4dbc8a926be48c9c1d SHA512 639cc5a5656e026f85e893009831f98420e3818f73bab95f0afd0a5bd64c901082826921e40c1b6e1f75cad82b3be2cf36787fa74ba7f0fd011dac070b24e0f8 +DIST numcodecs-0.11.0.tar.gz 4512454 BLAKE2B 8144120856437ca272e275430c6e169d3e2a88c12c54f71518a7f262a77f13161f61e36b8da75abc0ab4efc02cf0807e86272c1bcf5e21bfb76fba7c4cbc8863 SHA512 cd0bcd87320e3c5a4cc97f8b6b11062361ce007c55bf23d07afab7a85df256bf7bc3f16d49958e9238901e70b26deb90faaa7a006207b6325fdbe225b99139d2 +DIST numcodecs-0.12.1.tar.gz 4091415 BLAKE2B d7fa8cc549495c7c54130898f2047eb409559541b299640fb34a2332d874049afa64d5c14151426b24a1ab04c0e0444245477aa26f9336ce3ba7aefc8043abcf SHA512 716a1144c17b08cc1737bd429517b5434a7e5dbc9626ed613ca9ab4f9cda356ed97cb4ef0e2bba747a7681dc5b43818cb07c6db7f5537b4910790f6ea23c696c diff --git a/dev-python/numcodecs/files/numcodecs-0.11.0-nocov.patch b/dev-python/numcodecs/files/numcodecs-0.11.0-nocov.patch new file mode 100644 index 000000000..2d5e7f86e --- /dev/null +++ b/dev-python/numcodecs/files/numcodecs-0.11.0-nocov.patch @@ -0,0 +1,11 @@ +--- a/pyproject.toml ++++ b/pyproject.toml +@@ -87,7 +87,7 @@ exclude_lines = [ + ] + + [tool.pytest.ini_options] +-addopts = "--cov=numcodecs --cov-report xml --doctest-modules --doctest-glob=*.pyx" ++addopts = "--pyargs numcodecs --doctest-modules --doctest-glob=*.pyx" + doctest_optionflags = [ + "NORMALIZE_WHITESPACE", + "ELLIPSIS", diff --git a/dev-python/numcodecs/numcodecs-0.11.0.ebuild b/dev-python/numcodecs/numcodecs-0.11.0.ebuild new file mode 100644 index 000000000..500a52b89 --- /dev/null +++ b/dev-python/numcodecs/numcodecs-0.11.0.ebuild @@ -0,0 +1,49 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 pypi + +DESCRIPTION="Data storage buffer compression and transformation codecs" +HOMEPAGE="https://github.com/zarr-developers/numcodecs" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="test" + +RDEPEND=" + dev-python/cython[${PYTHON_USEDEP}] + dev-python/entrypoints[${PYTHON_USEDEP}] + dev-python/msgpack[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/py-cpuinfo[${PYTHON_USEDEP}] +" + +DEPEND=" + test? ( + ${RDEPEND} + dev-python/entrypoints[${PYTHON_USEDEP}] + ) +" + +PATCHES=( + "${FILESDIR}/${P}-nocov.patch" +) + +# Reported upstream: +# https://github.com/zarr-developers/numcodecs/issues/436 +EPYTEST_DESELECT=( + tests/test_json.py::test_non_numpy_inputs + tests/test_msgpacks.py::test_non_numpy_inputs +) + +distutils_enable_tests pytest + +python_test() { + cd "${T}" || die + epytest --pyargs numcodecs +} diff --git a/dev-python/numcodecs/numcodecs-0.12.1-r2.ebuild b/dev-python/numcodecs/numcodecs-0.12.1-r2.ebuild new file mode 100644 index 000000000..3d20684ba --- /dev/null +++ b/dev-python/numcodecs/numcodecs-0.12.1-r2.ebuild @@ -0,0 +1,43 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 pypi + +DESCRIPTION="Data storage buffer compression and transformation codecs" +HOMEPAGE="https://github.com/zarr-developers/numcodecs" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="test" + +RDEPEND=" + dev-python/cython[${PYTHON_USEDEP}] + dev-python/entrypoints[${PYTHON_USEDEP}] + dev-python/msgpack[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/py-cpuinfo[${PYTHON_USEDEP}] +" +DEPEND=" + test? ( + ${RDEPEND} + dev-python/entrypoints[${PYTHON_USEDEP}] + ) +" + +distutils_enable_tests pytest + +python_compile() { + local -x DISABLE_NUMCODECS_AVX2=1 + local -x DISABLE_NUMCODECS_SSE2=1 + distutils-r1_python_compile +} + +python_test() { + cd "${T}" || die + epytest --pyargs numcodecs +} diff --git a/dev-python/numcodecs/numcodecs-0.9.0.ebuild b/dev-python/numcodecs/numcodecs-0.9.0.ebuild deleted file mode 100644 index 7219b5b7b..000000000 --- a/dev-python/numcodecs/numcodecs-0.9.0.ebuild +++ /dev/null @@ -1,35 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{8..10} ) -inherit distutils-r1 - -DESCRIPTION="Data storage buffer compression and transformation codecs" -HOMEPAGE="https://github.com/zarr-developers/numcodecs" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="test" -# Fails to collect tests for yet unknown reasons: -# https://github.com/zarr-developers/numcodecs/issues/304 -RESTRICT="test" - -RDEPEND=" - dev-python/cython[${PYTHON_USEDEP}] - dev-python/msgpack[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/cython[${PYTHON_USEDEP}] -" - -DEPEND=" - test? ( - ${RDEPEND} - dev-python/entrypoints[${PYTHON_USEDEP}] - ) -" - -distutils_enable_tests pytest diff --git a/dev-python/numcodecs/numcodecs-0.9.1.ebuild b/dev-python/numcodecs/numcodecs-0.9.1.ebuild deleted file mode 100644 index 7219b5b7b..000000000 --- a/dev-python/numcodecs/numcodecs-0.9.1.ebuild +++ /dev/null @@ -1,35 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{8..10} ) -inherit distutils-r1 - -DESCRIPTION="Data storage buffer compression and transformation codecs" -HOMEPAGE="https://github.com/zarr-developers/numcodecs" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="test" -# Fails to collect tests for yet unknown reasons: -# https://github.com/zarr-developers/numcodecs/issues/304 -RESTRICT="test" - -RDEPEND=" - dev-python/cython[${PYTHON_USEDEP}] - dev-python/msgpack[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/cython[${PYTHON_USEDEP}] -" - -DEPEND=" - test? ( - ${RDEPEND} - dev-python/entrypoints[${PYTHON_USEDEP}] - ) -" - -distutils_enable_tests pytest diff --git a/dev-python/nwbinspector/Manifest b/dev-python/nwbinspector/Manifest index f5e2c79b7..d4db5e2f3 100644 --- a/dev-python/nwbinspector/Manifest +++ b/dev-python/nwbinspector/Manifest @@ -1 +1,2 @@ -DIST nwbinspector-0.3.9.tar.gz 443247 BLAKE2B 4d1adbca50ff0f5d8278d71063d1248a4b22da952de6dc3e4984d58285d1acecf5adfe85b2a624df20e8064a69fa2ffe2c4a23ec1d2a579446fc451e7cd04bd5 SHA512 e8752fadbfcdb9a46f5c16771d789995fdab378720861dbe15b100f8e07cfad58f99a75fbda8e7631f06ec5671e16b3ac48a002606b658b018d50dd62151cc5e +DIST nwbinspector-0.4.19.gh.tar.gz 570101 BLAKE2B f3950a8e24225fe490a6454ab5cd429bcb741eeee9cf12591089508600d283b4242ef70427e116960d16367e16c6d5a5869cfcedd829500ce920387d8ebca916 SHA512 3ecd7d1db1d53c0ec5db986a211e56b4818c165a376d15e7a79ede9c8ca45560b6f302e3c9b1e960153d632bfa759660be4e44540399e272be3728d76fd52a7c +DIST nwbinspector-0.4.26.gh.tar.gz 575576 BLAKE2B 5ec888fc578dd0225b346426b93193f1a08cf92fa9c11e7653773c6bd74603c9e3456514209b3e2a12cf9d868f6004b64700c98212f3837b4b77096dff23ea72 SHA512 901df8422aa3b8666f01e9a6389c22f7caca30007494cb8680ee228bb58a9192f4f35a2426f38f068df5e938fe192db6db4d5626d00ca96e766114dd301efce3 diff --git a/dev-python/nwbinspector/nwbinspector-0.3.9.ebuild b/dev-python/nwbinspector/nwbinspector-0.3.9.ebuild deleted file mode 100644 index 1e0352b88..000000000 --- a/dev-python/nwbinspector/nwbinspector-0.3.9.ebuild +++ /dev/null @@ -1,28 +0,0 @@ -# Copyright 2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -DISTUTILS_USE_PEP517=setuptools -PYTHON_COMPAT=( python3_{8..10} ) -inherit distutils-r1 - -DESCRIPTION="Inspect NWB files for compliance with NWB Best Practices" -HOMEPAGE="https://github.com/NeurodataWithoutBorders/nwbinspector" -SRC_URI="https://github.com/NeurodataWithoutBorders/nwbinspector/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="test" -RESTRICT="!test? ( test )" - -DEPEND="" -RDEPEND=" - dev-python/jsonschema[${PYTHON_USEDEP}] - dev-python/pynwb[${PYTHON_USEDEP}] - dev-python/pyyaml[${PYTHON_USEDEP}] -" -BDEPEND="" - -distutils_enable_tests pytest diff --git a/dev-python/nwbinspector/nwbinspector-0.4.19.ebuild b/dev-python/nwbinspector/nwbinspector-0.4.19.ebuild new file mode 100644 index 000000000..b4b5f7448 --- /dev/null +++ b/dev-python/nwbinspector/nwbinspector-0.4.19.ebuild @@ -0,0 +1,31 @@ +# Copyright 2022-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) +inherit distutils-r1 + +DESCRIPTION="Inspect NWB files for compliance with NWB Best Practices" +HOMEPAGE="https://github.com/NeurodataWithoutBorders/nwbinspector" +SRC_URI="https://github.com/NeurodataWithoutBorders/nwbinspector/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="test" +RESTRICT="!test? ( test )" + +DEPEND="" +RDEPEND=" + dev-python/click[${PYTHON_USEDEP}] + dev-python/jsonschema[${PYTHON_USEDEP}] + dev-python/natsort[${PYTHON_USEDEP}] + dev-python/pynwb[${PYTHON_USEDEP}] + dev-python/pyyaml[${PYTHON_USEDEP}] + dev-python/tqdm[${PYTHON_USEDEP}] +" +BDEPEND="" + +distutils_enable_tests pytest diff --git a/dev-python/nwbinspector/nwbinspector-0.4.26-r1.ebuild b/dev-python/nwbinspector/nwbinspector-0.4.26-r1.ebuild new file mode 100644 index 000000000..271dbfb1d --- /dev/null +++ b/dev-python/nwbinspector/nwbinspector-0.4.26-r1.ebuild @@ -0,0 +1,32 @@ +# Copyright 2022-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) +inherit distutils-r1 + +DESCRIPTION="Inspect NWB files for compliance with NWB Best Practices" +HOMEPAGE="https://github.com/NeurodataWithoutBorders/nwbinspector" +SRC_URI="https://github.com/NeurodataWithoutBorders/nwbinspector/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="test" +RESTRICT="!test? ( test )" + +DEPEND="" +RDEPEND=" + dev-python/click[${PYTHON_USEDEP}] + dev-python/isodate[${PYTHON_USEDEP}] + dev-python/jsonschema[${PYTHON_USEDEP}] + dev-python/natsort[${PYTHON_USEDEP}] + dev-python/pynwb[${PYTHON_USEDEP}] + dev-python/pyyaml[${PYTHON_USEDEP}] + dev-python/tqdm[${PYTHON_USEDEP}] +" +BDEPEND="" + +distutils_enable_tests pytest diff --git a/dev-python/palettable/Manifest b/dev-python/palettable/Manifest deleted file mode 100644 index 2fd3a2291..000000000 --- a/dev-python/palettable/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST palettable-3.3.0.tar.gz 105475 BLAKE2B bd3745e428b8273c1ce8ebca89cb99ba988fbf6bcfc11a387a946938dd8e573a8b9aadf3288b3a4c9a794add1c3b64f77519188a7025a1cb85de129e476429a4 SHA512 6689b009d3a7face36c0d3eaf2bee6a5e8f364f25f30e06924ec61d730c95921ef37cfc857a93b07a772a7b347e805ae8139f056478378a6c8669f853d5df810 diff --git a/dev-python/palettable/metadata.xml b/dev-python/palettable/metadata.xml deleted file mode 100644 index a5b9b813a..000000000 --- a/dev-python/palettable/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="person"> - <email>marbre@linux.sungazer.de</email> - <name>Marius Brehler</name> - </maintainer> - <maintainer type="project"> - <email>sci@gentoo.org</email> - <name>Gentoo Science Project</name> - </maintainer> - <upstream> - <remote-id type="github">jiffyclub/palettable</remote-id> - <remote-id type="pypi">palettable</remote-id> - </upstream> -</pkgmetadata> diff --git a/dev-python/palettable/palettable-3.3.0.ebuild b/dev-python/palettable/palettable-3.3.0.ebuild deleted file mode 100644 index 1288d9233..000000000 --- a/dev-python/palettable/palettable-3.3.0.ebuild +++ /dev/null @@ -1,34 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 -PYTHON_COMPAT=( python3_{7..9} ) - -inherit distutils-r1 - -DESCRIPTION="library of color palettes for python" -HOMEPAGE="https://github.com/jiffyclub/palettable" - -if [ ${PV} == "9999" ] ; then - inherit git-r3 - EGIT_REPO_URI="https://github.com/jiffyclub/palettable.git" -else - SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - KEYWORDS="~amd64" -fi - -LICENSE="MIT" -SLOT="0" - -RDEPEND=" - ${PYTHON_DEPS} - dev-python/matplotlib[${PYTHON_USEDEP}] -" -DEPEND="${RDEPEND}" - -distutils_enable_tests pytest - -python_test() { - distutils_install_for_testing - pytest -vv || die "tests failed for ${EPYTHON}" -} diff --git a/dev-python/palettable/palettable-9999.ebuild b/dev-python/palettable/palettable-9999.ebuild deleted file mode 100644 index 1288d9233..000000000 --- a/dev-python/palettable/palettable-9999.ebuild +++ /dev/null @@ -1,34 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 -PYTHON_COMPAT=( python3_{7..9} ) - -inherit distutils-r1 - -DESCRIPTION="library of color palettes for python" -HOMEPAGE="https://github.com/jiffyclub/palettable" - -if [ ${PV} == "9999" ] ; then - inherit git-r3 - EGIT_REPO_URI="https://github.com/jiffyclub/palettable.git" -else - SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - KEYWORDS="~amd64" -fi - -LICENSE="MIT" -SLOT="0" - -RDEPEND=" - ${PYTHON_DEPS} - dev-python/matplotlib[${PYTHON_USEDEP}] -" -DEPEND="${RDEPEND}" - -distutils_enable_tests pytest - -python_test() { - distutils_install_for_testing - pytest -vv || die "tests failed for ${EPYTHON}" -} diff --git a/dev-python/pandas-stubs/Manifest b/dev-python/pandas-stubs/Manifest new file mode 100644 index 000000000..856ff2fe2 --- /dev/null +++ b/dev-python/pandas-stubs/Manifest @@ -0,0 +1 @@ +DIST pandas-stubs-2.1.1.230928.gh.tar.gz 192865 BLAKE2B f3604def27a3ba7444969473c5800f7cc72fd4487f2363f326de6d637f1b6b60d2a8707f6cbb2647389691fbd856a2e7e5cf3710c0ad014ae106472c76dfb1c8 SHA512 5f9e71f187d1532388a98e0139852098c00d44d3ddf32fc3bad1c5199291c7dd4af82b2d73605b1e16b09a79f3b9df02752b37cf87fcb222faee9e704f52dd47 diff --git a/dev-python/pandas-stubs/metadata.xml b/dev-python/pandas-stubs/metadata.xml new file mode 100644 index 000000000..8cbc804ad --- /dev/null +++ b/dev-python/pandas-stubs/metadata.xml @@ -0,0 +1,16 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>python@gentoo.org</email> + <name>Gentoo Python Project</name> + </maintainer> + <maintainer type="person"> + <email>gentoo@chymera.eu</email> + <name>Horea Christian</name> + </maintainer> + <upstream> + <remote-id type="github">pandas-dev/pandas-stubs</remote-id> + <remote-id type="pypi">pandas-stubs</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/pandas-stubs/pandas-stubs-2.1.1.230928.ebuild b/dev-python/pandas-stubs/pandas-stubs-2.1.1.230928.ebuild new file mode 100644 index 000000000..e10fd1aca --- /dev/null +++ b/dev-python/pandas-stubs/pandas-stubs-2.1.1.230928.ebuild @@ -0,0 +1,52 @@ +# Copyright 2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=poetry +PYTHON_COMPAT=( python3_{10..11} ) +inherit distutils-r1 + +DESCRIPTION="Public type stubs for pandas" +HOMEPAGE="https://github.com/pandas-dev/pandas-stubs" +SRC_URI="https://github.com/pandas-dev/pandas-stubs/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" +# Allegedly also needs dev-python/types-pytz (available in ::guru), but somehow works without it... +# https://github.com/pandas-dev/pandas-stubs/blob/3c2affdaeb1cb03777cc59832dcdd4b030add27d/pyproject.toml#L34 +RDEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] +" +BDEPEND=" + test? ( + dev-python/xarray[${PYTHON_USEDEP}] + dev-python/pyarrow[${PYTHON_USEDEP}] + ) +" + +EPYTEST_DESELECT=( + # Package has a bunch of test deps missing from ::gentoo and ::science + tests/test_frame.py::test_to_markdown + tests/test_frame.py::test_types_to_feather + tests/test_io.py::test_orc + tests/test_io.py::test_orc_path + tests/test_io.py::test_orc_buffer + tests/test_io.py::test_orc_columns + tests/test_io.py::test_orc_bytes + tests/test_io.py::test_hdf + tests/test_io.py::test_hdfstore + tests/test_io.py::test_read_hdf_iterator + tests/test_io.py::test_hdf_context_manager + tests/test_io.py::test_hdf_series + tests/test_io.py::test_spss + tests/test_io.py::test_parquet + tests/test_io.py::test_parquet_options + tests/test_io.py::test_excel_writer_engine + tests/test_io.py::test_all_read_without_lxml_dtype_backend + tests/test_series.py::test_types_agg + tests/test_series.py::test_types_aggregate +) + +distutils_enable_tests pytest diff --git a/dev-python/panel/Manifest b/dev-python/panel/Manifest index dacf388f1..459ed3f61 100644 --- a/dev-python/panel/Manifest +++ b/dev-python/panel/Manifest @@ -1 +1 @@ -DIST panel-0.11.0.tar.gz 9682808 BLAKE2B 2f953aaa9e791433d254219ad3cf9efdd486164e713f41a3539628a6c87f5b7b800ebd166537d021799ce74dddd3bc259343e6ec4161d0d87393864502215a00 SHA512 6fa2e04dd758583db851fa7d36592b7fb10ad2838b1f51fb53cb9ead4b5504a975ca040525f3f210ff0a67e8ce579195d980570b2d7616308cc126c61a9e9f59 +DIST panel-0.14.2.tar.gz 20352366 BLAKE2B 429a2da7e92cc1b0f3a42fc120eddc4a8a54e3805c1ca249aad7c243cef0092959e62a13b0f9c64c4765a6d2533b6519a90640e85d4d512a257df40fff1a4522 SHA512 c611e4bc592edeca5920441102cf7baea336016b9f90778c05fc61c57a4b8b48c80e16c182daa1763440be10c6a0ffabb80699bf6aaa96e03566b4ac55b56f4b diff --git a/dev-python/panel/files/panel-0.14.1-disable_lite_build.patch b/dev-python/panel/files/panel-0.14.1-disable_lite_build.patch new file mode 100644 index 000000000..387cfb61b --- /dev/null +++ b/dev-python/panel/files/panel-0.14.1-disable_lite_build.patch @@ -0,0 +1,47 @@ +Subject: Prevent Panel from violating network sandboxing. + + * By default, "setup.py" invokes "npm" to rebuild Node.js packages bundled with Panel. + * Without this patch we get `error: HTTPSConnectionPool` + * A `sed` fix of the `_build_paneljs()` line will break the syntax. + * Using the `PANEL_LITE_BUILD` variable might do the trick instead of a patch, but thus far it didn't +Author: Horea Christian <gentoo@chymera.eu> +diff --git a/setup.py b/setup.py +index d2541dfb..8cfbf933 100644 +--- a/setup.py ++++ b/setup.py +@@ -54,8 +54,6 @@ class CustomDevelopCommand(develop): + """Custom installation for development mode.""" + + def run(self): +- if not PANEL_LITE_BUILD: +- _build_paneljs() + develop.run(self) + + +@@ -63,8 +61,6 @@ class CustomInstallCommand(install): + """Custom installation for install mode.""" + + def run(self): +- if not PANEL_LITE_BUILD: +- _build_paneljs() + install.run(self) + + +@@ -72,8 +68,6 @@ class CustomSdistCommand(sdist): + """Custom installation for sdist mode.""" + + def run(self): +- if not PANEL_LITE_BUILD: +- _build_paneljs() + sdist.run(self) + + +@@ -92,8 +86,6 @@ try: + + def run(self): + """Do nothing so the command intentionally fails.""" +- if not PANEL_LITE_BUILD: +- _build_paneljs() + bdist_wheel.run(self) + + _COMMANDS['bdist_wheel'] = CustomBdistWheelCommand diff --git a/dev-python/panel/panel-0.11.0.ebuild b/dev-python/panel/panel-0.11.0.ebuild deleted file mode 100644 index 594377dcd..000000000 --- a/dev-python/panel/panel-0.11.0.ebuild +++ /dev/null @@ -1,61 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7..9} ) - -# Panel imports from "distutils" at runtime. -DISTUTILS_USE_SETUPTOOLS=rdepend - -inherit distutils-r1 - -DESCRIPTION="High-level app and dashboarding solution for Python" -HOMEPAGE="https://panel.holoviz.org" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -# "setup.py" imports from Bokeh to rebuild Node.js packages, but we patch that -# away below. Our patched Panel thus requires Bokeh only at runtime. -DEPEND=" - >=dev-python/param-1.10.0[${PYTHON_USEDEP}] - >=dev-python/pyct-0.4.4[${PYTHON_USEDEP}] -" -RDEPEND="${DEPEND} - dev-python/markdown[${PYTHON_USEDEP}] - dev-python/requests[${PYTHON_USEDEP}] - dev-python/tqdm[${PYTHON_USEDEP}] - >=dev-python/bokeh-2.3.0[${PYTHON_USEDEP}] - >=dev-python/pyviz_comms-0.7.4[${PYTHON_USEDEP}] - >=net-libs/nodejs-15.11.0 -" - -src_prepare() { - # Install Jupyter configuration files to "/etc" rather than "/usr/etc". - sed -i -e 's~"etc/jupyter~"/etc/jupyter~' setup.py || die - - # Prevent Panel from violating network sandboxing. By default, "setup.py" - # invokes "npm" to rebuild Node.js packages bundled with Panel when these - # packages were built by Panel developers with a different version of Bokeh - # than that installed on the local system. Since disabling this - # functionality invites backend and frontend complications, we encourage - # server administrators to manually perform this functionality below. - sed -i -e '/^\s*_build_paneljs()$/d' setup.py || die - - default_src_prepare -} - -pkg_postinst() { - panel_pkg_postinst() { - PANEL_DIR="$(${EPYTHON} -c 'import os, panel; print(os.path.dirname(panel.__file__))')" - elog "Node.js packages bundled with Panel under ${EPYTHON} may be" - elog "desynchronized from Bokeh and require manual rebuilding with:" - elog " sudo ${EPYTHON} -m panel build \"${PANEL_DIR}\"" - elog - } - - python_foreach_impl panel_pkg_postinst -} diff --git a/dev-python/panel/panel-0.14.2-r1.ebuild b/dev-python/panel/panel-0.14.2-r1.ebuild new file mode 100644 index 000000000..4674f8161 --- /dev/null +++ b/dev-python/panel/panel-0.14.2-r1.ebuild @@ -0,0 +1,63 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools +# Panel imports from "distutils" at runtime. +#DISTUTILS_USE_SETUPTOOLS=rdepend +inherit distutils-r1 pypi + +DESCRIPTION="High-level app and dashboarding solution for Python" +HOMEPAGE="https://panel.holoviz.org" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +# "setup.py" imports from Bokeh to rebuild Node.js packages, but we patch that +# away below. Our patched Panel thus requires Bokeh only at runtime. +DEPEND=" + >=dev-python/param-1.10.0[${PYTHON_USEDEP}] + >=dev-python/pyct-0.4.4[${PYTHON_USEDEP}] + dev-python/bleach[${PYTHON_USEDEP}] +" +RDEPEND="${DEPEND} + dev-python/markdown[${PYTHON_USEDEP}] + dev-python/requests[${PYTHON_USEDEP}] + dev-python/tqdm[${PYTHON_USEDEP}] + >=dev-python/bokeh-2.3.0[${PYTHON_USEDEP}] + >=dev-python/pyviz_comms-0.7.4[${PYTHON_USEDEP}] + >=net-libs/nodejs-15.11.0 +" + +PATCHES=( "${FILESDIR}/${PN}-0.14.1-disable_lite_build.patch" ) + +# This does not work, need to patch.. +#export PANEL_LITE_BUILD=1 + +src_prepare() { + # Install Jupyter configuration files to "/etc" rather than "/usr/etc". + sed -i -e 's~"etc/jupyter~"/etc/jupyter~' setup.py || die + + default_src_prepare +} + +# This also does not work, still need patch :( +#src_compile() { +# export PANEL_LITE_BUILD=1 +# distutils-r1_src_compile +#} + +pkg_postinst() { + panel_pkg_postinst() { + PANEL_DIR="$(${EPYTHON} -c 'import os, panel; print(os.path.dirname(panel.__file__))')" + elog "Node.js packages bundled with Panel under ${EPYTHON} may be" + elog "desynchronized from Bokeh and require manual rebuilding with:" + elog " sudo ${EPYTHON} -m panel build \"${PANEL_DIR}\"" + elog + } + + python_foreach_impl panel_pkg_postinst +} diff --git a/dev-python/param/Manifest b/dev-python/param/Manifest index bec3c8061..d26e110b2 100644 --- a/dev-python/param/Manifest +++ b/dev-python/param/Manifest @@ -1 +1,2 @@ -DIST param-1.10.1.tar.gz 74216 BLAKE2B 98486a386b31f400647fa3da3d280867935a0e5c493de4b31dccfa7c5650a3b55e2590e09cbf15097d700e54dbdd33fda12ead4489ed745977ec0065b27735da SHA512 8f4693651b1abd12126248e1508b0bed7796a1a4d33cd0ed05cc1e176d1216f9bc504f8637220a92585e7682f2d0ad2600a5b24427702536d4ef679971e9c4a7 +DIST param-1.10.1.gh.tar.gz 132562 BLAKE2B ec4f8f6fada02aa91049cc665efddc75ab289a4f86cbd8951d9720c8174b5236415df884e630ede57b76d01da62b477a5db50b97cb46d04d46e37503ec0410a0 SHA512 ca035325829bbb9fdcfadc8fabac8d5a690e38b0942d30d8963f14259f0dc8ebeeba84723904aae8804898f6ea6d5cfa97d2a1103db29f0d6d3355577abe8d14 +DIST param-1.12.3.gh.tar.gz 460593 BLAKE2B 45e004f4df4d70ceb3d5ff654e260d2fdb28cd47c904408ccda86233502464907bc2e709840b060189a81242f348d3cd6e3f021a157be67962365f93a0b08327 SHA512 c7181dfb7ccffaab7521744566d601470678dc35a2ecd9b55fc5adda73a7cd4998f583f4a7b5930a5c811913cd5a9f2152fbc270a541b749c32b0901985cead2 diff --git a/dev-python/param/param-1.10.1.ebuild b/dev-python/param/param-1.10.1.ebuild index 3be942fe3..8e8ec8053 100644 --- a/dev-python/param/param-1.10.1.ebuild +++ b/dev-python/param/param-1.10.1.ebuild @@ -1,16 +1,22 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7..9} pypy3 ) +PYTHON_COMPAT=( python3_{10..11} pypy3 ) +DISTUTILS_USE_PEP517=setuptools inherit distutils-r1 DESCRIPTION="Make Python code clearer and more reliable by declaring Parameters" HOMEPAGE="https://param.holoviz.org" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" +# Pypi sources do not include tests +#SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" +SRC_URI="https://github.com/holoviz/param/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz" LICENSE="BSD" KEYWORDS="~amd64 ~x86" SLOT="0" + +# Some tests require nose: +#distutils_enable_tests unittest diff --git a/dev-python/param/param-1.12.3.ebuild b/dev-python/param/param-1.12.3.ebuild new file mode 100644 index 000000000..9ce9e3762 --- /dev/null +++ b/dev-python/param/param-1.12.3.ebuild @@ -0,0 +1,22 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} pypy3 ) +DISTUTILS_USE_PEP517=setuptools + +inherit distutils-r1 + +DESCRIPTION="Make Python code clearer and more reliable by declaring Parameters" +HOMEPAGE="https://param.holoviz.org" +# Pypi sources do not include tests, reported upstream: +# https://github.com/holoviz/param/issues/678 +#SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" +SRC_URI="https://github.com/holoviz/param/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="BSD" +KEYWORDS="~amd64 ~x86" +SLOT="0" + +distutils_enable_tests pytest diff --git a/dev-python/persim/Manifest b/dev-python/persim/Manifest index 44487ab15..b45fc4da3 100644 --- a/dev-python/persim/Manifest +++ b/dev-python/persim/Manifest @@ -1,4 +1 @@ -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/metadata.xml b/dev-python/persim/metadata.xml index 2f2c0b51c..ea34f9f89 100644 --- a/dev-python/persim/metadata.xml +++ b/dev-python/persim/metadata.xml @@ -9,4 +9,7 @@ <email>sci@gentoo.org</email> <name>Gentoo Science Project</name> </maintainer> + <upstream> + <remote-id type="pypi">persim</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/persim/persim-0.1.3.ebuild b/dev-python/persim/persim-0.1.3.ebuild deleted file mode 100644 index 722ae4d39..000000000 --- a/dev-python/persim/persim-0.1.3.ebuild +++ /dev/null @@ -1,26 +0,0 @@ -# Copyright 1999-2020 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/numpy[${PYTHON_USEDEP}] - dev-python/plotly[${PYTHON_USEDEP}] - dev-python/scipy[${PYTHON_USEDEP}] - sci-libs/scikit-learn[${PYTHON_USEDEP}] -" - -distutils_enable_tests pytest diff --git a/dev-python/persim/persim-0.2.0.ebuild b/dev-python/persim/persim-0.2.0.ebuild deleted file mode 100644 index 8ca453bf9..000000000 --- a/dev-python/persim/persim-0.2.0.ebuild +++ /dev/null @@ -1,26 +0,0 @@ -# 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[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/plotly[${PYTHON_USEDEP}] - dev-python/scipy[${PYTHON_USEDEP}] - sci-libs/scikit-learn[${PYTHON_USEDEP}] -" - -distutils_enable_tests pytest diff --git a/dev-python/persim/persim-0.3.0.ebuild b/dev-python/persim/persim-0.3.0.ebuild deleted file mode 100644 index 6e1d989aa..000000000 --- a/dev-python/persim/persim-0.3.0.ebuild +++ /dev/null @@ -1,28 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7..9} ) - -inherit distutils-r1 - -DESCRIPTION="Distances and representations of persistence diagrams" -HOMEPAGE="https://persim.scikit-tda.org/" -SRC_URI="mirror://pypi/${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 index 6e1d989aa..994dca206 100644 --- a/dev-python/persim/persim-0.3.1.ebuild +++ b/dev-python/persim/persim-0.3.1.ebuild @@ -1,21 +1,21 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7..9} ) +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools -inherit distutils-r1 +inherit distutils-r1 pypi DESCRIPTION="Distances and representations of persistence diagrams" HOMEPAGE="https://persim.scikit-tda.org/" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" LICENSE="MIT" SLOT="0" -KEYWORDS="~amd64 ~x86" +KEYWORDS="~amd64" -RDEPEND="${PYTHON_DEPS} +RDEPEND=" dev-python/hopcroftkarp[${PYTHON_USEDEP}] dev-python/matplotlib[${PYTHON_USEDEP}] dev-python/numpy[${PYTHON_USEDEP}] @@ -26,3 +26,21 @@ RDEPEND="${PYTHON_DEPS} BDEPEND="test? ( dev-python/deprecated[${PYTHON_USEDEP}] )" distutils_enable_tests pytest + +EPYTEST_DESELECT=( + # Reported upsream: + # https://github.com/scikit-tda/persim/issues/66 + test/test_landscapes.py::TestPersLandscapeExact::test_exact_critical_pairs + test/test_persim.py::test_integer_diagrams + test/test_persim.py::TestEmpty::test_empyt_diagram_list + test/test_persim.py::TestTransforms::test_lists_of_lists + test/test_persim.py::TestTransforms::test_n_pixels + test/test_persim.py::TestTransforms::test_multiple_diagrams + test/test_persistence_imager.py::test_empty_diagram_list + test/test_persistence_imager.py::test_fit_diagram + test/test_persistence_imager.py::test_fit_diagram_list + test/test_persistence_imager.py::test_mixed_pairs + test/test_persistence_imager.py::TestTransformOutput::test_lists_of_lists + test/test_persistence_imager.py::TestTransformOutput::test_n_pixels + test/test_persistence_imager.py::TestTransformOutput::test_multiple_diagrams +) diff --git a/dev-python/photutils/Manifest b/dev-python/photutils/Manifest index bbd7ab4a7..00cdad6e8 100644 --- a/dev-python/photutils/Manifest +++ b/dev-python/photutils/Manifest @@ -1 +1 @@ -DIST photutils-1.0.1.tar.gz 995604 BLAKE2B 552e66cfb20db193da97da570dfd6116eb6674b38c1510393c35e6929a7b9717ee75ecf06cfe874a628b6e096a57bd68ebc79a3f52c5ef94ef384e03e2543784 SHA512 3abcace35fde3b8c4de99c56afe813db50bde87bf1aeda65b1b37edf7c9409420f3aa62bd6b98ae4f381542c1fd3aff100b19220f6a7210f2a0c06f8a039f1b5 +DIST photutils-1.6.0.tar.gz 1062334 BLAKE2B dd694299ab52e561f3ba419bd3f2329d73017cefd2ab84dcd278dd93b290fb45457ccc6b9bd0cac769f0bce9a4e3ddd15c097a8345fc5a63af52b5c9aa577f4c SHA512 6d7e20f032f7417cedaaf29692b790a597b1a0e8a2d4e25605c2e598e6908de7e1a76e075f02cb1f281df586d9e6d45d0d61bc16eb3996c41568c9d1478725ed diff --git a/dev-python/photutils/metadata.xml b/dev-python/photutils/metadata.xml index 5c3d380b2..8069e65c7 100644 --- a/dev-python/photutils/metadata.xml +++ b/dev-python/photutils/metadata.xml @@ -12,5 +12,6 @@ centroid and shape parameters, and performing photometry. </longdescription> <upstream> <remote-id type="github">astropy/photutils</remote-id> + <remote-id type="pypi">photutils</remote-id> </upstream> </pkgmetadata> diff --git a/dev-python/photutils/photutils-1.0.1.ebuild b/dev-python/photutils/photutils-1.0.1.ebuild deleted file mode 100644 index ac34ff93a..000000000 --- a/dev-python/photutils/photutils-1.0.1.ebuild +++ /dev/null @@ -1,40 +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="Affiliated package for image photometry utilities" -HOMEPAGE="https://github.com/astropy/photutils" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -#TODO: Package all these pytest deps: -# pytest-doctestplus>=0.2.0 -# pytest-remotedata>=0.3.1 -# pytest-openfiles>=0.3.1 -# pytest-astropy-header>=0.1.2 -# pytest-arraydiff>=0.1 -# pytest-filter-subpackage>=0.1 -RESTRICT="test" - -RDEPEND=" - >=dev-python/astropy-0.4[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] -" - -distutils_enable_tests pytest -# TODO: Fix this -# NameError: name 'disabled_intersphinx_mapping' is not defined -#distutils_enable_sphinx docs \ -# dev-python/sphinx-astropy \ -# dev-python/scipy \ -# dev-python/matplotlib \ -# sci-libs/scikit-learn \ -# sci-libs/scikit-image \ diff --git a/dev-python/photutils/photutils-1.6.0.ebuild b/dev-python/photutils/photutils-1.6.0.ebuild new file mode 100644 index 000000000..a1fa5f2d2 --- /dev/null +++ b/dev-python/photutils/photutils-1.6.0.ebuild @@ -0,0 +1,40 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools + +inherit distutils-r1 pypi + +DESCRIPTION="Affiliated package for image photometry utilities" +HOMEPAGE="https://github.com/astropy/photutils" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +#TODO: Package all these pytest deps: +# pytest-doctestplus>=0.2.0 +# pytest-remotedata>=0.3.1 +# pytest-openfiles>=0.3.1 +# pytest-astropy-header>=0.1.2 +# pytest-arraydiff>=0.1 +# pytest-filter-subpackage>=0.1 +RESTRICT="test" + +RDEPEND=" + >=dev-python/astropy-0.4[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] +" + +distutils_enable_tests pytest +# TODO: Fix this +# NameError: name 'disabled_intersphinx_mapping' is not defined +#distutils_enable_sphinx docs \ +# dev-python/sphinx-astropy \ +# dev-python/scipy \ +# dev-python/matplotlib \ +# sci-libs/scikit-learn \ +# dev-python/scikit-image \ diff --git a/dev-python/plac/Manifest b/dev-python/plac/Manifest new file mode 100644 index 000000000..f50e462dc --- /dev/null +++ b/dev-python/plac/Manifest @@ -0,0 +1 @@ +DIST plac-1.4.2.tar.gz 37595 BLAKE2B 5205e9d8a5a775eb2e23ea7ad30e576417a8ba944cb196ccb7a16b514b6c4902856a7191b1bbf71ab0176910b5d8dc163ab36fe3fb0c5bb5765c02d16ae347b1 SHA512 c8c320cabda42f33071d7675b64befab8344bde746d0befe661a9bb26f658559435d2895dad0a27dc1d7c2dc59f07a359b529880e115d900b4fca8f245186742 diff --git a/dev-python/plac/metadata.xml b/dev-python/plac/metadata.xml new file mode 100644 index 000000000..98f0f918b --- /dev/null +++ b/dev-python/plac/metadata.xml @@ -0,0 +1,16 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>mschu.dev@gmail.com</email> + <name>Michael Schubert</name> + </maintainer> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <upstream> + <remote-id type="github">ialbert/plac</remote-id> + <remote-id type="pypi">plac</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/plac/plac-1.4.2.ebuild b/dev-python/plac/plac-1.4.2.ebuild new file mode 100644 index 000000000..50b269f42 --- /dev/null +++ b/dev-python/plac/plac-1.4.2.ebuild @@ -0,0 +1,23 @@ +# Copyright 1999-2018 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( pypy3 python3_{10..12} ) + +inherit pypi distutils-r1 + +DESCRIPTION="Parsing the Command Line the Easy Way" +HOMEPAGE="https://pypi.org/project/plac/" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" + +EPYTEST_DESELECT=( + # Missing index.rst + doc/test_plac.py::test_doctest +) + +distutils_enable_tests pytest diff --git a/dev-python/probeinterface/Manifest b/dev-python/probeinterface/Manifest new file mode 100644 index 000000000..189bbfcaf --- /dev/null +++ b/dev-python/probeinterface/Manifest @@ -0,0 +1,3 @@ +DIST probeinterface-0.2.14.gh.tar.gz 210232 BLAKE2B 5a2c4fb5bc0f1315777a70b4292a30b135022e3a70608584070088c5ff42b0e1474714472a306196b390e103b45eea70cb89e01cc5dca90b0c31ac4f44810c24 SHA512 e0f5cf5b6560f8c4e578cab708308c36ecf81446c0db684b520e1436e864f2f4e0dce0015461c7cfcba19a0c1c54345b2d55b972de5f4338b02b90731cff52c2 +DIST probeinterface-0.2.16.gh.tar.gz 302386 BLAKE2B e2124774f2f50779f1dc67b682085d87691c935909ab81591f005abd756c0925837b97e97bf651e2a84e2276f57bf6fd1df6de6289431b16227dc9caa6cea51c SHA512 7c38534dbcab837df1289074db054e31c0768bceefafeb6d70051f88a6ac289d664d77cd6c456f40e7c52a7b60a09e80a4a4fe5e8f491121157b0bbb4d5c1f84 +DIST probeinterface-0.2.20.gh.tar.gz 1930434 BLAKE2B 0087f82f8cea3e1eb225ba188487eb3862de8444cadb0cf76ebba1046f194eb1f369bab7b3ff35eb6b99c054409b902c1907037d42aa84d0d4253a47fa6009ce SHA512 16cee1845d4cd40f1bfdea654fff99ea5949fbd8606ffc038ea0ca27d6a4f3faa65e2dd448bcda1066c0d2984ce7e3995a0ead028ef57ae59743c34c6c5a4c39 diff --git a/dev-python/probeinterface/metadata.xml b/dev-python/probeinterface/metadata.xml new file mode 100644 index 000000000..58f800ce0 --- /dev/null +++ b/dev-python/probeinterface/metadata.xml @@ -0,0 +1,15 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>gentoo@chymera.eu</email> + <name>Horea Christian</name> + </maintainer> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <upstream> + <remote-id type="github">SpikeInterface/probeinterface</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/probeinterface/probeinterface-0.2.14.ebuild b/dev-python/probeinterface/probeinterface-0.2.14.ebuild new file mode 100644 index 000000000..75dd43bd4 --- /dev/null +++ b/dev-python/probeinterface/probeinterface-0.2.14.ebuild @@ -0,0 +1,37 @@ +# Copyright 2021-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) +inherit distutils-r1 + +DESCRIPTION="Python package to handle probe layout, geometry and wiring to device" +HOMEPAGE="https://github.com/SpikeInterface/probeinterface" +SRC_URI="https://github.com/SpikeInterface/probeinterface/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz" +# upstream doesn't pus test dir to pypi, https://github.com/SpikeInterface/probeinterface/issues/145 +#SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]" +BDEPEND=" + test? ( + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + ) +" + +EPYTEST_DESELECT=( + # Requires network access: + # https://github.com/SpikeInterface/probeinterface/issues/70 + tests/test_library.py::test_download_probeinterface_file + tests/test_library.py::test_get_from_cache + tests/test_library.py::test_get_probe + tests/test_wiring.py::test_wire_probe +) +distutils_enable_tests pytest diff --git a/dev-python/probeinterface/probeinterface-0.2.16.ebuild b/dev-python/probeinterface/probeinterface-0.2.16.ebuild new file mode 100644 index 000000000..75dd43bd4 --- /dev/null +++ b/dev-python/probeinterface/probeinterface-0.2.16.ebuild @@ -0,0 +1,37 @@ +# Copyright 2021-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) +inherit distutils-r1 + +DESCRIPTION="Python package to handle probe layout, geometry and wiring to device" +HOMEPAGE="https://github.com/SpikeInterface/probeinterface" +SRC_URI="https://github.com/SpikeInterface/probeinterface/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz" +# upstream doesn't pus test dir to pypi, https://github.com/SpikeInterface/probeinterface/issues/145 +#SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]" +BDEPEND=" + test? ( + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + ) +" + +EPYTEST_DESELECT=( + # Requires network access: + # https://github.com/SpikeInterface/probeinterface/issues/70 + tests/test_library.py::test_download_probeinterface_file + tests/test_library.py::test_get_from_cache + tests/test_library.py::test_get_probe + tests/test_wiring.py::test_wire_probe +) +distutils_enable_tests pytest diff --git a/dev-python/probeinterface/probeinterface-0.2.20.ebuild b/dev-python/probeinterface/probeinterface-0.2.20.ebuild new file mode 100644 index 000000000..75dd43bd4 --- /dev/null +++ b/dev-python/probeinterface/probeinterface-0.2.20.ebuild @@ -0,0 +1,37 @@ +# Copyright 2021-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) +inherit distutils-r1 + +DESCRIPTION="Python package to handle probe layout, geometry and wiring to device" +HOMEPAGE="https://github.com/SpikeInterface/probeinterface" +SRC_URI="https://github.com/SpikeInterface/probeinterface/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz" +# upstream doesn't pus test dir to pypi, https://github.com/SpikeInterface/probeinterface/issues/145 +#SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]" +BDEPEND=" + test? ( + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + ) +" + +EPYTEST_DESELECT=( + # Requires network access: + # https://github.com/SpikeInterface/probeinterface/issues/70 + tests/test_library.py::test_download_probeinterface_file + tests/test_library.py::test_get_from_cache + tests/test_library.py::test_get_probe + tests/test_wiring.py::test_wire_probe +) +distutils_enable_tests pytest diff --git a/dev-python/py2bit/Manifest b/dev-python/py2bit/Manifest index 4b58d5605..afd79913c 100644 --- a/dev-python/py2bit/Manifest +++ b/dev-python/py2bit/Manifest @@ -1 +1,2 @@ DIST py2bit-0.3.0.tar.gz 16059 BLAKE2B b66621b91db8c0370933d1531c25e3e9d2cf34cc453e085f5acf92175f16bc4a87368d5b97f4ad1f6b0aeb715ac91e02f752f27d660e733cbcf9788f7fb9ff0b SHA512 914ee4490605a005c5c83e914e5d469dcb860a76cf52dd2337086954d9a37f21addca7a581eb8ff612b77f7969334057de4ab5d5ce2c6e15fb88e56abd36e193 +DIST py2bit-0.3.1.tar.gz 16771 BLAKE2B 044f6c638bc001694a5ee1c0924bebfeccd26616dbeb7f7a692df71dde6937851227d8a4263c9f0c4e44a34d53900340bdf95818aa2c9c699d26b36a75e64158 SHA512 e9cb16e6f617f5f9c4a324abc949562da8aa0b4792e7011148103462ec49f3f38ab29a2c1821a374ec99726c292de2888de506966510a10211ee24295e9f775c diff --git a/dev-python/py2bit/py2bit-0.3.0.ebuild b/dev-python/py2bit/py2bit-0.3.0.ebuild index 7c6c27ef2..4b1c29658 100644 --- a/dev-python/py2bit/py2bit-0.3.0.ebuild +++ b/dev-python/py2bit/py2bit-0.3.0.ebuild @@ -1,9 +1,10 @@ -# Copyright 1999-2020 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7..9} ) +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools inherit distutils-r1 @@ -23,3 +24,9 @@ SLOT="0" DEPEND="sci-libs/lib2bit" RDEPEND="${DEPEND}" + +distutils_enable_tests pytest + +python_test() { + epytest "py2bitTest/test.py" +} diff --git a/dev-python/py2bit/py2bit-0.3.1.ebuild b/dev-python/py2bit/py2bit-0.3.1.ebuild new file mode 100644 index 000000000..4b1c29658 --- /dev/null +++ b/dev-python/py2bit/py2bit-0.3.1.ebuild @@ -0,0 +1,32 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools + +inherit distutils-r1 + +DESCRIPTION="Python library for accessing 2bit files" +HOMEPAGE="https://github.com/dpryan79/py2bit" + +if [[ ${PV} == 9999 ]] ; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/dpryan79/py2bit" +else + SRC_URI="https://github.com/dpryan79/py2bit/archive/${PV}.tar.gz -> ${P}.tar.gz" + KEYWORDS="~amd64 ~x86" +fi + +LICENSE="MIT" +SLOT="0" + +DEPEND="sci-libs/lib2bit" +RDEPEND="${DEPEND}" + +distutils_enable_tests pytest + +python_test() { + epytest "py2bitTest/test.py" +} diff --git a/dev-python/py2bit/py2bit-9999.ebuild b/dev-python/py2bit/py2bit-9999.ebuild index 7c6c27ef2..4b1c29658 100644 --- a/dev-python/py2bit/py2bit-9999.ebuild +++ b/dev-python/py2bit/py2bit-9999.ebuild @@ -1,9 +1,10 @@ -# Copyright 1999-2020 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7..9} ) +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools inherit distutils-r1 @@ -23,3 +24,9 @@ SLOT="0" DEPEND="sci-libs/lib2bit" RDEPEND="${DEPEND}" + +distutils_enable_tests pytest + +python_test() { + epytest "py2bitTest/test.py" +} diff --git a/dev-python/pyBigWig/Manifest b/dev-python/pyBigWig/Manifest index 96d66a343..b27a43a9b 100644 --- a/dev-python/pyBigWig/Manifest +++ b/dev-python/pyBigWig/Manifest @@ -1 +1,2 @@ DIST pyBigWig-0.3.17.tar.gz 65490 BLAKE2B 5ae3ad5792357ae36082022aa34548fb7ad105909eccc27305064f8f948714f462e1d239c3af7f9b75b84f5658bcb03231d7d1d3b0ebc8025c96d2e7835f1bfb SHA512 b52fec3a85984708660dd454f5569900a5cce7804d02e719bddbdc7ed2f9f4ab1131e55b0a01ae977b18bb0bbd079e13ec887d5df108d8abfebdd04ad56e503f +DIST pyBigWig-0.3.18.tar.gz 66478 BLAKE2B 0d2e20bed5f59fb8c79026f453c4d5c3e4f9b663e96614b3ef8cbb939357c8895edfa92184da018efdd40e14bbf357f13cc32f898d9cf89419382e7be89b01c8 SHA512 e782f059a8c47043498b2c4b1c0b63f3a1863d03f641c469995536bded220714c61fe0a2f1dbe5841152fe54d0d43b544e14ec4999447d4d808e01b452fa5e88 diff --git a/dev-python/pyBigWig/pyBigWig-0.3.17.ebuild b/dev-python/pyBigWig/pyBigWig-0.3.17.ebuild index eaa5d5375..acaca2306 100644 --- a/dev-python/pyBigWig/pyBigWig-0.3.17.ebuild +++ b/dev-python/pyBigWig/pyBigWig-0.3.17.ebuild @@ -1,9 +1,10 @@ -# Copyright 1999-2020 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7..9} ) +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools inherit distutils-r1 DESCRIPTION="quick access to and creation of bigWig files" diff --git a/dev-python/pyBigWig/pyBigWig-0.3.18.ebuild b/dev-python/pyBigWig/pyBigWig-0.3.18.ebuild new file mode 100644 index 000000000..acaca2306 --- /dev/null +++ b/dev-python/pyBigWig/pyBigWig-0.3.18.ebuild @@ -0,0 +1,25 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 + +DESCRIPTION="quick access to and creation of bigWig files" +HOMEPAGE="https://github.com/dpryan79/pyBigWig" + +if [[ ${PV} == 9999 ]] ; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/dpryan79/pyBigWig" +else + SRC_URI="https://github.com/dpryan79/pyBigWig/archive/${PV}.tar.gz -> ${P}.tar.gz" + KEYWORDS="~amd64 ~x86" +fi + +LICENSE="MIT" +SLOT="0" + +DEPEND="sci-biology/libBigWig" +RDEPEND="${DEPEND}" diff --git a/dev-python/pyBigWig/pyBigWig-9999.ebuild b/dev-python/pyBigWig/pyBigWig-9999.ebuild index eaa5d5375..acaca2306 100644 --- a/dev-python/pyBigWig/pyBigWig-9999.ebuild +++ b/dev-python/pyBigWig/pyBigWig-9999.ebuild @@ -1,9 +1,10 @@ -# Copyright 1999-2020 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7..9} ) +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools inherit distutils-r1 DESCRIPTION="quick access to and creation of bigWig files" diff --git a/dev-python/pyaml-env/Manifest b/dev-python/pyaml-env/Manifest new file mode 100644 index 000000000..06b54d70e --- /dev/null +++ b/dev-python/pyaml-env/Manifest @@ -0,0 +1 @@ +DIST pyaml_env-1.2.1.tar.gz 12759 BLAKE2B 5a037ccefaaa3c60ce393dae5847777eb43745549a31b763ef2f50feb3a6e216ef793f9501df9e80cb381f78782e54b888ee4b043736dc05bcd01619d839ff86 SHA512 1ef873fa66660e4949dc1064260405244c8b3a2ee4391831a0a52be30e503e99d0b80b087c78db78683e9fe2fc1fd73f2e30c1eacc4c94a1394000d8526c9d68 diff --git a/dev-python/pyaml-env/metadata.xml b/dev-python/pyaml-env/metadata.xml new file mode 100644 index 000000000..44769bf23 --- /dev/null +++ b/dev-python/pyaml-env/metadata.xml @@ -0,0 +1,12 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>mschu.dev@gmail.com</email> + <name>Michael Schubert</name> + </maintainer> + <upstream> + <remote-id type="github">mkaranasou/pyaml_env</remote-id> + <remote-id type="pypi">pyaml-env</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/pyaml-env/pyaml-env-1.2.1.ebuild b/dev-python/pyaml-env/pyaml-env-1.2.1.ebuild new file mode 100644 index 000000000..a5169040a --- /dev/null +++ b/dev-python/pyaml-env/pyaml-env-1.2.1.ebuild @@ -0,0 +1,22 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..12} ) + +inherit pypi distutils-r1 + +DESCRIPTION="Parse YAML configuration with environment variables in Python" +HOMEPAGE="https://pypi.org/project/pyaml-env/" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~amd64-linux" + +RDEPEND="dev-python/pyyaml[${PYTHON_USEDEP}]" + +# tests not included in pypi tarball +RESTRICT="test" +#distutils_enable_tests pytest diff --git a/dev-python/pybind11-stubgen/Manifest b/dev-python/pybind11-stubgen/Manifest index 783143fe7..7b5f755b5 100644 --- a/dev-python/pybind11-stubgen/Manifest +++ b/dev-python/pybind11-stubgen/Manifest @@ -1,3 +1 @@ DIST pybind11-stubgen-0.10.4.tar.gz 12605 BLAKE2B 5cb3e4301a896066ac26a7e6b9af83c77fb16fd5a3e48713a597e981a68e41cd90ddf0e351c177b7385966e8720100ef03b0524dfd381f17c87a2016a6eba808 SHA512 b43795c5fef6eee5198ec7590338f8a2dabbc4a2530de49f50a3b1a410da60188da86f7148a74ff014068c8d9ce5b058695902e236407ab221d640ac9b15903d -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/metadata.xml b/dev-python/pybind11-stubgen/metadata.xml index 2f2c0b51c..ad7b36abc 100644 --- a/dev-python/pybind11-stubgen/metadata.xml +++ b/dev-python/pybind11-stubgen/metadata.xml @@ -9,4 +9,8 @@ <email>sci@gentoo.org</email> <name>Gentoo Science Project</name> </maintainer> + <upstream> + <remote-id type="github">sizmailov/pybind11-stubgen</remote-id> + <remote-id type="pypi">pybind11-stubgen</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/pybind11-stubgen/pybind11-stubgen-0.10.4.ebuild b/dev-python/pybind11-stubgen/pybind11-stubgen-0.10.4.ebuild index f73f2dd4b..e1aaab3b6 100644 --- a/dev-python/pybind11-stubgen/pybind11-stubgen-0.10.4.ebuild +++ b/dev-python/pybind11-stubgen/pybind11-stubgen-0.10.4.ebuild @@ -3,12 +3,12 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) -inherit distutils-r1 +PYTHON_COMPAT=( python3_{10..11} ) +PYPI_NO_NORMALIZE=1 +inherit distutils-r1 pypi 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" diff --git a/dev-python/pybind11-stubgen/pybind11-stubgen-0.8.6.ebuild b/dev-python/pybind11-stubgen/pybind11-stubgen-0.8.6.ebuild deleted file mode 100644 index 9451a6082..000000000 --- a/dev-python/pybind11-stubgen/pybind11-stubgen-0.8.6.ebuild +++ /dev/null @@ -1,24 +0,0 @@ -# Copyright 1999-2020 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="${DEPEND}" - -# no tests in package diff --git a/dev-python/pybind11-stubgen/pybind11-stubgen-0.8.7.ebuild b/dev-python/pybind11-stubgen/pybind11-stubgen-0.8.7.ebuild deleted file mode 100644 index 3f2b0f779..000000000 --- a/dev-python/pybind11-stubgen/pybind11-stubgen-0.8.7.ebuild +++ /dev/null @@ -1,24 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7..9} ) -DISTUTILS_USE_SETUPTOOLS=rdepend -inherit distutils-r1 - -DESCRIPTION="PEP 561 type stubs generator for pybind11 modules" -HOMEPAGE="https://github.com/sizmailov/pybind11-stubgen" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -DEPEND=" - ${PYTHON_DEPS} - dev-python/pybind11[${PYTHON_USEDEP}] -" -RDEPEND="${DEPEND}" - -# no tests in package diff --git a/dev-python/pyct/pyct-0.4.8.ebuild b/dev-python/pyct/pyct-0.4.8.ebuild index f40dc6d49..d8ef9bfa2 100644 --- a/dev-python/pyct/pyct-0.4.8.ebuild +++ b/dev-python/pyct/pyct-0.4.8.ebuild @@ -1,18 +1,15 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 - -PYTHON_COMPAT=( python3_{7..9} pypy3 ) +EAPI=8 +PYTHON_COMPAT=( python3_{10..11} pypy3 ) # HoloViews imports from "distutils" at runtime. DISTUTILS_USE_SETUPTOOLS=rdepend - -inherit distutils-r1 +inherit distutils-r1 pypi DESCRIPTION="Python packaging Common Tasks" HOMEPAGE="https://holoviz.org" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" LICENSE="BSD" SLOT="0" diff --git a/dev-python/pyerfa/metadata.xml b/dev-python/pyerfa/metadata.xml index 4f4367037..5615e25d7 100644 --- a/dev-python/pyerfa/metadata.xml +++ b/dev-python/pyerfa/metadata.xml @@ -5,4 +5,8 @@ <email>sci-astronomy@gentoo.org</email> <name>Gentoo Astronomy Project</name> </maintainer> + <upstream> + <remote-id type="github">liberfa/pyerfa</remote-id> + <remote-id type="pypi">pyerfa</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/pyerfa/pyerfa-2.0.0.1-r2.ebuild b/dev-python/pyerfa/pyerfa-2.0.0.1-r2.ebuild new file mode 100644 index 000000000..11a68c169 --- /dev/null +++ b/dev-python/pyerfa/pyerfa-2.0.0.1-r2.ebuild @@ -0,0 +1,33 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools + +inherit distutils-r1 pypi + +DESCRIPTION="Python bindings for ERFA" +HOMEPAGE="https://github.com/liberfa/pyerfa/" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +# ImportError: cannot import name 'ufunc' from 'erfa' +RESTRICT="test" + +RDEPEND=" + sci-astronomy/erfa:0= + >=dev-python/numpy-1.17[${PYTHON_USEDEP}] +" +DEPEND="${RDEPEND}" +BDEPEND=" + dev-python/setuptools-scm[${PYTHON_USEDEP}] + test? ( + dev-python/pytest-doctestplus[${PYTHON_USEDEP}] + )" + +distutils_enable_tests pytest +#distutils_enable_sphinx docs dev-python/sphinx-astropy diff --git a/dev-python/pyerfa/pyerfa-2.0.0.1.ebuild b/dev-python/pyerfa/pyerfa-2.0.0.1.ebuild deleted file mode 100644 index 2e5bdf3e0..000000000 --- a/dev-python/pyerfa/pyerfa-2.0.0.1.ebuild +++ /dev/null @@ -1,32 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{8..10} ) - -inherit distutils-r1 - -DESCRIPTION="Python bindings for ERFA" -HOMEPAGE="https://github.com/liberfa/pyerfa/" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -# ImportError: cannot import name 'ufunc' from 'erfa' -#RESTRICT="test" - -RDEPEND=" - sci-astronomy/erfa:0= - >=dev-python/numpy-1.17[${PYTHON_USEDEP}] -" -BDEPEND="${RDEPEND} - dev-python/setuptools_scm[${PYTHON_USEDEP}] - test? ( - dev-python/pytest-doctestplus[${PYTHON_USEDEP}] - )" - -distutils_enable_tests pytest -distutils_enable_sphinx docs dev-python/sphinx-astropy diff --git a/dev-python/pynndescent/Manifest b/dev-python/pynndescent/Manifest deleted file mode 100644 index a92be64b7..000000000 --- a/dev-python/pynndescent/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST pynndescent-0.5.6.tar.gz 1135907 BLAKE2B 53f09045b14b3026ff1a2fa1ed27a4ce75f23e9c25ca0469c5ce207a51a25c778a7c2d3af51c3a724e1c0cd4eb148b3a8e73b6d39e819fc9c4cb0549240623be SHA512 9556754d4edbdfe442abf6b95b1970b8c606616a0012fc7a6875e1dfbe9a98b21b317eee84836c2b521dffb0db4e19ba6c8f1f9009498d43153ffda0f0a3b820 diff --git a/dev-python/pynndescent/metadata.xml b/dev-python/pynndescent/metadata.xml deleted file mode 100644 index 2f2c0b51c..000000000 --- a/dev-python/pynndescent/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>gentoo@aisha.cc</email> - <name>Aisha Tammy</name> - </maintainer> - <maintainer type="project"> - <email>sci@gentoo.org</email> - <name>Gentoo Science Project</name> - </maintainer> -</pkgmetadata> diff --git a/dev-python/pynndescent/pynndescent-0.5.6.ebuild b/dev-python/pynndescent/pynndescent-0.5.6.ebuild deleted file mode 100644 index 1e9eb00e4..000000000 --- a/dev-python/pynndescent/pynndescent-0.5.6.ebuild +++ /dev/null @@ -1,28 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{8..10} ) - -inherit distutils-r1 - -DESCRIPTION="nearest neighbor descent for approximate nearest neighbors" -HOMEPAGE="https://github.com/lmcinnes/pynndescent" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -RDEPEND=" - dev-python/joblib[${PYTHON_USEDEP}] - >=dev-python/numba-0.51.2[${PYTHON_USEDEP}] - >=dev-python/numpy-1.17[${PYTHON_USEDEP}] - >=dev-python/llvmlite-0.34[${PYTHON_USEDEP}] - >=dev-python/scipy-1.0[${PYTHON_USEDEP}] - >=sci-libs/scikit-learn-0.18.0[${PYTHON_USEDEP}] -" -DEPEND="${RDEPEND}" - -distutils_enable_tests pytest diff --git a/dev-python/pynrrd/Manifest b/dev-python/pynrrd/Manifest index b9c8e53d7..e174359e3 100644 --- a/dev-python/pynrrd/Manifest +++ b/dev-python/pynrrd/Manifest @@ -1 +1,3 @@ DIST pynrrd-0.4.2.tar.gz 43129 BLAKE2B 2001d151e38bbd02a648759475af13dd1be4bb7c12b7f8a3c7294e7fe1c281aeb9b35e39cce8254088b1c2f766aabe7343be0da4d48208375bb21be6dce9ba61 SHA512 8c5e4c1cb89dc84be3cf06e40d3f5bd45ea355c4e103027a62b088c4a73b03d1032cea1de0b153ef13fefd9b06d5a9b1954456a4542ae27cb74a278835b759ca +DIST pynrrd-0.4.3.tar.gz 43162 BLAKE2B 266c57029e48e923dd5371184f59471e069890668ac15a75cfafc178cfe1a718f33bc6bcc704172e0fca0bdc9c52091da79e404b6bfb85838eef0c3e0807409c SHA512 d6264fce3b270e5ae9d889e7d58a18ae7bf3fecf5a1fe168dc584dece2052efd32170b21a02fa630c35e0e45e7109c745069710169ec38819639a4585344e0f6 +DIST pynrrd-1.0.0.tar.gz 45061 BLAKE2B c08bcd70c3565cd690b228793651e57e08d2095a72b7f7102e6274f1518873acb1ee5645302fbb68b7cf1afafe3c5c734a33e561eea1caaacb5434c049dcc325 SHA512 c622812a4e000e6a4b5d82db2eac02822968c38bb9b8ab5d35cfa498a636bf221078d8722f8ac2cdd91b0430f0b5b6768fb33a63112c3045038f6d44d121e7b5 diff --git a/dev-python/pynrrd/pynrrd-0.4.2.ebuild b/dev-python/pynrrd/pynrrd-0.4.2.ebuild index c877ed1f3..2993f8f3a 100644 --- a/dev-python/pynrrd/pynrrd-0.4.2.ebuild +++ b/dev-python/pynrrd/pynrrd-0.4.2.ebuild @@ -1,9 +1,10 @@ -# Copyright 1999-2020 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7..9} ) +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) inherit distutils-r1 diff --git a/dev-python/pynrrd/pynrrd-0.4.3.ebuild b/dev-python/pynrrd/pynrrd-0.4.3.ebuild new file mode 100644 index 000000000..2993f8f3a --- /dev/null +++ b/dev-python/pynrrd/pynrrd-0.4.3.ebuild @@ -0,0 +1,27 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) + +inherit distutils-r1 + +DESCRIPTION="Simple pure-python module for reading and writing nrrd files" +HOMEPAGE="https://github.com/mhe/pynrrd" +SRC_URI="https://github.com/mhe/pynrrd/archive/v${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]" +DEPEND="test? ( ${RDEPEND} )" + +distutils_enable_tests unittest + +python_test() { + ${EPYTHON} -m unittest discover -v nrrd/tests || \ + die "unittests failed for ${EPYTHON}" +} diff --git a/dev-python/pynrrd/pynrrd-1.0.0.ebuild b/dev-python/pynrrd/pynrrd-1.0.0.ebuild new file mode 100644 index 000000000..d46aba486 --- /dev/null +++ b/dev-python/pynrrd/pynrrd-1.0.0.ebuild @@ -0,0 +1,30 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) + +inherit distutils-r1 + +DESCRIPTION="Simple pure-python module for reading and writing nrrd files" +HOMEPAGE="https://github.com/mhe/pynrrd" +SRC_URI="https://github.com/mhe/pynrrd/archive/v${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + dev-python/nptyping[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] +" +DEPEND="test? ( ${RDEPEND} )" + +distutils_enable_tests unittest + +python_test() { + ${EPYTHON} -m unittest discover -v nrrd/tests || \ + die "unittests failed for ${EPYTHON}" +} diff --git a/dev-python/pynwb/Manifest b/dev-python/pynwb/Manifest index 16b7c7287..0dffbb9ab 100644 --- a/dev-python/pynwb/Manifest +++ b/dev-python/pynwb/Manifest @@ -1,2 +1,2 @@ -DIST pynwb-2.0.0.post0.dev5.tar.gz 450799 BLAKE2B 02aef74992dda44139e776eebf3d29924caa46bfc2a12da400ceaadff5856295b6205c6ad230483935e713eed9dd868b9109c2d51d7c69291dc93db806ef4761 SHA512 840a33cd0a2de5c491e785530e4dab589945015b9a60384ed127a27fbfe4c527b1b10d74a9ffe2a795a29c3bba65aafd007975973a2da68fca73bf71260b7b8b -DIST pynwb-2.0.0.tar.gz 450082 BLAKE2B 3bfd17b8cbe5f12992630bc5a97144dbc7b3d583238e1fe0d59576029ae7a30acbd05b7af18ca89d6cba389df1bf543c97e75e83e04aeb4a4e44c4cd1a26be9d SHA512 4afc319fd9cce0c1e81589236237f9a28b69dd846d96849ae5cc554287a6dd124fd421f700736dbb714cfbe6f260e79f374d1dd63ee92c2776f5173654d61f9a +DIST pynwb-2.5.0.tar.gz 620770 BLAKE2B 470f5127560bf79f112061e9e8af208051d76833e449a66b03e31bb0828ffbfd6aa0b9efc136ecc0b7efba758334c3f15525a41ec4540c6f55d02f8afbd55ab2 SHA512 cad84e3ac6c3c67c3c28e3c3ec44402bfc94c4cf988fbe64ddfa461a67115398b24bb9bcac1bd00933e1b63d73048d9b20ec6cd736a51d9f2c7bf4d294edb261 +DIST pynwb-2.6.0.tar.gz 625188 BLAKE2B ac179af7e3c9de6ec4fb841dfd6279a1c3ba191b9d786553af02397a49c511f4a257a0e62f3b57a217ebb08588ad8ca64219fd435b3ec25776775d05e6a9ab9b SHA512 5c830cb37e8c6fe0643bd5bfee947565ddb1d0eff16dadadd3ebec7ec14a6e1ebcf34c3909ad05c3eedd8dd5f9e3669348216d695123f2013de0e969a403ec1c diff --git a/dev-python/pynwb/files/pynwb-2.0.0-versions.patch b/dev-python/pynwb/files/pynwb-2.0.0-versions.patch deleted file mode 100644 index d09c50594..000000000 --- a/dev-python/pynwb/files/pynwb-2.0.0-versions.patch +++ /dev/null @@ -1,21 +0,0 @@ -diff --git a/setup.py b/tmp/setup.py -index 39e75824..f7948f64 100755 ---- a/setup.py -+++ b/setup.py -@@ -19,11 +19,11 @@ print('found these packages:', pkgs) - schema_dir = 'nwb-schema/core' - - reqs = [ -- 'h5py>=2.9,<4', -- 'hdmf>=3.1.1,<4', -- 'numpy>=1.16,<1.22', -- 'pandas>=1.0.5,<2', -- 'python-dateutil>=2.7,<3', -+ 'h5py', -+ 'hdmf', -+ 'numpy', -+ 'pandas', -+ 'python-dateutil', - 'setuptools' - ] - diff --git a/dev-python/pynwb/metadata.xml b/dev-python/pynwb/metadata.xml index 99512b574..1e30097b2 100644 --- a/dev-python/pynwb/metadata.xml +++ b/dev-python/pynwb/metadata.xml @@ -17,4 +17,8 @@ data, focused on the dynamics of groups of neurons measured under a large range of experimental conditions. </longdescription> + <upstream> + <remote-id type="pypi">pynwb</remote-id> + <remote-id type="github">NeurodataWithoutBorders/pynwb</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/pynwb/pynwb-2.0.0.ebuild b/dev-python/pynwb/pynwb-2.0.0.ebuild deleted file mode 100644 index d9afd62e7..000000000 --- a/dev-python/pynwb/pynwb-2.0.0.ebuild +++ /dev/null @@ -1,46 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{8..10} ) -inherit distutils-r1 - -DESCRIPTION="A Python API for working with Neurodata stored in the NWB Format " -HOMEPAGE="https://github.com/NeurodataWithoutBorders/pynwb" -SRC_URI="https://github.com/NeurodataWithoutBorders/pynwb/releases/download/${PV}/${P}.tar.gz" - -SLOT="0" -LICENSE="BSD" -KEYWORDS="~amd64 ~x86" - -RDEPEND=" - sci-libs/hdf5[ros3(-)] - dev-python/hdmf[${PYTHON_USEDEP}] - dev-python/h5py[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/pandas[${PYTHON_USEDEP}] - dev-python/python-dateutil[${PYTHON_USEDEP}] - " -BDEPEND="" - -PATCHES=( - "${FILESDIR}/${P}-versions.patch" - ) - -EPYTEST_DESELECT=( - # Reported upsream: - # https://github.com/dandi/dandischema/issues/87 - tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached - tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached_bad_ns - tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached_hdmf_common - tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached_ignore - tests/validation/test_validate.py::TestValidateScript::test_validate_file_no_cache - tests/validation/test_validate.py::TestValidateScript::test_validate_file_no_cache_bad_ns - # Reported upstream and fixed in newer version: - # https://github.com/NeurodataWithoutBorders/pynwb/issues/1412#issuecomment-934153799 - tests/integration/ros3/test_ros3.py::TestRos3Streaming::test_dandi_read - tests/integration/ros3/test_ros3.py::TestRos3Streaming::test_read -) - -distutils_enable_tests pytest diff --git a/dev-python/pynwb/pynwb-2.0.0_p0.ebuild b/dev-python/pynwb/pynwb-2.0.0_p0.ebuild deleted file mode 100644 index 25672015c..000000000 --- a/dev-python/pynwb/pynwb-2.0.0_p0.ebuild +++ /dev/null @@ -1,47 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{8..10} ) -inherit distutils-r1 - -MY_PV="${PV/_p/.post}.dev5" -MY_P="${PN}-${MY_PV}" - -DESCRIPTION="A Python API for working with Neurodata stored in the NWB Format " -HOMEPAGE="https://github.com/NeurodataWithoutBorders/pynwb" -SRC_URI="https://github.com/NeurodataWithoutBorders/pynwb/releases/download/latest/${MY_P}.tar.gz" - -SLOT="0" -LICENSE="BSD" -KEYWORDS="~amd64 ~x86" - -RDEPEND=" - sci-libs/hdf5[ros3(-)] - dev-python/hdmf[${PYTHON_USEDEP}] - dev-python/h5py[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/pandas[${PYTHON_USEDEP}] - dev-python/python-dateutil[${PYTHON_USEDEP}] - " -BDEPEND="" - -PATCHES=( - "${FILESDIR}/${PN}-2.0.0-versions.patch" - ) - -S="${WORKDIR}/${MY_P}" - -EPYTEST_DESELECT=( - # Reported upsream - # https://github.com/dandi/dandischema/issues/87 - tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached - tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached_bad_ns - tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached_hdmf_common - tests/validation/test_validate.py::TestValidateScript::test_validate_file_cached_ignore - tests/validation/test_validate.py::TestValidateScript::test_validate_file_no_cache - tests/validation/test_validate.py::TestValidateScript::test_validate_file_no_cache_bad_ns -) - -distutils_enable_tests pytest diff --git a/dev-python/pynwb/pynwb-2.5.0.ebuild b/dev-python/pynwb/pynwb-2.5.0.ebuild new file mode 100644 index 000000000..ca11c3dbe --- /dev/null +++ b/dev-python/pynwb/pynwb-2.5.0.ebuild @@ -0,0 +1,50 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) +inherit distutils-r1 pypi + +DESCRIPTION="A Python API for working with Neurodata stored in the NWB Format " +HOMEPAGE="https://github.com/NeurodataWithoutBorders/pynwb" + +SLOT="0" +LICENSE="BSD" +KEYWORDS="~amd64 ~x86" + +RDEPEND=" + >=dev-python/hdmf-3.3.2[${PYTHON_USEDEP}] + >=sci-libs/hdf5-1.12.2 + dev-python/h5py[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + dev-python/python-dateutil[${PYTHON_USEDEP}] + dev-python/requests[${PYTHON_USEDEP}] + " + +EPYTEST_DESELECT=( + # Reported upsream: + # https://github.com/NeurodataWithoutBorders/pynwb/issues/1580 + tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached + tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_bad_ns + tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_core + tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_extension + tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_extension_pass_ns + tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_hdmf_common + tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_ignore + tests/validation/test_validate.py::TestValidateCLI::test_validate_file_invalid + tests/validation/test_validate.py::TestValidateCLI::test_validate_file_list_namespaces_core + tests/validation/test_validate.py::TestValidateCLI::test_validate_file_list_namespaces_extension + tests/validation/test_validate.py::TestValidateCLI::test_validate_file_no_cache + tests/validation/test_validate.py::TestValidateCLI::test_validate_file_no_cache_bad_ns + # Reported upstream: + # https://github.com/NeurodataWithoutBorders/pynwb/issues/1800 + tests/unit/test_file.py::TestNoCacheSpec::test_simple + # Not sandboxed, reported upstream: + # https://github.com/NeurodataWithoutBorders/pynwb/issues/1800 + tests/read_dandi/test_read_dandi.py::TestReadNWBDandisets::test_read_first_nwb_asset +) + +distutils_enable_tests pytest diff --git a/dev-python/pynwb/pynwb-2.6.0.ebuild b/dev-python/pynwb/pynwb-2.6.0.ebuild new file mode 100644 index 000000000..2f403981c --- /dev/null +++ b/dev-python/pynwb/pynwb-2.6.0.ebuild @@ -0,0 +1,51 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) +inherit distutils-r1 pypi + +DESCRIPTION="A Python API for working with Neurodata stored in the NWB Format " +HOMEPAGE="https://github.com/NeurodataWithoutBorders/pynwb" + +SLOT="0" +LICENSE="BSD" +KEYWORDS="~amd64 ~x86" + +RDEPEND=" + >=dev-python/hdmf-3.3.2[${PYTHON_USEDEP}] + >=sci-libs/hdf5-1.12.2 + dev-python/h5py[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + dev-python/python-dateutil[${PYTHON_USEDEP}] + dev-python/requests[${PYTHON_USEDEP}] + " + +EPYTEST_DESELECT=( + # Reported upsream: + # https://github.com/NeurodataWithoutBorders/pynwb/issues/1580 + tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached + tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_bad_ns + tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_core + tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_extension + tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_extension_pass_ns + tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_hdmf_common + tests/validation/test_validate.py::TestValidateCLI::test_validate_file_cached_ignore + tests/validation/test_validate.py::TestValidateCLI::test_validate_file_invalid + tests/validation/test_validate.py::TestValidateCLI::test_validate_file_list_namespaces_core + tests/validation/test_validate.py::TestValidateCLI::test_validate_file_list_namespaces_extension + tests/validation/test_validate.py::TestValidateCLI::test_validate_file_no_cache + tests/validation/test_validate.py::TestValidateCLI::test_validate_file_no_cache_bad_ns + # Reported upstream: + # https://github.com/NeurodataWithoutBorders/pynwb/issues/1800 + tests/unit/test_file.py::TestNoCacheSpec::test_simple + # Not sandboxed, reported upstream: + # https://github.com/NeurodataWithoutBorders/pynwb/issues/1800 + tests/read_dandi/test_read_dandi.py::TestReadNWBDandisets::test_read_first_nwb_asset + tests/unit/test_base.py::TestTimeSeries::test_repr_html +) + +distutils_enable_tests pytest diff --git a/dev-python/pyout/Manifest b/dev-python/pyout/Manifest index 551424495..5878b2e20 100644 --- a/dev-python/pyout/Manifest +++ b/dev-python/pyout/Manifest @@ -1,2 +1,2 @@ -DIST pyout-0.7.1.tar.gz 180439 BLAKE2B b64808edfa013c8460961afacbe70caad4f3c0520d8b87656e909e278534bf111154fd31a186f95246d3084671c841ea421ed52118ddeee3f08f21106f2f80b1 SHA512 66338ce6dbf1e4ee6a187993609f762fcd2f8dddd981bc976b3240b6ecd461ba1fd47b9f08b91fc29853ce88e26158c7047de0adfcf28a0dd66869adfad5ab71 DIST pyout-0.7.2.tar.gz 181753 BLAKE2B 780e536921151f81097e5dee7c74cfa086153f916fc9b9fd684f01008ada34102ba33ee7bdd3dd8cc4ccf89a8d9821ec0aecdbd87bc356abf25c6e4fe32d4c5a SHA512 e7be6f7829f6b09ead64c596cfdecfa45073af0a1da15401702327e141bbfae10e7968ee5e332358aa04bfc7ddf71b7b6caf2d5877aca8514e4ba544d3b1670a +DIST pyout-0.7.3.tar.gz 45726 BLAKE2B 4c5bc42b835fefd3db5d97db46c086ec2a7ca488a339813937f6e795a5fef699451dd67cd5078737f4f2bc47a36c96e2cb9f0010645fa45ebd288d24b5e0c3ba SHA512 784a7dd5b1eb811073466828f81783f89e3a251e05bc49edf124cdfc916c2447982299c83b087942845b61791481850f8c89379eea920e91d35c8abc2cbeb8ef diff --git a/dev-python/pyout/files/pyout-0.7.2-blessed.patch b/dev-python/pyout/files/pyout-0.7.2-blessed.patch new file mode 100644 index 000000000..89e189916 --- /dev/null +++ b/dev-python/pyout/files/pyout-0.7.2-blessed.patch @@ -0,0 +1,140 @@ +From 0f7c6d6f2abb304c9c473afb504cb03d17fef036 Mon Sep 17 00:00:00 2001 +From: Horea Christian <chr@chymera.eu> +Date: Sat, 7 Jan 2023 21:49:32 -0500 +Subject: [PATCH 1/2] Accepting either bless* library + +--- + pyout/field.py | 7 ++++++- + pyout/tabular.py | 9 +++++++-- + pyout/tests/terminal.py | 9 +++++++-- + pyout/tests/test_interface.py | 7 ++++++- + pyout/tests/test_tabular.py | 7 ++++++- + 5 files changed, 32 insertions(+), 7 deletions(-) + +diff --git a/pyout/field.py b/pyout/field.py +index 5105081..99c310f 100644 +--- a/pyout/field.py ++++ b/pyout/field.py +@@ -495,7 +495,12 @@ class TermProcessors(StyleProcessors): + + Parameters + ---------- +- term : blessings.Terminal ++ term : blessed.Terminal or blessings.Terminal ++ ++ Notes ++ ----- ++ * Eventually we may want to retire blessings: ++ https://github.com/pyout/pyout/issues/136 + """ + + def __init__(self, term): +diff --git a/pyout/tabular.py b/pyout/tabular.py +index 2a776a1..0d4797a 100644 +--- a/pyout/tabular.py ++++ b/pyout/tabular.py +@@ -7,7 +7,12 @@ + from logging import getLogger + import os + +-from blessings import Terminal ++# Eventually we may want to retire blessings: ++# https://github.com/pyout/pyout/issues/136 ++try: ++ from blessed import Terminal ++except ImportError: ++ from blessings import Terminal + + from pyout import interface + from pyout.field import TermProcessors +@@ -16,7 +21,7 @@ + + + class TerminalStream(interface.Stream): +- """Stream interface implementation using blessings.Terminal. ++ """Stream interface implementation using blessed/blessings.Terminal. + """ + + def __init__(self, stream=None, interactive=None): +diff --git a/pyout/tests/terminal.py b/pyout/tests/terminal.py +index 53aabd7..2d8857c 100644 +--- a/pyout/tests/terminal.py ++++ b/pyout/tests/terminal.py +@@ -6,12 +6,17 @@ + from functools import partial + import re + +-import blessings ++# Eventually we may want to retire blessings: ++# https://github.com/pyout/pyout/issues/136 ++try: ++ import blessed as bls ++except ImportError: ++ import blessings as bls + + from pyout.tests.utils import assert_contains + + +-class Terminal(blessings.Terminal): ++class Terminal(bls.Terminal): + + def __init__(self, *args, **kwargs): + super(Terminal, self).__init__( +diff --git a/pyout/tests/test_interface.py b/pyout/tests/test_interface.py +index 5205ef3..8348323 100644 +--- a/pyout/tests/test_interface.py ++++ b/pyout/tests/test_interface.py +@@ -1,6 +1,11 @@ + import pytest + +-pytest.importorskip("blessings") ++# Eventually we may want to retire blessings: ++# https://github.com/pyout/pyout/issues/136 ++try: ++ pytest.importorskip("blessed") ++except pytest.skip.Exception: ++ pytest.importorskip("blessings") + + import inspect + +diff --git a/pyout/tests/test_tabular.py b/pyout/tests/test_tabular.py +index 2044e92..a1d35e5 100644 +--- a/pyout/tests/test_tabular.py ++++ b/pyout/tests/test_tabular.py +@@ -1,7 +1,12 @@ + # -*- coding: utf-8 -*- + import pytest + +-pytest.importorskip("blessings") ++# Eventually we may want to retire blessings: ++# https://github.com/pyout/pyout/issues/136 ++try: ++ pytest.importorskip("blessed") ++except pytest.skip.Exception: ++ pytest.importorskip("blessings") + + from collections import Counter + from collections import OrderedDict + +From 5f6691c114578217a124d2ac1b24468993178e27 Mon Sep 17 00:00:00 2001 +From: Horea Christian <chr@chymera.eu> +Date: Sat, 7 Jan 2023 23:48:37 -0500 +Subject: [PATCH 2/2] Preferring blessings + +--- + setup.py | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/setup.py b/setup.py +index b376c2e..43005e7 100644 +--- a/setup.py ++++ b/setup.py +@@ -2,7 +2,7 @@ + + requires = { + "core": [ +- "blessings; sys_platform != 'win32'", ++ "blessed; sys_platform != 'win32'", + "jsonschema>=3.0.0", + ], + "tests": ["pytest", "pytest-timeout"], diff --git a/dev-python/pyout/pyout-0.7.1.ebuild b/dev-python/pyout/pyout-0.7.1.ebuild deleted file mode 100644 index 6cf80ec85..000000000 --- a/dev-python/pyout/pyout-0.7.1.ebuild +++ /dev/null @@ -1,32 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{8..10} ) -inherit distutils-r1 - -DESCRIPTION="Terminal styling for structured data" -HOMEPAGE="https://github.com/pyout/pyout" -SRC_URI="https://github.com/pyout/pyout/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz" - -SLOT="0" -LICENSE="MIT" -KEYWORDS="~amd64 ~x86" - -RDEPEND=" - dev-python/jsonschema[${PYTHON_USEDEP}] - dev-python/blessings[${PYTHON_USEDEP}] -" -DEPEND=" - test? ( - dev-python/pytest-timeout[${PYTHON_USEDEP}] - ) -" - -distutils_enable_tests pytest - -python_prepare_all() { - sed -i -e '/pytest-runner/d' setup.py || die - distutils-r1_python_prepare_all -} diff --git a/dev-python/pyout/pyout-0.7.2-r1.ebuild b/dev-python/pyout/pyout-0.7.2-r1.ebuild new file mode 100644 index 000000000..7e262b158 --- /dev/null +++ b/dev-python/pyout/pyout-0.7.2-r1.ebuild @@ -0,0 +1,34 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +inherit distutils-r1 + +DESCRIPTION="Terminal styling for structured data" +HOMEPAGE="https://github.com/pyout/pyout" +SRC_URI="https://github.com/pyout/pyout/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz" + +SLOT="0" +LICENSE="MIT" +KEYWORDS="~amd64 ~x86" + +RDEPEND=" + dev-python/jsonschema[${PYTHON_USEDEP}] + dev-python/blessed[${PYTHON_USEDEP}] +" +DEPEND=" + test? ( + dev-python/pytest-timeout[${PYTHON_USEDEP}] + ) +" + +distutils_enable_tests pytest + +PATCHES=( "${FILESDIR}/${P}-blessed.patch" ) + +python_prepare_all() { + sed -i -e '/pytest-runner/d' setup.py || die + distutils-r1_python_prepare_all +} diff --git a/dev-python/pyout/pyout-0.7.2.ebuild b/dev-python/pyout/pyout-0.7.2.ebuild deleted file mode 100644 index 6cf80ec85..000000000 --- a/dev-python/pyout/pyout-0.7.2.ebuild +++ /dev/null @@ -1,32 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{8..10} ) -inherit distutils-r1 - -DESCRIPTION="Terminal styling for structured data" -HOMEPAGE="https://github.com/pyout/pyout" -SRC_URI="https://github.com/pyout/pyout/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz" - -SLOT="0" -LICENSE="MIT" -KEYWORDS="~amd64 ~x86" - -RDEPEND=" - dev-python/jsonschema[${PYTHON_USEDEP}] - dev-python/blessings[${PYTHON_USEDEP}] -" -DEPEND=" - test? ( - dev-python/pytest-timeout[${PYTHON_USEDEP}] - ) -" - -distutils_enable_tests pytest - -python_prepare_all() { - sed -i -e '/pytest-runner/d' setup.py || die - distutils-r1_python_prepare_all -} diff --git a/dev-python/pyout/pyout-0.7.3.ebuild b/dev-python/pyout/pyout-0.7.3.ebuild new file mode 100644 index 000000000..7246139ee --- /dev/null +++ b/dev-python/pyout/pyout-0.7.3.ebuild @@ -0,0 +1,35 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..12} ) +inherit distutils-r1 pypi + +DESCRIPTION="Terminal styling for structured data" +HOMEPAGE="https://github.com/pyout/pyout" +#SRC_URI="https://github.com/pyout/pyout/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz" + +SLOT="0" +LICENSE="MIT" +KEYWORDS="~amd64 ~x86" + +RDEPEND=" + dev-python/jsonschema[${PYTHON_USEDEP}] + dev-python/blessed[${PYTHON_USEDEP}] +" +DEPEND=" + test? ( + dev-python/pytest-timeout[${PYTHON_USEDEP}] + ) +" + +distutils_enable_tests pytest + +#PATCHES=( "${FILESDIR}/${PN}-0.7.2-blessed.patch" ) + +python_prepare_all() { + sed -i -e '/pytest-runner/d' setup.py || die + distutils-r1_python_prepare_all +} diff --git a/dev-python/pyparsing/Manifest b/dev-python/pyparsing/Manifest deleted file mode 100644 index 736d09882..000000000 --- a/dev-python/pyparsing/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST pyparsing_2.4.7.tar.gz 648158 BLAKE2B 24525b4ee7876e245b9eb270f0e3e22fe2d8b398f9777ad3b3657b8a1227dcbd25983aa64a3f3018debdbffc1a042c732e6b3a09800e081c7acac7b97da15317 SHA512 c7a546729f86a2b5176e2482b566b9fd715b03e495aaef4d720b21307bb03f385dbc849247f8d266cb3d92be0a83c34ce4995b655ce85318355d5a0d42d6991e diff --git a/dev-python/pyparsing/metadata.xml b/dev-python/pyparsing/metadata.xml deleted file mode 100644 index 2692e21d7..000000000 --- a/dev-python/pyparsing/metadata.xml +++ /dev/null @@ -1,21 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci@gentoo.org</email> - <name>Science Project</name> - </maintainer> - <longdescription lang="en"> - The pyparsing module is an alternative approach to creating and - executing simple grammars, vs. the traditional lex/yacc approach, or the - use of regular expressions. The pyparsing module provides a library of - classes that client code uses to construct the grammar directly in - Python code. - </longdescription> - <stabilize-allarches/> - <upstream> - <remote-id type="sourceforge">pyparsing</remote-id> - <remote-id type="pypi">pyparsing</remote-id> - <remote-id type="github">pyparsing/pyparsing</remote-id> - </upstream> -</pkgmetadata> diff --git a/dev-python/pyparsing/pyparsing-2.4.7-r1.ebuild b/dev-python/pyparsing/pyparsing-2.4.7-r1.ebuild deleted file mode 100644 index 55da214a2..000000000 --- a/dev-python/pyparsing/pyparsing-2.4.7-r1.ebuild +++ /dev/null @@ -1,29 +0,0 @@ -# Copyright 2004-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -# please keep this ebuild at EAPI 7 -- sys-apps/portage dep -EAPI=7 - -PYTHON_COMPAT=( python3_{7..10} pypy3 ) -inherit distutils-r1 - -MY_P=${P/-/_} -DESCRIPTION="Easy-to-use Python module for text parsing" -HOMEPAGE="https://github.com/pyparsing/pyparsing https://pypi.org/project/pyparsing/" -SRC_URI="https://github.com/${PN}/${PN}/archive/${MY_P}.tar.gz" -S=${WORKDIR}/${PN}-${MY_P} - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~alpha ~amd64 ~arm ~arm64 ~hppa ~ia64 ~m68k ~mips ~ppc ~ppc64 ~riscv ~s390 ~sparc ~x86 ~x64-cygwin ~amd64-linux ~x86-linux ~ppc-macos ~x64-macos ~sparc-solaris ~sparc64-solaris ~x64-solaris ~x86-solaris" -IUSE="examples" - -distutils_enable_tests setup.py - -python_install_all() { - if use examples; then - docompress -x /usr/share/doc/${PF}/examples - dodoc -r examples - fi - distutils-r1_python_install_all -} diff --git a/dev-python/pysolar/Manifest b/dev-python/pysolar/Manifest index e8d002718..d353c6cbd 100644 --- a/dev-python/pysolar/Manifest +++ b/dev-python/pysolar/Manifest @@ -1 +1 @@ -DIST pysolar-0.8.tar.gz 1574747 BLAKE2B 7343cbed9c7e80deb1ee54406ceb96daebef76495d1595c44467aa5a025d161e730f3356a3c1b11ce27a1c96d1d47bd97a2f3e95b8864f6009b2fb3a14a1a722 SHA512 ca9d168c1fd5142998d07a18d3dde812ed38c667f1226fc62deb1fb148669039f6c5707bfed9aeea4bef8fbe962235495705e41043d7e381413caf55f9abba99 +DIST pysolar-0.10.tar.gz 1569021 BLAKE2B f1f30b32030e6dda00635257b6d2cbc5d75bf8122f27db2db6c0471339b73f4123627b116008c262a7547b5ca7a0664318ad90a92d6d4fc0b53d65de708cde29 SHA512 bccb41874bb6f344a64db694b8ed81137ddaa7c0df9b6011192c3ce3acb4b8f4d934e70000d91ced005936c5e1751043a80ad96b5d262ebf1d96ee061326e114 diff --git a/dev-python/pysolar/pysolar-0.10.ebuild b/dev-python/pysolar/pysolar-0.10.ebuild new file mode 100644 index 000000000..0e11e7967 --- /dev/null +++ b/dev-python/pysolar/pysolar-0.10.ebuild @@ -0,0 +1,38 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools + +AUTHOR=pingswept + +inherit distutils-r1 + +DESCRIPTION="Collection of Python libraries for simulating the irradiation by the sun" +HOMEPAGE="https://pysolar.org/" +SRC_URI="https://github.com/${AUTHOR}/${PN}/archive/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +# Still depends on nose +RESTRICT="test" + +RDEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/pytz[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] +" + +distutils_enable_tests pytest + +python_prepare_all() { + sed \ + -e "s:'testsolar', ::" \ + -e "s:'shade_test', ::" \ + -i setup.py || die # don't install tests + distutils-r1_python_prepare_all +} diff --git a/dev-python/pysolar/pysolar-0.8.ebuild b/dev-python/pysolar/pysolar-0.8.ebuild deleted file mode 100644 index 88f0505ef..000000000 --- a/dev-python/pysolar/pysolar-0.8.ebuild +++ /dev/null @@ -1,32 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7..9} ) - -AUTHOR=pingswept - -inherit distutils-r1 - -DESCRIPTION="Collection of Python libraries for simulating the irradiation by the sun" -HOMEPAGE="https://pysolar.org/" -SRC_URI="https://github.com/${AUTHOR}/${PN}/archive/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -RDEPEND=" - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/pytz[${PYTHON_USEDEP}] - dev-python/scipy[${PYTHON_USEDEP}] -" - -python_prepare_all() { - sed \ - -e "s:'testsolar', ::" \ - -e "s:'shade_test', ::" \ - -i setup.py || die # don't install tests - distutils-r1_python_prepare_all -} diff --git a/dev-python/pytest-doctestplus/Manifest b/dev-python/pytest-doctestplus/Manifest index 4a1e50d88..fa08cd21b 100644 --- a/dev-python/pytest-doctestplus/Manifest +++ b/dev-python/pytest-doctestplus/Manifest @@ -1 +1 @@ -DIST pytest-doctestplus-0.11.2.tar.gz 34943 BLAKE2B a45779ff3d65e1b920282f400d67b618f620a9a905da69edff96db799f30e1b93562e69bd567a49629194b962a080b1f675619b0c6995227a1391c3d0e74be20 SHA512 fed49a551be78f51db60161ccfa592e461719cca76e2a48e3267e8a22dbec60d02d8fbb757a88cb5cf4dc22143e27d3d20f25b51855be835254c72fd8260abbd +DIST pytest-doctestplus-0.12.1.tar.gz 36434 BLAKE2B 95baa9f6185423fdd3e61ec0c269de54a4cf3298f2db90087b1413608663e4200e48158240cf565c8cc267244fbf8d60a0a5241b3b8f1fa8c1187e34824b17ae SHA512 46b999abd5632fa5c5743900b8b78ee7b6be742959daeb85296ebdf820d7533cff0a78d1c8aed7f5d5a15436998b2f7fe3e571133be14fce056276900493fef9 diff --git a/dev-python/pytest-doctestplus/metadata.xml b/dev-python/pytest-doctestplus/metadata.xml index 4f4367037..33e3f0e33 100644 --- a/dev-python/pytest-doctestplus/metadata.xml +++ b/dev-python/pytest-doctestplus/metadata.xml @@ -5,4 +5,7 @@ <email>sci-astronomy@gentoo.org</email> <name>Gentoo Astronomy Project</name> </maintainer> + <upstream> + <remote-id type="pypi">pytest-doctestplus</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/pytest-doctestplus/pytest-doctestplus-0.11.2.ebuild b/dev-python/pytest-doctestplus/pytest-doctestplus-0.11.2.ebuild deleted file mode 100644 index 17b19cbb0..000000000 --- a/dev-python/pytest-doctestplus/pytest-doctestplus-0.11.2.ebuild +++ /dev/null @@ -1,24 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{8..10} ) - -inherit distutils-r1 - -DESCRIPTION="Pytest plugin with advanced doctest features" -HOMEPAGE="https://astropy.org/" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -# TODO: fix this -# AttributeError: type object 'reprec' has no attribute 'assertoutcome' -RESTRICT="test" - -RDEPEND="dev-python/pytest[${PYTHON_USEDEP}]" - -distutils_enable_tests pytest diff --git a/dev-python/pytest-doctestplus/pytest-doctestplus-0.12.1.ebuild b/dev-python/pytest-doctestplus/pytest-doctestplus-0.12.1.ebuild new file mode 100644 index 000000000..89f6c46eb --- /dev/null +++ b/dev-python/pytest-doctestplus/pytest-doctestplus-0.12.1.ebuild @@ -0,0 +1,41 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools +PYPI_NO_NORMALIZE=1 + +inherit distutils-r1 pypi + +DESCRIPTION="Pytest plugin with advanced doctest features" +HOMEPAGE="https://astropy.org/" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +RDEPEND=" + dev-python/pytest[${PYTHON_USEDEP}] + dev-python/packaging[${PYTHON_USEDEP}] +" + +BDEPEND=" + dev-python/setuptools-scm[${PYTHON_USEDEP}] + test? ( + dev-python/numpy[${PYTHON_USEDEP}] + ) +" + +# Skip the remote tests +EPYTEST_DESELECT=( + tests/test_doctestplus.py::test_remote_data_url + tests/test_doctestplus.py::test_remote_data_float_cmp + tests/test_doctestplus.py::test_remote_data_ignore_whitespace + tests/test_doctestplus.py::test_remote_data_ellipsis + tests/test_doctestplus.py::test_remote_data_requires + tests/test_doctestplus.py::test_remote_data_ignore_warnings +) + +distutils_enable_tests pytest diff --git a/dev-python/python-gantt/metadata.xml b/dev-python/python-gantt/metadata.xml index 3febd988f..18071f943 100644 --- a/dev-python/python-gantt/metadata.xml +++ b/dev-python/python-gantt/metadata.xml @@ -1,4 +1,4 @@ -<?xml version='1.0' encoding='UTF-8'?> +<?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -13,4 +13,7 @@ Python-Gantt makes it possible to easily draw gantt charts from Python and export outputs as scalable vector graphics (SVG). </longdescription> + <upstream> + <remote-id type="github">stefanSchinkel/gantt</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/python-gantt/python-gantt-0.6.0_p20200809.ebuild b/dev-python/python-gantt/python-gantt-0.6.0_p20200809.ebuild index 379816b05..b5fdf845b 100644 --- a/dev-python/python-gantt/python-gantt-0.6.0_p20200809.ebuild +++ b/dev-python/python-gantt/python-gantt-0.6.0_p20200809.ebuild @@ -1,8 +1,8 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 -PYTHON_COMPAT=( python3_{7..9} ) +EAPI=8 +PYTHON_COMPAT=( python3_10 ) inherit distutils-r1 @@ -30,7 +30,7 @@ python_prepare() { -e "s/matplotlib==3.0.3/matplotlib/g"\ -e "s/numpy==1.16.3/numpy/g"\ setup.py || die - distutils-r1_python_prepare_all + python_prepare_all } distutils_enable_tests pytest diff --git a/dev-python/python-igraph/Manifest b/dev-python/python-igraph/Manifest index bb22f152b..335664088 100644 --- a/dev-python/python-igraph/Manifest +++ b/dev-python/python-igraph/Manifest @@ -1 +1 @@ -DIST python-igraph-0.9.0.tar.gz 3366754 BLAKE2B baab83753bea4ee880564fe189b246c2ce0647a74ea1a41299062c3a2e203ec155abe1a3680c228d62a28e7bbf263e60e4529f151094b916ce4a1cae9f360705 SHA512 bd6071fc20c6c8f65034c71be6083e66367eb3047f376eb603e590da3606338fbd9890a2a74b8e0547fba2900c353f952683ea69b4d996f5643e84ee1c450b03 +DIST igraph-0.10.4.tar.gz 4209850 BLAKE2B 2f3b75569ea93d08b50c4af7331a1e072d1ded66a6437d52ca054ee2603f60cbbec9371107d8c6eeda5a8215b0fa5ee6eac420dbda9247ab2246d70b01d25aa5 SHA512 675388c3a9a346534c66ec96f4a427b34e88e15a1d401af4f283ee7f1f17fad85bd1636a85af58b6d1969238b40e0314d7b6db4b84723e0eb1f3afbc660f0300 diff --git a/dev-python/python-igraph/metadata.xml b/dev-python/python-igraph/metadata.xml index e97c4322a..4a86617fb 100644 --- a/dev-python/python-igraph/metadata.xml +++ b/dev-python/python-igraph/metadata.xml @@ -9,4 +9,7 @@ <email>sci@gentoo.org</email> <name>Gentoo Science Project</name> </maintainer> + <upstream> + <remote-id type="pypi">python-igraph</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/python-igraph/python-igraph-0.10.4.ebuild b/dev-python/python-igraph/python-igraph-0.10.4.ebuild new file mode 100644 index 000000000..3ee6e1eb4 --- /dev/null +++ b/dev-python/python-igraph/python-igraph-0.10.4.ebuild @@ -0,0 +1,50 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 pypi + +DESCRIPTION="Python interface for igraph" +HOMEPAGE="https://igraph.org" +SRC_URI="$(pypi_sdist_url igraph)" +S="${WORKDIR}/igraph-${PV}" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + >=dev-libs/igraph-$(ver_cut 1-2) + >=dev-python/texttable-1.6.2[${PYTHON_USEDEP}] +" +DEPEND="${RDEPEND}" +BDEPEND=" + test? ( + dev-python/cairocffi[${PYTHON_USEDEP}] + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/networkx[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + dev-python/plotly[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + ) +" + +distutils_enable_tests pytest + +python_prepare_all() { + # fix the igraph include path + cd src || die + find -type f -name "*.h" -exec sed -i -e 's@#include <igraph@#include <igraph/igraph@g' {} + || die + find -type f -name "*.c" -exec sed -i -e 's@#include <igraph@#include <igraph/igraph@g' {} + || die + cd .. || die + + distutils-r1_python_prepare_all +} + +python_compile() { + distutils-r1_python_compile --use-pkg-config +} diff --git a/dev-python/python-igraph/python-igraph-0.9.0.ebuild b/dev-python/python-igraph/python-igraph-0.9.0.ebuild deleted file mode 100644 index cec61215e..000000000 --- a/dev-python/python-igraph/python-igraph-0.9.0.ebuild +++ /dev/null @@ -1,46 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7..9} ) - -inherit distutils-r1 - -DESCRIPTION="Python interface for igraph" -HOMEPAGE="https://igraph.org" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -RDEPEND="${PYTHON_DEPS} - dev-libs/igraph - dev-python/texttable[${PYTHON_USEDEP}] - dev-python/pycairo[${PYTHON_USEDEP}] -" -DEPEND="${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() { - # fix the igraph include path - cd src || die - find -type f -name "*.h" -exec sed -i -e 's@#include <igraph@#include <igraph/igraph@g' {} + || die - find -type f -name "*.c" -exec sed -i -e 's@#include <igraph@#include <igraph/igraph@g' {} + || die - cd .. || die - - distutils-r1_python_prepare_all -} - -python_compile() { - distutils-r1_python_compile --use-pkg-config -} diff --git a/dev-python/python-vxi11/Manifest b/dev-python/python-vxi11/Manifest deleted file mode 100644 index 1f4c7aece..000000000 --- a/dev-python/python-vxi11/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST python-vxi11-0.9.tar.gz 21446 BLAKE2B 33d5af56aabf6583f630f4b8d7e31fc8fb962ef8c6952cf1894a69a304cd2f2f0c3d1bc2c17000a5b029c977c8a7c782657c9d9fab7ced484e41514ab77432f5 SHA512 d3136ca8d6cdd7bc695d52ab2adbad956936de6ab99b4be58f3b11111b1f0afc8720239ef6754da79f1c719bbd2ccec1c8a58249a4408b8536b7fd387c0164d0 diff --git a/dev-python/python-vxi11/metadata.xml b/dev-python/python-vxi11/metadata.xml deleted file mode 100644 index 80031f312..000000000 --- a/dev-python/python-vxi11/metadata.xml +++ /dev/null @@ -1,20 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>marbre@linux.sungazer.de</email> - <name>Marius Brehler</name> - </maintainer> - <maintainer type="project"> - <email>sci@gentoo.org</email> - <name>Gentoo Science Project</name> - </maintainer> - <longdescription> -Python VXI-11 is a Python implementation of the VXI-11 Ethernet -instrument control protocol. It is compatible with VXI-11, -LXI instruments and VXI-11 to GPIB bridges (HP E2050A, etc.). -</longdescription> - <upstream> - <remote-id type="github">python-ivi/python-vxi11</remote-id> - </upstream> -</pkgmetadata> diff --git a/dev-python/python-vxi11/python-vxi11-0.9.ebuild b/dev-python/python-vxi11/python-vxi11-0.9.ebuild deleted file mode 100644 index fe2292148..000000000 --- a/dev-python/python-vxi11/python-vxi11-0.9.ebuild +++ /dev/null @@ -1,21 +0,0 @@ -# Copyright 1999-2020 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="Provides a pure Python VXI-11 driver for controlling instruments over Ethernet" -HOMEPAGE="https://github.com/python-ivi/python-vxi11" - -if [[ ${PV} == 9999 ]] ; then - inherit git-r3 - EGIT_REPO_URI="https://github.com/python-ivi/python-vxi11" -else - SRC_URI="https://github.com/python-ivi/python-vxi11/archive/v${PV}.tar.gz -> ${P}.tar.gz" - KEYWORDS="~amd64" -fi - -LICENSE="MIT" -SLOT="0" diff --git a/dev-python/python-vxi11/python-vxi11-9999.ebuild b/dev-python/python-vxi11/python-vxi11-9999.ebuild deleted file mode 100644 index fe2292148..000000000 --- a/dev-python/python-vxi11/python-vxi11-9999.ebuild +++ /dev/null @@ -1,21 +0,0 @@ -# Copyright 1999-2020 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="Provides a pure Python VXI-11 driver for controlling instruments over Ethernet" -HOMEPAGE="https://github.com/python-ivi/python-vxi11" - -if [[ ${PV} == 9999 ]] ; then - inherit git-r3 - EGIT_REPO_URI="https://github.com/python-ivi/python-vxi11" -else - SRC_URI="https://github.com/python-ivi/python-vxi11/archive/v${PV}.tar.gz -> ${P}.tar.gz" - KEYWORDS="~amd64" -fi - -LICENSE="MIT" -SLOT="0" diff --git a/dev-python/pytorch-lightning/Manifest b/dev-python/pytorch-lightning/Manifest deleted file mode 100644 index f9f1f6b1d..000000000 --- a/dev-python/pytorch-lightning/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST pytorch-lightning-1.5.8.tar.gz 444592 BLAKE2B 7fa8e230811381a0aea43f4d098f9d833350183cfe10ea2f51aa6c4a8c9835ed979d103572b352c2831361d5802caf66a674da0fccf948ba9b14cdb7d77d325e SHA512 e9c08b5614f8041e2511977b0e42be5d209efbf20a80ae8067bf7ac4dedd5d30908a33542fb3f1601814dba769ffeb545ba8a66ff368ff038e8fdc5f630dc808 diff --git a/dev-python/pytorch-lightning/metadata.xml b/dev-python/pytorch-lightning/metadata.xml deleted file mode 100644 index 2e30eb3db..000000000 --- a/dev-python/pytorch-lightning/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci@gentoo.org</email> - <name>Science Project</name> - </maintainer> - <upstream> - <remote-id type="github">PyTorchLightning/pytorch-lightning</remote-id> - <remote-id type="pypi">pytorch-lightning</remote-id> - </upstream> -</pkgmetadata> diff --git a/dev-python/pytorch-lightning/pytorch-lightning-1.5.8.ebuild b/dev-python/pytorch-lightning/pytorch-lightning-1.5.8.ebuild deleted file mode 100644 index 7b3ad5e3f..000000000 --- a/dev-python/pytorch-lightning/pytorch-lightning-1.5.8.ebuild +++ /dev/null @@ -1,32 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{8..9} ) -DISTUTILS_SINGLE_IMPL=1 - -inherit distutils-r1 - -DESCRIPTION="Lightweight PyTorch wrapper for ML researchers" -HOMEPAGE="https://github.com/PyTorchLightning/pytorch-lightning" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="Apache-2.0" -SLOT="0" -KEYWORDS="~amd64" - -RDEPEND=" - sci-libs/pytorch[python,${PYTHON_SINGLE_USEDEP}] - $(python_gen_cond_dep ' - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/future[${PYTHON_USEDEP}] - dev-python/tqdm[${PYTHON_USEDEP}] - dev-python/pyyaml[${PYTHON_USEDEP}] - dev-python/fsspec[${PYTHON_USEDEP}] - sci-visualization/tensorboard[${PYTHON_USEDEP}] - dev-python/packaging[${PYTHON_USEDEP}] - dev-python/typing-extensions[${PYTHON_USEDEP}] - dev-python/ratelimit[${PYTHON_USEDEP}] - ') -" diff --git a/dev-python/pyvista/pyvista-0.33.2.ebuild b/dev-python/pyvista/pyvista-0.33.2.ebuild index c8b5a59dc..d59653fae 100644 --- a/dev-python/pyvista/pyvista-0.33.2.ebuild +++ b/dev-python/pyvista/pyvista-0.33.2.ebuild @@ -1,16 +1,14 @@ -# Copyright 1999-2022 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 -PYTHON_COMPAT=( python3_{8..9} ) +PYTHON_COMPAT=( python3_{10..10} ) DISTUTILS_SINGLE_IMPL=1 # because "sci-libs/vtk" inherits "python-single-r1" - -inherit distutils-r1 +inherit distutils-r1 pypi DESCRIPTION="Easier Pythonic interface to VTK" HOMEPAGE="https://docs.pyvista.org" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" LICENSE="MIT" KEYWORDS="~amd64 ~x86" diff --git a/dev-python/pyviz_comms/Manifest b/dev-python/pyviz_comms/Manifest index 315e51357..0d6a5ac51 100644 --- a/dev-python/pyviz_comms/Manifest +++ b/dev-python/pyviz_comms/Manifest @@ -1 +1 @@ -DIST pyviz_comms-2.0.1.tar.gz 125046 BLAKE2B d0913fb873396ddb11db2781cb65cd4b2a9dd22ce496af58a656a2c17c4d0ca1af1351a618b293c5eca964dc7f32840c577a831139a0e5e9cd7667886c97aa2c SHA512 da913ee537588cd7e643c034f14b141e28699ddddb1dcd89053b3b9482bc330582f381e4257cd07546049da67f20b1f25cf9ffb4d11c9ef457bd4915781a751c +DIST pyviz_comms-2.2.0.tar.gz 31910 BLAKE2B 42175d8750e9cb8dea4888970028898a9ee1e34b2ca5c895d2a1db40d9eec2f7eb86aec41090431b723ffcfdd0411016c04015e286d467a4c9d89eb710e7e08c SHA512 de6dba5b5d93a9a496b6895f4bf884dd80afd4124e1519bbd243b7672827f04f51d353f3941678be3780a250640e03b0c4ea0a3f87b8b9892980845bdca07439 diff --git a/dev-python/pyviz_comms/metadata.xml b/dev-python/pyviz_comms/metadata.xml index 8127bb8b0..3a0ec5dc8 100644 --- a/dev-python/pyviz_comms/metadata.xml +++ b/dev-python/pyviz_comms/metadata.xml @@ -7,7 +7,7 @@ </maintainer> <stabilize-allarches/> <upstream> - <remote-id type="pypi">pyviz_comms</remote-id> + <remote-id type="pypi">pyviz-comms</remote-id> <remote-id type="github">holoviz/pyviz_comms</remote-id> </upstream> </pkgmetadata> diff --git a/dev-python/pyviz_comms/pyviz_comms-2.0.1.ebuild b/dev-python/pyviz_comms/pyviz_comms-2.0.1.ebuild deleted file mode 100644 index df1d2bfe2..000000000 --- a/dev-python/pyviz_comms/pyviz_comms-2.0.1.ebuild +++ /dev/null @@ -1,18 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7..9} ) - -inherit distutils-r1 - -DESCRIPTION="Bidirectional communication for the HoloViz ecosystem" -HOMEPAGE="https://holoviz.org" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -RDEPEND="dev-python/param[${PYTHON_USEDEP}]" diff --git a/dev-python/pyviz_comms/pyviz_comms-2.2.0.ebuild b/dev-python/pyviz_comms/pyviz_comms-2.2.0.ebuild new file mode 100644 index 000000000..7f50fc279 --- /dev/null +++ b/dev-python/pyviz_comms/pyviz_comms-2.2.0.ebuild @@ -0,0 +1,20 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +inherit distutils-r1 pypi + +DESCRIPTION="Bidirectional communication for the HoloViz ecosystem" +HOMEPAGE="https://holoviz.org" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +RDEPEND="dev-python/param[${PYTHON_USEDEP}]" + +# Tarballs do not include tests, reported upstream: +# https://github.com/holoviz/pyviz_comms/issues/104 +#distutils_enable_tests pytest diff --git a/dev-python/pyvote/metadata.xml b/dev-python/pyvote/metadata.xml index d208f0f55..5fbf687f3 100644 --- a/dev-python/pyvote/metadata.xml +++ b/dev-python/pyvote/metadata.xml @@ -1,4 +1,4 @@ -<?xml version='1.0' encoding='UTF-8'?> +<?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -16,4 +16,7 @@ (or normal) probability density function for outcomes, or a fixed outcome probability. </longdescription> + <upstream> + <remote-id type="github">TheChymera/pyvote</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/pyvote/pyvote-0.1.ebuild b/dev-python/pyvote/pyvote-0.1.ebuild index b7ef458e2..95d95cb1b 100644 --- a/dev-python/pyvote/pyvote-0.1.ebuild +++ b/dev-python/pyvote/pyvote-0.1.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) inherit distutils-r1 diff --git a/dev-python/pyzo/Manifest b/dev-python/pyzo/Manifest index 53069b179..781107b6f 100644 --- a/dev-python/pyzo/Manifest +++ b/dev-python/pyzo/Manifest @@ -1 +1 @@ -DIST pyzo-4.11.2.tar.gz 5340033 BLAKE2B 0c5c89deac947878ab84e7744dd21ca1092e6a9448573ad85067a20861f7823727623eb45a4c3f598e0bb2056bdf153d6818daed29ec8485313bebe8fccac32f SHA512 f96e4db48b414c5d6c2d9cb723e1bef2c4e0bc461c35710b1d7bf533c935734c5a17824ade59894f273624c80823b6283f131b972cbbe7cef3d0d20ff206f7db +DIST pyzo-4.12.7.gh.tar.gz 2280468 BLAKE2B c71e29730c677cc0e75a16a10f752b26dd5675ab978493e98049a3cb6ff51449e554c22d9b171ade7e96d8908fcf4b09842c9107d09cbfee2b4e488a3ef3ed28 SHA512 974e4166227afb42ffb950f0abd8733264e57fbf5cb1c23fc72f76a41940be5cf7cc9bc39bc93353ce392aaf204a420853e62313c139814771fff92729dbe032 diff --git a/dev-python/pyzo/metadata.xml b/dev-python/pyzo/metadata.xml index ae9640ffb..8019eb9d1 100644 --- a/dev-python/pyzo/metadata.xml +++ b/dev-python/pyzo/metadata.xml @@ -5,4 +5,7 @@ <email>sci@gentoo.org</email> <name>Gentoo Science Project</name> </maintainer> + <upstream> + <remote-id type="github">pyzo/pyzo</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/pyzo/pyzo-4.11.2.ebuild b/dev-python/pyzo/pyzo-4.11.2.ebuild deleted file mode 100644 index 772793be5..000000000 --- a/dev-python/pyzo/pyzo-4.11.2.ebuild +++ /dev/null @@ -1,64 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{8..9} ) - -inherit distutils-r1 virtualx desktop xdg - -DESCRIPTION="The Python IDE for scientific computing" -HOMEPAGE="https://pyzo.org/" -SRC_URI="https://github.com/${PN}/${PN}/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="BSD-2" -SLOT="0" -KEYWORDS="~amd64" - -# For some reason this requires network access -# Qt: Session management error: Could not open network socket -RESTRICT="test" - -RDEPEND=" - dev-python/QtPy[${PYTHON_USEDEP}] -" -BDEPEND=" - test? ( - dev-python/visvis[${PYTHON_USEDEP}] - ) -" - -distutils_enable_tests pytest -distutils_enable_sphinx doc - -python_prepare_all() { - # Use relative path to avoid access violation - # Do not install the license file, install other data_files manually - sed -i \ - -e 's:/usr/share/metainfo:share/metainfo:g' \ - -e '/LICENSE.md/d' \ - setup.py || die - - distutils-r1_python_prepare_all -} - -src_test() { - virtx python_foreach_impl python_test -} - -python_install() { - distutils-r1_python_install - python_doscript pyzolauncher.py -} - -python_install_all() { - insinto /usr/share/metainfo/ - doins pyzo.appdata.xml - - for size in 16 32 48 64 128; do - newicon -s ${size} "${PN}/resources/appicons/pyzologo${size}.png" pyzologo.png - done - domenu "${PN}/resources/${PN}.desktop" - - distutils-r1_python_install_all -} diff --git a/dev-python/pyzo/pyzo-4.12.7.ebuild b/dev-python/pyzo/pyzo-4.12.7.ebuild new file mode 100644 index 000000000..f65ebcc7d --- /dev/null +++ b/dev-python/pyzo/pyzo-4.12.7.ebuild @@ -0,0 +1,67 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools + +inherit distutils-r1 virtualx desktop xdg + +DESCRIPTION="The Python IDE for scientific computing" +HOMEPAGE="https://pyzo.org/" +SRC_URI="https://github.com/${PN}/${PN}/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="BSD-2" +SLOT="0" +KEYWORDS="~amd64" + +# For some reason this requires network access +# Qt: Session management error: Could not open network socket +PROPERTIES="test_network" +RESTRICT="test" + +RDEPEND=" + dev-python/QtPy[${PYTHON_USEDEP}] +" +BDEPEND=" + dev-python/packaging[${PYTHON_USEDEP}] + test? ( + dev-python/visvis[${PYTHON_USEDEP}] + ) +" + +distutils_enable_tests pytest +distutils_enable_sphinx doc + +python_prepare_all() { + # Use relative path to avoid access violation + # Do not install the license file, install other data_files manually + sed -i \ + -e 's:/usr/share/metainfo:share/metainfo:g' \ + -e '/LICENSE.md/d' \ + setup.py || die + + distutils-r1_python_prepare_all +} + +python_test() { + virtx epytest +} + +python_install() { + distutils-r1_python_install + python_doscript pyzolauncher.py +} + +python_install_all() { + insinto /usr/share/metainfo/ + doins pyzo.appdata.xml + + for size in 16 32 48 64 128; do + newicon -s ${size} "${PN}/resources/appicons/pyzologo${size}.png" pyzologo.png + done + domenu "${PN}/resources/${PN}.desktop" + + distutils-r1_python_install_all +} diff --git a/dev-python/rasterio/rasterio-1.2.10-r1.ebuild b/dev-python/rasterio/rasterio-1.2.10-r1.ebuild index 7ae9776c7..c2aa347f1 100644 --- a/dev-python/rasterio/rasterio-1.2.10-r1.ebuild +++ b/dev-python/rasterio/rasterio-1.2.10-r1.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) DISTUTILS_USE_PEP517="setuptools" inherit distutils-r1 diff --git a/dev-python/rasterstats/rasterstats-0.16.0.ebuild b/dev-python/rasterstats/rasterstats-0.16.0.ebuild index 3567cdb42..5074a1566 100644 --- a/dev-python/rasterstats/rasterstats-0.16.0.ebuild +++ b/dev-python/rasterstats/rasterstats-0.16.0.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) DISTUTILS_USE_PEP517="setuptools" inherit distutils-r1 diff --git a/dev-python/regions/Manifest b/dev-python/regions/Manifest index e3051705f..7e2e2f89a 100644 --- a/dev-python/regions/Manifest +++ b/dev-python/regions/Manifest @@ -1 +1 @@ -DIST regions-0.4.tar.gz 1108822 BLAKE2B 7b2de2815c0a7a4e4d75aa08443520c8baf50772a0d2d892e6922d6223c32f4a05089acd464cdfba8a8737984de982b472329c800c9254f5d9ed3d8e649287d2 SHA512 571ab06c40a9abf0ebe5665b0efe7d09b0f2a9c6295fcd56f30ab25bfa506bfd80b89f7e88e83a5dbe68e084bb94e374abb01ecc043cd564a2b9cb78f6057acf +DIST regions-0.7.tar.gz 666091 BLAKE2B 7fd8cc1c9c34b236301c0493e11b99a3d2177e31c15c3ef43f38053eec653f8a68b84c4e0568395e38c940e987fcdf3a52a06e012a387a741de0cb46ec1995e8 SHA512 0e86b1cda4e479e29c00d151079788630a5b434f3d721d21ee81b4abcb03ea959e04351d61f48bfc19713dc938396fc9383c00998ba947f50fbbf9477db7d760 diff --git a/dev-python/regions/metadata.xml b/dev-python/regions/metadata.xml index a9f88e7d8..b0d9fd489 100644 --- a/dev-python/regions/metadata.xml +++ b/dev-python/regions/metadata.xml @@ -12,5 +12,6 @@ H.E.S.S, and CTA in primarily Galactic plane survey studies. </longdescription> <upstream> <remote-id type="github">gammapy/gammapy</remote-id> + <remote-id type="pypi">regions</remote-id> </upstream> </pkgmetadata> diff --git a/dev-python/regions/regions-0.4.ebuild b/dev-python/regions/regions-0.4.ebuild deleted file mode 100644 index eccec0eda..000000000 --- a/dev-python/regions/regions-0.4.ebuild +++ /dev/null @@ -1,32 +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} ) -DISTUTILS_USE_SETUPTOOLS=rdepend - -inherit distutils-r1 - -DESCRIPTION="Astropy affilated package for region handling" -HOMEPAGE="https://github.com/astropy/regions" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -# TODO: fix this -# E ModuleNotFoundError: No module named 'regions._geometry.circular_overlap' -RESTRICT="test" - -RDEPEND=" - >=dev-python/astropy-0.4[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/six[${PYTHON_USEDEP}] -" - -# TODO: fix this -# NameError: name 'disabled_intersphinx_mapping' is not defined -#distutils_enable_sphinx docs dev-python/sphinx-astropy -distutils_enable_tests pytest diff --git a/dev-python/regions/regions-0.7.ebuild b/dev-python/regions/regions-0.7.ebuild new file mode 100644 index 000000000..ef412a153 --- /dev/null +++ b/dev-python/regions/regions-0.7.ebuild @@ -0,0 +1,31 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools + +inherit distutils-r1 pypi + +DESCRIPTION="Astropy affilated package for region handling" +HOMEPAGE="https://github.com/astropy/regions" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +# TODO: fix this +# E ModuleNotFoundError: No module named 'regions._geometry.circular_overlap' +RESTRICT="test" + +RDEPEND=" + >=dev-python/astropy-0.4[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/six[${PYTHON_USEDEP}] +" + +# TODO: fix this +# NameError: name 'disabled_intersphinx_mapping' is not defined +#distutils_enable_sphinx docs dev-python/sphinx-astropy +distutils_enable_tests pytest diff --git a/dev-python/reproject/metadata.xml b/dev-python/reproject/metadata.xml index 4f4367037..56a54a20b 100644 --- a/dev-python/reproject/metadata.xml +++ b/dev-python/reproject/metadata.xml @@ -5,4 +5,7 @@ <email>sci-astronomy@gentoo.org</email> <name>Gentoo Astronomy Project</name> </maintainer> + <upstream> + <remote-id type="pypi">reproject</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/reproject/reproject-0.8.ebuild b/dev-python/reproject/reproject-0.8.ebuild index 2daccec83..cf57e7d73 100644 --- a/dev-python/reproject/reproject-0.8.ebuild +++ b/dev-python/reproject/reproject-0.8.ebuild @@ -3,13 +3,11 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) - -inherit distutils-r1 +PYTHON_COMPAT=( python3_10 ) +inherit distutils-r1 pypi DESCRIPTION="Reproject astronomical images" HOMEPAGE="https://reproject.readthedocs.io/" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" LICENSE="BSD" SLOT="0" @@ -24,7 +22,7 @@ KEYWORDS="~amd64 ~x86" # pytest-filter-subpackage>=0.1 RESTRICT="test" -BDEPEND="dev-python/setuptools_scm[${PYTHON_USEDEP}]" +BDEPEND="dev-python/setuptools-scm[${PYTHON_USEDEP}]" RDEPEND=" >=dev-python/astropy-3.2[${PYTHON_USEDEP}] diff --git a/dev-python/repsep_utils/Manifest b/dev-python/repsep_utils/Manifest index 489a3a719..1c65b16d9 100644 --- a/dev-python/repsep_utils/Manifest +++ b/dev-python/repsep_utils/Manifest @@ -1 +1,3 @@ DIST repsep_utils-0.2.tar.gz 11147 BLAKE2B 89726b7e163c954ae9826a32c6997f4c678e6586240db52b37355ca59c16743b8c19e89d12d175cb55435aced5498a22e9e825d0c2d95f9046a52ac6daadefb3 SHA512 ba499cecb3dac38c1ca8e91eee3e1f9edafbc906e8acc046cd1eaead8253a9ac61f489ffca23cdb4ac6a595ecef40cc6a3374b3618c8162a4f38f499c1a4cc4e +DIST repsep_utils-0.3.1.tar.gz 12021 BLAKE2B cfe6e0dbeaddf751a1f222a19e7c430b4c3acd4ea28061164ecc213cadccb7bcb42e9b1fe16bf73f93d735edba3887553ac49b04f763ec888177ab653d05b07b SHA512 a5897a6b2a778d8079f9d5947b22def7c42922d0c607e711f2c2957b569991098f1ed3ce53ff2f74183cb4466b87f87596aafec9f2e4c1efb38c317ef29df8da +DIST repsep_utils-0.3.tar.gz 11893 BLAKE2B b02ec74d55bbfbe15052573049660a39c87681862ff3d38a7560666191b9b2cec6ea230898349c8feef4d5654e1524b16fa90c13b1238ea1d5d51ae6eaffa283 SHA512 9df1fb77d09d18387625e7cceed9aa31faf35fd72d076425cbabc30c7020e6f8257161628940f131f6209ac2aab6336c07ffb3aa333c2ec48e2a3c47708cc2b4 diff --git a/dev-python/repsep_utils/metadata.xml b/dev-python/repsep_utils/metadata.xml index aa31ba351..228d0e4bf 100644 --- a/dev-python/repsep_utils/metadata.xml +++ b/dev-python/repsep_utils/metadata.xml @@ -1,15 +1,18 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="person"> - <email>chr@chymera.eu</email> - <name>Horea Christian</name> - </maintainer> - <longdescription lang="en"> - Utilities for compiling and developing RepSeP-style articles, such as the - reference implementation. The package contains generic boilerplate code for - PythonTeX-interaction, as used by all RepSeP-style articles, as well as an - executable file allowing single-script execution for development and - debugging purposes. - </longdescription> + <maintainer type="person"> + <email>chr@chymera.eu</email> + <name>Horea Christian</name> + </maintainer> + <longdescription lang="en"> + Utilities for compiling and developing RepSeP-style articles, such as the + reference implementation. The package contains generic boilerplate code for + PythonTeX-interaction, as used by all RepSeP-style articles, as well as an + executable file allowing single-script execution for development and + debugging purposes. + </longdescription> + <upstream> + <remote-id type="github">TheChymera/repsep_utils</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/repsep_utils/repsep_utils-0.3.1.ebuild b/dev-python/repsep_utils/repsep_utils-0.3.1.ebuild new file mode 100644 index 000000000..975d97f9d --- /dev/null +++ b/dev-python/repsep_utils/repsep_utils-0.3.1.ebuild @@ -0,0 +1,22 @@ +# Copyright 2019-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DESCRIPTION="Utilities Supporting RepSeP-style documents" +HOMEPAGE="https://github.com/TheChymera/repsep_utils" +SRC_URI="https://github.com/TheChymera/repsep_utils/archive/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +DEPEND="" +RDEPEND="dev-tex/pythontex" + +src_install() { + dobin "bin/repsep" + + insinto "/usr/share/repsep" + doins repsep/* +} diff --git a/dev-python/repsep_utils/repsep_utils-0.3.ebuild b/dev-python/repsep_utils/repsep_utils-0.3.ebuild new file mode 100644 index 000000000..975d97f9d --- /dev/null +++ b/dev-python/repsep_utils/repsep_utils-0.3.ebuild @@ -0,0 +1,22 @@ +# Copyright 2019-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DESCRIPTION="Utilities Supporting RepSeP-style documents" +HOMEPAGE="https://github.com/TheChymera/repsep_utils" +SRC_URI="https://github.com/TheChymera/repsep_utils/archive/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +DEPEND="" +RDEPEND="dev-tex/pythontex" + +src_install() { + dobin "bin/repsep" + + insinto "/usr/share/repsep" + doins repsep/* +} diff --git a/dev-python/reretry/Manifest b/dev-python/reretry/Manifest new file mode 100644 index 000000000..af408dac3 --- /dev/null +++ b/dev-python/reretry/Manifest @@ -0,0 +1 @@ +DIST reretry-0.11.8.gh.tar.gz 6629 BLAKE2B eb13ecce1ca29ce29932566e08b57a05d3f2426f41633b33b1c51eed1c4d880c5520adda4e5386ac13d064f7ff6bdc3831ce612c64c8dd24e63164a55907ae3b SHA512 e499e64cc06af8e1bb7e9fdd857c02305dcb76fd3205de128d389332a94493696c85a705efaf1e9ac0110b94a1cd443a44d49856f26b31a7eba8ad317f7deba4 diff --git a/dev-python/reretry/metadata.xml b/dev-python/reretry/metadata.xml new file mode 100644 index 000000000..64af0841d --- /dev/null +++ b/dev-python/reretry/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <upstream> + <remote-id type="github">leshchenko1979/reretry</remote-id> + <remote-id type="pypi">reretry</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/reretry/reretry-0.11.8.ebuild b/dev-python/reretry/reretry-0.11.8.ebuild new file mode 100644 index 000000000..64da7215b --- /dev/null +++ b/dev-python/reretry/reretry-0.11.8.ebuild @@ -0,0 +1,25 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools + +inherit distutils-r1 + +DESCRIPTION="An easy-to-use but functional retry decorator in python" +HOMEPAGE="https://github.com/leshchenko1979/reretry" +SRC_URI="https://github.com/leshchenko1979/reretry/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="~amd64" + +BDEPEND=" + test? ( + dev-python/pytest-asyncio[${PYTHON_USEDEP}] + ) +" + +distutils_enable_tests pytest diff --git a/dev-python/rich-click/Manifest b/dev-python/rich-click/Manifest new file mode 100644 index 000000000..ae8d92c2f --- /dev/null +++ b/dev-python/rich-click/Manifest @@ -0,0 +1 @@ +DIST rich-click-1.7.2.tar.gz 39362 BLAKE2B c4ad70d449ce9ceb3d9bbbccf7c7d3cd43386c35061d60c6395ff7845f606558af36a7c465a3393484008ece244f8e684ca9d71cea14463f04cac21803108543 SHA512 f4046e54874c4f3cc4f77651fdeb1f888d9435ff282f54d320c16c7c42f57c48018c0159230e780684336d29edff6e654454b8940b5b8df5a19139d2219c671b diff --git a/dev-python/rich-click/metadata.xml b/dev-python/rich-click/metadata.xml new file mode 100644 index 000000000..79a5238bd --- /dev/null +++ b/dev-python/rich-click/metadata.xml @@ -0,0 +1,12 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>mschu.dev@gmail.com</email> + <name>Michael Schubert</name> + </maintainer> + <upstream> + <remote-id type="github">ewels/rich-click</remote-id> + <remote-id type="pypi">rich-click</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/rich-click/rich-click-1.7.2.ebuild b/dev-python/rich-click/rich-click-1.7.2.ebuild new file mode 100644 index 000000000..e642303e2 --- /dev/null +++ b/dev-python/rich-click/rich-click-1.7.2.ebuild @@ -0,0 +1,25 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..12} ) + +PYPI_NO_NORMALIZE=1 +inherit pypi distutils-r1 + +DESCRIPTION="Format click help output nicely with rich" +HOMEPAGE="https://pypi.org/project/rich-click/" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~amd64-linux" + +RDEPEND="dev-python/click[${PYTHON_USEDEP}] + dev-python/rich[${PYTHON_USEDEP}] + dev-python/typing-extensions[${PYTHON_USEDEP}]" + +RESTRICT="test" +# ModuleNotFoundError: No module named 'tests.conftest' +#distutils_enable_tests pytest diff --git a/dev-python/ripser/Manifest b/dev-python/ripser/Manifest index 2a8f78db2..4f2515c0a 100644 --- a/dev-python/ripser/Manifest +++ b/dev-python/ripser/Manifest @@ -1 +1 @@ -DIST ripser-0.6.0.tar.gz 71420 BLAKE2B 28c34ccda4bcf5762d4ccf782aa0a1c6fe5e24fc6b84721da7ffb1475c9132b19115e7eb981ef966714f6fab2d745e2ca17f637489d1913d2fb14f82c9ed041b SHA512 1e091130c9a88eda6e29365c6616a2e12d93c9b65bda7eb5d21673f73940c24ab671ce88e716743a36bcc77ade673a49513f5e6840aa6a1810b7e17d8de741ee +DIST ripser-0.6.4.tar.gz 74642 BLAKE2B a6d7a39671415a86978ae4514f1f915f13ec791f246e632d3974553b53c398b971989e25b3cca2027a910831404c478994e646ed6e03010350b1e95438d7fc10 SHA512 b3fc216e75c807666e24d9f797a96296f2e1ffbddf3bba499220dab385690cdb6f47138cb55977eb68678dfbff9d750d7f1c4bcd8ea9267a940c9949a8dae360 diff --git a/dev-python/ripser/metadata.xml b/dev-python/ripser/metadata.xml index 2f2c0b51c..f983c3d4c 100644 --- a/dev-python/ripser/metadata.xml +++ b/dev-python/ripser/metadata.xml @@ -9,4 +9,7 @@ <email>sci@gentoo.org</email> <name>Gentoo Science Project</name> </maintainer> + <upstream> + <remote-id type="pypi">ripser</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/ripser/ripser-0.6.0.ebuild b/dev-python/ripser/ripser-0.6.0.ebuild deleted file mode 100644 index 5317a7208..000000000 --- a/dev-python/ripser/ripser-0.6.0.ebuild +++ /dev/null @@ -1,32 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7..9} ) - -inherit distutils-r1 - -DESCRIPTION="python frontend for the fast ripser tda tool" -HOMEPAGE="https://ripser.scikit-tda.org/" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND="${PYTHON_DEPS} - dev-python/cython[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/persim[${PYTHON_USEDEP}] - dev-python/scipy[${PYTHON_USEDEP}] - sci-libs/scikit-learn[${PYTHON_USEDEP}] -" -BDEPEND=" - test? ( - dev-python/hopcroftkarp[${PYTHON_USEDEP}] - dev-python/joblib[${PYTHON_USEDEP}] - ) -" -distutils_enable_tests pytest diff --git a/dev-python/ripser/ripser-0.6.4.ebuild b/dev-python/ripser/ripser-0.6.4.ebuild new file mode 100644 index 000000000..21d6b6ccd --- /dev/null +++ b/dev-python/ripser/ripser-0.6.4.ebuild @@ -0,0 +1,31 @@ +# Copyright 1999-2020 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools + +inherit distutils-r1 pypi + +DESCRIPTION="python frontend for the fast ripser tda tool" +HOMEPAGE="https://ripser.scikit-tda.org/" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + dev-python/cython[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/persim[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + sci-libs/scikit-learn[${PYTHON_USEDEP}] +" +BDEPEND=" + test? ( + dev-python/hopcroftkarp[${PYTHON_USEDEP}] + dev-python/joblib[${PYTHON_USEDEP}] + ) +" +distutils_enable_tests pytest diff --git a/dev-python/schema/Manifest b/dev-python/schema/Manifest deleted file mode 100644 index e69b4b33b..000000000 --- a/dev-python/schema/Manifest +++ /dev/null @@ -1 +0,0 @@ -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 deleted file mode 100644 index 440ea4da1..000000000 --- a/dev-python/schema/metadata.xml +++ /dev/null @@ -1,13 +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> - <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 deleted file mode 100644 index 05e8712bb..000000000 --- a/dev-python/schema/schema-0.7.4.ebuild +++ /dev/null @@ -1,28 +0,0 @@ -# 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/scooby-0.5.7.ebuild b/dev-python/scooby/scooby-0.5.7.ebuild index 19d343eca..4cd053b50 100644 --- a/dev-python/scooby/scooby-0.5.7.ebuild +++ b/dev-python/scooby/scooby-0.5.7.ebuild @@ -3,13 +3,11 @@ EAPI=7 -PYTHON_COMPAT=( python3_{8..10} ) - -inherit distutils-r1 +PYTHON_COMPAT=( python3_10 ) +inherit distutils-r1 pypi DESCRIPTION="Easily report Python package versions and hardware resources" -HOMEPAGE="https://pypi.org/project/scooby" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" +HOMEPAGE="https://pypi.org/project/scooby/" LICENSE="MIT" KEYWORDS="~amd64 ~x86" diff --git a/dev-python/smart-open/Manifest b/dev-python/smart-open/Manifest new file mode 100644 index 000000000..37703129f --- /dev/null +++ b/dev-python/smart-open/Manifest @@ -0,0 +1 @@ +DIST smart-open-6.3.0.gh.tar.gz 131300 BLAKE2B 816b2e42fca7783891eefbe767ac28423c533fe726707bf40be2b53107d7c928e74dec904db79542f7b0d41100f5aada78598478c9bc6ca23d3dbe2341575ad4 SHA512 78a63b22fc00b1ab9b60161ab0ea79d7c760539f1c69386cba1c9844099b597dc8a8a77940e019f126cb989ae63c3f2418493f4e8e86f6605662d7f2904108e4 diff --git a/dev-python/smart-open/metadata.xml b/dev-python/smart-open/metadata.xml new file mode 100644 index 000000000..6c86761f0 --- /dev/null +++ b/dev-python/smart-open/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <upstream> + <remote-id type="github">RaRe-Technologies/smart_open</remote-id> + <remote-id type="pypi">smart-open</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/smart-open/smart-open-6.3.0.ebuild b/dev-python/smart-open/smart-open-6.3.0.ebuild new file mode 100644 index 000000000..b585f1d4b --- /dev/null +++ b/dev-python/smart-open/smart-open-6.3.0.ebuild @@ -0,0 +1,35 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools + +inherit distutils-r1 + +DESCRIPTION="Utils for streaming large files (S3, HDFS, gzip, bz2...) " +HOMEPAGE="https://github.com/RaRe-Technologies/smart_open" +SRC_URI="https://github.com/RaRe-Technologies/smart_open/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz" +S="${WORKDIR}/${PN//-/_}-${PV}" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + dev-python/boto3[${PYTHON_USEDEP}] + dev-python/google-cloud-storage[${PYTHON_USEDEP}] + dev-python/requests[${PYTHON_USEDEP}] + dev-python/paramiko[${PYTHON_USEDEP}] +" + +BDEPEND=" + test? ( + dev-python/moto[${PYTHON_USEDEP}] + dev-python/responses[${PYTHON_USEDEP}] + dev-python/pytest-rerunfailures[${PYTHON_USEDEP}] + ) +" + +distutils_enable_tests pytest diff --git a/dev-python/snakemake/Manifest b/dev-python/snakemake/Manifest index d82883f77..eca03bc0e 100644 --- a/dev-python/snakemake/Manifest +++ b/dev-python/snakemake/Manifest @@ -1 +1 @@ -DIST snakemake-5.32.2.tar.gz 7010842 BLAKE2B 70526d55ae058d4658c9486cad993fd626308c2ae21cc8e4a484c4f0916d5835ab27b6205e500b13303cae13f659bd542442b1e9a255b7f7f4b7cb4878694a17 SHA512 aa9c53f451bcf454209df25c5bbc795c4d67f27d1b3fe641ce9b788ee1350826e0a4d92514a50fbce58e5a3a462cca9c4015a58646a36a6a3f043381cc5b929d +DIST snakemake-7.32.4.gh.tar.gz 8885863 BLAKE2B 6bb7ff4722dd06f0edf5e8079b42f5e54d6f55f41e2987b7dae7f9b75df0d4d836138e28340e5977107a5cc0b5afe793b0d7897c501246cc1b4340eb4eca2f17 SHA512 34fef61528b18facab798652c88ed5c698ef02161e023255fdd024b7c7781c4e582cdb04b2740fdff9b6f3600acaec719742984acee57920bb48ef3b5af99d9a diff --git a/dev-python/snakemake/metadata.xml b/dev-python/snakemake/metadata.xml index 440b5758f..74c76cce1 100644 --- a/dev-python/snakemake/metadata.xml +++ b/dev-python/snakemake/metadata.xml @@ -5,8 +5,12 @@ <email>mschu.dev@gmail.com</email> <name>Michael Schubert</name> </maintainer> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> <upstream> - <remote-id type="bitbucket">johanneskoester/snakemake</remote-id> <remote-id type="pypi">snakemake</remote-id> + <remote-id type="github">snakemake/snakemake</remote-id> </upstream> </pkgmetadata> diff --git a/dev-python/snakemake/snakemake-5.32.2.ebuild b/dev-python/snakemake/snakemake-5.32.2.ebuild deleted file mode 100644 index 59d2f061a..000000000 --- a/dev-python/snakemake/snakemake-5.32.2.ebuild +++ /dev/null @@ -1,56 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{8..9} ) -DISTUTILS_USE_SETUPTOOLS=rdepend - -inherit distutils-r1 - -DESCRIPTION="Make-like task language" -HOMEPAGE="https://snakemake.readthedocs.io" -SRC_URI="https://github.com/${PN}/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -# missing test dep google.cloud -RESTRICT="test" - -BDEPEND="test? ( - dev-python/requests-mock[${PYTHON_USEDEP}] - dev-python/google-api-python-client[${PYTHON_USEDEP}] - dev-python/jinja[${PYTHON_USEDEP}] - dev-python/networkx[${PYTHON_USEDEP}] - dev-python/pygments[${PYTHON_USEDEP}] - dev-python/pygraphviz[${PYTHON_USEDEP}] - dev-python/oauth2client[${PYTHON_USEDEP}] - net-libs/google-cloud-cpp -)" - -RDEPEND=" - dev-python/appdirs[${PYTHON_USEDEP}] - dev-python/ConfigArgParse[${PYTHON_USEDEP}] - dev-python/datrie[${PYTHON_USEDEP}] - dev-python/docutils[${PYTHON_USEDEP}] - dev-python/GitPython[${PYTHON_USEDEP}] - dev-python/jsonschema[${PYTHON_USEDEP}] - dev-python/nbformat[${PYTHON_USEDEP}] - dev-python/psutil[${PYTHON_USEDEP}] - dev-python/pyyaml[${PYTHON_USEDEP}] - dev-python/ratelimit[${PYTHON_USEDEP}] - dev-python/requests[${PYTHON_USEDEP}] - dev-python/toposort[${PYTHON_USEDEP}] - dev-python/wrapt[${PYTHON_USEDEP}] - sci-mathematics/pulp[${PYTHON_USEDEP}] -" - -distutils_enable_sphinx docs \ - dev-python/sphinxcontrib-napoleon \ - dev-python/sphinx-argparse \ - dev-python/sphinx_rtd_theme \ - dev-python/docutils \ - dev-python/recommonmark -distutils_enable_tests pytest diff --git a/dev-python/snakemake/snakemake-7.32.4.ebuild b/dev-python/snakemake/snakemake-7.32.4.ebuild new file mode 100644 index 000000000..711aac286 --- /dev/null +++ b/dev-python/snakemake/snakemake-7.32.4.ebuild @@ -0,0 +1,67 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools + +inherit distutils-r1 + +DESCRIPTION="Make-like task language" +HOMEPAGE="https://snakemake.readthedocs.io" +SRC_URI="https://github.com/${PN}/${PN}/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" + +# cannot import name '_helpers' from 'google.cloud' +RESTRICT="test" + +BDEPEND=" + dev-python/tomli[${PYTHON_USEDEP}] + test? ( + dev-python/requests-mock[${PYTHON_USEDEP}] + dev-python/google-api-python-client[${PYTHON_USEDEP}] + dev-python/networkx[${PYTHON_USEDEP}] + dev-python/pygments[${PYTHON_USEDEP}] + dev-python/pygraphviz[${PYTHON_USEDEP}] + net-libs/google-cloud-cpp + ) +" + +RDEPEND=" + dev-python/appdirs[${PYTHON_USEDEP}] + dev-python/ConfigArgParse[${PYTHON_USEDEP}] + dev-python/connection_pool[${PYTHON_USEDEP}] + dev-python/datrie[${PYTHON_USEDEP}] + dev-python/docutils[${PYTHON_USEDEP}] + dev-python/GitPython[${PYTHON_USEDEP}] + dev-python/humanfriendly[${PYTHON_USEDEP}] + dev-python/jinja[${PYTHON_USEDEP}] + dev-python/jsonschema[${PYTHON_USEDEP}] + dev-python/nbformat[${PYTHON_USEDEP}] + dev-python/packaging[${PYTHON_USEDEP}] + dev-python/psutil[${PYTHON_USEDEP}] + dev-python/pyyaml[${PYTHON_USEDEP}] + dev-python/requests[${PYTHON_USEDEP}] + dev-python/reretry[${PYTHON_USEDEP}] + dev-python/smart-open[${PYTHON_USEDEP}] + dev-python/stopit[${PYTHON_USEDEP}] + dev-python/tabulate[${PYTHON_USEDEP}] + dev-python/throttler[${PYTHON_USEDEP}] + dev-python/toposort[${PYTHON_USEDEP}] + dev-python/wrapt[${PYTHON_USEDEP}] + dev-python/yte[${PYTHON_USEDEP}] + sci-mathematics/pulp[${PYTHON_USEDEP}] +" + +distutils_enable_sphinx docs \ + dev-python/sphinxcontrib-napoleon \ + dev-python/sphinx-argparse \ + dev-python/sphinx-rtd-theme \ + dev-python/docutils \ + dev-python/recommonmark \ + dev-python/myst-parser +distutils_enable_tests pytest diff --git a/dev-python/snuggs/snuggs-1.4.7.ebuild b/dev-python/snuggs/snuggs-1.4.7.ebuild index ebae883ff..be3395de7 100644 --- a/dev-python/snuggs/snuggs-1.4.7.ebuild +++ b/dev-python/snuggs/snuggs-1.4.7.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) DISTUTILS_USE_PEP517="setuptools" inherit distutils-r1 diff --git a/dev-python/spectra/Manifest b/dev-python/spectra/Manifest new file mode 100644 index 000000000..97bcfc93a --- /dev/null +++ b/dev-python/spectra/Manifest @@ -0,0 +1 @@ +DIST spectra-0.0.11.tar.gz 18819 BLAKE2B 45ceefa8d2bab051a8fa8ee687f9fa25f6436e66987bb84c6982f64a522fb0b04120e068ef890f4b04f6626a130c5df1e81090913c143df1e82bda5ca3a01d4d SHA512 7b4e244ba200df8c6d7cff19ddf36a5af6cfe8cf6f89283f8dbb64345a3eb85b4f62456e3c75b7c8ce2d24e01c8a123a5763605b1e702903fe16839966e47b32 diff --git a/dev-python/spectra/metadata.xml b/dev-python/spectra/metadata.xml new file mode 100644 index 000000000..9332eceee --- /dev/null +++ b/dev-python/spectra/metadata.xml @@ -0,0 +1,12 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>mschu.dev@gmail.com</email> + <name>Michael Schubert</name> + </maintainer> + <upstream> + <remote-id type="github">jsvine/spectra</remote-id> + <remote-id type="pypi">spectra</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/spectra/spectra-0.0.11.ebuild b/dev-python/spectra/spectra-0.0.11.ebuild new file mode 100644 index 000000000..d0df23724 --- /dev/null +++ b/dev-python/spectra/spectra-0.0.11.ebuild @@ -0,0 +1,22 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..12} ) + +inherit pypi distutils-r1 + +DESCRIPTION="Easy color scales and color conversion for Python" +HOMEPAGE="https://pypi.org/project/spectra/" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~amd64-linux" + +RDEPEND="dev-python/colormath[${PYTHON_USEDEP}]" + +# requires nose +RESTRICT="test" +#distutils_enable_tests pytest diff --git a/dev-python/specutils/Manifest b/dev-python/specutils/Manifest index a612bb26f..9ee9c42c5 100644 --- a/dev-python/specutils/Manifest +++ b/dev-python/specutils/Manifest @@ -1 +1 @@ -DIST specutils-1.1.1.tar.gz 508922 BLAKE2B fb7eafae5ccdd1b7e73d2bf45c5e9b490ddfbae35cb583a1db5ba9bae7fa9e568f6064929395ddcba9a31ead5552d6e59c5b2da1c4684af09f5080fc5c43a284 SHA512 f20c7a3f3c8bd59d0fd3532ca3c52bea651c726d3d5ee7570d840babee73f83bbaeb6a18cd370393d739835358a768771b232ce81df211efee32b795fd61cddc +DIST specutils-1.9.1.tar.gz 665564 BLAKE2B 733bfecfdc61a03f85bc7f7588724eac869db66e135c4ef22993c3b1d537b67ef6ca784d03a0182741684282c4a7385642352f20d3fce948f0b26a4e950ba82f SHA512 f06e878539173b3c8a9220fd87f8deff15db744c3d267405afb1a43f98c181440c160c5396c636d2f6e2ed4373055537e6274e4a65e5f4e82f9163a446a6d450 diff --git a/dev-python/specutils/metadata.xml b/dev-python/specutils/metadata.xml index d8e354751..1055c50cb 100644 --- a/dev-python/specutils/metadata.xml +++ b/dev-python/specutils/metadata.xml @@ -12,5 +12,6 @@ into a class with special handling of 1D spectra. </longdescription> <upstream> <remote-id type="github">astropy/specutils</remote-id> + <remote-id type="pypi">specutils</remote-id> </upstream> </pkgmetadata> diff --git a/dev-python/specutils/specutils-1.1.1.ebuild b/dev-python/specutils/specutils-1.1.1.ebuild deleted file mode 100644 index 24f1d3118..000000000 --- a/dev-python/specutils/specutils-1.1.1.ebuild +++ /dev/null @@ -1,39 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7,8,9} ) -DISTUTILS_USE_SETUPTOOLS=rdepend - -inherit distutils-r1 - -DESCRIPTION="Package for spectroscopic astronomical data" -HOMEPAGE="https://github.com/astropy/specutils" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -# Requires access to the internet -RESTRICT="test" - -RDEPEND=" - dev-python/asdf[${PYTHON_USEDEP}] - >=dev-python/astropy-4.0[${PYTHON_USEDEP}] - dev-python/astropy-helpers[${PYTHON_USEDEP}] - dev-python/gwcs[${PYTHON_USEDEP}] - dev-python/scipy[${PYTHON_USEDEP}] -" - -# Bug: https://bugs.gentoo.org/703778 -#distutils_enable_sphinx docs dev-python/sphinx-astropy -distutils_enable_tests pytest - -python_prepare_all() { - # do not depend on pytest-datafiles - sed -i -e '/addopts =/d' setup.cfg || die - - distutils-r1_python_prepare_all -} diff --git a/dev-python/specutils/specutils-1.9.1.ebuild b/dev-python/specutils/specutils-1.9.1.ebuild new file mode 100644 index 000000000..c77a1078d --- /dev/null +++ b/dev-python/specutils/specutils-1.9.1.ebuild @@ -0,0 +1,38 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools + +inherit distutils-r1 pypi + +DESCRIPTION="Package for spectroscopic astronomical data" +HOMEPAGE="https://github.com/astropy/specutils" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +# Requires access to the internet +RESTRICT="test" + +RDEPEND=" + dev-python/asdf[${PYTHON_USEDEP}] + >=dev-python/astropy-4.0[${PYTHON_USEDEP}] + dev-python/astropy-helpers[${PYTHON_USEDEP}] + dev-python/gwcs[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] +" + +# Bug: https://bugs.gentoo.org/703778 +#distutils_enable_sphinx docs dev-python/sphinx-astropy +distutils_enable_tests pytest + +python_prepare_all() { + # do not depend on pytest-datafiles + sed -i -e '/addopts =/d' setup.cfg || die + + distutils-r1_python_prepare_all +} diff --git a/dev-python/sphinx-argparse/Manifest b/dev-python/sphinx-argparse/Manifest deleted file mode 100644 index cc6a6ba19..000000000 --- a/dev-python/sphinx-argparse/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST sphinx-argparse-0.3.1.tar.gz 42953 BLAKE2B 76c74a270a638b1b894548bc898918fbfa5fde6bcf1ccbf5e69a3daaada829bc1ae27ad8befd18e834646dc2fc3b025f36807c2be894911cc0c6d65294174898 SHA512 3d289c90165eb6a3d7a94dff8e6a429a49eb404ce373e80e007a0cd9abaae1e1236f5393df2fbf11701c349dade9d199640dc398064da4fd50a58a90eb3f8f12 diff --git a/dev-python/sphinx-argparse/metadata.xml b/dev-python/sphinx-argparse/metadata.xml deleted file mode 100644 index ae9640ffb..000000000 --- a/dev-python/sphinx-argparse/metadata.xml +++ /dev/null @@ -1,8 +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> -</pkgmetadata> diff --git a/dev-python/sphinx-argparse/sphinx-argparse-0.3.1.ebuild b/dev-python/sphinx-argparse/sphinx-argparse-0.3.1.ebuild deleted file mode 100644 index 5b380202e..000000000 --- a/dev-python/sphinx-argparse/sphinx-argparse-0.3.1.ebuild +++ /dev/null @@ -1,27 +0,0 @@ -# Copyright 2020-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{8..9} ) -DISTUTILS_USE_SETUPTOOLS=pyproject.toml -inherit distutils-r1 - -DESCRIPTION="Sphinx extension that automatically documents argparse commands and options" -HOMEPAGE="https://pypi.org/project/sphinx-argparse/ - https://github.com/ashb/sphinx-argparse" -SRC_URI="https://github.com/ashb/${PN}/archive/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -DEPEND="" -RDEPEND="${DEPEND} - dev-python/sphinx[${PYTHON_USEDEP}] - dev-python/commonmark[${PYTHON_USEDEP}] -" - -distutils_enable_tests pytest -# requires self to build own documentation -distutils_enable_sphinx docs dev-python/sphinx_rtd_theme dev-python/sphinx-argparse diff --git a/dev-python/sphinx-astropy/Manifest b/dev-python/sphinx-astropy/Manifest index 26a909677..7cbf6d7c8 100644 --- a/dev-python/sphinx-astropy/Manifest +++ b/dev-python/sphinx-astropy/Manifest @@ -1 +1 @@ -DIST sphinx-astropy-1.7.0.tar.gz 18266 BLAKE2B 363733c5a3e5974cdf0f62f879babc9a28617ff61d15292649acd189798e24611c2d84e69af5dc05b89241f395cc997233f966bdf8e8a84ccfe235f873d533c2 SHA512 4b9af1528805c5017695be6ad9d0b789437da4ea01080190d5c0e44a76d927098864002cfd2a59529924a8d2844e26d2e7635fb3f0417ed90502e7e47d0239d3 +DIST sphinx-astropy-1.8.0.tar.gz 18310 BLAKE2B 0d13ba59b2ffcb792e66e58d2a87057b79da811d38e6fd101b074b0edbf5ad6d76e79300f5863521b0bbb1b40921ba6773f8d37c32d68dd36078cb2d0497e2ff SHA512 f02fe8d3ed58ffeff190492c07e2df91a2bd5bcc8e82c6685002e543585a5fc1294ebd46821b7dc0a364540f3a45adacf1b90261b7da95657bc99dcd6130f4d5 diff --git a/dev-python/sphinx-astropy/metadata.xml b/dev-python/sphinx-astropy/metadata.xml index 4f4367037..8d01c3b18 100644 --- a/dev-python/sphinx-astropy/metadata.xml +++ b/dev-python/sphinx-astropy/metadata.xml @@ -5,4 +5,7 @@ <email>sci-astronomy@gentoo.org</email> <name>Gentoo Astronomy Project</name> </maintainer> + <upstream> + <remote-id type="pypi">sphinx-astropy</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/sphinx-astropy/sphinx-astropy-1.7.0.ebuild b/dev-python/sphinx-astropy/sphinx-astropy-1.7.0.ebuild deleted file mode 100644 index be4395414..000000000 --- a/dev-python/sphinx-astropy/sphinx-astropy-1.7.0.ebuild +++ /dev/null @@ -1,31 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{8..10} ) - -inherit distutils-r1 - -DESCRIPTION="Sphinx extensions and configuration specific to the Astropy project" -HOMEPAGE="https://astropy.org/" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -# Requires access to the internet -RESTRICT="test" - -RDEPEND=" - dev-python/packaging[${PYTHON_USEDEP}] - dev-python/astropy-sphinx-theme[${PYTHON_USEDEP}] - dev-python/numpydoc[${PYTHON_USEDEP}] - >=dev-python/sphinx-1.7[${PYTHON_USEDEP}] - dev-python/sphinx-automodapi[${PYTHON_USEDEP}] - dev-python/sphinx-gallery[${PYTHON_USEDEP}] - dev-python/pillow[${PYTHON_USEDEP}] -" - -distutils_enable_tests pytest diff --git a/dev-python/sphinx-astropy/sphinx-astropy-1.8.0.ebuild b/dev-python/sphinx-astropy/sphinx-astropy-1.8.0.ebuild new file mode 100644 index 000000000..89d58fc6b --- /dev/null +++ b/dev-python/sphinx-astropy/sphinx-astropy-1.8.0.ebuild @@ -0,0 +1,32 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools +PYPI_NO_NORMALIZE=1 + +inherit distutils-r1 pypi + +DESCRIPTION="Sphinx extensions and configuration specific to the Astropy project" +HOMEPAGE="https://www.astropy.org/" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +# Requires access to the internet +RESTRICT="test" + +RDEPEND=" + dev-python/packaging[${PYTHON_USEDEP}] + dev-python/astropy-sphinx-theme[${PYTHON_USEDEP}] + dev-python/numpydoc[${PYTHON_USEDEP}] + >=dev-python/sphinx-1.7[${PYTHON_USEDEP}] + dev-python/sphinx-automodapi[${PYTHON_USEDEP}] + dev-python/sphinx-gallery[${PYTHON_USEDEP}] + dev-python/pillow[${PYTHON_USEDEP}] +" + +distutils_enable_tests pytest diff --git a/dev-python/sphinx-automodapi/metadata.xml b/dev-python/sphinx-automodapi/metadata.xml index 4f4367037..092a8c5e9 100644 --- a/dev-python/sphinx-automodapi/metadata.xml +++ b/dev-python/sphinx-automodapi/metadata.xml @@ -5,4 +5,7 @@ <email>sci-astronomy@gentoo.org</email> <name>Gentoo Astronomy Project</name> </maintainer> + <upstream> + <remote-id type="pypi">sphinx-automodapi</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/sphinx-automodapi/sphinx-automodapi-0.14.1-r1.ebuild b/dev-python/sphinx-automodapi/sphinx-automodapi-0.14.1-r1.ebuild new file mode 100644 index 000000000..e64b9a0e0 --- /dev/null +++ b/dev-python/sphinx-automodapi/sphinx-automodapi-0.14.1-r1.ebuild @@ -0,0 +1,24 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools +PYPI_NO_NORMALIZE=1 + +inherit distutils-r1 pypi + +DESCRIPTION="Sphinx extension for auto-generating API documentation for entire modules" +HOMEPAGE="https://www.astropy.org/" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +# Requires network for some reason +RESTRICT="test" + +RDEPEND="dev-python/sphinx[${PYTHON_USEDEP}]" + +distutils_enable_tests pytest diff --git a/dev-python/sphinx-automodapi/sphinx-automodapi-0.14.1.ebuild b/dev-python/sphinx-automodapi/sphinx-automodapi-0.14.1.ebuild deleted file mode 100644 index f98b972ae..000000000 --- a/dev-python/sphinx-automodapi/sphinx-automodapi-0.14.1.ebuild +++ /dev/null @@ -1,23 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{8..10} ) - -inherit distutils-r1 - -DESCRIPTION="Sphinx extension for auto-generating API documentation for entire modules" -HOMEPAGE="https://astropy.org/" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -# Requires network for some reason -RESTRICT="test" - -RDEPEND="dev-python/sphinx[${PYTHON_USEDEP}]" - -distutils_enable_tests pytest diff --git a/dev-python/sphinxcontrib-napoleon/sphinxcontrib-napoleon-0.7-r1.ebuild b/dev-python/sphinxcontrib-napoleon/sphinxcontrib-napoleon-0.7-r1.ebuild new file mode 100644 index 000000000..0a962fd5e --- /dev/null +++ b/dev-python/sphinxcontrib-napoleon/sphinxcontrib-napoleon-0.7-r1.ebuild @@ -0,0 +1,30 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools +PYPI_NO_NORMALIZE=1 + +inherit distutils-r1 pypi + +DESCRIPTION="Allow a different format in dosctrings for better clarity" +HOMEPAGE="https://sphinxcontrib-napoleon.readthedocs.io/" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +RDEPEND=" + dev-python/sphinx[${PYTHON_USEDEP}] +" +DEPEND=" + dev-python/pockets[${PYTHON_USEDEP}] + dev-python/six[${PYTHON_USEDEP}] +" + +python_install_all() { + distutils-r1_python_install_all + find "${ED}" -name '*.pth' -delete || die +} diff --git a/dev-python/sphinxcontrib-napoleon/sphinxcontrib-napoleon-0.7.ebuild b/dev-python/sphinxcontrib-napoleon/sphinxcontrib-napoleon-0.7.ebuild deleted file mode 100644 index 7680d8206..000000000 --- a/dev-python/sphinxcontrib-napoleon/sphinxcontrib-napoleon-0.7.ebuild +++ /dev/null @@ -1,29 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{8..10} ) - -inherit distutils-r1 - -DESCRIPTION="Allow a different format in dosctrings for better clarity" -HOMEPAGE="https://sphinxcontrib-napoleon.readthedocs.io/" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -RDEPEND=" - dev-python/sphinx[${PYTHON_USEDEP}] -" -DEPEND=" - dev-python/pockets[${PYTHON_USEDEP}] - dev-python/six[${PYTHON_USEDEP}] -" - -python_install_all() { - distutils-r1_python_install_all - find "${ED}" -name '*.pth' -delete || die -} diff --git a/dev-python/spikeinterface/Manifest b/dev-python/spikeinterface/Manifest new file mode 100644 index 000000000..bdf3e4b60 --- /dev/null +++ b/dev-python/spikeinterface/Manifest @@ -0,0 +1,3 @@ +DIST spikeinterface-0.96.1.tar.gz 1596455 BLAKE2B 52b5d4f0b435433396e7d06b9a2ed83646280ebefb1f62f179f068a060f43898a822e41bf1500ec53087ad5410ee060806f415988606b0197d13d7a671a5603a SHA512 12de90a8d27e900489d36d0ca14edaac3d1abab1a29f0c41ff1d1648fbf11be09c6c01cb0bd1cc4e1d00a81303fab5ffcb4de596ae69be9508e0503edab768ef +DIST spikeinterface-0.97.0.tar.gz 6735715 BLAKE2B c11bee4306f8d96ae5cd09cf1b852e267c1db6caa13565f6364cd65ee36fe62c04589e8e0657517003ed1dd6d76d25f60bef226820403111db4ed7717e8a20cd SHA512 befdf3382de6aad2ef2c72e3bbdf64fbee1c1f72f83610ca8bba2f8693992c84b515f8c000dc6b3609825347b0bcd85b026747633e90777d7fdd30dc0ae0ef13 +DIST spikeinterface-0.99.1.tar.gz 11475537 BLAKE2B 9427079f70020b882c7bdbaadb9b60508827f1131f3aeb4fa8fdaaada73f2aa2cb3ec018f87467cd2a7505bea435d6bcf04d9784d921829533ebf41d686d72bb SHA512 4dd513aa6eb8af58fa9d1a80671973b01cb81643588c4522f3f87cfd0ccebcfb7a1f2926e554bc7dadbb2201fc0b2f2873b0003483dd5ca578b5a76d4cce05a2 diff --git a/dev-python/spikeinterface/metadata.xml b/dev-python/spikeinterface/metadata.xml new file mode 100644 index 000000000..f91c7a26c --- /dev/null +++ b/dev-python/spikeinterface/metadata.xml @@ -0,0 +1,19 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>gentoo@chymera.eu</email> + <name>Horea Christian</name> + </maintainer> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <use> + <flag name="extractors">support for all extractors</flag> + <flag name="full">support for all optional processing features</flag> + </use> + <upstream> + <remote-id type="github">SpikeInterface/spikeinterface</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/spikeinterface/spikeinterface-0.96.1.ebuild b/dev-python/spikeinterface/spikeinterface-0.96.1.ebuild new file mode 100644 index 000000000..ef6a472f4 --- /dev/null +++ b/dev-python/spikeinterface/spikeinterface-0.96.1.ebuild @@ -0,0 +1,93 @@ +# Copyright 2021-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 + +DESCRIPTION="A Python-based module for creating flexible and robust spike sorting pipelines." +HOMEPAGE="https://github.com/SpikeInterface/spikeinterface" +SRC_URI="https://github.com/SpikeInterface/spikeinterface/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" +IUSE="extractors full test" + +RDEPEND=" + dev-python/joblib[${PYTHON_USEDEP}] + dev-python/neo[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/probeinterface[${PYTHON_USEDEP}] + dev-python/threadpoolctl[${PYTHON_USEDEP}] + dev-python/tqdm[${PYTHON_USEDEP}] + extractors? ( + dev-python/pynwb[${PYTHON_USEDEP}] + dev-python/lxml[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + ) + full? ( + dev-python/distinctipy[${PYTHON_USEDEP}] + dev-python/h5py[${PYTHON_USEDEP}] + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/networkx[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + dev-python/xarray[${PYTHON_USEDEP}] + dev-python/zarr[${PYTHON_USEDEP}] + sci-libs/scikit-learn[${PYTHON_USEDEP}] + ) +" +# Also wants: +# # Extractors: +# MEArec +# pyedflib +# sonpy +# dev-python/hdf5storage (in ::science, masked) + +distutils_enable_tests pytest + +# Test failures reported upstream: +# https://github.com/SpikeInterface/spikeinterface/issues/307 +python_test() { + # Network sandboxing, mostly (?) + local EPYTEST_DESELECT=( + spikeinterface/core/tests/test_datasets.py::test_download_dataset + spikeinterface/sortingcomponents/tests/test_motion_estimation.py::test_motion_functions + spikeinterface/sortingcomponents/tests/test_motion_estimation.py::test_estimate_motion_rigid + spikeinterface/sortingcomponents/tests/test_motion_estimation.py::test_estimate_motion_non_rigid + spikeinterface/comparison/tests/test_multisortingcomparison.py::test_compare_multiple_sorters + spikeinterface/curation/tests/test_sortingview_curation.py::test_sortingview_curation + spikeinterface/exporters/tests/test_export_to_phy.py::test_export_to_phy + spikeinterface/exporters/tests/test_export_to_phy.py::test_export_to_phy_by_sparsity + spikeinterface/exporters/tests/test_report.py::test_export_report + spikeinterface/extractors/tests/test_neoextractors.py + spikeinterface/sorters/tests/test_launcher.py::test_run_sorters_with_dict + spikeinterface/sorters/tests/test_launcher.py::test_sorter_installation + spikeinterface/sorters/tests/test_runsorter.py::test_run_sorter_local + spikeinterface/sorters/tests/test_runsorter.py::test_run_sorter_docker + spikeinterface/sorters/tests/test_runsorter.py::test_run_sorter_singularity + spikeinterface/sorters/tests/test_si_based_sorters.py::SpykingCircus2SorterCommonTestSuite + spikeinterface/sorters/tests/test_si_based_sorters.py::Tridesclous2SorterCommonTestSuite::test_with_class + spikeinterface/sorters/tests/test_si_based_sorters.py::Tridesclous2SorterCommonTestSuite::test_with_run + spikeinterface/sortingcomponents/tests/test_clustering.py::test_find_cluster_from_peaks + spikeinterface/sortingcomponents/tests/test_features_from_peaks.py::test_features_from_peaks + spikeinterface/sortingcomponents/tests/test_peak_detection.py::test_detect_peaks + spikeinterface/sortingcomponents/tests/test_peak_localization.py::test_localize_peaks + spikeinterface/sortingcomponents/tests/test_peak_pipeline.py::test_run_peak_pipeline + spikeinterface/sortingcomponents/tests/test_peak_selection.py::test_detect_peaks + spikeinterface/sortingcomponents/tests/test_template_matching.py::test_find_spikes_from_templates + spikeinterface/widgets/tests/test_widgets.py::TestWidgets + ) + # Reported upstream: + # https://github.com/SpikeInterface/spikeinterface/issues/307#issuecomment-1410840998 + EPYTEST_DESELECT+=( + spikeinterface/sorters/tests/test_launcher.py::test_collect_sorting_outputs + ) + local EPYTEST_IGNORE=( + spikeinterface/widgets/_legacy_mpl_widgets/tests/* + ) + epytest +} diff --git a/dev-python/spikeinterface/spikeinterface-0.97.0.ebuild b/dev-python/spikeinterface/spikeinterface-0.97.0.ebuild new file mode 100644 index 000000000..2a25d4eee --- /dev/null +++ b/dev-python/spikeinterface/spikeinterface-0.97.0.ebuild @@ -0,0 +1,93 @@ +# Copyright 2021-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 + +DESCRIPTION="A Python-based module for creating flexible and robust spike sorting pipelines." +HOMEPAGE="https://github.com/SpikeInterface/spikeinterface" +SRC_URI="https://github.com/SpikeInterface/spikeinterface/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" +IUSE="extractors full test" + +RDEPEND=" + dev-python/joblib[${PYTHON_USEDEP}] + dev-python/neo[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + >=dev-python/probeinterface-0.2.16[${PYTHON_USEDEP}] + dev-python/threadpoolctl[${PYTHON_USEDEP}] + dev-python/tqdm[${PYTHON_USEDEP}] + extractors? ( + dev-python/pynwb[${PYTHON_USEDEP}] + dev-python/lxml[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + ) + full? ( + dev-python/distinctipy[${PYTHON_USEDEP}] + dev-python/h5py[${PYTHON_USEDEP}] + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/networkx[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + dev-python/xarray[${PYTHON_USEDEP}] + dev-python/zarr[${PYTHON_USEDEP}] + sci-libs/scikit-learn[${PYTHON_USEDEP}] + ) +" +# Also wants: +# # Extractors: +# MEArec +# pyedflib +# sonpy +# dev-python/hdf5storage (in ::science, masked) + +distutils_enable_tests pytest + +# Test failures reported upstream: +# https://github.com/SpikeInterface/spikeinterface/issues/307 +python_test() { + # Network sandboxing, mostly (?) + local EPYTEST_DESELECT=( + spikeinterface/core/tests/test_datasets.py::test_download_dataset + spikeinterface/sortingcomponents/tests/test_motion_estimation.py::test_motion_functions + spikeinterface/sortingcomponents/tests/test_motion_estimation.py::test_estimate_motion_rigid + spikeinterface/sortingcomponents/tests/test_motion_estimation.py::test_estimate_motion_non_rigid + spikeinterface/comparison/tests/test_multisortingcomparison.py::test_compare_multiple_sorters + spikeinterface/curation/tests/test_sortingview_curation.py::test_sortingview_curation + spikeinterface/exporters/tests/test_export_to_phy.py::test_export_to_phy + spikeinterface/exporters/tests/test_export_to_phy.py::test_export_to_phy_by_sparsity + spikeinterface/exporters/tests/test_report.py::test_export_report + spikeinterface/extractors/tests/test_neoextractors.py + spikeinterface/sorters/tests/test_launcher.py::test_run_sorters_with_dict + spikeinterface/sorters/tests/test_launcher.py::test_sorter_installation + spikeinterface/sorters/tests/test_runsorter.py::test_run_sorter_local + spikeinterface/sorters/tests/test_runsorter.py::test_run_sorter_docker + spikeinterface/sorters/tests/test_runsorter.py::test_run_sorter_singularity + spikeinterface/sorters/tests/test_si_based_sorters.py::SpykingCircus2SorterCommonTestSuite + spikeinterface/sorters/tests/test_si_based_sorters.py::Tridesclous2SorterCommonTestSuite::test_with_class + spikeinterface/sorters/tests/test_si_based_sorters.py::Tridesclous2SorterCommonTestSuite::test_with_run + spikeinterface/sortingcomponents/tests/test_clustering.py::test_find_cluster_from_peaks + spikeinterface/sortingcomponents/tests/test_features_from_peaks.py::test_features_from_peaks + spikeinterface/sortingcomponents/tests/test_peak_detection.py::test_detect_peaks + spikeinterface/sortingcomponents/tests/test_peak_localization.py::test_localize_peaks + spikeinterface/sortingcomponents/tests/test_peak_pipeline.py::test_run_peak_pipeline + spikeinterface/sortingcomponents/tests/test_peak_selection.py::test_detect_peaks + spikeinterface/sortingcomponents/tests/test_template_matching.py::test_find_spikes_from_templates + spikeinterface/widgets/tests/test_widgets.py::TestWidgets + ) + # Reported upstream: + # https://github.com/SpikeInterface/spikeinterface/issues/307#issuecomment-1410840998 + EPYTEST_DESELECT+=( + spikeinterface/sorters/tests/test_launcher.py::test_collect_sorting_outputs + ) + local EPYTEST_IGNORE=( + spikeinterface/widgets/_legacy_mpl_widgets/tests/* + ) + epytest +} diff --git a/dev-python/spikeinterface/spikeinterface-0.99.1.ebuild b/dev-python/spikeinterface/spikeinterface-0.99.1.ebuild new file mode 100644 index 000000000..a428775eb --- /dev/null +++ b/dev-python/spikeinterface/spikeinterface-0.99.1.ebuild @@ -0,0 +1,53 @@ +# Copyright 2021-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 + +DESCRIPTION="A Python-based module for creating flexible and robust spike sorting pipelines." +HOMEPAGE="https://github.com/SpikeInterface/spikeinterface" +SRC_URI="https://github.com/SpikeInterface/spikeinterface/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" +IUSE="extractors full test" +# Reported upstream: +# https://github.com/SpikeInterface/spikeinterface/issues/2339 +RESTRICT="test" + +RDEPEND=" + dev-python/joblib[${PYTHON_USEDEP}] + dev-python/neo[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + >=dev-python/probeinterface-0.2.16[${PYTHON_USEDEP}] + dev-python/threadpoolctl[${PYTHON_USEDEP}] + dev-python/tqdm[${PYTHON_USEDEP}] + extractors? ( + dev-python/pynwb[${PYTHON_USEDEP}] + dev-python/lxml[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + ) + full? ( + dev-python/distinctipy[${PYTHON_USEDEP}] + dev-python/h5py[${PYTHON_USEDEP}] + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/networkx[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + dev-python/xarray[${PYTHON_USEDEP}] + dev-python/zarr[${PYTHON_USEDEP}] + sci-libs/scikit-learn[${PYTHON_USEDEP}] + ) +" +# Also wants: +# # Extractors: +# MEArec +# pyedflib +# sonpy +# dev-python/hdf5storage (in ::science, masked) + +distutils_enable_tests pytest diff --git a/dev-python/stopit/Manifest b/dev-python/stopit/Manifest new file mode 100644 index 000000000..8509ce69f --- /dev/null +++ b/dev-python/stopit/Manifest @@ -0,0 +1 @@ +DIST stopit-1.1.2.tar.gz 18281 BLAKE2B 500c4c60f7a1ae65231f546c28c6406bb1b01c48b43ac97757b87db1c6cfe460b9fb96543a46ec4ff36640e6aa758dbea543f75628bf7bf237e1f76acd54e62e SHA512 5ddf93c12ac19e2a2bf52a22838de13da1cf50f1a4d2ef8958dc3ddccd1884b7edaa629edc29121071ba231bfc1e3188bfa089da6e8fc994364c134f0c7aa0c8 diff --git a/dev-python/stopit/metadata.xml b/dev-python/stopit/metadata.xml new file mode 100644 index 000000000..21d0546f4 --- /dev/null +++ b/dev-python/stopit/metadata.xml @@ -0,0 +1,11 @@ +<?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> + <upstream> + <remote-id type="pypi">stopit</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/stopit/stopit-1.1.2.ebuild b/dev-python/stopit/stopit-1.1.2.ebuild new file mode 100644 index 000000000..64d63502a --- /dev/null +++ b/dev-python/stopit/stopit-1.1.2.ebuild @@ -0,0 +1,16 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools + +inherit distutils-r1 pypi + +DESCRIPTION="Timeout control decorator and context managers" +HOMEPAGE="https://pypi.org/project/stopit" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" diff --git a/dev-python/texext/Manifest b/dev-python/texext/Manifest index acfea3010..3300b31c6 100644 --- a/dev-python/texext/Manifest +++ b/dev-python/texext/Manifest @@ -1 +1 @@ -DIST texext-0.6.6.tar.gz 38121 BLAKE2B 655ac678ecf1de5f7fa34148bff93c4ba8a28253117afccc197da3e44592024a6ec523452c2e02697275f4061ae2452beae74e9d3fa305eb1faddffb33c992ac SHA512 117a74c85fc36af8921a145e387b560e3c6c115090f777539178021cafac0075077fc81c62d18fa2bbee0b0f59e256274a9526f2a688d00a99ecbda2ac944ccd +DIST texext-0.6.7.gh.tar.gz 42823 BLAKE2B 224cb700f5ee74de75c41d8248a1cbb494f773f8124638974fbabdbffcd2bf72237c55b15e12ea8e5a5086dab02fde798efe5f3519befddb1a4535ed233414a3 SHA512 abdc57f9fd38b3d6e261347a3ba2d7d7400d8b7bd79c2763a40cc34aa72a079fe55dae1fc0117f2da604331a449b2d9168f320a6ecc2f13c62a6615c000523f8 diff --git a/dev-python/texext/texext-0.6.6.ebuild b/dev-python/texext/texext-0.6.6.ebuild deleted file mode 100644 index 15d6a83d1..000000000 --- a/dev-python/texext/texext-0.6.6.ebuild +++ /dev/null @@ -1,33 +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="Sphinx extensions for working with LaTeX math" -HOMEPAGE="https://github.com/matthew-brett/texext" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -# TODO: package sphinxtesters -# E ModuleNotFoundError: No module named 'sphinxtesters' -RESTRICT="test" - -RDEPEND=" - dev-python/sphinx[${PYTHON_USEDEP}] - dev-python/six[${PYTHON_USEDEP}] - dev-python/docutils[${PYTHON_USEDEP}] -" - -BDEPEND="test? ( - dev-python/matplotlib[${PYTHON_USEDEP}] - dev-python/sympy[${PYTHON_USEDEP}] -)" - -distutils_enable_tests pytest diff --git a/dev-python/texext/texext-0.6.7.ebuild b/dev-python/texext/texext-0.6.7.ebuild new file mode 100644 index 000000000..fdeb2350a --- /dev/null +++ b/dev-python/texext/texext-0.6.7.ebuild @@ -0,0 +1,33 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_10 ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 + +DESCRIPTION="Sphinx extensions for working with LaTeX math" +HOMEPAGE="https://github.com/matthew-brett/texext" +SRC_URI="https://github.com/matthew-brett/texext/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +# TODO: package sphinxtesters +# E ModuleNotFoundError: No module named 'sphinxtesters' +RESTRICT="test" + +RDEPEND=" + dev-python/sphinx[${PYTHON_USEDEP}] + dev-python/six[${PYTHON_USEDEP}] + dev-python/docutils[${PYTHON_USEDEP}] +" + +BDEPEND="test? ( + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/sympy[${PYTHON_USEDEP}] +)" + +distutils_enable_tests pytest diff --git a/dev-python/throttler/Manifest b/dev-python/throttler/Manifest new file mode 100644 index 000000000..fcd07b799 --- /dev/null +++ b/dev-python/throttler/Manifest @@ -0,0 +1 @@ +DIST throttler-1.2.2.gh.tar.gz 8874 BLAKE2B f4f62059483551d2516e0d744ce4de4de1d83c5d169583944f2fba390acc2f6aadd5f212158de2c59b85356d71396a02404051e9206dfffec25be95ae983686a SHA512 a45cba0400e2e6225bcc396d1a216e781be9264345c215aa0c9e009d463bb80fca449ef0cc6a67657c443f9624e0864644cd5187351e815292894176dd6f13bb diff --git a/dev-python/throttler/metadata.xml b/dev-python/throttler/metadata.xml new file mode 100644 index 000000000..dff8139fd --- /dev/null +++ b/dev-python/throttler/metadata.xml @@ -0,0 +1,12 @@ +<?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> + <upstream> + <remote-id type="github">uburuntu/throttler</remote-id> + <remote-id type="pypi">throttler</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/throttler/throttler-1.2.2.ebuild b/dev-python/throttler/throttler-1.2.2.ebuild new file mode 100644 index 000000000..0d0d62a16 --- /dev/null +++ b/dev-python/throttler/throttler-1.2.2.ebuild @@ -0,0 +1,25 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools + +inherit distutils-r1 + +DESCRIPTION="Easy throttling with asyncio support" +HOMEPAGE="https://github.com/uburuntu/throttler" +SRC_URI="https://github.com/uburuntu/throttler/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" + +BDEPEND=" + test? ( + dev-python/pytest-asyncio[${PYTHON_USEDEP}] + ) +" + +distutils_enable_tests pytest diff --git a/dev-python/traits/Manifest b/dev-python/traits/Manifest index 4c0fe0428..c33b93d1f 100644 --- a/dev-python/traits/Manifest +++ b/dev-python/traits/Manifest @@ -1,2 +1,2 @@ -DIST traits-6.0.0.tar.gz 441607 BLAKE2B d8f28e8ccdca8d65a4abb71210f6fe36d6fd2eb07ce5e8f1d374a64cf44e9ce95a318274c68b6791c91f2e105c4f9385e4a743d33434b608ce1d939693958e33 SHA512 b89f844b18c97e2fd2239fc74253e83f255aa231a3d02207a5acf27da7686c32c57cb7c36ffb92a59f7bfa4d98a5e1a95ae2b70e34aa4577a7ae82c8c6756e1e -DIST traits-6.1.1.tar.gz 567019 BLAKE2B 4b6ed46c87b1fda2a2001299106b5aacafbe8b148ba0564c4f39b67a8de76f6713366c8b00841db254a26c87a7b2b73b6935ecade770d92ad972aa8a0425cecf SHA512 7f7e9f11d4861c02164ae1ce595888859c8ce23213290cfc3ac11df100d33beeeea4c7def6799b70ef2d090b3f7bd98407f3605affff0867914d0fe0164dd50f +DIST traits-6.3.2.tar.gz 9517139 BLAKE2B 9c6209a24fd07def86699174a66e2e0b3332670d974a75ead9486187c37e1c2c25b2a0c47e5444a03577931411ce6938b3b9ba195261a46c86d660c5abe9b502 SHA512 792004d88d2a00a1e9ba03974d58ec692b620f3c45aaf3bd82f93396818df8663a86903d43806c877230a66c5c8fee4d68268ed9355c166af00b5d060ba14c7d +DIST traits-6.4.1.tar.gz 9527016 BLAKE2B 12036eeb845cc3014b0cba9984e1c1686a6720630678d440a2059c47916c08284b1f823ca566dcb6c1c86594ebec5400bb2a8c44d43d765a25d00e157fbbda74 SHA512 04b936195d57320c02fee9f0d5e7dbcfee28add422c151bd4aaa6d1c58c59f8de7fe54b4df039bb2023ffc9dae9570bba52210cd015ce462e0f736e9439327e5 diff --git a/dev-python/traits/metadata.xml b/dev-python/traits/metadata.xml index ec9460dd1..2e84467ab 100644 --- a/dev-python/traits/metadata.xml +++ b/dev-python/traits/metadata.xml @@ -21,6 +21,7 @@ * Visualization: With the TraitsUI package, GUIs can be generated automatically from traited objects. </longdescription> <upstream> + <remote-id type="github">enthought/traits</remote-id> <remote-id type="pypi">traits</remote-id> </upstream> </pkgmetadata> diff --git a/dev-python/traits/traits-6.0.0.ebuild b/dev-python/traits/traits-6.0.0.ebuild deleted file mode 100644 index 732c6247a..000000000 --- a/dev-python/traits/traits-6.0.0.ebuild +++ /dev/null @@ -1,44 +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="Enthought Tool Suite: Explicitly typed attributes for Python" -HOMEPAGE="https://docs.enthought.com/traits/ - https://github.com/enthought/traits - https://pypi.org/project/traits/" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~ppc ~ppc64 ~x86" -IUSE="test" -RESTRICT="!test? ( test )" - -RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]" - -DEPEND=" - dev-python/setuptools[${PYTHON_USEDEP}] - test? ( - dev-python/nose[${PYTHON_USEDEP}] - ${RDEPEND} - )" - -python_prepare_all() { - sed -i -e "s/'-O3'//g" setup.py || die - distutils-r1_python_prepare_all -} - -python_compile() { - python_is_python3 || local -x CFLAGS="${CFLAGS} -fno-strict-aliasing" - distutils-r1_python_compile -} - -python_test() { - cd "${BUILD_DIR}"/lib || die - ${EPYTHON} -m unittest discover || die -} diff --git a/dev-python/traits/traits-6.1.1.ebuild b/dev-python/traits/traits-6.1.1.ebuild deleted file mode 100644 index e0263e441..000000000 --- a/dev-python/traits/traits-6.1.1.ebuild +++ /dev/null @@ -1,35 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7,8,9} ) - -inherit distutils-r1 - -DESCRIPTION="Enthought Tool Suite: Explicitly typed attributes for Python" -HOMEPAGE="https://docs.enthought.com/traits/ - https://github.com/enthought/traits - https://pypi.org/project/traits/" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~ppc ~ppc64 ~x86" - -RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]" - -distutils_enable_tests nose -# ToDo: Fix doc building: -# AttributeError: 'NoDefaultSpecified' object has no attribute '__name__' -#distutils_enable_sphinx docs/source --no-autodoc - -python_prepare_all() { - sed -i -e "s/'-O3'//g" setup.py || die - distutils-r1_python_prepare_all -} - -python_test() { - cd "${BUILD_DIR}"/lib || die - ${EPYTHON} -m unittest discover || die -} diff --git a/dev-python/traits/traits-6.3.2.ebuild b/dev-python/traits/traits-6.3.2.ebuild new file mode 100644 index 000000000..4d3c699a5 --- /dev/null +++ b/dev-python/traits/traits-6.3.2.ebuild @@ -0,0 +1,35 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) + +inherit distutils-r1 pypi + +DESCRIPTION="Enthought Tool Suite: Explicitly typed attributes for Python" +HOMEPAGE=" + https://docs.enthought.com/traits/ + https://github.com/enthought/traits +" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~ppc64 ~x86" + +RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]" + +distutils_enable_tests unittest +# ToDo: Fix doc building: +# AttributeError: 'NoDefaultSpecified' object has no attribute '__name__' +#distutils_enable_sphinx docs/source --no-autodoc + +python_prepare_all() { + sed -i -e "s/'-O3'//g" setup.py || die + distutils-r1_python_prepare_all +} + +python_test() { + cd "${BUILD_DIR}"/lib || die + ${EPYTHON} -m unittest discover || die +} diff --git a/dev-python/traits/traits-6.4.1.ebuild b/dev-python/traits/traits-6.4.1.ebuild new file mode 100644 index 000000000..ebd3fb97a --- /dev/null +++ b/dev-python/traits/traits-6.4.1.ebuild @@ -0,0 +1,36 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) + +inherit distutils-r1 pypi + +DESCRIPTION="Enthought Tool Suite: Explicitly typed attributes for Python" +HOMEPAGE=" + https://docs.enthought.com/traits/ + https://github.com/enthought/traits +" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~ppc64 ~x86" + +RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]" + +distutils_enable_tests pytest +# ToDo: Fix doc building: +# AttributeError: 'NoDefaultSpecified' object has no attribute '__name__' +#distutils_enable_sphinx docs/source --no-autodoc + +python_prepare_all() { + sed -i -e "s/'-O3'//g" setup.py || die + distutils-r1_python_prepare_all +} + +python_test() { + cd "${T}" || die + epytest --pyargs traits +} diff --git a/dev-python/transforms3d/transforms3d-0.3.1.ebuild b/dev-python/transforms3d/transforms3d-0.3.1.ebuild index ed719c6a5..661d78acb 100644 --- a/dev-python/transforms3d/transforms3d-0.3.1.ebuild +++ b/dev-python/transforms3d/transforms3d-0.3.1.ebuild @@ -1,23 +1,22 @@ # Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) -DISTUTILS_USE_SETUPTOOLS=no +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools -inherit distutils-r1 +inherit distutils-r1 pypi DESCRIPTION="Functions for 3D coordinate transformations" -HOMEPAGE="https://matthew-brett.github.io/transforms3d" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" +HOMEPAGE="https://matthew-brett.github.io/transforms3d/" 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="${RDEPEND}" +RDEPEND=" + >=dev-python/numpy-1.5.1[${PYTHON_USEDEP}] +" -distutils_enable_tests nose +distutils_enable_tests pytest diff --git a/dev-python/typish/typish-1.9.3.ebuild b/dev-python/typish/typish-1.9.3.ebuild index 3c32b1184..a4ecbb65f 100644 --- a/dev-python/typish/typish-1.9.3.ebuild +++ b/dev-python/typish/typish-1.9.3.ebuild @@ -4,7 +4,7 @@ EAPI=8 DISTUTILS_USE_PEP517=setuptools -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) inherit distutils-r1 DESCRIPTION="Functionality for types" @@ -17,7 +17,7 @@ SRC_URI=" LICENSE="MIT" SLOT="0" -KEYWORDS="~amd64 ~arm ~arm64 ~hppa ~ia64 ~ppc ~ppc64 ~riscv ~s390 ~sparc ~x86" +KEYWORDS="~amd64" BDEPEND=" test? ( diff --git a/dev-python/ufl/Manifest b/dev-python/ufl/Manifest deleted file mode 100644 index 636d9ef3e..000000000 --- a/dev-python/ufl/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST ufl-2019.1.0.tar.gz 308107 BLAKE2B b89ac7bc5614d5fc61f3d5a91bdd64c8ef0b8589500e2ca4c0cc33a3488f17630ce006a9908ac53606cfa5867781943a247791ae043c8e15c040de1eabd20199 SHA512 2e79c5c05ddea1edc2aca55eafb5fcb246f24a31d9f7312dca19cfa284f7c039b1cb3d5450bbd628eed29b0881f3f3abdc9be106fd33f86a73720eaba5bea3d5 diff --git a/dev-python/ufl/metadata.xml b/dev-python/ufl/metadata.xml deleted file mode 100644 index 142da2a70..000000000 --- a/dev-python/ufl/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 Unified Form Language (UFL) is a domain specific language for -declaration of finite element discretizations of variational forms. More -precisely, it defines a flexible interface for choosing finite element -spaces and defining expressions for weak forms in a notation close to -mathematical notation. -</longdescription> - <upstream> - <remote-id type="bitbucket">fenics-project/ufl</remote-id> - </upstream> -</pkgmetadata> diff --git a/dev-python/ufl/ufl-2019.1.0.ebuild b/dev-python/ufl/ufl-2019.1.0.ebuild deleted file mode 100644 index ef75774a2..000000000 --- a/dev-python/ufl/ufl-2019.1.0.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 - -PYTHON_COMPAT=( python3_{7..9} ) - -inherit distutils-r1 optfeature - -DESCRIPTION="Unified Form Language for declaration of for FE discretizations" -HOMEPAGE="https://github.com/FEniCS/ufl" -SRC_URI="https://github.com/FEniCS/ufl/archive/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -RDEPEND="dev-python/numpy[${PYTHON_USEDEP}]" - -distutils_enable_tests pytest - -python_test() { - distutils_install_for_testing - pytest -vv || die "pytest failed for ${EPYTHON}" -} - -pkg_postinst() { - optfeature "Support for evaluating Bessel functions" dev-python/scipy -} diff --git a/dev-python/uhi/Manifest b/dev-python/uhi/Manifest new file mode 100644 index 000000000..199ee2a62 --- /dev/null +++ b/dev-python/uhi/Manifest @@ -0,0 +1 @@ +DIST uhi-0.4.0.tar.gz 52953 BLAKE2B b0c16c58c676f405d7b46398507968e92e4c3939a53224b49cbd935c3473800341903a9e9c5e3c598d68f171a9ec098feedaa774b2bbfe780581a663e99b2592 SHA512 4f7f0bdce3fef14c8789e0860956d6d4d2ab91e48eb95b6bceb67aef47b23a260f0f33a565c052fe48933f108adfe32f4c28c8cf874cc908929d407687bbc385 diff --git a/dev-python/uhi/metadata.xml b/dev-python/uhi/metadata.xml new file mode 100644 index 000000000..c1ee047a1 --- /dev/null +++ b/dev-python/uhi/metadata.xml @@ -0,0 +1,19 @@ +<?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> + <maintainer type="person"> + <email>alexander@neuwirth-informatik.de</email> + <name>Alexander Puck Neuwirth</name> + </maintainer> + <longdescription lang="en"> + This is a package meant primarily for documenting histogram indexing and the PlottableHistogram Protocol and any future cross-library standards. It also contains the code for the PlottableHistogram Protocol, to be used in type checking libraries wanting to conform to the protocol. Eventually, it might gain a set of tools for testing conformance to UHI indexing, as well. It is not usually a runtime dependency, but only a type checking, testing, and/or docs dependency in support of other libraries (such as boost-histogram 0.13+, hist 2.1+, mplhep 0.2.15+, uproot 4+, and histoprint 2+). There are a few useful runtime usable components (listed below). It requires Python 3.6+. See what's new. + </longdescription> + <upstream> + <remote-id type="pypi">uhi</remote-id> + <remote-id type="github">scikit-hep/uhi</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/uhi/uhi-0.4.0.ebuild b/dev-python/uhi/uhi-0.4.0.ebuild new file mode 100644 index 000000000..380e3bdbd --- /dev/null +++ b/dev-python/uhi/uhi-0.4.0.ebuild @@ -0,0 +1,27 @@ +EAPI=8 + +PYTHON_COMPAT=( python3_{10..12} ) +DISTUTILS_USE_PEP517=hatchling +SETUPTOOLS_SCM_PRETEND_VERSION=${PV} +inherit distutils-r1 pypi + +DESCRIPTION="Universal Histogram Interface" +HOMEPAGE="https://github.com/scikit-hep/uhi" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + >=dev-python/numpy-1.13.3[${PYTHON_USEDEP}] + test? ( + dev-python/pytest[${PYTHON_USEDEP}] + dev-python/boost-histogram[${PYTHON_USEDEP}] + ) +" +BDEPEND=" + ${RDEPEND} + dev-python/hatch-vcs[${PYTHON_USEDEP}] +" + +distutils_enable_tests pytest diff --git a/dev-python/umap-learn/Manifest b/dev-python/umap-learn/Manifest deleted file mode 100644 index 911c8ce27..000000000 --- a/dev-python/umap-learn/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST umap-learn-0.5.2.tar.gz 86805 BLAKE2B b1381647c947472a10472475477d3f4c91446606b1ee7235dd91c65606e4c54119a706864364845ad34d74db33760013f93fd6f2a3b7e75a5161bbbc216a2c5a SHA512 89d7e7680554c63429eee1c0702f6b0b03f5a29d7770af0630a15bd50aeeaa3c272d87f2380ec71a60accea96fe9936c7c807bfe4143c6afa1444741c865eef5 diff --git a/dev-python/umap-learn/metadata.xml b/dev-python/umap-learn/metadata.xml deleted file mode 100644 index 2f2c0b51c..000000000 --- a/dev-python/umap-learn/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>gentoo@aisha.cc</email> - <name>Aisha Tammy</name> - </maintainer> - <maintainer type="project"> - <email>sci@gentoo.org</email> - <name>Gentoo Science Project</name> - </maintainer> -</pkgmetadata> diff --git a/dev-python/umap-learn/umap-learn-0.5.2.ebuild b/dev-python/umap-learn/umap-learn-0.5.2.ebuild deleted file mode 100644 index f0dc3dab5..000000000 --- a/dev-python/umap-learn/umap-learn-0.5.2.ebuild +++ /dev/null @@ -1,26 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{8..10} ) - -inherit distutils-r1 - -DESCRIPTION="Uniform Manifold Approximation and Projection" -HOMEPAGE="https://umap-learn.readthedocs.io/" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -RDEPEND=" - >=dev-python/numba-0.49[${PYTHON_USEDEP}] - >=dev-python/numpy-1.17[${PYTHON_USEDEP}] - >=dev-python/pynndescent-0.5[${PYTHON_USEDEP}] - >=dev-python/scipy-1.0[${PYTHON_USEDEP}] - dev-python/tqdm[${PYTHON_USEDEP}] - >=sci-libs/scikit-learn-0.22[${PYTHON_USEDEP}] -" -DEPEND="${RDEPEND}" diff --git a/dev-python/unyt/Manifest b/dev-python/unyt/Manifest deleted file mode 100644 index 8120c74f7..000000000 --- a/dev-python/unyt/Manifest +++ /dev/null @@ -1,3 +0,0 @@ -DIST old_json_registry.txt 12950 BLAKE2B 54197911cbb4c3167ffe88673db87cc7dec96a55dd762162293eb0616996ec1324d91e6b4bbba4f77be227e63bf52013bcab155ca49a75e14844ae52d82337b7 SHA512 9fe6d46e24257542646e40e7364b93d52f21b6a449532cfaf4a7e913d47b76ac6c5b0579db4bc9449de816e127db90b6d330cb7620376846236829c4bc2f2346 -DIST unyt-2.7.2.tar.gz 584585 BLAKE2B 1ff1083709195510d915979c07e1aa0e0605897d41d8b3eb9497dfa21e86ba6cebc623d6cb42dba85580a416f0ad1c4c4a2be20fd492fc421e19a42c61f8c66a SHA512 73c8585b847baba927357e093336936c2505da28665dc06b79d29eb667604ef195d2c9a68aa851c0231a08f440dc7a711c4ea19ea334675dd78c11e7441aff72 -DIST unyt-2.8.0.tar.gz 324621 BLAKE2B b950ac0ca37795212edcf0a93a418c3287d5019fd9a6509bde50a62795433bcb828595508ffdc0f615b6e1e2426e7cfebf8cd3c65068e9754f79d58783ae7e7e SHA512 b3279023044d54b83833e2503876da67c6a8ce25fe1d3359e045cb9f5f8e5389bb3e1f5e1564479ebef3191c451614c3bd28b9f79ade89d3f9c00dceb04b021c diff --git a/dev-python/unyt/metadata.xml b/dev-python/unyt/metadata.xml deleted file mode 100644 index 2f2c0b51c..000000000 --- a/dev-python/unyt/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>gentoo@aisha.cc</email> - <name>Aisha Tammy</name> - </maintainer> - <maintainer type="project"> - <email>sci@gentoo.org</email> - <name>Gentoo Science Project</name> - </maintainer> -</pkgmetadata> diff --git a/dev-python/unyt/unyt-2.7.2.ebuild b/dev-python/unyt/unyt-2.7.2.ebuild deleted file mode 100644 index 893f0c03f..000000000 --- a/dev-python/unyt/unyt-2.7.2.ebuild +++ /dev/null @@ -1,32 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7..9} ) - -inherit distutils-r1 - -DESCRIPTION="package for handling numpy arrays with units" -HOMEPAGE="https://github.com/yt-project/unyt" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz - https://raw.githubusercontent.com/yt-project/unyt/v${PV}/unyt/tests/data/old_json_registry.txt -" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64" - -RDEPEND="${PYTHON_DEPS} - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/sympy[${PYTHON_USEDEP}] -" - -distutils_enable_tests pytest - -python_prepare_all() { - mkdir -p "${S}"/unyt/tests/data || die - mv "${DISTDIR}"/old_json_registry.txt "${S}"/unyt/tests/data/ - - distutils-r1_python_prepare_all -} diff --git a/dev-python/unyt/unyt-2.8.0.ebuild b/dev-python/unyt/unyt-2.8.0.ebuild deleted file mode 100644 index 893f0c03f..000000000 --- a/dev-python/unyt/unyt-2.8.0.ebuild +++ /dev/null @@ -1,32 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7..9} ) - -inherit distutils-r1 - -DESCRIPTION="package for handling numpy arrays with units" -HOMEPAGE="https://github.com/yt-project/unyt" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz - https://raw.githubusercontent.com/yt-project/unyt/v${PV}/unyt/tests/data/old_json_registry.txt -" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64" - -RDEPEND="${PYTHON_DEPS} - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/sympy[${PYTHON_USEDEP}] -" - -distutils_enable_tests pytest - -python_prepare_all() { - mkdir -p "${S}"/unyt/tests/data || die - mv "${DISTDIR}"/old_json_registry.txt "${S}"/unyt/tests/data/ - - distutils-r1_python_prepare_all -} diff --git a/dev-python/vector/Manifest b/dev-python/vector/Manifest new file mode 100644 index 000000000..541d150c6 --- /dev/null +++ b/dev-python/vector/Manifest @@ -0,0 +1,2 @@ +DIST vector-1.1.1.tar.gz 289916 BLAKE2B 35281c498f244b0307d744a20d0364c4cf664d0bd08a4f17d8d3110aa4eae6d7f66e3b51b4e9847f31d3a6ab943248115221dee4dcd3c3f2f8c47842001b553a SHA512 b1e195751de35ca2c67749b6b2b330db8a29e023f42e9b454adc8fc2408c29b5926b39e9ed6dc6a93f97006fbfb286a2217be8b14cb0eb2b96c9538f6c3943e6 +DIST vector-1.3.1.tar.gz 299581 BLAKE2B 36e99e814b5e8afc7a0179acce74f399db8f76e3c3c59ebbb5a2616bfa8f34ca2cfabe9e42752226dbabbdcd77fc15a4725c4e296f5329533a85cade8fcfae0c SHA512 524752789f6ea0201e1bb3dc09e7396a8bc64a1ee78ccab383bbe968134783bbf7499948784b141353612649f8188d0cb93147b53afdf37ba26f812d8ebd84b0 diff --git a/dev-python/vector/metadata.xml b/dev-python/vector/metadata.xml new file mode 100644 index 000000000..b6aaa9af7 --- /dev/null +++ b/dev-python/vector/metadata.xml @@ -0,0 +1,19 @@ +<?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> + <maintainer type="person"> + <email>alexander@neuwirth-informatik.de</email> + <name>Alexander Puck Neuwirth</name> + </maintainer> + <longdescription lang="en"> + Vector is a Python 3.8+ library (Python 3.6 and 3.7 supported till v0.9.0 and v1.0.0, respectively) for 2D, 3D, and Lorentz vectors, especially arrays of vectors, to solve common physics problems in a NumPy-like way. + </longdescription> + <upstream> + <remote-id type="pypi">vector</remote-id> + <remote-id type="github">scikit-hep/vector</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/vector/vector-1.1.1.ebuild b/dev-python/vector/vector-1.1.1.ebuild new file mode 100644 index 000000000..8b5a45c3d --- /dev/null +++ b/dev-python/vector/vector-1.1.1.ebuild @@ -0,0 +1,22 @@ +EAPI=8 + +PYTHON_COMPAT=( python3_{10..12} ) +DISTUTILS_USE_PEP517=hatchling +inherit distutils-r1 pypi + +DESCRIPTION="Vector classes and utilities" +HOMEPAGE="https://github.com/scikit-hep/vector" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + >=dev-python/numpy-1.13.3[${PYTHON_USEDEP}] +" +DEPEND="${RDEPEND}" +BDEPEND=" + dev-python/hatch-vcs[${PYTHON_USEDEP}] +" + +export SETUPTOOLS_SCM_PRETEND_VERSION=${PV} diff --git a/dev-python/vector/vector-1.3.1.ebuild b/dev-python/vector/vector-1.3.1.ebuild new file mode 100644 index 000000000..8b5a45c3d --- /dev/null +++ b/dev-python/vector/vector-1.3.1.ebuild @@ -0,0 +1,22 @@ +EAPI=8 + +PYTHON_COMPAT=( python3_{10..12} ) +DISTUTILS_USE_PEP517=hatchling +inherit distutils-r1 pypi + +DESCRIPTION="Vector classes and utilities" +HOMEPAGE="https://github.com/scikit-hep/vector" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + >=dev-python/numpy-1.13.3[${PYTHON_USEDEP}] +" +DEPEND="${RDEPEND}" +BDEPEND=" + dev-python/hatch-vcs[${PYTHON_USEDEP}] +" + +export SETUPTOOLS_SCM_PRETEND_VERSION=${PV} diff --git a/dev-python/visvis/Manifest b/dev-python/visvis/Manifest index 10c6f487a..2caf8e4e4 100644 --- a/dev-python/visvis/Manifest +++ b/dev-python/visvis/Manifest @@ -1 +1 @@ -DIST visvis-1.13.0.tar.gz 5095145 BLAKE2B 4c47002902d7ee15f4ccc684b53daec09657422d9e53438a0e91d11ea17b76fd8e413b6caab8fee63752116247b526454bc7830751db1d3bb6d12adab914cc1a SHA512 a2272250060e418c7b78acb51599bf5d440d6d20ffe41d5fbfb3b68f6486b6d9312300dfa94697ff23bdadb2e79a871dc75bf0ba53be3267107d392236693d6a +DIST visvis-1.14.0.tar.gz 4892032 BLAKE2B 564e328d4265676bec35798149ff1283b7289fe04e946ca78b6068ae6f70d1dff809a4ec19b94b1d49a9c3ac7f0b186996070736d3eb4ba4897feac7d03edb6a SHA512 d056ec8a83ac9cee4cbb05806145287fa9dab8064fbc910463255d4510f082ca29f393c309c7b649c6d625f1c368bf5ef28f44de1ebb30ccd1d5650fadb76a81 diff --git a/dev-python/visvis/metadata.xml b/dev-python/visvis/metadata.xml index ae9640ffb..7eac38327 100644 --- a/dev-python/visvis/metadata.xml +++ b/dev-python/visvis/metadata.xml @@ -5,4 +5,8 @@ <email>sci@gentoo.org</email> <name>Gentoo Science Project</name> </maintainer> + <upstream> + <remote-id type="pypi">visvis</remote-id> + <remote-id type="github">almarklein/visvis</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/visvis/visvis-1.13.0.ebuild b/dev-python/visvis/visvis-1.13.0.ebuild deleted file mode 100644 index 80704b0c3..000000000 --- a/dev-python/visvis/visvis-1.13.0.ebuild +++ /dev/null @@ -1,25 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -DISTUTILS_USE_SETUPTOOLS=no -PYTHON_COMPAT=( python3_{8..9} ) - -inherit distutils-r1 - -DESCRIPTION="An object oriented approach to visualization of 1D to 4D data" -HOMEPAGE="https://github.com/almarklein/visvis" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64" - -RDEPEND=" - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/pyopengl[${PYTHON_USEDEP}] - dev-python/imageio[${PYTHON_USEDEP}] -" - -distutils_enable_tests pytest diff --git a/dev-python/visvis/visvis-1.14.0.ebuild b/dev-python/visvis/visvis-1.14.0.ebuild new file mode 100644 index 000000000..1f210c0b4 --- /dev/null +++ b/dev-python/visvis/visvis-1.14.0.ebuild @@ -0,0 +1,24 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools + +inherit distutils-r1 pypi + +DESCRIPTION="An object oriented approach to visualization of 1D to 4D data" +HOMEPAGE="https://github.com/almarklein/visvis" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/pyopengl[${PYTHON_USEDEP}] + dev-python/imageio[${PYTHON_USEDEP}] +" + +distutils_enable_tests pytest diff --git a/dev-python/wraps/Manifest b/dev-python/wraps/Manifest new file mode 100644 index 000000000..44510a1dd --- /dev/null +++ b/dev-python/wraps/Manifest @@ -0,0 +1 @@ +DIST wraps-0.2.0.tar.gz 25308 BLAKE2B b68359d34995f7bc39535e97458807a5d55e3547124ccb8b34f9cd34fe1d3b38921a3a0c16df031410022f74d414aba97af9e9f60a20fb635428030bc400b130 SHA512 daf72785c3215db06f4bf06704f02c7ecfd1ef5c58dbf5c50b2dee14755d73b519f8a13be9658bf825c296689d9b3effd08aec4254779812583c1024522751f0 diff --git a/dev-python/wraps/files/wraps-0.1.0-poetry_groups.patch b/dev-python/wraps/files/wraps-0.1.0-poetry_groups.patch new file mode 100644 index 000000000..c1b2ccd3e --- /dev/null +++ b/dev-python/wraps/files/wraps-0.1.0-poetry_groups.patch @@ -0,0 +1,63 @@ +--- a/pyproject.toml 2022-06-28 11:08:09.624127900 -0400 ++++ b/pyproject.toml 2022-07-11 16:33:14.810411482 -0400 +@@ -36,31 +36,6 @@ + + typing-extensions = ">= 4.3.0" + +-[tool.poetry.group.format] +-optional = true +- +-[tool.poetry.group.format.dependencies] +-black = "22.8.0" +- +-[tool.poetry.group.format.dependencies.isort] +-version = "5.10.1" +-python = "^3.7" +- +-[tool.poetry.group.check] +-optional = true +- +-[tool.poetry.group.check.dependencies] +-mypy = "0.971" +- +-[tool.poetry.group.test] +-optional = true +- +-[tool.poetry.group.test.dependencies] +-pytest = "7.1.3" +-pytest-cov = "3.0.0" +-anyio = "3.6.1" +-trio = "0.21.0" +- + [tool.poetry.group.docs] + optional = true + +@@ -67,29 +44,6 @@ + line_length = 100 + profile = "black" + +-[tool.pytest.ini_options] +-addopts = "--cov wraps" +-testpaths = ["tests"] +- +-[tool.coverage.run] +-source = ["wraps"] +- +-[tool.coverage.report] +-ignore_errors = true +-exclude_lines = [ +- "pragma: never", +- "pragma: no cover", +- "if TYPE_CHECKING", +- "@overload", +- "@abstractmethod", +- "raise NotImplementedError", +- "raise AssertionError", +- "def __repr__", +-] +- +-[tool.coverage.html] +-directory = "coverage" +- + [tool.mypy] + show_column_numbers = true diff --git a/dev-python/wraps/metadata.xml b/dev-python/wraps/metadata.xml new file mode 100644 index 000000000..d94ee3bee --- /dev/null +++ b/dev-python/wraps/metadata.xml @@ -0,0 +1,16 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>gentoo@chymera.eu</email> + <name>Horea Christian</name> + </maintainer> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <upstream> + <remote-id type="github">nekitdev/wraps</remote-id> + <remote-id type="pypi">wraps</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/wraps/wraps-0.2.0.ebuild b/dev-python/wraps/wraps-0.2.0.ebuild new file mode 100644 index 000000000..b06b511cd --- /dev/null +++ b/dev-python/wraps/wraps-0.2.0.ebuild @@ -0,0 +1,28 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=poetry +PYTHON_COMPAT=( python3_{10..11} ) +inherit distutils-r1 pypi + +DESCRIPTION=" Meaningful and safe wrapping types. " +HOMEPAGE="https://github.com/nekitdev/wraps" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" +RESTRICT="test" +# package does not have test suite (yet) + +RDEPEND=" + >=dev-python/attrs-21.4.0[${PYTHON_USEDEP}] + >=dev-python/typing-extensions-4.2.0[${PYTHON_USEDEP}] + " + +PATCHES=( + "${FILESDIR}/${PN}-0.1.0-poetry_groups.patch" +) + +distutils_enable_tests pytest diff --git a/dev-python/xgboost/Manifest b/dev-python/xgboost/Manifest index 1bcc6ae18..b76de8dcc 100644 --- a/dev-python/xgboost/Manifest +++ b/dev-python/xgboost/Manifest @@ -1 +1,2 @@ -DIST xgboost-1.3.1.tar.gz 764139 BLAKE2B cde5e36b07fd4e2dba4961921bc169b730c775a12d8ec98a80d3f442a894f4bcc946094122df8d9fc5e76c8f505d4c57416e2deb13fe88751a9f51d8e4e09cad SHA512 ffe5851bd600d3a2f9b92850df6a028ec2c7d5f40ce4bad8e21b24e128a251e577e4344d8ce5cc50d6c17accf23bf283ff605d93fe6e12b9bfea6b544c57f428 +DIST xgboost-1.6.2.tar.gz 790950 BLAKE2B 07c7e65f6969d75b5741e7fb0d113dd98007d7fe296eb2f62cd02d88b39ec4d87c2e51e8f866ee9fb76d9cf73fbb2e0defea3a9d4d78373d170f9298a991ca22 SHA512 6e5221cf569765848484a7476acc1d8ccc7260807c70695047d0dac839404bd191e0f521a91d9e088af2c125770aec7c6a651c4bb830059c04482c4c799bb62b +DIST xgboost-2.0.3.tar.gz 1048322 BLAKE2B 2140b805aaed441da956e47cbfe08d84db1b0af96844771f4912480b05346b18632051886b237bef3e2b55a80f09c1db996be4dfeff48c942220079c4a4a149c SHA512 93614a9ad9d0a256cc31586b701c46eef4353df76c3eac26f39df23c8c02fa9ec95e72a0cea0b51bc3e416b81b3ac557ed361afeda246376a7b561bb6f7da579 diff --git a/dev-python/xgboost/files/xgboost-1.3.1-fix-install.patch b/dev-python/xgboost/files/xgboost-1.3.1-fix-install.patch deleted file mode 100644 index 8c2d3d180..000000000 --- a/dev-python/xgboost/files/xgboost-1.3.1-fix-install.patch +++ /dev/null @@ -1,31 +0,0 @@ -The BUILD_TEMP_DIR variable is set in the build phase but is no -longer available in the install phase. We write the variable to -a tmp file and read it later in the install phase as a workaround -diff --git a/setup.py b/setup.py -index 6244066..934e7cf 100644 ---- a/setup.py -+++ b/setup.py -@@ -137,6 +137,11 @@ class BuildExt(build_ext.build_ext): # pylint: disable=too-many-ancestors - build_dir = self.build_temp - global BUILD_TEMP_DIR # pylint: disable=global-statement - BUILD_TEMP_DIR = build_dir -+ tmp_workdir = os.environ["WORKDIR"] -+ py_vers = os.environ["EPYTHON"] -+ f = open(tmp_workdir + f"/build-path-{py_vers}.txt", "w") -+ f.write(BUILD_TEMP_DIR) -+ f.close() - libxgboost = os.path.abspath( - os.path.join(CURRENT_DIR, os.path.pardir, 'lib', lib_name())) - -@@ -229,6 +234,11 @@ class InstallLib(install_lib.install_lib): - dst = os.path.join(self.install_dir, 'xgboost', 'lib', lib_name()) - - global BUILD_TEMP_DIR # pylint: disable=global-statement -+ tmp_workdir = os.environ["WORKDIR"] -+ py_vers = os.environ["EPYTHON"] -+ f = open(tmp_workdir + f"/build-path-{py_vers}.txt", "r") -+ BUILD_TEMP_DIR = f.read() -+ f.close() - libxgboost_path = lib_name() - - dft_lib_dir = os.path.join(CURRENT_DIR, os.path.pardir, 'lib') diff --git a/dev-python/xgboost/metadata.xml b/dev-python/xgboost/metadata.xml index a83159655..f862a0379 100644 --- a/dev-python/xgboost/metadata.xml +++ b/dev-python/xgboost/metadata.xml @@ -5,4 +5,7 @@ SYSTEM 'http://www.gentoo.org/dtd/metadata.dtd'> <maintainer type="person"> <email>heroxbd@gentoo.org</email> </maintainer> + <upstream> + <remote-id type="pypi">xgboost</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-python/xgboost/xgboost-1.3.1.ebuild b/dev-python/xgboost/xgboost-1.3.1.ebuild deleted file mode 100644 index 25145f93d..000000000 --- a/dev-python/xgboost/xgboost-1.3.1.ebuild +++ /dev/null @@ -1,25 +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="XGBoost Python Package" -HOMEPAGE="https://xgboost.readthedocs.io" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="Apache-2.0" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -PATCHES=( "${FILESDIR}/${P}-fix-install.patch" ) - -RDEPEND=" - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/scipy[${PYTHON_USEDEP}] -" - -PATCHES=( "${FILESDIR}/${P}-fix-install.patch" ) diff --git a/dev-python/xgboost/xgboost-1.6.2.ebuild b/dev-python/xgboost/xgboost-1.6.2.ebuild new file mode 100644 index 000000000..780adec11 --- /dev/null +++ b/dev-python/xgboost/xgboost-1.6.2.ebuild @@ -0,0 +1,20 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 pypi + +DESCRIPTION="XGBoost Python Package" +HOMEPAGE="https://xgboost.readthedocs.io" + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +RDEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] +" diff --git a/dev-python/xgboost/xgboost-2.0.3.ebuild b/dev-python/xgboost/xgboost-2.0.3.ebuild new file mode 100644 index 000000000..60302a1cb --- /dev/null +++ b/dev-python/xgboost/xgboost-2.0.3.ebuild @@ -0,0 +1,27 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..12} ) +DISTUTILS_USE_PEP517="standalone" +inherit distutils-r1 pypi + +DESCRIPTION="XGBoost Python Package" +HOMEPAGE=" + https://xgboost.readthedocs.io + https://github.com/dmlc/xgboost/ +" + +REQUIRED_USE=" + ${PYTHON_REQUIRED_USE} +" + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +RDEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] +" diff --git a/dev-python/xopen/Manifest b/dev-python/xopen/Manifest deleted file mode 100644 index 7c783a2c0..000000000 --- a/dev-python/xopen/Manifest +++ /dev/null @@ -1,4 +0,0 @@ -DIST xopen-0.9.0.tar.gz 13334 BLAKE2B e3131bccf25b486eb9e23abcde03b09287edbff7fe78f558d158700e21219a330f3bf50390de4bd9f0598f1079261ff42b5d3bfd58a5b81e44b0051f592b2d7f SHA512 1cc8f32aaa9e626855e038ce3422d485a73c3d7d3af6e0957b8d735bc2c673f1780896686e9541a25fb25a57d7fe37d63099b23cada112ee2be382ccc0b52def -DIST xopen-1.0.0.tar.gz 17487 BLAKE2B b805c8bc9bbfd57027a83e6d12d5bfdcb53cd9a4d3d938e9c97160e05e0684ee061121b800bcfdbfa3eb84bd10205c1a29a9c787563377a015a962132ee3c4d5 SHA512 d0ca9118d7ff871ee71605e3bbdf8271aca1179d8fbc4ec4e4ce86c0d822dcd74bb4c7927a8aa5796f01cb5cd14ef88414d9dc1f26e734b0037e81a180fbff09 -DIST xopen-1.0.1.tar.gz 18237 BLAKE2B 4019176c80d135551de09a057fe24c1ae96ccff3a2dc59129dbc6262e13b95993618701deae7795df49bfc9cfeb6503c2c9de4d25f1d7499a6ccce91878e49fd SHA512 045fd685b1a9f2dcd91e4ec28b5d3e1dba5ff71bee22165b0b6f1ca4d0fec91fd9551118e1f096d94d543e67512f7bc0c5bf58954115908b03544cf7afcef7b7 -DIST xopen-1.1.0.tar.gz 17836 BLAKE2B bdc70e4b9f08bbacadc8ca7bfb543a554104d41d092c771524277d83e616d29d2425724c35f82b2480e42ee60b9671d18742537c157acfea857669007ba63979 SHA512 74e366febede75afd09760a0f04fe13738bc432fe6801507435efb8020d4431aa37aab9500e55d78de5030474f473b379aff7764205e07647454d12118a26997 diff --git a/dev-python/xopen/metadata.xml b/dev-python/xopen/metadata.xml deleted file mode 100644 index 822323020..000000000 --- a/dev-python/xopen/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="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="person"> - <email>gentoo@aisha.cc</email> - <name>Aisha Tammy</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/dev-python/xopen/xopen-0.9.0.ebuild b/dev-python/xopen/xopen-0.9.0.ebuild deleted file mode 100644 index 7c32e8298..000000000 --- a/dev-python/xopen/xopen-0.9.0.ebuild +++ /dev/null @@ -1,21 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7..9} ) -inherit distutils-r1 - -DESCRIPTION="Open compressed files transparently" -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=" - app-arch/pigz -" - -distutils_enable_tests pytest diff --git a/dev-python/xopen/xopen-1.0.0.ebuild b/dev-python/xopen/xopen-1.0.0.ebuild deleted file mode 100644 index 7c32e8298..000000000 --- a/dev-python/xopen/xopen-1.0.0.ebuild +++ /dev/null @@ -1,21 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7..9} ) -inherit distutils-r1 - -DESCRIPTION="Open compressed files transparently" -HOMEPAGE="https://pypi.python.org/pypi/xopen" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -RDEPEND=" - app-arch/pigz -" - -distutils_enable_tests pytest diff --git a/dev-python/xopen/xopen-1.0.1.ebuild b/dev-python/xopen/xopen-1.0.1.ebuild deleted file mode 100644 index 7c32e8298..000000000 --- a/dev-python/xopen/xopen-1.0.1.ebuild +++ /dev/null @@ -1,21 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7..9} ) -inherit distutils-r1 - -DESCRIPTION="Open compressed files transparently" -HOMEPAGE="https://pypi.python.org/pypi/xopen" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -RDEPEND=" - app-arch/pigz -" - -distutils_enable_tests pytest diff --git a/dev-python/xopen/xopen-1.1.0.ebuild b/dev-python/xopen/xopen-1.1.0.ebuild deleted file mode 100644 index 3c721232d..000000000 --- a/dev-python/xopen/xopen-1.1.0.ebuild +++ /dev/null @@ -1,21 +0,0 @@ -# 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="Open compressed files transparently" -HOMEPAGE="https://pypi.python.org/pypi/xopen" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -RDEPEND=" - app-arch/pigz -" - -distutils_enable_tests pytest diff --git a/dev-python/yte/Manifest b/dev-python/yte/Manifest new file mode 100644 index 000000000..2ad6d3366 --- /dev/null +++ b/dev-python/yte/Manifest @@ -0,0 +1 @@ +DIST yte-1.5.4.tar.gz 6352 BLAKE2B f304d1846c0f54949397570564f6bf9d048cd26a99a87feb62f8944403fd0f619546ed0989a2f9fda381c0f39adaa4d987ff66eb4e3bcbce107a460091c1b775 SHA512 eb61553d4c17f6d39f954ea5ab1a09a83009ab8f6f653afbf780b7a30f355e149b4508f8e3755a804f245246e0a1184c74be995f1477e1d2d27bc536bc1ff1f7 diff --git a/dev-python/yte/metadata.xml b/dev-python/yte/metadata.xml new file mode 100644 index 000000000..ea4e4616a --- /dev/null +++ b/dev-python/yte/metadata.xml @@ -0,0 +1,16 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>mschu.dev@gmail.com</email> + <name>Michael Schubert</name> + </maintainer> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <upstream> + <remote-id type="github">yte-template-engine/yte</remote-id> + <remote-id type="pypi">yte</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/yte/yte-1.5.4.ebuild b/dev-python/yte/yte-1.5.4.ebuild new file mode 100644 index 000000000..ad7b669b1 --- /dev/null +++ b/dev-python/yte/yte-1.5.4.ebuild @@ -0,0 +1,22 @@ +# Copyright 1999-2018 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=poetry +PYTHON_COMPAT=( python3_{10..12} ) + +inherit pypi distutils-r1 + +DESCRIPTION="A YAML template engine with Python expressions" +HOMEPAGE="https://pypi.org/project/yte/" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" + +RDEPEND=" + dev-python/dpath[${PYTHON_USEDEP}] + dev-python/plac[${PYTHON_USEDEP}] + dev-python/pyyaml[${PYTHON_USEDEP}] +" diff --git a/dev-python/zarr/Manifest b/dev-python/zarr/Manifest index 08592fdcc..bb2213da1 100644 --- a/dev-python/zarr/Manifest +++ b/dev-python/zarr/Manifest @@ -1,3 +1,3 @@ -DIST zarr-2.11.1.tar.gz 3492813 BLAKE2B ff31cc2d11f5f863770f91136694108ab76525c644dd57861a4a57ca03dae0bb8cde5c20a2654f3566ffb69900d581e7592f576b9c0d2746e4fb95ed6991c740 SHA512 e0079a69f65a1bc230049469f50bf52af036d85d84f7c163ecdc2a4a8d7b75b07b59c1fcdecd83f578682914a6463641e9341d2c18f939c57f1e78f298f6b7ea -DIST zarr-2.11.3.tar.gz 3492924 BLAKE2B ca7c5d4b4dd9a3ba4b108fb878e91418fda5b4020a09eb024c774ea8b06b1b329fd7537806632550d60b19ab16b6f6542b6e368cbaef1bbf43a8514b2347c5d6 SHA512 e11e08341769a730a22fcf9a14bbd6d284c4cb051d971dbd3a234ef42224a46e8119cb53360df1aa55580bc4912df61ddde42284c16173f68a3db1d666afbc65 DIST zarr-2.12.0.tar.gz 3571172 BLAKE2B f8c628d0ff1fdb75fa46dc923de413f4de5f7aeed822a14523c3c2277b2692852f4896c80d160c503c787d510270c25fc813a9556f1a1f54ed2ffa0147f41763 SHA512 300fc20e22def9b444629c5bb7d5ae9d8178100b88f02b5dc4ddeabc2007cc9d19e7fe9b1710f3b69ebf1aa2154f7e03b11b1a78809be9285caf294d4d49c4ee +DIST zarr-2.14.2.tar.gz 3589944 BLAKE2B 5e7de6c3a2bd9bd970b07bdfe1d51f14ad0e50bac37f2fbad91d98066d5239d237fa5af8cfef2f0a1ab4461dba4eeaed1db9fa0a4a1bfcd1757d54da4bbb15f7 SHA512 cc1eb40cd3723e87916e84f958d26df6353fc1e767e33a986068e182ad2a83c2dd7eb4939bf12ff45d4de49d822a0e6cb0afb5a5f1292d4c196f812d48939191 +DIST zarr-2.16.1.tar.gz 3597771 BLAKE2B 459f8022b3a4e3298b0f9650738713f6c13bb474ae50005b9387fefc87360f6358e4899037b26b9893d87298b14606d7b29bc1539fc8fa1479a08b30f2c8323b SHA512 e3b7c234c6376bea535d47304d83ee5b4d8b4bfc6952dde5e0bf1276833c1f427c98a7af0867f351e0139404d3729024b591a1f9b2242e219846a994e0762ee5 diff --git a/dev-python/zarr/zarr-2.11.1.ebuild b/dev-python/zarr/zarr-2.11.1.ebuild deleted file mode 100644 index 9822cb161..000000000 --- a/dev-python/zarr/zarr-2.11.1.ebuild +++ /dev/null @@ -1,56 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -DISTUTILS_USE_PEP517=setuptools -PYTHON_COMPAT=( python3_{8..10} ) - -inherit distutils-r1 - -DESCRIPTION="Chunked, compressed, N-dimensional arrays for Python" -HOMEPAGE="https://github.com/zarr-developers/zarr-python" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="test" -RESTRICT="!test? ( test )" - -RDEPEND=" - dev-python/asciitree[${PYTHON_USEDEP}] - dev-python/fasteners[${PYTHON_USEDEP}] - dev-python/numcodecs[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] -" - -DEPEND=" - test? ( - dev-python/msgpack[${PYTHON_USEDEP}] - ) -" - -# Reported upsream -# https://github.com/zarr-developers/zarr-python/issues/961 -EPYTEST_DESELECT=( - zarr/tests/test_core.py::TestArray::test_object_arrays_vlen_bytes - zarr/tests/test_core.py::TestArrayWithPath::test_object_arrays_vlen_bytes - zarr/tests/test_core.py::TestArrayWithChunkStore::test_object_arrays_vlen_bytes - zarr/tests/test_core.py::TestArrayWithDirectoryStore::test_object_arrays_vlen_bytes - zarr/tests/test_core.py::TestArrayWithNestedDirectoryStore::test_object_arrays_vlen_bytes - zarr/tests/test_core.py::TestArrayWithDBMStore::test_object_arrays_vlen_bytes - zarr/tests/test_core.py::TestArrayWithSQLiteStore::test_object_arrays_vlen_bytes - zarr/tests/test_core.py::TestArrayWithNoCompressor::test_object_arrays_vlen_bytes - zarr/tests/test_core.py::TestArrayWithBZ2Compressor::test_object_arrays_vlen_bytes - zarr/tests/test_core.py::TestArrayWithBloscCompressor::test_object_arrays_vlen_bytes - zarr/tests/test_core.py::TestArrayWithLZMACompressor::test_object_arrays_vlen_bytes - zarr/tests/test_core.py::TestArrayWithCustomMapping::test_object_arrays_vlen_bytes - zarr/tests/test_core.py::TestArrayNoCache::test_object_arrays_vlen_bytes - zarr/tests/test_core.py::TestArrayWithStoreCache::test_object_arrays_vlen_bytes - zarr/tests/test_sync.py::TestArray::test_object_arrays_vlen_bytes - zarr/tests/test_sync.py::TestArrayWithThreadSynchronizer::test_object_arrays_vlen_bytes - zarr/tests/test_sync.py::TestArrayWithProcessSynchronizer::test_object_arrays_vlen_bytes -) - -distutils_enable_tests pytest diff --git a/dev-python/zarr/zarr-2.11.3.ebuild b/dev-python/zarr/zarr-2.11.3.ebuild deleted file mode 100644 index 50ec85404..000000000 --- a/dev-python/zarr/zarr-2.11.3.ebuild +++ /dev/null @@ -1,57 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -DISTUTILS_USE_PEP517=setuptools -PYTHON_COMPAT=( python3_{8..10} ) - -inherit distutils-r1 - -DESCRIPTION="Chunked, compressed, N-dimensional arrays for Python" -HOMEPAGE="https://github.com/zarr-developers/zarr-python" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="test" -RESTRICT="!test? ( test )" - -RDEPEND=" - dev-python/asciitree[${PYTHON_USEDEP}] - dev-python/fasteners[${PYTHON_USEDEP}] - >=dev-python/numcodecs-0.6.4[${PYTHON_USEDEP}] - >=dev-python/numpy-1.7[${PYTHON_USEDEP}] -" - -DEPEND=" - test? ( - dev-python/msgpack[${PYTHON_USEDEP}] - ) -" - -# Reported upsream -# https://github.com/zarr-developers/zarr-python/issues/961 -EPYTEST_DESELECT=( - zarr/tests/test_core.py::TestArray::test_object_arrays_vlen_bytes - zarr/tests/test_core.py::TestArrayWithPath::test_object_arrays_vlen_bytes - zarr/tests/test_core.py::TestArrayWithChunkStore::test_object_arrays_vlen_bytes - zarr/tests/test_core.py::TestArrayWithDirectoryStore::test_object_arrays_vlen_bytes - zarr/tests/test_core.py::TestArrayWithNestedDirectoryStore::test_object_arrays_vlen_bytes - zarr/tests/test_core.py::TestArrayWithDBMStore::test_object_arrays_vlen_bytes - zarr/tests/test_core.py::TestArrayWithSQLiteStore::test_object_arrays_vlen_bytes - zarr/tests/test_core.py::TestArrayWithNoCompressor::test_object_arrays_vlen_bytes - zarr/tests/test_core.py::TestArrayWithBZ2Compressor::test_object_arrays_vlen_bytes - zarr/tests/test_core.py::TestArrayWithBloscCompressor::test_object_arrays_vlen_bytes - zarr/tests/test_core.py::TestArrayWithLZMACompressor::test_object_arrays_vlen_bytes - zarr/tests/test_core.py::TestArrayWithCustomMapping::test_object_arrays_vlen_bytes - zarr/tests/test_core.py::TestArrayNoCache::test_object_arrays_vlen_bytes - zarr/tests/test_core.py::TestArrayWithStoreCache::test_object_arrays_vlen_bytes - zarr/tests/test_sync.py::TestArray::test_object_arrays_vlen_bytes - zarr/tests/test_sync.py::TestArrayWithThreadSynchronizer::test_object_arrays_vlen_bytes - zarr/tests/test_sync.py::TestArrayWithProcessSynchronizer::test_object_arrays_vlen_bytes -) - -distutils_enable_tests pytest -distutils_enable_sphinx docs dev-python/numpydoc dev-python/sphinx-issues dev-python/sphinx_rtd_theme diff --git a/dev-python/zarr/zarr-2.12.0.ebuild b/dev-python/zarr/zarr-2.12.0.ebuild index 1fa4e9af9..f18e92d44 100644 --- a/dev-python/zarr/zarr-2.12.0.ebuild +++ b/dev-python/zarr/zarr-2.12.0.ebuild @@ -1,16 +1,15 @@ -# Copyright 1999-2022 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 DISTUTILS_USE_PEP517=setuptools -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_{10..11} ) -inherit distutils-r1 +inherit distutils-r1 pypi DESCRIPTION="Chunked, compressed, N-dimensional arrays for Python" HOMEPAGE="https://github.com/zarr-developers/zarr-python" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" LICENSE="MIT" SLOT="0" @@ -59,4 +58,4 @@ EPYTEST_DESELECT=( ) distutils_enable_tests pytest -distutils_enable_sphinx docs dev-python/numpydoc dev-python/sphinx-issues dev-python/sphinx_rtd_theme +distutils_enable_sphinx docs dev-python/numpydoc dev-python/sphinx-issues dev-python/sphinx-rtd-theme diff --git a/dev-python/zarr/zarr-2.14.2.ebuild b/dev-python/zarr/zarr-2.14.2.ebuild new file mode 100644 index 000000000..f18e92d44 --- /dev/null +++ b/dev-python/zarr/zarr-2.14.2.ebuild @@ -0,0 +1,61 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) + +inherit distutils-r1 pypi + +DESCRIPTION="Chunked, compressed, N-dimensional arrays for Python" +HOMEPAGE="https://github.com/zarr-developers/zarr-python" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="test" +RESTRICT="!test? ( test )" + +RDEPEND=" + dev-python/asciitree[${PYTHON_USEDEP}] + dev-python/fasteners[${PYTHON_USEDEP}] + >=dev-python/numcodecs-0.6.4[${PYTHON_USEDEP}] + >=dev-python/numpy-1.7[${PYTHON_USEDEP}] +" + +DEPEND=" + test? ( + dev-python/msgpack[${PYTHON_USEDEP}] + ) +" + +# Reported upsream +# https://github.com/zarr-developers/zarr-python/issues/961 +EPYTEST_DESELECT=( + zarr/tests/test_core.py::TestArray::test_object_arrays_vlen_bytes + zarr/tests/test_core.py::TestArrayWithPath::test_object_arrays_vlen_bytes + zarr/tests/test_core.py::TestArrayWithChunkStore::test_object_arrays_vlen_bytes + zarr/tests/test_core.py::TestArrayWithDirectoryStore::test_object_arrays_vlen_bytes + zarr/tests/test_core.py::TestArrayWithNestedDirectoryStore::test_object_arrays_vlen_bytes + zarr/tests/test_core.py::TestArrayWithDBMStore::test_object_arrays_vlen_bytes + zarr/tests/test_core.py::TestArrayWithSQLiteStore::test_object_arrays_vlen_bytes + zarr/tests/test_core.py::TestArrayWithNoCompressor::test_object_arrays_vlen_bytes + zarr/tests/test_core.py::TestArrayWithBZ2Compressor::test_object_arrays_vlen_bytes + zarr/tests/test_core.py::TestArrayWithBloscCompressor::test_object_arrays_vlen_bytes + zarr/tests/test_core.py::TestArrayWithLZMACompressor::test_object_arrays_vlen_bytes + zarr/tests/test_core.py::TestArrayWithCustomMapping::test_object_arrays_vlen_bytes + zarr/tests/test_core.py::TestArrayNoCache::test_object_arrays_vlen_bytes + zarr/tests/test_core.py::TestArrayWithStoreCache::test_object_arrays_vlen_bytes + zarr/tests/test_sync.py::TestArray::test_object_arrays_vlen_bytes + zarr/tests/test_sync.py::TestArrayWithThreadSynchronizer::test_object_arrays_vlen_bytes + zarr/tests/test_sync.py::TestArrayWithProcessSynchronizer::test_object_arrays_vlen_bytes + zarr/tests/test_core.py::TestArrayWithFSStore::test_object_arrays_vlen_bytes + zarr/tests/test_core.py::TestArrayWithFSStoreFromFilesystem::test_object_arrays_vlen_bytes + zarr/tests/test_core.py::TestArrayWithFSStorePartialRead::test_object_arrays_vlen_bytes + zarr/tests/test_core.py::TestArrayWithFSStoreNested::test_object_arrays_vlen_bytes + zarr/tests/test_core.py::TestArrayWithFSStoreNestedPartialRead::test_object_arrays_vlen_bytes +) + +distutils_enable_tests pytest +distutils_enable_sphinx docs dev-python/numpydoc dev-python/sphinx-issues dev-python/sphinx-rtd-theme diff --git a/dev-python/zarr/zarr-2.16.1.ebuild b/dev-python/zarr/zarr-2.16.1.ebuild new file mode 100644 index 000000000..f18e92d44 --- /dev/null +++ b/dev-python/zarr/zarr-2.16.1.ebuild @@ -0,0 +1,61 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) + +inherit distutils-r1 pypi + +DESCRIPTION="Chunked, compressed, N-dimensional arrays for Python" +HOMEPAGE="https://github.com/zarr-developers/zarr-python" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="test" +RESTRICT="!test? ( test )" + +RDEPEND=" + dev-python/asciitree[${PYTHON_USEDEP}] + dev-python/fasteners[${PYTHON_USEDEP}] + >=dev-python/numcodecs-0.6.4[${PYTHON_USEDEP}] + >=dev-python/numpy-1.7[${PYTHON_USEDEP}] +" + +DEPEND=" + test? ( + dev-python/msgpack[${PYTHON_USEDEP}] + ) +" + +# Reported upsream +# https://github.com/zarr-developers/zarr-python/issues/961 +EPYTEST_DESELECT=( + zarr/tests/test_core.py::TestArray::test_object_arrays_vlen_bytes + zarr/tests/test_core.py::TestArrayWithPath::test_object_arrays_vlen_bytes + zarr/tests/test_core.py::TestArrayWithChunkStore::test_object_arrays_vlen_bytes + zarr/tests/test_core.py::TestArrayWithDirectoryStore::test_object_arrays_vlen_bytes + zarr/tests/test_core.py::TestArrayWithNestedDirectoryStore::test_object_arrays_vlen_bytes + zarr/tests/test_core.py::TestArrayWithDBMStore::test_object_arrays_vlen_bytes + zarr/tests/test_core.py::TestArrayWithSQLiteStore::test_object_arrays_vlen_bytes + zarr/tests/test_core.py::TestArrayWithNoCompressor::test_object_arrays_vlen_bytes + zarr/tests/test_core.py::TestArrayWithBZ2Compressor::test_object_arrays_vlen_bytes + zarr/tests/test_core.py::TestArrayWithBloscCompressor::test_object_arrays_vlen_bytes + zarr/tests/test_core.py::TestArrayWithLZMACompressor::test_object_arrays_vlen_bytes + zarr/tests/test_core.py::TestArrayWithCustomMapping::test_object_arrays_vlen_bytes + zarr/tests/test_core.py::TestArrayNoCache::test_object_arrays_vlen_bytes + zarr/tests/test_core.py::TestArrayWithStoreCache::test_object_arrays_vlen_bytes + zarr/tests/test_sync.py::TestArray::test_object_arrays_vlen_bytes + zarr/tests/test_sync.py::TestArrayWithThreadSynchronizer::test_object_arrays_vlen_bytes + zarr/tests/test_sync.py::TestArrayWithProcessSynchronizer::test_object_arrays_vlen_bytes + zarr/tests/test_core.py::TestArrayWithFSStore::test_object_arrays_vlen_bytes + zarr/tests/test_core.py::TestArrayWithFSStoreFromFilesystem::test_object_arrays_vlen_bytes + zarr/tests/test_core.py::TestArrayWithFSStorePartialRead::test_object_arrays_vlen_bytes + zarr/tests/test_core.py::TestArrayWithFSStoreNested::test_object_arrays_vlen_bytes + zarr/tests/test_core.py::TestArrayWithFSStoreNestedPartialRead::test_object_arrays_vlen_bytes +) + +distutils_enable_tests pytest +distutils_enable_sphinx docs dev-python/numpydoc dev-python/sphinx-issues dev-python/sphinx-rtd-theme diff --git a/dev-python/zarr_checksum/Manifest b/dev-python/zarr_checksum/Manifest new file mode 100644 index 000000000..5ca7cc376 --- /dev/null +++ b/dev-python/zarr_checksum/Manifest @@ -0,0 +1,2 @@ +DIST zarr_checksum-0.2.8.tar.gz 11824 BLAKE2B b26b6e1b9559e6572c95fb3700afada3c9040dfa1d26f736dcf6edfe4272c2e513f209286e24d7690de9fa2789297075469258f65edc8a2999fa2c4eee58f3ee SHA512 5c79611568decc8b9a353002e96c6ca73ec2c378debcba11f89feecb62089a78a4c3a8f4948971dd1a120a476dba7f357b23ba0b6edcf93d3f44dbb7c531feb5 +DIST zarr_checksum-0.4.0.tar.gz 11618 BLAKE2B 90c963f6540fd9a7a667f0a683b6c3d4a70230b4d71eb08f62a1cfecb20b7eb46b515b4cafc12b90fbc6c80fb83d5c5779682c6313bc56a819a4a8a5ff1843dc SHA512 e903bbc04847767dd14a0e0ad7e2fae47e97b18b813911b3bdb835e75454f573e8e1021c68f79cbf44fa21af64a4833f41ecb754a5b263e5d46dc0c7dc83447f diff --git a/dev-python/zarr_checksum/metadata.xml b/dev-python/zarr_checksum/metadata.xml new file mode 100644 index 000000000..57bdec31a --- /dev/null +++ b/dev-python/zarr_checksum/metadata.xml @@ -0,0 +1,16 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>gentoo@chymera.eu</email> + <name>Horea Christian</name> + </maintainer> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <upstream> + <remote-id type="github">dandi/zarr_checksum</remote-id> + <remote-id type="pypi">zarr_checksum</remote-id> + </upstream> +</pkgmetadata> diff --git a/dev-python/zarr_checksum/zarr_checksum-0.2.8.ebuild b/dev-python/zarr_checksum/zarr_checksum-0.2.8.ebuild new file mode 100644 index 000000000..58cb87329 --- /dev/null +++ b/dev-python/zarr_checksum/zarr_checksum-0.2.8.ebuild @@ -0,0 +1,26 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=poetry + +inherit distutils-r1 pypi + +DESCRIPTION="Calculatine zarr checksums from local or cloud storage" +HOMEPAGE="https://github.com/dandi/zarr_checksum" + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +RDEPEND=" + dev-python/boto3[${PYTHON_USEDEP}] + dev-python/click[${PYTHON_USEDEP}] + dev-python/pydantic[${PYTHON_USEDEP}] + dev-python/tqdm[${PYTHON_USEDEP}] + dev-python/zarr[${PYTHON_USEDEP}] +" + +distutils_enable_tests pytest diff --git a/dev-python/zarr_checksum/zarr_checksum-0.4.0.ebuild b/dev-python/zarr_checksum/zarr_checksum-0.4.0.ebuild new file mode 100644 index 000000000..58cb87329 --- /dev/null +++ b/dev-python/zarr_checksum/zarr_checksum-0.4.0.ebuild @@ -0,0 +1,26 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=poetry + +inherit distutils-r1 pypi + +DESCRIPTION="Calculatine zarr checksums from local or cloud storage" +HOMEPAGE="https://github.com/dandi/zarr_checksum" + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +RDEPEND=" + dev-python/boto3[${PYTHON_USEDEP}] + dev-python/click[${PYTHON_USEDEP}] + dev-python/pydantic[${PYTHON_USEDEP}] + dev-python/tqdm[${PYTHON_USEDEP}] + dev-python/zarr[${PYTHON_USEDEP}] +" + +distutils_enable_tests pytest diff --git a/dev-util/makefile2graph/metadata.xml b/dev-util/makefile2graph/metadata.xml index 138cb7705..41bb35aa0 100644 --- a/dev-util/makefile2graph/metadata.xml +++ b/dev-util/makefile2graph/metadata.xml @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">lindenb/makefile2graph</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-util/plog/metadata.xml b/dev-util/plog/metadata.xml index 7203fb853..40a8e36c6 100644 --- a/dev-util/plog/metadata.xml +++ b/dev-util/plog/metadata.xml @@ -4,4 +4,7 @@ <maintainer type="person"> <email>heroxbd@gentoo.org</email> </maintainer> + <upstream> + <remote-id type="github">SergiusTheBest/plog</remote-id> + </upstream> </pkgmetadata> diff --git a/dev-util/waf/Manifest b/dev-util/waf/Manifest deleted file mode 100644 index f3196a0cf..000000000 --- a/dev-util/waf/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST waf-2.0.21.tar.bz2 684459 BLAKE2B ba7d85c50d4ba1ad566620f7da2779ac1a4e0a5fcc5bcc639c64a59750bf9df40318070f771098d21335cc8d494b4043ecbdae1baa67c4bce3ce791ce2e538d5 SHA512 b76c32d5992757af1f483dc59dc439e414d06d0325eaf1c8ac20bc20ee62bee25d8a97099d80e6d8e3a2ca9c9aeadf0543c2ba5005479e9617c1fbcfd60ba6b8 diff --git a/dev-util/waf/metadata.xml b/dev-util/waf/metadata.xml deleted file mode 100644 index 026cdb22b..000000000 --- a/dev-util/waf/metadata.xml +++ /dev/null @@ -1,8 +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> -</pkgmetadata> diff --git a/dev-util/waf/waf-2.0.21.ebuild b/dev-util/waf/waf-2.0.21.ebuild deleted file mode 100644 index e7d0a83bc..000000000 --- a/dev-util/waf/waf-2.0.21.ebuild +++ /dev/null @@ -1,65 +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} ) -PYTHON_REQ_USE="threads(+)" - -inherit python-single-r1 - -DESCRIPTION="Piece of software used to help building software projects" -HOMEPAGE="https://waf.io/" -SRC_URI="https://waf.io/${P}.tar.bz2" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -IUSE="doc examples" -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -BDEPEND="doc? ( $(python_gen_cond_dep \ - 'dev-python/sphinx[${PYTHON_USEDEP}]' ) -)" -DEPEND="${PYTHON_DEPS}" -RDEPEND="${PYTHON_DEPS}" - -src_prepare() { - rm waf || die - - default -} - -src_configure() { - ${EPYTHON} ./waf-light configure || die "waf configure failed" -} - -src_compile() { - ${EPYTHON} ./waf-light build || die "waf build failed" - use doc && build_sphinx docs/sphinx -} - -src_install() { - default - - # Set INSTALL to EPREFIX - # Set REVISION to PR - # set dirname to empty because python_get_sitedir - # installs directly to a dir with the correct name - # Set location of waflib to location of Gentoo - # Python sitedir - sed -e "/INSTALL=/s:=.*:='${EPREFIX}':" \ - -e "/REVISION=/s:=.*:='${PR}':" \ - -e "/dirname =/s:=.*:= '':" \ - -e "s:/lib/:$(python_get_sitedir)/:" \ - -e "/^#\(==>\|BZ\|<==\)/d" \ - -i waf || die - python_doscript waf - - python_domodule waflib - - if use examples ; then - dodoc -r demos - fi -} diff --git a/dev-vcs/dandi-cli/Manifest b/dev-vcs/dandi-cli/Manifest index cce81b9b2..f84e21730 100644 --- a/dev-vcs/dandi-cli/Manifest +++ b/dev-vcs/dandi-cli/Manifest @@ -1,3 +1,2 @@ -DIST dandi-cli-0.37.0.tar.gz 212121 BLAKE2B a38077439edb9975b25eaffd299cba633b538d7c5a93aefeb35e8403e07896f1e93eb6b42790ca84ab20ddfe0ead850a000f857cfd3ef8c6342eb76952b95b62 SHA512 fe96b760bb8526cf2670be4523121b389ede82699a8b13a9b46e4511012ab15390d9aec35b5403fa4d52dd79738a37980bcc83755df738b4039ae56eb6ca0f14 -DIST dandi-cli-0.38.0.tar.gz 322974 BLAKE2B 5451eb922019e0b06de1181161d23fac21ddbd772fb9ff5b23e296eb5ccc54c44b6c6c62d5d8f25bf075e6c93136f1db4d3ab72d372dfa7a28c84fc03008e0f3 SHA512 a77d834dadbd532ce016425fe25324582a5d2c442b52087d5751770d99c84fa9532a08525ee75f40d45ccb5c50ed11b9fbe0c29a24c7d1b24c253d218538e054 -DIST dandi-cli-0.39.4.tar.gz 329268 BLAKE2B c34674570c3474dbc12a2f96c0877a84ca3cddbf8d04cb1bc7cc47e6d03bbf4103cf8f36d4267f59bfb5da2504300e14dc007a3f23a5d807bb92cece506fb7b7 SHA512 8ac4ae25eb9b09530a017ca2812a490c578157caeb0cca2737630f9796ec4559fc2379f150764544e1cd474cf481f87bb08dd255d4bf4dcc7722c8006ae78c4b +DIST dandi-0.61.0.tar.gz 306755 BLAKE2B 8d279fddf4a9c390c91d09915d978f5709c297bb4284e8c8f3026ef9c94a9b2bab4b24409ff1d915550ab2564f8398a1afb236b226a41303264898de51deed42 SHA512 3cbd5c81c024cfca01c94fd2f9c794b22170f830a39c283f5cde1dfd998447287559457e324f81f46154fa38bf065720736da3be13a5668bc7453d091dd51869 +DIST dandi-0.61.2.tar.gz 306867 BLAKE2B 9a51c26f36d462e518241d40604726973727f17c70855136b6ea8e8402fb2c30ecc3adbbf7db6ed967bdb8c63a11da0809c09ae61f3a4996784b0b2083c1ec3a SHA512 9f4f3a02e62a3c4af3496a29faa18c696263e71dd2baf56c2925696c09e4c633a3a28a1fe30329764b98cba3006e4ccfe0884f5bae3d580f643f4cf946b2d291 diff --git a/dev-vcs/dandi-cli/dandi-cli-0.37.0.ebuild b/dev-vcs/dandi-cli/dandi-cli-0.37.0.ebuild deleted file mode 100644 index 08d652de9..000000000 --- a/dev-vcs/dandi-cli/dandi-cli-0.37.0.ebuild +++ /dev/null @@ -1,87 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -DISTUTILS_USE_PEP517=setuptools -PYTHON_COMPAT=( python3_{8..10} ) - -inherit distutils-r1 - -DESCRIPTION="DANDI command line client to facilitate common operations" -HOMEPAGE="https://github.com/dandi/dandi-cli" -SRC_URI="https://github.com/dandi/dandi-cli/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="Apache-2.0" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="test etelemetry" - -RDEPEND=" - dev-python/appdirs[${PYTHON_USEDEP}] - dev-python/click[${PYTHON_USEDEP}] - dev-python/click-didyoumean[${PYTHON_USEDEP}] - ~dev-python/dandi-schema-0.6.0[${PYTHON_USEDEP}] - dev-python/fasteners[${PYTHON_USEDEP}] - dev-python/fscacher[${PYTHON_USEDEP}] - dev-python/humanize[${PYTHON_USEDEP}] - dev-python/interleave[${PYTHON_USEDEP}] - dev-python/joblib[${PYTHON_USEDEP}] - dev-python/keyring[${PYTHON_USEDEP}] - dev-python/keyrings_alt[${PYTHON_USEDEP}] - dev-python/packaging[${PYTHON_USEDEP}] - dev-python/pycryptodome[${PYTHON_USEDEP}] - >=dev-python/pydantic-1.9.0[${PYTHON_USEDEP}] - dev-python/pynwb[${PYTHON_USEDEP}] - dev-python/pyout[${PYTHON_USEDEP}] - dev-python/python-dateutil[${PYTHON_USEDEP}] - dev-python/requests[${PYTHON_USEDEP}] - dev-python/ruamel-yaml[${PYTHON_USEDEP}] - dev-python/semantic_version[${PYTHON_USEDEP}] - dev-python/tenacity[${PYTHON_USEDEP}] - dev-python/wheel[${PYTHON_USEDEP}] - dev-python/zarr[${PYTHON_USEDEP}] -" - -DEPEND=" - test? ( - dev-python/anys[${PYTHON_USEDEP}] - dev-python/responses[${PYTHON_USEDEP}] - dev-python/pyfakefs[${PYTHON_USEDEP}] - dev-python/pytest-mock[${PYTHON_USEDEP}] - media-libs/opencv[ffmpeg,${PYTHON_USEDEP}] - ) -" -# Upstream might be amenable to dropping opencv: -# https://github.com/dandi/dandi-cli/issues/944 - -# Some tests require deep copy with git history -# https://github.com/dandi/dandi-cli/issues/878#issuecomment-1021720299 -EPYTEST_DESELECT=( - "dandi/tests/test_utils.py::test_get_instance_dandi_with_api" - "dandi/tests/test_utils.py::test_get_instance_url" - "dandi/tests/test_utils.py::test_get_instance_cli_version_too_old" - "dandi/tests/test_utils.py::test_get_instance_bad_cli_version" -) - -distutils_enable_tests pytest - -PATCHES=( - "${FILESDIR}/${PN}-0.37.0-pip-versioncheck.patch" - "${FILESDIR}/${PN}-0.37.0-pep517.patch" -) - -src_prepare() { - if use etelemetry; then - default - else - eapply "${FILESDIR}/${PN}-0.28.0-no-etelemetry.patch" - default - sed -i "/etelemetry/d" setup.cfg - fi -} - -python_test() { - export DANDI_TESTS_NONETWORK=1 - epytest -} diff --git a/dev-vcs/dandi-cli/dandi-cli-0.38.0.ebuild b/dev-vcs/dandi-cli/dandi-cli-0.38.0.ebuild deleted file mode 100644 index 08d652de9..000000000 --- a/dev-vcs/dandi-cli/dandi-cli-0.38.0.ebuild +++ /dev/null @@ -1,87 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -DISTUTILS_USE_PEP517=setuptools -PYTHON_COMPAT=( python3_{8..10} ) - -inherit distutils-r1 - -DESCRIPTION="DANDI command line client to facilitate common operations" -HOMEPAGE="https://github.com/dandi/dandi-cli" -SRC_URI="https://github.com/dandi/dandi-cli/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="Apache-2.0" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="test etelemetry" - -RDEPEND=" - dev-python/appdirs[${PYTHON_USEDEP}] - dev-python/click[${PYTHON_USEDEP}] - dev-python/click-didyoumean[${PYTHON_USEDEP}] - ~dev-python/dandi-schema-0.6.0[${PYTHON_USEDEP}] - dev-python/fasteners[${PYTHON_USEDEP}] - dev-python/fscacher[${PYTHON_USEDEP}] - dev-python/humanize[${PYTHON_USEDEP}] - dev-python/interleave[${PYTHON_USEDEP}] - dev-python/joblib[${PYTHON_USEDEP}] - dev-python/keyring[${PYTHON_USEDEP}] - dev-python/keyrings_alt[${PYTHON_USEDEP}] - dev-python/packaging[${PYTHON_USEDEP}] - dev-python/pycryptodome[${PYTHON_USEDEP}] - >=dev-python/pydantic-1.9.0[${PYTHON_USEDEP}] - dev-python/pynwb[${PYTHON_USEDEP}] - dev-python/pyout[${PYTHON_USEDEP}] - dev-python/python-dateutil[${PYTHON_USEDEP}] - dev-python/requests[${PYTHON_USEDEP}] - dev-python/ruamel-yaml[${PYTHON_USEDEP}] - dev-python/semantic_version[${PYTHON_USEDEP}] - dev-python/tenacity[${PYTHON_USEDEP}] - dev-python/wheel[${PYTHON_USEDEP}] - dev-python/zarr[${PYTHON_USEDEP}] -" - -DEPEND=" - test? ( - dev-python/anys[${PYTHON_USEDEP}] - dev-python/responses[${PYTHON_USEDEP}] - dev-python/pyfakefs[${PYTHON_USEDEP}] - dev-python/pytest-mock[${PYTHON_USEDEP}] - media-libs/opencv[ffmpeg,${PYTHON_USEDEP}] - ) -" -# Upstream might be amenable to dropping opencv: -# https://github.com/dandi/dandi-cli/issues/944 - -# Some tests require deep copy with git history -# https://github.com/dandi/dandi-cli/issues/878#issuecomment-1021720299 -EPYTEST_DESELECT=( - "dandi/tests/test_utils.py::test_get_instance_dandi_with_api" - "dandi/tests/test_utils.py::test_get_instance_url" - "dandi/tests/test_utils.py::test_get_instance_cli_version_too_old" - "dandi/tests/test_utils.py::test_get_instance_bad_cli_version" -) - -distutils_enable_tests pytest - -PATCHES=( - "${FILESDIR}/${PN}-0.37.0-pip-versioncheck.patch" - "${FILESDIR}/${PN}-0.37.0-pep517.patch" -) - -src_prepare() { - if use etelemetry; then - default - else - eapply "${FILESDIR}/${PN}-0.28.0-no-etelemetry.patch" - default - sed -i "/etelemetry/d" setup.cfg - fi -} - -python_test() { - export DANDI_TESTS_NONETWORK=1 - epytest -} diff --git a/dev-vcs/dandi-cli/dandi-cli-0.39.4.ebuild b/dev-vcs/dandi-cli/dandi-cli-0.39.4.ebuild deleted file mode 100644 index 11f322912..000000000 --- a/dev-vcs/dandi-cli/dandi-cli-0.39.4.ebuild +++ /dev/null @@ -1,89 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -DISTUTILS_USE_PEP517=setuptools -PYTHON_COMPAT=( python3_{8..10} ) - -inherit distutils-r1 - -DESCRIPTION="DANDI command line client to facilitate common operations" -HOMEPAGE="https://github.com/dandi/dandi-cli" -SRC_URI="https://github.com/dandi/dandi-cli/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="Apache-2.0" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="test etelemetry" - -RDEPEND=" - dev-python/appdirs[${PYTHON_USEDEP}] - dev-python/click[${PYTHON_USEDEP}] - dev-python/click-didyoumean[${PYTHON_USEDEP}] - ~dev-python/dandi-schema-0.6.0[${PYTHON_USEDEP}] - dev-python/fasteners[${PYTHON_USEDEP}] - dev-python/fscacher[${PYTHON_USEDEP}] - dev-python/humanize[${PYTHON_USEDEP}] - dev-python/interleave[${PYTHON_USEDEP}] - dev-python/joblib[${PYTHON_USEDEP}] - dev-python/keyring[${PYTHON_USEDEP}] - dev-python/keyrings_alt[${PYTHON_USEDEP}] - dev-python/nwbinspector[${PYTHON_USEDEP}] - dev-python/packaging[${PYTHON_USEDEP}] - dev-python/pycryptodome[${PYTHON_USEDEP}] - >=dev-python/pydantic-1.9.0[${PYTHON_USEDEP}] - dev-python/pynwb[${PYTHON_USEDEP}] - dev-python/pyout[${PYTHON_USEDEP}] - dev-python/python-dateutil[${PYTHON_USEDEP}] - dev-python/requests[${PYTHON_USEDEP}] - dev-python/ruamel-yaml[${PYTHON_USEDEP}] - dev-python/semantic_version[${PYTHON_USEDEP}] - dev-python/tenacity[${PYTHON_USEDEP}] - dev-python/versioneer[${PYTHON_USEDEP}] - dev-python/wheel[${PYTHON_USEDEP}] - dev-python/zarr[${PYTHON_USEDEP}] -" - -BDEPEND=" - test? ( - dev-python/anys[${PYTHON_USEDEP}] - dev-python/responses[${PYTHON_USEDEP}] - dev-python/pyfakefs[${PYTHON_USEDEP}] - dev-python/pytest-mock[${PYTHON_USEDEP}] - media-libs/opencv[ffmpeg,${PYTHON_USEDEP}] - ) -" -# Upstream might be amenable to dropping opencv: -# https://github.com/dandi/dandi-cli/issues/944 - -# Some tests require deep copy with git history -# https://github.com/dandi/dandi-cli/issues/878#issuecomment-1021720299 -EPYTEST_DESELECT=( - "dandi/tests/test_utils.py::test_get_instance_dandi_with_api" - "dandi/tests/test_utils.py::test_get_instance_url" - "dandi/tests/test_utils.py::test_get_instance_cli_version_too_old" - "dandi/tests/test_utils.py::test_get_instance_bad_cli_version" -) - -distutils_enable_tests pytest - -PATCHES=( - "${FILESDIR}/${PN}-0.37.0-pip-versioncheck.patch" - "${FILESDIR}/${PN}-0.37.0-pep517.patch" -) - -src_prepare() { - if use etelemetry; then - default - else - eapply "${FILESDIR}/${PN}-0.28.0-no-etelemetry.patch" - default - sed -i "/etelemetry/d" setup.cfg - fi -} - -python_test() { - export DANDI_TESTS_NONETWORK=1 - epytest -} diff --git a/dev-vcs/dandi-cli/dandi-cli-0.61.0.ebuild b/dev-vcs/dandi-cli/dandi-cli-0.61.0.ebuild new file mode 100644 index 000000000..35ac320f5 --- /dev/null +++ b/dev-vcs/dandi-cli/dandi-cli-0.61.0.ebuild @@ -0,0 +1,80 @@ +# Copyright 1999-2024 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) + +inherit distutils-r1 pypi + +MY_PN="dandi" +MY_P="${MY_PN}-${PV}" + +DESCRIPTION="DANDI command line client to facilitate common operations" +HOMEPAGE="https://github.com/dandi/dandi-cli" +SRC_URI="$(pypi_sdist_url dandi)" + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="~amd64" +IUSE="test etelemetry" + +RDEPEND=" + >=dev-python/dandi-schema-0.9.0[${PYTHON_USEDEP}] + >=dev-python/pydantic-2.0.0[${PYTHON_USEDEP}] + >=sci-biology/bidsschematools-0.7.0[${PYTHON_USEDEP}] + dev-python/click-didyoumean[${PYTHON_USEDEP}] + dev-python/click[${PYTHON_USEDEP}] + dev-python/fasteners[${PYTHON_USEDEP}] + dev-python/fscacher[${PYTHON_USEDEP}] + dev-python/humanize[${PYTHON_USEDEP}] + dev-python/interleave[${PYTHON_USEDEP}] + dev-python/joblib[${PYTHON_USEDEP}] + dev-python/keyring[${PYTHON_USEDEP}] + dev-python/keyrings-alt[${PYTHON_USEDEP}] + dev-python/nwbinspector[${PYTHON_USEDEP}] + dev-python/packaging[${PYTHON_USEDEP}] + dev-python/platformdirs[${PYTHON_USEDEP}] + dev-python/pycryptodome[${PYTHON_USEDEP}] + dev-python/pynwb[${PYTHON_USEDEP}] + dev-python/pyout[${PYTHON_USEDEP}] + dev-python/python-dateutil[${PYTHON_USEDEP}] + dev-python/requests[${PYTHON_USEDEP}] + dev-python/ruamel-yaml[${PYTHON_USEDEP}] + dev-python/semantic-version[${PYTHON_USEDEP}] + dev-python/tenacity[${PYTHON_USEDEP}] + dev-python/versioneer[${PYTHON_USEDEP}] + dev-python/wheel[${PYTHON_USEDEP}] + dev-python/zarr[${PYTHON_USEDEP}] + >=dev-python/zarr_checksum-0.4.0[${PYTHON_USEDEP}] +" + +BDEPEND=" + test? ( + dev-python/anys[${PYTHON_USEDEP}] + dev-python/pyfakefs[${PYTHON_USEDEP}] + dev-python/pytest-mock[${PYTHON_USEDEP}] + dev-python/pytest-rerunfailures[${PYTHON_USEDEP}] + dev-python/responses[${PYTHON_USEDEP}] + dev-python/vcrpy[${PYTHON_USEDEP}] + media-libs/opencv[ffmpeg,${PYTHON_USEDEP}] + ) +" +# Upstream might be amenable to dropping opencv: +# https://github.com/dandi/dandi-cli/issues/944 + +S="${WORKDIR}/${MY_P}" + +EPYTEST_DESELECT=( + # Reported upstream: + # https://github.com/dandi/dandi-cli/issues/1394 + dandi/cli/tests/test_command.py::test_no_heavy_imports +) + +distutils_enable_tests pytest + +python_test() { + export DANDI_TESTS_NONETWORK=1 + epytest +} diff --git a/dev-vcs/dandi-cli/dandi-cli-0.61.2.ebuild b/dev-vcs/dandi-cli/dandi-cli-0.61.2.ebuild new file mode 100644 index 000000000..760fb32b4 --- /dev/null +++ b/dev-vcs/dandi-cli/dandi-cli-0.61.2.ebuild @@ -0,0 +1,81 @@ +# Copyright 1999-2024 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) + +inherit distutils-r1 pypi + +MY_PN="dandi" +MY_P="${MY_PN}-${PV}" + +DESCRIPTION="DANDI command line client to facilitate common operations" +HOMEPAGE="https://github.com/dandi/dandi-cli" +SRC_URI="$(pypi_sdist_url dandi)" + +S="${WORKDIR}/${MY_P}" + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="~amd64" +IUSE="test etelemetry" + +RDEPEND=" + >=dev-python/dandi-schema-0.9.0[${PYTHON_USEDEP}] + >=dev-python/pydantic-2.0.0[${PYTHON_USEDEP}] + >=sci-biology/bidsschematools-0.7.0[${PYTHON_USEDEP}] + >=dev-python/zarr_checksum-0.4.0[${PYTHON_USEDEP}] + dev-python/click-didyoumean[${PYTHON_USEDEP}] + dev-python/click[${PYTHON_USEDEP}] + dev-python/fasteners[${PYTHON_USEDEP}] + dev-python/fscacher[${PYTHON_USEDEP}] + dev-python/humanize[${PYTHON_USEDEP}] + dev-python/interleave[${PYTHON_USEDEP}] + dev-python/joblib[${PYTHON_USEDEP}] + dev-python/keyring[${PYTHON_USEDEP}] + dev-python/keyrings-alt[${PYTHON_USEDEP}] + dev-python/nwbinspector[${PYTHON_USEDEP}] + dev-python/packaging[${PYTHON_USEDEP}] + dev-python/platformdirs[${PYTHON_USEDEP}] + dev-python/pycryptodome[${PYTHON_USEDEP}] + dev-python/pynwb[${PYTHON_USEDEP}] + dev-python/pyout[${PYTHON_USEDEP}] + dev-python/python-dateutil[${PYTHON_USEDEP}] + dev-python/requests[${PYTHON_USEDEP}] + dev-python/ruamel-yaml[${PYTHON_USEDEP}] + dev-python/semantic-version[${PYTHON_USEDEP}] + dev-python/tenacity[${PYTHON_USEDEP}] + dev-python/versioneer[${PYTHON_USEDEP}] + dev-python/wheel[${PYTHON_USEDEP}] + dev-python/yarl[${PYTHON_USEDEP}] + dev-python/zarr[${PYTHON_USEDEP}] +" + +BDEPEND=" + test? ( + dev-python/anys[${PYTHON_USEDEP}] + dev-python/pyfakefs[${PYTHON_USEDEP}] + dev-python/pytest-mock[${PYTHON_USEDEP}] + dev-python/pytest-rerunfailures[${PYTHON_USEDEP}] + dev-python/responses[${PYTHON_USEDEP}] + dev-python/vcrpy[${PYTHON_USEDEP}] + media-libs/opencv[ffmpeg,${PYTHON_USEDEP}] + ) +" +# Upstream might be amenable to dropping opencv: +# https://github.com/dandi/dandi-cli/issues/944 + +EPYTEST_DESELECT=( + # Reported upstream: + # https://github.com/dandi/dandi-cli/issues/1394 + dandi/cli/tests/test_command.py::test_no_heavy_imports +) + +distutils_enable_tests pytest + +python_test() { + export DANDI_TESTS_NONETWORK=1 + epytest +} diff --git a/dev-vcs/dandi-cli/files/dandi-cli-0.37.0-pep517.patch b/dev-vcs/dandi-cli/files/dandi-cli-0.37.0-pep517.patch deleted file mode 100644 index 4d4715f95..000000000 --- a/dev-vcs/dandi-cli/files/dandi-cli-0.37.0-pep517.patch +++ /dev/null @@ -1,46 +0,0 @@ -From a363b68b79b3dd2004912640c90958882a918537 Mon Sep 17 00:00:00 2001 -From: =?UTF-8?q?Micha=C5=82=20G=C3=B3rny?= <mgorny@gentoo.org> -Date: Wed, 4 May 2022 19:49:37 +0200 -Subject: [PATCH] Prepend to sys.path to fix versioneer in PEP517 mode - -Prepend the current directory to sys.path rather than appending it -in order to fix the build in PEP517 mode properly. If the path -is appended and versioneer is installed on the system, the system -versioneer.py (i.e. the module used to install versioneer into projects) -is imported rather than the local file, and the build fails: - -``` -Traceback (most recent call last): - File "/usr/lib/python-exec/python3.10/gpep517", line 4, in <module> - sys.exit(main()) - File "/usr/lib/python3.10/site-packages/gpep517/__main__.py", line 136, in main - return func(args) - File "/usr/lib/python3.10/site-packages/gpep517/__main__.py", line 44, in build_wheel - wheel_name = backend.build_wheel(args.wheel_dir, args.config_json) - File "/usr/lib/python3.10/site-packages/setuptools/build_meta.py", line 244, in build_wheel - return self._build_with_temp_dir(['bdist_wheel'], '.whl', - File "/usr/lib/python3.10/site-packages/setuptools/build_meta.py", line 229, in _build_with_temp_dir - self.run_setup() - File "/usr/lib/python3.10/site-packages/setuptools/build_meta.py", line 174, in run_setup - exec(compile(code, __file__, 'exec'), locals()) - File "setup.py", line 32, in <module> - "version": versioneer.get_version(), -AttributeError: module 'versioneer' has no attribute 'get_version' -``` ---- - setup.py | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/setup.py b/setup.py -index e8dddc985..05765009c 100755 ---- a/setup.py -+++ b/setup.py -@@ -23,7 +23,7 @@ - # This is needed for versioneer to be importable when building with PEP 517. - # See <https://github.com/warner/python-versioneer/issues/193> and links - # therein for more information. --sys.path.append(os.path.dirname(__file__)) -+sys.path.insert(0, os.path.dirname(__file__)) - - try: - import versioneer diff --git a/dev-vcs/dandi-cli/files/dandi-cli-0.37.0-pip-versioncheck.patch b/dev-vcs/dandi-cli/files/dandi-cli-0.37.0-pip-versioncheck.patch deleted file mode 100644 index bcc3853d3..000000000 --- a/dev-vcs/dandi-cli/files/dandi-cli-0.37.0-pip-versioncheck.patch +++ /dev/null @@ -1,13 +0,0 @@ ---- a/setup.cfg 2021-10-06 11:44:40.549337707 -0400 -+++ b/dsetup.cfg 2021-10-06 11:45:10.236935245 -0400 -@@ -30,8 +30,8 @@ - appdirs - click - click-didyoumean -- dandischema ~= 0.6.0 -- etelemetry >= 0.2.2 -+ dandischema -+ etelemetry - fasteners - fscacher - # Specifying != might be what causes pip 19.3.1 first to install hdmf 1.5.1 diff --git a/dev-vcs/dandi-cli/files/dandi-cli-0.55.0-hdf5.patch b/dev-vcs/dandi-cli/files/dandi-cli-0.55.0-hdf5.patch new file mode 100644 index 000000000..4cd55ca7e --- /dev/null +++ b/dev-vcs/dandi-cli/files/dandi-cli-0.55.0-hdf5.patch @@ -0,0 +1,29 @@ +From d16bf0855e9ef7c029e8aca969ddfa04c1d7fdfd Mon Sep 17 00:00:00 2001 +From: "John T. Wodder II" <git@varonathe.org> +Date: Thu, 25 May 2023 14:17:36 -0400 +Subject: [PATCH] Fix test for newer hdf5 + +--- + dandi/tests/test_files.py | 9 ++++++++- + 1 file changed, 8 insertions(+), 1 deletion(-) + +diff --git a/dandi/tests/test_files.py b/dandi/tests/test_files.py +index 4dbf0f223..3e44cf6b1 100644 +--- a/dandi/tests/test_files.py ++++ b/dandi/tests/test_files.py +@@ -374,7 +374,14 @@ def test_validate_bogus(tmp_path): + errors = dandi_file(path).get_validation_errors() + # ATM we would get 2 errors -- since could not be open in two places, + # but that would be too rigid to test. Let's just see that we have expected errors +- assert any(e.message.startswith("Unable to open file") for e in errors) ++ assert any( ++ e.message.startswith( ++ ("Unable to open file", "Unable to synchronously open file") ++ ) ++ for e in errors ++ ) ++ # Recent versions of hdf5 changed the error message, hence the need to ++ # check for two different patterns. + + + def test_upload_zarr(new_dandiset, tmp_path): diff --git a/dev-vcs/dandi-cli/files/dandi-cli-0.59.0-no-etelemetry.patch b/dev-vcs/dandi-cli/files/dandi-cli-0.59.0-no-etelemetry.patch new file mode 100644 index 000000000..4d4f42a03 --- /dev/null +++ b/dev-vcs/dandi-cli/files/dandi-cli-0.59.0-no-etelemetry.patch @@ -0,0 +1,40 @@ +diff --git a/dandi/files/bases.py b/dandi/files/bases.py +index 45f5929f..38bde34f 100644 +--- a/dandi/files/bases.py ++++ b/dandi/files/bases.py +@@ -18,7 +18,6 @@ from dandischema.digests.dandietag import DandiETag + from dandischema.models import BareAsset, CommonModel + from dandischema.models import Dandiset as DandisetMeta + from dandischema.models import get_schema_version +-from etelemetry import get_project + from packaging.version import Version + from pydantic import ValidationError + import requests +@@ -737,6 +736,7 @@ def _get_nwb_inspector_version(): + _current_nwbinspector_version = get_package_version(name="nwbinspector") + # Ensure latest version of NWB Inspector is installed and used client-side + try: ++ from etelemetry import get_project + max_version = Version( + get_project(repo="NeurodataWithoutBorders/nwbinspector")["version"] + ) +diff --git a/setup.cfg b/setup.cfg +--- a/setup.cfg 2024-01-09 14:08:33.952653200 -0500 ++++ b/setup.cfg 2024-01-25 01:45:34.594335960 -0500 +@@ -34,7 +34,6 @@ + click >= 7.1 + click-didyoumean + dandischema ~= 0.8.0 +- etelemetry >= 0.2.2 + fasteners + fscacher >= 0.3.0 + hdmf != 3.5.0 +@@ -147,9 +146,6 @@ + [mypy-click_didyoumean.*] + ignore_missing_imports = True + +-[mypy-etelemetry.*] +-ignore_missing_imports = True +- + [mypy-fasteners.*] + ignore_missing_imports = True diff --git a/dev-vcs/datalad/Manifest b/dev-vcs/datalad/Manifest index c4147a574..7875ed2b6 100644 --- a/dev-vcs/datalad/Manifest +++ b/dev-vcs/datalad/Manifest @@ -1,2 +1 @@ -DIST datalad-0.15.1.tar.gz 1357778 BLAKE2B 7c12c3ff1bd8d260e8e7cfd9e477a1f0798f6fc0fbdbc335229bcf88362ebc7280eeb92bb59c45e0f66677297680e4d8d7bc8f56c7ac171f921bc389c1ceef7c SHA512 d5ae7859486748cbf40bd27f3351fa5620b8342c6a4347b8e3e0cb331de5fa33b9384071adbb899fd7878641a210a11b360a9ea68d0c7437eae709244fa08fd1 -DIST datalad-0.15.2.tar.gz 1361038 BLAKE2B c515b374f0781693ed0f1d0d2c260a0bdb1c9e998b782a2232c501b4ab7c022adc38f00a79d0aed04ffde4ade5c696705d53bf16dbaec2378c74ef4ab35a7a15 SHA512 f0206855439c2d376172218ec6bf1ffa3277508256a5a49a2ec65a57bb5720e039481329c16459ed62eb1c9ed0126dc178ca34fa2c3b8dfdf8b8a0706a2b8658 +DIST datalad-0.19.6.tar.gz 1420979 BLAKE2B 49d8e19449652f284f89f99e6696c6d1abf7ddcc58a8eb00004c657be38ce2532ed9c11855dca4a0a8f82c55fbf1633f53ff2bdea063fd18ad946145d27a3404 SHA512 db7cd807a8106727f0b6f587be8c0ce3abcf0dc7cf72b4757e6b44650adca05482e6b0a6c1719050fba37660dcd5de2a6f27df044a8db180ac6855ee7ff8cbda diff --git a/dev-vcs/datalad/datalad-0.15.1.ebuild b/dev-vcs/datalad/datalad-0.15.1.ebuild deleted file mode 100644 index 2322ac254..000000000 --- a/dev-vcs/datalad/datalad-0.15.1.ebuild +++ /dev/null @@ -1,68 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{8,9} ) -inherit distutils-r1 - -DESCRIPTION="Keep code, data, containers under control with git and git-annex" -HOMEPAGE="https://github.com/datalad/datalad" -SRC_URI="https://github.com/datalad/datalad/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64" -IUSE="test +downloaders +metadata +publish misc" -RESTRICT="!test? ( test )" - -RDEPEND=" - app-arch/p7zip - dev-python/annexremote[${PYTHON_USEDEP}] - dev-python/appdirs[${PYTHON_USEDEP}] - >=dev-python/chardet-3.0.4[${PYTHON_USEDEP}] - dev-python/distro[${PYTHON_USEDEP}] - dev-python/iso8601[${PYTHON_USEDEP}] - dev-python/humanize[${PYTHON_USEDEP}] - dev-python/fasteners[${PYTHON_USEDEP}] - app-arch/patool[${PYTHON_USEDEP}] - dev-python/tqdm[${PYTHON_USEDEP}] - dev-python/wrapt[${PYTHON_USEDEP}] - downloaders? ( - dev-python/boto[${PYTHON_USEDEP}] - dev-python/keyring[${PYTHON_USEDEP}] - dev-python/keyrings_alt[${PYTHON_USEDEP}] - dev-python/msgpack[${PYTHON_USEDEP}] - dev-python/requests[${PYTHON_USEDEP}] - ) - metadata? ( - dev-python/simplejson[${PYTHON_USEDEP}] - dev-python/whoosh[${PYTHON_USEDEP}] - ) - misc? ( - dev-python/argcomplete[${PYTHON_USEDEP}] - dev-python/pyperclip[${PYTHON_USEDEP}] - dev-python/python-dateutil[${PYTHON_USEDEP}] - ) - publish? ( - dev-vcs/python-gitlab[${PYTHON_USEDEP}] - dev-python/PyGithub[${PYTHON_USEDEP}] - ) -" -DEPEND=" - dev-python/setuptools[${PYTHON_USEDEP}] - test? ( - dev-python/beautifulsoup4[${PYTHON_USEDEP}] - dev-python/httpretty[${PYTHON_USEDEP}] - dev-python/vcrpy[${PYTHON_USEDEP}] - ) -" - -distutils_enable_tests nose - -python_test() { - export DATALAD_TESTS_NONETWORK=1 - ${EPYTHON} -m nose -s -v -A "not(integration or usecase or slow or network or turtle)" datalad || die - # Full test suite takes for ever: - # ${EPYTHON} -m nose -s -v datalad || die -} diff --git a/dev-vcs/datalad/datalad-0.15.2.ebuild b/dev-vcs/datalad/datalad-0.15.2.ebuild deleted file mode 100644 index 2322ac254..000000000 --- a/dev-vcs/datalad/datalad-0.15.2.ebuild +++ /dev/null @@ -1,68 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{8,9} ) -inherit distutils-r1 - -DESCRIPTION="Keep code, data, containers under control with git and git-annex" -HOMEPAGE="https://github.com/datalad/datalad" -SRC_URI="https://github.com/datalad/datalad/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64" -IUSE="test +downloaders +metadata +publish misc" -RESTRICT="!test? ( test )" - -RDEPEND=" - app-arch/p7zip - dev-python/annexremote[${PYTHON_USEDEP}] - dev-python/appdirs[${PYTHON_USEDEP}] - >=dev-python/chardet-3.0.4[${PYTHON_USEDEP}] - dev-python/distro[${PYTHON_USEDEP}] - dev-python/iso8601[${PYTHON_USEDEP}] - dev-python/humanize[${PYTHON_USEDEP}] - dev-python/fasteners[${PYTHON_USEDEP}] - app-arch/patool[${PYTHON_USEDEP}] - dev-python/tqdm[${PYTHON_USEDEP}] - dev-python/wrapt[${PYTHON_USEDEP}] - downloaders? ( - dev-python/boto[${PYTHON_USEDEP}] - dev-python/keyring[${PYTHON_USEDEP}] - dev-python/keyrings_alt[${PYTHON_USEDEP}] - dev-python/msgpack[${PYTHON_USEDEP}] - dev-python/requests[${PYTHON_USEDEP}] - ) - metadata? ( - dev-python/simplejson[${PYTHON_USEDEP}] - dev-python/whoosh[${PYTHON_USEDEP}] - ) - misc? ( - dev-python/argcomplete[${PYTHON_USEDEP}] - dev-python/pyperclip[${PYTHON_USEDEP}] - dev-python/python-dateutil[${PYTHON_USEDEP}] - ) - publish? ( - dev-vcs/python-gitlab[${PYTHON_USEDEP}] - dev-python/PyGithub[${PYTHON_USEDEP}] - ) -" -DEPEND=" - dev-python/setuptools[${PYTHON_USEDEP}] - test? ( - dev-python/beautifulsoup4[${PYTHON_USEDEP}] - dev-python/httpretty[${PYTHON_USEDEP}] - dev-python/vcrpy[${PYTHON_USEDEP}] - ) -" - -distutils_enable_tests nose - -python_test() { - export DATALAD_TESTS_NONETWORK=1 - ${EPYTHON} -m nose -s -v -A "not(integration or usecase or slow or network or turtle)" datalad || die - # Full test suite takes for ever: - # ${EPYTHON} -m nose -s -v datalad || die -} diff --git a/dev-vcs/datalad/datalad-0.19.6-r1.ebuild b/dev-vcs/datalad/datalad-0.19.6-r1.ebuild new file mode 100644 index 000000000..c95bc935f --- /dev/null +++ b/dev-vcs/datalad/datalad-0.19.6-r1.ebuild @@ -0,0 +1,73 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) +inherit distutils-r1 pypi + +DESCRIPTION="Keep code, data, containers under control with git and git-annex" +HOMEPAGE="https://github.com/datalad/datalad" +#SRC_URI="https://github.com/datalad/datalad/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" +IUSE="test +downloaders +metadata +publish misc" +RESTRICT="!test? ( test )" + +RDEPEND=" + >=dev-python/chardet-3.0.4[${PYTHON_USEDEP}] + app-arch/p7zip + app-arch/patool[${PYTHON_USEDEP}] + dev-python/annexremote[${PYTHON_USEDEP}] + dev-python/distro[${PYTHON_USEDEP}] + dev-python/fasteners[${PYTHON_USEDEP}] + dev-python/humanize[${PYTHON_USEDEP}] + dev-python/iso8601[${PYTHON_USEDEP}] + dev-python/looseversion[${PYTHON_USEDEP}] + dev-python/platformdirs[${PYTHON_USEDEP}] + dev-python/tqdm[${PYTHON_USEDEP}] + dev-python/wraps[${PYTHON_USEDEP}] + dev-vcs/git-annex + downloaders? ( + dev-python/keyring[${PYTHON_USEDEP}] + dev-python/keyrings-alt[${PYTHON_USEDEP}] + dev-python/msgpack[${PYTHON_USEDEP}] + dev-python/requests[${PYTHON_USEDEP}] + ) + metadata? ( + dev-python/simplejson[${PYTHON_USEDEP}] + dev-python/whoosh[${PYTHON_USEDEP}] + ) + misc? ( + dev-python/argcomplete[${PYTHON_USEDEP}] + dev-python/pyperclip[${PYTHON_USEDEP}] + dev-python/python-dateutil[${PYTHON_USEDEP}] + ) + publish? ( + dev-vcs/python-gitlab[${PYTHON_USEDEP}] + ) +" +BDEPEND=" + dev-python/packaging[${PYTHON_USEDEP}] + test? ( + ${RDEPEND} + dev-python/beautifulsoup4[${PYTHON_USEDEP}] + dev-python/httpretty[${PYTHON_USEDEP}] + dev-python/mypy[${PYTHON_USEDEP}] + dev-python/vcrpy[${PYTHON_USEDEP}] + ) +" +# Also wants test dep: +# dev-python/types-requests +# dev-python/types-python-dateutil + +distutils_enable_tests pytest + +python_test() { + local -x DATALAD_TESTS_NONETWORK=1 + # see test groups in "tox.ini" + epytest -k "not turtle and not slow and not usecase" +} diff --git a/dev-vcs/datalad/metadata.xml b/dev-vcs/datalad/metadata.xml index 8a6c00a2d..9c40d4f36 100644 --- a/dev-vcs/datalad/metadata.xml +++ b/dev-vcs/datalad/metadata.xml @@ -26,5 +26,6 @@ </use> <upstream> <remote-id type="github">datalad/datalad</remote-id> + <remote-id type="pypi">datalad</remote-id> </upstream> </pkgmetadata> diff --git a/docs/meetings/logs/20130130.log b/docs/meetings/logs/20130130.log deleted file mode 100644 index cde74b5cc..000000000 --- a/docs/meetings/logs/20130130.log +++ /dev/null @@ -1,262 +0,0 @@ -[22:01:44] *** Joins: jlec (~jlec@gentoo/developer/jlec) -[22:01:53] <tomka> here -[22:01:53] <willikins> tomka, you have notes! [17:16] <darkside_> thats a fun OSX error o_0 [18:46] <hwoarang> how about moving the tatt source code to the arch-tools repository please?! -[22:02:13] <jlec> hi -[22:02:59] <bicatali> let's wait another minute or so, although not sure we'll be so many of us -[22:03:53] <jlec> Actually the science channel looks quite full -[22:04:32] <bicatali> may be we should switch the meeting there then -[22:04:53] <bicatali> ok, let's start -[22:05:06] <jlec> I am supressing the join/part messages so I don't know when they all joined -[22:05:06] <bicatali> 1. alternatives -[22:05:26] <jlec> Who is willing to work on that? -[22:06:03] <bicatali> i'm working on an eselect fork, some fixes are already on github.com/gentoo-science/eselect.git -[22:06:31] <tomka> I'm mostly in maintenance mode, not going to take over new projects, sorry. -[22:06:33] <jlec> How much work do you think needs to be done until we can start merging it into the main eselect? -[22:06:45] <bicatali> more fixes will follow this week end to do the alternatives_for into the eselect -[22:07:04] <jlec> is ulm following the changes? -[22:07:15] <bicatali> these last fixes should be enough for ulm to review and pull -[22:07:24] <jlec> perfect. -[22:07:41] <jlec> That you are taking care of eselect. -[22:07:45] <bicatali> then there is the ldscript issue, which i have not started -[22:07:46] <bicatali> yep -[22:08:12] <jlec> yeah about the ldscript thing. -[22:08:12] *** Joins: heroxbd (~user@gentoo/developer/heroxbd) -[22:08:17] <bicatali> after those fixes the eclass will need to be rewritten, but it should be much more simple -[22:08:31] <heroxbd> sorry I'm late, it's 5am here. -[22:08:44] <jlec> no problem -[22:08:48] <jlec> we just started -[22:08:55] <heroxbd> ;) -[22:09:07] <jlec> bicatali: so we are waiting for you to fix eselect -[22:09:21] <bicatali> so has anyone tried the eselect-9999 from the science overlay? -[22:09:39] <jlec> not yet, but I will switch to tomorrow -[22:10:11] * heroxbd is wondering if it is about blas/atlas/gotoblas selection -[22:10:19] <bicatali> i would like a tester for the current eclass/eselect with multiple blas -[22:10:25] <jlec> heroxbd: alternatives framework -[22:10:32] <heroxbd> I see -[22:10:53] <bicatali> heroxbd: you need to unmask eselect-9999::science -[22:11:13] <heroxbd> bicatali: I'd like to be a tester, too. -[22:11:19] <bicatali> the other issue is what we do with library sonames -[22:11:31] <jlec> right -[22:11:43] <jlec> But I still disagree with equalizing them -[22:12:02] <jlec> You are right we reduce the rebuilding when one implementation is drop -[22:12:04] <jlec> ped -[22:12:07] <bicatali> so debian changes soname for atlas and openblas to blas -[22:12:28] <jlec> But we loose the ability to use different blas implementations for different programms -[22:13:31] <jlec> What do we gain in addition to the rebuilds to set all sonames to blas? -[22:13:33] <bicatali> i don't think we want users to compile R against openblas-threaded and octave against atlas -[22:13:49] <jlec> Why not? -[22:14:37] <bicatali> it's calling for bugs while rebuilding, and what do we do if the user removes one provider? -[22:15:00] <jlec> portage should catch that and preserve libs. -[22:15:03] <bicatali> and truely, once you choose one, you don't move -[22:15:25] <jlec> Not that I would recommend using different blas for different apps -[22:15:31] <jlec> But it's about choice -[22:15:35] <bicatali> we could do more eselect modules: blas-threads, blas-serial, blas-int64 -[22:16:21] <heroxbd> just to confirm, they cannot be made ABI at all. So we are exclued with this probability, is that true? -[22:16:27] <jlec> so instead of splitting into different providers, splitting into different types of implementation. -[22:16:30] <heroxbd> ABI-compatible I mean -[22:16:59] <jlec> bicatali: that sounds like a good idea -[22:17:29] <bicatali> yes, so we would use the mutlibuild eclass for each, then add some use flags threads, int64, etc... for the dependent packages -[22:18:02] <jlec> bicatali: but what about the libs which are splitted in to different so files? How do you handle sonames there? -[22:18:15] <bicatali> this makes sense: sometimes a threaded program does want a serial blas to avoid oversuscribing -[22:18:38] <bicatali> same soname for a given eselect module? -[22:19:20] <bicatali> right now i would suggest lets split, then later on let's worry about soname/ldscript -[22:19:49] <jlec> split what? -[22:20:22] <bicatali> let's make several blas eselect modules: blas-serial, blas-threads, ... -[22:20:59] <bicatali> and add use flags to virtual/blas -[22:22:15] <jlec> And would that look for different providers for e.g. blas-serial? -[22:22:30] <jlec> so atlas and reference are installed and provide serial -[22:22:40] <jlec> How can the user choose? -[22:22:51] <bicatali> use flag? -[22:23:19] <bicatali> threads? ( virtual/blas[threads] ) -[22:23:56] <jlec> so we have can do eselect blas-thread set atlas ? -[22:23:59] <bicatali> the worry about this is: much work to change ebuilds -[22:24:34] <bicatali> eselect blas-threads to select atlas-threads -[22:24:47] <bicatali> eselect blas-serial to select atlas... -[22:25:14] <jlec> and what if want now reference ? -[22:25:44] <bicatali> only on eselect blas-serial and virtual/blas with -threads -[22:26:25] <jlec> So you want to control everything over virtual/blas? -[22:26:57] <bicatali> on the package level yes, or do several virtual/blas-* -[22:27:30] <bicatali> it seems it needs more thinking, so let's set this for another time -[22:27:56] <jlec> yes fine. Perhaps you could write up a draft of your ideas -[22:28:34] * heroxbd considers a written guideline for us and the users necessary -[22:28:41] <bicatali> so actions: i'll finish the eselect, heroxbd will test the current builds with it -[22:28:55] <jlec> I will also test -[22:29:13] <jlec> sounds good -[22:29:14] <bicatali> anyone wants to investigate multibuilds? -[22:29:16] <heroxbd> no problem -[22:29:29] <heroxbd> I've been googling for it -[22:29:34] <jlec> bicatali: I can take a look -[22:29:49] <jlec> but we need to have a chat about your exact ideas -[22:30:08] <bicatali> yes. and let's start an alternatives wiki page -[22:30:37] <bicatali> btw anyone with another word than 'alternatives' is welcome -[22:31:05] * jlec slowly gets bicatali plan -[22:31:39] <bicatali> time to switch to the 2. documentation -[22:31:52] <jlec> WE need more. -[22:32:04] <heroxbd> exactly -[22:32:23] <jlec> I am trying to work on the whole contribution/community part -[22:32:43] <jlec> And I am currently in progress to move the mpi.eclass/empi thing to the tree. -[22:33:08] <jlec> This also need more documentation, which is probably more a business of the clusterteam -[22:33:31] <jlec> Which other documentations are top priority? -[22:33:33] <bicatali> regarding https://wiki.gentoo.org/wiki/Project:Science: it would be nice if everyone reads all the pages/subpages and resources -[22:34:36] <bicatali> like the Gentoo Electronics project and herd are empty -[22:34:49] <bicatali> but is it? -[22:34:56] <bicatali> the mail alias is not -[22:35:26] <jlec> bicatali: I will go through it and send mails to the aliases. -[22:35:57] <jlec> !herd sci-electronics -[22:36:00] <willikins> jlec: (sci-electronics) calchan, rafaelmartins, tomjbe, xmw -[22:37:38] <jlec> And wee need to increase the staffing needs -[22:37:45] <jlec> As we really need staff -[22:37:58] <jlec> BTW please try to recruit -[22:38:19] <bicatali> so let's push some jobs in the next gmn -[22:38:19] <jlec> we are super fast in recruiting currently so the process is really fast -[22:38:28] <jlec> good idea -[22:39:10] <bicatali> who would like to review all the wiki pages to make them consistent? -[22:39:30] <heroxbd> I can, haven't read it carefully yet -[22:39:32] <bicatali> i've tried quite a bit already, but it needs more reviewing -[22:39:46] <tomka> What's inconsistent? -[22:39:57] <bicatali> jlec: want to ping the herds to include themselves in the wiki? -[22:40:06] <jlec> It seems to be quite consistent -[22:40:12] <bicatali> herds, members and mail aliases -[22:40:18] <jlec> bicatali: ask for input on their pages -[22:40:29] <jlec> I will also go through it -[22:41:04] <tomka> Recruitment looks pretty much boilerplate. -[22:41:09] <tomka> It's the same on every sub-page. -[22:41:23] <tomka> But missing on sci-biology -[22:41:27] <bicatali> just want to make sure we can get rid of http://www.gentoo.org/proj/en/science/index.xml -[22:41:28] <tomka> are they fully staffed? -[22:41:42] <bicatali> which is still the first google result for gentoo science -[22:43:08] <jlec> I will first take a look that everything from the old xml site is covered by the wiki and then clean/improve the wiki pages. -[22:43:12] <heroxbd> so the task is to review the wiki to make sure it has the full coverage of proj/science/xml and then redirect it. -[22:43:48] <bicatali> yes, the blas-lapack page i will start the rewrite with the alternatives -[22:43:48] <heroxbd> !herd sci-biology -[22:43:49] <willikins> heroxbd: (sci-biology) je_fro, jlec, weaver -[22:44:05] <bicatali> !herd sci-geosciences -[22:44:06] <willikins> bicatali: (sci-geosciences) fordfrog -[22:44:06] <jlec> heroxbd: it's just me -[22:44:20] <heroxbd> ;) -[22:44:32] <bicatali> so these sub-projects make sense? -[22:44:59] <jlec> you mean the packages in the wiki or the herd subdivision? -[22:45:05] <heroxbd> I think so, there would be more stuff. -[22:45:36] <bicatali> we have both sub-herds and sub-projects -[22:46:00] <bicatali> ok, let's keep it that way and get more people i guess -[22:46:28] <jlec> sub-projects don't make really sense. -[22:46:33] <jlec> sub-herds do -[22:47:17] <jlec> I think the sub-projects should be things like the alternative framework rather then different science fields -[22:47:29] <bicatali> well we had this: http://www.gentoo.org/proj/en/science/electronics/ -[22:48:09] <jlec> so we can add the electronics test bench sub project -[22:48:36] <bicatali> first make sure that electronics is active... -[22:49:02] <jlec> So I will ask the current sub-projects if they are willing to merge into the parent -[22:49:14] <jlec> or otherwise maintain their subpage -[22:49:24] <bicatali> yes, and then re-organize the wiki -[22:49:26] <jlec> rafaelmartins: what about sci-electronics? -[22:49:34] <jlec> !seen rafaelmartins -[22:49:37] <willikins> jlec: rafaelmartins was last seen 4 hours, 44 minutes and 31 seconds ago, joining #gentoo-prefix -[22:50:35] <heroxbd> we can make alternative framework itself a subproject in parallel to the fields. -[22:51:22] <bicatali> i'd rather see the alternatives part of the eselect, i'll talk to ulm -[22:51:32] <jlec> kk -[22:52:00] <rafaelmartins> jlec: hello -[22:52:05] <jlec> hi -[22:52:08] * rafaelmartins jumps in the meeting -[22:52:18] <heroxbd> hi -[22:52:21] <jlec> I will send around mails -[22:52:26] <jlec> that's better -[22:52:30] <rafaelmartins> so, we are having low activity lately -[22:52:31] <bicatali> actions: wiki review herobxd, jlec. wiki reorg: jlec?. alternatives write-up start: bicatali -[22:52:37] <bicatali> rafaelmartins: oi -[22:52:45] <rafaelmartins> bicatali: oi :) -[22:53:01] <jlec> bicatali: I will take care of the wiki -[22:54:14] <bicatali> finally: 3. new leader -[22:54:21] <bicatali> i nominate jlec -[22:54:46] * heroxbd nods -[22:54:46] <jlec> Thanks. I accept the nomination. -[22:54:53] <tomka> I second that. -[22:54:59] <rafaelmartins> about electronics, quickly: -[22:55:33] <rafaelmartins> I'am not doing a lot of work on this. mainly maintaining just the stuff I use to play for fun, not working with any eng-related stuff at this point -[22:56:12] <rafaelmartins> I assumed as lead mainly because calchan wasn't able to do it at that time, my plan is to schedule a subproject lead election soon -[22:56:37] <bicatali> rafaelmartins: pushing for new recruits and updating the wiki should be enough for electronics to survive -[22:56:42] <jlec> rafaelmartins: I will take care of the wiki and do the rest by mail to the alias -[22:56:50] <rafaelmartins> so, the subproject still exists, but with quite low activity at this point -[22:56:59] <heroxbd> rafaelmartins: or would like to merge the sub project into science? -[22:57:10] <rafaelmartins> bicatali: yeah, we got some people interested, but they disappear :( -[22:57:34] <rafaelmartins> heroxbd: I'd like to hear calchan's opinion on this -[22:57:52] <heroxbd> rafaelmartins: ok -[22:57:59] <rafaelmartins> we can keep everything as is now, just migrating the project page to the wiki and decide on it later -[22:58:05] <bicatali> rafaelmartins: could you help jlec merging the old page into https://wiki.gentoo.org/wiki/Project:Electronics -[22:58:16] <rafaelmartins> bicatali: of course -[22:58:49] *** Joins: fbissey (~fbissey@132.181.64.206) -[22:58:53] <bicatali> ok voting: i vote for jlec as new leader -[22:59:08] <rafaelmartins> +1 for jlec -[22:59:10] <fbissey> Just in time for the vote -[22:59:17] <bicatali> hey fbissey -[22:59:23] <heroxbd> I vote for jlec, too -[22:59:27] <heroxbd> fbissey: hi -[22:59:39] <fbissey> no surprise that jlec is put in the driving seat -[22:59:52] <tomka> +1 for jlec -[23:00:49] <bicatali> jlec: clearly you are our new leader, please someone kicks me out from this channel! -[23:01:08] <jlec> THank you everbody -[23:01:12] <heroxbd> bicatali: ;) -[23:01:15] <fbissey> congrats! -[23:01:50] <jlec> ANd thank you bicatali doing the work the last years -[23:01:55] <heroxbd> jlec: hey you haven't voted yet -[23:01:59] <tomka> yeah thanks bicatali -[23:02:24] <fbissey> thanks for putting up with us bicatali -[23:02:50] <heroxbd> bicatali: yeah, thanks. And may I ask why you stepped down and what's your plan with science herd next? -[23:03:02] <bicatali> i'll try to clean up my leadership with a bug free alternatives -[23:03:36] <fbissey> I remember jlec and I came to gentoo at the same time and he is lead and I haven't made it to developer yet -[23:03:52] <bicatali> heroxbd: jlec is more involved than me. i'm going to work on an automated gentoo -[23:04:07] <heroxbd> fbissey: wow -[23:04:38] <jlec> I think we set some nice clean up for the next months. -[23:04:39] <heroxbd> bicatali: that's cluster deployment? -[23:04:58] <jlec> Getting the alternatives into the tree should be top priority. -[23:05:11] <heroxbd> jlec: agreed. -[23:05:43] <heroxbd> jlec: and as the wiki reorg/review overlaps, you can assign me some jobs in detail. -[23:05:59] <bicatali> heroxbd: no, some minimal gentoo core + cvmfs ala coreos to automate stabilizing -[23:06:20] <bicatali> anyone keeping logs? -[23:06:31] <jlec> I am logging -[23:06:54] <heroxbd> ain't there a 4. open floor? -[23:07:15] <heroxbd> just some FYI: first some news from roverlay. -[23:07:18] <bicatali> heroxbd: yes you are right -[23:08:27] <heroxbd> I started co-maintaining the roverlay with calchan, it is automated generatedfrom cran. once it's mature, I'll write up some doc -[23:08:49] <bicatali> that is good news -[23:09:13] <heroxbd> sorry, creepy internet connection -[23:09:32] <bicatali> jlec: want to post meeting log on the wiki then? -[23:09:48] <jlec> bicatali: I will -[23:09:56] <fbissey> heroxbd: can it take other R repo like bioconductor? -[23:11:04] <heroxbd> fbissey, I think it high possible, as the overlay generation tools are actively developed by another student. -[23:11:13] <heroxbd> *highly -[23:11:32] <heroxbd> it has been a google summer of code project -[23:12:57] <heroxbd> FYI2, among the Prefix users, many are from academic field. They submit bugs, and are good candidatesfor recruitment. -[23:14:38] <jlec> heroxbd: sounds great. -[23:14:45] <bicatali> ok folks, thanks, i'm off the meeting -[23:14:53] <jlec> make them fix the quizzes and get them a bug -[23:14:57] <fbissey> bye bicatali -[23:15:05] <jlec> bicatali thanks for all -[23:15:07] <jlec> bye -[23:15:28] <heroxbd> bicatali: see you -[23:17:30] <jlec> Okay guys, anymore more openfloor topics? -[23:17:34] <heroxbd> are we waiting for closing the meeting? -[23:18:08] <fbissey> I have some stuff but I will probably post on list for discusion -[23:18:19] <jlec> If there is nothing else, I would close it -[23:18:47] <jlec> We can schedule the next meeting sooner, in 1-2 months or so -[23:19:12] <jlec> fbissey: Or do you want to discuss now. It is up to you. -[23:19:31] <fbissey> I can introduce it. -[23:19:58] <fbissey> blas/lapack setup in python package is horrible -[23:20:26] <fbissey> motivated by work I am doing with people in sage I trying to get stuff to simplify that -[23:20:27] <jlec> We should wait for this a little -[23:20:39] <heroxbd> fbissey: python build system tries to do all the smart but wrong guessing -[23:21:00] <jlec> After bicatali fixed eselect and we decided about the soname thing, we shoudl have an ldscript -[23:21:10] <jlec> then it will become easier -[23:21:13] <fbissey> there is a python module to interface with pkg-config that makes some things easier -[23:21:22] <heroxbd> good idea -[23:21:42] <jlec> fbissey: best would be to simply have libblas.so as ldscript -[23:21:57] <jlec> but that should be implemented after we fixed the rest -[23:21:59] <fbissey> that make things easy agreed. -[23:23:57] <fbissey> nothing more from me -[23:24:05] <jlec> fine -[23:24:18] <jlec> So I will close the meeting here. Thanks for attending. -[23:24:29] <jlec> I will post the meeting log on the wiki -[23:24:36] <heroxbd> Thanks all -[23:24:47] <tomka> thanks -[23:25:30] *** Parts: fbissey (~fbissey@132.181.64.206) ("Konversation terminated!") -[23:33:09] *** Quits: tomka (~tomka@gentoo/developer/tomka) (Quit: tomka) -[23:44:50] *** Joins: Calchan (~calchan@gentoo/developer/calchan) diff --git a/docs/meetings/sci-electronics-201010-agenda b/docs/meetings/sci-electronics-201010-agenda deleted file mode 100644 index 2e3c18a3c..000000000 --- a/docs/meetings/sci-electronics-201010-agenda +++ /dev/null @@ -1,14 +0,0 @@ -Topics ------- - -- Open bugs (http://xrl.us/bh4cdg). -- Packages lacking in the main tree: - - Add your package here... -- Creation of the sci-electronics subproject. - - -Schedule --------- - -- When: 2010-10-17 2000 UTC (rafaelmartins, dilfridge) -- Where: #gentoo-meetings @ Freenode diff --git a/docs/proj/contrib.xml b/docs/proj/contrib.xml deleted file mode 100644 index fd474808b..000000000 --- a/docs/proj/contrib.xml +++ /dev/null @@ -1,182 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE guide SYSTEM "/dtd/guide.dtd"> -<guide link="/doc/en/" lang="en"> - - <title>Contributing to the Scientific Project</title> - - <author title="Author"> - <mail link="bicatali@gentoo.org">Sébastien Fabbro</mail> - <!-- others add your name here --> - </author> - - <abstract> - This document provides information on how one can get involved and - help out with the Gentoo Scientific Project - </abstract> - - <!-- The content of this document is licensed under the CC-BY-SA license --> - <!-- See http://creativecommons.org/licenses/by-sa/2.5 --> - <license/> - - <version>0.1</version> - <date>2009-01-21</date> - - <chapter> - <title>Overview</title> - <section> - <body> - <p> - This document aims to provide information on how one can get - involved and help out with the Gentoo Scientific Project. - Scientific packages are very diverse and many of us want our - pet application in the main tree for easy installation. Due to - the small size of our team, we can not implement all of - them, so we really appreciate any contribution. - </p> - <p> - There are few obvious areas where one can help as we - describe below. The Scientific Project tends to set strong - requirements on testing, especially on core packages. - Comments, thoughts, and feedback is greatly welcomed! - </p> - </body> - </section> - </chapter> - - <chapter> - <title>Bugs</title> - <section> - <title>Reporting</title> - <body> - <p> - All good software has bugs. They are too many combinations of - compilers, USE flags and versions to test them all. So if - you find the time to report them, we would love to hear - about it. We have the standard bugzilla system for - this. Don't be afraid of all these fields to fill in, it's - not that bad! - </p> - </body> - </section> - <section> - <title>Resolving</title> - <body> - <p> - The Scientific Team in Gentoo has always had a high number of - bugs. Fortunately, many of them are new packages. Any help in resolving - issues, improving submitted ebuilds is greatly appreciated. - </p> - <p> - <uri link="http://tinyurl.com/2qxmvu">Bugs for the Scientific Team.</uri> - <uri link="http://tinyurl.com/2nm6ag">Bugs for the Biology Team.</uri> - <uri link="http://tinyurl.com/368f2d">Bugs for the Chemistry Team.</uri> - <uri link="http://tinyurl.com/2lknlo">Bugs for the Electronics Team.</uri> - <uri link="http://tinyurl.com/2pcntk">Bugs for the Mathematics Team.</uri> - <uri link="http://tinyurl.com/3789aa">Bugs for the Physics Team.</uri> - </p> - </body> - </section> - </chapter> - - <chapter> - <title>Writing ebuilds</title> - <section> - <body> - <p> - You don't see your application in the main tree or in the - overlays and you don't want to wait for someone else to - create the ebuilds? The most obvious solution is to develop - your own ebuilds. If you do so, it's always nice to share - them. You can post them to our bugzilla system and then one - of our devs will comment out. The <uri link="http://overlays.gentoo.org/proj/sunrise">sunrise - overlay</uri> allows you more directly to commit your - ebuilds if you don't want to wait for science access. - </p> - </body> - </section> - </chapter> - - <chapter> - <title>Communication</title> - <section> - <title>Mailing List</title> - <body> - <p> - Join our - <uri link="http://www.gentoo.org/main/en/lists.xml"> gentoo-science mailing list - </uri> and asking/answering questions. - </p> - </body> - </section> - <section> - <title>IRC</title> - <body> - <p> - Meet some of us in #gentoo-science. It is a fairly quiet - channel, but slowly growing and we are responsive. We can - answer your questions, help you developing your ebuilds, - share ideas, etc... - </p> - </body> - </section> - <title>Direct emails</title> - <body> - <p> - If you feel your questions are more private and don't need - to be known from the rest of the world, you can always - directly send an email to our developers - listed <uri link="http://www.gentoo.org/main/en/proj/science/index.xml">here</uri> - and the listed sub-projects. If you want to mail all of us, send a mail to the herd. - </p> - </body> - </chapter> - - <chapter> - <title>Writing Documentation</title> - <body> - <section> - <p> - You may not be interested in fixing ebuilds and testing - packages, but want to share your knowledge about some - software, configuration or tips and tricks. The best way to - do this is to write some documentation. You can even write - official Gentoo documentation such as our - <uri link="http://www.gentoo.org/main/en/proj/science/blas-lapack.xml">blas/lapack - guide</uri>. - </p> - </section> - </body> - </chapter> - - <chapter> - <title>Seriously getting involved</title> - <section> - <body> - <p> - If you would like to join our team of volunteers and become - an official Gentoo Developer, show activity in anywhere you - can: bugzilla, overlays, mailing lists, irc, forums,... - Please refer to - <uri link="http://www.gentoo.org/proj/en/devrel/handbook/handbook.xml?part=1&chap=2"> - Becoming a Developer</uri> in the - <uri link="http://www.gentoo.org/proj/en/devrel/handbook/handbook.xml"> - Gentoo Developer Handbook</uri>. - </p> - <p> - Benefits are huge :-) : - <dl> - <dd> - <ul> - <li>Receive a warm welcome from us</li> - <li>Impress your geek friends</li> - <!--<li>Loose your social life, but</li>--> - <li>Get a free beer first time we meet in person!</li> - </ul> - </dd> - </dl> - </p> - - </body> - </section> - </chapter> -</guide> diff --git a/docs/proj/index.xml b/docs/proj/index.xml deleted file mode 100644 index b672ed36e..000000000 --- a/docs/proj/index.xml +++ /dev/null @@ -1,106 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<?xml-stylesheet href="/xsl/project.xsl" type="text/xsl"?> -<?xml-stylesheet href="/xsl/guide.xsl" type="text/xsl"?> -<!DOCTYPE project SYSTEM "/dtd/project.dtd"> - -<project> - <name>Science</name> - <longname>The Gentoo Scientific Project</longname> - <date>2009-01-21</date> - <author title="author"> - <mail link="sci@gentoo.org">Science Team</mail> - </author> - - <description> - The Gentoo Scientific Project handles all Gentoo related Math and Science items. - </description> - - <longdescription> - <p> - The Gentoo Scientific Project handles math and science related activities in Gentoo. - This includes maintaining packages that belong to various math - and science related herds, fortran compilers, documentations and communications. - </p> - </longdescription> - - <goals> - <p> - The goals of Scientific Gentoo are to provide a simple but optimal - installation and configuration of a wide variety of math and - science applications. Scientific computing is an area where custom optimization - provides great benefit. We also provide tools to easily switch configurations, and relevant - documentations. We give special attention to ways to test the - packages, through regression suites, and benchmarks. - </p> - </goals> - - - <!-- Staff --> - <dev role="member" description="General package maintainer">bicatali</dev> - <dev role="contributor" description="Ebuild development, general bug fixing, electronics and physics">dilfridge</dev> - <dev role="member" description="General package maintainer">je_fro</dev> - <dev role="contributor" description="Ebuild development (sage), general bug fixing and keep opendx running">kiwifb</dev> - <dev role="member" description="General package maintainer, g-octave developer">rafaelmartins</dev> - <dev role="member" description="General package maintainer">xarthisius</dev> - <dev role="member" description="g-cran developer">tulcod</dev> - <dev role="member" description="General package maintainer, sci-electronics">tomjbe</dev> - <dev role="my role in the science project" description="what i do mainly">dev-username</dev> - - <!-- Subprojects - <subproject ref="/proj/en/science/astronomy/index.xml" /> - <subproject ref="/proj/en/science/biology/index.xml" /> - <subproject ref="/proj/en/science/chemistry/index.xml" /> - <subproject ref="/proj/en/science/electronics/index.xml" /> - <subproject ref="/proj/en/science/math/index.xml" /> - <subproject ref="/proj/en/science/physics/index.xml" /> - --> - - <resource link="contrib.xml">Guide on contributing to the science project</resource> - <resource link="http://overlays.gentoo.org/proj/science">Official overlay</resource> - <resource link="http://news.gmane.org/gmane.linux.gentoo.science/">Mailing list archives</resource> - <resource link="irc://irc.freenode.net/gentoo-science">#gentoo-science IRC Channel</resource> - -<extrachapter position="bottom"> -<title>The Science Overlay</title> -<section> -<body> -<p> - New packages and more complex version bumps are held in - an <uri link="http://overlays.gentoo.org/proj/science/">Overlay</uri>. They - help both the science and hp-cluster team and the wiki contains some - temporary information. -</p> -</body> -</section> -</extrachapter> - -<recruitment> - <job> - <summary>Scientific package maintainer</summary> - <details> - The sci team and its various subprojects are always looking for a - general package maintainer to help our understaffed - team. Tasks are troubleshooting, version bumping and - stabilizing, new ebuilds and eclassed introduction. - </details> - <requirements> - Experience with Linux, various package build systems (autotools, cmake) - and makefiles, and bash. - </requirements> - <contact>sci</contact> - </job> - <job> - <summary>CAD Programs</summary> - <details> - Computer Aided Design open source programs are getting more popular - and yet to have decent support in Gentoo. We need to put an end - on this. - </details> - <requirements> - Knowledge of a few CAD programs and good ebuild skills. - </requirements> - <contact>sci</contact> - </job> -</recruitment> - -</project> diff --git a/eclass/alternatives-2.eclass b/eclass/alternatives-2.eclass deleted file mode 100644 index 7237f0db3..000000000 --- a/eclass/alternatives-2.eclass +++ /dev/null @@ -1,142 +0,0 @@ -# Copyright 2010-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -# Based in part upon 'alternatives.exlib' from Exherbo, which is: -# Copyright 2008, 2009 Bo Ørsted Andresen -# Copyright 2008, 2009 Mike Kelly -# Copyright 2009 David Leverton - -# @ECLASS: alternatives-2.eclass -# @MAINTAINER: -# Gentoo Science Project <sci@gentoo.org> -# @BLURB: Manage alternative implementations. -# @DESCRIPTION: -# Autogenerate eselect modules for alternatives and ensure that valid provider -# is set. -# -# Remove eselect modules when last provider is unmerged. -# -# If your package provides pkg_postinst or pkg_prerm phases, you need to be -# sure you explicitly run alternatives-2_pkg_{postinst,prerm} where appropriate. - -case "${EAPI:-0}" in - 0|1|2|3|4) - die "Unsupported EAPI=${EAPI:-0} (too old) for ${ECLASS}" - ;; - 5|6|7) - ;; - *) - die "Unsupported EAPI=${EAPI} (unknown) for ${ECLASS}" - ;; -esac - -DEPEND=">=app-admin/eselect-1.4.13-r101" -RDEPEND="${DEPEND} - !app-eselect/eselect-blas - !app-eselect/eselect-cblas - !app-eselect/eselect-lapack" - -# @ECLASS-VARIABLE: ALTERNATIVES_DIR -# @INTERNAL -# @DESCRIPTION: -# Alternatives directory with symlinks managed by eselect. -ALTERNATIVES_DIR="/etc/env.d/alternatives" - -# @FUNCTION: alternatives_for -# @USAGE: <alternative> <provider> <importance> <source> <target> [<source> <target> [...]] -# @DESCRIPTION: -# Set up alternative provider. -# -# EXAMPLE: -# @CODE -# alternatives_for sh bash 0 \ -# /usr/bin/sh bash -# @CODE -alternatives_for() { - debug-print-function ${FUNCNAME} "${@}" - - dodir /etc/env.d/alternatives - - ALTERNATIVESDIR_ROOT="${D%/}" \ - eselect alternatives add ${@} || die - - ALTERNATIVES_CREATED+=( ${1} ) -} - -# @FUNCTION: cleanup_old_alternatives_module -# @USAGE: <alternative> -# @DESCRIPTION: -# Remove old alternatives module. -cleanup_old_alternatives_module() { - debug-print-function ${FUNCNAME} "${@}" - - local alt=${1} old_module="${EROOT%/}/usr/share/eselect/modules/${alt}.eselect" - - if [[ -f "${old_module}" && $(grep 'ALTERNATIVE=' "${old_module}" | cut -d '=' -f 2) == "${alt}" ]]; then - local version="$(grep 'VERSION=' "${old_module}" | grep -o '[0-9.]\+')" - if [[ "${version}" == "0.1" || "${version}" == "20080924" ]]; then - einfo "rm ${old_module}" - rm "${old_module}" || eerror "rm ${old_module} failed" - fi - fi -} - -# @FUNCTION: alternatives-2_pkg_postinst -# @DESCRIPTION: -# Create eselect modules for all provided alternatives if necessary and ensure -# that valid provider is set. -# -# Also remove old eselect modules for provided alternatives. -# -# Provided alternatives are set up using alternatives_for(). -alternatives-2_pkg_postinst() { - debug-print-function ${FUNCNAME} "${@}" - - local alt - - for alt in ${ALTERNATIVES_CREATED[@]}; do - if ! eselect ${alt} show > /dev/null; then - einfo "Creating Alternative for ${alt}" - eselect alternatives create ${alt} - fi - - # Set alternative provider if there is no valid provider selected - eselect alternatives update "${alt}" - - cleanup_old_alternatives_module ${alt} - done -} - -# @FUNCTION: alternatives-2_pkg_prerm -# @DESCRIPTION: -# Ensure a valid provider is set in case the package is unmerged and -# remove autogenerated eselect modules for alternative when last -# provider is unmerged. -# -# Provided alternatives are set up using alternatives_for(). -alternatives-2_pkg_prerm() { - debug-print-function ${FUNCNAME} "${@}" - - local alt ret - - # If we are uninstalling, update alternatives to valid provider - [[ -n ${REPLACED_BY_VERSION} ]] || ignore="--ignore" - for alt in ${ALTERNATIVES_CREATED[@]}; do - eselect alternatives update "${alt}" - ret=$? - - case ${ret} in - 0) : ;; - 2) - # This was last provider for the alternative, remove eselect module - einfo "Cleaning up unused alternatives module for ${alt}" - eselect alternatives delete "${alt}" || eerror "Failed to remove ${alt}" - ;; - *) - eerror "eselect alternatives update returned \"${ret}\"" - ;; - esac - done -} - -EXPORT_FUNCTIONS pkg_postinst pkg_prerm diff --git a/eclass/intel-sdp-r1.eclass b/eclass/intel-sdp-r1.eclass deleted file mode 100644 index 9d902395f..000000000 --- a/eclass/intel-sdp-r1.eclass +++ /dev/null @@ -1,571 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -# @ECLASS: intel-sdp-r1.eclass -# @MAINTAINER: -# Justin Lecher <jlec@gentoo.org> -# David Seifert <soap@gentoo.org> -# Sci Team <sci@gentoo.org> -# @BLURB: Handling of Intel's Software Development Products package management - -MULTILIB_COMPAT=( abi_x86_{32,64} ) - -inherit check-reqs eutils multilib-build - -EXPORT_FUNCTIONS src_unpack src_install pkg_postinst pkg_postrm pkg_pretend - -if [[ ! ${_INTEL_SDP_R1_ECLASS_} ]]; then - -case "${EAPI}" in - 7) ;; - *) die "EAPI=${EAPI} is not supported" ;; -esac - -# @ECLASS-VARIABLE: INTEL_DIST_NAME -# @DESCRIPTION: -# The package name to download from Intel. -# To determine its value, see the links to download in -# https://registrationcenter.intel.com/RegCenter/MyProducts.aspx -# -# e.g. parallel_studio_xe -# -# Must be defined before inheriting the eclass. -: ${INTEL_DIST_NAME:=parallel_studio_xe} - -# @ECLASS-VARIABLE: INTEL_DIST_PV -# @DEFAULT_UNSET -# @DESCRIPTION: -# The package download version from Intel. -# To determine its value, see the links to download in -# https://registrationcenter.intel.com/RegCenter/MyProducts.aspx -# -# e.g. 2016_update1 -# -# Must be defined before inheriting the eclass. - -# @ECLASS-VARIABLE: INTEL_DIST_TARX -# @DESCRIPTION: -# The package distfile suffix. -# To determine its value, see the links to download in -# https://registrationcenter.intel.com/RegCenter/MyProducts.aspx -# -# e.g. tgz -# -# Must be defined before inheriting the eclass. -: ${INTEL_DIST_TARX:=tgz} - -# @ECLASS-VARIABLE: INTEL_SUBDIR -# @DESCRIPTION: -# The package sub-directory (without version numbers) where it will end-up in /opt/intel -# -# e.g. compilers_and_libraries -# -# To determine its value, you have to do a raw install from the Intel tarball. -: ${INTEL_SUBDIR:=compilers_and_libraries} - -# @ECLASS-VARIABLE: INTEL_SKIP_LICENSE -# @DEFAULT_UNSET -# @DESCRIPTION: -# Possibility to skip the mandatory check for licenses. Only set this if there -# is really no fix. - -# @ECLASS-VARIABLE: INTEL_RPMS_DIR -# @DESCRIPTION: -# Main subdirectory which contains the rpms to extract. -: ${INTEL_RPMS_DIR:=rpm} - -# @ECLASS-VARIABLE: INTEL_DIST_BIN_RPMS -# @DESCRIPTION: -# Functional name of rpm without any version/arch tag. -# Has to be a bash array -# -# e.g. ("icc-l-all-devel") -# -# if the rpm is located in a directory other than INTEL_RPMS_DIR you can -# specify the full path -# -# e.g. ("CLI_install/rpm/intel-vtune-amplifier-xe-cli") -[[ ${INTEL_DIST_BIN_RPMS[@]} ]] || INTEL_DIST_BIN_RPMS=() - -# @ECLASS-VARIABLE: INTEL_DIST_AMD64_RPMS -# @DESCRIPTION: -# AMD64 single arch rpms. Same syntax as INTEL_DIST_BIN_RPMS. -# Has to be a bash array. -[[ ${INTEL_DIST_AMD64_RPMS[@]} ]] || INTEL_DIST_AMD64_RPMS=() - -# @ECLASS-VARIABLE: INTEL_DIST_X86_RPMS -# @DESCRIPTION: -# X86 single arch rpms. Same syntax as INTEL_DIST_BIN_RPMS. -# Has to be a bash array. -[[ ${INTEL_DIST_X86_RPMS[@]} ]] || INTEL_DIST_X86_RPMS=() - -# @ECLASS-VARIABLE: INTEL_DIST_DAT_RPMS -# @DESCRIPTION: -# Functional name of rpm of common data which are arch free -# without any version tag. Has to be a bash array. -# -# e.g. ("openmp-l-all-devel") -# -# if the rpm is located in a directory different to INTEL_RPMS_DIR you can -# specify the full path -# -# e.g. ("CLI_install/rpm/intel-vtune-amplifier-xe-cli-common") -[[ ${INTEL_DIST_DAT_RPMS[@]} ]] || INTEL_DIST_DAT_RPMS=() - -# @ECLASS-VARIABLE: INTEL_DIST_SPLIT_ARCH -# @DESCRIPTION: -# Set to "true" if arches are to be fetched separately, instead of using -# the combined tarball. -: ${INTEL_DIST_SPLIT_ARCH:=false} - -# @FUNCTION: _isdp_path_exists -# @INTERNAL -# @USAGE: [-a|-o] <paths> -# @DESCRIPTION: -# Check if the specified paths exist. Works for all types of paths -# (files/dirs/etc...). The -a and -o flags control the requirements -# of the paths. They correspond to "and" and "or" logic. So the -a -# flag means all the paths must exist while the -o flag means at least -# one of the paths must exist. The default behavior is "and". If no -# paths are specified, then the return value is "false". -_isdp_path_exists() { - local opt=$1 - [[ ${opt} == -[ao] ]] && shift || opt="-a" - - # no paths -> return false - # same behavior as: [[ -e "" ]] - [[ $# -eq 0 ]] && return 1 - - local p r=0 - for p in "$@" ; do - [[ -e ${p} ]] - : $(( r += $? )) - done - - case ${opt} in - -a) return $(( r != 0 )) ;; - -o) return $(( r == $# )) ;; - esac - eerror "path_exists has been removed. Please see the following post" - eerror "for a replacement snippet:" - eerror "https://blogs.gentoo.org/mgorny/2018/08/09/inlining-path_exists/" - die "path_exists is banned" -} - -# @FUNCTION: _isdp_get-sdp-year -# @INTERNAL -# @DESCRIPTION: -# Gets the year component from INTEL_DIST_PV -_isdp_get-sdp-year() { - local _intel_sdp_year - _intel_sdp_year=${INTEL_DIST_PV} - _intel_sdp_year=${_intel_sdp_year%_sp*} - _intel_sdp_year=${_intel_sdp_year%_update*} - echo "${_intel_sdp_year}" -} - -# @FUNCTION: isdp_get-sdp-dir -# @DESCRIPTION: -# Gets the full rootless path to the installation directory -# -# e.g. opt/intel/compilers_and_libraries_2016.1.150 -# opt/intel/vtune_amplifier_2018.2.0.551022 -isdp_get-sdp-dir() { - local _intel_sdp_dir="opt/intel/${INTEL_SUBDIR}_$(_isdp_get-sdp-year).$(ver_cut 3-)" - echo "${_intel_sdp_dir}" -} - -# @FUNCTION: isdp_get-sdp-edir -# @DESCRIPTION: -# Gets the full rooted/prefixed path to the installation directory -# -# e.g. /opt/intel/compilers_and_libraries_2016.1.150 -isdp_get-sdp-edir() { - local _intel_sdp_edir="${EPREFIX%/}/$(isdp_get-sdp-dir)" - echo "${_intel_sdp_edir}" -} - -SRC_URI="${INTEL_DIST_NAME}_${INTEL_DIST_PV}.${INTEL_DIST_TARX}" -LICENSE="Intel-SDP" -# TODO: Proper slotting -# Future work, #394411 -SLOT="0" - -RESTRICT="bindist mirror fetch" - -RDEPEND="" -DEPEND="app-arch/rpm2targz" - -S="${WORKDIR}" - -QA_PREBUILT="$(isdp_get-sdp-dir)/*" - -# @FUNCTION: isdp_convert2intel-arch -# @USAGE: <arch> -# @DESCRIPTION: -# Convert between portage arch (e.g. amd64, x86) and intel installed arch -# nomenclature (e.g. intel64, ia32) -isdp_convert2intel-arch() { - debug-print-function ${FUNCNAME} "${@}" - - case $1 in - *amd64*|abi_x86_64) - echo "intel64" - ;; - *x86*) - echo "ia32" - ;; - *) - die "Abi \'$1\' is unsupported" - ;; - esac -} - -# @FUNCTION: isdp_get-native-abi-arch -# @DESCRIPTION: -# Determine the the intel arch string of the native ABI -isdp_get-native-abi-arch() { - debug-print-function ${FUNCNAME} "${@}" - - use amd64 && echo "$(isdp_convert2intel-arch abi_x86_64)" - use x86 && echo "$(isdp_convert2intel-arch abi_x86_32)" -} - -# @FUNCTION: isdp_get-sdp-installed-arches -# @DESCRIPTION: -# Returns a space separated list of the arch suffixes used in directory -# names for enabled ABIs. Intel uses "ia32" for x86 and "intel64" for -# amd64. The result would be "ia32 intel64" if both ABIs were enabled. -isdp_get-sdp-installed-arches() { - local arch=() - use abi_x86_64 && arch+=($(isdp_convert2intel-arch abi_x86_64)) - use abi_x86_32 && arch+=($(isdp_convert2intel-arch abi_x86_32)) - echo "${arch[*]}" -} - -# @FUNCTION: _isdp_generate-list-install-rpms -# @INTERNAL -# @DESCRIPTION: -# Generates the list of fully expanded RPMs to be extracted. -_isdp_generate-list-install-rpms() { - debug-print-function ${FUNCNAME} "${@}" - - # Expand components into full RPM filenames - expand_component_into_full_rpm() { - local deref_var="${1}[@]" - local p rpm_prefix expanded_full_rpms=() - - for p in "${!deref_var}"; do - # check if a directory is prefixed - if [[ "${p}" == "${p##*/}" ]]; then - rpm_prefix="${INTEL_RPMS_DIR}/intel-" - else - rpm_prefix="" - fi - expanded_full_rpms+=( "${rpm_prefix}${p}" ) - done - echo ${expanded_full_rpms[*]} - } - - local vars_to_expand=("INTEL_DIST_BIN_RPMS" "INTEL_DIST_DAT_RPMS") - if use abi_x86_32; then - vars_to_expand+=("INTEL_DIST_X86_RPMS") - fi - if use abi_x86_64; then - vars_to_expand+=("INTEL_DIST_AMD64_RPMS") - fi - - local i fully_expanded_intel_rpms=() - for ((i=0; i<${#vars_to_expand[@]}; i++)); do - fully_expanded_intel_rpms+=($(expand_component_into_full_rpm "${vars_to_expand[i]}")) - done - echo ${fully_expanded_intel_rpms[*]} -} - -# @FUNCTION: _isdp_big-warning -# @USAGE: [pre-check | test-failed] -# @INTERNAL -# @DESCRIPTION: -# warn user that we really require a license -_isdp_big-warning() { - debug-print-function ${FUNCNAME} "${@}" - - case ${1} in - pre-check ) - ewarn "License file not found!" - ;; - - test-failed ) - ewarn "Function test failed. Most probably due to an invalid license." - ewarn "This means you already tried to bypass the license check once." - ;; - esac - - ewarn - ewarn "Make sure you have received an Intel license." - ewarn "To receive a non-commercial license, you need to register at:" - ewarn "https://software.intel.com/en-us/qualify-for-free-software" - ewarn "Install the license file into ${EPREFIX}/opt/intel/licenses" - - case ${1} in - pre-check ) - ewarn "before proceeding with installation of ${P}" - ;; - * ) - ;; - esac -} - -# @FUNCTION: _isdp_version_test -# @INTERNAL -# @DESCRIPTION: -# Testing for valid license by asking for version information of the compiler. -_isdp_version_test() { - debug-print-function ${FUNCNAME} "${@}" - - local comp - case ${PN} in - ifc ) - debug-print "Testing ifort" - comp=ifort - ;; - icc ) - debug-print "Testing icc" - comp=icc - ;; - *) - die "${PN} is not supported for testing" - ;; - esac - - local comp_full arch warn - for arch in $(isdp_get-sdp-installed-arches); do - case ${EBUILD_PHASE} in - install ) - comp_full="${ED%/}/$(isdp_get-sdp-dir)/linux/bin/${arch}/${comp}" - ;; - postinst ) - comp_full="$(isdp_get-sdp-edir)/linux/bin/${arch}/${comp}" - ;; - * ) - die "Compile test not supported in ${EBUILD_PHASE}" - ;; - esac - - debug-print "LD_LIBRARY_PATH=\"$(isdp_get-sdp-edir)/linux/bin/${arch}/\" \"${comp_full}\" -V" - - LD_LIBRARY_PATH="$(isdp_get-sdp-edir)/linux/bin/${arch}/" "${comp_full}" -V &>/dev/null || warn=yes - done - [[ ${warn} == yes ]] && _isdp_big-warning test-failed -} - -# @FUNCTION: _isdp_run-test -# @INTERNAL -# @DESCRIPTION: -# Test if installed compiler is working. -_isdp_run-test() { - debug-print-function ${FUNCNAME} "${@}" - - if [[ -z ${INTEL_SKIP_LICENSE} ]]; then - case ${PN} in - ifc | icc ) - _isdp_version_test - ;; - * ) - debug-print "No test available for ${PN}" - ;; - esac - fi -} - -# @FUNCTION: intel-sdp-r1_pkg_pretend -# @DESCRIPTION: -# -# * Check for a (valid) license before proceeding. -# -# * Check for space requirements being fulfilled. -# -intel-sdp-r1_pkg_pretend() { - debug-print-function ${FUNCNAME} "${@}" - - local warn=1 dir dirs ret arch a p - - : ${CHECKREQS_DISK_BUILD:=256M} - check-reqs_pkg_pretend - - if [[ -z ${INTEL_SKIP_LICENSE} ]]; then - if [[ ${INTEL_LICENSE_FILE} == *@* ]]; then - einfo "Looks like you are using following license server:" - einfo " ${INTEL_LICENSE_FILE}" - return 0 - fi - - dirs=( - "${EPREFIX}/opt/intel/licenses" - "$(isdp_get-sdp-edir)/licenses" - "$(isdp_get-sdp-edir)/Licenses" - ) - for dir in "${dirs[@]}" ; do - ebegin "Checking for a license in: ${dir}" - _isdp_path_exists "${dir}"/*lic && warn=0 - eend ${warn} && break - done - if [[ ${warn} == 1 ]]; then - _isdp_big-warning pre-check - die "Could not find license file" - fi - else - eqawarn "The ebuild doesn't check for presence of a proper intel license!" - eqawarn "This shouldn't be done unless there is a very good reason." - fi -} - -# @FUNCTION: intel-sdp-r1_pkg_nofetch -# @DESCRIPTION: -# Advice user to download the parallel studio tarball -pkg_nofetch() { - einfo "Please download" - einfo " ${SRC_URI}" - einfo "from" - einfo " https://registrationcenter.intel.com/RegCenter/MyProducts.aspx" - einfo "and place the tarball in your DISTDIR directory." -} - -# @FUNCTION: intel-sdp-r1_src_unpack -# @DESCRIPTION: -# Unpacking necessary rpms from tarball, extract them and rearrange the output. -intel-sdp-r1_src_unpack() { - local t - for t in ${A}; do - local r list=() source_rpms=($(_isdp_generate-list-install-rpms)) - for r in "${source_rpms[@]}"; do - list+=( ${t%%.*}/${r} ) - done - - local debug_list - debug_list="$(IFS=$'\n'; echo ${list[@]} )" - - debug-print "Adding to decompression list:" - debug-print ${debug_list} - - tar -xvf "${DISTDIR}"/${t} ${list[@]} &> "${T}"/rpm-extraction.log - - for r in ${list[@]}; do - einfo "Unpacking ${r}" - printf "\nUnpacking %s\n" "${r}" >> "${T}"/rpm-extraction.log - rpm2tar -O ${r} | tar -xvf - &>> "${T}"/rpm-extraction.log; assert "Unpacking ${r} failed" - done - done -} - -# @FUNCTION: intel-sdp-r1_src_install -# @DESCRIPTION: -# Install everything -intel-sdp-r1_src_install() { - debug-print-function ${FUNCNAME} "${@}" - - local i - # remove uninstall information - ebegin "Cleaning out uninstall" - while IFS='\n' read -r -d '' i; do - rm -r "${i}" || die - done < <(find opt -regextype posix-extended -regex '.*(uninstall|uninstall.sh)$' -print0) - eend - - # handle documentation - if _isdp_path_exists "opt/intel/documentation_$(_isdp_get-sdp-year)"; then - # normal man pages - if _isdp_path_exists "opt/intel/documentation_$(_isdp_get-sdp-year)/en/man/common/man1"; then - doman opt/intel/documentation_"$(_isdp_get-sdp-year)"/en/man/common/man1/* - rm -r opt/intel/documentation_"$(_isdp_get-sdp-year)"/en/man || die - fi - - use doc && dodoc -r opt/intel/documentation_"$(_isdp_get-sdp-year)"/* - - ebegin "Cleaning out documentation" - rm -r "opt/intel/documentation_$(_isdp_get-sdp-year)" || die - rm -rf "$(isdp_get-sdp-dir)"/linux/{documentation,man} || die - eend - fi - - # MPI man pages - if _isdp_path_exists "$(isdp_get-sdp-dir)/linux/mpi/man/man3"; then - doman "$(isdp_get-sdp-dir)"/linux/mpi/man/man3/* - rm -r "$(isdp_get-sdp-dir)"/linux/mpi/man || die - fi - - # licensing docs - if _isdp_path_exists "$(isdp_get-sdp-dir)/licensing/documentation"; then - dodoc -r "$(isdp_get-sdp-dir)/licensing/documentation"/* - rm -rf "$(isdp_get-sdp-dir)/licensing/documentation" || die - fi - - if _isdp_path_exists opt/intel/"${INTEL_DIST_NAME}"*/licensing; then - dodoc -r opt/intel/"${INTEL_DIST_NAME}"*/licensing - rm -rf opt/intel/"${INTEL_DIST_NAME}"* || die - fi - - # handle examples - if _isdp_path_exists "opt/intel/samples_$(_isdp_get-sdp-year)"; then - use examples && dodoc -r opt/intel/samples_"$(_isdp_get-sdp-year)"/* - - ebegin "Cleaning out examples" - rm -r "opt/intel/samples_$(_isdp_get-sdp-year)" || die - eend - fi - - # remove eclipse unconditionally - ebegin "Cleaning out eclipse files" - rm -rf opt/intel/ide_support_* || die - eend - - # repair shell scripts used for sourcing PATH (iccvars.sh and such) - ebegin "Tagging ${PN}" - find opt -name \*sh -type f -exec sed -i \ - -e "s:<.*DIR>:$(isdp_get-sdp-edir)/linux:g" \ - '{}' + || die - eend - - ebegin "Removing broken symlinks" - while IFS='\n' read -r -d '' i; do - rm "${i}" || die - done < <(find opt -xtype l -print0) - eend - - mv opt "${ED%/}"/ || die "moving files failed" - - keepdir "$(isdp_get-sdp-dir)"/licenses /opt/intel/ism/rm -} - -# @FUNCTION: intel-sdp-r1_pkg_postinst -# @DESCRIPTION: -# Test for all things working -intel-sdp-r1_pkg_postinst() { - debug-print-function ${FUNCNAME} "${@}" - - _isdp_run-test - - if [[ ${PN} = icc ]] && has_version ">=dev-util/ccache-3.1.9-r2" ; then - #add ccache links as icc might get installed after ccache - "${EROOT}"/usr/bin/ccache-config --install-links - fi - - elog "Beginning with the 2016 suite of Intel tools, Gentoo has removed" - elog "support for the eclipse plugin. If you require the IDE support," - elog "you will have to install the suite on your own, outside portage." -} - -# @FUNCTION: intel-sdp-r1_pkg_postrm -# @DESCRIPTION: -# Sanitize cache links -intel-sdp-r1_pkg_postrm() { - debug-print-function ${FUNCNAME} "${@}" - - if [[ ${PN} = icc ]] && has_version ">=dev-util/ccache-3.1.9-r2" && [[ -z ${REPLACED_BY_VERSION} ]]; then - # --remove-links would remove all links, --install-links updates them - "${EROOT}"/usr/bin/ccache-config --install-links - fi -} - -_INTEL_SDP_R1_ECLASS_=1 -fi diff --git a/eclass/numeric-int64-multibuild.eclass b/eclass/numeric-int64-multibuild.eclass deleted file mode 100644 index 9dd23cebf..000000000 --- a/eclass/numeric-int64-multibuild.eclass +++ /dev/null @@ -1,414 +0,0 @@ -# Copyright 1999-2021 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -# @ECLASS: numeric-int64-multibuild.eclass -# @MAINTAINER: -# sci team <sci@gentoo.org> -# @AUTHOR: -# Author: Mark Wright <gienah@gentoo.org> -# Author: Justin Lecher <jlec@gentoo.org> -# @BLURB: Build functions for Fortran multilib int64 multibuild packages -# @DESCRIPTION: -# The numeric-int64-multibuild.eclass exports USE flags and utility functions -# necessary to build packages for multilib int64 multibuild in a clean -# and uniform manner. - -if [[ ! ${_NUMERIC_INT64_MULTILIB_ECLASS} ]]; then - -# EAPI=5 is required for meaningful MULTILIB_USEDEP. -case ${EAPI:-0} in - 5) - inherit multilib ;; - 6|7) ;; - *) die "EAPI=${EAPI} is not supported" ;; -esac - -inherit alternatives-2 eutils fortran-2 multilib-build numeric toolchain-funcs - -IUSE="int64" - -# @ECLASS-VARIABLE: NUMERIC_INT32_SUFFIX -# @INTERNAL -# @DESCRIPTION: -# MULTIBUILD_ID suffix for int32 build -NUMERIC_INT32_SUFFIX="int32" - -# @ECLASS-VARIABLE: NUMERIC_INT64_SUFFIX -# @INTERNAL -# @DESCRIPTION: -# MULTIBUILD_ID suffix for int64 build -NUMERIC_INT64_SUFFIX="int64" - -# @ECLASS-VARIABLE: NUMERIC_STATIC_SUFFIX -# @INTERNAL -# @DESCRIPTION: -# MULTIBUILD_ID suffix for static build -NUMERIC_STATIC_SUFFIX="static" - -# @FUNCTION: numeric-int64_is_int64_build -# @DESCRIPTION: -# Returns shell true if the current multibuild is a int64 build, -# else returns shell false. -# -# Example: -# -# @CODE -# $(numeric-int64_is_int64_build) && \ -# openblas_abi_cflags+=" -DOPENBLAS_USE64BITINT" -# @CODE -numeric-int64_is_int64_build() { - debug-print-function ${FUNCNAME} "${@}" - if [[ "${MULTIBUILD_ID}" =~ "${NUMERIC_INT64_SUFFIX}" ]]; then - return 0 - else - return 1 - fi -} - -# @FUNCTION: numeric-int64_is_static_build -# @DESCRIPTION: -# Returns shell true if current multibuild is a static build, -# else returns shell false. -# -# Example: -# -# @CODE -# if $(numeric-int64_is_static_build); then -# dolib.a lib*a -# fi -# @CODE -numeric-int64_is_static_build() { - debug-print-function ${FUNCNAME} "${@}" - if [[ "${MULTIBUILD_ID}" =~ "${NUMERIC_STATIC_SUFFIX}" ]]; then - return 0 - else - return 1 - fi -} - -# @FUNCTION: numeric-int64_get_module_name -# @USAGE: [<module_name>] -# @DESCRIPTION: -# Return the numeric module name, without the .pc extension, -# for the current fortran int64 build. If the current build is not an int64 -# build, and the ebuild does not have dynamic, threads or openmp USE flags or -# they are disabled, then the module_name is ${NUMERIC_MODULE_NAME} or -# <module_name> if <module_name> is specified. -# -# Takes an optional <module_name> parameter. If no <module_name> is specified, -# uses ${NUMERIC_MODULE_NAME} as the base to calculate the module_name for the -# current build. -# -# Example: -# -# @CODE -# NUMERIC_MODULE_NAME=blas -# profname=$(numeric-int64_get_module_name) -# -# int32 build: -# -> profname == blas -# -# int64 build: -# -> profname == blas-int64 -# @CODE -numeric-int64_get_module_name() { - debug-print-function ${FUNCNAME} "${@}" - local module_name="${1:-${NUMERIC_MODULE_NAME}}" - if has dynamic ${IUSE} && use dynamic; then - module_name+="-dynamic" - fi - if $(numeric-int64_is_int64_build); then - module_name+="-${NUMERIC_INT64_SUFFIX}" - fi - # choose posix threads over openmp when the two are set - # yet to see the need of having the two profiles simultaneously - if in_iuse threads && use threads; then - module_name+="-threads" - elif in_iuse openmp && use openmp; then - module_name+="-openmp" - fi - echo "${module_name}" -} - -# @FUNCTION: _numeric-int64_get_numeric_alternative -# @INTERNAL -_numeric-int64_get_numeric_alternative() { - debug-print-function ${FUNCNAME} "${@}" - local alternative_name="${1}" - if $(numeric-int64_is_int64_build); then - alternative_name+="-${NUMERIC_INT64_SUFFIX}" - fi - echo "${alternative_name}" -} - -# @FUNCTION: numeric-int64_get_blas_alternative -# @DESCRIPTION: -# Returns the eselect blas alternative for the current -# int build type. Which is blas-int64 if called from an int64 build, -# or blas otherwise. -numeric-int64_get_blas_alternative() { - debug-print-function ${FUNCNAME} "${@}" - _numeric-int64_get_numeric_alternative blas -} - -# @FUNCTION: numeric-int64_get_cblas_alternative -# @DESCRIPTION: -# Returns the eselect cblas alternative for the current -# int build type. Which is cblas-int64 if called from an int64 build, -# or cblas otherwise. -numeric-int64_get_cblas_alternative() { - debug-print-function ${FUNCNAME} "${@}" - _numeric-int64_get_numeric_alternative cblas -} - -# @FUNCTION: numeric-int64_get_xblas_alternative -# @DESCRIPTION: -# Returns the eselect xblas alternative for the current -# int build type. Which is xblas-int64 if called from an int64 build, -# or xblas otherwise. -numeric-int64_get_xblas_alternative() { - debug-print-function ${FUNCNAME} "${@}" - _numeric-int64_get_numeric_alternative xblas -} - -# @FUNCTION: numeric-int64_get_lapack_alternative -# @DESCRIPTION: -# Returns the eselect lapack alternative for the current -# int build type. Which is lapack-int64 if called from an int64 build, -# or lapack otherwise. -numeric-int64_get_lapack_alternative() { - debug-print-function ${FUNCNAME} "${@}" - _numeric-int64_get_numeric_alternative lapack -} - -# @FUNCTION: numeric-int64_get_blas_module_name -# @DESCRIPTION: -# Returns the pkg-config file name, without the .pc extension, -# for the currently selected blas-int64 module if we are performing an int64 -# build, or the currently selected blas module otherwise. -numeric-int64_get_blas_module_name() { - debug-print-function ${FUNCNAME} "${@}" - local blas_alternative=$(numeric-int64_get_blas_alternative) - local blas_symlinks=( $(eselect "${blas_alternative}" files) ) - local blas_prof_symlink="$(readlink -f ${blas_symlinks[0]})" - local blas_prof_file="${blas_prof_symlink##*/}" - echo "${blas_prof_file%.pc}" -} - -# @FUNCTION: numeric-int64_get_xblas_module_name -# @DESCRIPTION: -# Returns the xblas pkg-config file name, -# without the .pc extension, for the current build. Which is xblas-int64 if -# we are performing an int64 build, or xblas otherwise. -numeric-int64_get_xblas_module_name() { - debug-print-function ${FUNCNAME} "${@}" - local xblas_provider="xblas" - if $(numeric-int64_is_int64_build); then - xblas_provider+="-${INT64_SUFFIX}" - fi - echo "${xblas_provider}" -} - -# @FUNCTION: numeric-int64_get_fortran_int64_abi_fflags -# @DESCRIPTION: -# Return the Fortran compiler flag to enable 64 bit integers for -# array indices if we are performing an int64 build, or the empty string -# otherwise. -# -# Example: -# -# @CODE -# src_configure() { -# my_configure() { -# export FCFLAGS="${FCFLAGS} $(get_abi_CFLAGS) $(numeric-int64_get_fortran_int64_abi_fflags)" -# econf $(use_enable fortran) -# } -# numeric-int64-multibuild_foreach_all_abi_variants run_in_build_dir my_configure -# } -# @CODE -numeric-int64_get_fortran_int64_abi_fflags() { - debug-print-function ${FUNCNAME} "${@}" - $(numeric-int64_is_int64_build) && echo "$(fortran_int64_abi_fflags)" -} - -# @FUNCTION: numeric-int64_get_multibuild_int_variants -# @DESCRIPTION: -# Returns the array of int64 and int32 -# multibuild combinations. -numeric-int64_get_multibuild_int_variants() { - debug-print-function ${FUNCNAME} "${@}" - local MULTIBUILD_VARIANTS=( int32 ) variant - - in_iuse int64 && use int64 && MULTIBUILD_VARIANTS+=( int64 ) - - echo "${MULTIBUILD_VARIANTS[@]}" -} - -# @FUNCTION: numeric-int64_get_multibuild_variants -# @DESCRIPTION: -# Returns the array of int64, int32 and static -# multibuild combinations. -numeric-int64_get_multibuild_variants() { - debug-print-function ${FUNCNAME} "${@}" - local MULTIBUILD_VARIANTS=$(numeric-int64_get_multibuild_int_variants) - if in_iuse static-libs && use static-libs; then - for variant in ${MULTIBUILD_VARIANTS[@]}; do - MULTIBUILD_VARIANTS+=( static_${variant} ) - done - fi - echo "${MULTIBUILD_VARIANTS[@]}" -} - -# @FUNCTION: numeric-int64_get_all_abi_variants -# @DESCRIPTION: -# Returns the array of int64, int32 and static build combinations -# combined with all multilib ABI variants. -numeric-int64_get_all_abi_variants() { - debug-print-function ${FUNCNAME} "${@}" - local abi ret=() variant - - for abi in $(multilib_get_enabled_abi_pairs); do - for variant in $(numeric-int64_get_multibuild_variants); do - if [[ ${variant} =~ int64 ]]; then - [[ ${abi} =~ amd64 ]] && ret+=( ${abi}_${variant} ) - else - ret+=( ${abi}_${variant} ) - fi - done - done - echo "${ret[@]}" -} - -# @FUNCTION: numeric-int64_ensure_blas_int_support -# @DESCRIPTION: -# Check the blas supports the necessary int types in the currently -# selected blas module. -# -# Example: -# -# @CODE -# src_prepare() { -# numeric-int64_ensure_blas_int_support -# ... -# @CODE -numeric-int64_ensure_blas_int_support() { - local MULTILIB_INT64_VARIANTS=( $(numeric-int64_get_multibuild_variants) ) - local MULTIBUILD_ID - for MULTIBUILD_ID in "${MULTILIB_INT64_VARIANTS[@]}"; do - local blas_module_name=$(numeric-int64_get_blas_module_name) - $(tc-getPKG_CONFIG) --exists "${blas_module_name}" \ - || die "${PN} requires the pkgbuild module ${blas_module_name}" - done -} - -# @FUNCTION: numeric-int64-multibuild_install_alternative -# @USAGE: <alternative name> <provider name> [extra files sources] [extra files dest] -# @DESCRIPTION: -# Install alternatives pc file and extra files for all providers for all multilib ABIs. -numeric-int64-multibuild_install_alternative() { - debug-print-function ${FUNCNAME} "${@}" - [[ $# -lt 2 ]] && die "${FUNCNAME} needs at least two arguments" - pc_file() { - debug-print-function ${FUNCNAME} "${@}" - numeric-int64_is_static_build && return - local alternative=$(_numeric-int64_get_numeric_alternative "$1") - local module_name=$(numeric-int64_get_module_name) - printf \ - "/usr/$(get_libdir)/pkgconfig/${alternative}.pc ${module_name}.pc " \ - >> "${T}"/alternative-${alternative}.sh || die - } - pc_install() { - debug-print-function ${FUNCNAME} "${@}" - numeric-int64_is_static_build && return - local alternative=$(_numeric-int64_get_numeric_alternative "$1") - local module_name=$(numeric-int64_get_module_name $2) - shift 2 - alternatives_for \ - ${alternative} ${module_name} 0 \ - $(cat "${T}"/alternative-${alternative}.sh) ${@} - rm "${T}"/alternative-${alternative}.sh || die - } - numeric-int64-multibuild_foreach_all_abi_variants pc_file ${@} - numeric-int64-multibuild_foreach_int_abi pc_install ${@} -} - -# @FUNCTION: numeric-int64-multibuild_multilib_wrapper -# @USAGE: <argv>... -# @DESCRIPTION: -# Initialize the environment for ABI selected for multibuild. -# -# Example: -# -# @CODE -# multibuild_foreach_variant run_in_build_dir \ -# numeric-int64-multibuild_multilib_wrapper my_src_install -# @CODE -numeric-int64-multibuild_multilib_wrapper() { - debug-print-function ${FUNCNAME} "${@}" - - local v="${MULTIBUILD_VARIANT%_*}" - # MULTIBUILD_VARIANT could be abi_x86_64.amd64_static_int32 - v=${v%_${NUMERIC_STATIC_SUFFIX}} - local ABI="${v#*.}" - # hack: our int64 and int32 ABIs can correspond to the same ABI - # in multilib, resulting in multiple sed replacements of headers - # and thus error like "Flag not listed in wrapper template." - # Using MULTILIB_ABI_FLAG="${ABI}", the corresponding header - # is ignored. - local MULTILIB_ABI_FLAG - case ${MULTIBUILD_VARIANT} in - *_${NUMERIC_STATIC_SUFFIX}*|*_${NUMERIC_INT64_SUFFIX}) - MULTILIB_ABI_FLAG="${ABI}" - ;; - *_${NUMERIC_INT32_SUFFIX}) - MULTILIB_ABI_FLAG="${v%.*}" - ;; - esac - - multilib_toolchain_setup "${ABI}" - readonly ABI - "${@}" || die -} - -# @FUNCTION: numeric-int64-multibuild_foreach_int_abi -# @USAGE: <argv> ... -# @DESCRIPTION: -# Run command for each enabled numeric variant (e.g. int32, int64) -numeric-int64-multibuild_foreach_int_abi() { - debug-print-function ${FUNCNAME} "${@}" - local MULTIBUILD_VARIANTS=( $(numeric-int64_get_multibuild_int_variants) ) - multibuild_foreach_variant numeric-int64-multibuild_multilib_wrapper "${@}" -} - -# @FUNCTION: numeric-int64-multibuild_foreach_variant -# @USAGE: <argv> ... -# @DESCRIPTION: -# Run command for each enabled numeric abi and static-libs (e.g. int32, int64, static) -numeric-int64-multibuild_foreach_variant() { - debug-print-function ${FUNCNAME} "${@}" - local MULTIBUILD_VARIANTS=( $(numeric-int64_get_multibuild_variants) ) - multibuild_foreach_variant numeric-int64-multibuild_multilib_wrapper "${@}" -} - -# @FUNCTION: numeric-int64-multibuild_foreach_all_abi_variants -# @USAGE: <argv> ... -# @DESCRIPTION: -# Run command for each enabled numeric variant (e.g. int32, int64, static) _AND_ -# enabled multilib ABI -numeric-int64-multibuild_foreach_all_abi_variants() { - debug-print-function ${FUNCNAME} "${@}" - local MULTIBUILD_VARIANTS=( $(numeric-int64_get_all_abi_variants) ) - multibuild_foreach_variant numeric-int64-multibuild_multilib_wrapper "${@}" -} - -# @FUNCTION: numeric-int64-multibuild_copy_sources -# @DESCRIPTION: -# Thin wrapper around multibuild_copy_sources() -numeric-int64-multibuild_copy_sources() { - debug-print-function ${FUNCNAME} "${@}" - local MULTIBUILD_VARIANTS=( $(numeric-int64_get_all_abi_variants) ) - multibuild_copy_sources -} - -_NUMERIC_INT64_MULTILIB_ECLASS=1 -fi diff --git a/eclass/numeric.eclass b/eclass/numeric.eclass deleted file mode 100644 index 431b7afec..000000000 --- a/eclass/numeric.eclass +++ /dev/null @@ -1,138 +0,0 @@ -# Copyright 1999-2017 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -# @ECLASS: numeric.eclass -# @MAINTAINER: -# jlec@gentoo.org -# @BLURB: Maintance bits needed for *lapack* and *blas* packages -# @DESCRIPTION: -# Various functions which make the maintenance numerical algebra packages -# easier. - -if [[ ! ${_NUMERIC_ECLASS} ]]; then - -case ${EAPI:-0} in - 0|1|2|3|4|5) - inherit multilib ;; - 6|7) ;; - *) die "EAPI=${EAPI} is not supported" ;; -esac - -# @VARIABLE: NUMERIC_MODULE_NAME -# @DESCRIPTION: -# The base pkg-config module name of the package being built. -# NUMERIC_MODULE_NAME is used by the numeric-int64_get_module_name to -# determine the pkg-config module name based on whether the package -# has dynamic, threads or openmp USE flags and if so, if the user has -# turned them or, and if the current multibuild is a int64 build or not. -# -# @CODE -# NUMERIC_MODULE_NAME="openblas" -# inherit ... numeric-int64-multibuild -# @CODE -: ${NUMERIC_MODULE_NAME:=blas} - -# @FUNCTION: create_pkgconfig -# @USAGE: [ additional arguments ] -# @DESCRIPTION: -# Creates and installs pkg-config file. The function should only be executed in -# src_install(). For further information about optional arguments please consult -# http://people.freedesktop.org/~dbn/pkg-config-guide.html -# -# @CODE -# Optional arguments are: -# -# -p | --prefix Offset for current package (${EPREFIX}/usr) -# -e | --exec-prefix Offset for current package (${prefix}) -# -L | --libdir Libdir to use (${prefix}/$(get_libdir)) -# -I | --includedir Includedir to use (${prefix}/include) -# -n | --name A human-readable name (PN} -# -d | --description A brief description (DESCRIPTION) -# -V | --version Version of the package (PV) -# -u | --url Web presents (HOMEPAGE) -# -r | --requires Packages required by this package (unset) -# -l | --libs Link flags specific to this package (unset) -# -c | --cflags Compiler flags specific to this package (unset) -# --requires-private Like --requires, but not exposed (unset) -# --conflicts Packages that this one conflicts with (unset) -# --libs-private Like --libs, but not exposed (unset) -# @CODE -create_pkgconfig() { - debug-print-function ${FUNCNAME} "${@}" - local pcfilename pcrequires pcrequirespriv pcconflicts pclibs pclibspriv pccflags - local pcprefix="${EPREFIX}/usr" - local pcexecprefix="${pcprefix}" - local pclibdir="${EPREFIX}/usr/$(get_libdir)" - local pcincldir="${pcprefix}/include" - local pcname=${PN} - local pcdescription="${DESCRIPTION}" - local pcurl=${HOMEPAGE} - local pcversion=${PV} - - [[ "${EBUILD_PHASE}" != "install" ]] && \ - die "create_pkgconfig should only be used in src_install()" - - while (($#)); do - case ${1} in - -p | --prefix ) - shift; pcprefix=${1} ;; - -e | --exec-prefix ) - shift; pcexecprefix=${1} ;; - -L | --libdir ) - shift; pclibdir=${1} ;; - -I | --includedir ) - shift; pcincldir=${1} ;; - -n | --name ) - shift; pcname=${1} ;; - -d | --description ) - shift; pcdescription=${1} ;; - -V | --version ) - shift; pcversion=${1} ;; - -u | --url ) - shift; pcurl=${1} ;; - -r | --requires ) - shift; pcrequires=${1} ;; - --requires-private ) - shift; pcrequirespriv=${1} ;; - --conflicts ) - shift; pcconflicts=${1};; - -l | --libs ) - shift; pclibs=${1} ;; - --libs-private ) - shift; pclibspriv=${1} ;; - -c | --cflags ) - shift; pccflags=${1} ;; - -* ) - ewarn "Unknown option ${1}" ;; - * ) - pcfilename=${1} ;; - esac - shift - done - - [[ -z ${pcfilename} ]] && die "Missing name for pkg-config file" - - cat > "${T}"/${pcfilename}.pc <<- EOF - prefix="${pcprefix}" - exec_prefix="${pcexecprefix}" - libdir="${pclibdir}" - includedir="${pcincldir}" - - Name: ${pcname} - Description: ${pcdescription} - Version: ${pcversion} - URL: ${pcurl} - Requires: ${pcrequires} - Requires.private: ${pcrequirespriv} - Conflicts: ${pcconflicts} - Libs: -L\${libdir} ${pclibs} - Libs.private: ${pclibspriv} - Cflags: -I\${includedir} ${pccflags} - EOF - - insinto /usr/$(get_libdir)/pkgconfig - doins "${T}"/${pcfilename}.pc -} - -_NUMERIC_ECLASS=1 -fi diff --git a/licenses/CeCILL-1.1 b/licenses/CeCILL-1.1 deleted file mode 100644 index b4efe1181..000000000 --- a/licenses/CeCILL-1.1 +++ /dev/null @@ -1,513 +0,0 @@ - FREE SOFTWARE LICENSING AGREEMENT CeCILL - ======================================== - - -Notice ------- - - -This Agreement is a free software license that is the result of discussions -between its authors in order to ensure compliance with the two main -principles guiding its drafting: - - firstly, its conformity with French law, both as regards the law of - torts and intellectual property law, and the protection that it offers - to authors and the holders of economic rights over software. - - secondly, compliance with the principles for the distribution of free - software: access to source codes, extended user-rights. - -The following bodies are the authors of this license CeCILL (Ce : CEA, C : -CNRS, I : INRIA, LL : Logiciel Libre): - -Commissariat à l'Energie Atomique - CEA, a public scientific, technical and -industrial establishment, having its principal place of business at 31-33 -rue de la Fédération, 75752 PARIS cedex 15, France. - -Centre National de la Recherche Scientifique - CNRS, a public scientific -and technological establishment, having its principal place of business at -3 rue Michel-Ange 75794 Paris cedex 16, France. - -Institut National de Recherche en Informatique et en Automatique - INRIA, a -public scientific and technological establishment, having its principal -place of business at Domaine de Voluceau, Rocquencourt, BP 105, 78153 Le -Chesnay cedex. - - -PREAMBLE --------- - - -The purpose of this Free Software Licensing Agreement is to grant users the -right to modify and redistribute the software governed by this license -within the framework of an "open source" distribution model. - -The exercising of these rights is conditional upon certain obligations for -users so as to ensure that this status is retained for subsequent -redistribution operations. - -As a counterpart to the access to the source code and rights to copy, modify -and redistribute granted by the license, users are provided only with a -limited warranty and the software's author, the holder of the economic -rights, and the successive licensors only have limited liability. - -In this respect, it is brought to the user's attention that the risks -associated with loading, using, modifying and/or developing or reproducing -the software by the user given its nature of Free Software, that may -mean that it is complicated to manipulate, and that also therefore means -that it is reserved for developers and experienced professionals having -in-depth computer knowledge. Users are therefore encouraged to load and test -the Software's suitability as regards their requirements in conditions -enabling the security of their systems and/or data to be ensured and, more -generally, to use and operate it in the same conditions of security. -This Agreement may be freely reproduced and published, provided it is -not altered, and that no Articles are either added or removed herefrom. - -This Agreement may apply to any or all software for which the holder of the -economic rights decides to submit the operation thereof to its provisions. - - -Article 1 - DEFINITIONS ------------------------- - - -For the purposes of this Agreement, when the following expressions commence -with a capital letter, they shall have the following meaning: - -Agreement: means this Licensing Agreement, and any or all of its subsequent -versions. - -Software: means the software in its Object Code and/or Source Code form -and, where applicable, its documentation, "as is" at the time when the -Licensee accepts the Agreement. - -Initial Software: means the Software in its Source Code and/or Object Code -form and, where applicable, its documentation, "as is" at the time when it -is distributed for the first time under the terms and conditions of the -Agreement. - -Modified Software: means the Software modified by at least one -Contribution. - -Source Code: means all the Software's instructions and program lines to -which access is required so as to modify the Software. - -Object Code: means the binary files originating from the compilation of the -Source Code. - -Holder: means the holder of the economic rights over the Initial -Software. - -Licensee(s): mean(s) the Software user(s) having accepted the Agreement. - -Contributor: means a Licensee having made at least one Contribution. - -Licensor: means the Holder, or any or all other individual or legal entity, -that distributes the Software under the Agreement. - -Contributions: mean any or all modifications, corrections, translations, -adaptations and/or new functionalities integrated into the Software by any -or all Contributor, and the Static Modules. - -Module: means a set of sources files including their documentation that, -once compiled in executable form, enables supplementary functionalities or -services to be developed in addition to those offered by the Software. - -Dynamic Module: means any or all module, created by the Contributor, that -is independent of the Software, so that this module and the Software are in -two different executable forms that are run in separate address spaces, -with one calling the other when they are run. - -Static Module: means any or all module, created by the Contributor and -connected to the Software by a static link that makes their object codes -interdependent. This module and the Software to which it is connected, are -combined in a single executable. - -Parties: mean both the Licensee and the Licensor. - -These expressions may be used both in singular and plural form. - - -Article 2 - PURPOSE -------------------- - - -The purpose of the Agreement is to enable the Licensor to grant the -Licensee a free, non-exclusive, transferable and worldwide License for the -Software as set forth in Article 5 hereinafter for the whole term of -protection of the rights over said Software. - - -Article 3 - ACCEPTANCE ----------------------- - - -3.1. The Licensee shall be deemed as having accepted the terms and -conditions of this Agreement by the occurrence of the first of the -following events: -- (i) loading the Software by any or all means, notably, by downloading - from a remote server, or by loading from a physical medium; -- (ii) the first time the Licensee exercises any of the rights granted - hereunder. - -3.2. One copy of the Agreement, containing a notice relating to the -specific nature of the Software, to the limited warranty, and to the -limitation to use by experienced users has been provided to the Licensee -prior to its acceptance as set forth in Article 3.1 hereinabove, and the -Licensee hereby acknowledges that it is aware thereof. - - -Article 4 - EFFECTIVE DATE AND TERM ------------------------------------ - - -4.1. EFFECTIVE DATE - -The Agreement shall become effective on the date when it is accepted by the -Licensee as set forth in Article 3.1. - -4.2. TERM - -The Agreement shall remain in force during the whole legal term of -protection of the economic rights over the Software. - - -Article 5 - SCOPE OF THE RIGHTS GRANTED ---------------------------------------- - - -The Licensor hereby grants to the Licensee, that accepts such, the -following rights as regards the Software for any or all use, and for the -term of the Agreement, on the basis of the terms and conditions set forth -hereinafter. - -Otherwise, the Licensor grants to the Licensee free of charge exploitation -rights on the patents he holds on whole or part of the inventions -implemented in the Software. - -5.1. RIGHTS OF USE - -The Licensee is authorized to use the Software, unrestrictedly, as regards -the fields of application, with it being hereinafter specified that this -relates to: -- permanent or temporary reproduction of all or part of the Software by - any or all means and in any or all form. -- loading, displaying, running, or storing the Software on any or all - medium. -- entitlement to observe, study or test the operation thereof so as to - establish the ideas and principles that form the basis for any or all - constituent elements of said Software. This shall apply when the - Licensee carries out any or all loading, displaying, running, - transmission or storage operation as regards the Software, that it is - entitled to carry out hereunder. - -5.2. entitlement to make CONTRIBUTIONS - -The right to make Contributions includes the right to translate, adapt, -arrange, or make any or all modification to the Software, and the right to -reproduce the resulting Software. - -The Licensee is authorized to make any or all Contribution to the Software -provided that it explicitly mentions its name as the author of said -Contribution and the date of the development thereof. - -5.3. DISTRIBUTION AND PUBLICATION RIGHTS - -In particular, the right of distribution and publication includes the right -to transmit and communicate the Software to the general public on any or -all medium, and by any or all means, and the right to market, either in -consideration of a fee, or free of charge, a copy or copies of the Software -by means of any or all process. -The Licensee is further authorized to redistribute copies of the modified -or unmodified Software to third parties according to the terms and -conditions set forth hereinafter. - -5.3.1. REDISTRIBUTION OF SOFTWARE WITHOUT MODIFICATION - -The Licensee is authorized to redistribute true copies of the Software in -Source Code or Object Code form, provided that said redistribution complies -with all the provisions of the Agreement and is accompanied by: -- a copy of the Agreement, -- a notice relating to the limitation of both the Licensor's warranty - and liability as set forth in Articles 8 and 9, -and that, in the event that only the Software's Object Code is -redistributed, the Licensee allows future Licensees unhindered access to -the Software's full Source Code by providing them with the terms and -conditions for access thereto, it being understood that the additional cost -of acquiring the Source Code shall not exceed the cost of transferring the -data. - -5.3.2. REDISTRIBUTION OF MODIFIED SOFTWARE - -When the Licensee makes a Contribution to the Software, the terms and -conditions for the redistribution of the Modified Software shall then be -subject to all the provisions hereof. - -The Licensee is authorized to redistribute the Modified Software, in Source -Code or Object Code form, provided that said redistribution complies with -all the provisions of the Agreement and is accompanied by: -- a copy of the Agreement, -- a notice relating to the limitation of both the Licensor's warranty - and liability as set forth in Articles 8 and 9, -and that, in the event that only the Modified Software's Object Code is -redistributed, the Licensee allows future Licensees unhindered access to -the Modified Software's full Source Code by providing them with the terms -and conditions for access thereto, it being understood that the additional -cost of acquiring the Source Code shall not exceed the cost of transferring -the data. - - -5.3.3. redistribution OF DYNAMIC MODULES - -When the Licensee has developed a Dynamic Module, the terms and conditions -hereof do not apply to said Dynamic Module, that may be distributed under -a separate Licensing Agreement. - -5.3.4. COMPATIBILITY WITH THE GPL LICENSE - -In the event that the Modified or unmodified Software is included in a code -that is subject to the provisions of the GPL License, the Licensee is -authorized to redistribute the whole under the GPL License. - -In the event that the Modified Software includes a code that is subject to -the provisions of the GPL License, the Licensee is authorized to -redistribute the Modified Software under the GPL License. - - -Article 6 - INTELLECTUAL PROPERTY ----------------------------------- - - -6.1. OVER THE INITIAL SOFTWARE - -The Holder owns the economic rights over the Initial Software. Any or all -use of the Initial Software is subject to compliance with the terms and -conditions under which the Holder has elected to distribute its work and no -one shall be entitled to and it shall have sole entitlement to modify the -terms and conditions for the distribution of said Initial Software. - -The Holder undertakes to maintain the distribution of the Initial Software -under the conditions of the Agreement, for the duration set forth in -article 4.2.. - -6.2. OVER THE CONTRIBUTIONS - -The intellectual property rights over the Contributions belong to the -holder of the economic rights as designated by effective legislation. - -6.3. OVER THE DYNAMIC MODULES - -The Licensee having developed a Dynamic Module is the holder of the -intellectual property rights over said Dynamic Module and is free to choose -the agreement that shall govern its distribution. - -6.4. JOINT PROVISIONS - -6.4.1. The Licensee expressly undertakes: -- not to remove, or modify, in any or all manner, the intellectual - property notices affixed to the Software; -- to reproduce said notices, in an identical manner, in the copies of - the Software. - -6.4.2. The Licensee undertakes not to directly or indirectly infringe the -intellectual property rights of the Holder and/or Contributors and to take, -where applicable, vis-à-vis its staff, any or all measures required to -ensure respect for said intellectual property rights of the Holder and/or -Contributors. - - -Article 7 - RELATED SERVICES ------------------------------ - - -7.1. Under no circumstances shall the Agreement oblige the Licensor to -provide technical assistance or maintenance services for the Software. - -However, the Licensor is entitled to offer this type of service. The -terms and conditions of such technical assistance, and/or such -maintenance, shall then be set forth in a separate instrument. Only the -Licensor offering said maintenance and/or technical assistance services -shall incur liability therefor. - -7.2. Similarly, any or all Licensor shall be entitled to offer to its -Licensees, under its own responsibility, a warranty, that shall only be -binding upon itself, for the redistribution of the Software and/or the -Modified Software, under terms and conditions that it shall decide upon -itself. Said warranty, and the financial terms and conditions of its -application, shall be subject to a separate instrument executed between the -Licensor and the Licensee. - - -Article 8 - LIABILITY ----------------------- - - -8.1. Subject to the provisions of Article 8.2, should the Licensor fail to -fulfill all or part of its obligations hereunder, the Licensee shall be -entitled to claim compensation for the direct loss suffered as a result of -a fault on the part of the Licensor, subject to providing evidence of it. - -8.2. The Licensor's liability is limited to the commitments made under this -Licensing Agreement and shall not be incurred as a result , in particular: -(i) of loss due the Licensee's total or partial failure to fulfill its -obligations, (ii) direct or consequential loss due to the Software's use or -performance that is suffered by the Licensee, when the latter is a -professional using said Software for professional purposes and (iii) -consequential loss due to the Software's use or performance. The Parties -expressly agree that any or all pecuniary or business loss (i.e. loss of -data, loss of profits, operating loss, loss of customers or orders, -opportunity cost, any disturbance to business activities) or any or all -legal proceedings instituted against the Licensee by a third party, shall -constitute consequential loss and shall not provide entitlement to any or -all compensation from the Licensor. - - -Article 9 - WARRANTY ---------------------- - - -9.1. The Licensee acknowledges that the current situation as regards -scientific and technical know-how at the time when the Software was -distributed did not enable all possible uses to be tested and verified, nor -for the presence of any or all faults to be detected. In this respect, the -Licensee's attention has been drawn to the risks associated with loading, -using, modifying and/or developing and reproducing the Software that are -reserved for experienced users. - -The Licensee shall be responsible for verifying, by any or all means, the -product's suitability for its requirements, its due and proper functioning, -and for ensuring that it shall not cause damage to either persons or -property. - -9.2. The Licensor hereby represents, in good faith, that it is entitled to -grant all the rights on the Software (including in particular the rights -set forth in Article 5 hereof over the Software). - -9.3. The Licensee acknowledges that the Software is supplied "as is" by the -Licensor without any or all other express or tacit warranty, other than -that provided for in Article 9.2 and, in particular, without any or all -warranty as to its market value, its secured, innovative or relevant -nature. - -Specifically, the Licensor does not warrant that the Software is free from -any or all error, that it shall operate continuously, that it shall be -compatible with the Licensee's own equipment and its software -configuration, nor that it shall meet the Licensee's requirements. - -9.4. The Licensor does not either expressly or tacitly warrant that the -Software does not infringe any or all third party intellectual right -relating to a patent, software or to any or all other property right. -Moreover, the Licensor shall not hold the Licensee harmless against any or -all proceedings for infringement that may be instituted in respect of the -use, modification and redistribution of the Software. Nevertheless, should -such proceedings be instituted against the Licensee, the Licensor shall -provide it with technical and legal assistance for its defense. Such -technical and legal assistance shall be decided upon on a case-by-case -basis between the relevant Licensor and the Licensee pursuant to a -memorandum of understanding. The Licensor disclaims any or all liability as -regards the Licensee's use of the Software's name. No warranty shall be -provided as regards the existence of prior rights over the name of the -Software and as regards the existence of a trademark. - - -Article 10 - TERMINATION -------------------------- - - -10.1. In the event of a breach by the Licensee of its obligations -hereunder, the Licensor may automatically terminate this Agreement thirty -(30) days after notice has been sent to the Licensee and has remained -ineffective. - -10.2. The Licensee whose Agreement is terminated shall no longer be -authorized to use, modify or distribute the Software. However, any or all -licenses that it may have granted prior to termination of the Agreement -shall remain valid subject to their having been granted in compliance with -the terms and conditions hereof. - - -Article 11 - MISCELLANEOUS PROVISIONS --------------------------------------- - - -11.1. EXCUSABLE EVENTS - -Neither Party shall be liable for any or all delay, or failure to perform -the Agreement, that may be attributable to an event of force majeure, an -act of God or an outside cause, such as, notably, defective functioning, or -interruptions affecting the electricity or telecommunications networks, -blocking of the network following a virus attack, the intervention of the -government authorities, natural disasters, water damage, earthquakes, fire, -explosions, strikes and labor unrest, war, etc. - -11.2. The fact that either Party may fail, on one or several occasions, to -invoke one or several of the provisions hereof, shall under no -circumstances be interpreted as being a waiver by the interested Party of -its entitlement to invoke said provision(s) subsequently. - -11.3. The Agreement cancels and replaces any or all previous agreement, -whether written or oral, between the Parties and having the same purpose, -and constitutes the entirety of the agreement between said Parties -concerning said purpose. No supplement or modification to the terms and -conditions hereof shall be effective as regards the Parties unless it is -made in writing and signed by their duly authorized representatives. - -11.4. In the event that one or several of the provisions hereof were to -conflict with a current or future applicable act or legislative text, said -act or legislative text shall take precedence, and the Parties shall make -the necessary amendments so as to be in compliance with said act or -legislative text. All the other provisions shall remain effective. -Similarly, the fact that a provision of the Agreement may be null and -void, for any reason whatsoever, shall not cause the Agreement as a whole -to be null and void. - -11.5. LANGUAGE - -The Agreement is drafted in both French and English. In the event of a -conflict as regards construction, the French version shall be deemed -authentic. - - -Article 12 - NEW VERSIONS OF THE AGREEMENT -------------------------------------------- - - -12.1. Any or all person is authorized to duplicate and distribute copies of -this Agreement. - -12.2. So as to ensure coherence, the wording of this Agreement is protected -and may only be modified by the authors of the License, that reserve the -right to periodically publish updates or new versions of the Agreement, -each with a separate number. These subsequent versions may address new issues -encountered by Free Software. - -12.3. Any or all Software distributed under a given version of the -Agreement may only be subsequently distributed under the same version of -the Agreement, or a subsequent version, subject to the provisions of -article 5.3.4. - - -Article 13 - GOVERNING LAW AND JURISDICTION -------------------------------------------- - - -13.1. The Agreement is governed by French law. The Parties agree to -endeavor to settle the disagreements or disputes that may arise during the -performance of the Agreement out-of-court. - -13.2. In the absence of an out-of-court settlement within two (2) months as -from their occurrence, and unless emergency proceedings are necessary, the -disagreements or disputes shall be referred to the Paris Courts having -jurisdiction, by the first Party to take action. - - - Version 1.1 of 10/26/2004 - - - - - - - - - - - diff --git a/licenses/GSL b/licenses/GSL new file mode 100644 index 000000000..38014b153 --- /dev/null +++ b/licenses/GSL @@ -0,0 +1,221 @@ + END USER LICENSE AGREEMENT + + NOTICE: THIS SOFTWARE END USER LICENSE AGREEMENT ("EULA") IS A LEGAL + AGREEMENT BETWEEN YOU (EITHER AS AN INDIVIDUAL OR AN ENTITY) AND GSL + BIOTECH LLC ("GSL"). PLEASE READ IT CAREFULLY BEFORE COMPLETING THE + INSTALLATION PROCESS AND USING THE SOFTWARE. THIS AGREEMENT PROVIDES A + LICENSE TO USE THE SOFTWARE AND CONTAINS WARRANTY INFORMATION AND + LIABILITY DISCLAIMERS. BY INSTALLING AND USING THE SOFTWARE, YOU ARE + CONFIRMING YOUR ACCEPTANCE OF THE SOFTWARE AND AGREEING TO BECOME BOUND BY + THE TERMS OF THIS AGREEMENT. IF YOU DO NOT AGREE TO BE BOUND BY THESE + TERMS, THEN DO NOT INSTALL THE SOFTWARE, AND RETURN THE SOFTWARE TO GSL. + + 1. Recitals + + 1. This End User License Agreement ("EULA") is a legal agreement + between you (either an individual person or a single legal + entity, who will be referred to in this EULA as "End User", and + GSL Biotech LLC ("GSL") for the SnapGene software product + ("Software") or SnapGene Viewer software product ("Freeware") + that accompanies this EULA, including any associated media, + printed materials and electronic documentation. + 2. The Software or Freeware also includes any software updates, + add-on components, web services and/or supplements that GSL may + provide to End User or make available to End User after the date + End User obtains the initial copy of the Software or Freeware, to + the extent that such items are not accompanied by a separate + license agreement or terms of use. By installing, copying, + downloading, accessing or otherwise using the Software or + Freeware, End User agrees to be bound by the terms of this EULA. + If End User does not agree to the terms of this EULA, End User + should not install, access or use the Software or Freeware. + + 2. License Grants + + 1. Freeware License. GSL grants End User an unlimited license to use + the Freeware. The install packages for the Freeware can be + redistributed without restriction, and can be used for both + commercial and non-commercial purposes. + 2. Trial Period License. End User may download and use the Software + for free for thirty (30) days after installation ("Trial + Period"). During the Trial Period, GSL grants End User a limited, + non-exclusive, non-transferable, non-renewable license to copy + and use the Software for evaluation purposes only. At GSL's + discretion, GSL may provide limited support through email or + discussion forums at GSL's website. The evaluation copy of the + Software contains a feature that will automatically disable + certain features of the Software at the end of Trial Period. GSL + will have no liability to End User if this feature disables the + Software. + 3. License After Trial Period. This Software is licensed, not sold. + End User has the option of paying a license fee in order to use + the Software after the expiration of the Trial Period. Upon + payment of the license fee, GSL provides End User with a + registration number, and grants End User a limited, + non-exclusive, non-transferable license as outlined in Sections + 2.d through Section 2.g and in Section 3. + 4. Computer-Specific License. Under the terms of a Computer-Specific + License for the Software, End User may activate each license only + on a single computer, and may use the Software only on that + computer. The Software may not be accessed remotely. + 5. Floating License. Under the terms of a Floating License for the + Software, End User may install the Software on an unlimited + number of computers. All computers using the Software must have + the ability to communicate with a license server. The number of + users who may run the Software concurrently must not at any time + exceed the number of Floating Licenses purchased. + 6. Unlimited License. Under the terms of an Unlimited License for + the Software, End User may install and use the Software on an + unlimited number of computers with IP addresses in a specified IP + range as agreed to by GSL and End User. + 7. The Software or Freeware is for educational and non-commercial or + commercial research purposes only. GSL makes no representation + that the Software or Freeware is a clinically approved medical + device, and End User understands and accepts that any result or + its display presented in whatever form obtained using the + Software or Freeware must not be used for any purpose other than + education or research. + + 3. License Restrictions + + 1. End User may use the Software only on the permitted number of + computers. + 2. End User may make one copy of the Software solely for backup + purposes. Any backup copy must contain all copyright notices and + any other proprietary legends on the original copy of the + Software. End User may not sell or transfer any copy of the + Software made for backup purposes. + 3. End User's license rights under this EULA are non-exclusive and + non-assignable. + 4. Other than as set forth in Section 3.b, End User may not make + copies of the Software or electronically transfer the Software + from one computer to another. + 5. End User may not alter, merge, modify, adapt, translate, + decompile, reverse engineer, disassemble, or otherwise reduce the + Software to a human-perceivable form. + 6. End User may not rent, lease, or sublicense the Software. + 7. End User may not create derivative works based upon the Software. + 8. End User may not export the Software into any country to which + such export is prohibited by the United States Export + Administration Act. + 9. In the event that End User fails to comply with this EULA, GSL + and its distributors may, in addition to seeking any damages, + terminate the license. Upon termination, End User must destroy + all copies of the Software (with all other rights of both parties + and all other provisions of this EULA surviving any such + termination). + + 4. Ownership + + The foregoing license gives End User a limited license to use the + Software. GSL retains all rights, title and interest, including all + copyright and intellectual property rights, in and to the Software and + all copies thereof. The Software is protected by the copyright laws of + the United States and other countries. All rights not expressly + granted in this EULA are reserved by GSL. + + 5. LIMITED WARRANTY AND DISCLAIMER + + 1. GSL warrants that, for a period of ninety (90) days, the Software + will perform in substantial conformance with published + specifications for the Software. + 2. EXCEPT AS SET FORTH IN THE FOREGOING LIMITED WARRANTY WITH + RESPECT TO THE SOFTWARE, GSL DISCLAIMS ALL OTHER WARRANTIES AND + REPRESENTATIONS, WHETHER EXPRESS, IMPLIED, OR OTHERWISE, + INCLUDING THE WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A + PARTICULAR PURPOSE. ALSO, THERE IS NO WARRANTY OF + NON-INFRINGEMENT AND TITLE OR QUIET ENJOYMENT. GSL DOES NOT + WARRANT THAT THE SOFTWARE IS ERROR-FREE OR WILL OPERATE WITHOUT + INTERRUPTION. THE SOFTWARE IS NOT DESIGNED, INTENDED OR LICENSED + FOR USE IN HAZARDOUS ENVIRONMENTS REQUIRING FAIL-SAFE CONTROLS. + 3. IF APPLICABLE LAW REQUIRES ANY WARRANTIES WITH RESPECT TO THE + SOFTWARE, ALL SUCH WARRANTIES ARE LIMITED IN DURATION TO NINETY + (90) DAYS FROM THE DATE OF DELIVERY. + 4. NO ORAL OR WRITTEN INFORMATION OR ADVICE GIVEN BY GSL SHALL + CREATE A WARRANTY OR IN ANY WAY INCREASE THE SCOPE OF ANY + WARRANTY PROVIDED HEREIN. + 5. (USA only) SOME STATES DO NOT ALLOW THE EXCLUSION OF IMPLIED + WARRANTIES, SO THE ABOVE EXCLUSION MAY NOT APPLY TO END USER. + THIS WARRANTY GIVES END USER SPECIFIC LEGAL RIGHTS AND END USER + MAY ALSO HAVE OTHER LEGAL RIGHTS THAT VARY FROM STATE TO STATE. + + 6. Exclusive Remedy + + End User's exclusive remedy is to return the Software to GSL. Provided + that any non-compliance with the above warranty is reported in writing + to GSL no more than ninety (90) days following delivery to End User, + GSL will use reasonable commercial efforts to supply End User with a + replacement copy of the Software that substantially conforms to + published specifications, provide a replacement for defective media, + or refund to End User the purchase price for the Software, at its + option. GSL shall have no responsibility if the Software has been + altered in any way, or if the media has been damaged by misuse, + accident, abuse, modification or misapplication. Any such misuse, + accident, abuse, modification or misapplication of the Software will + void the warranty above. THIS REMEDY IS THE SOLE AND EXCLUSIVE REMEDY + AVAILABLE TO END USER FOR BREACH OF EXPRESS OR IMPLIED WARRANTIES WITH + RESPECT TO THE SOFTWARE. + + 7. LIMITATION OF LIABILITY + + 1. GSL SHALL NOT BE LIABLE TO END USER OR ANY THIRD PARTY FOR ANY + INDIRECT, SPECIAL, INCIDENTAL, PUNITIVE, COVER OR CONSEQUENTIAL + DAMAGES (INCLUDING, BUT NOT LIMITED TO, DAMAGES FOR THE INABILITY + TO USE EQUIPMENT OR ACCESS DATA, LOSS OF BUSINESS, LOSS OF + PROFITS, BUSINESS INTERRUPTION OR THE LIKE), ARISING OUT OF THE + USE OF, OR INABILITY TO USE, THE SOFTWARE AND BASED ON ANY THEORY + OF LIABILITY INCLUDING BREACH OF CONTRACT, BREACH OF WARRANTY, + TORT (INCLUDING NEGLIGENCE), PRODUCT LIABILITY OR OTHERWISE, EVEN + IF GSL OR ITS REPRESENTATIVES HAVE BEEN ADVISED OF THE + POSSIBILITY OF SUCH DAMAGES AND EVEN IF A REMEDY SET FORTH HEREIN + IS FOUND TO HAVE FAILED IN ITS ESSENTIAL PURPOSE. + 2. GSL'S TOTAL LIABILITY TO END USER FOR ACTUAL DAMAGES FOR ANY + CAUSE WHATSOEVER WILL BE LIMITED TO THE AMOUNT END USER PAID FOR + THE SOFTWARE. + 3. (USA only) SOME STATES DO NOT ALLOW THE LIMITATION OR EXCLUSION + OF LIABILITY FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES, SO THE + ABOVE LIMITATION OR EXCLUSION MAY NOT APPLY TO END USER AND END + USER MAY ALSO HAVE OTHER LEGAL RIGHTS THAT VARY FROM STATE TO + STATE. + 4. THE FOREGOING LIMITATIONS ON LIABILITY ARE INTENDED TO APPLY TO + THE WARRANTIES AND DISCLAIMERS ABOVE AND ALL OTHER ASPECTS OF + THIS EULA. + + 8. U.S. GOVERNMENT RESTRICTED RIGHTS LEGEND + + This Software and the documentation are provided with "RESTRICTED + RIGHTS" applicable to private and public licenses alike. Without + limiting the foregoing, use, duplication, or disclosure by the U.S. + Government is subject to restrictions as set forth in this EULA and as + provided in DFARS 227.7202-1(a) and 227.7202-3(a) (1995), DFARS + 252.227-7013 (c)(1)(ii)(OCT 1988), FAR 12.212(a)(1995), FAR 52.227-19, + or FAR 52.227-14, as applicable. Manufacturer: GSL Biotech LLC + + 9. General + + This EULA shall be governed by the internal laws of the State of + Illinois, USA. In each case this EULA shall be construed and enforced + without regard to the United Nations Convention on the International + Sale of Goods. + + This EULA contains the complete agreement between the parties with + respect to the subject matter hereof, and supersedes all prior or + contemporaneous agreements or understandings, whether oral or written. + End User agrees that any varying or additional terms contained in any + purchase order or other written notification or document issued by End + User in relation to the Software licensed hereunder shall be of no + effect. 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Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. +2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. +3. In all cases, the software is, and all modifications and derivatives of the software shall be, licensed to you solely for use in conjunction with MathWorks products and service offerings. +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "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. 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\ No newline at end of file diff --git a/licenses/PGI b/licenses/PGI deleted file mode 100644 index a54f86c9b..000000000 --- a/licenses/PGI +++ /dev/null @@ -1,262 +0,0 @@ -PGI End-User License Agreement
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-11) Termination
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-13) Controlling Law and Complete Agreement
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diff --git a/licenses/estscan b/licenses/estscan deleted file mode 100644 index 46089aab6..000000000 --- a/licenses/estscan +++ /dev/null @@ -1,88 +0,0 @@ - ESTScan license - --------------- - -Copyright (c) Swiss Institute of Bioinformatics, Ludwig Institute for -Cancer Research (LICR), and Swiss Institute for Experimental Cancer -Research (ISREC), 1999, 2004. For the purposes of this copyright, the -Swiss Institute of Bioinformatics acts on behalf of its partners, LICR -and ISREC. - -The ESTScan software is the exclusive property of the copyright -owners, at UNIL - BEP, CH-1015 LAUSANNE, Switzerland. The Swiss -Institute of Bioinformatics provides the ESTScan program WITHOUT ANY -WARRANTY OF MERCHANTABILITY OR FITNESS FOR ANY PARTICULAR PURPOSE, OR -ANY OTHER WARRANTY, EXPRESS OR IMPLIED. - - -License Terms: - -Use, Modification and Redistribution (including distribution of any -modified or derived work) in source and binary forms is permitted only -if each of the following conditions is met: - -1. Redistributions qualify as "freeware" or "Open Source Software" under - one of the following terms: - - (a) Redistributions are made at no charge beyond the reasonable cost of - materials and delivery. - - (b) Redistributions are accompanied by a copy of the Source Code or by an - irrevocable offer to provide a copy of the Source Code for up to three - years at the cost of materials and delivery. Such redistributions - must allow further use, modification, and redistribution of the Source - Code under substantially the same terms as this license. For the - purposes of redistribution "Source Code" means the complete source - code of ESTScan including all modifications. - - Other forms of redistribution are allowed only under a separate royalty- - free agreement permitting such redistribution subject to standard - commercial terms and conditions. A copy of such agreement may be - obtained from the Swiss Institute of Bioinformatics at the above address. - -2. Redistributions of source code must retain the copyright notices as they - appear in each source code file, these license terms, and the - disclaimer/limitation of liability set forth in the introductory paragraph. - -3. Redistributions in binary form must reproduce the Copyright Notice, - these license terms, and the disclaimer/limitation of liability set - forth as above, in the documentation and/or other materials - provided with the distribution. For the purposes of binary distribution - the "Copyright Notice" refers to the following language: - "Copyright (c) 1999, 2004 Swiss Institute of Bioinformatics. - All rights reserved." - -4. Neither the name of the Swiss Institute of Bioinformatics nor - the names of its contributors may be used to endorse or promote - products derived from this software without specific prior written - permission. - -5. All redistributions must comply with the conditions imposed by the - Swiss Institute of Bioinformatics on certain embedded code, whose copyright - notice and conditions for redistribution are as follows: - - (a) Copyright (c) 1999, 2004 Swiss Institute of Bioinformatics. - All rights reserved. - - (b) Redistribution and use in source and binary forms, with or without - modification, are permitted provided that the following conditions - are met: - - (i) Redistributions of source code must retain the above copyright - notice, this list of conditions and the above disclaimer. - - (ii) Redistributions in binary form must reproduce the above - copyright notice, this list of conditions and the following - disclaimer in the documentation and/or other materials provided - with the distribution. - - (iii) All advertising materials mentioning features or use of this - software must display the following acknowledgement: "This - product includes software developed by the Swiss Institute of - Bioinformatics and its contributors." - - (iv) Neither the name of the Institute nor the names of its - contributors may be used to endorse or promote products derived - from this software without specific prior written permission. - -($Id: COPYRIGHT,v 1.1.1.1 2004/12/16 12:44:29 c4chris Exp $ -Version 1.1, last updated 9 December 2004) diff --git a/licenses/ligplot+ b/licenses/ligplot+ deleted file mode 100644 index 7457f6622..000000000 --- a/licenses/ligplot+ +++ /dev/null @@ -1,138 +0,0 @@ -LIGPLOT - Automated representation of protein-ligand interactions - ---------------------------------------------------------------- - - CONFIDENTIALITY AGREEMENT - ------------------------- - - - -In regard to the LIGPLOT , specified in the Appendix herewith -(the Software) supplied to us, the copyright and other -intellectual property rights to which belong to the authors, we - - - __________________________________________________________________ - -undertake to the authors that we shall be bound by the following terms -and conditions:- - -1. We will receive the Software and any related documentation in -confidence and will not use the same except for the purpose of the -department's own research. The Software will be used only by such of -our officers or employees to whom it must reasonably be communicated -to enable us to undertake our research and who agree to be bound by -the same confidence. The department shall procure and enforce such -agreement from its staff for the benefit of the authors. - -2. The publication of research using the Software must reference -"Wallace A C, Laskowski R A, Thornton J M (1995). LIGPLOT: A program -to generate schematic diagrams of protein-ligand interactions. Protein -Engineering, 8, 127-134." - -3. Research shall take place solely at the department's premises at - - - __________________________________________________________________ - -4. All forms of the Software will be kept in a reasonably secure place - to prevent unauthorised access. - -5. Each copy of the Software or, if not practicable then, any package -associated therewith shall be suitably marked (and such marking -maintained) with the following copyright notice: " Copyright 1994 -A C Wallace, R A Laskowski, & J M Thornton All Rights Reserved". - -6. The Software may be modified but any changes made shall be made -available to the authors. - -7. The Software shall be used exclusively for academic teaching and -research. The Software will not be used for any commercial research or -research associated with an industrial company. - -8. The confidentiality obligation in paragraph one shall not apply: - - (i) to information and data known to the department at the time of - receipt hereunder (as evidenced by its written records); - - (ii) to information and data which was at the time of receipt in the - public domain or thereafter becomes so through no wrongful act of - the department; - - (iii) to information and data which the department receives from a third - party not in breach of any obligation of confidentiality owed to - the authors. - -Please sign this Undertaking and return a copy of it to indicate that you -have read, understood and accepted the above terms. - - - - For and on behalf of _____________________________ - - _________________________________________________ - - .................................................. - - Dated ............................................ - - - -e-mail address ___________________________ - - - -Please complete the above form, sign it, and then send it, or fax it, to:- - - -Roman Laskowski -European Bioinformatics Institute, -Wellcome Trust Genome Campus, -Hinxton, -Cambridge, CB10 1SD, -United Kingdom - -Fax:- +44 (0)1223 494 468 - -roman@ebi.ac.uk - - -If you have any problems either installing the software or running it, -please e-mail your problems to:- - - roman@ebi.ac.uk - - -APPENDIX - Files supplied as part of the LIGPLOT program --------------------------------------------------------- - -Source program files:- -1. ligplot.c -2. ligplot.h -3. hbadd.c -4. hbadd.h -5. dimer.c -6. dimer.h - -Script files:- -1. ligplot.scr -2. ligonly.scr -3. dimplot.scr -4. dimonly.scr - -Parameter file:- -1. ligplot.prm - -Installation instructions:- -1. install.doc - -Documentation:- -1. manual.tar.Z -2. README - -Confidentiality Agreement:- -1. confid.txt - - - - v.4.4.2 - 7 Mar 2003 - diff --git a/licenses/mRNAmarkup b/licenses/mRNAmarkup deleted file mode 100644 index 884ed1bd3..000000000 --- a/licenses/mRNAmarkup +++ /dev/null @@ -1,25 +0,0 @@ -Copyright (c) 2000 Volker Brendel -All Rights Reserved. E-mail: vbrendel@iastate.edu - -Permission to use, copy, modify, and distribute this software and its -documentation for educational, research and non-profit purposes, without fee, -and without a written agreement is hereby granted, provided that the above -copyright notice, this paragraph and the following three paragraphs appear in -all copies. If you modify this file or included files you must cause the -modified files to carry prominent notices stating that you changed the files. - -Inqueries for permission to incorporate this software into commercial products -should be directed to the Office of Intellectual Property and Technology -Transfer, 310 Lab of Mechanics, Iowa State University, Ames, IA 50011, phone: -(515) 294-4740, E-mail: Licensing@iastate.edu. - -IN NO EVENT SHALL THE AUTHOR OR IOWA STATE UNIVERSITY BE LIABLE TO ANY PARTY FOR -DIRECT, INDIRECT, SPECIAL, INCIDENTAL, OR CONSEQUENTIAL DAMAGES, INCLUDING LOST -PROFITS, ARISING OUT OF THE USE OF THIS SOFTWARE AND ITS DOCUMENTATION, EVEN IF -IOWA STATE UNIVERSITY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - -IOWA STATE UNIVERSITY SPECIFICALLY DISCLAIMS ANY WARRANTIES, INCLUDING, BUT NOT -LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A -PARTICULAR PURPOSE. THE SOFTWARE PROVIDED HEREUNDER IS ON AN "AS IS" BASIS, -AND IOWA STATE UNIVERSITY HAS NO OBLIGATIONS TO PROVIDE MAINTENANCE, SUPPORT, -UPDATES, ENHANCEMENTS, OR MODIFICATIONS. diff --git a/licenses/polyphen b/licenses/polyphen deleted file mode 100644 index 250b86ed7..000000000 --- a/licenses/polyphen +++ /dev/null @@ -1,7 +0,0 @@ -The software provided herein is free for academic instruction and research -use only. Commercial licenses are available to legal entities, including -companies and organizations (both for-profit and non-profit), requiring the -software for general commercial use. To obtain a commercial license please, -contact us via e-mail. - -e-mail: iadzhubey@rics.bwh.harvard.edu
\ No newline at end of file diff --git a/licenses/signalp b/licenses/signalp deleted file mode 100644 index 7e5b15f19..000000000 --- a/licenses/signalp +++ /dev/null @@ -1,218 +0,0 @@ - ACADEMIC SOFTWARE LICENSE AGREEMENT FOR END-USERS AT PUBLICLY FUNDED - ACADEMIC, EDUCATION OR RESEARCH INSTITUTIONS FOR THE USE OF SignalP 3.0 - - By downloading the Software you are consenting to be bound by and become - a party to this agreement as the "Licensee". If you do not agree to all - of the terms of this agreement, you must not click the Acceptance - button, not install the product nor use the product, and you do not - become a LICENSEE under this agreement. - - If you are not a member of a publicly funded Academic and/or Education - and/or Research Institution you must obtain a commercial license, please - send mail to (software@cbs.dtu.dk). This software license agreement is - entered into by and between Center for Biological Sequence Analysis, - Technical University of Denmark (hereinafter "CBS") and the "LICENSEE". - - WHEREAS CBS has the right to license all copyrights and other property - rights in the Licensed Software identified as SignalP 3.0 and developed - by CBS and CBS desires to license the Software so that it becomes - available for public use and benefit. - - WHEREAS LICENSEE is a public funded Academic and/or Education and/or - Research Institution. - - WHEREAS LICENSEE desires to acquire a free non-exclusive license to use - the Software for internal research purposes only. - - NOW, THEREFORE, in consideration of the mutual promises and covenants - contained herein, the parties agree as follows: - - 1. Definitions - - "Licensed Software" means the specific version SignalP 3.0 pursuant - to this Agreement. Any opinion, findings, conclusions or recommendations - expressed in the Licensed Software are those of the authors and do not - necessarily reflect the views of CBS. - - 2. License - - Subject to the terms and conditions of this Agreement a non-exclusive, - non-transferable License to use and copy the Licensed Software is made - available free of charge for the LICENSEE which is a non-profit - educational, academic and/or research institution. The License is only - granted for personal and internal use in research only at one Site, - where a Site is defined as a set of contiguous buildings in one - location. The software will be used at only one location of LICENSEE. - - This license does not entitle Licensee to receive from CBS copies of the - Licensed software on disks, tapes or CD's, hard-copy documentation, - technical support, telephone assistance, or enhancements or updates to - the Licensed Software. - - The user and any research assistants, co-workers or other workers who - may use the Software agree to not give the program to third parties or - grant licenses on software, which include the Software, alone or - integrated into other software, to third parties. Modification of the - source code is prohibited without the prior written consent of CBS. - - 3. Ownership - - Except as expressly licensed in this Agreement, CBS shall retain title - to the Licensed Software, and any upgrades and modifications created by - CBS. - - 4. Consideration - - In consideration for the license rights granted by CBS, LICENSEE will - obtain this academic license free of charge. - - 5. Copies - - LICENSEE shall have the right to make copies of the Licensed Software - for internal use at the Site and for back-up purposes under this - Agreement, but agrees that all such copies shall contain the copyright - notices and all other reasonable and appropriate proprietary markings or - confidential legends that appear on the Licensed Software provided - hereunder. - - 6. Support - - CBS shall have no obligation to offer support services to LICENSEE, and - nothing contained herein shall be interpreted as to require CBS to - provide maintenance, installation services, version updates, debugging, - consultation or end-user support of any kind. - - 7. Software Protection - - LICENSEE acknowledges that the Licensed Software is proprietary to CBS. - The software code shall be treated as trade secrets and confidential - information of CBS, and LICENSEE agrees to use best efforts to hold the - same in confidence. LICENSEE's obligation for confidentiality shall not - extend to any information which is or becomes generally available to the - public, is already known to or subsequently disclosed by third parties - to LICENSEE and at its free disposal, or is independently developed by - LICENSEE or its affiliates without the use of the confidential - information disclosed by CBS, or is required by law or legal process. - - Except as other wise expressly permitted in this Agreement, Licensee my - not (i) modify or create any derivative works of the Licensed Software - or documentation, including customization, translation or localization; - (ii) decompile, disassemble, reverse engineer, or otherwise attempt to - derive the source code for the Product; (iii) redistribute, encumber, - sell, rent, lease, sublicense, or otherwise transfer rights to the - Licensed Software; (iv) remove or alter any trademark, logo, copyright - or other proprietary notices, legends, symbols or labels in the Product; - or (v) publish any results of benchmark tests run on the Product to a - third party without CBS's prior written consent. - - 8. Representations of CBS to LICENSEE - - CBS represents to LICENSEE that (i) CBS has the right to grant the - License and to enter into this agreement, (ii) that, to the best of - CBS's knowledge, the Licensed software does not infringe any patent, - copyright or trade secrets of any third party, provided however that - such representation and warranty shall not apply to any addition to, or - modifications or adaptation of, the Licensed Software made by LICENSEE - and (iii) CBS undertakes to use best efforts to cooperate with and - assist LICENSEE, at LICENSEE's expense, in defending itself against any - action based on the alleged infringement of any third party patent, - copyright or trade secret rights resulting from or relating to the use - or licensing of the Licensed Software by LICENSEE. - - 9. Indemnity and Disclaimer of Warranties - - Except as expressly set forth in this agreement, CBS makes no - representations or warranties, express or implied. - - The product is provided free of charge, and, therefore, on an "as is" - basis, without warranty of any kind, express or implied, including - without limitation the warranties that it is free of defects, virus - free, able to operate on an uninterrupted basis, merchantable, fit for a - particular purpose or non-interfering. The entire risk as to the quality - and performance of the Licensed Software is borne by LICENSEE. - - By way of example, but not limitation, CBS makes no representations or - warranties of merchantability or fitness for any particular application - or, except as set forth in paragraph 8, that the use of the Software - will not infringe any patents, copyrights or trademarks or other rights - of third parties. The entire risk as to the quality and performance of - the product is borne by LICENSEE. CBS shall not be liable for any - liability or damages with respect to any claim by LICENSEE or any third - party on account of, or arising from the license or use of the Software. - - Should the Licensed Software prove defective in any respect, LICENSEE - and not LICENSOR or it's affiliates should assume the entire cost of any - service and repair. This disclaimer of warranty constitutes an essential - part of this agreement. No use of the licensed product is authorized - hereunder except under this disclaimer. - - In no event will LICENSOR or its affiliates be liable for any indirect, - special, incidental or consequential damages arising out of the use of - or inability to use the product, including, without limitation, damages - for lost profits, loss of goodwill, work stoppage, computer failure or - malfunction, or any and all other commercial damages or losses, even if - advised of the possibility thereof, and regardless of the legal or - equitable theory (contract, tort or otherwise) upon which the claim is - based. - - 10. Promotional Advertising & References - - LICENSEE may not use the name of the Licensed Software in its - promotional advertising, product literature, and other similar - promotional materials to be disseminated to the public or any portion - thereof. LICENSEE agrees not to identify CBS in any promotional - advertising or other promotional materials to be disseminated to the - public, or any portion thereof without CBS's prior written consent. - LICENSEE agrees that any reference to the software for crystallographic - computations will cite one or more publications as set forth in the - manual and in agreement with common scientific practice. CBS shall not - use LICENSEE's name in publicity or advertising involving this Agreement - or otherwise without LICENSEE's prior written consent which may be - withheld at LICENSEE's sole discretion. - - 11. Term - - This Agreement and the license rights granted herein shall become - effective as of the date this Agreement is executed by both parties and - shall be perpetual unless terminated in accordance with this Section. - - CBS may terminate this Agreement at any time. - - Either party may terminate this Agreement at any time effective upon the - other party's breach of any agreement, covenant, or representation made - in this Agreement, such breach remaining uncorrected sixty (60) days - after written notice thereof. - - LICENSEE shall have the right, at any time, to terminate this Agreement - without cause by written notice to CBS specifying the date of - termination. - - Upon termination, LICENSEE shall destroy all full and partial copies of - the Licensed Software. - - 12. Governing Law - - This Agreement shall be construed in accordance with the laws of - Denmark. - - 13. General - - The parties agree that this Agreement is the complete and exclusive - agreement among the parties and supersedes all proposals and prior - agreements whether written or oral, and all other communications among - the parties relating to the subject matter of this Agreement. This - Agreement cannot be modified except in writing and signed by both - parties. Failure by either party at any time to enforce any of the - provisions of this Agreement shall not constitute a waiver by such party - of such provision nor in any way affect the validity of this Agreement. - - The invalidity of singular provisions does not affect the validity of - the entire understanding. The parties are obligated, however, to replace - the invalid provisions by a regulation which comes closest to the - economic intent of the invalid provision. The same shall apply mutatis - mutandis in case of a gap. - - IN WITNESS WHEREOF, the LICENSEE hereto have caused this Agreement to be - duly executed on the date of the download of the software and by - accepting the license conditions by pressing the Acceptance button. - diff --git a/licenses/staden b/licenses/staden deleted file mode 100644 index f2e77291a..000000000 --- a/licenses/staden +++ /dev/null @@ -1,76 +0,0 @@ -============================================================================= - -The Staden Package - -Copyright (c) 2003 MEDICAL RESEARCH COUNCIL -All rights reserved - -Redistribution and use in source and binary forms, with or without -modification, are permitted provided that the following conditions are met: - - . Redistributions of source code must retain the above copyright notice, -this list of conditions and the following disclaimer. - - . Redistributions in binary form must reproduce the above copyright notice, -this list of conditions and the following disclaimer in the documentation -and/or other materials provided with the distribution. - - . Neither the name of the MEDICAL RESEARCH COUNCIL, THE LABORATORY OF -MOLECULAR BIOLOGY nor the names of its contributors may be used to endorse or -promote products derived from this software without specific prior written -permission. - -THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "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 THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR -ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - -============================================================================= - -Portions of this code have been modified by the Wellcome Trust Sanger -Institute (Genome Research Limited). In some cases entirely new -programs and/or source files have been created. These are licenced -under essentially the same conditions as the MRC code (with just name -changes). - -The following licence only applies to files bearing the Genome -Research Limited copyright notice: - - - -Copyright (c) 2004 GENOME RESEARCH LIMITED -All rights reserved - -Redistribution and use in source and binary forms, with or without -modification, are permitted provided that the following conditions are met: - - . Redistributions of source code must retain the above copyright notice, -this list of conditions and the following disclaimer. - - . Redistributions in binary form must reproduce the above copyright notice, -this list of conditions and the following disclaimer in the documentation -and/or other materials provided with the distribution. - - . Neither the name of the GENOME RESEARCH LIMITED, the WELLCOME TRUST -SANGER INSTITUTE nor the names of its contributors may be used to endorse or -promote products derived from this software without specific prior written -permission. - -THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "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 THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR -ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES -(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; -LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON -ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT -(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS -SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. - -============================================================================= diff --git a/licenses/tmhmm b/licenses/tmhmm deleted file mode 100644 index 529d135d5..000000000 --- a/licenses/tmhmm +++ /dev/null @@ -1,217 +0,0 @@ - ACADEMIC SOFTWARE LICENSE AGREEMENT FOR END-USERS AT PUBLICLY FUNDED - ACADEMIC, EDUCATION OR RESEARCH INSTITUTIONS FOR THE USE OF TMHMM 2.0c - - By downloading the Software you are consenting to be bound by and become - a party to this agreement as the "Licensee". If you do not agree to all - of the terms of this agreement, you must not click the Acceptance - button, not install the product nor use the product, and you do not - become a LICENSEE under this agreement. - - If you are not a member of a publicly funded Academic and/or Education - and/or Research Institution you must obtain a commercial license, please - send mail to (software@cbs.dtu.dk). This software license agreement is - entered into by and between Center for Biological Sequence Analysis, - Technical University of Denmark (hereinafter "CBS") and the "LICENSEE". - - WHEREAS CBS has the right to license all copyrights and other property - rights in the Licensed Software identified as TMHMM 2.0c and developed - by CBS and CBS desires to license the Software so that it becomes - available for public use and benefit. - - WHEREAS LICENSEE is a public funded Academic and/or Education and/or - Research Institution. - - WHEREAS LICENSEE desires to acquire a free non-exclusive license to use - the Software for internal research purposes only. - - NOW, THEREFORE, in consideration of the mutual promises and covenants - contained herein, the parties agree as follows: - - 1. Definitions - - "Licensed Software" means the specific version TMHMM 2.0c pursuant - to this Agreement. Any opinion, findings, conclusions or recommendations - expressed in the Licensed Software are those of the authors and do not - necessarily reflect the views of CBS. - - 2. License - - Subject to the terms and conditions of this Agreement a non-exclusive, - non-transferable License to use and copy the Licensed Software is made - available free of charge for the LICENSEE which is a non-profit - educational, academic and/or research institution. The License is only - granted for personal and internal use in research only at one Site, - where a Site is defined as a set of contiguous buildings in one - location. The software will be used at only one location of LICENSEE. - - This license does not entitle Licensee to receive from CBS copies of the - Licensed software on disks, tapes or CD's, hard-copy documentation, - technical support, telephone assistance, or enhancements or updates to - the Licensed Software. - - The user and any research assistants, co-workers or other workers who - may use the Software agree to not give the program to third parties or - grant licenses on software, which include the Software, alone or - integrated into other software, to third parties. Modification of the - source code is prohibited without the prior written consent of CBS. - - 3. Ownership - - Except as expressly licensed in this Agreement, CBS shall retain title - to the Licensed Software, and any upgrades and modifications created by - CBS. - - 4. Consideration - - In consideration for the license rights granted by CBS, LICENSEE will - obtain this academic license free of charge. - - 5. Copies - - LICENSEE shall have the right to make copies of the Licensed Software - for internal use at the Site and for back-up purposes under this - Agreement, but agrees that all such copies shall contain the copyright - notices and all other reasonable and appropriate proprietary markings or - confidential legends that appear on the Licensed Software provided - hereunder. - - 6. Support - - CBS shall have no obligation to offer support services to LICENSEE, and - nothing contained herein shall be interpreted as to require CBS to - provide maintenance, installation services, version updates, debugging, - consultation or end-user support of any kind. - - 7. Software Protection - - LICENSEE acknowledges that the Licensed Software is proprietary to CBS. - The software code shall be treated as trade secrets and confidential - information of CBS, and LICENSEE agrees to use best efforts to hold the - same in confidence. LICENSEE's obligation for confidentiality shall not - extend to any information which is or becomes generally available to the - public, is already known to or subsequently disclosed by third parties - to LICENSEE and at its free disposal, or is independently developed by - LICENSEE or its affiliates without the use of the confidential - information disclosed by CBS, or is required by law or legal process. - - Except as other wise expressly permitted in this Agreement, Licensee my - not (i) modify or create any derivative works of the Licensed Software - or documentation, including customization, translation or localization; - (ii) decompile, disassemble, reverse engineer, or otherwise attempt to - derive the source code for the Product; (iii) redistribute, encumber, - sell, rent, lease, sublicense, or otherwise transfer rights to the - Licensed Software; (iv) remove or alter any trademark, logo, copyright - or other proprietary notices, legends, symbols or labels in the Product; - or (v) publish any results of benchmark tests run on the Product to a - third party without CBS's prior written consent. - - 8. Representations of CBS to LICENSEE - - CBS represents to LICENSEE that (i) CBS has the right to grant the - License and to enter into this agreement, (ii) that, to the best of - CBS's knowledge, the Licensed software does not infringe any patent, - copyright or trade secrets of any third party, provided however that - such representation and warranty shall not apply to any addition to, or - modifications or adaptation of, the Licensed Software made by LICENSEE - and (iii) CBS undertakes to use best efforts to cooperate with and - assist LICENSEE, at LICENSEE's expense, in defending itself against any - action based on the alleged infringement of any third party patent, - copyright or trade secret rights resulting from or relating to the use - or licensing of the Licensed Software by LICENSEE. - - 9. Indemnity and Disclaimer of Warranties - - Except as expressly set forth in this agreement, CBS makes no - representations or warranties, express or implied. - - The product is provided free of charge, and, therefore, on an "as is" - basis, without warranty of any kind, express or implied, including - without limitation the warranties that it is free of defects, virus - free, able to operate on an uninterrupted basis, merchantable, fit for a - particular purpose or non-interfering. The entire risk as to the quality - and performance of the Licensed Software is borne by LICENSEE. - - By way of example, but not limitation, CBS makes no representations or - warranties of merchantability or fitness for any particular application - or, except as set forth in paragraph 8, that the use of the Software - will not infringe any patents, copyrights or trademarks or other rights - of third parties. The entire risk as to the quality and performance of - the product is borne by LICENSEE. CBS shall not be liable for any - liability or damages with respect to any claim by LICENSEE or any third - party on account of, or arising from the license or use of the Software. - - Should the Licensed Software prove defective in any respect, LICENSEE - and not LICENSOR or it's affiliates should assume the entire cost of any - service and repair. This disclaimer of warranty constitutes an essential - part of this agreement. No use of the licensed product is authorized - hereunder except under this disclaimer. - - In no event will LICENSOR or its affiliates be liable for any indirect, - special, incidental or consequential damages arising out of the use of - or inability to use the product, including, without limitation, damages - for lost profits, loss of goodwill, work stoppage, computer failure or - malfunction, or any and all other commercial damages or losses, even if - advised of the possibility thereof, and regardless of the legal or - equitable theory (contract, tort or otherwise) upon which the claim is - based. - - 10. Promotional Advertising & References - - LICENSEE may not use the name of the Licensed Software in its - promotional advertising, product literature, and other similar - promotional materials to be disseminated to the public or any portion - thereof. LICENSEE agrees not to identify CBS in any promotional - advertising or other promotional materials to be disseminated to the - public, or any portion thereof without CBS's prior written consent. - LICENSEE agrees that any reference to the software for crystallographic - computations will cite one or more publications as set forth in the - manual and in agreement with common scientific practice. CBS shall not - use LICENSEE's name in publicity or advertising involving this Agreement - or otherwise without LICENSEE's prior written consent which may be - withheld at LICENSEE's sole discretion. - - 11. Term - - This Agreement and the license rights granted herein shall become - effective as of the date this Agreement is executed by both parties and - shall be perpetual unless terminated in accordance with this Section. - - CBS may terminate this Agreement at any time. - - Either party may terminate this Agreement at any time effective upon the - other party's breach of any agreement, covenant, or representation made - in this Agreement, such breach remaining uncorrected sixty (60) days - after written notice thereof. - - LICENSEE shall have the right, at any time, to terminate this Agreement - without cause by written notice to CBS specifying the date of - termination. - - Upon termination, LICENSEE shall destroy all full and partial copies of - the Licensed Software. - - 12. Governing Law - - This Agreement shall be construed in accordance with the laws of - Denmark. - - 13. General - - The parties agree that this Agreement is the complete and exclusive - agreement among the parties and supersedes all proposals and prior - agreements whether written or oral, and all other communications among - the parties relating to the subject matter of this Agreement. This - Agreement cannot be modified except in writing and signed by both - parties. Failure by either party at any time to enforce any of the - provisions of this Agreement shall not constitute a waiver by such party - of such provision nor in any way affect the validity of this Agreement. - - The invalidity of singular provisions does not affect the validity of - the entire understanding. The parties are obligated, however, to replace - the invalid provisions by a regulation which comes closest to the - economic intent of the invalid provision. The same shall apply mutatis - mutandis in case of a gap. - - IN WITNESS WHEREOF, the LICENSEE hereto have caused this Agreement to be - duly executed on the date of the download of the software and by - accepting the license conditions by pressing the Acceptance button. diff --git a/media-gfx/brlcad/brlcad-7.32.4.ebuild b/media-gfx/brlcad/brlcad-7.32.4.ebuild index aa70351e9..180542cac 100644 --- a/media-gfx/brlcad/brlcad-7.32.4.ebuild +++ b/media-gfx/brlcad/brlcad-7.32.4.ebuild @@ -43,7 +43,7 @@ DEPEND="${RDEPEND} ) doc? ( dev-libs/libxslt - app-doc/doxygen + app-text/doxygen )" # Install into /usr/ not recommended by upstream due to possible file conflicts diff --git a/media-gfx/brlcad/brlcad-9999.ebuild b/media-gfx/brlcad/brlcad-9999.ebuild index 5d6a345ce..5f7c0ad4c 100644 --- a/media-gfx/brlcad/brlcad-9999.ebuild +++ b/media-gfx/brlcad/brlcad-9999.ebuild @@ -41,7 +41,7 @@ DEPEND="${RDEPEND} ) doc? ( dev-libs/libxslt - app-doc/doxygen + app-text/doxygen )" # Install into /usr/ not recommended by upstream due to possible file conflicts diff --git a/media-libs/charls/Manifest b/media-libs/charls/Manifest new file mode 100644 index 000000000..5275ba74f --- /dev/null +++ b/media-libs/charls/Manifest @@ -0,0 +1 @@ +DIST charls-2.3.4.tar.gz 9483782 BLAKE2B 655bbe2f143df1c3b86f2bbb033217c9fa30f39cf9b449cb84ffd56ef2e3eb0ceb7088c8757cc1a59d6d9462363e59e62acee7dabcbe5a16fb68be0d5036b3eb SHA512 3f6e1a054d5f7cfa5309e3d1b280d0dbaaeac7f06b08619cefe15677367631d9f6eb96e54b3e5ec921ac50793a570c39178c3e4b52ce9837b731bbccd6a3d0ad diff --git a/media-libs/charls/charls-2.3.4.ebuild b/media-libs/charls/charls-2.3.4.ebuild new file mode 100644 index 000000000..155e910a8 --- /dev/null +++ b/media-libs/charls/charls-2.3.4.ebuild @@ -0,0 +1,30 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit cmake + +DESCRIPTION="C++ JPEG-LS library implementation" +HOMEPAGE="https://github.com/team-charls/charls" +SRC_URI="https://github.com/team-charls/charls/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +DEPEND="" +RDEPEND="${DEPEND}" +BDEPEND="" + +src_configure() { + # It doesn't seem like there is an automated way to run the test programs + # The samples option builds them, but do not install the resulting binaries + local mycmakeargs=( + -DCHARLS_BUILD_TESTS=OFF + -DCHARLS_BUILD_FUZZ_TEST=OFF + -DCHARLS_BUILD_SAMPLES=OFF + -DBUILD_SHARED_LIBS=ON + ) + cmake_src_configure +} diff --git a/media-libs/charls/metadata.xml b/media-libs/charls/metadata.xml new file mode 100644 index 000000000..3eef65eb8 --- /dev/null +++ b/media-libs/charls/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>fx.carton91@gmail.com</email> + <name>François-Xavier Carton</name> + </maintainer> + <upstream> + <remote-id type="github">team-charls/charls</remote-id> + </upstream> +</pkgmetadata> diff --git a/media-libs/imglib2/Manifest b/media-libs/imglib2/Manifest new file mode 100644 index 000000000..eaae671d4 --- /dev/null +++ b/media-libs/imglib2/Manifest @@ -0,0 +1 @@ +DIST imglib2-6.3.0-sources.tar.gz 1100228 BLAKE2B 65aba1c43980e98018154972bc143093d25e000148805d8ee75459f43dbe301cb0ae10463585fccc51dab28c926900e7c43df13696d408e79d2b4cb55ffadfc6 SHA512 9f6159379d1be6478a9cd53ee88241277761a5e569cd2042e26363f43394abc85d3ea2f72e592a57cff6f8b5f8f4cd46821a4168bf76939f7f77680844231748 diff --git a/media-libs/imglib2/imglib2-6.3.0.ebuild b/media-libs/imglib2/imglib2-6.3.0.ebuild new file mode 100644 index 000000000..4233e6795 --- /dev/null +++ b/media-libs/imglib2/imglib2-6.3.0.ebuild @@ -0,0 +1,53 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +JAVA_PKG_IUSE="doc source test" +JAVA_TESTING_FRAMEWORKS="junit-4" + +inherit java-pkg-2 java-pkg-simple + +DESCRIPTION="A multidimensional, type-agnostic image processing library." +HOMEPAGE=" + http://imglib2.net/ + https://github.com/imglib/imglib2 +" + +if [[ ${PV} == 9999 ]]; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/imglib/imglib2.git" + S="${WORKDIR}/${P}" + MAVEN_ID="net.imglib2:imglib2:9999" +else + SRC_URI=" + https://github.com/imglib/${PN}/archive/refs/tags/${P}.tar.gz -> ${P}-sources.tar.gz + " + S="${WORKDIR}/${PN}-${P}" + MAVEN_ID="net.imglib2:imglib2:6.3.0" + KEYWORDS="~amd64" +fi + +LICENSE="BSD-2" +SLOT="0" + +# jmh-core: According to the pom version 1.36 is required, +# however, jmh-core-1.35 is latest available in Gentoo +BDEPEND=" + >=virtual/jdk-1.8:* + test? ( + >=dev-java/jama-1.0.3 + >=dev-java/junit-4.13.2 + >=dev-java/jmh-core-1.35 + ) +" + +RDEPEND=" + >=virtual/jre-1.8:* +" + +JAVA_SRC_DIR="src/main/java" +JAVA_MAIN_CLASS="" + +JAVA_TEST_GENTOO_CLASSPATH="jama,junit-4,jmh-core" +JAVA_TEST_SRC_DIR="src/test/java" diff --git a/media-libs/imglib2/imglib2-9999.ebuild b/media-libs/imglib2/imglib2-9999.ebuild new file mode 100644 index 000000000..4233e6795 --- /dev/null +++ b/media-libs/imglib2/imglib2-9999.ebuild @@ -0,0 +1,53 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +JAVA_PKG_IUSE="doc source test" +JAVA_TESTING_FRAMEWORKS="junit-4" + +inherit java-pkg-2 java-pkg-simple + +DESCRIPTION="A multidimensional, type-agnostic image processing library." +HOMEPAGE=" + http://imglib2.net/ + https://github.com/imglib/imglib2 +" + +if [[ ${PV} == 9999 ]]; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/imglib/imglib2.git" + S="${WORKDIR}/${P}" + MAVEN_ID="net.imglib2:imglib2:9999" +else + SRC_URI=" + https://github.com/imglib/${PN}/archive/refs/tags/${P}.tar.gz -> ${P}-sources.tar.gz + " + S="${WORKDIR}/${PN}-${P}" + MAVEN_ID="net.imglib2:imglib2:6.3.0" + KEYWORDS="~amd64" +fi + +LICENSE="BSD-2" +SLOT="0" + +# jmh-core: According to the pom version 1.36 is required, +# however, jmh-core-1.35 is latest available in Gentoo +BDEPEND=" + >=virtual/jdk-1.8:* + test? ( + >=dev-java/jama-1.0.3 + >=dev-java/junit-4.13.2 + >=dev-java/jmh-core-1.35 + ) +" + +RDEPEND=" + >=virtual/jre-1.8:* +" + +JAVA_SRC_DIR="src/main/java" +JAVA_MAIN_CLASS="" + +JAVA_TEST_GENTOO_CLASSPATH="jama,junit-4,jmh-core" +JAVA_TEST_SRC_DIR="src/test/java" diff --git a/media-libs/imglib2/metadata.xml b/media-libs/imglib2/metadata.xml new file mode 100644 index 000000000..b5cf3918a --- /dev/null +++ b/media-libs/imglib2/metadata.xml @@ -0,0 +1,16 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <longdescription> + ImgLib2 is a general-purpose, multidimensional image processing library. + + It provides an interface-driven design that supports numeric and non-numeric data types (8-bit unsigned integer, 32-bit floating point, etc.) in an extensible way. It implements several data sources and sample organizations, including one single primitive array, one array per plane, N-dimensional array “cells†cached to and from disk on demand, and planes read on demand from disk. + </longdescription> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <upstream> + <remote-id type="github">imglib/imglib2</remote-id> + </upstream> +</pkgmetadata> diff --git a/media-libs/libgfx/metadata.xml b/media-libs/libgfx/metadata.xml index ae9640ffb..2103548da 100644 --- a/media-libs/libgfx/metadata.xml +++ b/media-libs/libgfx/metadata.xml @@ -5,4 +5,7 @@ <email>sci@gentoo.org</email> <name>Gentoo Science Project</name> </maintainer> + <upstream> + <remote-id type="github">mjgarland/libgfx</remote-id> + </upstream> </pkgmetadata> diff --git a/media-libs/mmg/metadata.xml b/media-libs/mmg/metadata.xml index 2b9123050..bd7221f19 100644 --- a/media-libs/mmg/metadata.xml +++ b/media-libs/mmg/metadata.xml @@ -13,4 +13,7 @@ <flag name="scotch">Use SCOTCH TOOL for renumbering</flag> <flag name="vtk">Use VTK I/O</flag> </use> + <upstream> + <remote-id type="github">MmgTools/mmg</remote-id> + </upstream> </pkgmetadata> diff --git a/media-libs/mmg/mmg-5.5.0.ebuild b/media-libs/mmg/mmg-5.5.0.ebuild index e5fa82146..1e8e4d8cb 100644 --- a/media-libs/mmg/mmg-5.5.0.ebuild +++ b/media-libs/mmg/mmg-5.5.0.ebuild @@ -22,7 +22,7 @@ DEPEND=" " RDEPEND="${DEPEND}" BDEPEND=" - app-doc/doxygen + app-text/doxygen " src_configure() { diff --git a/media-libs/mmg/mmg-5.5.1.ebuild b/media-libs/mmg/mmg-5.5.1.ebuild index e5fa82146..1e8e4d8cb 100644 --- a/media-libs/mmg/mmg-5.5.1.ebuild +++ b/media-libs/mmg/mmg-5.5.1.ebuild @@ -22,7 +22,7 @@ DEPEND=" " RDEPEND="${DEPEND}" BDEPEND=" - app-doc/doxygen + app-text/doxygen " src_configure() { diff --git a/media-libs/mmg/mmg-5.5.2.ebuild b/media-libs/mmg/mmg-5.5.2.ebuild index e5fa82146..1e8e4d8cb 100644 --- a/media-libs/mmg/mmg-5.5.2.ebuild +++ b/media-libs/mmg/mmg-5.5.2.ebuild @@ -22,7 +22,7 @@ DEPEND=" " RDEPEND="${DEPEND}" BDEPEND=" - app-doc/doxygen + app-text/doxygen " src_configure() { diff --git a/media-libs/scifio-jai-imageio/Manifest b/media-libs/scifio-jai-imageio/Manifest new file mode 100644 index 000000000..3d8ce4b51 --- /dev/null +++ b/media-libs/scifio-jai-imageio/Manifest @@ -0,0 +1 @@ +DIST scifio-jai-imageio-1.1.1-sources.tar.gz 826853 BLAKE2B 5bd31431f2b3b1286005ac740d0847281d46f2a4784d823f2a668544a0a69fd006b8b449919008bb51a15a07031a2c8f8c41046ed2f240632c4e7a47616b66da SHA512 041c743c3d5d64110d0f20396bf8d40e06b7806addc40165d6cde1e00edd37ffa22fc1b9887a00c14c701f59c549b3aebf9a7238a71efdac91d018627764e73a diff --git a/media-libs/scifio-jai-imageio/metadata.xml b/media-libs/scifio-jai-imageio/metadata.xml new file mode 100644 index 000000000..ff4226a63 --- /dev/null +++ b/media-libs/scifio-jai-imageio/metadata.xml @@ -0,0 +1,14 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <longdescription> + SCIFIO version of the Java Advanced Imaging Image I/O Tools API Core. Java API to handle JPEG and JPEG2000 files. Used by Bio-Formats to read images compressed with JPEG2000 and lossless JPEG. + </longdescription> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <upstream> + <remote-id type="github">scifio/scifio-jai-imageio</remote-id> + </upstream> +</pkgmetadata> diff --git a/media-libs/scifio-jai-imageio/scifio-jai-imageio-1.1.1.ebuild b/media-libs/scifio-jai-imageio/scifio-jai-imageio-1.1.1.ebuild new file mode 100644 index 000000000..bdc989735 --- /dev/null +++ b/media-libs/scifio-jai-imageio/scifio-jai-imageio-1.1.1.ebuild @@ -0,0 +1,37 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +JAVA_PKG_IUSE="doc source" + +inherit java-pkg-2 java-pkg-simple + +DESCRIPTION="SCIFIO version of the Java Advanced Imaging Image I/O Tools API Core." +HOMEPAGE="http://jai-imageio.dev.java.net/" + +if [[ ${PV} == 9999 ]]; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/scifio/scifio-jai-imageio.git" + S="${WORKDIR}/${P}" + MAVEN_ID="io.scif:scifio-jai-imageio:9999" +else + SRC_URI=" + https://github.com/scifio/${PN}/archive/refs/tags/${P}.tar.gz -> ${P}-sources.tar.gz + " + S="${WORKDIR}/${PN}-${P}" + MAVEN_ID="io.scif:scifio-jai-imageio:1.1.2" + KEYWORDS="~amd64" +fi + +LICENSE="BSD-2" +SLOT="0" + +DEPEND=">=virtual/jdk-1.8:*" +RDEPEND=">=virtual/jre-1.8:*" + +JAVA_SRC_DIR="src/main/java" +JAVA_MAIN_CLASS="" +JAVA_RESOURCE_DIRS=( + "src/main/resources" +) diff --git a/media-libs/scifio-jai-imageio/scifio-jai-imageio-9999.ebuild b/media-libs/scifio-jai-imageio/scifio-jai-imageio-9999.ebuild new file mode 100644 index 000000000..bdc989735 --- /dev/null +++ b/media-libs/scifio-jai-imageio/scifio-jai-imageio-9999.ebuild @@ -0,0 +1,37 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +JAVA_PKG_IUSE="doc source" + +inherit java-pkg-2 java-pkg-simple + +DESCRIPTION="SCIFIO version of the Java Advanced Imaging Image I/O Tools API Core." +HOMEPAGE="http://jai-imageio.dev.java.net/" + +if [[ ${PV} == 9999 ]]; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/scifio/scifio-jai-imageio.git" + S="${WORKDIR}/${P}" + MAVEN_ID="io.scif:scifio-jai-imageio:9999" +else + SRC_URI=" + https://github.com/scifio/${PN}/archive/refs/tags/${P}.tar.gz -> ${P}-sources.tar.gz + " + S="${WORKDIR}/${PN}-${P}" + MAVEN_ID="io.scif:scifio-jai-imageio:1.1.2" + KEYWORDS="~amd64" +fi + +LICENSE="BSD-2" +SLOT="0" + +DEPEND=">=virtual/jdk-1.8:*" +RDEPEND=">=virtual/jre-1.8:*" + +JAVA_SRC_DIR="src/main/java" +JAVA_MAIN_CLASS="" +JAVA_RESOURCE_DIRS=( + "src/main/resources" +) diff --git a/metadata/pkgcheck.conf b/metadata/pkgcheck.conf new file mode 100644 index 000000000..b39b6e490 --- /dev/null +++ b/metadata/pkgcheck.conf @@ -0,0 +1,2 @@ +[DEFAULT] +profiles = stable,dev,-default/linux/amd64/17.0/musl,-default/linux/amd64/17.0/x32 diff --git a/net-misc/cernbox-client/Manifest b/net-misc/cernbox-client/Manifest index ad8668437..5916259b7 100644 --- a/net-misc/cernbox-client/Manifest +++ b/net-misc/cernbox-client/Manifest @@ -1,3 +1,4 @@ -DIST cernbox-client-2.7.1-2596.src.rpm 15434250 BLAKE2B 3ef3fcc4010b3f292aee9b6bba7b5f9a72e4fbca1236e1e85e6523cd4e38d980fe4542c5f019647a19040be64628159651630a61ee8894cb7bcf4b69d342ccd0 SHA512 e329b84fc7aa62068f934bf8a9f47432709094adc618274c1b8ddbf7331094cb71b6208d3a777150ee426141301e0279cb219d65b123335f2e198a9b87980e5d -DIST ownCloud-2.10.0.6519.tar.xz 5791912 BLAKE2B 3cf02ef89a6af249ab8f9d1b0a4cc899fbb11f49bf47ffb0ce042442da984d8dbf49619cf3344cf1837f1f3437e70f6e6d302f4e4c67a7df5f547368be4252ba SHA512 ab1e8aebefa049a73c436325b3b6e1d03e9a74f93ab6e090adbc71ccdd1cf56297898f004b12312ebba82158f5c2e299d9d0b13c14e291b855dcf267bac490f2 -DIST ownCloud-2.10.1.7389.tar.xz 5598044 BLAKE2B 8558a8a7b7bd4b8a0685b703f0882d6b5619c4902217d40feb4cf5587555b9a85363c7f61834e4c85a84789142fca8c73910fce66544f491ec5968818c816605 SHA512 2a0893d48786b88f8210966a2b6b48f5bdada82818d4115e68ecc6c0c926ba62bc74df03c4ab35eb271aef2f3a43b36b1a6a115585efe3739fd4a6164f9c45a1 +DIST cernbox-client-4.1.0-11373.src.rpm 4621882 BLAKE2B db5106e4e214cee38f729543017adc45a7f4a00e95e57953c6d18b5272e6db88a7d5d820e68272e17d80c3ce962ad3ce689f053a2cff5fe0b7ec2788885cc0d8 SHA512 2deb9c19cbfffd7c37ac06c244c94e996a369ac511d4d71634b7f86f16093cfe7e6d44a97446bcf919924ded392669903344ea38da8bb70cc47317729d355cee +DIST libregraphapi-1.0.1.tar.gz 105266 BLAKE2B b5122ca5bb757c58bba0f29eaf119685c0ed119a9a72951f4098d8180e5bf05332b36fa6c884ca29b0414051c9c6d6ca081e3c7eeb7b9810202f11c1a70c5190 SHA512 aaa710642c36b4038dc61e7df4fc904a82a2ab6c34da03c3f5328075e41ab319f6616866b7f9ae472ff256b421751f8f5ce7ce0a6d3451bda75cfa3b307df082 +DIST ownCloud-4.1.0.11250.tar.xz 4122856 BLAKE2B 63bdd6047a75e07f6097fec37fb8092675ede50aada272bb8817e0d6ac1aa690cb7257a3d984bac58ed6320543f038cd2c89c49d9161d70ec8a3268997c42af3 SHA512 5f8f43cc8e3ceb2beeebe11fd93937df54e66ce9020a628da232523176815968364667a093cdea6bdf44dca9e1b67878ef76f38c48287327efc0fc3f85f22fb5 +DIST ownCloud-4.2.0.11670.tar.xz 4126004 BLAKE2B 60a5855239b32bfb6769d38de3eced3dcb6c642d702fa33439dfebdc97947dfaed1f0081d2ec8913edc7ab8688872115abd739e21eae7d06e96cbcd92abb5565 SHA512 277d18581155f663c0c18b44a6c0fb9b31c84695e0980da486028b91c1d1c9f5a7ba956afbc11fb2e7fc4679e46a30c2d737667208f5c0599a39bf91a109ce99 diff --git a/net-misc/cernbox-client/cernbox-client-2.10.0.6519.ebuild b/net-misc/cernbox-client/cernbox-client-2.10.0.6519.ebuild deleted file mode 100644 index c4eeaa7be..000000000 --- a/net-misc/cernbox-client/cernbox-client-2.10.0.6519.ebuild +++ /dev/null @@ -1,82 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -inherit cmake rpm xdg - -DESCRIPTION="Synchronize files from CERNBox EOS with your computer" - -# Origin is classic owncloud-client, branded for CERN during compilation. -ORIGIN_PN="ownCloud" -BRANDED_P="cernbox" -BRANDED_PV="2.7.1" -BRANDED_REL="2596" -HOMEPAGE="https://cernbox.cern.ch/" -SRC_URI="https://download.owncloud.com/desktop/${ORIGIN_PN}/stable/${PV}/source/${ORIGIN_PN}-${PV}.tar.xz - https://cernbox.cern.ch/cernbox/doc/Linux/repo/CentOS_7/src/${PN}-${BRANDED_PV}-${BRANDED_REL}.src.rpm - https://cern.ch/ofreyerm/gentoo/cernbox/${PN}-${BRANDED_PV}-${BRANDED_REL}.src.rpm" - -LICENSE="CC-BY-3.0 GPL-2" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="dolphin gnome-keyring nautilus test" - -COMMON_DEPEND=">=dev-db/sqlite-3.4:3 - dev-libs/qtkeychain[gnome-keyring?,qt5(+)] - dev-qt/qtconcurrent:5 - dev-qt/qtcore:5 - dev-qt/qtdbus:5 - dev-qt/qtgui:5 - dev-qt/qtnetwork:5[ssl] - dev-qt/qtsql:5 - dev-qt/qtwidgets:5 - dev-qt/qtxml:5 - sys-fs/inotify-tools - dolphin? ( - kde-frameworks/kcoreaddons:5 - kde-frameworks/kio:5 - ) - nautilus? ( dev-python/nautilus-python )" - -RDEPEND="${COMMON_DEPEND}" -DEPEND="${COMMON_DEPEND} - dev-qt/linguist-tools:5 - kde-frameworks/extra-cmake-modules - test? ( - dev-util/cmocka - dev-qt/qttest:5 - )" - -RESTRICT="!test? ( test )" - -S=${WORKDIR}/${ORIGIN_PN}-${PV} - -PATCHES=( "${FILESDIR}"/cernbox-theme-2.9.1.patch ) - -src_unpack() { - rpm_src_unpack ${PN}-${BRANDED_PV}-${BRANDED_REL}.src.rpm || die "failed to extract branding RPM" - mv ${PN%-*}-${BRANDED_PV}.${BRANDED_REL}/branding "${S}" || die "failed to extract branding" -} - -src_prepare() { - # Keep tests in ${T} - sed -i -e "s#\"/tmp#\"${T}#g" test/test*.cpp || die - - if ! use nautilus; then - pushd shell_integration > /dev/null || die - cmake_comment_add_subdirectory nautilus - popd > /dev/null || die - fi - cmake_src_prepare -} - -src_configure() { - local mycmakeargs=( - -DCMAKE_INSTALL_DOCDIR=/usr/share/doc/${PF} - -DBUILD_SHELL_INTEGRATION_DOLPHIN=$(usex dolphin) - -DBUILD_TESTING=$(usex test) - ) - - cmake_src_configure -} diff --git a/net-misc/cernbox-client/cernbox-client-2.10.1.7389.ebuild b/net-misc/cernbox-client/cernbox-client-2.10.1.7389.ebuild deleted file mode 100644 index c4eeaa7be..000000000 --- a/net-misc/cernbox-client/cernbox-client-2.10.1.7389.ebuild +++ /dev/null @@ -1,82 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -inherit cmake rpm xdg - -DESCRIPTION="Synchronize files from CERNBox EOS with your computer" - -# Origin is classic owncloud-client, branded for CERN during compilation. -ORIGIN_PN="ownCloud" -BRANDED_P="cernbox" -BRANDED_PV="2.7.1" -BRANDED_REL="2596" -HOMEPAGE="https://cernbox.cern.ch/" -SRC_URI="https://download.owncloud.com/desktop/${ORIGIN_PN}/stable/${PV}/source/${ORIGIN_PN}-${PV}.tar.xz - https://cernbox.cern.ch/cernbox/doc/Linux/repo/CentOS_7/src/${PN}-${BRANDED_PV}-${BRANDED_REL}.src.rpm - https://cern.ch/ofreyerm/gentoo/cernbox/${PN}-${BRANDED_PV}-${BRANDED_REL}.src.rpm" - -LICENSE="CC-BY-3.0 GPL-2" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="dolphin gnome-keyring nautilus test" - -COMMON_DEPEND=">=dev-db/sqlite-3.4:3 - dev-libs/qtkeychain[gnome-keyring?,qt5(+)] - dev-qt/qtconcurrent:5 - dev-qt/qtcore:5 - dev-qt/qtdbus:5 - dev-qt/qtgui:5 - dev-qt/qtnetwork:5[ssl] - dev-qt/qtsql:5 - dev-qt/qtwidgets:5 - dev-qt/qtxml:5 - sys-fs/inotify-tools - dolphin? ( - kde-frameworks/kcoreaddons:5 - kde-frameworks/kio:5 - ) - nautilus? ( dev-python/nautilus-python )" - -RDEPEND="${COMMON_DEPEND}" -DEPEND="${COMMON_DEPEND} - dev-qt/linguist-tools:5 - kde-frameworks/extra-cmake-modules - test? ( - dev-util/cmocka - dev-qt/qttest:5 - )" - -RESTRICT="!test? ( test )" - -S=${WORKDIR}/${ORIGIN_PN}-${PV} - -PATCHES=( "${FILESDIR}"/cernbox-theme-2.9.1.patch ) - -src_unpack() { - rpm_src_unpack ${PN}-${BRANDED_PV}-${BRANDED_REL}.src.rpm || die "failed to extract branding RPM" - mv ${PN%-*}-${BRANDED_PV}.${BRANDED_REL}/branding "${S}" || die "failed to extract branding" -} - -src_prepare() { - # Keep tests in ${T} - sed -i -e "s#\"/tmp#\"${T}#g" test/test*.cpp || die - - if ! use nautilus; then - pushd shell_integration > /dev/null || die - cmake_comment_add_subdirectory nautilus - popd > /dev/null || die - fi - cmake_src_prepare -} - -src_configure() { - local mycmakeargs=( - -DCMAKE_INSTALL_DOCDIR=/usr/share/doc/${PF} - -DBUILD_SHELL_INTEGRATION_DOLPHIN=$(usex dolphin) - -DBUILD_TESTING=$(usex test) - ) - - cmake_src_configure -} diff --git a/net-misc/cernbox-client/cernbox-client-4.1.0.11250.ebuild b/net-misc/cernbox-client/cernbox-client-4.1.0.11250.ebuild new file mode 100644 index 000000000..741aa66f1 --- /dev/null +++ b/net-misc/cernbox-client/cernbox-client-4.1.0.11250.ebuild @@ -0,0 +1,92 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit cmake rpm xdg + +DESCRIPTION="Synchronize files from CERNBox EOS with your computer" + +# Origin is classic owncloud-client, branded for CERN during compilation. +ORIGIN_PN="ownCloud" +BRANDED_P="cernbox" +BRANDED_PV="4.1.0" +BRANDED_REL="11373" +REGRAPHAPI_PV="1.0.1" +HOMEPAGE="https://cernbox.cern.ch/" +SRC_URI="https://download.owncloud.com/desktop/${ORIGIN_PN}/stable/${PV}/source/${ORIGIN_PN}-${PV}.tar.xz + https://cernboxdistr.web.cern.ch/cernboxdistr/Linux/repo.future/Fedora_38/src/${PN}-${BRANDED_PV}-${BRANDED_REL}.src.rpm + https://cern.ch/ofreyerm/gentoo/cernbox/${PN}-${BRANDED_PV}-${BRANDED_REL}.src.rpm + https://github.com/owncloud/libre-graph-api-cpp-qt-client/archive/refs/tags/v${REGRAPHAPI_PV}.tar.gz + -> libregraphapi-${REGRAPHAPI_PV}.tar.gz" + +LICENSE="CC-BY-3.0 GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="dolphin keyring nautilus test" +RESTRICT="!test? ( test )" + +RDEPEND=">=dev-db/sqlite-3.4:3 + dev-libs/qtkeychain[keyring?,qt5(+)] + dev-qt/qtconcurrent:5 + dev-qt/qtcore:5 + dev-qt/qtdbus:5 + dev-qt/qtgui:5 + dev-qt/qtnetwork:5[ssl] + dev-qt/qtsql:5 + dev-qt/qtwidgets:5 + dev-qt/qtxml:5 + sys-fs/inotify-tools + dolphin? ( + kde-frameworks/kcoreaddons:5 + kde-frameworks/kio:5 + ) + nautilus? ( dev-python/nautilus-python )" + +DEPEND="${RDEPEND} + test? ( + dev-util/cmocka + dev-qt/qttest:5 + )" + +BDEPEND=" + dev-qt/linguist-tools:5 + kde-frameworks/extra-cmake-modules" + +S=${WORKDIR}/${ORIGIN_PN}-${PV} + +src_unpack() { + rpm_src_unpack ${PN}-${BRANDED_PV}-${BRANDED_REL}.src.rpm || die "failed to extract branding RPM" + mv ${PN%-*}-${BRANDED_PV}.${BRANDED_REL}/branding "${S}" || die "failed to extract branding" +} + +PATCHES=( + "${FILESDIR}"/owncloud-client-3.1.0.9872-no_cmake_fetch.patch + "${FILESDIR}"/owncloud-client-3.2.0.10193-no_fortify_override.patch + "${FILESDIR}"/owncloud-client-4.1.0.11250-fix-mirall.patch +) + +src_prepare() { + mv ../libre-graph-api-cpp-qt-client-${REGRAPHAPI_PV} \ + src/libsync/libregraphapisrc-src || die + + # Keep tests in ${T} + sed -i -e "s#\"/tmp#\"${T}#g" test/test*.cpp || die + + if ! use nautilus; then + pushd shell_integration > /dev/null || die + cmake_comment_add_subdirectory nautilus + popd > /dev/null || die + fi + cmake_src_prepare +} + +src_configure() { + local mycmakeargs=( + -DCMAKE_INSTALL_DOCDIR=/usr/share/doc/${PF} + -DBUILD_SHELL_INTEGRATION_DOLPHIN=$(usex dolphin) + -DBUILD_TESTING=$(usex test) + ) + + cmake_src_configure +} diff --git a/net-misc/cernbox-client/cernbox-client-4.2.0.11670.ebuild b/net-misc/cernbox-client/cernbox-client-4.2.0.11670.ebuild new file mode 100644 index 000000000..741aa66f1 --- /dev/null +++ b/net-misc/cernbox-client/cernbox-client-4.2.0.11670.ebuild @@ -0,0 +1,92 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit cmake rpm xdg + +DESCRIPTION="Synchronize files from CERNBox EOS with your computer" + +# Origin is classic owncloud-client, branded for CERN during compilation. +ORIGIN_PN="ownCloud" +BRANDED_P="cernbox" +BRANDED_PV="4.1.0" +BRANDED_REL="11373" +REGRAPHAPI_PV="1.0.1" +HOMEPAGE="https://cernbox.cern.ch/" +SRC_URI="https://download.owncloud.com/desktop/${ORIGIN_PN}/stable/${PV}/source/${ORIGIN_PN}-${PV}.tar.xz + https://cernboxdistr.web.cern.ch/cernboxdistr/Linux/repo.future/Fedora_38/src/${PN}-${BRANDED_PV}-${BRANDED_REL}.src.rpm + https://cern.ch/ofreyerm/gentoo/cernbox/${PN}-${BRANDED_PV}-${BRANDED_REL}.src.rpm + https://github.com/owncloud/libre-graph-api-cpp-qt-client/archive/refs/tags/v${REGRAPHAPI_PV}.tar.gz + -> libregraphapi-${REGRAPHAPI_PV}.tar.gz" + +LICENSE="CC-BY-3.0 GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="dolphin keyring nautilus test" +RESTRICT="!test? ( test )" + +RDEPEND=">=dev-db/sqlite-3.4:3 + dev-libs/qtkeychain[keyring?,qt5(+)] + dev-qt/qtconcurrent:5 + dev-qt/qtcore:5 + dev-qt/qtdbus:5 + dev-qt/qtgui:5 + dev-qt/qtnetwork:5[ssl] + dev-qt/qtsql:5 + dev-qt/qtwidgets:5 + dev-qt/qtxml:5 + sys-fs/inotify-tools + dolphin? ( + kde-frameworks/kcoreaddons:5 + kde-frameworks/kio:5 + ) + nautilus? ( dev-python/nautilus-python )" + +DEPEND="${RDEPEND} + test? ( + dev-util/cmocka + dev-qt/qttest:5 + )" + +BDEPEND=" + dev-qt/linguist-tools:5 + kde-frameworks/extra-cmake-modules" + +S=${WORKDIR}/${ORIGIN_PN}-${PV} + +src_unpack() { + rpm_src_unpack ${PN}-${BRANDED_PV}-${BRANDED_REL}.src.rpm || die "failed to extract branding RPM" + mv ${PN%-*}-${BRANDED_PV}.${BRANDED_REL}/branding "${S}" || die "failed to extract branding" +} + +PATCHES=( + "${FILESDIR}"/owncloud-client-3.1.0.9872-no_cmake_fetch.patch + "${FILESDIR}"/owncloud-client-3.2.0.10193-no_fortify_override.patch + "${FILESDIR}"/owncloud-client-4.1.0.11250-fix-mirall.patch +) + +src_prepare() { + mv ../libre-graph-api-cpp-qt-client-${REGRAPHAPI_PV} \ + src/libsync/libregraphapisrc-src || die + + # Keep tests in ${T} + sed -i -e "s#\"/tmp#\"${T}#g" test/test*.cpp || die + + if ! use nautilus; then + pushd shell_integration > /dev/null || die + cmake_comment_add_subdirectory nautilus + popd > /dev/null || die + fi + cmake_src_prepare +} + +src_configure() { + local mycmakeargs=( + -DCMAKE_INSTALL_DOCDIR=/usr/share/doc/${PF} + -DBUILD_SHELL_INTEGRATION_DOLPHIN=$(usex dolphin) + -DBUILD_TESTING=$(usex test) + ) + + cmake_src_configure +} diff --git a/net-misc/cernbox-client/files/cernbox-theme-2.9.1.patch b/net-misc/cernbox-client/files/cernbox-theme-2.9.1.patch deleted file mode 100644 index c2ccbcc5e..000000000 --- a/net-misc/cernbox-client/files/cernbox-theme-2.9.1.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- a/branding/cernbox-theme.h 2021-10-21 13:10:22.832842670 +0200 -+++ b/branding/cernbox-theme.h 2021-10-21 13:14:57.394479817 +0200 -@@ -62,7 +62,7 @@ - - - QString about() const { -- QString devString = tr("<p>Version %1. For more information visit <a href=\"%2\">https://%3</a></p>").arg(Utility::escape(QStringLiteral(MIRALL_VERSION_STRING)), Utility::escape(QStringLiteral("https://" MIRALL_STRINGIFY(APPLICATION_DOMAIN))), Utility::escape(QStringLiteral(MIRALL_STRINGIFY(APPLICATION_DOMAIN)))); -+ QString devString = tr("<p>Version %1. For more information visit <a href=\"%2\">https://%3</a></p>").arg(Utility::escape(QStringLiteral(MIRALL_VERSION_STRING)), Utility::escape(QStringLiteral("https://" APPLICATION_DOMAIN)), Utility::escape(QStringLiteral(APPLICATION_DOMAIN))); - - - return devString; diff --git a/net-misc/cernbox-client/files/owncloud-client-3.1.0.9872-no_cmake_fetch.patch b/net-misc/cernbox-client/files/owncloud-client-3.1.0.9872-no_cmake_fetch.patch new file mode 100644 index 000000000..d9762292e --- /dev/null +++ b/net-misc/cernbox-client/files/owncloud-client-3.1.0.9872-no_cmake_fetch.patch @@ -0,0 +1,17 @@ +Index: ownCloud-3.1.0.9872/src/libsync/CMakeLists.txt +--- ownCloud-3.1.0.9872/src/libsync/CMakeLists.txt.orig ++++ ownCloud-3.1.0.9872/src/libsync/CMakeLists.txt +@@ -3,12 +3,7 @@ set(LibreGraphAPIVersion v0.13.2) + find_package(LibreGraphAPI QUIET) + if (NOT TARGET OpenAPI::LibreGraphAPI) + message(WARNING "Failed to find system OpenAPI::LibreGraphAPI: fetching ${LibreGraphAPIVersion}") +- include(FetchContent) +- FetchContent_Populate(LibreGraphAPISrc +- QUIET +- GIT_REPOSITORY https://github.com/owncloud/libre-graph-api-cpp-qt-client.git +- GIT_TAG ${LibreGraphAPIVersion}) +- add_subdirectory(${libregraphapisrc_SOURCE_DIR}/client ${libregraphapisrc_BINARY_DIR}/client EXCLUDE_FROM_ALL) ++ add_subdirectory(libregraphapisrc-src/client libregraphapisrc-src/client EXCLUDE_FROM_ALL) + endif() + + set(libsync_SRCS diff --git a/net-misc/cernbox-client/files/owncloud-client-3.2.0.10193-no_fortify_override.patch b/net-misc/cernbox-client/files/owncloud-client-3.2.0.10193-no_fortify_override.patch new file mode 100644 index 000000000..266596b7b --- /dev/null +++ b/net-misc/cernbox-client/files/owncloud-client-3.2.0.10193-no_fortify_override.patch @@ -0,0 +1,16 @@ +diff -Naur ownCloud-3.2.0.10193.orig/src/CMakeLists.txt ownCloud-3.2.0.10193/src/CMakeLists.txt +--- ownCloud-3.2.0.10193.orig/src/CMakeLists.txt 2023-02-15 18:27:55.000000000 +0100 ++++ ownCloud-3.2.0.10193/src/CMakeLists.txt 2023-02-22 22:55:29.352847663 +0100 +@@ -16,12 +16,6 @@ + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fstack-protector-strong") + endif() + endif() +- +- string(TOLOWER "${CMAKE_BUILD_TYPE}" CMAKE_BUILD_TYPE_LOWER) +- if(CMAKE_BUILD_TYPE_LOWER MATCHES "(release|relwithdebinfo|minsizerel)") +- set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -D_FORTIFY_SOURCE=2") +- set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -D_FORTIFY_SOURCE=2") +- endif() + endif() + + if(WIN32) diff --git a/net-misc/cernbox-client/files/owncloud-client-4.1.0.11250-fix-mirall.patch b/net-misc/cernbox-client/files/owncloud-client-4.1.0.11250-fix-mirall.patch new file mode 100644 index 000000000..5e00e23aa --- /dev/null +++ b/net-misc/cernbox-client/files/owncloud-client-4.1.0.11250-fix-mirall.patch @@ -0,0 +1,73 @@ +From: Fabian Müller <fmueller@owncloud.com> +Bug: https://github.com/owncloud/client/pull/10969 + +Fix installation of branded client in parallel to unbranded client. + +diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt +index 4d73f2cc3..49228dbb6 100644 +--- a/src/CMakeLists.txt ++++ b/src/CMakeLists.txt +@@ -54,10 +54,12 @@ endif(NOT BUILD_LIBRARIES_ONLY) + + add_subdirectory(plugins) + +-install(EXPORT ownCloudConfig DESTINATION "${KDE_INSTALL_CMAKEPACKAGEDIR}/ownCloud" NAMESPACE ownCloud::) ++install(EXPORT ${APPLICATION_SHORTNAME}Config DESTINATION "${KDE_INSTALL_CMAKEPACKAGEDIR}/${APPLICATION_SHORTNAME}" NAMESPACE ownCloud::) + +-ecm_setup_version(PROJECT VARIABLE_PREFIX ownCloud +- PACKAGE_VERSION_FILE "${CMAKE_CURRENT_BINARY_DIR}/ownCloudConfigVersion.cmake" +- SOVERSION ${MIRALL_SOVERSION}) ++ecm_setup_version(PROJECT ++ VARIABLE_PREFIX ${APPLICATION_SHORTNAME} ++ PACKAGE_VERSION_FILE "${CMAKE_CURRENT_BINARY_DIR}/${APPLICATION_SHORTNAME}ConfigVersion.cmake" ++ SOVERSION ${MIRALL_SOVERSION} ++) + +-install(FILES "${CMAKE_CURRENT_BINARY_DIR}/ownCloudConfigVersion.cmake" DESTINATION "${KDE_INSTALL_CMAKEPACKAGEDIR}/ownCloud") ++install(FILES "${CMAKE_CURRENT_BINARY_DIR}/${APPLICATION_SHORTNAME}ConfigVersion.cmake" DESTINATION "${KDE_INSTALL_CMAKEPACKAGEDIR}/${APPLICATION_SHORTNAME}") +diff --git a/src/csync/CMakeLists.txt b/src/csync/CMakeLists.txt +index fcf665e44..15c0a8130 100644 +--- a/src/csync/CMakeLists.txt ++++ b/src/csync/CMakeLists.txt +@@ -98,10 +98,10 @@ INSTALL( + ../common/filesystembase.h + ../common/utility.h + DESTINATION +- ${INCLUDE_INSTALL_DIR}/ownCloud/common ++ ${INCLUDE_INSTALL_DIR}/${APPLICATION_SHORTNAME}/common + ) + +-INSTALL(TARGETS csync EXPORT ownCloudConfig ${KDE_INSTALL_TARGETS_DEFAULT_ARGS}) ++INSTALL(TARGETS csync EXPORT ${APPLICATION_SHORTNAME}Config ${KDE_INSTALL_TARGETS_DEFAULT_ARGS}) + + configure_file(config_csync.h.cmake ${CMAKE_CURRENT_BINARY_DIR}/config_csync.h) + +diff --git a/src/libsync/CMakeLists.txt b/src/libsync/CMakeLists.txt +index 3995bcfe9..eeaef8450 100644 +--- a/src/libsync/CMakeLists.txt ++++ b/src/libsync/CMakeLists.txt +@@ -85,7 +85,7 @@ INSTALL( + ${CMAKE_CURRENT_BINARY_DIR}/owncloudlib.h + logger.h + accessmanager.h +- DESTINATION ${INCLUDE_INSTALL_DIR}/ownCloud/libsync ++ DESTINATION ${INCLUDE_INSTALL_DIR}/${APPLICATION_SHORTNAME}/libsync + ) + + add_library(libsync SHARED ${libsync_SRCS}) +@@ -138,4 +138,4 @@ set_target_properties(libsync PROPERTIES + VERSION ${MIRALL_VERSION} + SOVERSION ${MIRALL_SOVERSION} + ) +-install(TARGETS libsync EXPORT ownCloudConfig ${KDE_INSTALL_TARGETS_DEFAULT_ARGS}) ++install(TARGETS libsync EXPORT ${APPLICATION_SHORTNAME}Config ${KDE_INSTALL_TARGETS_DEFAULT_ARGS}) +diff --git a/src/resources/CMakeLists.txt b/src/resources/CMakeLists.txt +index 6f50bf3be..7e0ff05b7 100644 +--- a/src/resources/CMakeLists.txt ++++ b/src/resources/CMakeLists.txt +@@ -42,4 +42,4 @@ if(Qt5LinguistTools_FOUND) + ) + endif() + +-install(TARGETS owncloudResources EXPORT ownCloudConfig ${KDE_INSTALL_TARGETS_DEFAULT_ARGS}) ++install(TARGETS owncloudResources EXPORT ${APPLICATION_SHORTNAME}Config ${KDE_INSTALL_TARGETS_DEFAULT_ARGS}) diff --git a/net-misc/cernbox-client/metadata.xml b/net-misc/cernbox-client/metadata.xml index c67ea7b66..e8384eb02 100644 --- a/net-misc/cernbox-client/metadata.xml +++ b/net-misc/cernbox-client/metadata.xml @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> <email>o.freyermuth@googlemail.com</email> @@ -26,5 +26,7 @@ </use> <upstream> <doc>https://cernbox.web.cern.ch/cernbox/</doc> + <remote-id type="github">owncloud/client</remote-id> + <remote-id type="github">owncloud/libre-graph-api-cpp-qt-client</remote-id> </upstream> </pkgmetadata> diff --git a/profiles/default/linux/amd64/17.0/x32/package.mask b/profiles/default/linux/amd64/17.0/x32/package.mask deleted file mode 100644 index 4f9228f91..000000000 --- a/profiles/default/linux/amd64/17.0/x32/package.mask +++ /dev/null @@ -1,3 +0,0 @@ -# Cecil Curry <leycec@gmail.com> (2021-10-07) -# Panel requires Node.js, which fails to support the x32 ABI. -dev-python/panel diff --git a/profiles/desc/lhapdf_sets.desc b/profiles/desc/lhapdf_sets.desc new file mode 100644 index 000000000..66da0763c --- /dev/null +++ b/profiles/desc/lhapdf_sets.desc @@ -0,0 +1,19 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +# This file contains descriptions of LHAPDF_SETS USE_EXPAND flags. + +nnpdf31_nnlo_as_0118_luxqed - NNPDF31_nnlo_as_0118_luxqed LHAPDF grid +pdf4lhc15_nlo_asvar - PDF4LHC15_nlo_asvar LHAPDF grid +ct14qed_proton - CT14qed_proton LHAPDF grid +ct14lo - CT14lo LHAPDF grid +ct14nlo - CT14nlo LHAPDF grid +ct10 - CT10 LHAPDF grid +mrst2007lomod - MRST2007lomod LHAPDF grid +nnpdf23_nlo_as_0119_qed_mc - NNPDF23_nlo_as_0119_qed_mc LHAPDF grid +nnpdf23_nnlo_as_0119_qed_mc - NNPDF23_nnlo_as_0119_qed_mc LHAPDF grid +cteq66 - CTEQ66 LHAPDF grid +cteq6l1 - CTEQ6L1 LHAPDF grid +mrst2004qed - MRST2004qed LHAPDF grid +nnpdf23_nlo_as_0118 - nnpdf23_nlo_as_0118 grid +nnpdf31_nnlo_as_0118 - nnpdf31_nnlo_as_0118 grid
\ No newline at end of file diff --git a/profiles/license_groups b/profiles/license_groups index c505c87d8..5221d37f1 100644 --- a/profiles/license_groups +++ b/profiles/license_groups @@ -1 +1 @@ -EULA OpenSIFT +EULA OpenSIFT MathWorks diff --git a/profiles/make.defaults b/profiles/make.defaults new file mode 100644 index 000000000..88d3fe603 --- /dev/null +++ b/profiles/make.defaults @@ -0,0 +1 @@ +USE_EXPAND="LHAPDF_SETS"
\ No newline at end of file diff --git a/profiles/package.mask b/profiles/package.mask index b338c8d20..d39812beb 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -29,9 +29,3 @@ ## app-misc/some-package #--- END OF EXAMPLES --- - -# Andrew Ammerlaan <andrewammerlaan@gentoo.org> (15 May 2022) -# Requires old and removed batik:1.9::gentoo -# No updates since 2019 -# Mask for removal in 30 days -dev-java/jeuclid-core diff --git a/profiles/package.use.mask b/profiles/package.use.mask index 92d1d843a..39a6df0b7 100644 --- a/profiles/package.use.mask +++ b/profiles/package.use.mask @@ -15,20 +15,6 @@ ## =media-video/mplayer-0.90_pre5-r1 foo # -# Andrew Savchenko <bircoph@gentoo.org> (02 Jun 2016) -# doesn't link with plotutils-2.6 -sci-physics/qcl plotutils - -# Christoph Junghans <ottxor@gentoo.org> (12 Sep 2014) -# icc and ifc don't work on no-multilib -sci-biology/estscan icc ifc - -# Christoph Junghans <ottxor@gentoo.org> (05 Nov 2013) -# gui sandbox error -dev-lang/conceptual gui - -# Andrew Ammerlaan <andrewammerlaan@gentoo.org> (15 Jan 2022) -# dependencies not available -# https://github.com/gentoo/sci/issues/1085 -# https://github.com/gentoo/sci/issues/1084 -sci-libs/mlpack go R +# Andrew Ammerlaan <andrewammerlaan@gentoo.org> (23 Aug 2022) +# vtk<9 no longer available in ::gentoo +sci-libs/gdcm python diff --git a/profiles/updates/4Q-2022 b/profiles/updates/4Q-2022 new file mode 100644 index 000000000..b80d5a910 --- /dev/null +++ b/profiles/updates/4Q-2022 @@ -0,0 +1 @@ +move sci-mathematics/netgen media-gfx/netgen diff --git a/sci-biology/ABI-connectivity-data/ABI-connectivity-data-0.1-r1.ebuild b/sci-biology/ABI-connectivity-data/ABI-connectivity-data-0.1-r1.ebuild index 4b5476138..fe4926644 100644 --- a/sci-biology/ABI-connectivity-data/ABI-connectivity-data-0.1-r1.ebuild +++ b/sci-biology/ABI-connectivity-data/ABI-connectivity-data-0.1-r1.ebuild @@ -1,13 +1,13 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 inherit check-reqs DESCRIPTION="Connectivity data from the Allen Mouse Brain data portal" HOMEPAGE="https://github.com/IBT-FMI/ABI-connectivity-data_generator" -SRC_URI="http://resources.chymera.eu/distfiles/${P}.tar.xz" +SRC_URI="https://resources.chymera.eu/distfiles/${P}.tar.xz" LICENSE="fairuse" SLOT="0" diff --git a/sci-biology/ABI-connectivity-data/ABI-connectivity-data-0.2.ebuild b/sci-biology/ABI-connectivity-data/ABI-connectivity-data-0.2.ebuild index 4b5476138..fe4926644 100644 --- a/sci-biology/ABI-connectivity-data/ABI-connectivity-data-0.2.ebuild +++ b/sci-biology/ABI-connectivity-data/ABI-connectivity-data-0.2.ebuild @@ -1,13 +1,13 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 inherit check-reqs DESCRIPTION="Connectivity data from the Allen Mouse Brain data portal" HOMEPAGE="https://github.com/IBT-FMI/ABI-connectivity-data_generator" -SRC_URI="http://resources.chymera.eu/distfiles/${P}.tar.xz" +SRC_URI="https://resources.chymera.eu/distfiles/${P}.tar.xz" LICENSE="fairuse" SLOT="0" diff --git a/sci-biology/ABI-connectivity-data/metadata.xml b/sci-biology/ABI-connectivity-data/metadata.xml index 6de417d21..4f11f95ba 100644 --- a/sci-biology/ABI-connectivity-data/metadata.xml +++ b/sci-biology/ABI-connectivity-data/metadata.xml @@ -9,4 +9,7 @@ <email>sci@gentoo.org</email> <name>Gentoo Science Project</name> </maintainer> + <upstream> + <remote-id type="github">IBT-FMI/ABI-connectivity-data_generator</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/ABI-expression-data/ABI-expression-data-0.2.ebuild b/sci-biology/ABI-expression-data/ABI-expression-data-0.2.ebuild index e28aa18be..2016de083 100644 --- a/sci-biology/ABI-expression-data/ABI-expression-data-0.2.ebuild +++ b/sci-biology/ABI-expression-data/ABI-expression-data-0.2.ebuild @@ -8,7 +8,7 @@ inherit check-reqs DESCRIPTION="Gene expression data form the Allen Mouse Brain data portal" HOMEPAGE="https://github.com/IBT-FMI/ABI-expression-data_generator" SRC_URI=" - http://resources.chymera.eu/distfiles/${P}.tar.xz + https://resources.chymera.eu/distfiles/${P}.tar.xz " LICENSE="fairuse" diff --git a/sci-biology/BEP032tools/BEP032tools-0.0.1_alpha.ebuild b/sci-biology/BEP032tools/BEP032tools-0.0.1_alpha.ebuild new file mode 100644 index 000000000..ec394603d --- /dev/null +++ b/sci-biology/BEP032tools/BEP032tools-0.0.1_alpha.ebuild @@ -0,0 +1,44 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) + +inherit distutils-r1 + +MY_HASH="a7059ef691e74aeb018edaf37df49c99f6efed60" + +DESCRIPTION="Conversion and validation tools for BEP 032" +HOMEPAGE="https://github.com/INT-NIT/BEP032tools" +SRC_URI="https://github.com/INT-NIT/BEP032tools/archive/${MY_HASH}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + dev-python/pandas[${PYTHON_USEDEP}] + dev-python/pynwb[${PYTHON_USEDEP}] + dev-python/neo[${PYTHON_USEDEP}] +" +BDEPEND=" + dev-python/parameterized[${PYTHON_USEDEP}] +" + +S="${WORKDIR}/${PN}-${MY_HASH}" + +# Require nixio +EPYTEST_DESELECT=( + "bep032tools/generator/tests/test_BEP032Generator.py::Test_BEP032Data_ece::test_data_file_conversion_0_nix" + "bep032tools/generator/tests/test_BEP032Generator.py::Test_BEP032Data_ece::test_data_file_conversion_multi_split" + "bep032tools/generator/tests/test_BEP032Generator.py::Test_BEP032Data_ice::test_data_file_conversion_0_nix" +) +# Require dynamically fetched data +EPYTEST_DESELECT+=( + "bep032tools/generator/tests/test_nwb2bidsgenerator.py::TestNwbBIDSGenerator::test_nwb_to_bids" + "bep032tools/generator/tests/test_nwb2bidsgenerator.py::TestNwbBIDSGenerator::test_validation" +) + +distutils_enable_tests pytest diff --git a/sci-biology/BEP032tools/Manifest b/sci-biology/BEP032tools/Manifest new file mode 100644 index 000000000..1e97ed9b1 --- /dev/null +++ b/sci-biology/BEP032tools/Manifest @@ -0,0 +1 @@ +DIST BEP032tools-0.0.1_alpha.gh.tar.gz 79175 BLAKE2B dc3d999401d2d4361bfc66b72a39fa02bd6148a377bf63b5bdcc788f4018e486e89743b35ad8f61e232b22f79fed6199dad462aaab60e3bbd1425de117b9c576 SHA512 bf929e5f00cfdd47bbdb9f2240bab97468da5bcb72857e8272eb25857ce7d525b6a97cbc459ace8629d67eb9238b8ddd537e2b6269b73d0173a945b39d5eb59e diff --git a/sci-biology/BEP032tools/metadata.xml b/sci-biology/BEP032tools/metadata.xml new file mode 100644 index 000000000..8d24d17e7 --- /dev/null +++ b/sci-biology/BEP032tools/metadata.xml @@ -0,0 +1,16 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>gentoo@chymera.eu</email> + <name>Horea Christian</name> + </maintainer> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <upstream> + <remote-id type="github">INT-NIT/BEP032tools</remote-id> + <remote-id type="pypi">BEP032tools</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/BRAKER/metadata.xml b/sci-biology/BRAKER/metadata.xml index 138cb7705..aa4766e73 100644 --- a/sci-biology/BRAKER/metadata.xml +++ b/sci-biology/BRAKER/metadata.xml @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">Gaius-Augustus/BRAKER</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/BlastToSam/BlastToSam-1.1.ebuild b/sci-biology/BlastToSam/BlastToSam-1.1.ebuild deleted file mode 100644 index 775889330..000000000 --- a/sci-biology/BlastToSam/BlastToSam-1.1.ebuild +++ /dev/null @@ -1,32 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit git-r3 java-pkg-2 java-ant-2 - -DESCRIPTION="Convert NCBI BLAST+ Pairwise/XML (-outfmt 0 or 5) output to SAM v1.4" -HOMEPAGE="https://github.com/AstrorEnales/BlastToSam" -EGIT_REPO_URI="https://github.com/AstrorEnales/BlastToSam.git" -EGIT_COMMIT="8f543ff1640b64e44701cb534e2959ff46469b2e" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -RDEPEND=">=virtual/jre-1.5:*" -DEPEND="${RDEPEND} - >=virtual/jdk-1.5:* - dev-java/ant-core - dev-java/jython -" - -src_compile() { - ant compile || die -} - -src_install() { - java-pkg_dojar build/jar/BlastToSam.jar - java-pkg_dolauncher - dodoc README.md -} diff --git a/sci-biology/BlastToSam/metadata.xml b/sci-biology/BlastToSam/metadata.xml deleted file mode 100644 index 5a3c7d51d..000000000 --- a/sci-biology/BlastToSam/metadata.xml +++ /dev/null @@ -1,15 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="github">AstrorEnales/BlastToSam</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/CAT/CAT-1.3.ebuild b/sci-biology/CAT/CAT-1.3.ebuild index a2c4233c9..508ca4c36 100644 --- a/sci-biology/CAT/CAT-1.3.ebuild +++ b/sci-biology/CAT/CAT-1.3.ebuild @@ -4,9 +4,7 @@ EAPI=7 DESCRIPTION="Codon usage bias (composition) and its statistical significance" -HOMEPAGE=" - https://bigd.big.ac.cn/tools/cat - http://cbb.big.ac.cn/Software" +HOMEPAGE="https://bigd.big.ac.cn/tools/cat" SRC_URI="ftp://download.big.ac.cn/bigd/tools/${PN}${PV}.tar.gz -> ${P}.tar.gz" LICENSE="GPL-3+" diff --git a/sci-biology/FLASH/metadata.xml b/sci-biology/FLASH/metadata.xml index 0f267b755..7dc91092f 100644 --- a/sci-biology/FLASH/metadata.xml +++ b/sci-biology/FLASH/metadata.xml @@ -10,6 +10,6 @@ <name>Gentoo Biology Project</name> </maintainer> <upstream> - <remote-id type="sourceforge">downloads</remote-id> + <remote-id type="sourceforge">flashpage</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/Fastaq/Fastaq-3.17.0.ebuild b/sci-biology/Fastaq/Fastaq-3.17.0.ebuild index 28ff526f6..443fb3342 100644 --- a/sci-biology/Fastaq/Fastaq-3.17.0.ebuild +++ b/sci-biology/Fastaq/Fastaq-3.17.0.ebuild @@ -1,9 +1,10 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7,8,9} ) +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools inherit distutils-r1 @@ -15,4 +16,6 @@ LICENSE="GPL-3" SLOT="0" KEYWORDS="~amd64" -distutils_enable_tests nose +distutils_enable_tests pytest +# Nominally upstream still uses nose, though it does not encumber us, and tests pass: +# https://github.com/sanger-pathogens/Fastaq/issues/84 diff --git a/sci-biology/GAL/metadata.xml b/sci-biology/GAL/metadata.xml index 138cb7705..480ba370b 100644 --- a/sci-biology/GAL/metadata.xml +++ b/sci-biology/GAL/metadata.xml @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">The-Sequence-Ontology/GAL</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/MaSuRCA/MaSuRCA-4.0.1.ebuild b/sci-biology/MaSuRCA/MaSuRCA-4.0.1.ebuild index 8e6d2925e..7b070e595 100644 --- a/sci-biology/MaSuRCA/MaSuRCA-4.0.1.ebuild +++ b/sci-biology/MaSuRCA/MaSuRCA-4.0.1.ebuild @@ -1,17 +1,19 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 DESCRIPTION="de Bruijn and OLC assembler for Sanger, Roche 454, Illumina, Pacbio, Nanopore" HOMEPAGE="http://www.genome.umd.edu/masurca.html http://bioinformatics.oxfordjournals.org/content/29/21/2669 - https://biorxiv.org/content/biorxiv/early/2016/07/26/066100.full.pdf" + https://github.com/alekseyzimin/masurca" SRC_URI="https://github.com/alekseyzimin/masurca/releases/download/v${PV}/${P}.tar.gz" LICENSE="BSD GPL-2 GPL-3" SLOT="0" -KEYWORDS="~amd64" +# Known to produce build failure: +# https://github.com/alekseyzimin/masurca/issues/323 +KEYWORDS="" DEPEND=" >=dev-lang/perl-5.8 diff --git a/sci-biology/MaSuRCA/MaSuRCA-4.1.0.ebuild b/sci-biology/MaSuRCA/MaSuRCA-4.1.0.ebuild new file mode 100644 index 000000000..7b070e595 --- /dev/null +++ b/sci-biology/MaSuRCA/MaSuRCA-4.1.0.ebuild @@ -0,0 +1,29 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DESCRIPTION="de Bruijn and OLC assembler for Sanger, Roche 454, Illumina, Pacbio, Nanopore" +HOMEPAGE="http://www.genome.umd.edu/masurca.html + http://bioinformatics.oxfordjournals.org/content/29/21/2669 + https://github.com/alekseyzimin/masurca" +SRC_URI="https://github.com/alekseyzimin/masurca/releases/download/v${PV}/${P}.tar.gz" + +LICENSE="BSD GPL-2 GPL-3" +SLOT="0" +# Known to produce build failure: +# https://github.com/alekseyzimin/masurca/issues/323 +KEYWORDS="" + +DEPEND=" + >=dev-lang/perl-5.8 + app-arch/bzip2 +" +RDEPEND="${DEPEND}" + +src_compile(){ + ./install.sh || die +} +src_install(){ + dobin masurca +} diff --git a/sci-biology/MaSuRCA/Manifest b/sci-biology/MaSuRCA/Manifest index 330ac8de3..fd6029f04 100644 --- a/sci-biology/MaSuRCA/Manifest +++ b/sci-biology/MaSuRCA/Manifest @@ -1 +1,2 @@ DIST MaSuRCA-4.0.1.tar.gz 26502309 BLAKE2B 658c3a85d3d16bc966f50def9b0f98503f25f89893a18f6b7c361592dc2b20875f4c2b78e55e7279e47d0d381e9f973185da7cf7a1529c617c82b0789dea4183 SHA512 5a52dc6667b501ef5ee33f8c30a516a466b39b061ae3bee93f3e6a9cc9dd21503365671d93858165290b3200c859772324fdb12f8bdab235b3ff08c158c4dd66 +DIST MaSuRCA-4.1.0.tar.gz 26532049 BLAKE2B 93cf8cc2bcb4d2c56961f66c0e045ad7776011b4a5f78e5944c5e9b74004c553fc38e542a163aa2efca0aff0e2726fc38eea1aba8f2da287c5154c9eae4e9bcf SHA512 6de57abff87de2fd8c30bcc7efbd6c37358d37eab518d36ccbe48f036af6e1bc22a655abb59f32df613d99c84a5deca272c8c894395f255bcbceb4da5368e64a diff --git a/sci-biology/MaSuRCA/metadata.xml b/sci-biology/MaSuRCA/metadata.xml index 138cb7705..8a631d677 100644 --- a/sci-biology/MaSuRCA/metadata.xml +++ b/sci-biology/MaSuRCA/metadata.xml @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">alekseyzimin/masurca</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/MeV/metadata.xml b/sci-biology/MeV/metadata.xml index bd7adb92f..334d55097 100644 --- a/sci-biology/MeV/metadata.xml +++ b/sci-biology/MeV/metadata.xml @@ -9,6 +9,6 @@ <name>Gentoo Biology Project</name> </maintainer> <upstream> - <remote-id type="sourceforge">downloads</remote-id> + <remote-id type="sourceforge">mev-tm4</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/RAILS/metadata.xml b/sci-biology/RAILS/metadata.xml index 138cb7705..a3f152e56 100644 --- a/sci-biology/RAILS/metadata.xml +++ b/sci-biology/RAILS/metadata.xml @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">bcgsc/RAILS</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/RSeQC/Manifest b/sci-biology/RSeQC/Manifest deleted file mode 100644 index 5319e5fa5..000000000 --- a/sci-biology/RSeQC/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST RSeQC-4.0.0.tar.gz 101873 BLAKE2B 0a63ef39d3aa27e8ad419ad4d4e335563d870600d03e131fd02e4d4fd8fb403007f8b3a7ec0d57e8731ac616c6a4e07f3d6664668ea0e79aef911c1e54088afb SHA512 77ec4ad2c0f460b8bafe00dcfac6b1d9ddf65f933a55892c376eb7009f5820531dd167acc675b07186e81daa2a904914643dfcb7c220ef7b290d0c8ad3833c42 -DIST fetchChromSizes 2695 BLAKE2B a41f8e0085121f097c0fe93922b221b276f00a5d6af1da76f347ca121882e5d899d482900f51a0da4bff22b0b3158f0e274a67c60d7b7499c1bc3ead96beccd6 SHA512 23405beabb4f42b5cc5b569d9948d070e354ef2be10030b51ba3510865ab4e25bee8aab7283d9b6cbd7df454159a6f89e58ad8f5ee6a541046ad5a72f65019e8 diff --git a/sci-biology/RSeQC/RSeQC-4.0.0-r1.ebuild b/sci-biology/RSeQC/RSeQC-4.0.0-r1.ebuild deleted file mode 100644 index 9df8930e5..000000000 --- a/sci-biology/RSeQC/RSeQC-4.0.0-r1.ebuild +++ /dev/null @@ -1,34 +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="Utilities for RNA-seq data quality control" -HOMEPAGE="https://sourceforge.net/projects/rseqc/" -SRC_URI="https://sourceforge.net/projects/rseqc/files/RSeQC-${PV}.tar.gz - https://sourceforge.net/projects/rseqc/files/other/fetchChromSizes" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="~amd64" - -BDEPEND=" - dev-python/cython[${PYTHON_USEDEP}] - dev-python/nose[${PYTHON_USEDEP}] -" -RDEPEND=" - >=sci-biology/pysam-0.7.5[${PYTHON_USEDEP}] - sci-biology/bx-python[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/pyBigWig[${PYTHON_USEDEP}] -" - -python_prepare_all() { - distutils-r1_python_prepare_all - # avoid file collision with bx-python - rm lib/psyco_full.py || die -} diff --git a/sci-biology/RSeQC/metadata.xml b/sci-biology/RSeQC/metadata.xml deleted file mode 100644 index 5c8442330..000000000 --- a/sci-biology/RSeQC/metadata.xml +++ /dev/null @@ -1,15 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">rseqc</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/SPAdes/Manifest b/sci-biology/SPAdes/Manifest index 57f4fc569..cf724a82a 100644 --- a/sci-biology/SPAdes/Manifest +++ b/sci-biology/SPAdes/Manifest @@ -1,4 +1,4 @@ -DIST SPAdes-3.15.3.tar.gz 13687286 BLAKE2B d1c2204889ecd4e95306f10ca1bc4c1243369737822ba882ed141aa203005ce5240698b421e6f9c867684567abe971afb7562b837ad5464cfd91ce572d5e7af4 SHA512 e1b454c03f1edc857b552ebca9b5f4cd842d8e23caebdf11bb0cd05cb16a45e45421a03c67a5ecb04ea6dba0f30ec2652f0bf07afded39e823563518dc8080f4 -DIST SPAdes-3.15.3_manual.html 80507 BLAKE2B 14510ed5ff2ee1b7a6643f7e39761479180a022c6bae7b1bfac7a07fdf8d5f7889e619fc8bbd6c8354aa7b775241a34b0ab14aa6bf92c0b5af2d0e1588d5c4a7 SHA512 73538e487da7056b42715ec46dacd41e8abef0e268d3a4fe2997b49d208db402367913f3a86acd9643c8ff6a9cadd6d1ff109a2bc511ffb63de059633fe3255b -DIST SPAdes-3.15.3_rnaspades_manual.html 8624 BLAKE2B b549a6cae6b02c98cae08fd5d8975210f3593c47f2b4757f19a9445a759e332229620885a6fa2f1dc0662096974548e3d0362079d12c47e6738c0261d755a2af SHA512 2d0b169efd8aa7064d59bed8ad406477c72150f23ae0438227903645071c8f66f26fe062f7dd44b584edf8ef7c709ad6c220237e68917ec23c63cfb3139666b8 -DIST SPAdes-3.15.3_truspades_manual.html 10821 BLAKE2B eb466697f774d3421053cf0fd290c82d9b2059cafd787f10c616c1363537c59960cb8ca41a8a02983ec199e0e1a27567c5850009ad6d2173df45e38f7d3120f7 SHA512 1f3bcdbe5397a23ee94820f6aaf3b85c48aca357276f58f66607140d25529c28b31298c5c8e681df3c61dabed478ac67abeb0975885aa9b7e365e14d6aac06fd +DIST SPAdes-3.15.5.tar.gz 13692466 BLAKE2B c4fe59e6b253c91a6e409cf3c2e5a8181f3c0e93892e3b87f603aa75a6d025d5f1466a87ada5c86d6602f74de9048639e9b057d2abfbe449265f9c1796c608d1 SHA512 98b17f1ab0019a45e6abaf1bc7128a5edb5102120d50a47ddfbd5e30fc7130c7895a096cef16ba8e40be71c8a1f0feff38da54f02f9d2e62bd39d2d91a54f9bd +DIST SPAdes-3.15.5_manual.html 91156 BLAKE2B e5776ec98e972f52eb630cb2048f8cd12318f0cfc020ce464bbe72e14f3716b72199d5ea34f219351d79b3fd0f4201c99f68ca487edde0d258d8794aea1f4675 SHA512 b21cc705a1f3a224dad882fce26e15dfd6d249c46627172189b285584a11d2846d0fa3c4b5aa01ca6436a494cec552122cffd4b79f6cc31446a03d610486dfaa +DIST SPAdes-3.15.5_rnaspades_manual.html 8624 BLAKE2B b549a6cae6b02c98cae08fd5d8975210f3593c47f2b4757f19a9445a759e332229620885a6fa2f1dc0662096974548e3d0362079d12c47e6738c0261d755a2af SHA512 2d0b169efd8aa7064d59bed8ad406477c72150f23ae0438227903645071c8f66f26fe062f7dd44b584edf8ef7c709ad6c220237e68917ec23c63cfb3139666b8 +DIST SPAdes-3.15.5_truspades_manual.html 10821 BLAKE2B eb466697f774d3421053cf0fd290c82d9b2059cafd787f10c616c1363537c59960cb8ca41a8a02983ec199e0e1a27567c5850009ad6d2173df45e38f7d3120f7 SHA512 1f3bcdbe5397a23ee94820f6aaf3b85c48aca357276f58f66607140d25529c28b31298c5c8e681df3c61dabed478ac67abeb0975885aa9b7e365e14d6aac06fd diff --git a/sci-biology/SPAdes/SPAdes-3.15.3.ebuild b/sci-biology/SPAdes/SPAdes-3.15.3.ebuild deleted file mode 100644 index 553c21e21..000000000 --- a/sci-biology/SPAdes/SPAdes-3.15.3.ebuild +++ /dev/null @@ -1,36 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{8..10} ) -inherit python-single-r1 - -DESCRIPTION="De novo de Bruijn genome assembler overcoming uneven coverage" -HOMEPAGE="https://cab.spbu.ru/software/spades" -SRC_URI=" - https://github.com/ablab/spades/releases/download/v${PV}/${P}.tar.gz - https://cab.spbu.ru/files/release${PV}/manual.html -> ${P}_manual.html - https://cab.spbu.ru/files/release${PV}/rnaspades_manual.html -> ${P}_rnaspades_manual.html - https://cab.spbu.ru/files/release${PV}/truspades_manual.html -> ${P}_truspades_manual.html -" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64" -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -DEPEND=" - sys-libs/zlib - app-arch/bzip2 - dev-python/regex - ${PYTHON_DEPS} -" -RDEPEND="${DEPEND}" -BDEPEND="dev-util/cmake" - -src_install(){ - einstalldocs - # WORKAROUND: This script does both compile and install in one go - PREFIX="${ED}"/usr ./spades_compile.sh || die -} diff --git a/sci-biology/SPAdes/SPAdes-3.15.5.ebuild b/sci-biology/SPAdes/SPAdes-3.15.5.ebuild new file mode 100644 index 000000000..026dd0476 --- /dev/null +++ b/sci-biology/SPAdes/SPAdes-3.15.5.ebuild @@ -0,0 +1,42 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..12} ) +inherit python-single-r1 + +DESCRIPTION="De novo de Bruijn genome assembler overcoming uneven coverage" +HOMEPAGE="https://cab.spbu.ru/software/spades" +SRC_URI=" + https://github.com/ablab/spades/releases/download/v${PV}/${P}.tar.gz + https://cab.spbu.ru/files/release${PV}/manual.html -> ${P}_manual.html + https://cab.spbu.ru/files/release${PV}/rnaspades_manual.html -> ${P}_rnaspades_manual.html + https://cab.spbu.ru/files/release${PV}/truspades_manual.html -> ${P}_truspades_manual.html +" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64" +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +DEPEND=" + sys-libs/zlib + app-arch/bzip2 + dev-python/regex + ${PYTHON_DEPS} +" +RDEPEND="${DEPEND}" +BDEPEND="dev-build/cmake" + +# Remove for next release: +# https://github.com/ablab/spades/issues/1238#issuecomment-1904427831 +PATCHES=( + "${FILESDIR}/${P}-gcc13.patch" +) + +src_install(){ + einstalldocs + # WORKAROUND: This script does both compile and install in one go + PREFIX="${ED}"/usr ./spades_compile.sh || die +} diff --git a/sci-biology/SPAdes/files/SPAdes-3.15.5-gcc13.patch b/sci-biology/SPAdes/files/SPAdes-3.15.5-gcc13.patch new file mode 100644 index 000000000..3dd3f8c02 --- /dev/null +++ b/sci-biology/SPAdes/files/SPAdes-3.15.5-gcc13.patch @@ -0,0 +1,49 @@ +From 3e802fa51d156fc958c36e25d607f20bf756f0bf Mon Sep 17 00:00:00 2001 +From: Bo YU <tsu.yubo@gmail.com> +Date: Wed, 19 Jul 2023 18:42:04 +0800 +Subject: [PATCH] fix build issues due to gcc-13 + +Signed-off-by: Bo YU <tsu.yubo@gmail.com> +--- + ext/include/llvm/Support/Signals.h | 1 + + src/common/pipeline/library_data.hpp | 1 + + src/common/sequence/nucl.hpp | 2 ++ + 3 files changed, 4 insertions(+) + +diff --git a/assembler/ext/include/llvm/Support/Signals.h b/assembler/ext/include/llvm/Support/Signals.h +index e0a18e72f..148216b8f 100644 +--- a/ext/include/llvm/Support/Signals.h ++++ b/ext/include/llvm/Support/Signals.h +@@ -14,6 +14,7 @@ + #ifndef LLVM_SUPPORT_SIGNALS_H + #define LLVM_SUPPORT_SIGNALS_H + ++#include <cstdint> + #include <string> + + namespace llvm { +diff --git a/assembler/src/common/pipeline/library_data.hpp b/assembler/src/common/pipeline/library_data.hpp +index 3cbaf0adb..1ffaa7b37 100644 +--- a/src/common/pipeline/library_data.hpp ++++ b/src/common/pipeline/library_data.hpp +@@ -8,6 +8,7 @@ + + #include <map> + #include <string> ++#include <cstdint> + + // Forward decls for LLVM YAML API + namespace llvm { namespace yaml { class IO; template<typename T> struct MappingTraits; } } +diff --git a/assembler/src/common/sequence/nucl.hpp b/assembler/src/common/sequence/nucl.hpp +index 9c7d6de13..e10e7f583 100755 +--- a/src/common/sequence/nucl.hpp ++++ b/src/common/sequence/nucl.hpp +@@ -8,6 +8,8 @@ + #ifndef NUCL_HPP_ + #define NUCL_HPP_ + ++#include <cstdint> ++ + #include "utils/verify.hpp" + + /** diff --git a/sci-biology/SPAdes/metadata.xml b/sci-biology/SPAdes/metadata.xml index 0845ad7a4..5f573393e 100644 --- a/sci-biology/SPAdes/metadata.xml +++ b/sci-biology/SPAdes/metadata.xml @@ -10,8 +10,11 @@ <name>Gentoo Biology Project</name> </maintainer> <longdescription> -truSPAdes includes support for Illumina TruSeq Synthetic Long Read technology reads. -hammer and ionhammer are read error correcting modules for Illumina /IonTorrent reads, resp. -dipspades is assembly module for highly polymorphic diploid genomes -</longdescription> + truSPAdes includes support for Illumina TruSeq Synthetic Long Read technology reads. + hammer and ionhammer are read error correcting modules for Illumina /IonTorrent reads, resp. + dipspades is assembly module for highly polymorphic diploid genomes + </longdescription> + <upstream> + <remote-id type="github">ablab/spades</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/Trinotate/Manifest b/sci-biology/Trinotate/Manifest deleted file mode 100644 index cb1b89168..000000000 --- a/sci-biology/Trinotate/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST Trinotate-3.2.2.tar.gz 12902856 BLAKE2B 741b5b7386c5de646a4a1f3aa4ffc7ed9c4891e64a977efc5cd482eb0cd9315fbddc1db35f20f6fbbf136e28942542f72d33c078524971968a932f5af5d6551b SHA512 9e302eee948974c647fdcc6a352b17d55f3bd1331f6d3ddc49e0fc35f5603dcc370e9c6020e7b33dcd57324a954eab2ed3e81f2e34ef83af2fd97c793f1dfc48 diff --git a/sci-biology/Trinotate/Trinotate-3.2.2.ebuild b/sci-biology/Trinotate/Trinotate-3.2.2.ebuild deleted file mode 100644 index 794de03ae..000000000 --- a/sci-biology/Trinotate/Trinotate-3.2.2.ebuild +++ /dev/null @@ -1,43 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -inherit perl-module - -DESCRIPTION="Annotation and analysis pipeline for de novo assembled transcriptomes" -HOMEPAGE="https://github.com/Trinotate/Trinotate.github.io/wiki" -SRC_URI="https://github.com/Trinotate/Trinotate/archive/${PN}-v${PV}.tar.gz -> ${P}.tar.gz" -S="${WORKDIR}/${PN}-${PN}-v${PV}" - -LICENSE="BSD-BroadInstitute" -SLOT="0" -KEYWORDS="~amd64" - -DEPEND="" -RDEPEND="${DEPEND} - sci-biology/ncbi-tools++ - sci-biology/trinityrnaseq - sci-biology/TransDecoder -" - -# http://www.cbs.dtu.dk/cgi-bin/sw_request?rnammer -# >=sci-biology/rnammer-2.3.2 -# -# http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?signalp -# >=sci-biology/signalp-4 -# -# http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?tmhmm - -# We suggest you rename this version of hmmsearch from hmmer-2 package to 'hmmsearch2'. -# In the 'rnammer' software configuration, edit the rnammer script to point -# $HMMSEARCH_BINARY = "/path/to/hmmsearch2"; - -src_install(){ - perl_set_version - dobin Trinotate - insinto /usr/share/"${PN}" - doins -r admin sample_data util TrinotateWeb - perl_domodule -r PerlLib/* - dodoc notes README.md README.txt Changelog.txt -} diff --git a/sci-biology/Trinotate/metadata.xml b/sci-biology/Trinotate/metadata.xml deleted file mode 100644 index eaf731f09..000000000 --- a/sci-biology/Trinotate/metadata.xml +++ /dev/null @@ -1,15 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="github">Trinotate/Trinotate</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/VarScan/VarScan-2.4.4.ebuild b/sci-biology/VarScan/VarScan-2.4.4.ebuild index 72a3c94df..039a68f06 100644 --- a/sci-biology/VarScan/VarScan-2.4.4.ebuild +++ b/sci-biology/VarScan/VarScan-2.4.4.ebuild @@ -18,9 +18,11 @@ KEYWORDS="~amd64" DEPEND=" >=virtual/jdk-1.5:* - !sci-biology/VarScan-bin" +" RDEPEND=">=virtual/jre-1.5:* - sci-biology/bam-readcount" + sci-biology/bam-readcount + !sci-biology/VarScan-bin +" S="${WORKDIR}"/net/sf/varscan diff --git a/sci-biology/VelvetOptimiser/metadata.xml b/sci-biology/VelvetOptimiser/metadata.xml index 138cb7705..cc34f33b5 100644 --- a/sci-biology/VelvetOptimiser/metadata.xml +++ b/sci-biology/VelvetOptimiser/metadata.xml @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">tseemann/VelvetOptimiser</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/abacas/abacas-1.3.1.ebuild b/sci-biology/abacas/abacas-1.3.1.ebuild index 9abddf036..c347b508b 100644 --- a/sci-biology/abacas/abacas-1.3.1.ebuild +++ b/sci-biology/abacas/abacas-1.3.1.ebuild @@ -6,8 +6,8 @@ EAPI=7 inherit optfeature DESCRIPTION="Order and orientate DNA contigs even via 6-frame protein alignments" -HOMEPAGE="http://abacas.sourceforge.net" -SRC_URI="https://downloads.sourceforge.net/project/abacas/abacas.1.3.1.pl" +HOMEPAGE="https://abacas.sourceforge.net" +SRC_URI="https://downloads.sourceforge.net/project/abacas/abacas.${PV}.pl" LICENSE="GPL-2+" SLOT="0" @@ -21,7 +21,7 @@ RDEPEND="${DEPEND} S="${WORKDIR}" src_prepare(){ - cp -p "${DISTDIR}"/abacas.1.3.1.pl abacas.pl || die + cp -p "${DISTDIR}"/abacas.${PV}.pl abacas.pl || die sed \ -i 's#/usr/local/bin/perl#/usr/bin/perl#' \ -i abacas.pl || die diff --git a/sci-biology/abacas/metadata.xml b/sci-biology/abacas/metadata.xml index 0f267b755..0bb7ca029 100644 --- a/sci-biology/abacas/metadata.xml +++ b/sci-biology/abacas/metadata.xml @@ -10,6 +10,6 @@ <name>Gentoo Biology Project</name> </maintainer> <upstream> - <remote-id type="sourceforge">downloads</remote-id> + <remote-id type="sourceforge">abacas</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/afni/Manifest b/sci-biology/afni/Manifest index e8caa43d1..d1e783ff1 100644 --- a/sci-biology/afni/Manifest +++ b/sci-biology/afni/Manifest @@ -1,3 +1,4 @@ -DIST afni-20.1.16.tar.gz 43355499 BLAKE2B ad7750e64dd9f4c2ca7e5c67bd99faeb8595a41d8a16192e77202f3d307e912083affc11dcbb5da3530079b9e3cf3c2b6b470050f57d5d7af2bb35cc2322772f SHA512 e6fdb8baea6165865bae5bb186375bd65e862564c48470523a8fe026a12f00715fd21bd852bd77c4077ea444a97642c4c3d2ca8060640ba5ddd57bd7883901a6 -DIST afni-20.3.03.tar.gz 43263734 BLAKE2B 7fdaf3de874edff9b32950a2724ba8b4cbcdda538b09effb12658a042326d5c8badf48f1a4dfb4555eb069347099cf3cdb08c4fe1a12999e6eca3ca6f8dca639 SHA512 3c5007f59d6c46093d38f9419c72aa36fb5701314690811f757d9568561b386cf3cd602ddf910ae08fd071ea7ae1e51f5762081217f7a29b23e32f1490f5db65 -DIST afni-22.0.21.tar.gz 43934548 BLAKE2B 3efd5b7fcbbb7b98000e8de51c363ec936a691fcbd505871ff406824ba6ecd5fef358102f6dd2e4d0991b0a40589db6416c1ef14966138c5c36499d7efa3b089 SHA512 1c741e36227075bd8b4f9983510eef95528084cbc4971f9d6d028726ffc2bb211da7a74df98991538d8f6caed041633fdceb0c4366e04d6594faa0160a0e6d2b +DIST afni-24.0.04.gh.tar.gz 52888143 BLAKE2B db414b9ac9489aaab824e6f99cae54a1982e600d3b6d93a01cf3f175220ab76923a53ce6da647e4d8be87d3b50699c1b9603f8f0de43d812d34ceb1a65bde19d SHA512 aff673b63453a18c1f687775a6316614ee7495ff583e86c341aa0eed40d5f99b15cb599dea79baf05f8f8b77fea292436e3adc51b906dc13589968a8bdffa3d8 +DIST afni-24.0.08.gh.tar.gz 52917832 BLAKE2B 4cf61f3474c2c69d8373fbf9413c2236fbda77408535b142e6860effbf49ebcc6007ef9fb18943c07299b4815be6692477cc79423d7ac5a09bfe3d125565058c SHA512 90a9c8a48e1084dcc19d90e62b313057f0e71e87740f6ac63a305d19a4ded8ee01722b55546d2aaa2d4dfbfd0a206d4a9d25969592646c101cabe4743b8962c6 +DIST gifti-d3e873d8539d9b469daf7db04093da1d7e73d4f7.tar.gz 107745 BLAKE2B b8162fe08446d5c934762e8dce051e93c8c90fd574dca55757988ccc45be20bfdd07b7a401ef6c536afbe097e6bc05fd3b7f09c4404af4fad4e21fbada7109de SHA512 c458074c6976245cffc48c1e1e57811ec3c0cc5959345bdbc8d674eed6c8a8f93e9f9762bf3acce7142e004dc37930d14bed8cfb97c5b7e92b3f39598da924e2 +DIST nifti-da476fd27f46098f37f5c9c4c1baee01e559572c.tar.gz 451578 BLAKE2B 6bb92ae3ab48dba435b067f7ec0b6d417658ee1a46efe05070bf18fd6d46b8339eaffd09c2fea4971d2685f211496a700b36c255ffb164994636e535b64fe4f5 SHA512 df92345ed580e8bf0579f2ea3ed55a4c4c678a0fe3bfad1e62379e5bf16961272bb2d3e7fda89b96b503cda51c1bf2fb8eb74adba6aad9c73b6830d7d884d1f5 diff --git a/sci-biology/afni/afni-20.1.16.ebuild b/sci-biology/afni/afni-20.1.16.ebuild deleted file mode 100644 index e3e16f834..000000000 --- a/sci-biology/afni/afni-20.1.16.ebuild +++ /dev/null @@ -1,73 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -inherit toolchain-funcs - -DESCRIPTION="An open-source environment for processing and displaying functional MRI data" -HOMEPAGE="http://afni.nimh.nih.gov/" -SRC_URI="https://github.com/afni/afni/archive/AFNI_${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="GPL-3+" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -RDEPEND="dev-libs/expat - media-libs/glu - media-libs/netpbm - media-libs/qhull - media-video/mpeg-tools - sci-libs/gsl - sys-devel/llvm:* - media-libs/libjpeg-turbo:0 - x11-libs/libGLw - x11-libs/libXft - x11-libs/libXi - x11-libs/libXpm - x11-libs/motif[-static-libs]" - -# x11-libs/motif[static-libs] breaks the build. -# See upstream discussion -# http://afni.nimh.nih.gov/afni/community/board/read.php?1,85348,85348#msg-85348 - -DEPEND="${RDEPEND} - app-shells/tcsh" - -S="${WORKDIR}/${PN}-AFNI_${PV}/src" -BUILD="linux_fedora_19_64" -BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count mpeg_encode) - -src_prepare() { - eapply "${FILESDIR}/${P}-python.patch" || die - find -type f -exec sed -i -e "s/-lXp //g" {} + - cp other_builds/Makefile.${BUILD} Makefile || die "Could not copy Makefile" - # Unbundle imcat - sed -e "s/ imcat / /g" \ - -i Makefile.INCLUDE || die "Could not edit includes files." - sed -e "s~CC = /usr/bin/gcc -O2 -m64~CC = $(tc-getCC) \$(CFLAGS)~" \ - -e "s~CCMIN = /usr/bin/gcc -m64~CCMIN = $(tc-getCC) \$(CFLAGS)~" \ - -e "s~LD = /usr/bin/gcc~LD = $(tc-getCC)~" \ - -e "s~AR = /usr/bin/ar~AR = $(tc-getAR)~" \ - -e "s~RANLIB = /usr/bin/ranlib~RANLIB = $(tc-getRANLIB)~" \ - -i Makefile || die "Could not edit Makefile" - # they provide somewhat problematic makefiles :( - sed -e "s~ifeq ($(CC),gcc)~ifeq (1,1)~"\ - -i SUMA/SUMA_Makefile || die "Could not edit SUMA/SUMA_Makefile" - # upstream checks if $CC is EXACTLY gcc, else sets variables for Mac - find "${S}" -iname "*Makefile*" | xargs sed -e "s~/usr/~${EPREFIX}/usr/~g;" -i - default -} - -src_compile() { - emake -j1 all plugins suma_exec -} - -src_install() { - emake INSTALLDIR="${ED}/usr/bin" -j1 install install_plugins - emake INSTALLDIR="${ED}/usr/$(get_libdir)" install_lib - for CONFLICT in ${BIN_CONFLICTS[@]}; do - rm "${ED}/usr/bin/${CONFLICT}" - done -} diff --git a/sci-biology/afni/afni-20.3.03.ebuild b/sci-biology/afni/afni-20.3.03.ebuild deleted file mode 100644 index 1d9043ebb..000000000 --- a/sci-biology/afni/afni-20.3.03.ebuild +++ /dev/null @@ -1,73 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -inherit toolchain-funcs - -DESCRIPTION="An open-source environment for processing and displaying functional MRI data" -HOMEPAGE="http://afni.nimh.nih.gov/" -SRC_URI="https://github.com/afni/afni/archive/AFNI_${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="GPL-3+" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -RDEPEND="dev-libs/expat - media-libs/glu - media-libs/netpbm - media-libs/qhull - media-video/mpeg-tools - sci-libs/gsl - sys-devel/llvm:* - media-libs/libjpeg-turbo:0 - x11-libs/libGLw - x11-libs/libXft - x11-libs/libXi - x11-libs/libXpm - x11-libs/motif[-static-libs]" - -# x11-libs/motif[static-libs] breaks the build. -# See upstream discussion -# http://afni.nimh.nih.gov/afni/community/board/read.php?1,85348,85348#msg-85348 - -DEPEND="${RDEPEND} - app-shells/tcsh" - -S="${WORKDIR}/${PN}-AFNI_${PV}/src" -BUILD="linux_fedora_19_64" -BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count mpeg_encode) - -src_prepare() { - eapply "${FILESDIR}/${PN}-20.1.16-python.patch" || die - find -type f -exec sed -i -e "s/-lXp //g" {} + - cp other_builds/Makefile.${BUILD} Makefile || die "Could not copy Makefile" - # Unbundle imcat - sed -e "s/ imcat / /g" \ - -i Makefile.INCLUDE || die "Could not edit includes files." - sed -e "s~CC = /usr/bin/gcc -O2 -m64~CC = $(tc-getCC) \$(CFLAGS)~" \ - -e "s~CCMIN = /usr/bin/gcc -m64~CCMIN = $(tc-getCC) \$(CFLAGS)~" \ - -e "s~LD = /usr/bin/gcc~LD = $(tc-getCC)~" \ - -e "s~AR = /usr/bin/ar~AR = $(tc-getAR)~" \ - -e "s~RANLIB = /usr/bin/ranlib~RANLIB = $(tc-getRANLIB)~" \ - -i Makefile || die "Could not edit Makefile" - # they provide somewhat problematic makefiles :( - sed -e "s~ifeq ($(CC),gcc)~ifeq (1,1)~"\ - -i SUMA/SUMA_Makefile || die "Could not edit SUMA/SUMA_Makefile" - # upstream checks if $CC is EXACTLY gcc, else sets variables for Mac - find "${S}" -iname "*Makefile*" | xargs sed -e "s~/usr/~${EPREFIX}/usr/~g;" -i - default -} - -src_compile() { - emake -j1 all plugins suma_exec -} - -src_install() { - emake INSTALLDIR="${ED}/usr/bin" -j1 install install_plugins - emake INSTALLDIR="${ED}/usr/$(get_libdir)" install_lib - for CONFLICT in ${BIN_CONFLICTS[@]}; do - rm "${ED}/usr/bin/${CONFLICT}" - done -} diff --git a/sci-biology/afni/afni-22.0.21.ebuild b/sci-biology/afni/afni-22.0.21.ebuild deleted file mode 100644 index 149deede8..000000000 --- a/sci-biology/afni/afni-22.0.21.ebuild +++ /dev/null @@ -1,75 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -inherit toolchain-funcs - -DESCRIPTION="An open-source environment for processing and displaying functional MRI data" -HOMEPAGE="http://afni.nimh.nih.gov/" -SRC_URI="https://github.com/afni/afni/archive/AFNI_${PV}.tar.gz -> ${P}.tar.gz" -S="${WORKDIR}/${PN}-AFNI_${PV}/src" - -LICENSE="GPL-3+" -SLOT="0" -# SUMA error: https://ppb.chymera.eu/4223de.log -KEYWORDS="" - -RDEPEND=" - dev-libs/libf2c - dev-libs/expat - media-libs/freeglut - media-libs/glu - media-libs/netpbm - media-libs/qhull - media-video/mpeg-tools - sci-libs/gsl - sys-devel/llvm:* - media-libs/libjpeg-turbo:0 - x11-libs/libGLw - x11-libs/libXft - x11-libs/libXi - x11-libs/libXpm - x11-libs/motif -" - -DEPEND="${RDEPEND} - app-shells/tcsh -" - -BUILD="linux_fedora_19_64" -BIN_CONFLICTS=(qdelaunay whirlgif djpeg cjpeg qhull rbox count) - -src_prepare() { - # more easily applied here than via PATCHES at phase end. - eapply "${FILESDIR}/${PN}-20.1.16-python.patch" || die - find -type f -exec sed -i -e "s/-lXp //g" {} + || die - cp other_builds/Makefile.${BUILD} Makefile || die "Could not copy Makefile" - # Unbundle imcat - sed -e "s/ imcat / /g" \ - -i Makefile.INCLUDE || die "Could not edit includes files." - sed -e "s~CC = /usr/bin/gcc -O2 -m64~CC = $(tc-getCC) \$(CFLAGS)~" \ - -e "s~CCMIN = /usr/bin/gcc -m64~CCMIN = $(tc-getCC) \$(CFLAGS)~" \ - -e "s~LD = /usr/bin/gcc~LD = $(tc-getCC)~" \ - -e "s~AR = /usr/bin/ar~AR = $(tc-getAR)~" \ - -e "s~RANLIB = /usr/bin/ranlib~RANLIB = $(tc-getRANLIB)~" \ - -i Makefile || die "Could not edit Makefile" - # they provide somewhat problematic makefiles :( - sed -e "s~ifeq (\$(CC),gcc)~ifeq (1,1)~"\ - -i SUMA/SUMA_Makefile || die "Could not edit SUMA/SUMA_Makefile" - # upstream checks if $CC is EXACTLY gcc, else sets variables for Mac - find "${S}" -iname "*Makefile*" | xargs sed -e "s~/usr/~${EPREFIX}/usr/~g;" -i || die - default -} - -src_compile() { - emake -j1 all plugins suma_exec -} - -src_install() { - emake INSTALLDIR="${ED}/usr/bin" install install_plugins - emake INSTALLDIR="${ED}/usr/$(get_libdir)" install_lib - for CONFLICT in ${BIN_CONFLICTS[@]}; do - rm "${ED}/usr/bin/${CONFLICT}" || die - done -} diff --git a/sci-biology/afni/afni-24.0.04-r1.ebuild b/sci-biology/afni/afni-24.0.04-r1.ebuild new file mode 100644 index 000000000..557fbd579 --- /dev/null +++ b/sci-biology/afni/afni-24.0.04-r1.ebuild @@ -0,0 +1,110 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..12} ) + +DISTUTILS_USE_PEP517=setuptools +inherit cmake distutils-r1 toolchain-funcs + +GTS_HASH="962155a01f5a1b87bd64e3e3d880b4dbc2347ac7" +NIFTI_HASH="da476fd27f46098f37f5c9c4c1baee01e559572c" +GIFTI_HASH="d3e873d8539d9b469daf7db04093da1d7e73d4f7" + +DESCRIPTION="Advanced Normalitazion Tools for neuroimaging" +HOMEPAGE="http://stnava.github.io/ANTs/" +SRC_URI=" + https://github.com/afni/afni/archive/refs/tags/AFNI_${PV}.tar.gz -> ${P}.gh.tar.gz + https://github.com/NIFTI-Imaging/nifti_clib/archive/${NIFTI_HASH}.tar.gz -> nifti-${NIFTI_HASH}.tar.gz + https://github.com/NIFTI-Imaging/gifti_clib/archive/${GIFTI_HASH}.tar.gz -> gifti-${GIFTI_HASH}.tar.gz + " + +SLOT="0" +LICENSE="GPL-3+" +KEYWORDS="~amd64 ~x86" +IUSE="test whirlgif" +RESTRICT="!test? ( test )" + +RDEPEND=" + dev-libs/glib:2 + dev-libs/libf2c + dev-libs/expat + dev-build/ninja + media-libs/freeglut + media-libs/glu + media-libs/netpbm + media-libs/qhull + media-video/mpeg-tools + sci-libs/gsl + sci-libs/gts + sys-devel/llvm:* + sys-libs/libomp + virtual/jpeg-compat:62 + x11-libs/libGLw + x11-libs/libXft + x11-libs/libXi + x11-libs/libXmu + x11-libs/libXpm + x11-libs/libXt + x11-libs/motif[-static-libs] + " +DEPEND=" + ${RDEPEND} + app-shells/tcsh + " + +S="${WORKDIR}/afni-AFNI_${PV}" + +src_prepare() { + tar xf "${DISTDIR}/nifti-${NIFTI_HASH}.tar.gz" || die + tar xf "${DISTDIR}/gifti-${GIFTI_HASH}.tar.gz" || die + cmake_src_prepare + default + } + +src_configure() { + if use !whirlgif; then + eapply "${FILESDIR}/${P}-whirlgif.patch" + fi + export CFLAGS="-pthread ${CFLAGS}" + export GIT_REPO_VERSION=3.0.1.1 + local mycmakeargs=( + -DLIBDIR=/usr/$(get_libdir) + -DNIFTI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir) + -DGIFTI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir) + -DGIFTI_INSTALL_LIB_DIR=/usr/$(get_libdir) + -DAFNI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir) + -DCMAKE_INSTALL_LIBDIR=/usr/$(get_libdir) + -DCOMP_COREBINARIES=ON + -DUSE_SYSTEM_NIFTI=OFF + -DUSE_SYSTEM_GIFTI=OFF + -DUSE_SYSTEM_XMHTML=OFF + -DUSE_SYSTEM_GTS=ON + -DFETCHCONTENT_SOURCE_DIR_NIFTI_CLIB="${WORKDIR}/nifti_clib-${NIFTI_HASH}" + -DFETCHCONTENT_SOURCE_DIR_GIFTI_CLIB="${WORKDIR}/gifti_clib-${GIFTI_HASH}" + -DCOMP_GUI=ON + -DCOMP_PLUGINS=ON + -DUSE_OMP=ON + -DCOMP_PYTHON=OFF + -DUSE_SYSTEM_F2C=ON + ) + tc-export CC + cmake_src_configure +} + +src_compile() { + cmake_src_compile + pushd src/python_scripts + distutils-r1_src_compile + popd +} + +src_install() { + cmake_src_install + pushd src/python_scripts + distutils-r1_src_install + popd + cd "${D}" + rm usr/bin/mpeg_encode +} diff --git a/sci-biology/afni/afni-24.0.08-r1.ebuild b/sci-biology/afni/afni-24.0.08-r1.ebuild new file mode 100644 index 000000000..20293877f --- /dev/null +++ b/sci-biology/afni/afni-24.0.08-r1.ebuild @@ -0,0 +1,114 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..12} ) + +DISTUTILS_USE_PEP517=setuptools +inherit cmake distutils-r1 toolchain-funcs + +GTS_HASH="962155a01f5a1b87bd64e3e3d880b4dbc2347ac7" +NIFTI_HASH="da476fd27f46098f37f5c9c4c1baee01e559572c" +GIFTI_HASH="d3e873d8539d9b469daf7db04093da1d7e73d4f7" + +DESCRIPTION="Advanced Normalitazion Tools for neuroimaging" +HOMEPAGE="http://stnava.github.io/ANTs/" +SRC_URI=" + https://github.com/afni/afni/archive/refs/tags/AFNI_${PV}.tar.gz -> ${P}.gh.tar.gz + https://github.com/NIFTI-Imaging/nifti_clib/archive/${NIFTI_HASH}.tar.gz -> nifti-${NIFTI_HASH}.tar.gz + https://github.com/NIFTI-Imaging/gifti_clib/archive/${GIFTI_HASH}.tar.gz -> gifti-${GIFTI_HASH}.tar.gz + " + +SLOT="0" +LICENSE="GPL-3+" +KEYWORDS="~amd64 ~x86" +IUSE="test whirlgif" +RESTRICT="!test? ( test )" + +RDEPEND=" + dev-libs/glib:2 + dev-libs/libf2c + dev-libs/expat + dev-build/ninja + media-libs/freeglut + media-libs/glu + media-libs/netpbm + media-libs/qhull + media-video/mpeg-tools + sci-libs/gsl + sci-libs/gts + sys-devel/llvm:* + sys-libs/libomp + virtual/jpeg-compat:62 + x11-libs/libGLw + x11-libs/libXft + x11-libs/libXi + x11-libs/libXmu + x11-libs/libXpm + x11-libs/libXt + x11-libs/motif[-static-libs] + " +DEPEND=" + ${RDEPEND} + app-shells/tcsh + " +# Prospectively: +#Update jpeg-compat to virtual/jpeg:0 +# look for xmhtlm + +S="${WORKDIR}/afni-AFNI_${PV}" + + #tar xf "${DISTDIR}/${GTS_HASH}.tar.gz" || die +src_prepare() { + tar xf "${DISTDIR}/nifti-${NIFTI_HASH}.tar.gz" || die + tar xf "${DISTDIR}/gifti-${GIFTI_HASH}.tar.gz" || die + cmake_src_prepare + default + } + +src_configure() { + if use !whirlgif; then + eapply "${FILESDIR}/${PN}-24.0.04-whirlgif.patch" + fi + export CFLAGS="-pthread ${CFLAGS}" + export GIT_REPO_VERSION=3.0.1.1 + local mycmakeargs=( + -DLIBDIR=/usr/$(get_libdir) + -DNIFTI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir) + -DGIFTI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir) + -DGIFTI_INSTALL_LIB_DIR=/usr/$(get_libdir) + -DAFNI_INSTALL_LIBRARY_DIR=/usr/$(get_libdir) + -DCMAKE_INSTALL_LIBDIR=/usr/$(get_libdir) + -DCOMP_COREBINARIES=ON + -DUSE_SYSTEM_NIFTI=OFF + -DUSE_SYSTEM_GIFTI=OFF + -DUSE_SYSTEM_XMHTML=OFF + -DUSE_SYSTEM_GTS=ON + -DFETCHCONTENT_SOURCE_DIR_NIFTI_CLIB="${WORKDIR}/nifti_clib-${NIFTI_HASH}" + -DFETCHCONTENT_SOURCE_DIR_GIFTI_CLIB="${WORKDIR}/gifti_clib-${GIFTI_HASH}" + -DCOMP_GUI=ON + -DCOMP_PLUGINS=ON + -DUSE_OMP=ON + -DCOMP_PYTHON=OFF + -DUSE_SYSTEM_F2C=ON + ) + tc-export CC + cmake_src_configure +} + +src_compile() { + cmake_src_compile + pushd src/python_scripts + distutils-r1_src_compile + popd +} + +src_install() { + cmake_src_install + pushd src/python_scripts + distutils-r1_src_install + popd + cd "${D}" + rm usr/bin/mpeg_encode +} diff --git a/sci-biology/afni/files/afni-20.1.16-python.patch b/sci-biology/afni/files/afni-20.1.16-python.patch deleted file mode 100644 index 8c3e859f5..000000000 --- a/sci-biology/afni/files/afni-20.1.16-python.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- a/other_builds/Makefile.linux_fedora_19_64 2020-10-09 07:07:58.348874414 -0400 -+++ b/other_builds/Makefile.linux_fedora_19_64 2020-10-10 01:15:22.337755934 -0400 -@@ -11,8 +11,6 @@ - - # ------------------------------ - # python from C --IPYTHON = -DSELENIUM_READY -I/usr/include/python2.7 --LDPYTHON = -lpython2.7 - - # ---------------------------------------------------------------------- - # X configuration diff --git a/sci-biology/afni/files/afni-24.0.04-whirlgif.patch b/sci-biology/afni/files/afni-24.0.04-whirlgif.patch new file mode 100644 index 000000000..a357799e6 --- /dev/null +++ b/sci-biology/afni/files/afni-24.0.04-whirlgif.patch @@ -0,0 +1,39 @@ +diff --git a/packaging/installation_components.txt b/packaging/installation_components.txt +index 127193338..ba8825a7b 100644 +--- a/packaging/installation_components.txt ++++ b/packaging/installation_components.txt +@@ -347,7 +347,6 @@ uniq_images, corebinaries + unu, corebinaries + waver, corebinaries + whereami, corebinaries +-whirlgif, corebinaries + 3dMax, tcsh + 3dPAR2AFNI.pl, tcsh + @1dDiffMag, tcsh +diff --git a/src/CMakeLists_binaries.txt b/src/CMakeLists_binaries.txt +index d53368390..8c8e9e1fb 100644 +--- a/src/CMakeLists_binaries.txt ++++ b/src/CMakeLists_binaries.txt +@@ -209,7 +209,6 @@ foreach( + uniq_images + unu + whereami +- whirlgif + ) + + add_afni_executable(${target} ${target}.c) +diff --git a/src/Makefile.INCLUDE b/src/Makefile.INCLUDE +index f44103def..7ac08a87d 100644 +--- a/src/Makefile.INCLUDE ++++ b/src/Makefile.INCLUDE +@@ -3495,11 +3495,6 @@ help_format:help_format.o + ibinom:ibinom.o + $(CC) -o ibinom ibinom.o $(LFLAGS) $(LLIBS) + +-## GIF animation +- +-whirlgif:whirlgif.h whirlgif.c +- $(CC) -o whirlgif whirlgif.c $(INFLAGS) $(LFLAGS) $(LLIBS) +- + extor.o:extor.c + $(CCFAST) -c extor.c $(INFLAGS) diff --git a/sci-biology/afni/metadata.xml b/sci-biology/afni/metadata.xml index acf637dca..39ec69d08 100644 --- a/sci-biology/afni/metadata.xml +++ b/sci-biology/afni/metadata.xml @@ -13,4 +13,10 @@ Analysis of Functional NeuroImages (AFNI) is an open-source environment for processing and displaying functional MRI data—a technique for mapping human brain activity. </longdescription> + <use> + <flag name="whirlgif">Build optional whirlgif binary</flag> + </use> + <upstream> + <remote-id type="github">afni/afni</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/angsd/metadata.xml b/sci-biology/angsd/metadata.xml index 138cb7705..ed9e5b12d 100644 --- a/sci-biology/angsd/metadata.xml +++ b/sci-biology/angsd/metadata.xml @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">ANGSD/angsd</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/ants/Manifest b/sci-biology/ants/Manifest index 867a142eb..ef2d97caf 100644 --- a/sci-biology/ants/Manifest +++ b/sci-biology/ants/Manifest @@ -1,2 +1,2 @@ -DIST ants-2.3.4.tar.gz 2455843 BLAKE2B c00a2d3edebc0a121fa3b6618982c64fd986db9ea6aed1a1b2c7ced2f77ab154837a47e5bcb01f432b937160de2248b30a2bb7b526952852946e686858334e12 SHA512 084161505671a19530bec40c8209a67510d7de6e9d5afd151b806755ca703dadbea17c0a8d5c6472c7a81185821e17213ebf1488bc0325bfe858af783e8e6575 -DIST ants_testdata-2.3.4.tar.xz 25056552 BLAKE2B 6478ffe0c98fd3700a6de201f1271339276b45b461b02d4753acdcd1335c83196aa2ed89a89b5b4b0b3df33026f77b231ba1418c9eb7a2380356d4e224f9b310 SHA512 a266fbf2de0003ee689a9369c424c97c92cdf7e4d08ba713623948276d96c9f0f02ab14480c329f462db0059217138680bfe39654f9ec4ac99bf947f51da853d +DIST ants-2.4.3.tar.gz 2474986 BLAKE2B 56a057673ff65e7ed3037ee34cea481e960122f32d2fd04b347644126793a2ba0a9249823b45e360abf2019136659b3ba4a24e49677458d69cc0b614266faca1 SHA512 50b42e30bec9077a00450253a39a8296ca841a3b3511f623a759071e6fbda9b6ab480b4f26566c621dc85107913f2782f2a1c4ecdeaa8361dc132209a432c544 +DIST ants_testdata-2.4.3.tar.xz 25058064 BLAKE2B ca3bb9998d7ded8fc9821a341a3a5b847a40fe93cccbc61458b5a6f9bab102a14fa297aad2425a5602b70c51e756edab2609213b01e06f7dc63eca2e67846351 SHA512 2689bdf1cb6bc4e608511efab574c8a0a5de839a376e9af91e277bae352744fa58463258ea604ea73041b7b596a3ab3a36e0f5a28c098ee5e7a1a9f8b8873779 diff --git a/sci-biology/ants/ants-2.3.4.ebuild b/sci-biology/ants/ants-2.3.4.ebuild deleted file mode 100644 index 95eb6355b..000000000 --- a/sci-biology/ants/ants-2.3.4.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 - -CMAKE_MAKEFILE_GENERATOR="emake" - -inherit cmake - -MY_PN="ANTs" - -DESCRIPTION="Advanced Normalitazion Tools for neuroimaging" -HOMEPAGE="http://stnava.github.io/ANTs/" -SRC_URI=" - https://github.com/ANTsX/ANTs/archive/v${PV}.tar.gz -> ${P}.tar.gz - test? ( - http://resources.chymera.eu/distfiles/ants_testdata-${PV}.tar.xz - ) -" - -SLOT="0" -LICENSE="BSD" -KEYWORDS="~amd64 ~x86" -IUSE="test vtk" -RESTRICT="!test? ( test )" - -DEPEND=" - vtk? ( - ~sci-libs/itk-5.1.0[vtkglue] - sci-libs/vtk - ) - !vtk? ( ~sci-libs/itk-5.1.0 ) -" -RDEPEND="${DEPEND}" - -PATCHES=( - "${FILESDIR}/${P}-version.patch" - "${FILESDIR}/${P}-libdir.patch" -) - -S="${WORKDIR}/${MY_PN}-${PV}" - -src_unpack() { - default - if use test; then - mkdir -p "${S}/.ExternalData/MD5" || die "Could not create test data directory." - tar xvf "${DISTDIR}/ants_testdata-${PV}.tar.xz" -C "${S}/.ExternalData/MD5/" > /dev/null || die "Could not unpack test data." - fi -} - -src_configure() { - local mycmakeargs=( - -DUSE_SYSTEM_ITK=ON - -DITK_DIR="${EPREFIX}/usr/include/ITK-5.1/" - -DBUILD_TESTING="$(usex test ON OFF)" - -DUSE_VTK=$(usex vtk ON OFF) - -DUSE_SYSTEM_VTK=$(usex vtk ON OFF) - -DANTS_SNAPSHOT_VERSION:STRING=${PV} - ) - use vtk && mycmakeargs+=( - -DVTK_DIR="${EPREFIX}/usr/include/vtk-8.1/" - ) - use test && mycmakeargs+=( - -DExternalData_OBJECT_STORES="${S}/.ExternalData/MD5" - ) - cmake_src_configure -} - -src_install() { - BUILD_DIR="${WORKDIR}/${P}_build/ANTS-build" - cmake_src_install - cd "${S}/Scripts" || die "scripts dir not found" - dobin *.sh - dodir /usr/$(get_libdir)/ants - insinto "/usr/$(get_libdir)/ants" - doins * - doenvd "${FILESDIR}"/99ants -} diff --git a/sci-biology/ants/ants-2.4.3.ebuild b/sci-biology/ants/ants-2.4.3.ebuild new file mode 100644 index 000000000..2dfa2a56d --- /dev/null +++ b/sci-biology/ants/ants-2.4.3.ebuild @@ -0,0 +1,69 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +CMAKE_MAKEFILE_GENERATOR="emake" +inherit cmake + +MY_PN="ANTs" + +DESCRIPTION="Advanced Normalitazion Tools for neuroimaging" +HOMEPAGE="https://stnava.github.io/ANTs/" +SRC_URI=" + https://github.com/ANTsX/ANTs/archive/v${PV}.tar.gz -> ${P}.tar.gz + test? ( + https://resources.chymera.eu/distfiles/ants_testdata-${PV}.tar.xz + ) +" +S="${WORKDIR}/${MY_PN}-${PV}" + +SLOT="0" +LICENSE="BSD" +KEYWORDS="~amd64 ~x86" +IUSE="test vtk" +RESTRICT="!test? ( test )" + +DEPEND=" + !vtk? ( =sci-libs/itk-5.3*[fftw,-vtkglue] ) + vtk? ( + =sci-libs/itk-5.3*[fftw,vtkglue] + =sci-libs/vtk-9.2* + ) +" +RDEPEND="${DEPEND}" + +src_unpack() { + default + if use test; then + mkdir -p "${S}/.ExternalData/SHA512" || die "Could not create test data directory." + tar xvf "${DISTDIR}/ants_testdata-${PV}.tar.xz" -C "${S}/.ExternalData/SHA512/" > /dev/null || die "Could not unpack test data." + fi +} + +src_configure() { + local mycmakeargs=( + -DBUILD_EXAMPLES=OFF + -DUSE_SYSTEM_ITK=ON + -DITK_USE_SYSTEM_FFTW=ON + -DITK_DIR="${EPREFIX}/usr/include/ITK-5.3/" + -DBUILD_TESTING="$(usex test ON OFF)" + -DUSE_VTK=$(usex vtk ON OFF) + -DUSE_SYSTEM_VTK=$(usex vtk ON OFF) + ) + use vtk && mycmakeargs+=( + -DVTK_DIR="${EPREFIX}/usr/include/vtk-9.2/" + ) + cmake_src_configure +} + +src_install() { + BUILD_DIR="${WORKDIR}/${MY_PN}-${PV}_build/ANTS-build" + cmake_src_install + cd "${S}/Scripts" || die "scripts dir not found" + dobin *.sh + dodir /usr/$(get_libdir)/ants + insinto "/usr/$(get_libdir)/ants" + doins * + doenvd "${FILESDIR}"/99ants +} diff --git a/sci-biology/ants/files/ants-2.3.1_p20191013-logic.patch b/sci-biology/ants/files/ants-2.3.1_p20191013-logic.patch deleted file mode 100644 index 932da9954..000000000 --- a/sci-biology/ants/files/ants-2.3.1_p20191013-logic.patch +++ /dev/null @@ -1,37 +0,0 @@ -From b2c828ff8e5ce537d7096af04b086e965fede9e8 Mon Sep 17 00:00:00 2001 -From: "Gabriel A. Devenyi" <gdevenyi@gmail.com> -Date: Mon, 7 Oct 2019 22:01:51 -0400 -Subject: [PATCH] Fix install logic - ---- - ANTS.cmake | 3 ++- - SuperBuild.cmake | 2 ++ - 2 files changed, 4 insertions(+), 1 deletion(-) - -diff --git a/ANTS.cmake b/ANTS.cmake -index a1baf845..95ffdc74 100644 ---- a/ANTS.cmake -+++ b/ANTS.cmake -@@ -172,7 +172,8 @@ install(PROGRAMS Scripts/ANTSpexec.sh - COMPONENT SCRIPTS - ) - --if(BUILD_SHARED_LIBS AND NOT (USE_SYSTEM_ITK AND USE_SYSTEM_VTK)) -+#Only install ITK/VTK libraries if shared build and superbuild is used -+if(BUILD_SHARED_LIBS AND ((NOT USE_SYSTEM_ITK) OR ((NOT USE_SYSTEM_VTK) AND USE_VTK))) - install(DIRECTORY ${CMAKE_BINARY_DIR}/../staging/lib/ - DESTINATION lib) - endif() -diff --git a/SuperBuild.cmake b/SuperBuild.cmake -index f4630e64..32b930c2 100644 ---- a/SuperBuild.cmake -+++ b/SuperBuild.cmake -@@ -207,6 +207,8 @@ list(APPEND ${CMAKE_PROJECT_NAME}_SUPERBUILD_EP_VARS - CMAKE_C_COMPILER_LAUNCHER:STRING - CMAKE_CXX_COMPILER_LAUNCHER:STRING - CMAKE_CUDA_COMPILER_LAUNCHER:STRING -+ USE_SYSTEM_ITK:BOOL -+ USE_SYSTEM_VTK:BOOL - ) - - _expand_external_project_vars() diff --git a/sci-biology/ants/files/ants-2.3.1_p20191013-paths.patch b/sci-biology/ants/files/ants-2.3.1_p20191013-paths.patch deleted file mode 100644 index aaea92808..000000000 --- a/sci-biology/ants/files/ants-2.3.1_p20191013-paths.patch +++ /dev/null @@ -1,40 +0,0 @@ -diff --git a/Examples/CMakeLists.txt b/Examples/CMakeLists.txt ---- a/Examples/CMakeLists.txt -+++ b/Examples/CMakeLists.txt -@@ -16,8 +16,9 @@ -+include(GNUInstallDirs) - install(TARGETS antsUtilities -- RUNTIME DESTINATION bin -+ RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} - COMPONENT RUNTIME_antsUtilities -- LIBRARY DESTINATION lib -+ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} - COMPONENT RUNTIME_antsUtilities -- ARCHIVE DESTINATION lib -+ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR} - COMPONENT DEVELOPMENT_antsUtilities - ) -@@ -38,8 +38,8 @@ - install(TARGETS l_${ANTS_FUNCTION_NAME} ${ANTS_FUNCTION_NAME} -- RUNTIME DESTINATION bin -+ RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} - COMPONENT RUNTIME_${ANTS_FUNCTION_NAME} -- LIBRARY DESTINATION lib -+ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} - COMPONENT RUNTIME_${ANTS_FUNCTION_NAME} -- ARCHIVE DESTINATION lib -+ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR} - COMPONENT DEVELOPMENT_${ANTS_FUNCTION_NAME} - ) -@@ -61,8 +61,8 @@ - install(TARGETS l_${ANTS_FUNCTION_NAME} ${ANTS_FUNCTION_NAME} -- RUNTIME DESTINATION bin -+ RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} - COMPONENT RUNTIME_${ANTS_FUNCTION_NAME} -- LIBRARY DESTINATION lib -+ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} - COMPONENT RUNTIME_${ANTS_FUNCTION_NAME} -- ARCHIVE DESTINATION lib -+ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR} - COMPONENT DEVELOPMENT_${ANTS_FUNCTION_NAME} - ) diff --git a/sci-biology/ants/files/ants-2.3.4-libdir.patch b/sci-biology/ants/files/ants-2.3.4-libdir.patch deleted file mode 100644 index b593c2778..000000000 --- a/sci-biology/ants/files/ants-2.3.4-libdir.patch +++ /dev/null @@ -1,117 +0,0 @@ -From 329a7be631b33294d9cf3d58e8cdeb62e0aa993c Mon Sep 17 00:00:00 2001 -From: Philip A Cook <cookpa@pennmedicine.upenn.edu> -Date: Fri, 26 Jun 2020 18:23:08 +0000 -Subject: [PATCH] ENH: Use GNUInstallDirs CMake module - -Trying to enable installation to the correct lib dir for each platform ---- - Common.cmake | 7 +++++-- - Examples/CMakeLists.txt | 32 ++++++++++++++++---------------- - 2 files changed, 21 insertions(+), 18 deletions(-) - -diff --git a/Common.cmake b/Common.cmake -index 5e52d7f1..1e604113 100644 ---- a/Common.cmake -+++ b/Common.cmake -@@ -103,8 +103,6 @@ if(PLATFORM_CHECK) - endif() - endif() - -- -- - #------------------------------------------------------------------------- - # Augment compiler flags - #------------------------------------------------------------------------- -@@ -124,3 +122,8 @@ if(NOT CMAKE_POSITION_INDEPENDENT_CODE) - set(CMAKE_POSITION_INDEPENDENT_CODE ON) - endif() - endif() -+ -+#------------------------------------------------------------------------- -+# Define install dirs for different platforms -+#------------------------------------------------------------------------- -+include(GNUInstallDirs) -diff --git a/Examples/CMakeLists.txt b/Examples/CMakeLists.txt -index 61781f56..cb352748 100644 ---- a/Examples/CMakeLists.txt -+++ b/Examples/CMakeLists.txt -@@ -1,4 +1,4 @@ --SET(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib") -+SET(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_LIBDIR}") - ## Note that the antsUtilities can always be built static. It will then be linked - ## Directly into the other libraries. - add_library(antsUtilities antsUtilities.cxx -@@ -14,11 +14,11 @@ add_library(antsUtilities antsUtilities.cxx - ) - target_link_libraries(antsUtilities ${ITK_LIBRARIES} ) - install(TARGETS antsUtilities -- RUNTIME DESTINATION bin -+ RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} - COMPONENT RUNTIME_antsUtilities -- LIBRARY DESTINATION lib -+ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} - COMPONENT RUNTIME_antsUtilities -- ARCHIVE DESTINATION lib -+ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR} - COMPONENT DEVELOPMENT_antsUtilities - ) - -@@ -34,22 +34,22 @@ macro(STATIC_ANTS_BUILD ANTS_FUNCTION_NAME EXTRA_LIBS) - - if (ANTS_INSTALL_LIBS_ONLY) - install(TARGETS l_${ANTS_FUNCTION_NAME} -- # RUNTIME DESTINATION bin -+ # RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} - # COMPONENT RUNTIME_${ANTS_FUNCTION_NAME} -- LIBRARY DESTINATION lib -+ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} - COMPONENT RUNTIME_${ANTS_FUNCTION_NAME} -- ARCHIVE DESTINATION lib -+ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR} - COMPONENT DEVELOPMENT_${ANTS_FUNCTION_NAME} - ) - else() - add_executable( ${ANTS_FUNCTION_NAME} cli_${ANTS_FUNCTION_NAME}.cxx ) - target_link_libraries( ${ANTS_FUNCTION_NAME} l_${ANTS_FUNCTION_NAME} ) - install(TARGETS l_${ANTS_FUNCTION_NAME} ${ANTS_FUNCTION_NAME} -- RUNTIME DESTINATION bin -+ RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} - COMPONENT RUNTIME_${ANTS_FUNCTION_NAME} -- LIBRARY DESTINATION lib -+ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} - COMPONENT RUNTIME_${ANTS_FUNCTION_NAME} -- ARCHIVE DESTINATION lib -+ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR} - COMPONENT DEVELOPMENT_${ANTS_FUNCTION_NAME} - ) - endif() -@@ -68,11 +68,11 @@ macro(DYNAMIC_ANTS_BUILD ANTS_FUNCTION_NAME EXTRA_LIBS) - - if (ANTS_INSTALL_LIBS_ONLY) - install(TARGETS l_${ANTS_FUNCTION_NAME} -- # RUNTIME DESTINATION bin -+ # RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} - # COMPONENT RUNTIME_${ANTS_FUNCTION_NAME} -- LIBRARY DESTINATION lib -+ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} - COMPONENT RUNTIME_${ANTS_FUNCTION_NAME} -- ARCHIVE DESTINATION lib -+ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR} - COMPONENT DEVELOPMENT_${ANTS_FUNCTION_NAME} - ) - else() -@@ -80,11 +80,11 @@ macro(DYNAMIC_ANTS_BUILD ANTS_FUNCTION_NAME EXTRA_LIBS) - target_link_libraries( ${ANTS_FUNCTION_NAME} l_${ANTS_FUNCTION_NAME} ) - - install(TARGETS l_${ANTS_FUNCTION_NAME} ${ANTS_FUNCTION_NAME} -- RUNTIME DESTINATION bin -+ RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} - COMPONENT RUNTIME_${ANTS_FUNCTION_NAME} -- LIBRARY DESTINATION lib -+ LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} - COMPONENT RUNTIME_${ANTS_FUNCTION_NAME} -- ARCHIVE DESTINATION lib -+ ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR} - COMPONENT DEVELOPMENT_${ANTS_FUNCTION_NAME} - ) - endif() diff --git a/sci-biology/ants/files/ants-2.3.4-version.patch b/sci-biology/ants/files/ants-2.3.4-version.patch deleted file mode 100644 index 487151d69..000000000 --- a/sci-biology/ants/files/ants-2.3.4-version.patch +++ /dev/null @@ -1,17 +0,0 @@ ---- a/ANTS.cmake 2020-06-08 12:11:14.000000000 -0400 -+++ b/ANTS.cmake 2020-08-03 16:44:00.826633506 -0400 -@@ -37,7 +37,6 @@ - set(${PROJECT_NAME}_VERSION_MAJOR 0) - set(${PROJECT_NAME}_VERSION_MINOR 0) - set(${PROJECT_NAME}_VERSION_PATCH 0) -- set(${PROJECT_NAME}_VERSION_TWEAK 0) - set(${PROJECT_NAME}_VERSION "snapshot-${ANTS_SNAPSHOT_VERSION}") - endif() - -@@ -46,7 +45,6 @@ - set(${PROJECT_NAME}_VERSION_MAJOR 0) - set(${PROJECT_NAME}_VERSION_MINOR 0) - set(${PROJECT_NAME}_VERSION_PATCH 0) -- set(${PROJECT_NAME}_VERSION_TWEAK 0) - set(${PROJECT_NAME}_VERSION "0.0.0.0") - endif() diff --git a/sci-biology/ants/metadata.xml b/sci-biology/ants/metadata.xml index 9f969ddf9..e8372d21b 100644 --- a/sci-biology/ants/metadata.xml +++ b/sci-biology/ants/metadata.xml @@ -21,4 +21,7 @@ <use> <flag name="vtk">Optional support for a number of surface enabled tools (via sci-libs/vtk).</flag> </use> + <upstream> + <remote-id type="github">ANTsX/ANTs</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/bambus/bambus-2.33-r2.ebuild b/sci-biology/bambus/bambus-2.33-r2.ebuild index 475c7f0b1..1cb7aad1b 100644 --- a/sci-biology/bambus/bambus-2.33-r2.ebuild +++ b/sci-biology/bambus/bambus-2.33-r2.ebuild @@ -11,7 +11,7 @@ HOMEPAGE=" https://sourceforge.net/projects/amos/files/bambus" SRC_URI=" https://sourceforge.net/projects/amos/files/bambus/${PV}/${P}.tar.gz - http://mira-assembler.sourceforge.net/docs/scaffolding_MIRA_BAMBUS.pdf" # no https + https://mira-assembler.sourceforge.net/docs/scaffolding_MIRA_BAMBUS.pdf" LICENSE="Artistic" SLOT="0" diff --git a/sci-biology/bamql/metadata.xml b/sci-biology/bamql/metadata.xml index 138cb7705..927a160ba 100644 --- a/sci-biology/bamql/metadata.xml +++ b/sci-biology/bamql/metadata.xml @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">BoutrosLaboratory/bamql</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/barrnap/barrnap-0.9.ebuild b/sci-biology/barrnap/barrnap-0.9.ebuild index 999f065c1..6b7176e14 100644 --- a/sci-biology/barrnap/barrnap-0.9.ebuild +++ b/sci-biology/barrnap/barrnap-0.9.ebuild @@ -6,7 +6,7 @@ EAPI=7 inherit perl-module DESCRIPTION="Predict Bacterial and Archaeal rRNA genes and output in GFF3 format" -HOMEPAGE="https://vicbioinformatics.com/software.barrnap.shtml" +HOMEPAGE="https://github.com/tseemann/barrnap" SRC_URI="https://github.com/tseemann/barrnap/archive/${PV}.tar.gz -> ${P}.tar.gz" LICENSE="GPL-3" diff --git a/sci-biology/barrnap/metadata.xml b/sci-biology/barrnap/metadata.xml index 138cb7705..9183ef1ec 100644 --- a/sci-biology/barrnap/metadata.xml +++ b/sci-biology/barrnap/metadata.xml @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">tseemann/barrnap</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/behaviopy/Manifest b/sci-biology/behaviopy/Manifest deleted file mode 100644 index 916b93320..000000000 --- a/sci-biology/behaviopy/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST behaviopy-0.2.tar.gz 36812 BLAKE2B 099f245027ddbbd38478bc48df1746e25e5a2b8d32a381f3352cb4c1339f9aa7a101ff0a3b797bceb543db1656044470911dd2e3addd44f5d2cd8d661e20a0cf SHA512 b7939ac3dcbbc445b5459a2bb96e413ca71e720c14e441d3d9864422be13c6b78178c5a1006f851d141c70a3f1ab9635ea636841610e0f210ca3f35a0f12f9bc diff --git a/sci-biology/behaviopy/behaviopy-0.2.ebuild b/sci-biology/behaviopy/behaviopy-0.2.ebuild deleted file mode 100644 index ca6700729..000000000 --- a/sci-biology/behaviopy/behaviopy-0.2.ebuild +++ /dev/null @@ -1,42 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{8..10} ) - -inherit distutils-r1 - -DESCRIPTION="Neuroimaging tools for Python" -HOMEPAGE="https://github.com/TheChymera/behaviopy" -SRC_URI="https://github.com/TheChymera/behaviopy/archive/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="GPL-3" -SLOT="0" -IUSE="evaluation" -KEYWORDS="~amd64 ~x86" - -RDEPEND=" - dev-python/matplotlib[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/pandas[${PYTHON_USEDEP}] - dev-python/seaborn[${PYTHON_USEDEP}] - dev-python/statsmodels[${PYTHON_USEDEP}] - dev-python/scipy[${PYTHON_USEDEP}] -" - -python_prepare_all() { - if ! use evaluation; then - rm behaviopy/evaluation.py || die - fi - distutils-r1_python_prepare_all -} - -python_test() { - cd behaviopy/examples || die - echo "backend : Agg" > matplotlibrc || die - for i in *py; do - echo "Executing $i" - ${EPYTHON} $i || die - done -} diff --git a/sci-biology/behaviopy/metadata.xml b/sci-biology/behaviopy/metadata.xml deleted file mode 100644 index a33886a68..000000000 --- a/sci-biology/behaviopy/metadata.xml +++ /dev/null @@ -1,26 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>gentoo@chymera.eu</email> - <name>Horea Christian</name> - </maintainer> - <maintainer type="project"> - <email>sci@gentoo.org</email> - <name>Gentoo Science Project</name> - </maintainer> - <longdescription lang="en"> - BehavioPy is a Python toolkit providing evaluation (e.g. event - tracking) and plotting functions for behavioural data. Manual event - tracking is done via a simple and configurable PsychoPy-based - interface. Plotting functions are designed to work with preformatted - data in CSV format (e.g. as exported by pandas), and use Seaborn and - custom BehavioPy styles for maximum beautification. - </longdescription> - <upstream> - <remote-id type="github">TheChymera/behaviopy</remote-id> - </upstream> - <use> - <flag name="evaluation">Installs evaluation submodule.</flag> - </use> -</pkgmetadata> diff --git a/sci-biology/bidsschematools/Manifest b/sci-biology/bidsschematools/Manifest new file mode 100644 index 000000000..283f2cedf --- /dev/null +++ b/sci-biology/bidsschematools/Manifest @@ -0,0 +1,3 @@ +DIST bidsschematools-0.6.0.tar.gz 1162053 BLAKE2B b46ae2c19b96416908786347890db33aded14c0656b2af3f8396395a7decd9e74808b1ba54df3d049473eda038b706d7b0561f2e21c97ab5e9534f57c41a560a SHA512 32e2a679b85cb8c57e2a91783f315092b3e976e8cadc661a67822b499685b128a9f5abda70d2124ddcee42163a9357665474de6c3f96cf369c33cefe1586b7f1 +DIST bidsschematools-0.7.0.tar.gz 1227313 BLAKE2B 350621d8052ca8ee45be970c4f8973c34d5c7dfd9da0777758009d8f725691efaa665926d9f97723e2331f5511aedf3601fd1df520746b6ec4aebd6ef27a2cf6 SHA512 391e3ed1a96202bada1486de377ea4d96e8622cced132cbb014a697578dbd1c5fdfa3eb2ce6f44b5031136c987e2298a5bc702c1c5751e35479512cfe57a383b +DIST bidsschematools-0.7.1.tar.gz 1226794 BLAKE2B 6bbc672ac047bd1475b5b79f5cb74b61f190207531be810018768a6cf62e2cae36ccef4893bee041a53ed546f8ae6f104bb64d2f0b89550c80c911d6a48fcee5 SHA512 8cf9e94496108c15360bcc25a1c8e5900350e1fb3da9886c2d089481ae69c94a634ea0cf67e2a1120a93c2982c07061cda8d0d8ecba9715f848c01388108517e diff --git a/sci-biology/bidsschematools/bidsschematools-0.6.0.ebuild b/sci-biology/bidsschematools/bidsschematools-0.6.0.ebuild new file mode 100644 index 000000000..96b6cd57f --- /dev/null +++ b/sci-biology/bidsschematools/bidsschematools-0.6.0.ebuild @@ -0,0 +1,37 @@ +# Copyright 2022-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) + +inherit distutils-r1 pypi + +DESCRIPTION="A Python library for working with the BIDS schema" +HOMEPAGE="https://github.com/bids-standard/bids-specification" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="render" + +RDEPEND=" + dev-python/pyyaml[${PYTHON_USEDEP}] + render? ( + dev-python/markdown-it-py[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + dev-python/tabulate[${PYTHON_USEDEP}] + ) +" +DEPEND="" + +distutils_enable_tests pytest + +src_prepare() { + if ! use render; then + rm "${S}/bidsschematools/render.py" + rm "${S}/bidsschematools/tests/test_render.py" + fi + default +} diff --git a/sci-biology/bidsschematools/bidsschematools-0.7.0.ebuild b/sci-biology/bidsschematools/bidsschematools-0.7.0.ebuild new file mode 100644 index 000000000..98b773243 --- /dev/null +++ b/sci-biology/bidsschematools/bidsschematools-0.7.0.ebuild @@ -0,0 +1,46 @@ +# Copyright 2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) + +inherit distutils-r1 pypi + +DESCRIPTION="A Python library for working with the BIDS schema" +HOMEPAGE="https://github.com/bids-standard/bids-specification" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="render" +# Documented upstream: +# https://github.com/conda-forge/bidsschematools-feedstock/pull/2 +#RESTRICT="test" + +RDEPEND=" + dev-python/pyyaml[${PYTHON_USEDEP}] + render? ( + dev-python/markdown-it-py[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + dev-python/tabulate[${PYTHON_USEDEP}] + ) +" +DEPEND="" + +distutils_enable_tests pytest + +# Reported upstream: +# https://github.com/bids-standard/bids-specification/issues/1500 +EPYTEST_DESELECT=( + "bidsschematools/tests/test_validator.py::test_bids_datasets[ds000248]" +) + +src_prepare() { + if ! use render; then + rm "${S}/bidsschematools/render.py" + rm "${S}/bidsschematools/tests/test_render.py" + fi + default +} diff --git a/sci-biology/bidsschematools/bidsschematools-0.7.1.ebuild b/sci-biology/bidsschematools/bidsschematools-0.7.1.ebuild new file mode 100644 index 000000000..b5b12165d --- /dev/null +++ b/sci-biology/bidsschematools/bidsschematools-0.7.1.ebuild @@ -0,0 +1,37 @@ +# Copyright 2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) + +inherit distutils-r1 pypi + +DESCRIPTION="A Python library for working with the BIDS schema" +HOMEPAGE="https://github.com/bids-standard/bids-specification" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="render" + +RDEPEND=" + dev-python/pyyaml[${PYTHON_USEDEP}] + render? ( + dev-python/markdown-it-py[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + dev-python/tabulate[${PYTHON_USEDEP}] + ) +" +DEPEND="" + +distutils_enable_tests pytest + +src_prepare() { + if ! use render; then + rm "${S}/bidsschematools/render.py" + rm "${S}/bidsschematools/tests/test_render.py" + fi + default +} diff --git a/sci-biology/bidsschematools/metadata.xml b/sci-biology/bidsschematools/metadata.xml new file mode 100644 index 000000000..3fac5f14b --- /dev/null +++ b/sci-biology/bidsschematools/metadata.xml @@ -0,0 +1,19 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>gentoo@chymera.eu</email> + <name>Horea Christian</name> + </maintainer> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <upstream> + <remote-id type="github">bids-standard/bids-specification</remote-id> + <remote-id type="pypi">bidsschematools</remote-id> + </upstream> + <use> + <flag name="render">Support for schema table rendering</flag> + </use> +</pkgmetadata> diff --git a/sci-biology/bismark/metadata.xml b/sci-biology/bismark/metadata.xml index 4c433a8ca..4ee13c559 100644 --- a/sci-biology/bismark/metadata.xml +++ b/sci-biology/bismark/metadata.xml @@ -20,4 +20,7 @@ and gapped alignments; (4) Alignment seed length, number of mismatches etc. are adjustable; (5) Output discriminates between cytosine methylation in CpG, CHG and CHH context. </longdescription> + <upstream> + <remote-id type="github">FelixKrueger/Bismark</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/blasr/Manifest b/sci-biology/blasr/Manifest deleted file mode 100644 index 7819d5a37..000000000 --- a/sci-biology/blasr/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST blasr-5.3.5.tar.gz 2709986 BLAKE2B 48a8d12e4a47159c00d5febab4222dec5e2f4e5ce4d7a481243b4b62e0ba693eb9e1aa2a11b5de36606ec977db3947178cfdd0a1a09ccfea213e1a1567402e74 SHA512 79155f29076e4a9fe1d66d9e8310d38d3b6690fe1959be923627607ed4d7dfe97c020ff9f9134a3cffcb8e1cd5eb1b3a861d10cb476f9c3866c87e85e6ae93e7 diff --git a/sci-biology/blasr/blasr-5.3.5.ebuild b/sci-biology/blasr/blasr-5.3.5.ebuild deleted file mode 100644 index 85e4ea66d..000000000 --- a/sci-biology/blasr/blasr-5.3.5.ebuild +++ /dev/null @@ -1,24 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -inherit meson - -DESCRIPTION="The PacBio long read aligner" -HOMEPAGE="http://www.smrtcommunity.com/SMRT-Analysis/Algorithms/BLASR" -SRC_URI="https://github.com/PacificBiosciences/blasr/archive/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="blasr" -SLOT="0" -KEYWORDS="~amd64" - -BDEPEND=" - dev-util/cmake - virtual/pkgconfig -" -DEPEND=" - sci-biology/libblasr - dev-libs/boost:= -" -RDEPEND="${DEPEND}" diff --git a/sci-biology/blasr/metadata.xml b/sci-biology/blasr/metadata.xml deleted file mode 100644 index 8417d1580..000000000 --- a/sci-biology/blasr/metadata.xml +++ /dev/null @@ -1,8 +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-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/brkraw/Manifest b/sci-biology/brkraw/Manifest new file mode 100644 index 000000000..6bc79d823 --- /dev/null +++ b/sci-biology/brkraw/Manifest @@ -0,0 +1 @@ +DIST brkraw-0.3.11.gh.tar.gz 3919122 BLAKE2B 9881f53bb3fef038385eab4043f76d21c2e5391131c80daa49c909e7882359ed9d0b41b84fc82acd0432f4bac820a75061842de85b75cceff6f33d6f14988aea SHA512 a1e2725b6f50ff82ea6c4f9eacbd044ccb1c966aa26f2753c0872e3ee5e6469821dad336c9ef221dc6e15df2bed537ed9d31d5b09ff432694b757ab30af53631 diff --git a/sci-biology/brkraw/brkraw-0.3.11.ebuild b/sci-biology/brkraw/brkraw-0.3.11.ebuild new file mode 100644 index 000000000..60a7767b1 --- /dev/null +++ b/sci-biology/brkraw/brkraw-0.3.11.ebuild @@ -0,0 +1,36 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) + +DISTUTILS_USE_PEP517=setuptools + +inherit distutils-r1 pypi + +DESCRIPTION="Fast and easy statistical learning on NeuroImaging data" +HOMEPAGE="https://github.com/BrkRaw/brkraw" +SRC_URI="https://github.com/BrkRaw/brkraw/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="test" +# Strange test infrastructure involving dynamic download via make: +# https://github.com/BrkRaw/brkraw/blob/main/.github/workflows/test.yml +RESTRICT="test" + +RDEPEND=" + >=dev-python/numpy-1.18[${PYTHON_USEDEP}] + >=dev-python/pillow-7.1.1[${PYTHON_USEDEP}] + >=dev-python/tqdm-4.45.0[${PYTHON_USEDEP}] + >=dev-python/openpyxl-3.0.3[${PYTHON_USEDEP}] + >=dev-python/xlrd-1.1.0[${PYTHON_USEDEP}] + >=dev-python/pandas-1[${PYTHON_USEDEP}] + >=sci-libs/nibabel-3.0.2[${PYTHON_USEDEP}] +" + +PATCHES=( "${FILESDIR}/${P}-testexclusion.patch" ) + +distutils_enable_tests pytest diff --git a/sci-biology/brkraw/files/brkraw-0.3.11-testexclusion.patch b/sci-biology/brkraw/files/brkraw-0.3.11-testexclusion.patch new file mode 100644 index 000000000..40cc8fc4a --- /dev/null +++ b/sci-biology/brkraw/files/brkraw-0.3.11-testexclusion.patch @@ -0,0 +1,11 @@ +--- a/setup.py 2023-07-05 17:09:42.000000000 -0400 ++++ b/setup.py 2023-11-28 12:38:07.726369571 -0500 +@@ -24,7 +24,7 @@ + author_email=__email__, + url=__url__, + license='GNLv3', +- packages=find_packages(), ++ packages=find_packages(exclude=["tests", "tests.*"]), + install_requires=['nibabel>=3.0.2', + 'numpy>=1.18.0', + 'pandas>=1.0.0', diff --git a/sci-biology/brkraw/metadata.xml b/sci-biology/brkraw/metadata.xml new file mode 100644 index 000000000..5c436db45 --- /dev/null +++ b/sci-biology/brkraw/metadata.xml @@ -0,0 +1,16 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>gentoo@chymera.eu</email> + <name>Horea Christian</name> + </maintainer> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <upstream> + <remote-id type="github">BrkRaw/brkraw</remote-id> + <remote-id type="pypi">brkraw</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/bruker2nifti/bruker2nifti-1.0.4.ebuild b/sci-biology/bruker2nifti/bruker2nifti-1.0.4.ebuild index 7a9c238ce..dc0c49e6f 100644 --- a/sci-biology/bruker2nifti/bruker2nifti-1.0.4.ebuild +++ b/sci-biology/bruker2nifti/bruker2nifti-1.0.4.ebuild @@ -1,10 +1,10 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 DISTUTILS_USE_SETUPTOOLS="rdepend" -PYTHON_COMPAT=( python3_{7,8,9} ) +PYTHON_COMPAT=( python3_{10..11} ) inherit distutils-r1 diff --git a/sci-biology/btl_bloomfilter/metadata.xml b/sci-biology/btl_bloomfilter/metadata.xml index 138cb7705..1e02bb596 100644 --- a/sci-biology/btl_bloomfilter/metadata.xml +++ b/sci-biology/btl_bloomfilter/metadata.xml @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">bcgsc/btl_bloomfilter</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/bx-python/Manifest b/sci-biology/bx-python/Manifest index 80552af85..90147dff7 100644 --- a/sci-biology/bx-python/Manifest +++ b/sci-biology/bx-python/Manifest @@ -1 +1,2 @@ -DIST bx-python-0.8.9.tar.gz 1651514 BLAKE2B ee75d08aaae8102c2af5be0175c75200382e157abc0c0c723a67b55d5542ab2d4b6ccd4e256975b0a2d00b39b2249d73df0c6f4324b3a74757c3e18e2aeb6c1a SHA512 37863c92258dc06a12b566b02697502f68bbf7e4d9decd8fc63af10ee58b614dd0e7cff35e9977ba1ddf913f176c49e7969728d8e64a9f78ac7100da4a3d70ea +DIST bx-python-0.8.9.gh.tar.gz 1651514 BLAKE2B ee75d08aaae8102c2af5be0175c75200382e157abc0c0c723a67b55d5542ab2d4b6ccd4e256975b0a2d00b39b2249d73df0c6f4324b3a74757c3e18e2aeb6c1a SHA512 37863c92258dc06a12b566b02697502f68bbf7e4d9decd8fc63af10ee58b614dd0e7cff35e9977ba1ddf913f176c49e7969728d8e64a9f78ac7100da4a3d70ea +DIST bx-python-0.9.0.gh.tar.gz 1667445 BLAKE2B 0814792a2af8bfb7af5ef5fe1ddc184ed14a68df060a8286f4eba334388497363dc002f6c0de72836b5654452fe28f4cef67cd31b765a4a121c84f3af0634ea0 SHA512 955f396614d8e6d19a74e94a6612f7752a45f752a4a59c95853474dd363ed1960d20a340f17eb1815fda3aaf26d907dc30d37aa8c23608d718742b68864ca1bc diff --git a/sci-biology/bx-python/bx-python-0.8.9.ebuild b/sci-biology/bx-python/bx-python-0.8.9.ebuild index a0d3ae3df..6cffba1be 100644 --- a/sci-biology/bx-python/bx-python-0.8.9.ebuild +++ b/sci-biology/bx-python/bx-python-0.8.9.ebuild @@ -1,28 +1,35 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7..9} ) +PYTHON_COMPAT=( python3_{10..10} ) inherit distutils-r1 DESCRIPTION="Library for rapid implementation of genome scale analyses" HOMEPAGE="https://github.com/bxlab/bx-python" -SRC_URI="https://github.com/bxlab/bx-python/archive/v${PV}.tar.gz -> ${P}.tar.gz" +SRC_URI="https://github.com/bxlab/bx-python/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz" LICENSE="MIT" SLOT="0" KEYWORDS="~amd64 ~x86" +# Tests require dev-python/pytest-cython (currently not in ::gentoo or ::science) +# (and might need some more work beyond that) +RESTRICT=test RDEPEND=" dev-python/numpy[${PYTHON_USEDEP}] dev-python/six[${PYTHON_USEDEP}] " -BDEPEND="dev-python/cython[${PYTHON_USEDEP}]" +BDEPEND=" + dev-python/cython[${PYTHON_USEDEP}] +" # has file collision with sci-biology/RSeQC # ToDo: fix doc building: # Reason: TemplateNotFound('i') #distutils_enable_sphinx doc/source + +distutils_enable_tests pytest diff --git a/sci-biology/bx-python/bx-python-0.9.0.ebuild b/sci-biology/bx-python/bx-python-0.9.0.ebuild new file mode 100644 index 000000000..6cffba1be --- /dev/null +++ b/sci-biology/bx-python/bx-python-0.9.0.ebuild @@ -0,0 +1,35 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..10} ) + +inherit distutils-r1 + +DESCRIPTION="Library for rapid implementation of genome scale analyses" +HOMEPAGE="https://github.com/bxlab/bx-python" +SRC_URI="https://github.com/bxlab/bx-python/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" +# Tests require dev-python/pytest-cython (currently not in ::gentoo or ::science) +# (and might need some more work beyond that) +RESTRICT=test + +RDEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/six[${PYTHON_USEDEP}] +" +BDEPEND=" + dev-python/cython[${PYTHON_USEDEP}] +" + +# has file collision with sci-biology/RSeQC + +# ToDo: fix doc building: +# Reason: TemplateNotFound('i') +#distutils_enable_sphinx doc/source + +distutils_enable_tests pytest diff --git a/sci-biology/bx-python/bx-python-9999.ebuild b/sci-biology/bx-python/bx-python-9999.ebuild index 6f0b1c9ca..b29975b58 100644 --- a/sci-biology/bx-python/bx-python-9999.ebuild +++ b/sci-biology/bx-python/bx-python-9999.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7..9} ) +PYTHON_COMPAT=( python3_{10..10} ) inherit distutils-r1 git-r3 @@ -14,15 +14,22 @@ EGIT_REPO_URI="https://github.com/bxlab/bx-python" LICENSE="MIT" SLOT="0" KEYWORDS="" +# Tests require dev-python/pytest-cython (currently not in ::gentoo or ::science) +# (and might need some more work beyond that) +RESTRICT=test RDEPEND=" dev-python/numpy[${PYTHON_USEDEP}] dev-python/six[${PYTHON_USEDEP}] " -BDEPEND="dev-python/cython[${PYTHON_USEDEP}]" +BDEPEND=" + dev-python/cython[${PYTHON_USEDEP}] +" # has file collision with sci-biology/RSeQC # ToDo: fix doc building: # Reason: TemplateNotFound('i') #distutils_enable_sphinx doc/source + +distutils_enable_tests pytest diff --git a/sci-biology/bx-python/metadata.xml b/sci-biology/bx-python/metadata.xml index 3e13342e3..f1fc4360e 100644 --- a/sci-biology/bx-python/metadata.xml +++ b/sci-biology/bx-python/metadata.xml @@ -10,7 +10,7 @@ <name>Gentoo Biology Project</name> </maintainer> <upstream> - <remote-id type="bitbucket">james_taylor/bx-python</remote-id> + <remote-id type="github">bxlab/bx-python</remote-id> <remote-id type="pypi">bx-python</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/caftools/Manifest b/sci-biology/caftools/Manifest deleted file mode 100644 index 761665281..000000000 --- a/sci-biology/caftools/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST caftools-2.0.2.tar.gz 2645554 BLAKE2B a48d8fb71500b5dc07da37467a9dc8d5972dfd7f63ae19cf7ca016774c3a23c4a9cd0f4caa1bde8efe5ef74c2576b8143f8b7375f9bf34414edcb14ed34a17d2 SHA512 0c1a7f2127538ef932139cfee6bc6acb2411765d1006d508e65647ec74d1677a6ecd25b98cc37075bd8e5b0b1a245c11c1029cbbc51eefb46023bd121fdb2f1d -DIST caftools-2.0.tar.gz 2644892 BLAKE2B 76aa90bf18d7543eb8f39de3e3be5fbca9a549e47341b032dd569394865ae02e269ea54a607acca2d88d404d271f78e1b97399bc8bdc1a107937163c89642323 SHA512 0b2b5d09d503b900b275efd61dfa1c5b01259e53c392d68626d9c5081add27ca87b324b5702ec18293415b788208c547eb31e461861f1244b759e28221244417 diff --git a/sci-biology/caftools/caftools-2.0.2.ebuild b/sci-biology/caftools/caftools-2.0.2.ebuild deleted file mode 100644 index 7d58f3375..000000000 --- a/sci-biology/caftools/caftools-2.0.2.ebuild +++ /dev/null @@ -1,45 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DESCRIPTION="Manipulate CAF files and convert to GAP4 format (not GAP5), ACE, PHRAP" -HOMEPAGE="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC310697/" -SRC_URI=" - ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/src/${P}.tar.gz - ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/src/${PN}-2.0.tar.gz" - -LICENSE="GRL" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -DEPEND=" - sci-libs/io_lib - dev-lang/perl" -RDEPEND="${DEPEND}" - -PATCHES=( - "${FILESDIR}"/Makefile.in-"${PV}".patch -) - -src_prepare(){ - default - mv "${WORKDIR}"/caftools-2.0/man/*.{1,5} "${S}"/man/ || die -} - -src_configure(){ - default - sed \ - -e 's:prefix = /usr:prefix = $(DESTDIR)/usr:' \ - -i Makefile src/Makefile || die -} - -# TODO: the 2.0.2 archive lacks manpages compared to 2.0, FIXME -# The man/Makefile.in is screwed in 2.0.2 so we cannot use it to install the manpage files, -# not even copying over whole caftools-2.0/man/ to caftools-2.0.2/man does not help. -src_install(){ - default - doman man/*.[1-5] || die - elog "Some usage info is at http://sarton.imb-jena.de/software/consed2gap/" - elog "for some reason caf_find_misassemblies is gone from 2.0.2 version" -} diff --git a/sci-biology/caftools/files/Makefile.in-2.0.2.patch b/sci-biology/caftools/files/Makefile.in-2.0.2.patch deleted file mode 100644 index 1e5160487..000000000 --- a/sci-biology/caftools/files/Makefile.in-2.0.2.patch +++ /dev/null @@ -1,43 +0,0 @@ ---- src/Makefile.in.ori 2010-12-05 22:59:40.000000000 +0100 -+++ src/Makefile.in 2010-12-05 23:01:19.000000000 +0100 -@@ -32,8 +32,6 @@ - includedir = @includedir@ - oldincludedir = /usr/include - --DESTDIR = -- - pkgdatadir = $(datadir)/@PACKAGE@ - pkglibdir = $(libdir)/@PACKAGE@ - pkgincludedir = $(includedir)/@PACKAGE@ -@@ -323,18 +321,18 @@ - - install-binPROGRAMS: $(bin_PROGRAMS) - @$(NORMAL_INSTALL) -- $(mkinstalldirs) $(DESTDIR)$(bindir) -+ $(mkinstalldirs) $(bindir) - @list='$(bin_PROGRAMS)'; for p in $$list; do \ - if test -f $$p; then \ -- echo " $(INSTALL_PROGRAM) $$p $(DESTDIR)$(bindir)/`echo $$p|sed 's/$(EXEEXT)$$//'|sed '$(transform)'|sed 's/$$/$(EXEEXT)/'`"; \ -- $(INSTALL_PROGRAM) $$p $(DESTDIR)$(bindir)/`echo $$p|sed 's/$(EXEEXT)$$//'|sed '$(transform)'|sed 's/$$/$(EXEEXT)/'`; \ -+ echo " $(INSTALL_PROGRAM) $$p $(bindir)/`echo $$p|sed 's/$(EXEEXT)$$//'|sed '$(transform)'|sed 's/$$/$(EXEEXT)/'`"; \ -+ $(INSTALL_PROGRAM) $$p $(bindir)/`echo $$p|sed 's/$(EXEEXT)$$//'|sed '$(transform)'|sed 's/$$/$(EXEEXT)/'`; \ - else :; fi; \ - done - - uninstall-binPROGRAMS: - @$(NORMAL_UNINSTALL) - list='$(bin_PROGRAMS)'; for p in $$list; do \ -- rm -f $(DESTDIR)$(bindir)/`echo $$p|sed 's/$(EXEEXT)$$//'|sed '$(transform)'|sed 's/$$/$(EXEEXT)/'`; \ -+ rm -f $(bindir)/`echo $$p|sed 's/$(EXEEXT)$$//'|sed '$(transform)'|sed 's/$$/$(EXEEXT)/'`; \ - done - - .c.o: -@@ -579,7 +577,7 @@ - $(MAKE) $(AM_MAKEFLAGS) AM_INSTALL_PROGRAM_FLAGS=-s install - installdirs: installdirs-recursive - installdirs-am: -- $(mkinstalldirs) $(DESTDIR)$(bindir) -+ $(mkinstalldirs) $(bindir) - - - mostlyclean-generic: diff --git a/sci-biology/caftools/files/Makefile.in.patch b/sci-biology/caftools/files/Makefile.in.patch deleted file mode 100644 index 4ddd9f628..000000000 --- a/sci-biology/caftools/files/Makefile.in.patch +++ /dev/null @@ -1,49 +0,0 @@ ---- src/Makefile.in.ori 2010-12-05 22:08:50.000000000 +0100 -+++ src/Makefile.in 2010-12-05 22:10:07.000000000 +0100 -@@ -18,7 +18,7 @@ - srcdir = @srcdir@ - top_srcdir = @top_srcdir@ - VPATH = @srcdir@ --prefix = @prefix@ -+prefix = $(DESTDIR)/@prefix@ - exec_prefix = @exec_prefix@ - - bindir = @bindir@ -@@ -394,14 +394,14 @@ - binPROGRAMS_INSTALL = $(INSTALL_PROGRAM) - install-binPROGRAMS: $(bin_PROGRAMS) - @$(NORMAL_INSTALL) -- $(mkinstalldirs) $(DESTDIR)$(bindir) -+ $(mkinstalldirs) $(bindir) - @list='$(bin_PROGRAMS)'; for p in $$list; do \ - p1=`echo $$p|sed 's/$(EXEEXT)$$//'`; \ - if test -f $$p \ - ; then \ - f=`echo "$$p1" | sed 's,^.*/,,;$(transform);s/$$/$(EXEEXT)/'`; \ -- echo " $(INSTALL_PROGRAM_ENV) $(binPROGRAMS_INSTALL) $$p $(DESTDIR)$(bindir)/$$f"; \ -- $(INSTALL_PROGRAM_ENV) $(binPROGRAMS_INSTALL) $$p $(DESTDIR)$(bindir)/$$f; \ -+ echo " $(INSTALL_PROGRAM_ENV) $(binPROGRAMS_INSTALL) $$p $(bindir)/$$f"; \ -+ $(INSTALL_PROGRAM_ENV) $(binPROGRAMS_INSTALL) $$p $(bindir)/$$f; \ - else :; fi; \ - done - -@@ -409,8 +409,8 @@ - @$(NORMAL_UNINSTALL) - @list='$(bin_PROGRAMS)'; for p in $$list; do \ - f=`echo "$$p" | sed 's,^.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/'`; \ -- echo " rm -f $(DESTDIR)$(bindir)/$$f"; \ -- rm -f $(DESTDIR)$(bindir)/$$f; \ -+ echo " rm -f $(bindir)/$$f"; \ -+ rm -f $(bindir)/$$f; \ - done - - clean-binPROGRAMS: -@@ -663,7 +663,7 @@ - all-am: Makefile $(PROGRAMS) config.h - installdirs: installdirs-recursive - installdirs-am: -- $(mkinstalldirs) $(DESTDIR)$(bindir) -+ $(mkinstalldirs) $(bindir) - - install: install-recursive - install-exec: install-exec-recursive diff --git a/sci-biology/caftools/metadata.xml b/sci-biology/caftools/metadata.xml deleted file mode 100644 index 224641279..000000000 --- a/sci-biology/caftools/metadata.xml +++ /dev/null @@ -1,17 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <longdescription> -CAF is a text format for describing sequence assemblies. It is acedb-compliant -and is an extension of the ace-file format used earlier, but with support for -base quality measures and a more extensive description of the Sequence data. -</longdescription> -</pkgmetadata> diff --git a/sci-biology/canu/Manifest b/sci-biology/canu/Manifest deleted file mode 100644 index f7859b395..000000000 --- a/sci-biology/canu/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST canu-2.1.1.tar.xz 2281796 BLAKE2B ada9326054e0455fac824545baa0ed86d5e53325256a388b9a1bdfa393a2b9ad8926f64b5c871bc10acc9b2d8bac96bcb80682e6ed7c19d01d6ed3b7764111af SHA512 9be64df3c46c6eb98dde915959df346292ac033e650b428b16187e700637b91a87e67ccdf23a241dfbcef7bdb3df289e412d38a2233831eba855fd84dc6ea7c0 diff --git a/sci-biology/canu/canu-2.1.1.ebuild b/sci-biology/canu/canu-2.1.1.ebuild deleted file mode 100644 index 987fb99f2..000000000 --- a/sci-biology/canu/canu-2.1.1.ebuild +++ /dev/null @@ -1,70 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7,8,9} ) - -inherit java-pkg-2 perl-module python-r1 - -DESCRIPTION="Fork of a wgs-assembler for Oxfordnanopore and PacBio sequences" -HOMEPAGE="https://canu.readthedocs.io/en/latest" -SRC_URI="https://github.com/marbl/canu/releases/download/v${PV}/${P}.tar.xz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND="${PYTHON_DEPS} - >=virtual/jre-1.8:* - dev-lang/perl - virtual/perl-File-Path - sci-visualization/gnuplot - sci-biology/minimap2 -" -# =sci-biology/mhap-2.1.3 if we unbundle it -DEPEND="${RDEPEND} - >=virtual/jdk-1.8:* - dev-java/ant-core -" - -# Detected file collision(s): -# * sci-biology/wgs-assembler-8.3_rc2:0::science -# * /usr/bin/bogart -# * /usr/bin/bogus -# * /usr/bin/fastqAnalyze -# * /usr/bin/fastqSample -# * /usr/bin/fastqSimulate -# * /usr/bin/fastqSimulate-sort -# * /usr/bin/meryl -# * /usr/bin/overlapInCore -# * /usr/bin/utgcns - -# Perl 5.12.0, or File::Path 2.08 -# Java SE 8 -# https://github.com/marbl/MHAP uses Apache maven - -# contains bundled mhap-2.1.3.jar, kmer, pbutgcns, FALCON - -src_compile(){ - cd src || die - emake -} - -src_install(){ - # installs - # /usr/bin - # /usr/lib/libcanu.a - # /usr/lib64/perl5/vendor_perl/5.28.0/lib/site_perl/canu - # /usr/share/java/classes/mhap-2.1.3.jar - rm -rf Linux-amd64/obj - insinto /usr - doins -r Linux-amd64/{bin,share} - insinto /usr/$(get_libdir) - dolib.a Linux-amd64/lib/libcanu.a - rm Linux-amd64/lib/libcanu.a || die - perl_set_version - perl_domodule -r Linux-amd64/lib -} diff --git a/sci-biology/canu/metadata.xml b/sci-biology/canu/metadata.xml deleted file mode 100644 index 138cb7705..000000000 --- a/sci-biology/canu/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>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/chiron/Manifest b/sci-biology/chiron/Manifest deleted file mode 100644 index 2cde5a081..000000000 --- a/sci-biology/chiron/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST chiron-0.6.1.1.tar.gz 53281188 BLAKE2B 56c623ec0d2f8970cd03d892d321362145b44890a0384d5209a2bd8c19b22509ec0557e539f021240a447e836ca6cd3531f3c9ac827b6ece715b086fca73d9f3 SHA512 b74e7f3cea9d206bc0c456189ec643de684a866bdb2dd6fd9d05ac11efd2b980d1aa09f7fc2a2aa3d5df56ca60e7a57c23d63e20df3df10f3ab82c5289d8a52f diff --git a/sci-biology/chiron/chiron-0.6.1.1.ebuild b/sci-biology/chiron/chiron-0.6.1.1.ebuild deleted file mode 100644 index 162a03129..000000000 --- a/sci-biology/chiron/chiron-0.6.1.1.ebuild +++ /dev/null @@ -1,29 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{8..9} ) -DISTUTILS_USE_SETUPTOOLS=rdepend - -inherit distutils-r1 - -DESCRIPTION="A deep neural network basecaller for nanopore sequencing" -HOMEPAGE="https://github.com/haotianteng/chiron - https://www.biorxiv.org/content/early/2017/09/12/179531" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="MPL-2.0" -SLOT="0" -KEYWORDS="~amd64" - -RDEPEND=" - dev-python/h5py[${PYTHON_USEDEP}] - sci-biology/mappy[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/statsmodels[${PYTHON_USEDEP}] - dev-python/tqdm[${PYTHON_USEDEP}] - sci-biology/biopython[${PYTHON_USEDEP}] - dev-python/packaging[${PYTHON_USEDEP}] - sci-libs/tensorflow[${PYTHON_USEDEP}] -" diff --git a/sci-biology/chiron/metadata.xml b/sci-biology/chiron/metadata.xml deleted file mode 100644 index 138cb7705..000000000 --- a/sci-biology/chiron/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>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/cluster/files/cluster-1.38-helpmenu-fix.patch b/sci-biology/cluster/files/cluster-1.38-helpmenu-fix.patch deleted file mode 100644 index 69f3a963e..000000000 --- a/sci-biology/cluster/files/cluster-1.38-helpmenu-fix.patch +++ /dev/null @@ -1,30 +0,0 @@ ---- X11/gui.c 2007-05-05 00:21:30.000000000 -0500 -+++ X11/gui.c-new 2007-08-09 04:25:53.000000000 -0500 -@@ -1786,15 +1786,15 @@ - { int item_no = (int) client_data; - switch (item_no) - { case CMD_HELP_HTMLHELP: -- { system("netscape "PREFIX"/cluster/html/index.html &"); -+ { system("xdg-open "PREFIX"/share/doc/cluster-1.36/html/index.html &"); - break; - } - case CMD_HELP_MANUAL: -- { system("acroread "PREFIX"/cluster/doc/cluster3.pdf &"); -+ { system("xpdf "PREFIX"/share/doc/cluster-1.36/cluster3.pdf &"); - break; - } - case CMD_HELP_DOWNLOAD: -- { system("netscape http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/manual/index.html &"); -+ { system("xdg-open http://bonsai.ims.u-tokyo.ac.jp/~mdehoon/software/cluster/manual/index.html &"); - break; - } - case CMD_HELP_FILEFORMAT: -@@ -1852,7 +1852,7 @@ - XtManageChild(widget); - free(helptext); - n = 0; -- pixmap = XmGetPixmap(XtScreen(dialog),PREFIX"/cluster/format.xpm",0,0); -+ pixmap = XmGetPixmap(XtScreen(dialog),PREFIX"/share/doc/cluster-1.36/format.xpm",0,0); - XtSetArg(args[n], XmNx, 10); n++; - XtSetArg(args[n], XmNy, 410); n++; - XtSetArg(args[n],XmNlabelType, XmPIXMAP); n++; diff --git a/sci-biology/clview/Manifest b/sci-biology/clview/Manifest deleted file mode 100644 index 271e4eb76..000000000 --- a/sci-biology/clview/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST clview_linux_i386.tar.gz 1050318 BLAKE2B c5c52662df29a0f70a5355c0f2f563e8fef0ec473a707aed0c51d79bd1f1d7e9555139a21bb0c83c509fbac549d8c532d2af8d9ecb9af77b329be581f255493f SHA512 2fbd5ed5ef7bb96a715537a1b1d8f0957e5733d2603aacc5a0dba5a5002a27483ca57dd53780204a98d5ce05ac1090e3d04a3b2784cec021f0afc545e98b35b1 -DIST clview_src.tar.gz 62178 BLAKE2B b116a03c6ddba0caf77168fdd9e39bb86f4b1eccc0535dcd9f81a1e7c2a9b81c1219a4786ae37944abeb4913633acd9cf6b94824adba9851359a955440d9f21f SHA512 24c115b76041981d6dba731180485108d92cccc4719fe6982a135d73c3d18deed2e89ebb6d7daeb8d79941084ec912be2c3333369ec0bf403f96a156932909b9 diff --git a/sci-biology/clview/clview-0.1.ebuild b/sci-biology/clview/clview-0.1.ebuild deleted file mode 100644 index 2f200426d..000000000 --- a/sci-biology/clview/clview-0.1.ebuild +++ /dev/null @@ -1,108 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DESCRIPTION="clview is an assembly .ace file viewer from TIGR Gene Indices project tools" -HOMEPAGE="https://sourceforge.net/projects/clview" -SRC_URI=" - https://sourceforge.net/projects/clview/files/source%20code/clview_src.tar.gz - ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/clview/clview_src.tar.gz - ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/clview/clview_linux_i386.tar.gz" - -# the ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/tgicl/tgi_cpp_library.tar.gz -# contain maybe an older but definitely larger set of .cpp files compared to clview/gcl/ -# contents. clview compiles against both versions with same warning messages from g++. -# -# mokrejs@vrapenec$ ls -la /var/tmp/portage/sci-biology/clview-0.1/work/gclib/ -# total 188 -# drwxr-xr-x 2 mmokrejs mmokrejs 4096 Dec 2 22:23 . -# drwx------ 5 mmokrejs portage 4096 Dec 2 22:23 .. -# -rw-r--r-- 1 mmokrejs mmokrejs 11632 Sep 17 2008 AceParser.cpp -# -rw-r--r-- 1 mmokrejs mmokrejs 906 Sep 14 2008 AceParser.h -# -rw-r--r-- 1 mmokrejs mmokrejs 32276 Dec 2 22:23 AceParser.o -# -rw-r--r-- 1 mmokrejs mmokrejs 11012 Jan 22 2009 GBase.cpp -# -rw-r--r-- 1 mmokrejs mmokrejs 9200 Dec 16 2008 GBase.h -# -rw-r--r-- 1 mmokrejs mmokrejs 8844 Dec 2 22:23 GBase.o -# -rw-r--r-- 1 mmokrejs mmokrejs 16813 Jul 29 2008 GHash.hh -# -rw-r--r-- 1 mmokrejs mmokrejs 16516 Sep 10 2008 GList.hh -# -rw-r--r-- 1 mmokrejs mmokrejs 11221 Jan 22 2009 LayoutParser.cpp -# -rw-r--r-- 1 mmokrejs mmokrejs 6246 Sep 14 2008 LayoutParser.h -# -rw-r--r-- 1 mmokrejs mmokrejs 32956 Dec 2 22:23 LayoutParser.o -# mokrejs@vrapenec$ ls -la /var/tmp/portage/sci-biology/clview-0.1/work/tgi_cl/gcl/ -# total 268 -# drwxr-xr-x 2 mmokrejs mmokrejs 4096 Nov 18 2008 . -# drwxr-xr-x 3 mmokrejs mmokrejs 4096 Oct 18 2006 .. -# -rw-r--r-- 1 mmokrejs mmokrejs 9515 Nov 7 2005 AceParser.cpp -# -rw-r--r-- 1 mmokrejs mmokrejs 886 Nov 7 2005 AceParser.h -# -rw-r--r-- 1 mmokrejs mmokrejs 10768 Nov 7 2005 BitHash.hh -# -rw-r--r-- 1 mmokrejs mmokrejs 7250 Nov 7 2005 GArgs.cpp -# -rw-r--r-- 1 mmokrejs mmokrejs 2507 Nov 7 2005 GArgs.h -# -rw-r--r-- 1 mmokrejs mmokrejs 10156 Nov 18 2008 GBase.cpp -# -rw-r--r-- 1 mmokrejs mmokrejs 8142 Nov 18 2008 GBase.h -# -rw-r--r-- 1 mmokrejs mmokrejs 14742 Nov 7 2005 GCdbYank.cpp -# -rw-r--r-- 1 mmokrejs mmokrejs 1831 Nov 7 2005 GCdbYank.h -# -rw-r--r-- 1 mmokrejs mmokrejs 16723 Nov 7 2005 GFastaFile.h -# -rw-r--r-- 1 mmokrejs mmokrejs 16245 Nov 7 2005 GHash.hh -# -rw-r--r-- 1 mmokrejs mmokrejs 15561 Nov 7 2005 GList.hh -# -rw-r--r-- 1 mmokrejs mmokrejs 28 Nov 7 2005 GReadBuf.cpp -# -rw-r--r-- 1 mmokrejs mmokrejs 4022 Nov 7 2005 GReadBuf.h -# -rw-r--r-- 1 mmokrejs mmokrejs 48 Nov 7 2005 GShMem.cpp -# -rw-r--r-- 1 mmokrejs mmokrejs 4012 Nov 7 2005 GShMem.h -# -rw-r--r-- 1 mmokrejs mmokrejs 32875 Nov 7 2005 GString.cpp -# -rw-r--r-- 1 mmokrejs mmokrejs 8453 Nov 7 2005 GString.h -# -rw-r--r-- 1 mmokrejs mmokrejs 11157 Nov 7 2005 LayoutParser.cpp -# -rw-r--r-- 1 mmokrejs mmokrejs 6063 Nov 7 2005 LayoutParser.h -# -rw-r--r-- 1 mmokrejs mmokrejs 20253 Nov 7 2005 gcdb.cpp -# -rw-r--r-- 1 mmokrejs mmokrejs 6941 Nov 7 2005 gcdb.h -# -rw-r--r-- 1 mmokrejs mmokrejs 8998 Nov 7 2005 gcompress.cpp -# -rw-r--r-- 1 mmokrejs mmokrejs 3670 Nov 7 2005 gcompress.h -# - -LICENSE="Artistic" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -DEPEND="=x11-libs/fox-1.6*" -RDEPEND="${DEPEND}" - -S=${WORKDIR} - -src_unpack() { - unpack clview_src.tar.gz -} - -src_prepare() { - default - # FIXME: we have to run `/usr/bin/fox-config --cflags' to yield - # `-I/usr/include/fox-1.6' - # similarly `fox-config --libs' to yield e.g. - # `-lFOX-1.6 -lXext -lX11 -lXft -lXrender -lfontconfig -lfreetype -lz -lX11 - # -lXcursor -lXrandr -ldl -lpthread -lrt -ljpeg -lpng -ltiff -lz -lbz2 -lm - # -lcups -lnsl -lGLU -lGL' - FOXVERSION=`WANT_FOX="1.6" fox-config --version` - FOXPREFIX=`WANT_FOX="1.6" fox-config --prefix` - FOXINCPATH=`WANT_FOX="1.6" fox-config --cflags` - FOXLIBS=`WANT_FOX="1.6" fox-config --libs` - einfo "Discovered path to fox ${FOXVERSION} files: ${FOXINCPATH}\n${FOXLIBS}" - - sed -i "s#FOXPREFIX = /mylocal/geo#FOXPREFIX = ${FOXPREFIX}#" clview/Makefile || die "Failed to hack FOXPREFIX in clview/Makefile" - sed -i "s#FOXINCDIR := .*#FOXINCDIR := ${FOXINCPATH}#" clview/Makefile || die "Failed to hack FOXINCDIR in clview/Makefile" - sed -i "s#-I\${FOXINCDIR}#\${FOXINCDIR}#" clview/Makefile || die "Failed to revert the extra -I we introduced on a previous line to clview/Makefile" - sed -i "s#FOXLIBDIR := .*#FOXLIBDIR := ${FOXPREFIX}/lib#" clview/Makefile || die "Failed to hack FOXLIBDIR in clview/Makefile" - sed -i "s#LOADLIBS :=.*#LOADLIBS := ${FOXLIBS}#" clview/Makefile || die "Failed to hack LOADLIBS in clview/Makefile" - sed -i "s#-I-#-I #" clview/Makefile || die - - # see tgi_cl/gcl/ - sed -i "s#TGICLASSDIR := /tucan/geo/src/tgi_cl#TGICLASSDIR := ../gcl#" clview/Makefile || die -} - -src_compile(){ - cd "${S}"/clview || die - default -} - -src_install() { - # install at least the binaries for clview when we cannot compile it - dobin clview/clview -} diff --git a/sci-biology/clview/metadata.xml b/sci-biology/clview/metadata.xml deleted file mode 100644 index 7adf609cd..000000000 --- a/sci-biology/clview/metadata.xml +++ /dev/null @@ -1,15 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">clview</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/codonw/codonw-1.4.4-r2.ebuild b/sci-biology/codonw/codonw-1.4.4-r2.ebuild index 6478e9169..49bf65452 100644 --- a/sci-biology/codonw/codonw-1.4.4-r2.ebuild +++ b/sci-biology/codonw/codonw-1.4.4-r2.ebuild @@ -6,9 +6,9 @@ EAPI=7 inherit toolchain-funcs DESCRIPTION="Multivariate statistical analysis of codon and amino acid usage" -HOMEPAGE="http://codonw.sourceforge.net/" +HOMEPAGE="https://codonw.sourceforge.net/" SRC_URI="mirror://sourceforge/${PN}/CodonWSourceCode_${PV//./_}.tar.gz - http://codonw.sourceforge.net/JohnPedenThesisPressOpt_water.pdf" + https://codonw.sourceforge.net/JohnPedenThesisPressOpt_water.pdf" LICENSE="GPL-2" SLOT="0" diff --git a/sci-biology/coral/coral-1.4.1.ebuild b/sci-biology/coral/coral-1.4.1.ebuild index bfa2fc85a..0481e5e80 100644 --- a/sci-biology/coral/coral-1.4.1.ebuild +++ b/sci-biology/coral/coral-1.4.1.ebuild @@ -6,8 +6,8 @@ EAPI=7 inherit toolchain-funcs DESCRIPTION="Error corrector for Illumina and Roche/454 reads using multiple alignment info" -HOMEPAGE="http://www.cs.helsinki.fi/u/lmsalmel/coral" -SRC_URI="http://www.cs.helsinki.fi/u/lmsalmel/coral/${P}.tar.gz" +HOMEPAGE="https://www.cs.helsinki.fi/u/lmsalmel/coral" +SRC_URI="https://www.cs.helsinki.fi/u/lmsalmel/coral/${P}.tar.gz" LICENSE="GPL-3" SLOT="0" diff --git a/sci-biology/cutadapt/Manifest b/sci-biology/cutadapt/Manifest deleted file mode 100644 index 30063661a..000000000 --- a/sci-biology/cutadapt/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -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-2.10.ebuild b/sci-biology/cutadapt/cutadapt-2.10.ebuild deleted file mode 100644 index c0c263469..000000000 --- a/sci-biology/cutadapt/cutadapt-2.10.ebuild +++ /dev/null @@ -1,42 +0,0 @@ -# Copyright 1999-2020 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 - dev-python/sphinx - dev-python/sphinx-issues - ) -" - -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/cutadapt-3.3.ebuild b/sci-biology/cutadapt/cutadapt-3.3.ebuild deleted file mode 100644 index e1990f222..000000000 --- a/sci-biology/cutadapt/cutadapt-3.3.ebuild +++ /dev/null @@ -1,42 +0,0 @@ -# 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 deleted file mode 100644 index c2dc2a741..000000000 --- a/sci-biology/cutadapt/files/cutadapt-3.3-skiptest.patch +++ /dev/null @@ -1,13 +0,0 @@ -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/cutadapt/metadata.xml b/sci-biology/cutadapt/metadata.xml deleted file mode 100644 index 6a2aeb852..000000000 --- a/sci-biology/cutadapt/metadata.xml +++ /dev/null @@ -1,20 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="person"> - <email>gentoo@aisha.cc</email> - <name>Aisha Tammy</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="github">marcelm/cutadapt</remote-id> - <remote-id type="pypi">cutadapt</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/dcm2niix/metadata.xml b/sci-biology/dcm2niix/metadata.xml index 9c9e19081..773e706a6 100644 --- a/sci-biology/dcm2niix/metadata.xml +++ b/sci-biology/dcm2niix/metadata.xml @@ -19,4 +19,7 @@ format to the NIfTI format. ICOM provides many ways to store/compress image data, known as transfer syntaxes. </longdescription> + <upstream> + <remote-id type="github">rordenlab/dcm2niix</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/dcmstack/Manifest b/sci-biology/dcmstack/Manifest index ca8d74137..ab8414c4e 100644 --- a/sci-biology/dcmstack/Manifest +++ b/sci-biology/dcmstack/Manifest @@ -1 +1 @@ -DIST dcmstack-0.8.tar.gz 1740289 BLAKE2B d57276c02db3f6a64874635528cb98d874cbc4f64464cfe47aa7217db96caddd46465e9275fced32363a22076b0b75e8c27649aac2fc15133d1354d7dd3b039e SHA512 c6ba0933e173f63426af60fb34fe671c9b49d3cf958628c15920f99925368a14f40c7821c1972c247e7f91c73be3bba288bf8794f334f32fef1feba4c5d5e7c1 +DIST dcmstack-0.9.gh.tar.gz 1739820 BLAKE2B 08b65589b1317ab7ac16a5ac126cf6fba7933941b0b929baa689fb72425f590fb98ae967908b358d5316f5009aa6443787e7077c13f22f156d3fae67a9b8396c SHA512 8061f55c0fa467c3fae94f8790f01331d377d8552cf7a896d705b3cf895340051aad7a4a79237cc225f587d2411be23255635970ab4067d1e5a37f82407b4b39 diff --git a/sci-biology/dcmstack/dcmstack-0.8.ebuild b/sci-biology/dcmstack/dcmstack-0.8.ebuild deleted file mode 100644 index de4dfde54..000000000 --- a/sci-biology/dcmstack/dcmstack-0.8.ebuild +++ /dev/null @@ -1,25 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7..9} ) - -inherit distutils-r1 - -DESCRIPTION="DICOM to Nifti coversion" -HOMEPAGE="https://dcmstack.readthedocs.org/en/latest/" -SRC_URI="https://github.com/moloney/dcmstack/archive/v${PV}.tar.gz -> ${P}.tar.gz" -EGIT_REPO_URI="https://github.com/moloney/dcmstack" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -RDEPEND=" - sci-libs/nibabel[${PYTHON_USEDEP}] - sci-libs/pydicom[${PYTHON_USEDEP}] -" - -distutils_enable_tests setup.py diff --git a/sci-biology/dcmstack/dcmstack-0.9.ebuild b/sci-biology/dcmstack/dcmstack-0.9.ebuild new file mode 100644 index 000000000..d207526c0 --- /dev/null +++ b/sci-biology/dcmstack/dcmstack-0.9.ebuild @@ -0,0 +1,25 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) + +inherit distutils-r1 + +DESCRIPTION="DICOM to Nifti coversion" +HOMEPAGE="https://dcmstack.readthedocs.org/en/latest/" +SRC_URI="https://github.com/moloney/dcmstack/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" + +RDEPEND=" + sci-libs/nibabel[${PYTHON_USEDEP}] + sci-libs/pydicom[${PYTHON_USEDEP}] +" + +distutils_enable_tests pytest diff --git a/sci-biology/dcmstack/metadata.xml b/sci-biology/dcmstack/metadata.xml index ae9640ffb..0272cf14e 100644 --- a/sci-biology/dcmstack/metadata.xml +++ b/sci-biology/dcmstack/metadata.xml @@ -5,4 +5,7 @@ <email>sci@gentoo.org</email> <name>Gentoo Science Project</name> </maintainer> + <upstream> + <remote-id type="github">moloney/dcmstack</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/deeptools-intervals/deeptools-intervals-0.1.9.ebuild b/sci-biology/deeptools-intervals/deeptools-intervals-0.1.9.ebuild index 1eecdd1b9..38f9aea0f 100644 --- a/sci-biology/deeptools-intervals/deeptools-intervals-0.1.9.ebuild +++ b/sci-biology/deeptools-intervals/deeptools-intervals-0.1.9.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7,8,9} ) +PYTHON_COMPAT=( python3_{10..11} ) inherit distutils-r1 diff --git a/sci-biology/deeptools-intervals/metadata.xml b/sci-biology/deeptools-intervals/metadata.xml index 08881e6e4..853bd539c 100644 --- a/sci-biology/deeptools-intervals/metadata.xml +++ b/sci-biology/deeptools-intervals/metadata.xml @@ -6,6 +6,6 @@ <name>Gentoo Biology Project</name> </maintainer> <upstream> - <remote-id type="github">fidelram/deepTools_intervals</remote-id> + <remote-id type="github">deeptools/deeptools_intervals</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/deeptools/Manifest b/sci-biology/deeptools/Manifest index 31a5bdb90..649a31cdf 100644 --- a/sci-biology/deeptools/Manifest +++ b/sci-biology/deeptools/Manifest @@ -1 +1,2 @@ DIST deeptools-3.5.0.tar.gz 62553343 BLAKE2B a8cd1520b96c50ad36667405677cf422a74376d88f0716f83cc0c6f58d01aefcf47ac1b862aa98b8801e61445d59831dbc9246660e2f41a5b3e0ed3d6573ad50 SHA512 699734c8a863ec76dfead728e3227bbe3ec04d62e91f447269a6aa8406d627ff618837b85ab2e31cc635c671e1d62230c4db0992106bbe921281b81164387b38 +DIST deeptools-3.5.1.tar.gz 62552044 BLAKE2B 3c785ba478b88fbbe7ba2617e2d05984b8a897f787e85d6f8f144f596af07b9e16ba920c8adee35efc4b1b067f255e81f66cf746aaea43e5ee61c23c4d15c9c3 SHA512 f7618f1a51b975d42712a38e13e9ab2ddfeafffe24d81fdab41f1ef7c2e44fd09da0351210670b0036bf72e7af11b679417275adce300ae9fabe4b5339ee9810 diff --git a/sci-biology/deeptools/deeptools-3.5.0.ebuild b/sci-biology/deeptools/deeptools-3.5.0.ebuild index f53a19bcb..7c2eaa739 100644 --- a/sci-biology/deeptools/deeptools-3.5.0.ebuild +++ b/sci-biology/deeptools/deeptools-3.5.0.ebuild @@ -1,9 +1,10 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7,8,9} ) +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) inherit distutils-r1 @@ -13,7 +14,7 @@ SRC_URI="https://github.com/deeptools/deepTools/archive/${PV}.tar.gz -> ${P}.tar LICENSE="BSD" SLOT="0" -KEYWORDS="~amd64 ~x86" +KEYWORDS="~amd64" # TODO: fix this RESTRICT="test" @@ -23,7 +24,7 @@ RDEPEND=" >=dev-python/numpy-1.9.0[${PYTHON_USEDEP}] >=dev-python/numpydoc-0.5[${PYTHON_USEDEP}] >=dev-python/scipy-0.17.0[${PYTHON_USEDEP}] - >=dev-python/plotly-2.0.0[${PYTHON_USEDEP}] + dev-python/plotly[${PYTHON_USEDEP}] >=dev-python/py2bit-0.2.0[${PYTHON_USEDEP}] >=dev-python/pyBigWig-0.2.1[${PYTHON_USEDEP}] >=sci-biology/pysam-0.14.0[${PYTHON_USEDEP}] @@ -32,5 +33,5 @@ RDEPEND=" S="${WORKDIR}/deepTools-${PV}" -distutils_enable_sphinx docs dev-python/sphinx_rtd_theme dev-python/sphinx-argparse -distutils_enable_tests nose +distutils_enable_sphinx docs dev-python/sphinx-rtd-theme dev-python/sphinx-argparse +#distutils_enable_tests nose diff --git a/sci-biology/deeptools/deeptools-3.5.1.ebuild b/sci-biology/deeptools/deeptools-3.5.1.ebuild new file mode 100644 index 000000000..7c2eaa739 --- /dev/null +++ b/sci-biology/deeptools/deeptools-3.5.1.ebuild @@ -0,0 +1,37 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) + +inherit distutils-r1 + +DESCRIPTION="Extract reads from BAM files, normalize, draw figures, convert BAM to bigWig" +HOMEPAGE="https://github.com/deeptools/deepTools" +SRC_URI="https://github.com/deeptools/deepTools/archive/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" + +# TODO: fix this +RESTRICT="test" + +RDEPEND=" + >=sci-biology/deeptools-intervals-0.1.8[${PYTHON_USEDEP}] + >=dev-python/numpy-1.9.0[${PYTHON_USEDEP}] + >=dev-python/numpydoc-0.5[${PYTHON_USEDEP}] + >=dev-python/scipy-0.17.0[${PYTHON_USEDEP}] + dev-python/plotly[${PYTHON_USEDEP}] + >=dev-python/py2bit-0.2.0[${PYTHON_USEDEP}] + >=dev-python/pyBigWig-0.2.1[${PYTHON_USEDEP}] + >=sci-biology/pysam-0.14.0[${PYTHON_USEDEP}] + >=dev-python/matplotlib-3.1.0[${PYTHON_USEDEP}] +" + +S="${WORKDIR}/deepTools-${PV}" + +distutils_enable_sphinx docs dev-python/sphinx-rtd-theme dev-python/sphinx-argparse +#distutils_enable_tests nose diff --git a/sci-biology/diamond/metadata.xml b/sci-biology/diamond/metadata.xml index 138cb7705..ac7dfc24a 100644 --- a/sci-biology/diamond/metadata.xml +++ b/sci-biology/diamond/metadata.xml @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">bbuchfink/diamond</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/dipy/dipy-1.1.1.ebuild b/sci-biology/dipy/dipy-1.1.1.ebuild index c2c9f724e..3656d6dc8 100644 --- a/sci-biology/dipy/dipy-1.1.1.ebuild +++ b/sci-biology/dipy/dipy-1.1.1.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7..9} ) +PYTHON_COMPAT=( python3_10 ) inherit distutils-r1 diff --git a/sci-biology/dipy/dipy-9999.ebuild b/sci-biology/dipy/dipy-9999.ebuild deleted file mode 100644 index a1b162df6..000000000 --- a/sci-biology/dipy/dipy-9999.ebuild +++ /dev/null @@ -1,37 +0,0 @@ -# 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 git-r3 - -DESCRIPTION="Computational neuroanatomy project focusing on diffusion MRI" -HOMEPAGE="https://github.com/nipy/dipy" -SRC_URI="" -EGIT_REPO_URI="https://github.com/nipy/dipy" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="" -IUSE="test" -RESTRICT="!test? ( test )" - -RDEPEND=" - sci-libs/nibabel[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/scipy[${PYTHON_USEDEP}] -" -DEPEND=" - dev-python/cython[${PYTHON_USEDEP}] - dev-python/h5py[${PYTHON_USEDEP}] - dev-python/setuptools[${PYTHON_USEDEP}] - test? ( dev-python/nose[${PYTHON_USEDEP}] ) -" - -python_test() { - distutils_install_for_testing - cd "${TEST_DIR}"/lib || die - nosetests || die -} diff --git a/sci-biology/drlfom_bidsdata/drlfom_bidsdata-1.1.ebuild b/sci-biology/drlfom_bidsdata/drlfom_bidsdata-1.1.ebuild index 227aafd54..8ddd4007e 100644 --- a/sci-biology/drlfom_bidsdata/drlfom_bidsdata-1.1.ebuild +++ b/sci-biology/drlfom_bidsdata/drlfom_bidsdata-1.1.ebuild @@ -1,12 +1,12 @@ -# Copyright 1999-2022 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 inherit check-reqs DESCRIPTION="BIDS data files released with the DRLFOM publication" -HOMEPAGE="http://www.aic-fmi.ethz.ch/" +HOMEPAGE="https://chymera.eu/docs/focus/open-science/" SRC_URI=" https://zenodo.org/record/3598424/files/${P}.tar.xz " @@ -15,9 +15,6 @@ LICENSE="CC-BY-SA-4.0" SLOT="0" KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -RDEPEND="" -DEPEND="" - pkg_pretend() { CHECKREQS_DISK_BUILD="21G" check-reqs_pkg_pretend diff --git a/sci-biology/estscan/Manifest b/sci-biology/estscan/Manifest deleted file mode 100644 index 79281bc74..000000000 --- a/sci-biology/estscan/Manifest +++ /dev/null @@ -1,9 +0,0 @@ -DIST At.smat.gz 32314 BLAKE2B c48c043fa7e7e26e406a677587380e0ade911aafb5878988668da9b9f09a978a369e636c931d2d4d65b6efc65398723e1a78c032805cfc71f2927a42d87788c4 SHA512 aeb3dec65b730570d70e8f49930bf85cc73fe39696d2ccc08e6a804cfe435ea43423f1f4a02b192c68da03727b628bb43ec0ba27bb4549e59f743eccd203df09 -DIST BTLib-0.19.tar.gz 36283 BLAKE2B 53d26fdc7fee3325104a7f2041617bbde464421c540b29c7d47381c60d8f837601e7274d9f0ef5694d1b86b3e2cc7e9a0b289090c3c957a343542e3e7305cd50 SHA512 00261daa7fab4d16dec9e9d4f9e382cc804a10c0ed6b813d6223902b53f6b260dc0a242acfab93897afa750e949ab3f21ecae537206d81eb712f06289387f7d2 -DIST Dm.smat.gz 31711 BLAKE2B 5e8da0668d0788ce2e70535605cb85ced4ec052c4e736b11d838919c0328c6978170aed8e6102d62c6f8770a99a7f49aad373492ddc79328df3238486b7ee703 SHA512 fe141598291fd1bead1f0918c2e52533db1f5c5f60d4c71838a16298ccf60a8a1857a02379f58979dbab3cfad4e0ac64556cf629fcb65d9a0e6861fe4ca163a4 -DIST Dr.smat.gz 8813 BLAKE2B 465d980cc9c1d61f8a83e4c3dd203852b2cfa4bde5730de268655d7a05db9d018f6cff6357246bbfc42002f3993aebf44c9fc27c2d31fa6657194600e5a364b0 SHA512 1880981db252ed08a762fdc8a321b27063ea2341cde56c40146cc7eeed0fdfa620e9b4c71c245fffee6521ae1efbc89b52e6558cd84aef89138e8b26b60460de -DIST Hs.smat.gz 62935 BLAKE2B 4089dbcc54af5544071d9fc270a9048c758fef15e4846f92dc9c61abd5c60ba9d8ba4a25b9064f4d418cbe1a8a277c5bba49af9a85f51dd9f3bcaac30a7b568d SHA512 7ac3af9b018992014643fbbd83abc4128df4c8b9c516fb1b6b16e1fdc65b23df07811fa5b23ecec5ef2993de71e3efaec5bee3fc1626bcf2984794f13e343447 -DIST Mm.smat.gz 62711 BLAKE2B c65aeb6f8833e4effb360de29e3c25985184e4a9822272f370fc292ec2142843b78ac66485ec98b017aac3a18b7936fc45b510f58cb2db909d5230291573bdf3 SHA512 4ee5fac326bee7e4fe17ad9eab608a90007485a90b479557a181eb49628ff5fee22d04a3ef360b6bc29a76709723faa0a9df8ef1cdb40421d772a0b2dc9f3fc5 -DIST Rn.smat.gz 32388 BLAKE2B 06144cce26cd35eeb15d94db5f169a9cf6c6ab02b4c4f213e42140b2fe864473e7c107c910092620f255384eadd1e07a366e58a21d3df570e63e2843e537aaa3 SHA512 e517d95aa4d1928f766ac9cc885f277d9f980d27265dcc7a2c5d747b1023a5606bccb2dbce2fa9ff76fc0f0333fadd3bc0b7abe9ea4aa82396b57bb06b8dcf43 -DIST estscan-3.0.3.tar.gz 46412 BLAKE2B 998f4f117503e044492495d52e5b064fcb62c3800adb4ec4b357042ea90d8c6ce86902257e5b28ee119c2b332044389c8775101bad6875cba069db6961f73931 SHA512 d3ddb91a71a700a67807a63f7b9c9e2a1c45af847a7808afd757f60f276f7410e22adde6e0ffadbfef8e579890b79fe785b8a05e28cb3d67345464cd2035f69c -DIST user_guide_fev_07.pdf 327005 BLAKE2B 5d66466c122c12618c5aadb2f12a404159b553b57e80fa421d707d8c3e70d795da7285a6976beacd67b7c6462297fde7843b89b48ed773752cdc0e00bfd1c36c SHA512 de1f046656c3e01a9b3e3930aadc7a91cb10d907a9d6af8fc1c2b0abe6ef0d1305baaeee463c80df0c700951a03b1c26a211fdd14e76fbf41ac5fca3467e49c1 diff --git a/sci-biology/estscan/estscan-3.0.3.ebuild b/sci-biology/estscan/estscan-3.0.3.ebuild deleted file mode 100644 index a0992b76b..000000000 --- a/sci-biology/estscan/estscan-3.0.3.ebuild +++ /dev/null @@ -1,124 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit fortran-2 perl-module toolchain-funcs - -DESCRIPTION="Prediction of coding regions in DNA/RNA sequences" -HOMEPAGE="https://sourceforge.net/projects/estscan/" -SRC_URI=" - https://downloads.sourceforge.net/${PN}/${P}.tar.gz - https://downloads.sourceforge.net/${PN}/At.smat.gz - https://downloads.sourceforge.net/${PN}/Dm.smat.gz - https://downloads.sourceforge.net/${PN}/Dr.smat.gz - https://downloads.sourceforge.net/${PN}/Hs.smat.gz - https://downloads.sourceforge.net/${PN}/Mm.smat.gz - https://downloads.sourceforge.net/${PN}/Rn.smat.gz - https://downloads.sourceforge.net/${PN}/user_guide_fev_07.pdf - https://downloads.sourceforge.net/${PN}/BTLib-0.19.tar.gz" - -SLOT="0" -LICENSE="estscan" -KEYWORDS="~amd64 ~x86" -IUSE="icc ifc" - -DEPEND=" - dev-perl/BTLib - icc? ( dev-lang/icc ) - ifc? ( dev-lang/ifc )" -RDEPEND="${DEPEND}" - -S="${WORKDIR}" - -src_prepare() { - default - sed \ - -e 's/\\rm -f/rm -rf/' \ - -e 's/^ LDFLAGS = -lm/LDFLAGS = -lm/' \ - -i "${P}"/Makefile || die "failed to edit Makefile" - - # fix hard-coded paths - sed -e 's+/usr/molbio/share/ESTScan+/usr/share/ESTscan+' -i "${P}"/${PN}.c || die - sed -e 's+/usr/molbio/share/ESTScan+/usr/share/ESTscan+' -i "${P}"/${PN}.spec || die - - if ! use icc; then - sed \ - -e 's/^ CFLAGS = -O2/#CFLAGS = ${CFLAGS}/' -i "${P}"/Makefile || die - fi - - if ! use ifc; then - sed \ - -e 's/^ FFLAGS = -O2/#FFLAGS = ${FFLAGS}/' \ - -e "s/^ F77 = g77/F77 = $(tc-getF77)/" -i "${P}"/Makefile \ - || die - fi - - if use icc; then - # FIXME: I would use $(tc-getCC) instead of hard-coded icc but it gives - # me gcc instead, same for $(tc-getF77) - # Moreover, the if/else logic here should separate users having only icc - # while not ifort (and vice-versa) from those having only - # gcc/gfortran/g77 - # - # FIXME: below as a dirty hack I force gfortran instead of ifort for - # my testing purposes. Didn't ebuild contain "PROVIDES" line? - # Same for FFLAGS. - sed \ - -e "s:^# CC = icc:CC = icc:" \ - -e "s:^# CFLAGS = -O3 -ipo -axP:#CFLAGS = -O3 -ipo -axP:" \ - -e "s/^ CFLAGS = -O2/#CFLAGS = -O2/" \ - -e "s/^ CC = gcc/# CC = gcc/" \ - -i "${P}"/Makefile || die "sed failed to fix CFLAGS and CC" - - fi - - if use ifc; then - sed \ - -e "s:^# FFLAGS = -O3 -ipo -axP:#FFLAGS = -O3 -ipo -axP:" \ - -e "s/^# F77 = ifort/F77 = gfortran/" \ - -e "s/^ FFLAGS = -O2/#FFLAGS = -O2/" \ - -e "s/^ F77 = g77/# F77 = g77/" \ - -i "${P}"/Makefile || die "sed failed to fix FFLAGS and F77" - fi -} - -src_compile() { - emake -C ${P} -} - -src_install() { - # FIXME: Some kind of documentation is in {P}/${PN}.spec - cd ${P} || die "Failed to chdir to ${P}" - dobin \ - build_model ${PN} evaluate_model extract_EST extract_UG_EST \ - extract_mRNA makesmat maskred prepare_data winsegshuffle - # the file build_model_utils.pl should go into some PERL site-packages dir - # see {P}/${PN}.spec - - # install the doc (but is not in ${WORKDIR} because src_unpack() failed on it as it has .pdf extension - insinto /usr/share/doc/${PN} - # grab the file directly from ../distdir/ - doins "${DISTDIR}"/user_guide_fev_07.pdf - - # install the default precomputed matrices - cd "${WORKDIR}" || die "Failed to chdir to ${WORKDIR}" - insinto /usr/share/${PN} - doins *.smat - - # install BTlib (in perl) - # dobin fetch indexer netfetch - insinto /usr/share/${PN}/ - # install the config file which is packed inside the BTLib tarball while is not - # being installed by dev-perl/BTLib - doins "${WORKDIR}"/BTLib-0.19/fetch.conf - - # FIXME: install the *.pm files from BTLib-0.19 - # cd "${WORKDIR}"/BTLib-0.19 || die "Failed to chdir to "${WORKDIR}"/BTLib-0.19 - # myinst="DESTDIR=${D}" - # perl-module_src_install - - einfo "Please edit /usr/share/${PN}/fetch.conf to fit your local database layout." - einfo "Also create your own scoring matrices and place them into /usr/share/${PN}/." - einfo "You may follow the hints from http://${PN}.sourceforge.net/" -} diff --git a/sci-biology/estscan/metadata.xml b/sci-biology/estscan/metadata.xml deleted file mode 100644 index c79c2d1b5..000000000 --- a/sci-biology/estscan/metadata.xml +++ /dev/null @@ -1,19 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <use> - <flag name="icc">Undocumented USE</flag> - <flag name="ifc">Undocumented USE</flag> - </use> - <upstream> - <remote-id type="sourceforge">downloads</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/fastp/Manifest b/sci-biology/fastp/Manifest new file mode 100644 index 000000000..c158050fa --- /dev/null +++ b/sci-biology/fastp/Manifest @@ -0,0 +1 @@ +DIST fastp-0.23.4.tar.gz 164071 BLAKE2B 58745d494b83bbf9ae34593159228dbef5c854ab856af91fea8770fef171ed7b3053a4cac8c31053af3dcd91d4298fddb7594670a32963f53f75bd5fa1ec3a68 SHA512 2c929e974708f8cd2d8cab95d59c0a5fd01bea912f6ba5d08841fd929f0f5019ef89e506c771057bd02b879836ae30564b8417271866b6bbcb4917fbeb387e76 diff --git a/sci-biology/fastp/fastp-0.23.4.ebuild b/sci-biology/fastp/fastp-0.23.4.ebuild new file mode 100644 index 000000000..70d5ce330 --- /dev/null +++ b/sci-biology/fastp/fastp-0.23.4.ebuild @@ -0,0 +1,20 @@ +# Copyright 1999-2023 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DESCRIPTION="An ultra-fast all-in-one FASTQ preprocessor" +HOMEPAGE="https://github.com/OpenGene/fastp" +SRC_URI="https://github.com/OpenGene/fastp/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz" +KEYWORDS="~amd64" + +LICENSE="MIT" +SLOT="0" + +DEPEND="app-arch/libdeflate + dev-libs/isa-l" + +src_install() { + dodir /usr/bin + emake PREFIX="${ED}"/usr install +} diff --git a/sci-biology/fastp/metadata.xml b/sci-biology/fastp/metadata.xml new file mode 100644 index 000000000..d51d87c5a --- /dev/null +++ b/sci-biology/fastp/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>mschu.dev@gmail.com</email> + <name>Michael Schubert</name> + </maintainer> + <upstream> + <remote-id type="github">OpenGene/fastp</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/fastqc/metadata.xml b/sci-biology/fastqc/metadata.xml index 7c86089a2..f13c6ccba 100644 --- a/sci-biology/fastqc/metadata.xml +++ b/sci-biology/fastqc/metadata.xml @@ -13,4 +13,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">s-andrews/FastQC</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/ffindex/metadata.xml b/sci-biology/ffindex/metadata.xml index 138cb7705..a9577a9c3 100644 --- a/sci-biology/ffindex/metadata.xml +++ b/sci-biology/ffindex/metadata.xml @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">ahcm/ffindex</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/fsa/fsa-1.15.9.ebuild b/sci-biology/fsa/fsa-1.15.9.ebuild index 44e1d5cff..f77ae61aa 100644 --- a/sci-biology/fsa/fsa-1.15.9.ebuild +++ b/sci-biology/fsa/fsa-1.15.9.ebuild @@ -1,10 +1,10 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 DESCRIPTION="Distance-based probabilistic multiple sequence alignment algo for DNA/RNA/prot" -HOMEPAGE="http://fsa.sourceforge.net" +HOMEPAGE="https://fsa.sourceforge.net" SRC_URI="https://downloads.sourceforge.net/project/fsa/${P}.tar.gz" LICENSE="GPL-3+" diff --git a/sci-biology/fsa/metadata.xml b/sci-biology/fsa/metadata.xml index 0f267b755..e8c9d160f 100644 --- a/sci-biology/fsa/metadata.xml +++ b/sci-biology/fsa/metadata.xml @@ -10,6 +10,6 @@ <name>Gentoo Biology Project</name> </maintainer> <upstream> - <remote-id type="sourceforge">downloads</remote-id> + <remote-id type="sourceforge">fsa</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/fsl/files/fsl-6.0.2-cuda_buildsettings.patch b/sci-biology/fsl/files/fsl-6.0.2-cuda_buildsettings.patch deleted file mode 100644 index a3872acf0..000000000 --- a/sci-biology/fsl/files/fsl-6.0.2-cuda_buildsettings.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff -Naur fsl.orig/config/buildSettings.mk fsl/config/buildSettings.mk ---- fsl.orig/config/buildSettings.mk 2020-07-23 15:43:42.277064365 -0400 -+++ fsl/config/buildSettings.mk 2020-07-23 15:45:17.705069496 -0400 -@@ -141,7 +141,7 @@ - # CUDA development environment - CUDAVER := $(or $(CUDAVER),9.1) - #$(info $$CUDAVER is [${CUDAVER}]) --CUDA_INSTALLATION = /opt/cuda-${CUDAVER} -+CUDA_INSTALLATION = /opt/cuda - GENCODE_FLAGS = $(shell ${FSLDIR}/config/common/supportedGencodes.sh ${CUDA_INSTALLATION}) - LIB_CUDA = ${CUDA_INSTALLATION}/lib64 - INC_CUDA = ${CUDA_INSTALLATION}/include diff --git a/sci-biology/fsl/files/fsl-6.0.2-eddy_cuda.patch b/sci-biology/fsl/files/fsl-6.0.2-eddy_cuda.patch deleted file mode 100644 index 40409ec08..000000000 --- a/sci-biology/fsl/files/fsl-6.0.2-eddy_cuda.patch +++ /dev/null @@ -1,21 +0,0 @@ -diff -Naur fsl.orig/src/eddy/Makefile fsl/src/eddy/Makefile ---- fsl.orig/src/eddy/Makefile 2020-07-30 14:30:06.414884410 -0400 -+++ fsl/src/eddy/Makefile 2020-07-30 14:33:03.400889914 -0400 -@@ -29,6 +29,8 @@ - TMPCXXFLAGS_2= - TMPNAME_1= - TMPNAME_2= -+cuda=1 -+cpu=1 - - ifndef cuda - ifndef cpu #Default single cpu, no threading -@@ -74,7 +75,7 @@ - ifdef NVCC11 - NVCC=${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-6.0.2-gcc10_include.patch b/sci-biology/fsl/files/fsl-6.0.2-gcc10_include.patch deleted file mode 100644 index 9ddb11a2b..000000000 --- a/sci-biology/fsl/files/fsl-6.0.2-gcc10_include.patch +++ /dev/null @@ -1,10 +0,0 @@ ---- a/src/newimage/newimageio.h 2020-06-18 06:05:51.287864975 -0400 -+++ b/src/newimage/newimageio.h 2020-06-18 06:06:27.535129711 -0400 -@@ -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-6.0.2-setup.patch b/sci-biology/fsl/files/fsl-6.0.2-setup.patch deleted file mode 100644 index 39737fd85..000000000 --- a/sci-biology/fsl/files/fsl-6.0.2-setup.patch +++ /dev/null @@ -1,198 +0,0 @@ -From baae97cc3c8d0cadcabb7ed16559f4e4de26ddbe Mon Sep 17 00:00:00 2001 -From: François Bissey <frp.bissey@gmail.com> -Date: Mon, 20 Jan 2020 11:54:37 +1300 -Subject: [PATCH] Adjust the build system so it doesnt build packages - externally provided by portage. Make the compilation flags more generic and - easily adjustable. Make the build system stop at the first fault. - ---- - build | 6 +++--- - config/buildSettings.mk | 20 ++++++++++---------- - config/common/buildproj | 8 +++++--- - config/common/vars.mk | 10 +++++----- - extras/build | 8 ++++---- - src/mist-clean/Makefile | 2 +- - 6 files changed, 28 insertions(+), 26 deletions(-) - -diff --git a/build b/build -index 05dac06c..d90e407b 100755 ---- a/build -+++ b/build -@@ -3,7 +3,7 @@ - if [ $# -ge 1 ] ; then - PROJECTS="$@"; - else -- MASTERPROJECTS="CiftiLib-master utils znzlib NewNifti niftiio fslio giftiio miscmaths newimage libhfunc libvis first_lib \ -+ MASTERPROJECTS="utils znzlib NewNifti niftiio fslio giftiio miscmaths newimage libhfunc libvis first_lib \ - meshclass fslvtkio misc_tcl basisfield warpfns bint shapeModel MVdisc fslvtkconv fslsurface libmeshutils newmesh \ - DiscreteOpt FastPDlib MSMRegLib misc_c dpm topup \ - asl_mfree \ -@@ -80,8 +80,8 @@ xtract"; - done - fi - --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 --git a/config/buildSettings.mk b/config/buildSettings.mk -index b2e1f150..04532fc2 100644 ---- a/config/buildSettings.mk -+++ b/config/buildSettings.mk -@@ -18,7 +18,7 @@ MV = /bin/mv - CHMOD = /bin/chmod - MKDIR = /bin/mkdir - INSTALL = install -p --TCLSH = ${FSLDIR}/bin/fsltclsh -+TCLSH = tclsh - DEPENDFLAGS = -MM - MACHDBGFLAGS = -g - ##################################################################### -@@ -124,19 +124,19 @@ endif # if Darwin - ##################################################################### - ifeq ($(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) -@@ -148,8 +148,8 @@ INC_CUDA = ${CUDA_INSTALLATION}/include - NVCC = ${CUDA_INSTALLATION}/bin/nvcc - ############### External Libs ##################################### - # ZLIB library --LIB_ZLIB = /lib64 --INC_ZLIB = /usr/include -+#LIB_ZLIB = /lib64 -+#INC_ZLIB = /usr/include - # QT library - QTDIR = /usr/lib/qt3 - LIB_QT = ${QTDIR}/lib -diff --git a/config/common/buildproj b/config/common/buildproj -index 2f0f2b8f..48624a1f 100755 ---- a/config/common/buildproj -+++ b/config/common/buildproj -@@ -11,10 +11,10 @@ if [ X$1 = X-strict ] ; then - fi - PROJECTS="$@" ; 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 @@ for projname in $PROJECTS; do - 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 @@ for projname in $PROJECTS; do - if [ $installok = false ] ; then - echo " " - echo "ERROR::Could not install $projname successfully" ; -+ exit 1 - fi - else - echo " " -@@ -90,6 +91,7 @@ for projname in $PROJECTS; do - echo " " - echo " " - errorprojs="$errorprojs $projname" ; export errorprojs ; -+ exit 1 - fi - fi - done -diff --git a/config/common/vars.mk b/config/common/vars.mk -index b027b010..aeeae67c 100755 ---- a/config/common/vars.mk -+++ b/config/common/vars.mk -@@ -24,15 +24,15 @@ USRINCFLAGS = - 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} ${USERCXXFLAGS} - - HFILES = *.h - AFILES = *.a -diff --git a/extras/build b/extras/build -index 59e7a2ed..0d68232e 100755 ---- a/extras/build -+++ b/extras/build -@@ -96,16 +96,16 @@ if [ X"${OS}" = "XDarwin" ]; then - 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 --git a/src/mist-clean/Makefile b/src/mist-clean/Makefile -index 20402cca..6918bee4 100755 ---- a/src/mist-clean/Makefile -+++ b/src/mist-clean/Makefile -@@ -52,6 +52,6 @@ installpython: - cp -r python/* ${DESTDIR}/python/mist - - clean: -- rm -f ${OBJS} mist/mist.o mist/mist -+ rm -f ${OBJS} mist/mist.o mist/mist || echo "CLEAN could not locate some files scheduled for deletion." - - .PHONY: all clean installdata --- -2.24.1 - diff --git a/sci-biology/fsl/fsl-6.0.4.ebuild b/sci-biology/fsl/fsl-6.0.4.ebuild index cd91cf192..6e5d6e779 100644 --- a/sci-biology/fsl/fsl-6.0.4.ebuild +++ b/sci-biology/fsl/fsl-6.0.4.ebuild @@ -151,8 +151,8 @@ src_compile() { # define the default build system to match upstream official standard # -> individual projects may overwrite the '-std=' flag - export ANSI_CFLAGS="-std=c99" - export ANSI_CXXFLAGS="-std=c++98" + export ANSI_CFLAGS="-std=c11" + export ANSI_CXXFLAGS="-std=c++11" export USERLDFLAGS="${LDFLAGS}" export USERCFLAGS="${CFLAGS}" diff --git a/sci-biology/gemini/Manifest b/sci-biology/gemini/Manifest deleted file mode 100644 index e85205a03..000000000 --- a/sci-biology/gemini/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST gemini-0.30.2.tar.gz 1629220 BLAKE2B cbcbcb367817550d39f5385617fa577895d13a084ef2f7e8be2aa3895f9f22e9df2d453673993962819cdfa1705b1a8fa5f7f899d836f055eff753a7f6c5ae2f SHA512 08f88cc54631bc6f9fca72eaa996457dff1f19e4a5791b5ce11a2c2983e3ca23101aa572d2dcbd2fb1340d4e3ed1ea87d99e88530b25f2bfc533f879ac584b6d diff --git a/sci-biology/gemini/gemini-0.30.2.ebuild b/sci-biology/gemini/gemini-0.30.2.ebuild deleted file mode 100644 index f041c2c48..000000000 --- a/sci-biology/gemini/gemini-0.30.2.ebuild +++ /dev/null @@ -1,45 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7,8,9} ) - -inherit distutils-r1 - -DESCRIPTION="Lightweight VCF to DB framework for disease and population genetics" -HOMEPAGE="https://github.com/arq5x/gemini - http://gemini.readthedocs.org/en/latest" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -RDEPEND=" - dev-python/bottle[${PYTHON_USEDEP}] - dev-python/cython[${PYTHON_USEDEP}] - dev-python/ipyparallel[${PYTHON_USEDEP}] - dev-python/jinja[${PYTHON_USEDEP}] - dev-python/networkx[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/numexpr[${PYTHON_USEDEP}] - dev-python/openpyxl[${PYTHON_USEDEP}] - dev-python/pandas[${PYTHON_USEDEP}] - dev-python/pyyaml[${PYTHON_USEDEP}] - dev-python/unidecode[${PYTHON_USEDEP}] - dev-python/sqlalchemy[${PYTHON_USEDEP}] - sci-biology/bx-python[${PYTHON_USEDEP}] - sci-libs/htslib - sci-biology/pybedtools[${PYTHON_USEDEP}] - sci-biology/pysam[${PYTHON_USEDEP}] -" - -distutils_enable_sphinx docs - -python_prepare_all() { - # this has been renamed in newer versions of sphinx - sed -i -e 's/sphinx.ext.pngmath/sphinx.ext.imgmath/g' docs/conf.py || die - - distutils-r1_python_prepare_all -} diff --git a/sci-biology/gemini/metadata.xml b/sci-biology/gemini/metadata.xml deleted file mode 100644 index 260a8b4ae..000000000 --- a/sci-biology/gemini/metadata.xml +++ /dev/null @@ -1,15 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="github">arq5x/gemini</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/genomeview-bin/genomeview-bin-2450.ebuild b/sci-biology/genomeview-bin/genomeview-bin-2450.ebuild index 8de34c9fa..9d4480272 100644 --- a/sci-biology/genomeview-bin/genomeview-bin-2450.ebuild +++ b/sci-biology/genomeview-bin/genomeview-bin-2450.ebuild @@ -6,7 +6,7 @@ EAPI=7 inherit java-pkg-opt-2 java-ant-2 DESCRIPTION="Genome browser and annotation tool" -HOMEPAGE="http://genomeview.sourceforge.net" +HOMEPAGE="https://genomeview.sourceforge.net" SRC_URI="https://downloads.sourceforge.net/project/genomeview/GenomeView/genomeview-2450.zip" LICENSE="GPL-2" diff --git a/sci-biology/genomeview-bin/metadata.xml b/sci-biology/genomeview-bin/metadata.xml index 0f267b755..b6476ca7b 100644 --- a/sci-biology/genomeview-bin/metadata.xml +++ b/sci-biology/genomeview-bin/metadata.xml @@ -10,6 +10,6 @@ <name>Gentoo Biology Project</name> </maintainer> <upstream> - <remote-id type="sourceforge">downloads</remote-id> + <remote-id type="sourceforge">genomeview</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/gffcompare/files/Makefile.patch b/sci-biology/gffcompare/files/Makefile.patch deleted file mode 100644 index afb52b2e1..000000000 --- a/sci-biology/gffcompare/files/Makefile.patch +++ /dev/null @@ -1,79 +0,0 @@ ---- gffcompare-0.10.5/Makefile 2018-06-26 09:24:06.058542487 +0200 -+++ gffcompare-0.10.5/Makefile 2018-06-26 09:28:08.045119603 +0200 -@@ -16,7 +16,7 @@ - endif - - # CVS checked in --CC := g++ -+CXX ?= g++ - BASEFLAGS = -Wall -Wextra ${INCDIRS} $(MARCH) \ - -fno-exceptions -fno-rtti -D_REENTRANT - -@@ -24,7 +24,8 @@ - - ifneq (,$(filter %release %static, $(MAKECMDGOALS))) - # -- release build -- CFLAGS = -O3 -DNDEBUG $(BASEFLAGS) -+ CXXFLAGS ?= -O3 -g -+ CXXFLAGS += -DNDEBUG $(BASEFLAGS) - LDFLAGS = - LIBS = - ifneq (,$(findstring static,$(MAKECMDGOALS))) -@@ -37,16 +38,16 @@ - ifeq "$(GCCVER49)" "0" - $(error gcc version 4.9 or greater is required for this build target) - endif -- CFLAGS := -fno-omit-frame-pointer -fsanitize=undefined -fsanitize=address -+ CXXFLAGS += -fno-omit-frame-pointer -fsanitize=undefined -fsanitize=address - GCCVER5 := $(shell expr `g++ -dumpversion | cut -f1 -d.` \>= 5) - ifeq "$(GCCVER5)" "1" -- CFLAGS += -fsanitize=bounds -fsanitize=float-divide-by-zero -fsanitize=vptr -- CFLAGS += -fsanitize=float-cast-overflow -fsanitize=object-size -- #CFLAGS += -fcheck-pointer-bounds -mmpx -+ CXXFLAGS += -fsanitize=bounds -fsanitize=float-divide-by-zero -fsanitize=vptr -+ CXXFLAGS += -fsanitize=float-cast-overflow -fsanitize=object-size -+ #CXXFLAGS += -fcheck-pointer-bounds -mmpx - endif -- CFLAGS += $(BASEFLAGS) -- CFLAGS := -g -DDEBUG -D_DEBUG -DGDEBUG -fno-common -fstack-protector $(CFLAGS) -- LDFLAGS := -g -+ CXXFLAGS += $(BASEFLAGS) -+ CXXFLAGS += -DDEBUG -D_DEBUG -DGDEBUG -fno-common -fstack-protector -+ LDFLAGS ?= -g - #LIBS := -Wl,-Bstatic -lasan -lubsan -Wl,-Bdynamic -ldl $(LIBS) - LIBS := -lasan -lubsan -ldl $(LIBS) - else -@@ -55,26 +56,26 @@ - # GMEMTRACE=1 - #endif - #--- just plain debug build --- -- CFLAGS = -g -DDEBUG -D_DEBUG -DGDEBUG $(BASEFLAGS) -- LDFLAGS = -g -+ CXXFLAGS += -DDEBUG -D_DEBUG -DGDEBUG $(BASEFLAGS) -+ LDFLAGS += -g - LIBS = - endif - endif - - %.o : %.c -- ${CC} ${CFLAGS} -c $< -o $@ -+ ${CXX} ${CXXFLAGS} -c $< -o $@ - - %.o : %.cc -- ${CC} ${CFLAGS} -c $< -o $@ -+ ${CXX} ${CXXFLAGS} -c $< -o $@ - - %.o : %.C -- ${CC} ${CFLAGS} -c $< -o $@ -+ ${CXX} ${CXXFLAGS} -c $< -o $@ - - %.o : %.cpp -- ${CC} ${CFLAGS} -c $< -o $@ -+ ${CXX} ${CXXFLAGS} -c $< -o $@ - - %.o : %.cxx -- ${CC} ${CFLAGS} -c $< -o $@ -+ ${CXX} ${CXXFLAGS} -c $< -o $@ - - # C/C++ linker - diff --git a/sci-biology/gffutils/Manifest b/sci-biology/gffutils/Manifest index a697f0784..e8b006cbf 100644 --- a/sci-biology/gffutils/Manifest +++ b/sci-biology/gffutils/Manifest @@ -1,2 +1 @@ -DIST gffutils-0.10.1.tar.gz 1636628 BLAKE2B ca539bdcf2a2e199d264194e23c3d1b52e1f4b141d2a43a1346024c008020ff531d5b642c63bd4c3a34cd97de2a399975eea430163f16218f5a1d671521e69b6 SHA512 21f56e013abdf1368756db97afcea0be6d0edc56cb0636e9e796603959570c7c3ba0cecf1bf90a69ab7afd2c4c831d3d42b92960a8c34f9b645be7e47d42190a -DIST gffutils-0.8.7.1.tar.gz 1541112 BLAKE2B 65676cf0b910ad0fee478315409dba808a13d11922d0ab254694939ebd01f10b62c2237ae517d941999c6cf9bcb08d903bde8b9055bcf7a67116e14439ec4cca SHA512 4739dd402963d402f34a5e3da9cca7ba9586dcbbe62efbad89bf85c5dbb0feff0e260eea20563340911756e6817289c1556c261ef973a61f4e66e50efdfc8aa8 +DIST gffutils-0.11.1.tar.gz 1646787 BLAKE2B 96e573cf366844c8a348aff062362aeaea1a46360c74ae75a2d8d730d37cd69f0e6c658d1d0f348ca8f8e8c49d9a7c923c52619341e8d2dabd92a329fb43b677 SHA512 1844e9d7626a800549def2ba09b4d97e60c8a1a0fce2da60d7841cf4c4347da50aea850e8c1a67b07de08d4e6cf737b0d5c2bf8eb5fc87900427866282e82bdb diff --git a/sci-biology/gffutils/gffutils-0.10.1.ebuild b/sci-biology/gffutils/gffutils-0.10.1.ebuild deleted file mode 100644 index c7a437264..000000000 --- a/sci-biology/gffutils/gffutils-0.10.1.ebuild +++ /dev/null @@ -1,39 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7..9} ) - -inherit distutils-r1 - -DESCRIPTION="GFF and GTF file manipulation and interconversion" -HOMEPAGE="https://pythonhosted.org/gffutils/" -SRC_URI="https://github.com/daler/gffutils/archive/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -RDEPEND=" - dev-python/simplejson[${PYTHON_USEDEP}] - dev-python/argh[${PYTHON_USEDEP}] - dev-python/argcomplete[${PYTHON_USEDEP}] - sci-biology/biopython[${PYTHON_USEDEP}] - sci-biology/pybedtools[${PYTHON_USEDEP}] - sci-biology/pyfaidx[${PYTHON_USEDEP}] -" -DEPEND="${RDEPEND}" - -python_prepare_all() { - if use test; then - sed -i -e "s:/tmp/gffutils-test:${T}:g" gffutils/test/test.py || die - fi - distutils-r1_python_prepare_all -} - -distutils_enable_tests nose -python_test() { - distutils_install_for_testing - nosetests -v -x --with-doctest -a '!slow' || die -} diff --git a/sci-biology/gffutils/gffutils-0.11.1.ebuild b/sci-biology/gffutils/gffutils-0.11.1.ebuild new file mode 100644 index 000000000..8ee8fd4b5 --- /dev/null +++ b/sci-biology/gffutils/gffutils-0.11.1.ebuild @@ -0,0 +1,42 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) + +inherit distutils-r1 + +DESCRIPTION="GFF and GTF file manipulation and interconversion" +HOMEPAGE="https://gffutils.readthedocs.io/en/latest/" +SRC_URI="https://github.com/daler/gffutils/archive/v${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="test" +# Nose tests no longer supported, migration on next release +#RESTRICT="test" +RESTRICT="!test? ( test )" + +RDEPEND=" + dev-python/simplejson[${PYTHON_USEDEP}] + dev-python/argh[${PYTHON_USEDEP}] + dev-python/argcomplete[${PYTHON_USEDEP}] + sci-biology/biopython[${PYTHON_USEDEP}] + sci-biology/pybedtools[${PYTHON_USEDEP}] + sci-biology/pyfaidx[${PYTHON_USEDEP}] +" +DEPEND="${RDEPEND}" + +python_prepare_all() { + if use test; then + sed -i -e "s:/tmp/gffutils-test:${T}:g" gffutils/test/test.py || die + fi + distutils-r1_python_prepare_all +} + +python_test() { + distutils_install_for_testing + nosetests -v -x --with-doctest -a '!slow' || die +} diff --git a/sci-biology/gffutils/gffutils-0.8.7.1.ebuild b/sci-biology/gffutils/gffutils-0.8.7.1.ebuild deleted file mode 100644 index c6b304fb1..000000000 --- a/sci-biology/gffutils/gffutils-0.8.7.1.ebuild +++ /dev/null @@ -1,23 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7..9} ) - -inherit distutils-r1 - -DESCRIPTION="GFF and GTF file manipulation and interconversion" -HOMEPAGE="https://pythonhosted.org/gffutils/" -SRC_URI="https://github.com/daler/gffutils/archive/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -RDEPEND=" - sci-biology/pyfaidx[${PYTHON_USEDEP}] - dev-python/simplejson[${PYTHON_USEDEP}] - dev-python/argh[${PYTHON_USEDEP}] - dev-python/argcomplete[${PYTHON_USEDEP}]" -DEPEND="${RDEPEND}" diff --git a/sci-biology/glean/glean-1.0.1.ebuild b/sci-biology/glean/glean-1.0.1.ebuild index d459d664b..507f76900 100644 --- a/sci-biology/glean/glean-1.0.1.ebuild +++ b/sci-biology/glean/glean-1.0.1.ebuild @@ -6,7 +6,7 @@ EAPI=7 inherit perl-module DESCRIPTION="Merge various gene prediction into one (unsupervised learning system)" -HOMEPAGE="https://sourceforge.net/projects/glean-gene" +HOMEPAGE="https://sourceforge.net/projects/glean-gene/" SRC_URI="https://downloads.sourceforge.net/project/glean-gene/GLEAN/glean-${PV//./-}/glean-${PV//./-}.tar.gz" LICENSE="Artistic" diff --git a/sci-biology/glean/metadata.xml b/sci-biology/glean/metadata.xml index 0f267b755..26831499b 100644 --- a/sci-biology/glean/metadata.xml +++ b/sci-biology/glean/metadata.xml @@ -10,6 +10,6 @@ <name>Gentoo Biology Project</name> </maintainer> <upstream> - <remote-id type="sourceforge">downloads</remote-id> + <remote-id type="sourceforge">glean-gene</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/hisat2/hisat2-2.2.1.ebuild b/sci-biology/hisat2/hisat2-2.2.1.ebuild index 8841bd445..9a30d7aef 100644 --- a/sci-biology/hisat2/hisat2-2.2.1.ebuild +++ b/sci-biology/hisat2/hisat2-2.2.1.ebuild @@ -1,15 +1,15 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7,8,9} ) +PYTHON_COMPAT=( python3_{10..11} ) inherit python-r1 DESCRIPTION="Align DNA reads to a population of genomes" HOMEPAGE=" - https://ccb.jhu.edu/software/hisat2 + https://daehwankimlab.github.io/hisat2 https://github.com/DaehwanKimLab/hisat2" SRC_URI="https://github.com/DaehwanKimLab/hisat2/archive/v${PV}.tar.gz -> ${P}.tar.gz" diff --git a/sci-biology/hisat2/metadata.xml b/sci-biology/hisat2/metadata.xml index 2a70cba7e..7954bc741 100644 --- a/sci-biology/hisat2/metadata.xml +++ b/sci-biology/hisat2/metadata.xml @@ -10,6 +10,6 @@ <name>Gentoo Biology Project</name> </maintainer> <upstream> - <remote-id type="github">infphilo/hisat2</remote-id> + <remote-id type="github">DaehwanKimLab/hisat2</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/imagej/Manifest b/sci-biology/imagej/Manifest index 1d4db507e..4c5068f0a 100644 --- a/sci-biology/imagej/Manifest +++ b/sci-biology/imagej/Manifest @@ -1,3 +1,3 @@ DIST ImageJ.png 13012 BLAKE2B b42ee855e6214b275cbdcc722f6c7b095fe83de477a151714c4afec8e23abe12b2d0bf62ae81a4f9c4ccefc9245a9e144085b844ee3f92121a88f7d27106acf5 SHA512 60c2ff73bcfc668931c59b0dfb299723a369b741601bdd591a407302e30fc58c6c626525b3f08b955a5dab37729d3f704db689317b42a94e7a3ccbfb72abc9b3 -DIST ij153.zip 6394791 BLAKE2B 1b942f808e600fee95f0442f7ec6439164585276b130c295845f6d3c4cf6bcaba1befafc12394fb59a289aab3263d684c89f6c3b1d3be04f443a3a39396baad0 SHA512 3c367a502d3fd46272756228c6cefba2e94e635db74edbd117ca083a8c8dc68a2eef4da6deefcdcece5d68c7c03b67233de8ff7a6c33aad0c30a58abd0f0786a -DIST ij153g-src.zip 1498513 BLAKE2B d1ab359b061896644ed003ec5c331418bd89445c90e792b127b88f000cea5a20e621d18b5a1912d541668a33dcaf02a857f9a0cb5c5e354dd12daddfd521ef2a SHA512 5be0e6e53139f8954983f5f7a9c48f911e71849832b6915e8ae02aabc6fc274ef886523285bc90590a23a767ab8aa51aa2837e147da0005d9b83c88f540848f7 +DIST ij154.zip 6677151 BLAKE2B acd99e95c8123461710e3565a31121e475ac9bd1bb993649dc9569c1e17a055e6e0aad9a3fa482b4a021f39cd3467e779529a1512be557a370277c6091fa7b08 SHA512 92c9f13335e9d2cc111bf08851a6fb747d1d1eac8f3088563f42669e225cff6fd2ffbfd4ea474e7baaa266656c4a433107a3264539f9744412aa6400094cb2c9 +DIST imagej-1.54h.gh.tar.gz 5822723 BLAKE2B a293a4b3c2f5f998822c61e67586124491c0b902c5c91538d7ab7eb7d84f6f8ce79759eaa5f4e5de60731566923cc4b837277539c9522c2efe7bc079c6c13455 SHA512 6061fad8c11b26cdf7537f945abc26f9e4a10f34ed151701f6f89e794028be646dc8013437605c6889073acf803ea6784457f47e3cd645c54265fef24bfeb615 diff --git a/sci-biology/imagej/imagej-1.53g.ebuild b/sci-biology/imagej/imagej-1.53g.ebuild deleted file mode 100644 index 6c9fdf736..000000000 --- a/sci-biology/imagej/imagej-1.53g.ebuild +++ /dev/null @@ -1,120 +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 desktop - -MY_PN="ij" -MY_PV=${PV//.} -IJ_PV=${MY_PV::-1} - -DESCRIPTION="Image Processing and Analysis in Java" -HOMEPAGE="https://imagej.nih.gov/ij/" - -SRC_URI="https://imagej.nih.gov/ij/download/src/${MY_PN}${MY_PV}-src.zip - https://rsb.info.nih.gov/ij/images/ImageJ.png - plugins? ( https://wsr.imagej.net/distros/cross-platform/${MY_PN}${IJ_PV}.zip )" -# plugins are under a different licenses and can be installed into user's $IJ_HOME/plugins -# plugins? ( http://rsb.info.nih.gov/ij/download/zips/${MY_PN}${IJ_PV}.zip )" - -LICENSE="public-domain" # http://imagej.net/disclaimer.html -SLOT="0" - -KEYWORDS="~amd64" - -IUSE="doc plugins debug" - -RDEPEND=" - >=virtual/jre-1.7:* - dev-java/java-config -" -DEPEND="${RDEPEND} - >=virtual/jdk-1.7:* - dev-java/ant-core - app-arch/unzip -" - -S="${WORKDIR}/source" -IJ_S=${WORKDIR}/ImageJ - -src_prepare() { - cp "${DISTDIR}"/ImageJ.png "${WORKDIR}/${PN}.png" || die - - if ! use debug ; then - sed -i 's: debug="on">: debug="off">:' "${S}"/build.xml || die - fi - default -} - -src_compile() { - local antflags="build" - use doc && antflags="${antflags} javadocs" - - ant ${antflags} || die "ant build failed" - - # Max memory usage depends on available memory and CPU type - MEM=$(grep MemTotal /proc/meminfo | cut -d':' -f2 | grep -o [0-9]*) - IJ_MAX_MEM=$(expr ${MEM} / 1024) - if use x86 && $IJ_MAX_MEM -gt 2048 ; then - IJ_MAX_MEM=2048 - fi - # build finished, generate startup wrapper - cat <<EOF > "${T}/${PN}" -#!${EPREFIX}/bin/bash -IJ_LIB=${EPREFIX}/usr/share/${PN}/lib -if !([ "\${IJ_HOME}" ]) ; then - IJ_HOME=\${HOME}/.imagej -fi -if [ -d \${IJ_HOME}/plugins ] ; then - IJ_PLG=\${IJ_HOME} -else - IJ_PLG=${EPREFIX}/usr/share/${PN}/lib -fi -if !([ "\$IJ_MEM" ]) ; then - IJ_MEM=${IJ_MAX_MEM} -fi -if !([ "\$IJ_CP" ]) ; then - IJ_CP=\$(java-config -p imagej):\$(java-config -O)/lib/tools.jar -else - IJ_CP=\$(java-config -p imagej):\$(java-config -O)/lib/tools.jar:\${IJ_CP} -fi -\$(java-config --java) \\ - -Xmx\${IJ_MEM}m -Dswing.aatext=true \\ - -Dawt.useSystemAAFontSettings=on\\ - -cp \${IJ_CP} \\ - -Duser.home=\${IJ_HOME} \\ - -Dplugins.dir=\${IJ_PLG} \\ - ij.ImageJ "\$@" -EOF -} - -src_install() { - java-pkg_dojar *.jar - dobin "${T}/${PN}" - - if use plugins ; then - cp -R "${IJ_S}"/plugins "${ED}"/usr/share/"${PN}"/lib/ - cp -R "${IJ_S}"/macros "${ED}"/usr/share/"${PN}"/lib/ - fi - - use doc && java-pkg_dohtml -r "${WORKDIR}"/api - - insinto /usr/share/pixmaps - doins "${WORKDIR}/${PN}".png - make_desktop_entry "${PN}" ImageJ "${PN}" Graphics -} - -pkg_postinst() { - einfo "" - einfo "You can configure the path of a folder, which contains \"plugins\" directory and IJ_Prefs.txt," - einfo "by setting the environmental variable, \$IJ_HOME." - einfo "Default setting is \$IJ_HOME=\${HOME}/.imagej, i.e. \${HOME}/.imagej/plugins and \${HOME}/.imagej/IJ_Prefs.txt." - einfo "" - einfo "You can also configure the memory size by setting the environmental variable, \$IJ_MEM," - einfo "and the class path by setting the environmental variable, \$IJ_CP." - einfo "" - einfo "If you want to use much more plugins, please see http://rsb.info.nih.gov/ij/plugins/index.html" - einfo "and add *.class files to \$IJ_HOME/plugins folder" - einfo "" -} diff --git a/sci-biology/imagej/imagej-1.54h-r1.ebuild b/sci-biology/imagej/imagej-1.54h-r1.ebuild new file mode 100644 index 000000000..0252d6613 --- /dev/null +++ b/sci-biology/imagej/imagej-1.54h-r1.ebuild @@ -0,0 +1,144 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit java-pkg-2 java-ant-2 desktop + +MY_PN="ij" +IJ_PV="154" #plugins now available for 154 + +DESCRIPTION="Image Processing and Analysis in Java" + +HOMEPAGE=" + https://imagej.nih.gov/ij/ + https://github.com/imagej +" + +SRC_URI=" + https://imagej.nih.gov/ij/images/ImageJ.png + plugins? ( https://wsr.imagej.net/distros/cross-platform/${MY_PN}${IJ_PV}.zip )" +# plugins are under a different licenses and can be installed into user's $IJ_HOME/plugins + +if [[ ${PV} == 9999 ]]; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/imagej/ImageJ" + IJ_S="${S}/ImageJ" +else + SRC_URI+=" + https://github.com/imagej/ImageJ/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz + " + S="${WORKDIR}/ImageJ-${PV}" + IJ_S="${WORKDIR}/ImageJ" + KEYWORDS="~amd64" +fi + +LICENSE="public-domain" + +SLOT="0" + +IUSE="doc plugins debug" + +RDEPEND=" + >=virtual/jre-1.7:* + dev-java/java-config +" + +DEPEND=" + ${RDEPEND} + >=virtual/jdk-1.7:* +" + +BDEPEND=" + dev-java/ant-core + app-arch/unzip +" + +src_prepare() { + cp "${DISTDIR}"/ImageJ.png "${WORKDIR}/${PN}.png" || die + + if [[ ${PV} == 9999 ]]; then + if use plugins ; then + unpack "${MY_PN}${IJ_PV}.zip" + fi + fi + + if ! use debug ; then + sed -i 's: debug="on">: debug="off">:' "${S}"/build.xml || die + fi + default +} + +src_compile() { + local antflags="build" + use doc && antflags="${antflags} javadocs" + + ant ${antflags} || die "ant build failed" + + # Max memory usage depends on available memory and CPU type + MEM=$(grep MemTotal /proc/meminfo | cut -d':' -f2 | grep -o [0-9]*) + IJ_MAX_MEM=$(expr ${MEM} / 1024) + + if use x86 && $IJ_MAX_MEM -gt 2048 ; then + IJ_MAX_MEM=2048 + fi + + # build finished, generate startup wrapper + cat <<EOF > "${T}/${PN}" +#!${EPREFIX}/bin/bash +IJ_LIB=${EPREFIX}/usr/share/${PN}/lib +if !([ "\${IJ_HOME}" ]) ; then + IJ_HOME=\${HOME}/.imagej +fi +if [ -d \${IJ_HOME}/plugins ] ; then + IJ_PLG=\${IJ_HOME} +else + IJ_PLG=${EPREFIX}/usr/share/${PN}/lib +fi +if !([ "\$IJ_MEM" ]) ; then + IJ_MEM=${IJ_MAX_MEM} +fi +if !([ "\$IJ_CP" ]) ; then + IJ_CP=\$(java-config -p imagej):\$(java-config -O)/lib/tools.jar +else + IJ_CP=\$(java-config -p imagej):\$(java-config -O)/lib/tools.jar:\${IJ_CP} +fi +\$(java-config --java) \\ + -Xmx\${IJ_MEM}m -Dswing.aatext=true \\ + -Dawt.useSystemAAFontSettings=on\\ + -cp \${IJ_CP} \\ + -Duser.home=\${IJ_HOME} \\ + -Dplugins.dir=\${IJ_PLG} \\ + ij.ImageJ "\$@" +EOF +} + +src_install() { + java-pkg_dojar *.jar + dobin "${T}/${PN}" + + if use plugins ; then + cp -R "${IJ_S}"/plugins "${ED}"/usr/share/"${PN}"/lib/ + cp -R "${IJ_S}"/macros "${ED}"/usr/share/"${PN}"/lib/ + fi + + use doc && java-pkg_dohtml -r "${WORKDIR}"/api + + insinto /usr/share/pixmaps + doins "${WORKDIR}/${PN}".png + make_desktop_entry "${PN}" ImageJ "${PN}" Graphics +} + +pkg_postinst() { + einfo "" + einfo "You can configure the path of a folder, which contains \"plugins\" directory and IJ_Prefs.txt," + einfo "by setting the environmental variable, \$IJ_HOME." + einfo "Default setting is \$IJ_HOME=\${HOME}/.imagej, i.e. \${HOME}/.imagej/plugins and \${HOME}/.imagej/IJ_Prefs.txt." + einfo "" + einfo "You can also configure the memory size by setting the environmental variable, \$IJ_MEM," + einfo "and the class path by setting the environmental variable, \$IJ_CP." + einfo "" + einfo "If you want to use much more plugins, please see http://rsb.info.nih.gov/ij/plugins/index.html" + einfo "and add *.class files to \$IJ_HOME/plugins folder" + einfo "" +} diff --git a/sci-biology/imagej/imagej-9999.ebuild b/sci-biology/imagej/imagej-9999.ebuild new file mode 100644 index 000000000..0252d6613 --- /dev/null +++ b/sci-biology/imagej/imagej-9999.ebuild @@ -0,0 +1,144 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit java-pkg-2 java-ant-2 desktop + +MY_PN="ij" +IJ_PV="154" #plugins now available for 154 + +DESCRIPTION="Image Processing and Analysis in Java" + +HOMEPAGE=" + https://imagej.nih.gov/ij/ + https://github.com/imagej +" + +SRC_URI=" + https://imagej.nih.gov/ij/images/ImageJ.png + plugins? ( https://wsr.imagej.net/distros/cross-platform/${MY_PN}${IJ_PV}.zip )" +# plugins are under a different licenses and can be installed into user's $IJ_HOME/plugins + +if [[ ${PV} == 9999 ]]; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/imagej/ImageJ" + IJ_S="${S}/ImageJ" +else + SRC_URI+=" + https://github.com/imagej/ImageJ/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz + " + S="${WORKDIR}/ImageJ-${PV}" + IJ_S="${WORKDIR}/ImageJ" + KEYWORDS="~amd64" +fi + +LICENSE="public-domain" + +SLOT="0" + +IUSE="doc plugins debug" + +RDEPEND=" + >=virtual/jre-1.7:* + dev-java/java-config +" + +DEPEND=" + ${RDEPEND} + >=virtual/jdk-1.7:* +" + +BDEPEND=" + dev-java/ant-core + app-arch/unzip +" + +src_prepare() { + cp "${DISTDIR}"/ImageJ.png "${WORKDIR}/${PN}.png" || die + + if [[ ${PV} == 9999 ]]; then + if use plugins ; then + unpack "${MY_PN}${IJ_PV}.zip" + fi + fi + + if ! use debug ; then + sed -i 's: debug="on">: debug="off">:' "${S}"/build.xml || die + fi + default +} + +src_compile() { + local antflags="build" + use doc && antflags="${antflags} javadocs" + + ant ${antflags} || die "ant build failed" + + # Max memory usage depends on available memory and CPU type + MEM=$(grep MemTotal /proc/meminfo | cut -d':' -f2 | grep -o [0-9]*) + IJ_MAX_MEM=$(expr ${MEM} / 1024) + + if use x86 && $IJ_MAX_MEM -gt 2048 ; then + IJ_MAX_MEM=2048 + fi + + # build finished, generate startup wrapper + cat <<EOF > "${T}/${PN}" +#!${EPREFIX}/bin/bash +IJ_LIB=${EPREFIX}/usr/share/${PN}/lib +if !([ "\${IJ_HOME}" ]) ; then + IJ_HOME=\${HOME}/.imagej +fi +if [ -d \${IJ_HOME}/plugins ] ; then + IJ_PLG=\${IJ_HOME} +else + IJ_PLG=${EPREFIX}/usr/share/${PN}/lib +fi +if !([ "\$IJ_MEM" ]) ; then + IJ_MEM=${IJ_MAX_MEM} +fi +if !([ "\$IJ_CP" ]) ; then + IJ_CP=\$(java-config -p imagej):\$(java-config -O)/lib/tools.jar +else + IJ_CP=\$(java-config -p imagej):\$(java-config -O)/lib/tools.jar:\${IJ_CP} +fi +\$(java-config --java) \\ + -Xmx\${IJ_MEM}m -Dswing.aatext=true \\ + -Dawt.useSystemAAFontSettings=on\\ + -cp \${IJ_CP} \\ + -Duser.home=\${IJ_HOME} \\ + -Dplugins.dir=\${IJ_PLG} \\ + ij.ImageJ "\$@" +EOF +} + +src_install() { + java-pkg_dojar *.jar + dobin "${T}/${PN}" + + if use plugins ; then + cp -R "${IJ_S}"/plugins "${ED}"/usr/share/"${PN}"/lib/ + cp -R "${IJ_S}"/macros "${ED}"/usr/share/"${PN}"/lib/ + fi + + use doc && java-pkg_dohtml -r "${WORKDIR}"/api + + insinto /usr/share/pixmaps + doins "${WORKDIR}/${PN}".png + make_desktop_entry "${PN}" ImageJ "${PN}" Graphics +} + +pkg_postinst() { + einfo "" + einfo "You can configure the path of a folder, which contains \"plugins\" directory and IJ_Prefs.txt," + einfo "by setting the environmental variable, \$IJ_HOME." + einfo "Default setting is \$IJ_HOME=\${HOME}/.imagej, i.e. \${HOME}/.imagej/plugins and \${HOME}/.imagej/IJ_Prefs.txt." + einfo "" + einfo "You can also configure the memory size by setting the environmental variable, \$IJ_MEM," + einfo "and the class path by setting the environmental variable, \$IJ_CP." + einfo "" + einfo "If you want to use much more plugins, please see http://rsb.info.nih.gov/ij/plugins/index.html" + einfo "and add *.class files to \$IJ_HOME/plugins folder" + einfo "" +} diff --git a/sci-biology/imagej/metadata.xml b/sci-biology/imagej/metadata.xml index ca2867d8c..8b8ebd7d9 100644 --- a/sci-biology/imagej/metadata.xml +++ b/sci-biology/imagej/metadata.xml @@ -12,4 +12,7 @@ <use> <flag name="plugins">Install additional plugins</flag> </use> + <upstream> + <remote-id type="github">imagej/ImageJ</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/irsabi_bidsdata/irsabi_bidsdata-1.4.ebuild b/sci-biology/irsabi_bidsdata/irsabi_bidsdata-1.4.ebuild index d50ebf927..021929bad 100644 --- a/sci-biology/irsabi_bidsdata/irsabi_bidsdata-1.4.ebuild +++ b/sci-biology/irsabi_bidsdata/irsabi_bidsdata-1.4.ebuild @@ -6,7 +6,7 @@ EAPI=7 inherit check-reqs DESCRIPTION="BIDS data files released with the IRSABI publication" -HOMEPAGE="http://www.aic-fmi.ethz.ch/" +HOMEPAGE="https://chymera.eu/docs/focus/open-science/" SRC_URI=" https://zenodo.org/record/3601531/files/${P}.tar.xz " diff --git a/sci-biology/jellyfish/jellyfish-1.1.12.ebuild b/sci-biology/jellyfish/jellyfish-1.1.12.ebuild index b2e6ea25b..a6989c2bf 100644 --- a/sci-biology/jellyfish/jellyfish-1.1.12.ebuild +++ b/sci-biology/jellyfish/jellyfish-1.1.12.ebuild @@ -1,10 +1,10 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 DESCRIPTION="k-mer counter within reads for assemblies" -HOMEPAGE="http://www.cbcb.umd.edu/software/jellyfish" +HOMEPAGE="https://genome.umd.edu/jellyfish.html" SRC_URI="https://github.com/gmarcais/Jellyfish/releases/download/v${PV}/${P}.tar.gz" # older version is hidden in trinityrnaseq_r20140413p1/trinity-plugins/jellyfish-1.1.11 diff --git a/sci-biology/jellyfish/jellyfish-2.3.0.ebuild b/sci-biology/jellyfish/jellyfish-2.3.0.ebuild index e8e3c8fd0..2237173e0 100644 --- a/sci-biology/jellyfish/jellyfish-2.3.0.ebuild +++ b/sci-biology/jellyfish/jellyfish-2.3.0.ebuild @@ -1,10 +1,10 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 DESCRIPTION="k-mer counter within reads for assemblies" -HOMEPAGE="http://www.genome.umd.edu/jellyfish.html" +HOMEPAGE="https://genome.umd.edu/jellyfish.html" SRC_URI="https://github.com/gmarcais/Jellyfish/releases/download/v${PV}/${P}.tar.gz" # older version is hidden in trinityrnaseq_r20140413p1/trinity-plugins/jellyfish-1.1.11 diff --git a/sci-biology/jellyfish/metadata.xml b/sci-biology/jellyfish/metadata.xml index 138cb7705..f2c1cd819 100644 --- a/sci-biology/jellyfish/metadata.xml +++ b/sci-biology/jellyfish/metadata.xml @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">gmarcais/Jellyfish</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/jtreeview-bin/jtreeview-bin-1.2.0.ebuild b/sci-biology/jtreeview-bin/jtreeview-bin-1.2.0.ebuild index d146efd5a..63ec84d2f 100644 --- a/sci-biology/jtreeview-bin/jtreeview-bin-1.2.0.ebuild +++ b/sci-biology/jtreeview-bin/jtreeview-bin-1.2.0.ebuild @@ -8,7 +8,7 @@ inherit java-pkg-2 java-ant-2 perl-module S="${WORKDIR}"/TreeView-1.1.6r4-bin DESCRIPTION="Viewer for Microarray Data in PCL or CDT formats" -HOMEPAGE="http://jtreeview.sourceforge.net/" # no https +HOMEPAGE="https://jtreeview.sourceforge.net/" SRC_URI=" https://sourceforge.net/projects/jtreeview/files/jtreeview/${PV}/TreeView-${PV}-bin.tar.gz https://sourceforge.net/projects/jtreeview/files/helper-scripts/0.0.2/helper-scripts-0.0.2.tar.gz diff --git a/sci-biology/kat/Manifest b/sci-biology/kat/Manifest deleted file mode 100644 index 0bdd2dd15..000000000 --- a/sci-biology/kat/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST kat-2.4.2.tar.gz 21829118 BLAKE2B 52a0056f322dfb405c005b31a0cb182c739a6af05173123dc1cef1d986f515a8318c1481f1ed0f8c247c01c6b460c951147d81f904709f4e27a7d3d1f47bda3d SHA512 696e3b9ed307ed17085790b24d617195f47fbdb7180be13ee644718c2464c429ffd964959857fc8d1317a451d57b74f6d7b2857fe3764573d9605d58a53b2a0c diff --git a/sci-biology/kat/files/kat-2.4.2-ignore-bundled-deps.patch b/sci-biology/kat/files/kat-2.4.2-ignore-bundled-deps.patch deleted file mode 100644 index 46d343294..000000000 --- a/sci-biology/kat/files/kat-2.4.2-ignore-bundled-deps.patch +++ /dev/null @@ -1,79 +0,0 @@ -diff --git a/lib/Makefile.am b/lib/Makefile.am -index ac23917..0ca4be9 100644 ---- a/lib/Makefile.am -+++ b/lib/Makefile.am -@@ -6,7 +6,6 @@ pkgconfig_DATA = kat.pc - lib_LTLIBRARIES = libkat.la - - libkat_la_LDFLAGS = \ -- -L$(top_builddir)/deps/boost/build/lib/ \ - -version-info 2:4:2 - - LIBS = \ -@@ -41,7 +40,6 @@ library_include_HEADERS = $(KI)/distance_metrics.hpp \ - - libkat_la_CPPFLAGS = \ - -I$(top_srcdir)/deps/jellyfish-2.2.0/include \ -- -I$(top_srcdir)/deps/boost/build/include \ - -I$(top_srcdir)/lib/include \ - -DKAT_SITE_PKGS='"$(prefix)/lib/python$(PYTHON_VERSION)/site-packages"' \ - @AM_CPPFLAGS@ -diff --git a/src/Makefile.am b/src/Makefile.am -index 1cdf7e0..dfa878b 100644 ---- a/src/Makefile.am -+++ b/src/Makefile.am -@@ -14,7 +14,6 @@ kat_CXXFLAGS = \ - kat_CPPFLAGS = \ - -I$(top_srcdir)/deps/seqan-library-2.0.0/include \ - -I$(top_srcdir)/deps/jellyfish-2.2.0/include \ -- -I$(top_srcdir)/deps/boost/build/include \ - -I$(top_srcdir)/lib/include \ - -DKAT_SCRIPTS='"$(datarootdir)/scripts"' \ - -DKAT_SITE_PKGS='"$(prefix)/lib/python$(PYTHON_VERSION)/site-packages"' \ -@@ -25,13 +24,13 @@ kat_LDFLAGS = \ - @AM_LDFLAGS@ - - kat_LDADD = \ -- $(top_builddir)/deps/boost/build/lib/libboost_timer.a \ -- $(top_builddir)/deps/boost/build/lib/libboost_chrono.a \ -- $(top_builddir)/deps/boost/build/lib/libboost_filesystem.a \ -- $(top_builddir)/deps/boost/build/lib/libboost_program_options.a \ -- $(top_builddir)/deps/boost/build/lib/libboost_system.a \ -- $(top_builddir)/deps/jellyfish-2.2.0/.libs/libkat_jellyfish.la \ - $(top_builddir)/lib/libkat.la \ -+ $(top_builddir)/deps/jellyfish-2.2.0/.libs/libkat_jellyfish.la \ -+ -lboost_timer \ -+ -lboost_chrono \ -+ -lboost_filesystem \ -+ -lboost_program_options \ -+ -lboost_system \ - @AM_LIBS@ - - noinst_HEADERS = \ -diff --git a/tests/Makefile.am b/tests/Makefile.am -index eee4e8b..dec2a5f 100644 ---- a/tests/Makefile.am -+++ b/tests/Makefile.am -@@ -31,7 +31,6 @@ AM_CPPFLAGS = \ - -I$(top_srcdir)/lib/include \ - -I$(top_srcdir)/deps/seqan-library-2.0.0/include \ - -I$(top_srcdir)/deps/jellyfish-2.2.0/include \ -- -I$(top_srcdir)/deps/boost/build/include \ - -DDATADIR=\"$(srcdir)/data\" \ - -DKAT_SITE_PKGS='"$(prefix)/lib/python$(PYTHON_VERSION)/site-packages"' \ - @AM_CPPFLAGS@ -@@ -58,13 +57,11 @@ check_unit_tests_SOURCES = \ - - check_unit_tests_LDFLAGS = \ - -static \ -- -L$(top_builddir)/deps/boost/build/lib \ -- -Wl,-rpath $(top_builddir)/deps/boost/build/lib \ - @AM_LDFLAGS@ - - check_unit_tests_LDADD = \ - libgtest.la \ -- $(top_builddir)/lib/libkat.la \ -+ $(top_builddir)/lib/libkat.la \ - -lboost_timer \ - -lboost_chrono \ - -lboost_filesystem \ diff --git a/sci-biology/kat/files/kat-2.4.2-no_static_build.patch b/sci-biology/kat/files/kat-2.4.2-no_static_build.patch deleted file mode 100644 index 48ad6d562..000000000 --- a/sci-biology/kat/files/kat-2.4.2-no_static_build.patch +++ /dev/null @@ -1,56 +0,0 @@ -diff --git a/configure.ac b/configure.ac -index 9acc141..24a4b14 100644 ---- a/configure.ac -+++ b/configure.ac -@@ -178,8 +178,6 @@ define([PC_FILE], lib/kat-2.2.pc) - - AM_CXXFLAGS="-g -O2 -std=c++11" - AC_SUBST([AM_CXXFLAGS]) --AM_LDFLAGS="-static-libstdc++" --AC_SUBST([AM_LDFLAGS]) - - if [[ "${make_pykat}" == "yes" ]]; then - AM_CPPFLAGS="${PYTHON_CPPFLAGS}" -diff --git a/deps/jellyfish-2.2.0/Makefile.am b/deps/jellyfish-2.2.0/Makefile.am -index 83192d9..e3b1694 100644 ---- a/deps/jellyfish-2.2.0/Makefile.am -+++ b/deps/jellyfish-2.2.0/Makefile.am -@@ -7,7 +7,7 @@ man1_MANS = doc/kat_jellyfish.man - pkgconfigdir = $(libdir)/pkgconfig - pkgconfig_DATA = kat_jellyfish.pc - --AM_LDFLAGS = -lz -lpthread -static-libstdc++ # $(VALGRIND_LIBS) -+AM_LDFLAGS = -lz -lpthread # $(VALGRIND_LIBS) - AM_CPPFLAGS = -I$(top_srcdir) -I$(top_srcdir)/include # $(VALGRIND_CFLAGS) - AM_CXXFLAGS = $(ALL_CXXFLAGS) -Wall -Wnon-virtual-dtor -Wno-deprecated-declarations - -diff --git a/src/Makefile.am b/src/Makefile.am -index 2d5cd72..cb5cb0e 100644 ---- a/src/Makefile.am -+++ b/src/Makefile.am -@@ -18,10 +18,6 @@ kat_CPPFLAGS = \ - -DKAT_SCRIPTS='"$(datadir)/scripts"' \ - @AM_CPPFLAGS@ - --kat_LDFLAGS = \ -- -static \ -- @AM_LDFLAGS@ -- - kat_LDADD = \ - $(top_builddir)/lib/libkat.la \ - $(top_builddir)/deps/jellyfish-2.2.0/.libs/libkat_jellyfish.la \ -diff --git a/tests/Makefile.am b/tests/Makefile.am -index d96363a..90e4f61 100644 ---- a/tests/Makefile.am -+++ b/tests/Makefile.am -@@ -54,10 +54,6 @@ check_unit_tests_SOURCES = \ - check_compcounters.cc \ - check_main.cc - --check_unit_tests_LDFLAGS = \ -- -static \ -- @AM_LDFLAGS@ -- - check_unit_tests_LDADD = \ - libgtest.la \ - $(top_builddir)/lib/libkat.la \ diff --git a/sci-biology/kat/kat-2.4.2.ebuild b/sci-biology/kat/kat-2.4.2.ebuild deleted file mode 100644 index a915d1491..000000000 --- a/sci-biology/kat/kat-2.4.2.ebuild +++ /dev/null @@ -1,83 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7,8,9} ) -DISTUTILS_USE_SETUPTOOLS=rdepend -# https://github.com/Ensembl/Bio-DB-HTS/issues/30 - -inherit autotools distutils-r1 - -DESCRIPTION="K-mer Analysis Toolkit (histogram, filter, compare sets, plot)" -HOMEPAGE="https://github.com/TGAC/KAT" -SRC_URI="https://github.com/TGAC/KAT/archive/Release-${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="GPL-3+" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="cpu_flags_x86_sse static-libs test" - -CDEPEND=" - >=dev-libs/boost-1.52[${PYTHON_USEDEP}] - sys-libs/zlib - dev-python/tabulate[${PYTHON_USEDEP}] - dev-python/matplotlib[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/scipy[${PYTHON_USEDEP}] -" -DEPEND="${CDEPEND} - test? ( sys-process/time )" -RDEPEND="${CDEPEND}" -# contains bundled and *modified* version of jellyfish-2.2.0 -# (libkat_jellyfish.{a,so} and "kat_" prefixes are added to all binaries) -# https://github.com/TGAC/KAT/issues/93#issuecomment-383377666 -# contains embedded sci-biology/seqan headers - -PATCHES=( - "${FILESDIR}"/kat-2.4.2-ignore-bundled-deps.patch - "${FILESDIR}"/kat-2.4.2-no_static_build.patch - ) - -S="${WORKDIR}"/KAT-Release-"${PV}" - -distutils_enable_sphinx "${S}/doc/source" --no-autodoc -distutils_enable_tests pytest - -src_prepare(){ - default - rm -rf deps/boost || die "Failed to zap bundled boost" - eautoreconf -} - -src_configure(){ - python_setup - local myconf=() - myconf+=( - --disable-gnuplot - --disable-pykat-install - $(use_enable static-libs static) - ) # python3 does better image rendering, no need for gnuplot - # pass down to jellyfish-2.2.0/configure - use cpu_flags_x86_sse && myconf+=( $(use_with cpu_flags_x86_sse sse) ) - econf ${myconf[@]} -} - -src_compile(){ - default - pushd scripts >/dev/null || die - distutils-r1_src_compile - popd > /dev/null || die -} - -src_install(){ - default - pushd scripts >/dev/null || die - distutils-r1_src_install - popd > /dev/null || die -} - -src_test(){ - default - python_foreach_impl python_test -} diff --git a/sci-biology/kat/kat-9999.ebuild b/sci-biology/kat/kat-9999.ebuild deleted file mode 100644 index acbdac423..000000000 --- a/sci-biology/kat/kat-9999.ebuild +++ /dev/null @@ -1,84 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7,8,9} ) -DISTUTILS_USE_SETUPTOOLS=rdepend -# https://github.com/Ensembl/Bio-DB-HTS/issues/30 - -inherit autotools distutils-r1 git-r3 - -DESCRIPTION="K-mer Analysis Toolkit (histogram, filter, compare sets, plot)" -HOMEPAGE="https://github.com/TGAC/KAT" -EGIT_REPO_URI="https://github.com/TGAC/KAT.git" -EGIT_CHECKOUT_DIR="${WORKDIR}"/KAT-Release-"${PV}" - -LICENSE="GPL-3+" -SLOT="0" -KEYWORDS="" -IUSE="cpu_flags_x86_sse static-libs test" - -CDEPEND=" - >=dev-libs/boost-1.52[${PYTHON_USEDEP}] - sys-libs/zlib - dev-python/tabulate[${PYTHON_USEDEP}] - dev-python/matplotlib[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/scipy[${PYTHON_USEDEP}] -" -DEPEND="${CDEPEND} - test? ( sys-process/time )" -RDEPEND="${CDEPEND}" -# contains bundled and *modified* version of jellyfish-2.2.0 -# (libkat_jellyfish.{a,so} and "kat_" prefixes are added to all binaries) -# https://github.com/TGAC/KAT/issues/93#issuecomment-383377666 -# contains embedded sci-biology/seqan headers - -PATCHES=( - "${FILESDIR}"/kat-2.4.2-ignore-bundled-deps.patch - "${FILESDIR}"/kat-2.4.2-no_static_build.patch - ) - -S="${WORKDIR}"/KAT-Release-"${PV}" - -distutils_enable_sphinx "${S}/doc/source" --no-autodoc -distutils_enable_tests pytest - -src_prepare(){ - default - rm -rf deps/boost || die "Failed to zap bundled boost" - eautoreconf -} - -src_configure(){ - python_setup - local myconf=() - myconf+=( - --disable-gnuplot - --disable-pykat-install - $(use_enable static-libs static) - ) # python3 does better image rendering, no need for gnuplot - # pass down to jellyfish-2.2.0/configure - use cpu_flags_x86_sse && myconf+=( $(use_with cpu_flags_x86_sse sse) ) - econf ${myconf[@]} -} - -src_compile(){ - default - pushd scripts >/dev/null || die - distutils-r1_src_compile - popd > /dev/null || die -} - -src_install(){ - default - pushd scripts >/dev/null || die - distutils-r1_src_install - popd > /dev/null || die -} - -src_test(){ - default - python_foreach_impl python_test -} diff --git a/sci-biology/kat/metadata.xml b/sci-biology/kat/metadata.xml deleted file mode 100644 index 6810aabae..000000000 --- a/sci-biology/kat/metadata.xml +++ /dev/null @@ -1,15 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="github">TGAC/KAT</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/khmer/Manifest b/sci-biology/khmer/Manifest deleted file mode 100644 index 18a85fae6..000000000 --- a/sci-biology/khmer/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST khmer-2.1.1.tar.gz 8507798 BLAKE2B e4db949736c6d01f0878140d0d7be0a91916532bc6709845eeb8d458e145349c868bc381c35ae007716b3c9b7c7a9ca5171965cf187c838a59033b1b969bf177 SHA512 aca35d2b12812470afb271c17eb521e9d80ecaefedde60312ed676bbf73a8662a581e722ebaa4bee6572adc65021a4bc010adbfb84d5393b11c0552139614914 diff --git a/sci-biology/khmer/khmer-2.1.1.ebuild b/sci-biology/khmer/khmer-2.1.1.ebuild deleted file mode 100644 index 11c4231e8..000000000 --- a/sci-biology/khmer/khmer-2.1.1.ebuild +++ /dev/null @@ -1,34 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7,8,9} ) - -inherit distutils-r1 - -DESCRIPTION="In-memory K-mer counting in DNA/RNA/protein sequences" -HOMEPAGE="https://github.com/dib-lab/khmer" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -# ToDo: Fix this: -# ModuleNotFoundError: No module named 'khmer._khmer' -# even happens with --install option for enable_tests -RESTRICT="test" - -RDEPEND=" - sci-biology/screed[${PYTHON_USEDEP}] - dev-python/bz2file[${PYTHON_USEDEP}] -" - -distutils_enable_tests pytest - -python_prepare_all() { - # do not depend on pytest-runner - sed -i "/pytest-runner/d" setup.py || die - distutils-r1_python_prepare_all -} diff --git a/sci-biology/khmer/metadata.xml b/sci-biology/khmer/metadata.xml deleted file mode 100644 index 91ed395d8..000000000 --- a/sci-biology/khmer/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="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="github">ged-lab/khmer</remote-id> - <remote-id type="pypi">khmer</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/kmergenie/Manifest b/sci-biology/kmergenie/Manifest deleted file mode 100644 index f38792478..000000000 --- a/sci-biology/kmergenie/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST kmergenie-1.7048.tar.gz 664034 BLAKE2B 1835cf7a9a360e125d1f793091b9000b106ca7816ff400caf8c79a8ae8bb304e6ab6ea3ac4c29dee3cd7cf65b45db42c11b44c606f9f5808fc068037a222a68b SHA512 7c98a329f39443b689ad6431feb7fdb36b0f0bd8a4d8d7637b7af44064d12c8949690771f50e109660ce5e598c592fe8c0ea32ded27f1055e1b1c203d60938f7 diff --git a/sci-biology/kmergenie/kmergenie-1.7048.ebuild b/sci-biology/kmergenie/kmergenie-1.7048.ebuild deleted file mode 100644 index 3a0d6a105..000000000 --- a/sci-biology/kmergenie/kmergenie-1.7048.ebuild +++ /dev/null @@ -1,22 +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="Estimate best k-mer length to be used in novo assemblies" -HOMEPAGE="http://kmergenie.bx.psu.edu/" -SRC_URI="http://kmergenie.bx.psu.edu/${P}.tar.gz" - -LICENSE="CeCILL-1.1" -SLOT="0" -KEYWORDS="~amd64" - -DEPEND=" - dev-python/docopt[${PYTHON_USEDEP}] - dev-lang/R -" -RDEPEND="${DEPEND}" diff --git a/sci-biology/kmergenie/metadata.xml b/sci-biology/kmergenie/metadata.xml deleted file mode 100644 index 138cb7705..000000000 --- a/sci-biology/kmergenie/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/kraken/Manifest b/sci-biology/kraken/Manifest deleted file mode 100644 index bb9fb5722..000000000 --- a/sci-biology/kraken/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST kraken-1.1.1.tar.gz 76541 BLAKE2B 74a302196c9e40757981094838a4a31b24f803ce49941b11be955f7fafc1f89a0e63ab2d8661a7c099c82058959744206c057d047c852693c80df627efa66ba8 SHA512 9f4897d7738b8aed2839581b4f629eff9229ce8333e2a99aa0d2a90fee34036a9f8dd89b4aecbdaf46b785b7d1080b3a014cf89f88efa4d49acf1d36638dedcb -DIST kraken-2.1.1.tar.gz 193878 BLAKE2B d5494038f715e0bb9bd7325a7a0f5430ff3062b0589f0cbd154d671a98aadbd85ce3334f7f3c7844b6becaafdc06889893f427d2da76db71bca71cb8dd7073a5 SHA512 3b5c24955deff63d23017ee5e798648ebd2319a1ead77e85d285b6a1735d38155799f5988c6d1c69121bd7902dde1aaa03782a7d72b841b74c93e314f8a81bfe diff --git a/sci-biology/kraken/kraken-1.1.1-r2.ebuild b/sci-biology/kraken/kraken-1.1.1-r2.ebuild deleted file mode 100644 index 3dd599b83..000000000 --- a/sci-biology/kraken/kraken-1.1.1-r2.ebuild +++ /dev/null @@ -1,51 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit perl-functions - -DESCRIPTION="Detect sequencing project contaminants by mapping reads to taxonomic groups" -HOMEPAGE="https://ccb.jhu.edu/software/kraken" -SRC_URI="https://github.com/DerrickWood/kraken/archive/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="GPL-3" -SLOT="1" -KEYWORDS="~amd64" - -DEPEND="" -RDEPEND="${DEPEND} - dev-lang/perl - net-misc/wget - sci-biology/jellyfish:1 -" - -src_prepare(){ - default - sed -e 's/^CXX = /CXX ?= /' -e 's/^CXXFLAGS = /CXXFLAGS ?= /' -i src/Makefile || die - echo "exit 0" >> install_kraken.sh || die -} - -src_compile(){ - ./install_kraken.sh destdir || die -} - -src_install(){ - dodoc -r docs - perl_set_version - perl_domodule destdir/*.pm - dosym ../../"${VENDOR_LIB//${EPREFIX/}}/krakenlib.pm" /usr/bin/krakenlib.pm - insinto /usr/share/${PN}/util - doins destdir/*.pl - chmod -R a+rx "${ED}/usr/share/${PN}/util" - rm -f destdir/krakenlib.pm - dobin destdir/* -} - -pkg_postinst(){ - ewarn "Kraken may optionally need <=sci-biology/jellyfish-2 if you want to build your own dbs" - ewarn "Kraken needs high network bandwidth for its huge downloads, be sure to read" - ewarn "https://ccb.jhu.edu/software/kraken and prepare at least 160GB of disk space" - ewarn "Consider placing the db files in ramfs (needs root permissions) taking >75GB RAM" - ewarn "Results can be visualized with https://sourceforge.net/p/krona/home/krona" -} diff --git a/sci-biology/kraken/kraken-2.1.1.ebuild b/sci-biology/kraken/kraken-2.1.1.ebuild deleted file mode 100644 index 0991f94fa..000000000 --- a/sci-biology/kraken/kraken-2.1.1.ebuild +++ /dev/null @@ -1,55 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit perl-functions - -DESCRIPTION="Detect sequencing project contaminants by mapping reads to taxonomic groups" -HOMEPAGE="https://ccb.jhu.edu/software/kraken2/" -SRC_URI="https://github.com/DerrickWood/kraken2/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="MIT" -SLOT="2" -KEYWORDS="~amd64" - -# TODO: somehow avoid the file conflict with kraken-1 -DEPEND="" -RDEPEND="${DEPEND} - sci-biology/ncbi-tools++ - dev-lang/perl - net-misc/wget - !sci-biology/kraken:1 -" - -S="${WORKDIR}/${PN}2-${PV}" - -src_prepare(){ - default - sed -e 's/^CXX = /CXX ?= /' -e 's/^CXXFLAGS = /CXXFLAGS ?= /' -i src/Makefile || die - echo "exit 0" >> install_kraken2.sh || die -} - -src_compile(){ - ./install_kraken2.sh destdir || die -} - -src_install(){ - dodoc -r docs - perl_set_version - perl_domodule destdir/*.pm - dosym ../../"${VENDOR_LIB//${EPREFIX/}}/krakenlib.pm" /usr/bin/krakenlib.pm - insinto /usr/share/${PN}/util - doins destdir/*.pl - chmod -R a+rx "${ED}/usr/share/${PN}/util" - rm -f destdir/krakenlib.pm - dobin destdir/* -} - -pkg_postinst(){ - ewarn "Kraken may optionally need <=sci-biology/jellyfish-2 if you want to build your own dbs" - ewarn "Kraken needs high network bandwidth for its huge downloads, be sure to read" - ewarn "https://ccb.jhu.edu/software/kraken and prepare at least 160GB of disk space" - ewarn "Consider placing the db files in ramfs (needs root permissions) taking >75GB RAM" - ewarn "Results can be visualized with https://sourceforge.net/p/krona/home/krona" -} diff --git a/sci-biology/kraken/metadata.xml b/sci-biology/kraken/metadata.xml deleted file mode 100644 index 138cb7705..000000000 --- a/sci-biology/kraken/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>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/last/Manifest b/sci-biology/last/Manifest deleted file mode 100644 index 1f6d0efe0..000000000 --- a/sci-biology/last/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST last-1179.zip 808701 BLAKE2B 9bbb0da004ccc0b20786c5f631dd48e266e5fecc1719eec040311d53785d4e95657d52ab5addf823709555a07d3617a98eb5e858d110660dea56afcfa84dfc1d SHA512 36aaa5be6a932e9a9c340d18f049d1e735e0ff6f41430c83c7b36bef39540a75a34dff91052c53ddc580e81d0d9a0cb24b5c50125341e0c6ecfd033ff4db84e1 diff --git a/sci-biology/last/last-1179.ebuild b/sci-biology/last/last-1179.ebuild deleted file mode 100644 index 6972a0312..000000000 --- a/sci-biology/last/last-1179.ebuild +++ /dev/null @@ -1,37 +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 toolchain-funcs python-single-r1 - -DESCRIPTION="Genome-scale comparison of biological sequences" -HOMEPAGE="http://last.cbrc.jp/" -SRC_URI="http://last.cbrc.jp/${P}.zip" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -RDEPEND="${PYTHON_DEPS}" -DEPEND="app-arch/unzip" - -src_configure() { - tc-export CC CXX -} - -src_install() { - local DOCS=( doc/*.txt ChangeLog.txt README.txt ) - local HTML_DOCS=( doc/*html ) - einstalldocs - - dobin src/lastdb src/lastal src/last-split src/last-merge-batches \ - src/last-pair-probs src/lastdb8 src/lastal8 src/last-split8 - - cd scripts || die - dobin * -} diff --git a/sci-biology/last/metadata.xml b/sci-biology/last/metadata.xml deleted file mode 100644 index 8417d1580..000000000 --- a/sci-biology/last/metadata.xml +++ /dev/null @@ -1,8 +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-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/libBigWig/Manifest b/sci-biology/libBigWig/Manifest index 4a1880c5f..249395f6f 100644 --- a/sci-biology/libBigWig/Manifest +++ b/sci-biology/libBigWig/Manifest @@ -1 +1,2 @@ DIST libBigWig-0.4.4.tar.gz 272926 BLAKE2B ffde5fced9991b28cf1fdb8b296a88744d949ea6f044d3bc6f5bbcb3405bc8a08906d94a614d489758fbfc625361b910bbbdcf9ea721fa22dee0edf2f286fc08 SHA512 85e0b60e4ce541eb1328528d834f54ea827cc79b5890093688661dfc9bc72e417c8d293cfe5b93987973b4584b042f10a6edd77adca6ea6b1e57ed3741edba71 +DIST libBigWig-0.4.7.tar.gz 302341 BLAKE2B 667aff6153dc11a3491362e19673b64ff72a0779f5c722508d21f2af8ce4c5e9fb410c9685fc2ecfc3a1fade85454f40ada8d2969948eb1d3336b13ed3a816be SHA512 52f1b7c8e21e16238b3bb07baef6aa3611797b1b5ff44d912c874f8f4527c516a0676877fad21c103b8b25a733e84bef48530f28dc224a79d43f7764eae7ed40 diff --git a/sci-biology/libBigWig/libBigWig-0.4.7.ebuild b/sci-biology/libBigWig/libBigWig-0.4.7.ebuild new file mode 100644 index 000000000..7dc83ceed --- /dev/null +++ b/sci-biology/libBigWig/libBigWig-0.4.7.ebuild @@ -0,0 +1,31 @@ +# Copyright 1999-2020 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DESCRIPTION="C library for handling bigWig files (functionally replacing Jim Kent's lib)" +HOMEPAGE="https://github.com/dpryan79/libBigWig" + +if [[ ${PV} == 9999 ]] ; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/dpryan79/libBigWig" +else + SRC_URI="https://github.com/dpryan79/libBigWig/archive/${PV}.tar.gz -> ${P}.tar.gz" + KEYWORDS="~amd64 ~x86" +fi + +LICENSE="MIT" +SLOT="0" + +DEPEND="net-misc/curl" +RDEPEND="${DEPEND}" + +src_prepare(){ + default + sed -e 's#/usr/local#$(DESTDIR)/usr#' -i Makefile || die + sed -e "s:/lib:/$(get_libdir):" -i Makefile || die +} + +src_install(){ + emake install DESTDIR="${ED}" +} diff --git a/sci-biology/libblasr/Manifest b/sci-biology/libblasr/Manifest deleted file mode 100644 index c575f4081..000000000 --- a/sci-biology/libblasr/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST libblasr-5.3.5.tar.gz 3950694 BLAKE2B 879910dbbfc60592528fab4de0e3bd975f8d12b7e68ca80e031577c9b18a6959a95c76186455fbdecbe3d8455320ba5b83db2c88318467d50a2470569860c514 SHA512 45997fce4fba12ff40c4624bc152990a683e4298d898b404f82e645493557a0565476ead2420fd9c28790e1985cdf3a88401c30181fdc57f84bbd61a707a8b5e diff --git a/sci-biology/libblasr/libblasr-5.3.5.ebuild b/sci-biology/libblasr/libblasr-5.3.5.ebuild deleted file mode 100644 index a12dc25ac..000000000 --- a/sci-biology/libblasr/libblasr-5.3.5.ebuild +++ /dev/null @@ -1,25 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -inherit meson - -DESCRIPTION="Library for blasr" -HOMEPAGE="http://www.smrtcommunity.com/SMRT-Analysis/Algorithms/BLASR" -SRC_URI="https://github.com/PacificBiosciences/blasr_libcpp/archive/${PV}.tar.gz -> ${P}.tar.gz" -S="${WORKDIR}/blasr_libcpp-${PV}" - -LICENSE="blasr" -SLOT="0" -KEYWORDS="~amd64" - -BDEPEND=" - dev-util/cmake - virtual/pkgconfig -" -DEPEND=" - sci-biology/pbbam - sci-libs/hdf5[cxx] -" -RDEPEND="${DEPEND}" diff --git a/sci-biology/libblasr/metadata.xml b/sci-biology/libblasr/metadata.xml deleted file mode 100644 index 8417d1580..000000000 --- a/sci-biology/libblasr/metadata.xml +++ /dev/null @@ -1,8 +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-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/longstitch/metadata.xml b/sci-biology/longstitch/metadata.xml index 138cb7705..b25087121 100644 --- a/sci-biology/longstitch/metadata.xml +++ b/sci-biology/longstitch/metadata.xml @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">bcgsc/LongStitch</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/lucy/lucy-1.20.ebuild b/sci-biology/lucy/lucy-1.20.ebuild index 4084ba298..a47e5fcf8 100644 --- a/sci-biology/lucy/lucy-1.20.ebuild +++ b/sci-biology/lucy/lucy-1.20.ebuild @@ -4,7 +4,7 @@ EAPI=7 DESCRIPTION="DNA sequence quality and vector trimming tool" -HOMEPAGE="http://lucy.sourceforge.net/" # no https +HOMEPAGE="https://lucy.sourceforge.net/" SRC_URI="https://sourceforge.net/projects/lucy/files/lucy/lucy%201.20/lucy${PV}.tar.gz" LICENSE="Artistic" diff --git a/sci-biology/mRNAmarkup/Manifest b/sci-biology/mRNAmarkup/Manifest deleted file mode 100644 index fb61347b3..000000000 --- a/sci-biology/mRNAmarkup/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST mRNAmarkup-5-21-2019.tar.gz 192535480 BLAKE2B 5aa385ddae79f2d18649ab70ac2939a478714abd84a59621d852888e9f7df4fd666baea8b8e905756a0f259471a35c6ca1fb5f7c2fa7a50769b4cf7c32dd431b SHA512 c05b685db7992e6278b56b34ad4e77c1f1c4bfb5b9f4880062fa07b5674272e5b950480bbfdd5cbfc037e6b87c10544d0fc67a8b55370037649203ce1c730d2a diff --git a/sci-biology/mRNAmarkup/mRNAmarkup-5.21.2019.ebuild b/sci-biology/mRNAmarkup/mRNAmarkup-5.21.2019.ebuild deleted file mode 100644 index fb37b69f9..000000000 --- a/sci-biology/mRNAmarkup/mRNAmarkup-5.21.2019.ebuild +++ /dev/null @@ -1,55 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DESCRIPTION="Transcript annotation workflow" -HOMEPAGE="http://brendelgroup.org/bioinformatics2go/mRNAmarkup.php" -SRC_URI="http://www.brendelgroup.org/bioinformatics2go/Download/mRNAmarkup-${PV//./-}.tar.gz" # 184MB - -LICENSE="mRNAmarkup" -SLOT="0" -KEYWORDS="~amd64" - -DEPEND=" - sci-biology/ncbi-tools++ - sci-biology/estscan" -# sci-biology/MuSeqBox has fetch-restrict and probably only works with old BLAST plaintex output -# but, mRNAmarkup/INSTALL says: -# 'For convenience, a copy of the MuSeqBox code distribution is included in directory src/contributed -# -# has a slightly modified estscan copy in src/contributed -RDEPEND="${DEPEND}" - -S="${WORKDIR}/${PN}" - -src_prepare(){ - default - sed -e \ - "s#configfile=$installdir/mRNAmarkup.conf#configfile=/usr/share/mRNAmarkup/etc/mRNAmarkup.conf#" \ - -i bin/mRNAmarkup.orig || die - sed -e \ - "s#$installdir/bin/ESTScan.conf#/usr/share/mRNAmarkup/etc/ESTScan.conf#" \ - -i bin/mRNAmarkup.orig -} - -src_compile(){ - cd src - emake -} - -src_install(){ - mv bin/mRNAmarkup.orig bin/mRNAmarkup - sed -e 's#INSTALLDIR#/usr/share/mRNAmarkup/etc/#' -i bin/mRNAmarkup - dobin bin/mRNAmarkup bin/*.pl bin/dnatopro bin/genestat - # TODO: there are some more files in bin/ , sigh! - insinto /usr/share/mRNAmarkup/etc - mv mRNAmarkup.conf.orig mRNAmarkup.conf - doins mRNAmarkup.conf - doins bin/ESTScan.conf - dodoc 0README INSTALL -} - -pkg_postinst(){ - einfo "Please obtain a local copy of NCBI CDD dastabase" -} diff --git a/sci-biology/mRNAmarkup/metadata.xml b/sci-biology/mRNAmarkup/metadata.xml deleted file mode 100644 index 138cb7705..000000000 --- a/sci-biology/mRNAmarkup/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>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/mappy/Manifest b/sci-biology/mappy/Manifest index c39d0ea60..ff114e6ea 100644 --- a/sci-biology/mappy/Manifest +++ b/sci-biology/mappy/Manifest @@ -1 +1,2 @@ DIST mappy-2.24.tar.gz 140859 BLAKE2B af8ecf8f00c33951b2c7e81bec1e45fe39b7b41da1692fc8c4804b3ad5465320f453e2d53f771c09ce88fa681ad60c0c3706334ace8a682eee8b6f4ebccb02fc SHA512 5500b76ffb0f530aa8f1433c01f1805f5b95e329445ab103847e6ec6e0977a54e5c0dabe405869c7dd8d9103646db0b3cff0ef13b79d7021752ed266002a1dd4 +DIST mappy-2.26.tar.gz 135105 BLAKE2B 26c4c94eae3b719cfaadf2fe31a84faeaef4894b8b8c9ad6bbba46dbb17f609c62c61ecfd42e3be07a7eace38545d029ab03d1fee611868ac6839b3d3362698d SHA512 75949b705561455c317713bfb4bca2de24368881e6c0bb3bf2d11841db9f9e792c7eef0e46f00a7b27e38fe143db5b00be5f281fe058dca32130b745057dcb75 diff --git a/sci-biology/mappy/mappy-2.24.ebuild b/sci-biology/mappy/mappy-2.24.ebuild index 3e25ed1eb..0fa703188 100644 --- a/sci-biology/mappy/mappy-2.24.ebuild +++ b/sci-biology/mappy/mappy-2.24.ebuild @@ -1,15 +1,15 @@ -# Copyright 1999-2022 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) -inherit distutils-r1 +inherit distutils-r1 pypi DESCRIPTION="Minimap2 python binding" HOMEPAGE="https://github.com/haotianteng/chiron" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" LICENSE="MIT" SLOT="0" diff --git a/sci-biology/mappy/mappy-2.26.ebuild b/sci-biology/mappy/mappy-2.26.ebuild new file mode 100644 index 000000000..0fa703188 --- /dev/null +++ b/sci-biology/mappy/mappy-2.26.ebuild @@ -0,0 +1,16 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) + +inherit distutils-r1 pypi + +DESCRIPTION="Minimap2 python binding" +HOMEPAGE="https://github.com/haotianteng/chiron" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" diff --git a/sci-biology/mappy/metadata.xml b/sci-biology/mappy/metadata.xml index 8417d1580..2b83a776c 100644 --- a/sci-biology/mappy/metadata.xml +++ b/sci-biology/mappy/metadata.xml @@ -5,4 +5,8 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">haotianteng/chiron</remote-id> + <remote-id type="pypi">mappy</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/minimap2/metadata.xml b/sci-biology/minimap2/metadata.xml index c9e82c96a..604410dd8 100644 --- a/sci-biology/minimap2/metadata.xml +++ b/sci-biology/minimap2/metadata.xml @@ -10,6 +10,6 @@ <name>Gentoo Biology Project</name> </maintainer> <upstream> - <remote-id type="github">minimap2</remote-id> + <remote-id type="github">lh3/minimap2</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/minimap2/minimap2-2.24.ebuild b/sci-biology/minimap2/minimap2-2.24.ebuild index f39de8ead..6934f2a74 100644 --- a/sci-biology/minimap2/minimap2-2.24.ebuild +++ b/sci-biology/minimap2/minimap2-2.24.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) DISTUTILS_OPTIONAL=1 inherit distutils-r1 diff --git a/sci-biology/mouse-brain-atlases/Manifest b/sci-biology/mouse-brain-atlases/Manifest deleted file mode 100644 index 262bc49f7..000000000 --- a/sci-biology/mouse-brain-atlases/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST mouse-brain-atlases-0.5.3.tar.xz 591935168 BLAKE2B ceabe728d65b9a73afc9ec18dde14146e26c8465a71b53fdb607ad05ff4626a748ac8cc3d56c2876a2dabf53015db9da0caa66dc48ce83fbaddffcd19c0becce SHA512 7d7ca79f99d03e4a9a97ccf6517fc6570770bee0cea80c2b31e7c4fb4500b8eb49ffb7df5579901c12dd982fd3efb6fc93490dcf53da715c167d47939ea44bdb -DIST mouse-brain-atlasesHD-0.5.3.tar.xz 915990788 BLAKE2B 3be900c9421849a32473a9f1fb1188f73b9fffd36f1e4edc7b6ead91b485bde3cfe211d03f73c4e09cfe194debdc92aad8639e72a64f66036d9a45f08a29cf47 SHA512 46c74d41d323d4cdd7cdf5e8c8ceec03eecf5e7b5c83bb95b7ad4814e55dc32ada7f781710dc40145ffd751d650d35eb5727c460920b831135ab706f5e136718 diff --git a/sci-biology/mouse-brain-atlases/metadata.xml b/sci-biology/mouse-brain-atlases/metadata.xml deleted file mode 100644 index 16fcf156a..000000000 --- a/sci-biology/mouse-brain-atlases/metadata.xml +++ /dev/null @@ -1,15 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>gentoo@chymera.eu</email> - <name>Horea Christian</name> - </maintainer> - <maintainer type="project"> - <email>sci@gentoo.org</email> - <name>Gentoo Science Project</name> - </maintainer> - <use> - <flag name="hires">Also install high-resolution atlases.</flag> - </use> -</pkgmetadata> diff --git a/sci-biology/mouse-brain-atlases/mouse-brain-atlases-0.5.3.ebuild b/sci-biology/mouse-brain-atlases/mouse-brain-atlases-0.5.3.ebuild deleted file mode 100644 index 0709fb65d..000000000 --- a/sci-biology/mouse-brain-atlases/mouse-brain-atlases-0.5.3.ebuild +++ /dev/null @@ -1,44 +0,0 @@ -# Copyright 1999-2018 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit check-reqs - -DESCRIPTION="A collection of mouse brain atlases in NIfTI format" -HOMEPAGE="https://github.com/IBT-FMI/mouse-brain-atlases" -SRC_URI=" - http://resources.chymera.eu/distfiles/${P}.tar.xz - hires? ( http://resources.chymera.eu/distfiles/${PN}HD-${PV}.tar.xz ) - " - -LICENSE="fairuse" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="hires" - -RDEPEND="" -DEPEND="" - -pkg_pretend() { - if use hires; then - CHECKREQS_DISK_BUILD="4G" - CHECKREQS_DISK_USR="4G" - CHECKREQS_DISK_VAR="8G" - else - CHECKREQS_DISK_BUILD="500M" - fi - check-reqs_pkg_pretend -} - -# We disable this phase to not check requirements twice. -pkg_setup() { :; } - -src_install() { - insinto "/usr/share/${PN}" - doins * - if use hires; then - cd "../${PN}HD-${PV}" - doins * - fi -} diff --git a/sci-biology/mouse-brain-templates/metadata.xml b/sci-biology/mouse-brain-templates/metadata.xml index 16fcf156a..97fbbcbf2 100644 --- a/sci-biology/mouse-brain-templates/metadata.xml +++ b/sci-biology/mouse-brain-templates/metadata.xml @@ -12,4 +12,7 @@ <use> <flag name="hires">Also install high-resolution atlases.</flag> </use> + <upstream> + <remote-id type="github">IBT-FMI/mouse-brain-templates_generator</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/mouse-brain-templates/mouse-brain-templates-0.5.3.ebuild b/sci-biology/mouse-brain-templates/mouse-brain-templates-0.5.3.ebuild index 79c042a2a..60d06f934 100644 --- a/sci-biology/mouse-brain-templates/mouse-brain-templates-0.5.3.ebuild +++ b/sci-biology/mouse-brain-templates/mouse-brain-templates-0.5.3.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 @@ -6,10 +6,10 @@ EAPI=7 inherit check-reqs DESCRIPTION="A collection of mouse brain templates in NIfTI format" -HOMEPAGE="https://github.com/IBT-FMI/mouse-brain-atlases" +HOMEPAGE="https://github.com/IBT-FMI/mouse-brain-templates_generator" SRC_URI=" - http://resources.chymera.eu/distfiles/${P}.tar.xz - hires? ( http://resources.chymera.eu/distfiles/${PN}HD-${PV}.tar.xz ) + https://resources.chymera.eu/distfiles/${P}.tar.xz + hires? ( https://resources.chymera.eu/distfiles/${PN}HD-${PV}.tar.xz ) " LICENSE="fairuse" diff --git a/sci-biology/mreps/metadata.xml b/sci-biology/mreps/metadata.xml index 8417d1580..a60e8c1b5 100644 --- a/sci-biology/mreps/metadata.xml +++ b/sci-biology/mreps/metadata.xml @@ -5,4 +5,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">gregorykucherov/mreps</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/multiqc/Manifest b/sci-biology/multiqc/Manifest new file mode 100644 index 000000000..3585038a3 --- /dev/null +++ b/sci-biology/multiqc/Manifest @@ -0,0 +1 @@ +DIST multiqc-1.19.tar.gz 1159781 BLAKE2B 32d592dba5675f8cb673c8fced9f8ed32977ecd2baf1407aff4ef16b88d8bdad6a9541748717b90d5ab755f6354166e2de62cb1abd282d0e5ce9d1c89529d249 SHA512 75ef5a1b6c6433d68b878e2a1d51b6f420b8c77831cb1279a0b87aff5d6dee7a65bcca5d1f4deb04d4957feef0f27a1155198e244bd165404b08a23bfc8a9354 diff --git a/sci-biology/multiqc/metadata.xml b/sci-biology/multiqc/metadata.xml new file mode 100644 index 000000000..09bd2b6e6 --- /dev/null +++ b/sci-biology/multiqc/metadata.xml @@ -0,0 +1,12 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>mschu.dev@gmail.com</email> + <name>Michael Schubert</name> + </maintainer> + <upstream> + <remote-id type="github">ewels/MultiQC</remote-id> + <remote-id type="pypi">multiqc</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/multiqc/multiqc-1.19.ebuild b/sci-biology/multiqc/multiqc-1.19.ebuild new file mode 100644 index 000000000..187f06c22 --- /dev/null +++ b/sci-biology/multiqc/multiqc-1.19.ebuild @@ -0,0 +1,40 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) + +inherit pypi distutils-r1 + +DESCRIPTION="Aggregate bioinformatics results across many samples into a single report" +HOMEPAGE="https://multiqc.info/" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~amd64-linux" + +RDEPEND="dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/networkx[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/click[${PYTHON_USEDEP}] + dev-python/coloredlogs[${PYTHON_USEDEP}] + dev-python/future[${PYTHON_USEDEP}] + dev-python/jinja[${PYTHON_USEDEP}] + dev-python/lzstring[${PYTHON_USEDEP}] + dev-python/markdown[${PYTHON_USEDEP}] + dev-python/packaging[${PYTHON_USEDEP}] + dev-python/pyyaml[${PYTHON_USEDEP}] + dev-python/requests[${PYTHON_USEDEP}] + dev-python/rich[${PYTHON_USEDEP}] + dev-python/rich-click[${PYTHON_USEDEP}] + dev-python/simplejson[${PYTHON_USEDEP}] + dev-python/spectra[${PYTHON_USEDEP}] + dev-python/importlib-metadata[$PYTHON_USEDEP] + dev-python/humanize[$PYTHON_USEDEP] + dev-python/pyaml-env[$PYTHON_USEDEP]" + +# pypi tarball does not include tests +RESTRICT="test" +#distutils_enable_tests pytest diff --git a/sci-biology/ncbi-blast+/Manifest b/sci-biology/ncbi-blast+/Manifest deleted file mode 100644 index afe8a43ef..000000000 --- a/sci-biology/ncbi-blast+/Manifest +++ /dev/null @@ -1,5 +0,0 @@ -DIST ncbi-blast-2.11.0+-src.tar.gz 58493096 BLAKE2B cfd6e7c66b379bee7065d306d2e426b798ec13fea5ed736c05c48b45c2fd7389c5050cc920b67d5e0f58102a4ef1108decbde791012fab28fe7402f9c8747808 SHA512 617994a0e3a4675a5f7048f165ac405bbd6a715ece9aba115d7c26b6be446b889b817dd496a2e15673545e5b594684c83fc4edb22cb5ecca2fd6d342c3bd642e -DIST ncbi-blast-2.2.30+-src.tar.gz 18985378 BLAKE2B 59e749964ee5c6e30ac0286fc928fa8806abfd01aa70d937751642929de4d4e8ebc2109061f5dc82baf7e517a8718e1e11b9372c84f8be3b4140f55708ab264b SHA512 501727486aaa384ee5c40368332243ec2e19f22ab88f50c9396b4d33738bde4dbb5d3a1025ae599c1b5f4b4dd3d065ba4d0eb30305f42bfc781c95bbc4140a17 -DIST ncbi-blast-2.2.31+-src.tar.gz 18971327 BLAKE2B 4f6b124ddf6c892a0be36cbdcb00fe20a15b6f7a49af3f022e31a757ebd48d95c52219ecb2d56fa7787f936dbc08853affe07250ddf5461aff2f7fa5a9742be7 SHA512 2681a4394cc250d1ee545cd85dc962d73b1dbbdd987790a029bf51a58e74cbb08b5c8cf4a02b9b7c95916e3fb0d1613e2ed8631bb7ad683156759421081bb4ca -DIST ncbi-blast-2.6.0+-src.tar.gz 20025526 BLAKE2B d97d1245e3f2030025e99323d67d889e6cecaa719fe525dbe1574a916e5f8b7b620880d44efe51851d64b9d1cdd0538f13161bfea8e233dcca6a223548d5090d SHA512 ea6444892a0b10459193d33d243b5960ad206b702e01e94a554a5ebda0291ff45e1ce43479713c23a96eba676b40bb8c57a7ef9dd2118729feef6b2cd98560c6 -DIST ncbi-blast-2.8.1+-src.tar.gz 24973554 BLAKE2B d13dee5cdd0218cb409898ac999fe5613e534375958c4b814a4c52d9954152a8da491d4866d6090c11bbb94916542be4809744a7f474c189a3b2f3dc9bc8e207 SHA512 3f408c5f76704183578828df3272bab7d59dd6052364e73e1831cd005b87d87dcc086bb1799b316b09e639e4af0edea6404b93a4b3e3c159d27cef34fff93d6f diff --git a/sci-biology/ncbi-blast+/files/disable-testsuite-compilation.txt b/sci-biology/ncbi-blast+/files/disable-testsuite-compilation.txt deleted file mode 100644 index aeaf75e45..000000000 --- a/sci-biology/ncbi-blast+/files/disable-testsuite-compilation.txt +++ /dev/null @@ -1,3 +0,0 @@ -.* --.*/test --.*/unit_test diff --git a/sci-biology/ncbi-blast+/files/ncbi-blast+-2.2.30__fix_lib_deps.patch b/sci-biology/ncbi-blast+/files/ncbi-blast+-2.2.30__fix_lib_deps.patch deleted file mode 100644 index 13dffeee7..000000000 --- a/sci-biology/ncbi-blast+/files/ncbi-blast+-2.2.30__fix_lib_deps.patch +++ /dev/null @@ -1,668 +0,0 @@ -Subject: ensure that all libraries link against all direct dependencies
-
- * src/**/Makefile.*.lib: set DLL_(D)LIB correctly. Break the dependency
- loop between libxblast and libxalgoblastdbindex by having the former
- provide only the C++ BLAST API, leaving the C core only in libblast.
- * src/build-system/library_relations.txt: Change xblast's
- relationship to blast from includes to needs, accordingly.
- * src/algo/blast/dbindex*/*/Makefile.*.app: Link against libxconnect
- rather than libconnect for consistency with libblast, which uses the
- former to keep the aforementioned cycle-breaking from causing
- inconsistency elsewhere.
-
-Debian-Bug: 633567.
-Author: Aaron M. Ucko <ucko@debian.org>
-Last-Update: 2014-12-02
---- a/c++/src/algo/blast/core/Makefile.blast.lib
-+++ b/c++/src/algo/blast/core/Makefile.blast.lib
-@@ -21,6 +21,7 @@ LIB = blast
- CFLAGS = $(FAST_CFLAGS)
- LDFLAGS = $(FAST_LDFLAGS)
-
-+DLL_LIB = composition_adjustment xconnect tables
-
- WATCHERS = madden camacho
-
---- a/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib
-+++ b/c++/src/algo/blast/dbindex/Makefile.xalgoblastdbindex.lib
-@@ -11,6 +11,8 @@ SRC = sequence_istream_fasta \
- CXXFLAGS = -DDO_INLINE $(FAST_CXXFLAGS)
- LDFLAGS = $(FAST_LDFLAGS)
-
-+DLL_LIB = blast seqdb xobjread xobjutil xobjmgr seqset seq xser xutil xncbi
-+
- ASN_DEP = seqset
-
- WATCHERS = morgulis
---- a/c++/src/algo/blast/format/Makefile.xblastformat.lib
-+++ b/c++/src/algo/blast/format/Makefile.xblastformat.lib
-@@ -7,7 +7,8 @@ SRC = blastfmtutil blastxml_format blast
-
- CPPFLAGS = -DNCBI_MODULE=BLASTFORMAT $(ORIG_CPPFLAGS)
-
--DLL_LIB = align_format blastxml blastxml2 xhtml xcgi
-+DLL_LIB = xblast align_format xalnmgr xobjmgr xnetblast scoremat blastxml \
-+ seq general xser tables xncbi blastxml2
-
- WATCHERS = jianye zaretska madden camacho fongah2
-
---- a/c++/src/algo/winmask/Makefile.xalgowinmask.lib
-+++ b/c++/src/algo/winmask/Makefile.xalgowinmask.lib
-@@ -21,7 +21,7 @@ SRC = seq_masker seq_masker_score_mean s
- CXXFLAGS = $(FAST_CXXFLAGS)
- LDFLAGS = $(FAST_LDFLAGS)
-
--
-+DLL_LIB = seqmasks_io xobjread xobjutil xobjmgr seq xncbi
-
- USES_LIBRARIES = \
- seqmasks_io
---- a/c++/src/cgi/Makefile.cgi.lib
-+++ b/c++/src/cgi/Makefile.cgi.lib
-@@ -9,6 +9,8 @@ SRC = ncbicgi cgiapp cgictx ncbicgir ncb
- user_agent
- LIB = xcgi
-
-+DLL_LIB = xutil xncbi
-+
- CPPFLAGS = $(ORIG_CPPFLAGS) $(FASTCGI_INCLUDE)
-
- WATCHERS = vakatov
---- a/c++/src/html/Makefile.html.lib
-+++ b/c++/src/html/Makefile.html.lib
-@@ -7,6 +7,8 @@ SRC = node html htmlhelper page pager se
- commentdiag indentstream html_exception writer_htmlenc
- LIB = xhtml
-
-+DLL_LIB = xncbi
-+
- WATCHERS = ivanov
-
-
---- a/c++/src/objects/blast/Makefile.xnetblastcli.lib
-+++ b/c++/src/objects/blast/Makefile.xnetblastcli.lib
-@@ -3,6 +3,7 @@ ASN_DEP = xnetblast
- LIB = xnetblastcli
- SRC = blastclient blastclient_
-
-+DLL_LIB = xnetblast xser xconnect xutil xncbi
-
- USES_LIBRARIES = \
- xconnect xnetblast
---- a/c++/src/objtools/align_format/Makefile.align_format.lib
-+++ b/c++/src/objtools/align_format/Makefile.align_format.lib
-@@ -13,6 +13,10 @@ SRC = format_flags align_format_util sho
-
- CPPFLAGS = -DNCBI_MODULE=BLASTFORMAT $(ORIG_CPPFLAGS)
-
-+DLL_LIB = xalnmgr ncbi_xloader_genbank seqdb blast_services xobjread xobjutil \
-+ xobjmgr xnetblast blastdb gene_info seqset seq general xser \
-+ xcgi xhtml tables xncbi
-+
- ### EXAMPLES OF OTHER SETTINGS THAT MIGHT BE OF INTEREST
- # CFLAGS = $(FAST_CFLAGS)
- # CXXFLAGS = $(FAST_CXXFLAGS)
---- a/c++/src/objtools/alnmgr/Makefile.alnmgr.lib
-+++ b/c++/src/objtools/alnmgr/Makefile.alnmgr.lib
-@@ -12,7 +12,7 @@ SRC = aln_builders aln_converters aln_ge
-
- WATCHERS = todorov dicuccio grichenk
-
--
-+DLL_LIB = xobjmgr seqset seq xser tables xncbi
-
- USES_LIBRARIES = \
- tables xobjutil
---- a/c++/src/objtools/readers/Makefile.xobjread.lib
-+++ b/c++/src/objtools/readers/Makefile.xobjread.lib
-@@ -21,7 +21,7 @@ SRC = read_util format_guess_ex \
- message_listener line_error
-
-
--DLL_LIB = creaders
-+DLL_LIB = submit seqset seq pub general xser creaders sequtil xutil xncbi
-
-
-
---- a/c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib
-+++ b/c++/src/objtools/seqmasks_io/Makefile.seqmasks_io.lib
-@@ -12,7 +12,7 @@ mask_writer_seqloc \
- mask_writer_blastdb_maskinfo
-
- ASN_DEP = seqset
--DLL_LIB = seqdb blastdb
-+DLL_LIB = seqdb xobjread xobjutil xobjmgr blastdb seqset seq xser xncbi
-
- WATCHERS = morgulis camacho
-
---- a/c++/src/objtools/simple/Makefile.xobjsimple.lib
-+++ b/c++/src/objtools/simple/Makefile.xobjsimple.lib
-@@ -7,6 +7,8 @@ WATCHERS = jcherry
-
- ASN_DEP = seqset
-
-+DLL_LIB = ncbi_xloader_genbank xobjmgr seq xncbi
-+
- LIB = xobjsimple
- SRC = simple_om
-
---- a/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib
-+++ b/c++/src/objtools/blast/seqdb_reader/Makefile.seqdb.lib
-@@ -24,6 +24,8 @@ seqdbobj
-
- LIB = seqdb
-
-+DLL_LIB = blastdb xobjmgr seq general xser sequtil xncbi
-+
- CFLAGS = $(FAST_CFLAGS)
- CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS)
- CXXFLAGS = $(FAST_CXXFLAGS)
---- a/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib
-+++ b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib
-@@ -7,6 +7,8 @@ CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_
-
- ASN_DEP = blastdb seqset
-
-+DLL_LIB = seqdb xobjmgr seqset seq xncbi
-+
- WATCHERS = camacho
-
-
---- a/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib
-+++ b/c++/src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib
-@@ -5,6 +5,8 @@ SRC = bdbloader_rmt remote_blastdb_adapt
-
- CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS)
-
-+DLL_LIB = ncbi_xloader_blastdb blast_services xobjmgr seq xncbi
-+
- ASN_DEP = blastdb xnetblast
-
- WATCHERS = camacho
---- a/c++/src/algo/blast/api/Makefile.xblast.lib
-+++ b/c++/src/algo/blast/api/Makefile.xblast.lib
-@@ -74,14 +74,15 @@ cdd_pssm_input \
- deltablast_options \
- deltablast
-
--SRC = $(SRC_C:%=.core_%) $(SRC_CXX)
-+SRC = $(SRC_CXX) # $(SRC_C:%=.core_%)
-
- LIB = xblast
-
- DLL_LIB = xalgoblastdbindex composition_adjustment xalgowinmask \
- xalgodustmask seqmasks_io seqdb $(OBJREAD_LIBS) xobjutil \
- blastdb xnetblastcli xnetblast scoremat xconnect tables \
-- $(SOBJMGR_LIBS)
-+ $(SOBJMGR_LIBS) blast seqdb seqset seq general \
-+ xser xconnect sequtil tables xutil xncbi
-
- CFLAGS = $(FAST_CFLAGS)
- CPPFLAGS = -DNCBI_MODULE=BLAST $(ORIG_CPPFLAGS)
---- a/c++/src/algo/blast/blastinput/Makefile.blastinput.lib
-+++ b/c++/src/algo/blast/blastinput/Makefile.blastinput.lib
-@@ -24,7 +24,9 @@ SRC = $(SRC_CXX)
-
- LIB = blastinput
-
--DLL_LIB = xblast align_format ncbi_xloader_blastdb_rmt ncbi_xloader_blastdb seqdb $(OBJREAD_LIBS) $(OBJMGR_LIBS) xutil
-+ DLL_LIB = xblast align_format ncbi_xloader_blastdb_rmt ncbi_xloader_blastdb seqdb xobjread \
-+ $(OBJREAD_LIBS) $(OBJMGR_LIBS) xutil ncbi_xloader_genbank ncbi_xreader_id2 ncbi_xreader \
-+ scoremat seqset seq xser xutil xncbi
-
- # should be redundant, given the above :-/
- ASN_DEP = seqset xnetblast
---- a/c++/src/algo/dustmask/Makefile.xalgodustmask.lib
-+++ b/c++/src/algo/dustmask/Makefile.xalgodustmask.lib
-@@ -8,6 +8,8 @@ LIB = xalgodustmask
-
- SRC = symdust
-
-+DLL_LIB = xobjmgr seq xncbi
-+
- CXXFLAGS = $(FAST_CXXFLAGS)
- LDFLAGS = $(FAST_LDFLAGS)
-
---- a/c++/src/connect/Makefile.xconnect.lib
-+++ b/c++/src/connect/Makefile.xconnect.lib
-@@ -14,6 +14,8 @@ UNIX_SRC = $(LOCAL_LBSM)
- LIB = xconnect
- PROJ_TAG = core
-
-+DLL_LIB = xncbi
-+
- LIBS = $(NETWORK_LIBS) $(ORIG_LIBS)
-
- WATCHERS = lavr
---- a/c++/src/connect/ext/Makefile.xconnext.lib
-+++ b/c++/src/connect/ext/Makefile.xconnext.lib
-@@ -6,6 +6,8 @@ SRC = $(SRC_C) ncbi_dblb_svcmapper
-
- LIB = xconnext
-
-+DLL_LIB = xconnect xncbi
-+
- WATCHERS = lavr
-
-
---- a/c++/src/objects/blast/Makefile.blast.lib
-+++ b/c++/src/objects/blast/Makefile.blast.lib
-@@ -1,6 +1,8 @@
- LIB = xnetblast
- SRC = blast__ blast___ names
-
-+DLL_LIB = scoremat seqset seq xser xncbi
-+
- WATCHERS = camacho
-
-
---- a/c++/src/objects/blastxml/Makefile.blastxml.lib
-+++ b/c++/src/objects/blastxml/Makefile.blastxml.lib
-@@ -1,6 +1,8 @@
- LIB = blastxml
- SRC = blastxml__ blastxml___
-
-+DLL_LIB = xser xncbi
-+
-
- USES_LIBRARIES = \
- xser
---- a/c++/src/objects/scoremat/Makefile.scoremat.lib
-+++ b/c++/src/objects/scoremat/Makefile.scoremat.lib
-@@ -1,6 +1,8 @@
- LIB = scoremat
- SRC = scoremat__ scoremat___
-
-+DLL_LIB = seqset seq general xser xncbi
-+
-
- USES_LIBRARIES = \
- seqset
---- a/c++/src/objects/seqedit/Makefile.seqedit.lib
-+++ b/c++/src/objects/seqedit/Makefile.seqedit.lib
-@@ -1,6 +1,7 @@
- LIB = seqedit
- SRC = seqedit__ seqedit___
--
-+
-+DLL_LIB = seqset seq general xser xncbi
-
-
- USES_LIBRARIES = \
---- a/c++/src/objects/submit/Makefile.submit.lib
-+++ b/c++/src/objects/submit/Makefile.submit.lib
-@@ -1,6 +1,8 @@
- LIB = submit
- SRC = submit__ submit___
-
-+DLL_LIB = seqset seq biblio general xser xncbi
-+
-
- USES_LIBRARIES = \
- seqset
---- a/c++/src/objmgr/util/Makefile.util.lib
-+++ b/c++/src/objmgr/util/Makefile.util.lib
-@@ -8,6 +8,8 @@ ASN_DEP = submit
- SRC = weight sequence feature seqtitle create_defline obj_sniff seq_loc_util seq_align_util seq_trimmer bioseqgaps_ci
- LIB = xobjutil
-
-+DLL_LIB = xobjmgr seqset seq pub biblio general xser sequtil xutil xncbi
-+
- WATCHERS = ucko vasilche kornbluh
-
-
---- a/c++/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib
-+++ b/c++/src/objtools/blast/blastdb_format/Makefile.blastdb_format.lib
-@@ -11,6 +11,7 @@ SRC = seq_writer blastdb_dataextract bla
-
- CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS)
-
-+DLL_LIB = seqdb xobjutil xobjmgr seq xser sequtil xutil xncbi
-
- ### EXAMPLES OF OTHER SETTINGS THAT MIGHT BE OF INTEREST
- # CFLAGS = $(FAST_CFLAGS)
---- a/c++/src/objtools/blast/services/Makefile.blast_services.lib
-+++ b/c++/src/objtools/blast/services/Makefile.blast_services.lib
-@@ -8,6 +8,8 @@ SRC = blast_services
-
- LIB = blast_services
-
-+DLL_LIB = xnetblastcli xnetblast xser xconnect xutil xncbi
-+
- CFLAGS = $(FAST_CFLAGS)
- CPPFLAGS = -DNCBI_MODULE=NETBLAST $(ORIG_CPPFLAGS)
- CXXFLAGS = $(FAST_CXXFLAGS)
---- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib
-+++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xloader_genbank.lib
-@@ -12,6 +12,9 @@ LIB_OR_DLL = both
- # Dependencies for shared library
- DLL_LIB = ncbi_xreader$(DLL)
-
-+DLL_DLIB = ncbi_xreader_cache ncbi_xreader_id1 ncbi_xreader_id2 \
-+ id2 id1 ncbi_xreader xobjmgr seq xutil xncbi
-+
- WATCHERS = vasilche
-
-
---- a/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib
-+++ b/c++/src/objtools/data_loaders/genbank/Makefile.ncbi_xreader.lib
-@@ -15,6 +15,9 @@ LIB_OR_DLL = both
- DLL_LIB =
- DLL_DLIB = $(GENBANK_READER_LDEP)
-
-+DLL_DLIB = xobjmgr id2 seqsplit id1 seqset seq general \
-+ xser xconnect xcompress xutil xncbi
-+
- WATCHERS = vasilche
-
-
---- a/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib
-+++ b/c++/src/objtools/data_loaders/genbank/cache/Makefile.ncbi_xreader_cache.lib
-@@ -12,6 +12,8 @@ LIB_OR_DLL = both
- # Dependencies for shared library
- DLL_LIB = ncbi_xreader$(DLL)
-
-+DLL_DLIB = ncbi_xreader xobjmgr seq xser xncbi
-+
- CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
-
- WATCHERS = vasilche
---- a/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib
-+++ b/c++/src/objtools/data_loaders/genbank/id1/Makefile.ncbi_xreader_id1.lib
-@@ -12,6 +12,8 @@ LIB_OR_DLL = both
- # Dependencies for shared library
- DLL_LIB = xconnect ncbi_xreader$(DLL)
-
-+DLL_DLIB = ncbi_xreader xobjmgr id1 seq general xser xconnect xutil xncbi
-+
- CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
-
- WATCHERS = vasilche
---- a/c++/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib
-+++ b/c++/src/objtools/data_loaders/genbank/id2/Makefile.ncbi_xreader_id2.lib
-@@ -12,7 +12,10 @@ LIB_OR_DLL = both
- CPPFLAGS = $(ORIG_CPPFLAGS) $(Z_INCLUDE)
-
- # Dependencies for shared library (disabled due to problems on Darwin)
--# DLL_LIB = xconnect ncbi_xreader$(DLL)
-+DLL_LIB = xconnect ncbi_xreader$(DLL)
-+
-+DLL_DLIB = ncbi_xreader xobjmgr id2 seqsplit seq xser xconnect xncbi
-+
-
- WATCHERS = vasilche
-
---- a/c++/src/util/compress/api/Makefile.compress.lib
-+++ b/c++/src/util/compress/api/Makefile.compress.lib
-@@ -7,7 +7,7 @@ LIB = xcompress
-
- CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
-
--DLL_LIB = $(BZ2_LIB) $(Z_LIB) $(LZO_LIB)
-+DLL_LIB = $(BZ2_LIB) $(Z_LIB) $(LZO_LIB) xutil xncbi
- LIBS = $(BZ2_LIBS) $(Z_LIBS) $(LZO_LIBS) $(ORIG_LIBS)
-
- WATCHERS = ivanov
---- a/c++/src/util/sequtil/Makefile.sequtil.lib
-+++ b/c++/src/util/sequtil/Makefile.sequtil.lib
-@@ -3,6 +3,8 @@
- LIB = sequtil
- SRC = sequtil sequtil_convert sequtil_convert_imp sequtil_manip sequtil_tables sequtil_shared
-
-+DLL_LIB = xncbi
-+
- WATCHERS = shomrat
-
-
---- a/c++/src/corelib/Makefile.test_boost.lib
-+++ b/c++/src/corelib/Makefile.test_boost.lib
-@@ -3,6 +3,8 @@
- SRC = test_boost teamcity_messages
- LIB = test_boost
-
-+DLL_LIB = xncbi
-+
- CPPFLAGS = $(ORIG_CPPFLAGS) $(BOOST_INCLUDE)
-
- REQUIRES = Boost.Test.Included
---- a/c++/src/corelib/Makefile.test_mt.lib
-+++ b/c++/src/corelib/Makefile.test_mt.lib
-@@ -3,6 +3,8 @@
- SRC = test_mt
- LIB = test_mt
-
-+DLL_LIB = xncbi
-+
- # REQUIRES = MT
-
- USE_PCH = no
---- a/c++/src/objects/biblio/Makefile.biblio.lib
-+++ b/c++/src/objects/biblio/Makefile.biblio.lib
-@@ -1,6 +1,8 @@
- LIB = biblio
- SRC = biblio__ biblio___ citation_base
-
-+DLL_LIB = general xser xncbi
-+
-
- USES_LIBRARIES = \
- general
---- a/c++/src/objects/blastdb/Makefile.blastdb.lib
-+++ b/c++/src/objects/blastdb/Makefile.blastdb.lib
-@@ -1,5 +1,7 @@
- # $Id: Makefile.blastdb.lib 427424 2014-02-20 13:38:50Z gouriano $
-
-+
-+DLL_LIB = seq xser xncbi
- LIB = blastdb
- SRC = blastdb__ blastdb___
-
---- a/c++/src/objects/general/Makefile.general.lib
-+++ b/c++/src/objects/general/Makefile.general.lib
-@@ -1,6 +1,8 @@
- LIB = general
- SRC = general__ general___ uoconv
-
-+DLL_LIB = xser xncbi
-+
-
- USES_LIBRARIES = \
- xser
---- a/c++/src/objects/genomecoll/Makefile.genome_collection.lib
-+++ b/c++/src/objects/genomecoll/Makefile.genome_collection.lib
-@@ -3,6 +3,8 @@
- LIB = genome_collection
- SRC = genome_collection__ genome_collection___
-
-+DLL_LIB = seq general xser xncbi
-+
- WATCHERS = dicuccio
-
-
---- a/c++/src/objects/id1/Makefile.id1.lib
-+++ b/c++/src/objects/id1/Makefile.id1.lib
-@@ -3,6 +3,8 @@ ASN_DEP = seq
- LIB = id1
- SRC = id1__ id1___
-
-+DLL_LIB = seqset seq xser xncbi
-+
- WATCHERS = vasilche
-
-
---- a/c++/src/objects/id2/Makefile.id2.lib
-+++ b/c++/src/objects/id2/Makefile.id2.lib
-@@ -1,6 +1,8 @@
- LIB = id2
- SRC = id2__ id2___
-
-+DLL_LIB = seqsplit seq xser xncbi
-+
- WATCHERS = vasilche
-
-
---- a/c++/src/objects/medline/Makefile.medline.lib
-+++ b/c++/src/objects/medline/Makefile.medline.lib
-@@ -1,6 +1,8 @@
- LIB = medline
- SRC = medline__ medline___
-
-+DLL_LIB = biblio general xser xncbi
-+
-
- USES_LIBRARIES = \
- biblio
---- a/c++/src/objects/pub/Makefile.pub.lib
-+++ b/c++/src/objects/pub/Makefile.pub.lib
-@@ -1,6 +1,8 @@
- LIB = pub
- SRC = pub__ pub___
-
-+DLL_LIB = medline biblio xser xncbi
-+
-
- USES_LIBRARIES = \
- medline
---- a/c++/src/objects/seq/Makefile.seq.lib
-+++ b/c++/src/objects/seq/Makefile.seq.lib
-@@ -12,6 +12,8 @@ SRC = $(ASN:%=%__) $(ASN:%=%___) seqport
- seq_loc_mapper_base seq_align_mapper_base seqlocinfo sofa_map \
- seq_loc_from_string seq_loc_reverse_complementer
-
-+DLL_LIB = seqcode pub biblio general xser sequtil xutil xncbi
-+
- WATCHERS = vasilche grichenk
-
-
---- a/c++/src/objects/seqcode/Makefile.seqcode.lib
-+++ b/c++/src/objects/seqcode/Makefile.seqcode.lib
-@@ -1,6 +1,8 @@
- LIB = seqcode
- SRC = seqcode__ seqcode___
-
-+DLL_LIB = xser xncbi
-+
-
- USES_LIBRARIES = \
- xser
---- a/c++/src/objects/seqset/Makefile.seqset.lib
-+++ b/c++/src/objects/seqset/Makefile.seqset.lib
-@@ -1,6 +1,8 @@
- LIB = seqset
- SRC = seqset__ seqset___ gb_release_file
-
-+DLL_LIB = seq general xser xncbi
-+
-
- USES_LIBRARIES = \
- $(SEQ_LIBS) pub
---- a/c++/src/objects/seqsplit/Makefile.seqsplit.lib
-+++ b/c++/src/objects/seqsplit/Makefile.seqsplit.lib
-@@ -1,6 +1,8 @@
- LIB = seqsplit
- SRC = seqsplit__ seqsplit___
-
-+DLL_LIB = seqset seq xser xncbi
-+
- WATCHERS = vasilche
-
-
---- a/c++/src/serial/Makefile.serial.lib
-+++ b/c++/src/serial/Makefile.serial.lib
-@@ -18,6 +18,8 @@ SRC = \
-
- LIB = xser
-
-+DLL_LIB = xutil xncbi
-+
- WATCHERS = gouriano
-
-
---- a/c++/src/util/Makefile.util.lib
-+++ b/c++/src/util/Makefile.util.lib
-@@ -12,6 +12,7 @@ SRC = random_gen utf8 checksum bytesrc s
- LIB = xutil
- PROJ_TAG = core
-
-+DLL_LIB = xncbi
- LIBS = $(ORIG_LIBS)
-
- WATCHERS = vakatov kornbluh
---- a/c++/src/util/xregexp/Makefile.xregexp.lib
-+++ b/c++/src/util/xregexp/Makefile.xregexp.lib
-@@ -6,7 +6,7 @@ LIB = xregexp
-
- CPPFLAGS = $(ORIG_CPPFLAGS) $(PCRE_INCLUDE)
-
--DLL_LIB = $(PCRE_LIB)
-+DLL_LIB = $(PCRE_LIB) xncbi
- LIBS = $(PCRE_LIBS)
-
- WATCHERS = ivanov
---- a/c++/src/algo/segmask/Makefile.xalgosegmask.lib
-+++ b/c++/src/algo/segmask/Makefile.xalgosegmask.lib
-@@ -8,6 +8,8 @@ LIB = xalgosegmask
-
- SRC = segmask
-
-+DLL_LIB = blast xobjmgr xncbi
-+
- CXXFLAGS = $(FAST_CXXFLAGS)
- LDFLAGS = $(FAST_LDFLAGS)
-
---- a/c++/src/objmgr/split/Makefile.id2_split.lib
-+++ b/c++/src/objmgr/split/Makefile.id2_split.lib
-@@ -17,7 +17,7 @@ LIB = id2_split
-
- CPPFLAGS = $(ORIG_CPPFLAGS) $(CMPRS_INCLUDE)
-
--DLL_LIB = $(SOBJMGR_LIBS)
-+DLL_LIB = xobjmgr seqsplit seqset seq general xser xcompress xncbi
-
- WATCHERS = vasilche
-
---- a/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib
-+++ b/c++/src/objtools/blast/seqdb_writer/Makefile.writedb.lib
-@@ -8,6 +8,9 @@ SRC = writedb writedb_impl writedb_volum
-
- LIB = writedb
-
-+DLL_LIB = seqdb xobjread xobjmgr blastdb seqset seq general \
-+ xser sequtil xutil xncbi
-+
- CFLAGS = $(FAST_CFLAGS)
- CPPFLAGS = -DNCBI_MODULE=BLASTDB $(ORIG_CPPFLAGS)
- CXXFLAGS = $(FAST_CXXFLAGS)
---- a/c++/src/algo/blast/Makefile.blast_macros.mk
-+++ b/c++/src/algo/blast/Makefile.blast_macros.mk
-@@ -18,7 +18,7 @@ BLAST_INPUT_LIBS = blastinput \
- BLAST_SRA_LIBS=blast_sra $(SRAXF_LIBS) vxf $(SRA_LIBS)
-
- # BLAST_FORMATTER_LIBS and BLAST_INPUT_LIBS need $BLAST_LIBS
--BLAST_LIBS = xblast xalgoblastdbindex composition_adjustment \
-+BLAST_LIBS = xblast xalgoblastdbindex blast composition_adjustment \
- xalgodustmask xalgowinmask seqmasks_io seqdb blast_services xobjutil \
- $(OBJREAD_LIBS) xnetblastcli xnetblast blastdb scoremat tables xalnmgr
- # BLAST additionally needs xconnect $(SOBJMGR_LIBS) or $(OBJMGR_LIBS)
---- a/c++/src/algo/blast/dbindex/makeindex/Makefile.makeindex.app
-+++ b/c++/src/algo/blast/dbindex/makeindex/Makefile.makeindex.app
-@@ -2,7 +2,7 @@ APP = makembindex
- SRC = main mkindex_app
-
- LIB_ = xalgoblastdbindex blast composition_adjustment seqdb blastdb \
-- $(OBJREAD_LIBS) xobjutil tables connect $(SOBJMGR_LIBS)
-+ $(OBJREAD_LIBS) xobjutil tables xconnect $(SOBJMGR_LIBS)
- LIB = $(LIB_:%=%$(STATIC))
-
- CXXFLAGS = $(FAST_CXXFLAGS)
---- a/c++/src/build-system/library_relations.txt
-+++ b/c++/src/build-system/library_relations.txt
-@@ -1189,7 +1189,7 @@ xasmcompare needs $(SEQ_LIBS)
- xasmcompare needs pub
- xasn needs xhtml
- xasn needs3party $(NCBI_C_ncbi)
--xblast includes blast
-+xblast needs blast
- xblast needs xalgoblastdbindex
- xblast needs xalgodustmask
- xblast needs xalgowinmask
diff --git a/sci-biology/ncbi-blast+/metadata.xml b/sci-biology/ncbi-blast+/metadata.xml deleted file mode 100644 index 93556eaa7..000000000 --- a/sci-biology/ncbi-blast+/metadata.xml +++ /dev/null @@ -1,23 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <use> - <flag name="boost">Undocumented USE</flag> - <flag name="cppunit">Undocumented USE</flag> - <flag name="freetype">Undocumented USE</flag> - <flag name="mesa">Undocumented USE</flag> - <flag name="muparser">Undocumented USE</flag> - <flag name="sablotron">Undocumented USE</flag> - <flag name="xerces">Undocumented USE</flag> - <flag name="xalan">Undocumented USE</flag> - <flag name="xslt">Undocumented USE</flag> - </use> -</pkgmetadata> diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild deleted file mode 100644 index 527acfadf..000000000 --- a/sci-biology/ncbi-blast+/ncbi-blast+-2.11.0.ebuild +++ /dev/null @@ -1,360 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7,8,9} ) - -inherit python-single-r1 toolchain-funcs - -MY_P="ncbi-blast-${PV}+-src" -# workdir/ncbi-blast-2.2.30+-src -# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-src.tar.gz -# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.3.0+-src.tar.gz - -DESCRIPTION="A subset of NCBI C++ Toolkit containing just the NCBI BLAST+" -HOMEPAGE="https://ncbi.github.io/cxx-toolkit/" -SRC_URI=" - ftp://ftp.ncbi.nih.gov/blast/executables/blast+/${PV}/${MY_P}.tar.gz" -# http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz" - -# should also install ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz -# see http://www.biostars.org/p/76551/ and http://blastedbio.blogspot.cz/2012/05/blast-tabular-missing-descriptions.html -LICENSE="public-domain" -SLOT="0" -IUSE=" - debug static-libs static threads pch - test wxwidgets odbc - berkdb boost bzip2 cppunit curl expat fltk freetype gif - glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python - sablotron sqlite tiff xerces xalan xml xpm xslt X" -KEYWORDS="~amd64 ~x86" -RESTRICT="!test? ( test )" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -# sys-libs/db should be compiled with USE=cxx -DEPEND=" - <sys-devel/gcc-10:= - !sci-biology/ncbi-tools++ - berkdb? ( sys-libs/db:=[cxx(-)] ) - boost? ( dev-libs/boost ) - curl? ( net-misc/curl ) - sqlite? ( dev-db/sqlite:3 ) - mysql? ( virtual/mysql ) - fltk? ( x11-libs/fltk ) - opengl? ( virtual/opengl media-libs/glew:0= ) - mesa? ( media-libs/mesa[osmesa] ) - glut? ( media-libs/freeglut ) - freetype? ( media-libs/freetype ) - gnutls? ( net-libs/gnutls ) - python? ( ${PYTHON_DEPS} ) - cppunit? ( dev-util/cppunit ) - icu? ( dev-libs/icu ) - expat? ( dev-libs/expat ) - sablotron? ( app-text/sablotron ) - xml? ( dev-libs/libxml2 ) - xslt? ( dev-libs/libxslt ) - xerces? ( dev-libs/xerces-c ) - xalan? ( dev-libs/xalan-c ) - muparser? ( dev-cpp/muParser ) - hdf5? ( sci-libs/hdf5[cxx] ) - gif? ( media-libs/giflib ) - jpeg? ( media-libs/libjpeg-turbo:0= ) - png? ( media-libs/libpng:0= ) - tiff? ( media-libs/tiff:0= ) - xpm? ( x11-libs/libXpm ) - dev-libs/lzo - app-arch/bzip2 - dev-libs/libpcre - dev-db/lmdb" -# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge -# Intentionally omitted USE flags: -# ftds? ( dev-db/freetds ) # support for outside FreeTDS installations is currently broken. -# The default (heavily patched) embedded copy should work, or you can -# leave it off altogether -- the only public apps that make use of it are -# samples and tests, since NCBI's database servers are of course firewalled. - -# seems muParser is required, also glew is required. configure exits otherwise if these are explicitly passed to it (due to USE flag enabled) - -RDEPEND="${DEPEND}" - -S="${WORKDIR}/${MY_P}/c++" -# ncbi-blast-2.2.30+-src/c++ - -src_prepare() { -# filter-ldflags -Wl,--as-needed -# append-ldflags -Wl,--no-undefined -# sed -i -e 's/-print-file-name=libstdc++.a//' \ -# -e '/sed/ s/\([gO]\[0-9\]\)\*/\1\\+/' \ -# src/build-system/configure || die -# epatch \ -# "${FILESDIR}"/${PN}-${PV#0.}-fix-order-of-libs.patch \ -# "${FILESDIR}"/curl-types.patch \ -# "${FILESDIR}"/malloc_initialize_upstream_fix.patch \ -# "${FILESDIR}"/respect_CXXFLAGS_configure.ac.patch \ -# "${FILESDIR}"/respect_CXXFLAGS_configure.patch \ -# "${FILESDIR}"/report_project_settings_configure.ac.patch \ -# "${FILESDIR}"/report_project_settings_configure.patch \ -# "${FILESDIR}"/make_install.patch - -# "${FILESDIR}"/${PN}-${PV#0.}-disable_test_compress.patch - -# "${FILESDIR}"/${PN}-${PV#0.}-gcc46.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-gcc47.patch \ -# "${WORKDIR}"/${PN}-${PV#0.}-asneeded.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-libpng15.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-glibc-214.patch - -# use prefix && append-ldflags -Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/${PN}" - -# The conf-opts.patch and as-needed.patch need to be adjusted for 12.0.0 line numbers -## local PATCHES=( -## "${FILESDIR}"/${P}-conf-opts.patch -## "${FILESDIR}"/${P}-fix-svn-URL-upstream.patch -## "${FILESDIR}"/${P}-linkage-tuneups.patch -## "${FILESDIR}"/${P}-more-patches.patch -## "${FILESDIR}"/${P}-linkage-tuneups-addons.patch -## "${FILESDIR}"/${P}-configure.patch -## "${FILESDIR}"/${P}-drop-STATIC-from-LIB.patch -## "${FILESDIR}"/${P}-fix-install.patch -## ) - # "${FILESDIR}"/${P}-support-autoconf-2.60.patch -## epatch ${PATCHES[@]} - - # use a Debian patch from http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ncbi-blast%2B/trunk/debian/patches/fix_lib_deps?revision=18535&view=markup - # the patches for 2.2.30+ do not apply to 2.2.31, mostly DLL_LIB is gone but somewhere - # it is still present, plus in a few places was something else patched - # staying without any patches for now and lets see is it works on Gentoo - # epatch "${FILESDIR}"/fix_lib_deps.patch - # make sure this one is the last one and contains the actual patches applied unless we can have autoconf-2.59 or 2.60 - # https://bugs.gentoo.org/show_bug.cgi?id=514706 - - tc-export CXX CC - -## cd src/build-system || die -# eautoreconf - - # Temporarily disabling eautoconf because we patch configure via ${P}-support-autoconf-2.60.patch - # eautoconf # keep it disabled until we can ensure 2.59 is installed - # beware 12.0.0. and previous required autoconf-2.59, a patch for 12.0.0 brings autoconf-2.60 support - default -} - -# possibly place modified contents of ${W}/src/build-system/config.site.ncbi and {W}/src/build-system/config.site.ex into ${W}/src/build-system/config.site -src_configure() { - local myconf=() - #--without-optimization turn off optimization flags in non-debug mode - #--with-profiling build profiled versions of libs and apps - #--with-tcheck(=DIR) build for Intel Thread Checker (in DIR) - #--with-plugin-auto-load always enable the plugin manager by default - #--with-bundles build bundles in addition to dylibs on Mac OS X - #--with-bin-release build executables suitable for public release - # no dll and such - #--with-64 compile to 64-bit code - #--with-universal build universal binaries on Mac OS X - #--with-universal=CPUs build universal binaries targeting the given CPUs - #--without-exe do not build executables - #--with-relative-runpath=P specify an executable-relative DLL search path - #--with-hard-runpath hard-code runtime path, ignoring LD_LIBRARY_PATH - #--with-limited-linker don't attempt to build especially large projects - #--with-extra-action= script to call after the configuration is complete - #--with-autodep automatic generation of dependencies (GNU make) - #--with-fake-root=DIR appear to have been built under DIR - #--with-build-root-sfx=X add a user-specified suffix to the build dir name - #--without-execopy do not copy built executables to the BIN area - #--with-lib-rebuilds ensure that apps use up-to-date libraries - #--with-lib-rebuilds=ask ask whether to update each app's libraries - #--without-deactivation keep old copies of libraries that no longer build - #--without-makefile-auto-update do not auto-update generated makefiles - #--with-projects=FILE build projects listed in FILE by default - #--without-flat-makefile do not generate an all-encompassing flat makefile - #--with-configure-dialog allow interactive flat makefile project selection - #--with-saved-settings=F load configuration settings from the file F - #--with-check-tools=... use the specified tools for testing - #--with-ncbi-public ensure compatibility for all in-house platforms - #--with-sybase-local=DIR use local SYBASE install (DIR is optional) - #--with-sybase-new use newer SYBASE install (12.5 rather than 12.0) - #--without-sp do not use SP libraries - #--without-orbacus do not use ORBacus CORBA libraries - #--with-orbacus=DIR use ORBacus installation in DIR - #--with-jni(=JDK-DIR) build Java bindings (against the JDK in JDK-DIR) - #--with-sablot=DIR use Sablotron installation in DIR - #--without-sablot, do not use Sablotron - #--with-oechem=DIR use OpenEye OEChem installation in DIR - #--without-oechem do not use OEChem - #--with-sge=DIR use Sun Grid Engine installation in DIR - #--without-sge do not use Sun Grid Engine - #--with-magic=DIR use libmagic installation in DIR - #--without-magic do not use libmagic - #--without-local-lbsm turn off support for IPC with locally running LBSMD - #--without-ncbi-crypt use a dummy stubbed-out version of ncbi_crypt - #--without-connext do not build non-public CONNECT library extensions - #--without-serial do not build the serialization library and tools - #--without-objects do not generate/build serializeable objects from ASNs - #--without-dbapi do not build database connectivity libraries - #--without-app do not build standalone applications like ID1_FETCH - #--without-gui do not build most graphical projects - #--without-algo do not build CPU-intensive algorithms - #--without-internal do not build internal projects - #--with-gbench ensure that Genome Workbench can be built - #--without-gbench do not build Genome Workbench - myconf+=( - --with-dll - --with-lfs - --with-build-root="${S}"_build - --without-suffix - --without-hostspec - --without-version - --with-bincopy - --without-strip - --without-ccache - --without-distcc -# --with-ncbi-c - --without-ctools -# --with-sss -# --with-sssutils -# --with-sssdb -# --with-included-sss - --with-z="${EPREFIX}/usr" - --with-bz2="${EPREFIX}/usr" - --without-sybase - --with-autodep -# --with-3psw=std:netopt favor standard (system) builds of the above pkgs - $(use_with debug) - $(use_with debug max-debug) - $(use_with debug symbols) - $(use_with static-libs static) - $(use_with static static-exe) - $(use_with threads mt) - $(use_with prefix runpath "${EPREFIX}/usr/$(get_libdir)/${PN}") - $(use_with test check) - $(use_with pch) - $(use_with lzo lzo "${EPREFIX}/usr") - $(use_with pcre pcre "${EPREFIX}/usr") - $(use_with gnutls gnutls "${EPREFIX}/usr") - $(use_with mysql mysql "${EPREFIX}/usr") - $(use_with muparser muparser "${EPREFIX}/usr") - $(usex fltk --with-fltk="${EPREFIX}/usr" "") - $(use_with opengl opengl "${EPREFIX}/usr") - $(use_with mesa mesa "${EPREFIX}/usr") - $(use_with opengl glut "${EPREFIX}/usr") - $(use_with opengl glew "${EPREFIX}/usr") - # - # GLEW 2.0 dropped support for this, see https://bugs.gentoo.org/show_bug.cgi?id=611302 - # $(use_with opengl glew-mx) - $(use_with wxwidgets wxwidgets "${EPREFIX}/usr") - $(use_with wxwidgets wxwidgets-ucs) - $(use_with freetype freetype "${EPREFIX}/usr") -# $(use_with berkdb bdb "${EPREFIX}/usr") # not in ncbi-blast+ - $(usex odbc --with-odbc="${EPREFIX}/usr" "") - $(use_with python python "${EPREFIX}/usr") - $(use_with boost boost "${EPREFIX}/usr") - $(use_with sqlite sqlite3 "${EPREFIX}/usr") - $(use_with icu icu "${EPREFIX}/usr") - $(use_with expat expat "${EPREFIX}/usr") - $(use_with xml libxml "${EPREFIX}/usr") - $(use_with xml libxslt "${EPREFIX}/usr") - $(use_with xerces xerces "${EPREFIX}/usr") - $(use_with hdf5 hdf5 "${EPREFIX}/usr") - $(use_with xalan xalan "${EPREFIX}/usr") -# $(use_with gif gif "${EPREFIX}/usr") # prevent compilation failure in "ncbi-tools++-12.0.0/src/util/image/image_io_gif.cpp:351: error: 'QuantizeBuffer' was not declared in this scope" - --without-gif - $(use_with jpeg jpeg "${EPREFIX}/usr") - $(use_with tiff tiff "${EPREFIX}/usr") - $(use_with png png "${EPREFIX}/usr") - $(use_with xpm xpm "${EPREFIX}/usr") - $(use_with curl curl "${EPREFIX}/usr") -# $(use_with X x "${EPREFIX}/usr") -# $(use_with X x) # there is no --with-x option - # prevent downloading VDB sources from https://github.com/ncbi/ncbi-vdb.git during configure execution - --without-vdb - ) - - # http://www.ncbi.nlm.nih.gov/books/NBK7167/ - use test || myconf+=( --with-projects="${FILESDIR}"/disable-testsuite-compilation.txt ) - - # TODO - # copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure - # otherwise your -O2 will be dropped in some subdirectories and replaced by e.g. -O9 - - einfo "bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}/usr" --libdir=/usr/lib64 ${myconf[@]}" - -# ECONF_SOURCE="src/build-system" \ -# econf \ - bash \ - ./src/build-system/configure \ - --srcdir="${S}" \ - --prefix="${EPREFIX}/usr" \ - --libdir=/usr/lib64 \ - --with-flat-makefile \ - ${myconf[@]} || die "Maybe try new src/build-system/cmake/cmake-configure instead?" -#--without-debug \ -# --with-bin-release \ -# --with-bincopy \ -# --without-static \ -# --with-dll \ -# --with-mt \ -# --with-openmp \ -# --with-lfs \ -# --prefix="${ED}"/usr \ -# --libdir="${ED}"/usr/$(get_libdir)/"${PN}" \ -# ${myconf} LDFLAGS="-Wl,--no-as-needed" \ -# || die -# econf ${myconf[@]} -} - -src_compile() { - ## all_r would ignore the --with-projects contents and build more - ## emake all_r -C GCC*-Release*/build || die - ## all_p with compile only selected/required components - ##cd "${S}"_build &&\ - ##emake all_p -C GCC*-Release*/build || die "gcc-4.5.3 crashes at src/objects/valerr/ValidError.cpp:226:1: internal compiler error: Segmentation fault, right?" - #emake all_p -C "${S}"_build/build - - # - # Re: /usr/lib64/ncbi-tools++/libdbapi_driver.so: undefined reference to `ncbi::NcbiGetlineEOL(std::istream&, std::string&)' - # - # The next release should automatically address such underlinking, albeit - # only in --with-flat-makefile configurations. For now (12.0.0), you'll need to - # add or extend more DLL_LIB settings, to which end you may find the - # resources at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/ - # helpful. For instance, - # - # http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/dbapi_driver.html - # - # indicates that src/dbapi/driver/Makefile.dbapi_driver.lib should set - # - # DLL_LIB = xncbi - # - # (You can find the path to that makefile by examining - # .../status/.dbapi_driver.dep or .../build/Makefile.flat.) - # - # To take full advantage of --with-flat-makefile, you'll need the following (instead of 'emake all_p -C "${S}"_build/build') and call configure --with-flat-makefile: - emake -C "${S}"_build/build -f Makefile.flat -} - -src_install() { - rm -rvf "${S}"_build/lib/ncbi || die - emake install prefix="${ED}/usr" libdir="${ED}/usr/$(get_libdir)/${PN}" - -# dobin "${S}"_build/bin/* -# dolib.so "${S}"_build/lib/*so* -# dolib.a "${S}"_build/lib/*.a -# doheader "${S}"_build/inc/* - - # File collisions with sci-biology/ncbi-tools - mv "${ED}"/usr/bin/asn2asn "${ED}"/usr/bin/asn2asn+ - mv "${ED}"/usr/bin/rpsblast "${ED}"/usr/bin/rpsblast+ - mv -f "${ED}"/usr/bin/test_regexp "${ED}"/usr/bin/test_regexp+ # drop the eventually mistakenly compiled binaries - mv "${ED}"/usr/bin/vecscreen "${ED}"/usr/bin/vecscreen+ - mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop+ - - echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}" > ${S}/99${PN} - doenvd "${S}/99${PN}" -} - -pkg_postinst() { - einfo 'Please run "source /etc/profile" before using this package in the current shell.' - einfo 'Documentation is at http://www.ncbi.nlm.nih.gov/books/NBK7167/' -} diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild deleted file mode 100644 index e90652f38..000000000 --- a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.30.ebuild +++ /dev/null @@ -1,350 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit toolchain-funcs - -MY_P="ncbi-blast-${PV}+-src" -# workdir/ncbi-blast-2.2.30+-src -# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-src.tar.gz - -DESCRIPTION="A subset of NCBI C++ Toolkit containing just the NCBI BLAST+" -HOMEPAGE="https://ncbi.github.io/cxx-toolkit/" -SRC_URI=" - ftp://ftp.ncbi.nih.gov/blast/executables/blast+/${PV}/${MY_P}.tar.gz" -# http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz" - -# should also install ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz -# see http://www.biostars.org/p/76551/ and http://blastedbio.blogspot.cz/2012/05/blast-tabular-missing-descriptions.html -LICENSE="public-domain" -SLOT="0" -IUSE=" - debug static-libs static threads pch - test wxwidgets odbc - berkdb boost bzip2 cppunit curl expat fltk freetype gif - glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png - sablotron sqlite tiff xerces xalan xml xpm xslt X" -KEYWORDS="~amd64 ~x86" -RESTRICT="!test? ( test )" - -# sys-libs/db should be compiled with USE=cxx -DEPEND=" - <sys-devel/gcc-10:= - !sci-biology/ncbi-tools++ - berkdb? ( sys-libs/db:=[cxx(-)] ) - boost? ( dev-libs/boost ) - curl? ( net-misc/curl ) - sqlite? ( dev-db/sqlite:3 ) - mysql? ( virtual/mysql ) - fltk? ( x11-libs/fltk ) - opengl? ( virtual/opengl media-libs/glew:0= ) - mesa? ( media-libs/mesa[osmesa] ) - glut? ( media-libs/freeglut ) - freetype? ( media-libs/freetype ) - gnutls? ( net-libs/gnutls ) - cppunit? ( dev-util/cppunit ) - icu? ( dev-libs/icu ) - expat? ( dev-libs/expat ) - sablotron? ( app-text/sablotron ) - xml? ( dev-libs/libxml2 ) - xslt? ( dev-libs/libxslt ) - xerces? ( dev-libs/xerces-c ) - xalan? ( dev-libs/xalan-c ) - muparser? ( dev-cpp/muParser ) - hdf5? ( sci-libs/hdf5[cxx] ) - gif? ( media-libs/giflib ) - jpeg? ( media-libs/libjpeg-turbo:0= ) - png? ( media-libs/libpng:0= ) - tiff? ( media-libs/tiff:0= ) - xpm? ( x11-libs/libXpm ) - dev-libs/lzo - app-arch/bzip2 - dev-libs/libpcre" -# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge -# Intentionally omitted USE flags: -# ftds? ( dev-db/freetds ) # support for outside FreeTDS installations is currently broken. -# The default (heavily patched) embedded copy should work, or you can -# leave it off altogether -- the only public apps that make use of it are -# samples and tests, since NCBI's database servers are of course firewalled. - -# seems muParser is required, also glew is required. configure exits otherwise if these are explicitly passed to it (due to USE flag enabled) - -RDEPEND="${DEPEND}" - -S="${WORKDIR}/${MY_P}/c++" -# ncbi-blast-2.2.30+-src/c++ - -PATCHES=( - "${FILESDIR}"/"${P}"__fix_lib_deps.patch -) - -src_prepare() { -# filter-ldflags -Wl,--as-needed -# append-ldflags -Wl,--no-undefined -# sed -i -e 's/-print-file-name=libstdc++.a//' \ -# -e '/sed/ s/\([gO]\[0-9\]\)\*/\1\\+/' \ -# src/build-system/configure || die -# epatch \ -# "${FILESDIR}"/${PN}-${PV#0.}-fix-order-of-libs.patch \ -# "${FILESDIR}"/curl-types.patch \ -# "${FILESDIR}"/malloc_initialize_upstream_fix.patch \ -# "${FILESDIR}"/respect_CXXFLAGS_configure.ac.patch \ -# "${FILESDIR}"/respect_CXXFLAGS_configure.patch \ -# "${FILESDIR}"/report_project_settings_configure.ac.patch \ -# "${FILESDIR}"/report_project_settings_configure.patch \ -# "${FILESDIR}"/make_install.patch - -# "${FILESDIR}"/${PN}-${PV#0.}-disable_test_compress.patch - -# "${FILESDIR}"/${PN}-${PV#0.}-gcc46.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-gcc47.patch \ -# "${WORKDIR}"/${PN}-${PV#0.}-asneeded.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-libpng15.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-glibc-214.patch - -# use prefix && append-ldflags -Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/${PN}" - -# The conf-opts.patch and as-needed.patch need to be adjusted for 12.0.0 line numbers -## local PATCHES=( -## "${FILESDIR}"/${P}-conf-opts.patch -## "${FILESDIR}"/${P}-fix-svn-URL-upstream.patch -## "${FILESDIR}"/${P}-linkage-tuneups.patch -## "${FILESDIR}"/${P}-more-patches.patch -## "${FILESDIR}"/${P}-linkage-tuneups-addons.patch -## "${FILESDIR}"/${P}-configure.patch -## "${FILESDIR}"/${P}-drop-STATIC-from-LIB.patch -## "${FILESDIR}"/${P}-fix-install.patch -## ) - # "${FILESDIR}"/${P}-support-autoconf-2.60.patch -## epatch ${PATCHES[@]} - - # use a Debian patch from http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ncbi-blast%2B/trunk/debian/patches/fix_lib_deps?revision=18535&view=markup - # make sure this one is the last one and contains the actual patches applied unless we can have autoconf-2.59 or 2.60 - # https://bugs.gentoo.org/show_bug.cgi?id=514706 - - tc-export CXX CC - -## cd src/build-system || die -# eautoreconf - - # Temporarily disabling eautoconf because we patch configure via ${P}-support-autoconf-2.60.patch - # eautoconf # keep it disabled until we can ensure 2.59 is installed - # beware 12.0.0. and previous required autoconf-2.59, a patch for 12.0.0 brings autoconf-2.60 support - default -} - -# possibly place modified contents of ${W}/src/build-system/config.site.ncbi and {W}/src/build-system/config.site.ex into ${W}/src/build-system/config.site -src_configure() { - local myconf=() - #--without-optimization turn off optimization flags in non-debug mode - #--with-profiling build profiled versions of libs and apps - #--with-tcheck(=DIR) build for Intel Thread Checker (in DIR) - #--with-plugin-auto-load always enable the plugin manager by default - #--with-bundles build bundles in addition to dylibs on Mac OS X - #--with-bin-release build executables suitable for public release - # no dll and such - #--with-64 compile to 64-bit code - #--with-universal build universal binaries on Mac OS X - #--with-universal=CPUs build universal binaries targeting the given CPUs - #--without-exe do not build executables - #--with-relative-runpath=P specify an executable-relative DLL search path - #--with-hard-runpath hard-code runtime path, ignoring LD_LIBRARY_PATH - #--with-limited-linker don't attempt to build especially large projects - #--with-extra-action= script to call after the configuration is complete - #--with-autodep automatic generation of dependencies (GNU make) - #--with-fake-root=DIR appear to have been built under DIR - #--with-build-root-sfx=X add a user-specified suffix to the build dir name - #--without-execopy do not copy built executables to the BIN area - #--with-lib-rebuilds ensure that apps use up-to-date libraries - #--with-lib-rebuilds=ask ask whether to update each app's libraries - #--without-deactivation keep old copies of libraries that no longer build - #--without-makefile-auto-update do not auto-update generated makefiles - #--with-projects=FILE build projects listed in FILE by default - #--without-flat-makefile do not generate an all-encompassing flat makefile - #--with-configure-dialog allow interactive flat makefile project selection - #--with-saved-settings=F load configuration settings from the file F - #--with-check-tools=... use the specified tools for testing - #--with-ncbi-public ensure compatibility for all in-house platforms - #--with-sybase-local=DIR use local SYBASE install (DIR is optional) - #--with-sybase-new use newer SYBASE install (12.5 rather than 12.0) - #--without-sp do not use SP libraries - #--without-orbacus do not use ORBacus CORBA libraries - #--with-orbacus=DIR use ORBacus installation in DIR - #--with-jni(=JDK-DIR) build Java bindings (against the JDK in JDK-DIR) - #--with-sablot=DIR use Sablotron installation in DIR - #--without-sablot, do not use Sablotron - #--with-oechem=DIR use OpenEye OEChem installation in DIR - #--without-oechem do not use OEChem - #--with-sge=DIR use Sun Grid Engine installation in DIR - #--without-sge do not use Sun Grid Engine - #--with-magic=DIR use libmagic installation in DIR - #--without-magic do not use libmagic - #--without-local-lbsm turn off support for IPC with locally running LBSMD - #--without-ncbi-crypt use a dummy stubbed-out version of ncbi_crypt - #--without-connext do not build non-public CONNECT library extensions - #--without-serial do not build the serialization library and tools - #--without-objects do not generate/build serializeable objects from ASNs - #--without-dbapi do not build database connectivity libraries - #--without-app do not build standalone applications like ID1_FETCH - #--without-gui do not build most graphical projects - #--without-algo do not build CPU-intensive algorithms - #--without-internal do not build internal projects - #--with-gbench ensure that Genome Workbench can be built - #--without-gbench do not build Genome Workbench - myconf+=( - --with-dll - --with-lfs - --with-build-root="${S}"_build - --without-suffix - --without-hostspec - --without-version - --with-bincopy - --without-strip - --without-ccache - --without-distcc -# --with-ncbi-c - --without-ctools -# --with-sss -# --with-sssutils -# --with-sssdb -# --with-included-sss - --with-z="${EPREFIX}/usr" - --with-bz2="${EPREFIX}/usr" - --without-sybase - --with-autodep -# --with-3psw=std:netopt favor standard (system) builds of the above pkgs - $(use_with debug) - $(use_with debug max-debug) - $(use_with debug symbols) - $(use_with static-libs static) - $(use_with static static-exe) - $(use_with threads mt) - $(use_with prefix runpath "${EPREFIX}/usr/$(get_libdir)/${PN}") - $(use_with test check) - $(use_with pch) - $(use_with lzo lzo "${EPREFIX}/usr") - $(use_with pcre pcre "${EPREFIX}/usr") - $(use_with gnutls gnutls "${EPREFIX}/usr") - $(use_with mysql mysql "${EPREFIX}/usr") - $(use_with muparser muparser "${EPREFIX}/usr") - $(usex fltk --with-fltk="${EPREFIX}/usr" "") - $(use_with opengl opengl "${EPREFIX}/usr") - $(use_with mesa mesa "${EPREFIX}/usr") - $(use_with opengl glut "${EPREFIX}/usr") - $(use_with opengl glew "${EPREFIX}/usr") - $(use_with opengl glew-mx) - $(use_with wxwidgets wxwidgets "${EPREFIX}/usr") - $(use_with wxwidgets wxwidgets-ucs) - $(use_with freetype freetype "${EPREFIX}/usr") -# $(use_with berkdb bdb "${EPREFIX}/usr") # not in ncbi-blast+ - $(usex odbc --with-odbc="${EPREFIX}/usr" "") - # is python2 - --without-python - $(use_with boost boost "${EPREFIX}/usr") - $(use_with sqlite sqlite3 "${EPREFIX}/usr") - $(use_with icu icu "${EPREFIX}/usr") - $(use_with expat expat "${EPREFIX}/usr") - $(use_with xml libxml "${EPREFIX}/usr") - $(use_with xml libxslt "${EPREFIX}/usr") - $(use_with xerces xerces "${EPREFIX}/usr") - $(use_with hdf5 hdf5 "${EPREFIX}/usr") - $(use_with xalan xalan "${EPREFIX}/usr") -# $(use_with gif gif "${EPREFIX}/usr") # prevent compilation failure in "ncbi-tools++-12.0.0/src/util/image/image_io_gif.cpp:351: error: 'QuantizeBuffer' was not declared in this scope" - --without-gif - $(use_with jpeg jpeg "${EPREFIX}/usr") - $(use_with tiff tiff "${EPREFIX}/usr") - $(use_with png png "${EPREFIX}/usr") - $(use_with xpm xpm "${EPREFIX}/usr") - $(use_with curl curl "${EPREFIX}/usr") -# $(use_with X x "${EPREFIX}/usr") -# $(use_with X x) # there is no --with-x option - ) - - # http://www.ncbi.nlm.nih.gov/books/NBK7167/ - use test || myconf+=( --with-projects="${FILESDIR}"/disable-testsuite-compilation.txt ) - - # TODO - # copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure - # otherwise your -O2 will be dropped in some subdirectories and replaced by e.g. -O9 - - einfo "bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}/usr" --libdir=/usr/lib64 ${myconf[@]}" - -# ECONF_SOURCE="src/build-system" \ -# econf \ - bash \ - ./src/build-system/configure \ - --srcdir="${S}" \ - --prefix="${EPREFIX}/usr" \ - --libdir=/usr/lib64 \ - --with-flat-makefile \ - ${myconf[@]} || die "gcc 7 or newer were not used by upstream hence unsupported" -#--without-debug \ -# --with-bin-release \ -# --with-bincopy \ -# --without-static \ -# --with-dll \ -# --with-mt \ -# --with-openmp \ -# --with-lfs \ -# --prefix="${ED}"/usr \ -# --libdir="${ED}"/usr/$(get_libdir)/"${PN}" \ -# ${myconf} LDFLAGS="-Wl,--no-as-needed" \ -# || die -# econf ${myconf[@]} -} - -src_compile() { - ## all_r would ignore the --with-projects contents and build more - ## emake all_r -C GCC*-Release*/build || die - ## all_p with compile only selected/required components - ##cd "${S}"_build &&\ - ##emake all_p -C GCC*-Release*/build || die "gcc-4.5.3 crashes at src/objects/valerr/ValidError.cpp:226:1: internal compiler error: Segmentation fault, right?" - #emake all_p -C "${S}"_build/build - - # - # Re: /usr/lib64/ncbi-tools++/libdbapi_driver.so: undefined reference to `ncbi::NcbiGetlineEOL(std::istream&, std::string&)' - # - # The next release should automatically address such underlinking, albeit - # only in --with-flat-makefile configurations. For now (12.0.0), you'll need to - # add or extend more DLL_LIB settings, to which end you may find the - # resources at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/ - # helpful. For instance, - # - # http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/dbapi_driver.html - # - # indicates that src/dbapi/driver/Makefile.dbapi_driver.lib should set - # - # DLL_LIB = xncbi - # - # (You can find the path to that makefile by examining - # .../status/.dbapi_driver.dep or .../build/Makefile.flat.) - # - # To take full advantage of --with-flat-makefile, you'll need the following (instead of 'emake all_p -C "${S}"_build/build') and call configure --with-flat-makefile: - emake -C "${S}"_build/build -f Makefile.flat -} - -src_install() { - rm -rvf "${S}"_build/lib/ncbi || die - emake install prefix="${ED}/usr" libdir="${ED}/usr/$(get_libdir)/${PN}" - -# dobin "${S}"_build/bin/* -# dolib.so "${S}"_build/lib/*so* -# dolib.a "${S}"_build/lib/*.a -# doheader "${S}"_build/inc/* - - # File collisions with sci-biology/ncbi-tools - mv "${ED}"/usr/bin/asn2asn "${ED}"/usr/bin/asn2asn+ - mv "${ED}"/usr/bin/rpsblast "${ED}"/usr/bin/rpsblast+ - mv -f "${ED}"/usr/bin/test_regexp "${ED}"/usr/bin/test_regexp+ # drop the eventually mistakenly compiled binaries - mv "${ED}"/usr/bin/vecscreen "${ED}"/usr/bin/vecscreen+ - mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop+ - - echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}" > ${S}/99${PN} - doenvd "${S}/99${PN}" -} - -pkg_postinst() { - einfo 'Please run "source /etc/profile" before using this package in the current shell.' - einfo 'Documentation is at http://www.ncbi.nlm.nih.gov/books/NBK7167/' -} diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild deleted file mode 100644 index ddeeac07d..000000000 --- a/sci-biology/ncbi-blast+/ncbi-blast+-2.2.31.ebuild +++ /dev/null @@ -1,350 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit toolchain-funcs - -MY_P="ncbi-blast-${PV}+-src" -# workdir/ncbi-blast-2.2.30+-src -# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-src.tar.gz - -DESCRIPTION="A subset of NCBI C++ Toolkit containing just the NCBI BLAST+" -HOMEPAGE="https://ncbi.github.io/cxx-toolkit/t" -SRC_URI=" - ftp://ftp.ncbi.nih.gov/blast/executables/blast+/${PV}/${MY_P}.tar.gz" -# http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz" - -# should also install ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz -# see http://www.biostars.org/p/76551/ and http://blastedbio.blogspot.cz/2012/05/blast-tabular-missing-descriptions.html -LICENSE="public-domain" -SLOT="0" -IUSE=" - debug static-libs static threads pch - test wxwidgets odbc - berkdb boost bzip2 cppunit curl expat fltk freetype gif - glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png - sablotron sqlite tiff xerces xalan xml xpm xslt X" -KEYWORDS="~amd64 ~x86" -RESTRICT="!test? ( test )" - -# sys-libs/db should be compiled with USE=cxx -DEPEND=" - <sys-devel/gcc-10:= - !sci-biology/ncbi-tools++ - berkdb? ( sys-libs/db:=[cxx(-)] ) - boost? ( dev-libs/boost ) - curl? ( net-misc/curl ) - sqlite? ( dev-db/sqlite:3 ) - mysql? ( virtual/mysql ) - fltk? ( x11-libs/fltk ) - opengl? ( virtual/opengl media-libs/glew:0= ) - mesa? ( media-libs/mesa[osmesa] ) - glut? ( media-libs/freeglut ) - freetype? ( media-libs/freetype ) - gnutls? ( net-libs/gnutls ) - cppunit? ( dev-util/cppunit ) - icu? ( dev-libs/icu ) - expat? ( dev-libs/expat ) - sablotron? ( app-text/sablotron ) - xml? ( dev-libs/libxml2 ) - xslt? ( dev-libs/libxslt ) - xerces? ( dev-libs/xerces-c ) - xalan? ( dev-libs/xalan-c ) - muparser? ( dev-cpp/muParser ) - hdf5? ( sci-libs/hdf5[cxx] ) - gif? ( media-libs/giflib ) - jpeg? ( media-libs/libjpeg-turbo:0= ) - png? ( media-libs/libpng:0= ) - tiff? ( media-libs/tiff:0= ) - xpm? ( x11-libs/libXpm ) - dev-libs/lzo - app-arch/bzip2 - dev-libs/libpcre" -# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge -# Intentionally omitted USE flags: -# ftds? ( dev-db/freetds ) # support for outside FreeTDS installations is currently broken. -# The default (heavily patched) embedded copy should work, or you can -# leave it off altogether -- the only public apps that make use of it are -# samples and tests, since NCBI's database servers are of course firewalled. - -# seems muParser is required, also glew is required. configure exits otherwise if these are explicitly passed to it (due to USE flag enabled) - -RDEPEND="${DEPEND}" - -S="${WORKDIR}/${MY_P}/c++" -# ncbi-blast-2.2.30+-src/c++ - -src_prepare() { -# filter-ldflags -Wl,--as-needed -# append-ldflags -Wl,--no-undefined -# sed -i -e 's/-print-file-name=libstdc++.a//' \ -# -e '/sed/ s/\([gO]\[0-9\]\)\*/\1\\+/' \ -# src/build-system/configure || die -# epatch \ -# "${FILESDIR}"/${PN}-${PV#0.}-fix-order-of-libs.patch \ -# "${FILESDIR}"/curl-types.patch \ -# "${FILESDIR}"/malloc_initialize_upstream_fix.patch \ -# "${FILESDIR}"/respect_CXXFLAGS_configure.ac.patch \ -# "${FILESDIR}"/respect_CXXFLAGS_configure.patch \ -# "${FILESDIR}"/report_project_settings_configure.ac.patch \ -# "${FILESDIR}"/report_project_settings_configure.patch \ -# "${FILESDIR}"/make_install.patch - -# "${FILESDIR}"/${PN}-${PV#0.}-disable_test_compress.patch - -# "${FILESDIR}"/${PN}-${PV#0.}-gcc46.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-gcc47.patch \ -# "${WORKDIR}"/${PN}-${PV#0.}-asneeded.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-libpng15.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-glibc-214.patch - -# use prefix && append-ldflags -Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/${PN}" - -# The conf-opts.patch and as-needed.patch need to be adjusted for 12.0.0 line numbers -## local PATCHES=( -## "${FILESDIR}"/${P}-conf-opts.patch -## "${FILESDIR}"/${P}-fix-svn-URL-upstream.patch -## "${FILESDIR}"/${P}-linkage-tuneups.patch -## "${FILESDIR}"/${P}-more-patches.patch -## "${FILESDIR}"/${P}-linkage-tuneups-addons.patch -## "${FILESDIR}"/${P}-configure.patch -## "${FILESDIR}"/${P}-drop-STATIC-from-LIB.patch -## "${FILESDIR}"/${P}-fix-install.patch -## ) - # "${FILESDIR}"/${P}-support-autoconf-2.60.patch -## epatch ${PATCHES[@]} - - # use a Debian patch from http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ncbi-blast%2B/trunk/debian/patches/fix_lib_deps?revision=18535&view=markup - # the patches for 2.2.30+ do not apply to 2.2.31, mostly DLL_LIB is gone but somewhere - # it is still present, plus in a few places was something else patched - # staying without any patches for now and lets see is it works on Gentoo - # epatch "${FILESDIR}"/fix_lib_deps.patch - # make sure this one is the last one and contains the actual patches applied unless we can have autoconf-2.59 or 2.60 - # https://bugs.gentoo.org/show_bug.cgi?id=514706 - - tc-export CXX CC - -## cd src/build-system || die -# eautoreconf - - # Temporarily disabling eautoconf because we patch configure via ${P}-support-autoconf-2.60.patch - # eautoconf # keep it disabled until we can ensure 2.59 is installed - # beware 12.0.0. and previous required autoconf-2.59, a patch for 12.0.0 brings autoconf-2.60 support - default -} - -# possibly place modified contents of ${W}/src/build-system/config.site.ncbi and {W}/src/build-system/config.site.ex into ${W}/src/build-system/config.site -src_configure() { - local myconf=() - #--without-optimization turn off optimization flags in non-debug mode - #--with-profiling build profiled versions of libs and apps - #--with-tcheck(=DIR) build for Intel Thread Checker (in DIR) - #--with-plugin-auto-load always enable the plugin manager by default - #--with-bundles build bundles in addition to dylibs on Mac OS X - #--with-bin-release build executables suitable for public release - # no dll and such - #--with-64 compile to 64-bit code - #--with-universal build universal binaries on Mac OS X - #--with-universal=CPUs build universal binaries targeting the given CPUs - #--without-exe do not build executables - #--with-relative-runpath=P specify an executable-relative DLL search path - #--with-hard-runpath hard-code runtime path, ignoring LD_LIBRARY_PATH - #--with-limited-linker don't attempt to build especially large projects - #--with-extra-action= script to call after the configuration is complete - #--with-autodep automatic generation of dependencies (GNU make) - #--with-fake-root=DIR appear to have been built under DIR - #--with-build-root-sfx=X add a user-specified suffix to the build dir name - #--without-execopy do not copy built executables to the BIN area - #--with-lib-rebuilds ensure that apps use up-to-date libraries - #--with-lib-rebuilds=ask ask whether to update each app's libraries - #--without-deactivation keep old copies of libraries that no longer build - #--without-makefile-auto-update do not auto-update generated makefiles - #--with-projects=FILE build projects listed in FILE by default - #--without-flat-makefile do not generate an all-encompassing flat makefile - #--with-configure-dialog allow interactive flat makefile project selection - #--with-saved-settings=F load configuration settings from the file F - #--with-check-tools=... use the specified tools for testing - #--with-ncbi-public ensure compatibility for all in-house platforms - #--with-sybase-local=DIR use local SYBASE install (DIR is optional) - #--with-sybase-new use newer SYBASE install (12.5 rather than 12.0) - #--without-sp do not use SP libraries - #--without-orbacus do not use ORBacus CORBA libraries - #--with-orbacus=DIR use ORBacus installation in DIR - #--with-jni(=JDK-DIR) build Java bindings (against the JDK in JDK-DIR) - #--with-sablot=DIR use Sablotron installation in DIR - #--without-sablot, do not use Sablotron - #--with-oechem=DIR use OpenEye OEChem installation in DIR - #--without-oechem do not use OEChem - #--with-sge=DIR use Sun Grid Engine installation in DIR - #--without-sge do not use Sun Grid Engine - #--with-magic=DIR use libmagic installation in DIR - #--without-magic do not use libmagic - #--without-local-lbsm turn off support for IPC with locally running LBSMD - #--without-ncbi-crypt use a dummy stubbed-out version of ncbi_crypt - #--without-connext do not build non-public CONNECT library extensions - #--without-serial do not build the serialization library and tools - #--without-objects do not generate/build serializeable objects from ASNs - #--without-dbapi do not build database connectivity libraries - #--without-app do not build standalone applications like ID1_FETCH - #--without-gui do not build most graphical projects - #--without-algo do not build CPU-intensive algorithms - #--without-internal do not build internal projects - #--with-gbench ensure that Genome Workbench can be built - #--without-gbench do not build Genome Workbench - myconf+=( - --with-dll - --with-lfs - --with-build-root="${S}"_build - --without-suffix - --without-hostspec - --without-version - --with-bincopy - --without-strip - --without-ccache - --without-distcc -# --with-ncbi-c - --without-ctools -# --with-sss -# --with-sssutils -# --with-sssdb -# --with-included-sss - --with-z="${EPREFIX}/usr" - --with-bz2="${EPREFIX}/usr" - --without-sybase - --with-autodep -# --with-3psw=std:netopt favor standard (system) builds of the above pkgs - $(use_with debug) - $(use_with debug max-debug) - $(use_with debug symbols) - $(use_with static-libs static) - $(use_with static static-exe) - $(use_with threads mt) - $(use_with prefix runpath "${EPREFIX}/usr/$(get_libdir)/${PN}") - $(use_with test check) - $(use_with pch) - $(use_with lzo lzo "${EPREFIX}/usr") - $(use_with pcre pcre "${EPREFIX}/usr") - $(use_with gnutls gnutls "${EPREFIX}/usr") - $(use_with mysql mysql "${EPREFIX}/usr") - $(use_with muparser muparser "${EPREFIX}/usr") - $(usex fltk --with-fltk="${EPREFIX}/usr" "") - $(use_with opengl opengl "${EPREFIX}/usr") - $(use_with mesa mesa "${EPREFIX}/usr") - $(use_with opengl glut "${EPREFIX}/usr") - $(use_with opengl glew "${EPREFIX}/usr") - $(use_with opengl glew-mx) - $(use_with wxwidgets wxwidgets "${EPREFIX}/usr") - $(use_with wxwidgets wxwidgets-ucs) - $(use_with freetype freetype "${EPREFIX}/usr") -# $(use_with berkdb bdb "${EPREFIX}/usr") # not in ncbi-blast+ - $(usex odbc --with-odbc="${EPREFIX}/usr" "") - # is python2 - --without-python - $(use_with boost boost "${EPREFIX}/usr") - $(use_with sqlite sqlite3 "${EPREFIX}/usr") - $(use_with icu icu "${EPREFIX}/usr") - $(use_with expat expat "${EPREFIX}/usr") - $(use_with xml libxml "${EPREFIX}/usr") - $(use_with xml libxslt "${EPREFIX}/usr") - $(use_with xerces xerces "${EPREFIX}/usr") - $(use_with hdf5 hdf5 "${EPREFIX}/usr") - $(use_with xalan xalan "${EPREFIX}/usr") -# $(use_with gif gif "${EPREFIX}/usr") # prevent compilation failure in "ncbi-tools++-12.0.0/src/util/image/image_io_gif.cpp:351: error: 'QuantizeBuffer' was not declared in this scope" - --without-gif - $(use_with jpeg jpeg "${EPREFIX}/usr") - $(use_with tiff tiff "${EPREFIX}/usr") - $(use_with png png "${EPREFIX}/usr") - $(use_with xpm xpm "${EPREFIX}/usr") - $(use_with curl curl "${EPREFIX}/usr") -# $(use_with X x "${EPREFIX}/usr") -# $(use_with X x) # there is no --with-x option - ) - - # http://www.ncbi.nlm.nih.gov/books/NBK7167/ - use test || myconf+=( --with-projects="${FILESDIR}"/disable-testsuite-compilation.txt ) - - # TODO - # copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure - # otherwise your -O2 will be dropped in some subdirectories and replaced by e.g. -O9 - - einfo "bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}/usr" --libdir=/usr/lib64 ${myconf[@]}" - -# ECONF_SOURCE="src/build-system" \ -# econf \ - bash \ - ./src/build-system/configure \ - --srcdir="${S}" \ - --prefix="${EPREFIX}/usr" \ - --libdir=/usr/lib64 \ - --with-flat-makefile \ - ${myconf[@]} || die "gcc 7 or newer were not used by upstream hence unsupported" -#--without-debug \ -# --with-bin-release \ -# --with-bincopy \ -# --without-static \ -# --with-dll \ -# --with-mt \ -# --with-openmp \ -# --with-lfs \ -# --prefix="${ED}"/usr \ -# --libdir="${ED}"/usr/$(get_libdir)/"${PN}" \ -# ${myconf} LDFLAGS="-Wl,--no-as-needed" \ -# || die -# econf ${myconf[@]} -} - -src_compile() { - ## all_r would ignore the --with-projects contents and build more - ## emake all_r -C GCC*-Release*/build || die - ## all_p with compile only selected/required components - ##cd "${S}"_build &&\ - ##emake all_p -C GCC*-Release*/build || die "gcc-4.5.3 crashes at src/objects/valerr/ValidError.cpp:226:1: internal compiler error: Segmentation fault, right?" - #emake all_p -C "${S}"_build/build - - # - # Re: /usr/lib64/ncbi-tools++/libdbapi_driver.so: undefined reference to `ncbi::NcbiGetlineEOL(std::istream&, std::string&)' - # - # The next release should automatically address such underlinking, albeit - # only in --with-flat-makefile configurations. For now (12.0.0), you'll need to - # add or extend more DLL_LIB settings, to which end you may find the - # resources at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/ - # helpful. For instance, - # - # http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/dbapi_driver.html - # - # indicates that src/dbapi/driver/Makefile.dbapi_driver.lib should set - # - # DLL_LIB = xncbi - # - # (You can find the path to that makefile by examining - # .../status/.dbapi_driver.dep or .../build/Makefile.flat.) - # - # To take full advantage of --with-flat-makefile, you'll need the following (instead of 'emake all_p -C "${S}"_build/build') and call configure --with-flat-makefile: - emake -C "${S}"_build/build -f Makefile.flat -} - -src_install() { - rm -rvf "${S}"_build/lib/ncbi || die - emake install prefix="${ED}/usr" libdir="${ED}/usr/$(get_libdir)/${PN}" - -# dobin "${S}"_build/bin/* -# dolib.so "${S}"_build/lib/*so* -# dolib.a "${S}"_build/lib/*.a -# doheader "${S}"_build/inc/* - - # File collisions with sci-biology/ncbi-tools - mv "${ED}"/usr/bin/asn2asn "${ED}"/usr/bin/asn2asn+ - mv "${ED}"/usr/bin/rpsblast "${ED}"/usr/bin/rpsblast+ - mv -f "${ED}"/usr/bin/test_regexp "${ED}"/usr/bin/test_regexp+ # drop the eventually mistakenly compiled binaries - mv "${ED}"/usr/bin/vecscreen "${ED}"/usr/bin/vecscreen+ - mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop+ - - echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}" > ${S}/99${PN} - doenvd "${S}/99${PN}" -} - -pkg_postinst() { - einfo 'Please run "source /etc/profile" before using this package in the current shell.' - einfo 'Documentation is at http://www.ncbi.nlm.nih.gov/books/NBK7167/' -} diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild deleted file mode 100644 index 976ea3804..000000000 --- a/sci-biology/ncbi-blast+/ncbi-blast+-2.6.0.ebuild +++ /dev/null @@ -1,355 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit toolchain-funcs - -MY_P="ncbi-blast-${PV}+-src" -# workdir/ncbi-blast-2.2.30+-src -# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-src.tar.gz -# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.3.0+-src.tar.gz - -DESCRIPTION="A subset of NCBI C++ Toolkit containing just the NCBI BLAST+" -HOMEPAGE="https://ncbi.github.io/cxx-toolkit/" -SRC_URI=" - ftp://ftp.ncbi.nih.gov/blast/executables/blast+/${PV}/${MY_P}.tar.gz" -# http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz" - -# should also install ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz -# see http://www.biostars.org/p/76551/ and http://blastedbio.blogspot.cz/2012/05/blast-tabular-missing-descriptions.html -LICENSE="public-domain" -SLOT="0" -IUSE=" - debug static-libs static threads pch - test wxwidgets odbc - berkdb boost bzip2 cppunit curl expat fltk freetype gif - glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png - sablotron sqlite tiff xerces xalan xml xpm xslt X" -KEYWORDS="~amd64 ~x86" -RESTRICT="!test? ( test )" - -# sys-libs/db should be compiled with USE=cxx -DEPEND=" - <sys-devel/gcc-10:= - !sci-biology/ncbi-tools++ - berkdb? ( sys-libs/db:=[cxx(-)] ) - boost? ( dev-libs/boost ) - curl? ( net-misc/curl ) - sqlite? ( dev-db/sqlite:3 ) - mysql? ( virtual/mysql ) - fltk? ( x11-libs/fltk ) - opengl? ( virtual/opengl media-libs/glew:0= ) - mesa? ( media-libs/mesa[osmesa] ) - glut? ( media-libs/freeglut ) - freetype? ( media-libs/freetype ) - gnutls? ( net-libs/gnutls ) - cppunit? ( dev-util/cppunit ) - icu? ( dev-libs/icu ) - expat? ( dev-libs/expat ) - sablotron? ( app-text/sablotron ) - xml? ( dev-libs/libxml2 ) - xslt? ( dev-libs/libxslt ) - xerces? ( dev-libs/xerces-c ) - xalan? ( dev-libs/xalan-c ) - muparser? ( dev-cpp/muParser ) - hdf5? ( sci-libs/hdf5[cxx] ) - gif? ( media-libs/giflib ) - jpeg? ( media-libs/libjpeg-turbo:0= ) - png? ( media-libs/libpng:0= ) - tiff? ( media-libs/tiff:0= ) - xpm? ( x11-libs/libXpm ) - dev-libs/lzo - app-arch/bzip2 - dev-libs/libpcre" -# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge -# Intentionally omitted USE flags: -# ftds? ( dev-db/freetds ) # support for outside FreeTDS installations is currently broken. -# The default (heavily patched) embedded copy should work, or you can -# leave it off altogether -- the only public apps that make use of it are -# samples and tests, since NCBI's database servers are of course firewalled. - -# seems muParser is required, also glew is required. configure exits otherwise if these are explicitly passed to it (due to USE flag enabled) - -RDEPEND="${DEPEND}" - -S="${WORKDIR}/${MY_P}/c++" -# ncbi-blast-2.2.30+-src/c++ - -src_prepare() { -# filter-ldflags -Wl,--as-needed -# append-ldflags -Wl,--no-undefined -# sed -i -e 's/-print-file-name=libstdc++.a//' \ -# -e '/sed/ s/\([gO]\[0-9\]\)\*/\1\\+/' \ -# src/build-system/configure || die -# epatch \ -# "${FILESDIR}"/${PN}-${PV#0.}-fix-order-of-libs.patch \ -# "${FILESDIR}"/curl-types.patch \ -# "${FILESDIR}"/malloc_initialize_upstream_fix.patch \ -# "${FILESDIR}"/respect_CXXFLAGS_configure.ac.patch \ -# "${FILESDIR}"/respect_CXXFLAGS_configure.patch \ -# "${FILESDIR}"/report_project_settings_configure.ac.patch \ -# "${FILESDIR}"/report_project_settings_configure.patch \ -# "${FILESDIR}"/make_install.patch - -# "${FILESDIR}"/${PN}-${PV#0.}-disable_test_compress.patch - -# "${FILESDIR}"/${PN}-${PV#0.}-gcc46.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-gcc47.patch \ -# "${WORKDIR}"/${PN}-${PV#0.}-asneeded.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-libpng15.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-glibc-214.patch - -# use prefix && append-ldflags -Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/${PN}" - -# The conf-opts.patch and as-needed.patch need to be adjusted for 12.0.0 line numbers -## local PATCHES=( -## "${FILESDIR}"/${P}-conf-opts.patch -## "${FILESDIR}"/${P}-fix-svn-URL-upstream.patch -## "${FILESDIR}"/${P}-linkage-tuneups.patch -## "${FILESDIR}"/${P}-more-patches.patch -## "${FILESDIR}"/${P}-linkage-tuneups-addons.patch -## "${FILESDIR}"/${P}-configure.patch -## "${FILESDIR}"/${P}-drop-STATIC-from-LIB.patch -## "${FILESDIR}"/${P}-fix-install.patch -## ) - # "${FILESDIR}"/${P}-support-autoconf-2.60.patch -## epatch ${PATCHES[@]} - - # use a Debian patch from http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ncbi-blast%2B/trunk/debian/patches/fix_lib_deps?revision=18535&view=markup - # the patches for 2.2.30+ do not apply to 2.2.31, mostly DLL_LIB is gone but somewhere - # it is still present, plus in a few places was something else patched - # staying without any patches for now and lets see is it works on Gentoo - # epatch "${FILESDIR}"/fix_lib_deps.patch - # make sure this one is the last one and contains the actual patches applied unless we can have autoconf-2.59 or 2.60 - # https://bugs.gentoo.org/show_bug.cgi?id=514706 - - tc-export CXX CC - -## cd src/build-system || die -# eautoreconf - - # Temporarily disabling eautoconf because we patch configure via ${P}-support-autoconf-2.60.patch - # eautoconf # keep it disabled until we can ensure 2.59 is installed - # beware 12.0.0. and previous required autoconf-2.59, a patch for 12.0.0 brings autoconf-2.60 support - default -} - -# possibly place modified contents of ${W}/src/build-system/config.site.ncbi and {W}/src/build-system/config.site.ex into ${W}/src/build-system/config.site -src_configure() { - local myconf=() - #--without-optimization turn off optimization flags in non-debug mode - #--with-profiling build profiled versions of libs and apps - #--with-tcheck(=DIR) build for Intel Thread Checker (in DIR) - #--with-plugin-auto-load always enable the plugin manager by default - #--with-bundles build bundles in addition to dylibs on Mac OS X - #--with-bin-release build executables suitable for public release - # no dll and such - #--with-64 compile to 64-bit code - #--with-universal build universal binaries on Mac OS X - #--with-universal=CPUs build universal binaries targeting the given CPUs - #--without-exe do not build executables - #--with-relative-runpath=P specify an executable-relative DLL search path - #--with-hard-runpath hard-code runtime path, ignoring LD_LIBRARY_PATH - #--with-limited-linker don't attempt to build especially large projects - #--with-extra-action= script to call after the configuration is complete - #--with-autodep automatic generation of dependencies (GNU make) - #--with-fake-root=DIR appear to have been built under DIR - #--with-build-root-sfx=X add a user-specified suffix to the build dir name - #--without-execopy do not copy built executables to the BIN area - #--with-lib-rebuilds ensure that apps use up-to-date libraries - #--with-lib-rebuilds=ask ask whether to update each app's libraries - #--without-deactivation keep old copies of libraries that no longer build - #--without-makefile-auto-update do not auto-update generated makefiles - #--with-projects=FILE build projects listed in FILE by default - #--without-flat-makefile do not generate an all-encompassing flat makefile - #--with-configure-dialog allow interactive flat makefile project selection - #--with-saved-settings=F load configuration settings from the file F - #--with-check-tools=... use the specified tools for testing - #--with-ncbi-public ensure compatibility for all in-house platforms - #--with-sybase-local=DIR use local SYBASE install (DIR is optional) - #--with-sybase-new use newer SYBASE install (12.5 rather than 12.0) - #--without-sp do not use SP libraries - #--without-orbacus do not use ORBacus CORBA libraries - #--with-orbacus=DIR use ORBacus installation in DIR - #--with-jni(=JDK-DIR) build Java bindings (against the JDK in JDK-DIR) - #--with-sablot=DIR use Sablotron installation in DIR - #--without-sablot, do not use Sablotron - #--with-oechem=DIR use OpenEye OEChem installation in DIR - #--without-oechem do not use OEChem - #--with-sge=DIR use Sun Grid Engine installation in DIR - #--without-sge do not use Sun Grid Engine - #--with-magic=DIR use libmagic installation in DIR - #--without-magic do not use libmagic - #--without-local-lbsm turn off support for IPC with locally running LBSMD - #--without-ncbi-crypt use a dummy stubbed-out version of ncbi_crypt - #--without-connext do not build non-public CONNECT library extensions - #--without-serial do not build the serialization library and tools - #--without-objects do not generate/build serializeable objects from ASNs - #--without-dbapi do not build database connectivity libraries - #--without-app do not build standalone applications like ID1_FETCH - #--without-gui do not build most graphical projects - #--without-algo do not build CPU-intensive algorithms - #--without-internal do not build internal projects - #--with-gbench ensure that Genome Workbench can be built - #--without-gbench do not build Genome Workbench - myconf+=( - --with-dll - --with-lfs - --with-build-root="${S}"_build - --without-suffix - --without-hostspec - --without-version - --with-bincopy - --without-strip - --without-ccache - --without-distcc -# --with-ncbi-c - --without-ctools -# --with-sss -# --with-sssutils -# --with-sssdb -# --with-included-sss - --with-z="${EPREFIX}/usr" - --with-bz2="${EPREFIX}/usr" - --without-sybase - --with-autodep -# --with-3psw=std:netopt favor standard (system) builds of the above pkgs - $(use_with debug) - $(use_with debug max-debug) - $(use_with debug symbols) - $(use_with static-libs static) - $(use_with static static-exe) - $(use_with threads mt) - $(use_with prefix runpath "${EPREFIX}/usr/$(get_libdir)/${PN}") - $(use_with test check) - $(use_with pch) - $(use_with lzo lzo "${EPREFIX}/usr") - $(use_with pcre pcre "${EPREFIX}/usr") - $(use_with gnutls gnutls "${EPREFIX}/usr") - $(use_with mysql mysql "${EPREFIX}/usr") - $(use_with muparser muparser "${EPREFIX}/usr") - $(usex fltk --with-fltk="${EPREFIX}/usr" "") - $(use_with opengl opengl "${EPREFIX}/usr") - $(use_with mesa mesa "${EPREFIX}/usr") - $(use_with opengl glut "${EPREFIX}/usr") - $(use_with opengl glew "${EPREFIX}/usr") - # - # GLEW 2.0 dropped support for this, see https://bugs.gentoo.org/show_bug.cgi?id=611302 - # $(use_with opengl glew-mx) - $(use_with wxwidgets wxwidgets "${EPREFIX}/usr") - $(use_with wxwidgets wxwidgets-ucs) - $(use_with freetype freetype "${EPREFIX}/usr") -# $(use_with berkdb bdb "${EPREFIX}/usr") # not in ncbi-blast+ - $(usex odbc --with-odbc="${EPREFIX}/usr" "") - # is python2 - --without-python - $(use_with boost boost "${EPREFIX}/usr") - $(use_with sqlite sqlite3 "${EPREFIX}/usr") - $(use_with icu icu "${EPREFIX}/usr") - $(use_with expat expat "${EPREFIX}/usr") - $(use_with xml libxml "${EPREFIX}/usr") - $(use_with xml libxslt "${EPREFIX}/usr") - $(use_with xerces xerces "${EPREFIX}/usr") - $(use_with hdf5 hdf5 "${EPREFIX}/usr") - $(use_with xalan xalan "${EPREFIX}/usr") -# $(use_with gif gif "${EPREFIX}/usr") # prevent compilation failure in "ncbi-tools++-12.0.0/src/util/image/image_io_gif.cpp:351: error: 'QuantizeBuffer' was not declared in this scope" - --without-gif - $(use_with jpeg jpeg "${EPREFIX}/usr") - $(use_with tiff tiff "${EPREFIX}/usr") - $(use_with png png "${EPREFIX}/usr") - $(use_with xpm xpm "${EPREFIX}/usr") - $(use_with curl curl "${EPREFIX}/usr") -# $(use_with X x "${EPREFIX}/usr") -# $(use_with X x) # there is no --with-x option - # prevent downloading VDB sources from https://github.com/ncbi/ncbi-vdb.git during configure execution - --without-vdb - ) - - # http://www.ncbi.nlm.nih.gov/books/NBK7167/ - use test || myconf+=( --with-projects="${FILESDIR}"/disable-testsuite-compilation.txt ) - - # TODO - # copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure - # otherwise your -O2 will be dropped in some subdirectories and replaced by e.g. -O9 - - einfo "bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}/usr" --libdir=/usr/lib64 ${myconf[@]}" - -# ECONF_SOURCE="src/build-system" \ -# econf \ - bash \ - ./src/build-system/configure \ - --srcdir="${S}" \ - --prefix="${EPREFIX}/usr" \ - --libdir=/usr/lib64 \ - --with-flat-makefile \ - ${myconf[@]} || die -#--without-debug \ -# --with-bin-release \ -# --with-bincopy \ -# --without-static \ -# --with-dll \ -# --with-mt \ -# --with-openmp \ -# --with-lfs \ -# --prefix="${ED}"/usr \ -# --libdir="${ED}"/usr/$(get_libdir)/"${PN}" \ -# ${myconf} LDFLAGS="-Wl,--no-as-needed" \ -# || die -# econf ${myconf[@]} -} - -src_compile() { - ## all_r would ignore the --with-projects contents and build more - ## emake all_r -C GCC*-Release*/build || die - ## all_p with compile only selected/required components - ##cd "${S}"_build &&\ - ##emake all_p -C GCC*-Release*/build || die "gcc-4.5.3 crashes at src/objects/valerr/ValidError.cpp:226:1: internal compiler error: Segmentation fault, right?" - #emake all_p -C "${S}"_build/build - - # - # Re: /usr/lib64/ncbi-tools++/libdbapi_driver.so: undefined reference to `ncbi::NcbiGetlineEOL(std::istream&, std::string&)' - # - # The next release should automatically address such underlinking, albeit - # only in --with-flat-makefile configurations. For now (12.0.0), you'll need to - # add or extend more DLL_LIB settings, to which end you may find the - # resources at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/ - # helpful. For instance, - # - # http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/dbapi_driver.html - # - # indicates that src/dbapi/driver/Makefile.dbapi_driver.lib should set - # - # DLL_LIB = xncbi - # - # (You can find the path to that makefile by examining - # .../status/.dbapi_driver.dep or .../build/Makefile.flat.) - # - # To take full advantage of --with-flat-makefile, you'll need the following (instead of 'emake all_p -C "${S}"_build/build') and call configure --with-flat-makefile: - emake -C "${S}"_build/build -f Makefile.flat -} - -src_install() { - rm -rvf "${S}"_build/lib/ncbi || die - emake install prefix="${ED}/usr" libdir="${ED}/usr/$(get_libdir)/${PN}" - -# dobin "${S}"_build/bin/* -# dolib.so "${S}"_build/lib/*so* -# dolib.a "${S}"_build/lib/*.a -# doheader "${S}"_build/inc/* - - # File collisions with sci-biology/ncbi-tools - mv "${ED}"/usr/bin/asn2asn "${ED}"/usr/bin/asn2asn+ - mv "${ED}"/usr/bin/rpsblast "${ED}"/usr/bin/rpsblast+ - mv -f "${ED}"/usr/bin/test_regexp "${ED}"/usr/bin/test_regexp+ # drop the eventually mistakenly compiled binaries - mv "${ED}"/usr/bin/vecscreen "${ED}"/usr/bin/vecscreen+ - mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop+ - - echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}" > ${S}/99${PN} - doenvd "${S}/99${PN}" -} - -pkg_postinst() { - einfo 'Please run "source /etc/profile" before using this package in the current shell.' - einfo 'Documentation is at http://www.ncbi.nlm.nih.gov/books/NBK7167/' -} diff --git a/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild b/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild deleted file mode 100644 index 527acfadf..000000000 --- a/sci-biology/ncbi-blast+/ncbi-blast+-2.8.1.ebuild +++ /dev/null @@ -1,360 +0,0 @@ -# Copyright 1999-2022 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 toolchain-funcs - -MY_P="ncbi-blast-${PV}+-src" -# workdir/ncbi-blast-2.2.30+-src -# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.30/ncbi-blast-2.2.30+-src.tar.gz -# ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.3.0+-src.tar.gz - -DESCRIPTION="A subset of NCBI C++ Toolkit containing just the NCBI BLAST+" -HOMEPAGE="https://ncbi.github.io/cxx-toolkit/" -SRC_URI=" - ftp://ftp.ncbi.nih.gov/blast/executables/blast+/${PV}/${MY_P}.tar.gz" -# http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz" - -# should also install ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz -# see http://www.biostars.org/p/76551/ and http://blastedbio.blogspot.cz/2012/05/blast-tabular-missing-descriptions.html -LICENSE="public-domain" -SLOT="0" -IUSE=" - debug static-libs static threads pch - test wxwidgets odbc - berkdb boost bzip2 cppunit curl expat fltk freetype gif - glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python - sablotron sqlite tiff xerces xalan xml xpm xslt X" -KEYWORDS="~amd64 ~x86" -RESTRICT="!test? ( test )" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -# sys-libs/db should be compiled with USE=cxx -DEPEND=" - <sys-devel/gcc-10:= - !sci-biology/ncbi-tools++ - berkdb? ( sys-libs/db:=[cxx(-)] ) - boost? ( dev-libs/boost ) - curl? ( net-misc/curl ) - sqlite? ( dev-db/sqlite:3 ) - mysql? ( virtual/mysql ) - fltk? ( x11-libs/fltk ) - opengl? ( virtual/opengl media-libs/glew:0= ) - mesa? ( media-libs/mesa[osmesa] ) - glut? ( media-libs/freeglut ) - freetype? ( media-libs/freetype ) - gnutls? ( net-libs/gnutls ) - python? ( ${PYTHON_DEPS} ) - cppunit? ( dev-util/cppunit ) - icu? ( dev-libs/icu ) - expat? ( dev-libs/expat ) - sablotron? ( app-text/sablotron ) - xml? ( dev-libs/libxml2 ) - xslt? ( dev-libs/libxslt ) - xerces? ( dev-libs/xerces-c ) - xalan? ( dev-libs/xalan-c ) - muparser? ( dev-cpp/muParser ) - hdf5? ( sci-libs/hdf5[cxx] ) - gif? ( media-libs/giflib ) - jpeg? ( media-libs/libjpeg-turbo:0= ) - png? ( media-libs/libpng:0= ) - tiff? ( media-libs/tiff:0= ) - xpm? ( x11-libs/libXpm ) - dev-libs/lzo - app-arch/bzip2 - dev-libs/libpcre - dev-db/lmdb" -# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge -# Intentionally omitted USE flags: -# ftds? ( dev-db/freetds ) # support for outside FreeTDS installations is currently broken. -# The default (heavily patched) embedded copy should work, or you can -# leave it off altogether -- the only public apps that make use of it are -# samples and tests, since NCBI's database servers are of course firewalled. - -# seems muParser is required, also glew is required. configure exits otherwise if these are explicitly passed to it (due to USE flag enabled) - -RDEPEND="${DEPEND}" - -S="${WORKDIR}/${MY_P}/c++" -# ncbi-blast-2.2.30+-src/c++ - -src_prepare() { -# filter-ldflags -Wl,--as-needed -# append-ldflags -Wl,--no-undefined -# sed -i -e 's/-print-file-name=libstdc++.a//' \ -# -e '/sed/ s/\([gO]\[0-9\]\)\*/\1\\+/' \ -# src/build-system/configure || die -# epatch \ -# "${FILESDIR}"/${PN}-${PV#0.}-fix-order-of-libs.patch \ -# "${FILESDIR}"/curl-types.patch \ -# "${FILESDIR}"/malloc_initialize_upstream_fix.patch \ -# "${FILESDIR}"/respect_CXXFLAGS_configure.ac.patch \ -# "${FILESDIR}"/respect_CXXFLAGS_configure.patch \ -# "${FILESDIR}"/report_project_settings_configure.ac.patch \ -# "${FILESDIR}"/report_project_settings_configure.patch \ -# "${FILESDIR}"/make_install.patch - -# "${FILESDIR}"/${PN}-${PV#0.}-disable_test_compress.patch - -# "${FILESDIR}"/${PN}-${PV#0.}-gcc46.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-gcc47.patch \ -# "${WORKDIR}"/${PN}-${PV#0.}-asneeded.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-libpng15.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-glibc-214.patch - -# use prefix && append-ldflags -Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/${PN}" - -# The conf-opts.patch and as-needed.patch need to be adjusted for 12.0.0 line numbers -## local PATCHES=( -## "${FILESDIR}"/${P}-conf-opts.patch -## "${FILESDIR}"/${P}-fix-svn-URL-upstream.patch -## "${FILESDIR}"/${P}-linkage-tuneups.patch -## "${FILESDIR}"/${P}-more-patches.patch -## "${FILESDIR}"/${P}-linkage-tuneups-addons.patch -## "${FILESDIR}"/${P}-configure.patch -## "${FILESDIR}"/${P}-drop-STATIC-from-LIB.patch -## "${FILESDIR}"/${P}-fix-install.patch -## ) - # "${FILESDIR}"/${P}-support-autoconf-2.60.patch -## epatch ${PATCHES[@]} - - # use a Debian patch from http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ncbi-blast%2B/trunk/debian/patches/fix_lib_deps?revision=18535&view=markup - # the patches for 2.2.30+ do not apply to 2.2.31, mostly DLL_LIB is gone but somewhere - # it is still present, plus in a few places was something else patched - # staying without any patches for now and lets see is it works on Gentoo - # epatch "${FILESDIR}"/fix_lib_deps.patch - # make sure this one is the last one and contains the actual patches applied unless we can have autoconf-2.59 or 2.60 - # https://bugs.gentoo.org/show_bug.cgi?id=514706 - - tc-export CXX CC - -## cd src/build-system || die -# eautoreconf - - # Temporarily disabling eautoconf because we patch configure via ${P}-support-autoconf-2.60.patch - # eautoconf # keep it disabled until we can ensure 2.59 is installed - # beware 12.0.0. and previous required autoconf-2.59, a patch for 12.0.0 brings autoconf-2.60 support - default -} - -# possibly place modified contents of ${W}/src/build-system/config.site.ncbi and {W}/src/build-system/config.site.ex into ${W}/src/build-system/config.site -src_configure() { - local myconf=() - #--without-optimization turn off optimization flags in non-debug mode - #--with-profiling build profiled versions of libs and apps - #--with-tcheck(=DIR) build for Intel Thread Checker (in DIR) - #--with-plugin-auto-load always enable the plugin manager by default - #--with-bundles build bundles in addition to dylibs on Mac OS X - #--with-bin-release build executables suitable for public release - # no dll and such - #--with-64 compile to 64-bit code - #--with-universal build universal binaries on Mac OS X - #--with-universal=CPUs build universal binaries targeting the given CPUs - #--without-exe do not build executables - #--with-relative-runpath=P specify an executable-relative DLL search path - #--with-hard-runpath hard-code runtime path, ignoring LD_LIBRARY_PATH - #--with-limited-linker don't attempt to build especially large projects - #--with-extra-action= script to call after the configuration is complete - #--with-autodep automatic generation of dependencies (GNU make) - #--with-fake-root=DIR appear to have been built under DIR - #--with-build-root-sfx=X add a user-specified suffix to the build dir name - #--without-execopy do not copy built executables to the BIN area - #--with-lib-rebuilds ensure that apps use up-to-date libraries - #--with-lib-rebuilds=ask ask whether to update each app's libraries - #--without-deactivation keep old copies of libraries that no longer build - #--without-makefile-auto-update do not auto-update generated makefiles - #--with-projects=FILE build projects listed in FILE by default - #--without-flat-makefile do not generate an all-encompassing flat makefile - #--with-configure-dialog allow interactive flat makefile project selection - #--with-saved-settings=F load configuration settings from the file F - #--with-check-tools=... use the specified tools for testing - #--with-ncbi-public ensure compatibility for all in-house platforms - #--with-sybase-local=DIR use local SYBASE install (DIR is optional) - #--with-sybase-new use newer SYBASE install (12.5 rather than 12.0) - #--without-sp do not use SP libraries - #--without-orbacus do not use ORBacus CORBA libraries - #--with-orbacus=DIR use ORBacus installation in DIR - #--with-jni(=JDK-DIR) build Java bindings (against the JDK in JDK-DIR) - #--with-sablot=DIR use Sablotron installation in DIR - #--without-sablot, do not use Sablotron - #--with-oechem=DIR use OpenEye OEChem installation in DIR - #--without-oechem do not use OEChem - #--with-sge=DIR use Sun Grid Engine installation in DIR - #--without-sge do not use Sun Grid Engine - #--with-magic=DIR use libmagic installation in DIR - #--without-magic do not use libmagic - #--without-local-lbsm turn off support for IPC with locally running LBSMD - #--without-ncbi-crypt use a dummy stubbed-out version of ncbi_crypt - #--without-connext do not build non-public CONNECT library extensions - #--without-serial do not build the serialization library and tools - #--without-objects do not generate/build serializeable objects from ASNs - #--without-dbapi do not build database connectivity libraries - #--without-app do not build standalone applications like ID1_FETCH - #--without-gui do not build most graphical projects - #--without-algo do not build CPU-intensive algorithms - #--without-internal do not build internal projects - #--with-gbench ensure that Genome Workbench can be built - #--without-gbench do not build Genome Workbench - myconf+=( - --with-dll - --with-lfs - --with-build-root="${S}"_build - --without-suffix - --without-hostspec - --without-version - --with-bincopy - --without-strip - --without-ccache - --without-distcc -# --with-ncbi-c - --without-ctools -# --with-sss -# --with-sssutils -# --with-sssdb -# --with-included-sss - --with-z="${EPREFIX}/usr" - --with-bz2="${EPREFIX}/usr" - --without-sybase - --with-autodep -# --with-3psw=std:netopt favor standard (system) builds of the above pkgs - $(use_with debug) - $(use_with debug max-debug) - $(use_with debug symbols) - $(use_with static-libs static) - $(use_with static static-exe) - $(use_with threads mt) - $(use_with prefix runpath "${EPREFIX}/usr/$(get_libdir)/${PN}") - $(use_with test check) - $(use_with pch) - $(use_with lzo lzo "${EPREFIX}/usr") - $(use_with pcre pcre "${EPREFIX}/usr") - $(use_with gnutls gnutls "${EPREFIX}/usr") - $(use_with mysql mysql "${EPREFIX}/usr") - $(use_with muparser muparser "${EPREFIX}/usr") - $(usex fltk --with-fltk="${EPREFIX}/usr" "") - $(use_with opengl opengl "${EPREFIX}/usr") - $(use_with mesa mesa "${EPREFIX}/usr") - $(use_with opengl glut "${EPREFIX}/usr") - $(use_with opengl glew "${EPREFIX}/usr") - # - # GLEW 2.0 dropped support for this, see https://bugs.gentoo.org/show_bug.cgi?id=611302 - # $(use_with opengl glew-mx) - $(use_with wxwidgets wxwidgets "${EPREFIX}/usr") - $(use_with wxwidgets wxwidgets-ucs) - $(use_with freetype freetype "${EPREFIX}/usr") -# $(use_with berkdb bdb "${EPREFIX}/usr") # not in ncbi-blast+ - $(usex odbc --with-odbc="${EPREFIX}/usr" "") - $(use_with python python "${EPREFIX}/usr") - $(use_with boost boost "${EPREFIX}/usr") - $(use_with sqlite sqlite3 "${EPREFIX}/usr") - $(use_with icu icu "${EPREFIX}/usr") - $(use_with expat expat "${EPREFIX}/usr") - $(use_with xml libxml "${EPREFIX}/usr") - $(use_with xml libxslt "${EPREFIX}/usr") - $(use_with xerces xerces "${EPREFIX}/usr") - $(use_with hdf5 hdf5 "${EPREFIX}/usr") - $(use_with xalan xalan "${EPREFIX}/usr") -# $(use_with gif gif "${EPREFIX}/usr") # prevent compilation failure in "ncbi-tools++-12.0.0/src/util/image/image_io_gif.cpp:351: error: 'QuantizeBuffer' was not declared in this scope" - --without-gif - $(use_with jpeg jpeg "${EPREFIX}/usr") - $(use_with tiff tiff "${EPREFIX}/usr") - $(use_with png png "${EPREFIX}/usr") - $(use_with xpm xpm "${EPREFIX}/usr") - $(use_with curl curl "${EPREFIX}/usr") -# $(use_with X x "${EPREFIX}/usr") -# $(use_with X x) # there is no --with-x option - # prevent downloading VDB sources from https://github.com/ncbi/ncbi-vdb.git during configure execution - --without-vdb - ) - - # http://www.ncbi.nlm.nih.gov/books/NBK7167/ - use test || myconf+=( --with-projects="${FILESDIR}"/disable-testsuite-compilation.txt ) - - # TODO - # copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure - # otherwise your -O2 will be dropped in some subdirectories and replaced by e.g. -O9 - - einfo "bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}/usr" --libdir=/usr/lib64 ${myconf[@]}" - -# ECONF_SOURCE="src/build-system" \ -# econf \ - bash \ - ./src/build-system/configure \ - --srcdir="${S}" \ - --prefix="${EPREFIX}/usr" \ - --libdir=/usr/lib64 \ - --with-flat-makefile \ - ${myconf[@]} || die "Maybe try new src/build-system/cmake/cmake-configure instead?" -#--without-debug \ -# --with-bin-release \ -# --with-bincopy \ -# --without-static \ -# --with-dll \ -# --with-mt \ -# --with-openmp \ -# --with-lfs \ -# --prefix="${ED}"/usr \ -# --libdir="${ED}"/usr/$(get_libdir)/"${PN}" \ -# ${myconf} LDFLAGS="-Wl,--no-as-needed" \ -# || die -# econf ${myconf[@]} -} - -src_compile() { - ## all_r would ignore the --with-projects contents and build more - ## emake all_r -C GCC*-Release*/build || die - ## all_p with compile only selected/required components - ##cd "${S}"_build &&\ - ##emake all_p -C GCC*-Release*/build || die "gcc-4.5.3 crashes at src/objects/valerr/ValidError.cpp:226:1: internal compiler error: Segmentation fault, right?" - #emake all_p -C "${S}"_build/build - - # - # Re: /usr/lib64/ncbi-tools++/libdbapi_driver.so: undefined reference to `ncbi::NcbiGetlineEOL(std::istream&, std::string&)' - # - # The next release should automatically address such underlinking, albeit - # only in --with-flat-makefile configurations. For now (12.0.0), you'll need to - # add or extend more DLL_LIB settings, to which end you may find the - # resources at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/ - # helpful. For instance, - # - # http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/dbapi_driver.html - # - # indicates that src/dbapi/driver/Makefile.dbapi_driver.lib should set - # - # DLL_LIB = xncbi - # - # (You can find the path to that makefile by examining - # .../status/.dbapi_driver.dep or .../build/Makefile.flat.) - # - # To take full advantage of --with-flat-makefile, you'll need the following (instead of 'emake all_p -C "${S}"_build/build') and call configure --with-flat-makefile: - emake -C "${S}"_build/build -f Makefile.flat -} - -src_install() { - rm -rvf "${S}"_build/lib/ncbi || die - emake install prefix="${ED}/usr" libdir="${ED}/usr/$(get_libdir)/${PN}" - -# dobin "${S}"_build/bin/* -# dolib.so "${S}"_build/lib/*so* -# dolib.a "${S}"_build/lib/*.a -# doheader "${S}"_build/inc/* - - # File collisions with sci-biology/ncbi-tools - mv "${ED}"/usr/bin/asn2asn "${ED}"/usr/bin/asn2asn+ - mv "${ED}"/usr/bin/rpsblast "${ED}"/usr/bin/rpsblast+ - mv -f "${ED}"/usr/bin/test_regexp "${ED}"/usr/bin/test_regexp+ # drop the eventually mistakenly compiled binaries - mv "${ED}"/usr/bin/vecscreen "${ED}"/usr/bin/vecscreen+ - mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop+ - - echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}" > ${S}/99${PN} - doenvd "${S}/99${PN}" -} - -pkg_postinst() { - einfo 'Please run "source /etc/profile" before using this package in the current shell.' - einfo 'Documentation is at http://www.ncbi.nlm.nih.gov/books/NBK7167/' -} diff --git a/sci-biology/ncbi-genome-download/Manifest b/sci-biology/ncbi-genome-download/Manifest deleted file mode 100644 index 57adfb8ee..000000000 --- a/sci-biology/ncbi-genome-download/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST ncbi-genome-download-0.3.0.tar.gz 37355 BLAKE2B c8061f29c2130d26ee97e310ce702db304d30794735af26cb2d804db5acb38e32b05b30d7770c195fb627f3d005b33bff038208b49612380de52278823914dc2 SHA512 5bcd6e0d731bc4bb6792821dc6d233e2f7acac6ee6819ddd14014a881d475c43ad084ff000d78e12fc2528d179be0e3db076fbe15da4b83dc6815c37c188ab61 diff --git a/sci-biology/ncbi-genome-download/metadata.xml b/sci-biology/ncbi-genome-download/metadata.xml deleted file mode 100644 index a394f7ee4..000000000 --- a/sci-biology/ncbi-genome-download/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>freeh4cker@gmail.com</email> - <name>Bertrand Néron</name> - </maintainer> - <upstream> - <remote-id type="github">kblin/ncbi-genome-download</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/ncbi-genome-download/ncbi-genome-download-0.3.0.ebuild b/sci-biology/ncbi-genome-download/ncbi-genome-download-0.3.0.ebuild deleted file mode 100644 index 1afb771c5..000000000 --- a/sci-biology/ncbi-genome-download/ncbi-genome-download-0.3.0.ebuild +++ /dev/null @@ -1,24 +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} ) -DISTUTILS_USE_SETUPTOOLS=rdepend - -inherit distutils-r1 - -DESCRIPTION="Download genomes from the NCBI FTP servers" -HOMEPAGE="https://github.com/kblin/ncbi-genome-download" -SRC_URI="https://github.com/kblin/${PN}/archive/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="Apache-2.0" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -BDEPEND="test? ( - dev-python/requests-mock[${PYTHON_USEDEP}] - dev-python/pytest-mock[${PYTHON_USEDEP}] -)" - -distutils_enable_tests pytest diff --git a/sci-biology/ncbi-tools++/Manifest b/sci-biology/ncbi-tools++/Manifest deleted file mode 100644 index 9dd3a53d8..000000000 --- a/sci-biology/ncbi-tools++/Manifest +++ /dev/null @@ -1,3 +0,0 @@ -DIST ncbi_cxx--12_0_0.tar.gz 37925914 BLAKE2B 45490961293d8b3ace24c21602f4039041003f9b45d9f1763957c97ba1e55d6d336c33b6116262b2e774cc26b9366cc3d61bead0c0c7fbd4c461cad2921d80d4 SHA512 1a79f2d95960efde6263289814102499460ec235dad36337dd398d668665e44015e06e40fd0e66a8fb16f526d326949adcaadcb667debeba5d8570b1a92e30ed -DIST ncbi_cxx--18_0_0.tar.gz 69807228 BLAKE2B 2221232e4ab38845708a9ec5601a94f1dd25c5dd6fff265bde3c3d64b9108eec00b8480a1888d2517881f25abe9127e547ba88528b95398480ecd09d133482a7 SHA512 70dd07597aafa3f48881640530bf2aeebcac6fa13843fada4c590ca101cb8fdfa1aabf240ed0177d371a1fc36c6d231d667125279096006cd1eba119ea9514f5 -DIST ncbi_cxx--22_0_0.tar.gz 56042079 BLAKE2B 8a358f9f09e2844c4007b99f4b1c5212e254f804237c26c2eb6620448755b88029d492ff124fff3fdb515189219400f3edaaa195eb4f0fa539ac7b122af4d7e1 SHA512 f6624b09aae1f27b30196b7036f3d962125f2c57e1369bef013b15c116828e2daf264e018a1c1e71fb57c55462d71c5df7580e429fcf9d736e02f89c71cbfbd0 diff --git a/sci-biology/ncbi-tools++/files/curl-types.patch b/sci-biology/ncbi-tools++/files/curl-types.patch deleted file mode 100644 index 3e6079057..000000000 --- a/sci-biology/ncbi-tools++/files/curl-types.patch +++ /dev/null @@ -1,24 +0,0 @@ -Index: libs/kns/url-fetcher-curl.c -=================================================================== ---- src/sra/sdk/libs/kns/url-fetcher-curl.c (revision 11878) -+++ src/sra/sdk/libs/kns/url-fetcher-curl.c (revision 11880) -@@ -38,7 +38,6 @@ - #include <string.h> - - #include <curl/curl.h> --#include <curl/types.h> - #include <curl/easy.h> - - /*-------------------------------------------------------------------------- -Index: tools/refseq-load/refseq-load.c -=================================================================== ---- src/sra/sdk/tools/refseq-load/refseq-load.c (revision 11878) -+++ src/sra/sdk/tools/refseq-load/refseq-load.c (revision 11880) -@@ -41,7 +41,6 @@ - #include <sysalloc.h> - - #include <curl/curl.h> --#include <curl/types.h> - #include <curl/easy.h> - - #include <stdlib.h> diff --git a/sci-biology/ncbi-tools++/files/disable-testsuite-compilation.txt b/sci-biology/ncbi-tools++/files/disable-testsuite-compilation.txt deleted file mode 100644 index fa27aa13b..000000000 --- a/sci-biology/ncbi-tools++/files/disable-testsuite-compilation.txt +++ /dev/null @@ -1,8 +0,0 @@ -.* --.*/test --.*/unit_test --.*/unit_tests --dbapi/driver/ftds.*/freetds/.*/unittests --sample --.*/demo --.*/samples diff --git a/sci-biology/ncbi-tools++/files/make_install.patch b/sci-biology/ncbi-tools++/files/make_install.patch deleted file mode 100644 index e98f1110d..000000000 --- a/sci-biology/ncbi-tools++/files/make_install.patch +++ /dev/null @@ -1,14 +0,0 @@ ---- src/build-system/Makefile.in.top.old 2013-01-07 23:07:29.970141951 +0100 -+++ src/build-system/Makefile.in.top 2013-01-07 23:08:37.940990190 +0100 -@@ -39,7 +39,10 @@ - -$(RMDIR) $(pincludedir) - $(INSTALL) -d $(bindir) $(libdir) $(pincludedir) - $(INSTALL) $(lbindir)/* $(bindir) -- $(INSTALL) -m 644 $(llibdir)/* $(libdir) -+ $(INSTALL) -m 644 $(llibdir)/*.* $(libdir) -+ if test -d $(llibdir)/ncbi; then \ -+ cp -pPR $(llibdir)/ncbi $(libdir)/; \ -+ fi - -rm -f $(libdir)/lib*-static.a - cd $(libdir) && \ - for x in *.a; do ln -s "$$x" "`basename \"$$x\" .a`-static.a"; done diff --git a/sci-biology/ncbi-tools++/files/malloc_initialize_upstream_fix.patch b/sci-biology/ncbi-tools++/files/malloc_initialize_upstream_fix.patch deleted file mode 100644 index 4900e529a..000000000 --- a/sci-biology/ncbi-tools++/files/malloc_initialize_upstream_fix.patch +++ /dev/null @@ -1,100 +0,0 @@ ---- trunk/c++/src/app/netcache/nc_memory.cpp 2011/12/16 17:42:54 52330 -+++ trunk/c++/src/app/netcache/nc_memory.cpp 2012/02/27 14:38:30 53136 -@@ -360,7 +360,7 @@ - m_ObjLock.Lock(); - ++m_SysFrees; - m_SystemMem -= alloced_size; -- m_LostMem -= alloced_size -= asked_size; -+ m_LostMem -= alloced_size - asked_size; - m_ObjLock.Unlock(); - } - -@@ -2539,7 +2539,7 @@ - bool - CNCMemManager::InitializeApp(void) - { -- try { -+ /*try { - CSQLITE_Global::SetCustomMallocFuncs(&s_NCMallocMethods); - } - catch (CSQLITE_Exception& ex) { -@@ -2547,13 +2547,15 @@ - return false; - } - -- return CNCMMCentral::RunLateInit(); -+ return CNCMMCentral::RunLateInit();*/ -+ g_InitNCThreadIndexes(); -+ return true; - } - - void - CNCMemManager::FinalizeApp(void) - { -- CNCMMCentral::PrepareToStop(); -+ //CNCMMCentral::PrepareToStop(); - } - - void -@@ -2571,28 +2573,29 @@ - void - CNCMemManager::PrintStats(CPrintTextProxy& proxy) - { -- CNCMMStats stats_sum; -+ /*CNCMMStats stats_sum; - CNCMMStats::CollectAllStats(&stats_sum); -- stats_sum.Print(proxy); -+ stats_sum.Print(proxy);*/ - } - - size_t - CNCMemManager::GetMemoryLimit(void) - { -- return CNCMMCentral::GetMemLimit(); -+ return 0;//CNCMMCentral::GetMemLimit(); - } - - size_t - CNCMemManager::GetMemoryUsed(void) - { -- CNCMMStats stat; -+ /*CNCMMStats stat; - CNCMMStats::CollectAllStats(&stat); -- return stat.GetSystemMem(); -+ return stat.GetSystemMem();*/ -+ return 0; - } - - END_NCBI_SCOPE - -- -+/* - void* - operator new (size_t size) - #ifndef NCBI_COMPILER_MSVC -@@ -2626,13 +2629,13 @@ - { - NCBI_NS_NCBI::CNCMMCentral::DeallocMemory(ptr); - } -- -+*/ - #ifdef __GLIBC__ - // glibc has special method of overriding C library allocation functions. - - #include <malloc.h> - -- -+/* - void* s_NCMallocHook(size_t size, const void* caller) - { - return NCBI_NS_NCBI::CNCMMCentral::AllocMemory(size); -@@ -2656,7 +2659,7 @@ - } - - void (*__malloc_initialize_hook) (void) = s_NCInitMallocHook; -- -+*/ - #elif !defined(NCBI_OS_MSWIN) - // Changing of C library allocation functions on Windows is very tricky (if - // possible at all) and NetCache will never run in production on Windows. So - diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-bdb6.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-bdb6.patch deleted file mode 100644 index 9589481d4..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-bdb6.patch +++ /dev/null @@ -1,114 +0,0 @@ -Index: include/db/bdb/bdb_file.hpp -=================================================================== ---- include/db/bdb/bdb_file.hpp (revision 470126) -+++ include/db/bdb/bdb_file.hpp (working copy) -@@ -660,6 +660,9 @@ - void x_ConstructKeyBuf(); - void x_ConstructDataBuf(); - -+ static int x_CompareShim(DB* db, const DBT* dbt1, const DBT* dbt2, -+ size_t* locp); -+ - private: - auto_ptr<CBDB_BufferManager> m_KeyBuf; - auto_ptr<CBDB_BufferManager> m_DataBuf; -Index: src/db/bdb/bdb_blob.cpp -=================================================================== ---- src/db/bdb/bdb_blob.cpp (revision 470126) -+++ src/db/bdb/bdb_blob.cpp (working copy) -@@ -583,12 +583,31 @@ - return m_DBT_Data->size; - } - -+#if DB_VERSION_MAJOR >= 6 -+extern "C" { -+ typedef int (*BDB_CompareFunction_V6)(DB*, const DBT*, const DBT*, -+ size_t*); -+ int BDB_Uint4Compare_V6(DB* db, const DBT* dbt1, const DBT* dbt2, size_t*) -+ { return BDB_Uint4Compare(db, dbt1, dbt2); } -+ int BDB_ByteSwap_Uint4Compare_V6(DB* db, const DBT* dbt1, const DBT* dbt2, -+ size_t*) -+ { return BDB_ByteSwap_Uint4Compare(db, dbt1, dbt2); } -+} -+#endif -+ - void CBDB_LobFile::SetCmp(DB*) - { -+#if DB_VERSION_MAJOR >= 6 -+ BDB_CompareFunction_V6 func = BDB_Uint4Compare_V6; -+ if (IsByteSwapped()) { -+ func = BDB_ByteSwap_Uint4Compare_V6; -+ } -+#else - BDB_CompareFunction func = BDB_Uint4Compare; - if (IsByteSwapped()) { - func = BDB_ByteSwap_Uint4Compare; - } -+#endif - - _ASSERT(func); - int ret = m_DB->set_bt_compare(m_DB, func); -Index: src/db/bdb/bdb_file.cpp -=================================================================== ---- src/db/bdb/bdb_file.cpp (revision 470126) -+++ src/db/bdb/bdb_file.cpp (working copy) -@@ -1535,12 +1535,27 @@ - } - - -+#if DB_VERSION_MAJOR >= 6 -+int CBDB_File::x_CompareShim(DB* db, const DBT* dbt1, const DBT* dbt2, size_t*) -+{ -+ const CBDB_BufferManager* key_buf -+ = static_cast<const CBDB_BufferManager*>(db->app_private); -+ _ASSERT(key_buf); -+ return (key_buf->GetCompareFunction())(db, dbt1, dbt2); -+} -+#endif -+ -+ - void CBDB_File::SetCmp(DB* db) - { - _ASSERT(m_DB_Type == eBtree); -+#if DB_VERSION_MAJOR >= 6 -+ int ret = db->set_bt_compare(db, x_CompareShim); -+#else - BDB_CompareFunction func = m_KeyBuf->GetCompareFunction(); - _ASSERT(func); - int ret = db->set_bt_compare(db, func); -+#endif - BDB_CHECK(ret, 0); - - if (m_PrefixCompress) { -@@ -2056,12 +2071,31 @@ - BindKey("id", &IdKey); - } - -+#if DB_VERSION_MAJOR >= 6 -+extern "C" { -+ typedef int (*BDB_CompareFunction_V6)(DB*, const DBT*, const DBT*, -+ size_t*); -+ int BDB_Int4Compare_V6(DB* db, const DBT* dbt1, const DBT* dbt2, size_t*) -+ { return BDB_Int4Compare(db, dbt1, dbt2); } -+ int BDB_ByteSwap_Int4Compare_V6(DB* db, const DBT* dbt1, const DBT* dbt2, -+ size_t*) -+ { return BDB_ByteSwap_Int4Compare(db, dbt1, dbt2); } -+} -+#endif -+ - void CBDB_IdFile::SetCmp(DB* /* db */) - { -+#if DB_VERSION_MAJOR >= 6 -+ BDB_CompareFunction_V6 func = BDB_Int4Compare_V6; -+ if (IsByteSwapped()) { -+ func = BDB_ByteSwap_Int4Compare_V6; -+ } -+#else - BDB_CompareFunction func = BDB_Int4Compare; - if (IsByteSwapped()) { - func = BDB_ByteSwap_Int4Compare; - } -+#endif - - _ASSERT(func); - int ret = m_DB->set_bt_compare(m_DB, func); diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-conf-opts.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-conf-opts.patch deleted file mode 100644 index 3ed3e7d5f..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-conf-opts.patch +++ /dev/null @@ -1,64 +0,0 @@ - src/build-system/configure.ac | 17 ++++++++++++++--- - 1 file changed, 14 insertions(+), 3 deletions(-) - -diff --git a/src/build-system/configure.ac b/src/build-system/configure.ac -index 03e34b4..336453d 100644 ---- a/src/build-system/configure.ac -+++ b/src/build-system/configure.ac -@@ -224,7 +224,7 @@ AC_ARG_WITH(ncbi-c, - AC_ARG_WITH(sss, - [ --without-sss do not use NCBI SSS libraries]) - AC_ARG_WITH(sssutils, -- [ --without-utils do not use NCBI SSS UTIL library]) -+ [ --without-sssutils do not use NCBI SSS UTIL library]) - AC_ARG_WITH(sssdb, - [ --without-sssdb do not use NCBI SSS DB library]) - AC_ARG_WITH(included-sss, -@@ -490,13 +490,13 @@ check ncbi-public strip pch caution ccache distcc \ - ncbi-c wxwidgets wxwidgets-ucs fastcgi sss sssdb sssutils included-sss \ - geo included-geo \ - z bz2 lzo pcre gcrypt gnutls openssl krb5 sybase sybase-local sybase-new \ --ftds mysql orbacus freetype ftgl opengl mesa glut glew glew-mx \ -+ftds mysql orbacus odbc freetype ftgl opengl mesa glut glew glew-mx \ - bdb python perl jni sqlite3 icu boost boost-tag \ - sp expat sablot libxml libxslt libexslt xerces xalan zorba \ - oechem sge muparser hdf5 \ - gif jpeg tiff png xpm magic curl mimetic 3psw \ - local-lbsm ncbi-crypt connext \ --serial objects dbapi app ctools gui algo internal gbench" -+serial objects dbapi app ctools gui algo internal gbench x" - - changequote(, )dnl - x_with_list=`echo "$x_with_list" | sed 's/\([^ ][^ ]*\)/--with-\1 --without-\1/g'` -@@ -522,6 +522,7 @@ for x_arg in "$@" ; do - case "$x_arg" in - --with-extra-action= | --exec-prefix= | --with-projects= | --srcdir= \ - | --cache-file= | --build= | --host= | --target= | --with-runpath= \ -+ | --mandir= | --infodir= | --datadir= | --sysconfdir= | --localstatedir= \ - | --with-relative-runpath= | --x-includes= | --x-libraries= ) - AC_MSG_ERROR([$x_arg: requires value; use --help to show usage]) - ;; -@@ -532,6 +533,7 @@ for x_arg in "$@" ; do - | --with-universal=* | --with-tcheck=* \ - | --cache-file=* | --build=* | --host=* | --prefix=* | --exec-prefix=* \ - | --libdir=* | --bindir=* | --includedir=* | --srcdir=* \ -+ | --mandir=* | --infodir=* | --datadir=* | --sysconfdir=* | --localstatedir=* \ - | [[A-Z]*=*] \ - | --with-z=* | --with-bz2=* | --with-lzo=* \ - | --with-pcre=* \ -@@ -647,6 +649,15 @@ if test -z "${DEF_FAST_FLAGS}${FAST_CXXFLAGS}"; then - *\ -O* | *\ -xO* ) skip_fast_flags=yes ;; - esac - fi -+if test -n "$with_projects"; then -+ case "$with_projects" in -+ /* ) abs_projects=$with_projects ;; -+ yes) abs_projects=$srcdir/projects ;; -+ * ) abs_projects=$srcdir/$with_projects ;; -+ esac -+ test -r "$abs_projects" || \ -+ AC_MSG_ERROR([unable to read requested projects file "$abs_projects".]) -+fi - - #### Always define this - AC_DEFINE(NCBI_CXX_TOOLKIT, 1, [This is the NCBI C++ Toolkit.]) diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-configure.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-configure.patch deleted file mode 100644 index d44993da2..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-configure.patch +++ /dev/null @@ -1,216 +0,0 @@ ---- ncbi_cxx--12_0_0/src/build-system/configure.ori 2014-06-25 23:47:05.000000000 +0200 -+++ ncbi_cxx--12_0_0/src/build-system/configure 2014-06-25 23:52:35.000000000 +0200 -@@ -927,7 +927,7 @@ - --without-distcc do not automatically use distcc if available - --without-ncbi-c do not use NCBI C Toolkit - --without-sss do not use NCBI SSS libraries -- --without-utils do not use NCBI SSS UTIL library -+ --without-sssutils do not use NCBI SSS UTIL library - --without-sssdb do not use NCBI SSS DB library - --with-included-sss use the in-tree copy of SSS - --with-z=DIR use zlib installation in DIR -@@ -2965,13 +2965,13 @@ - ncbi-c wxwidgets wxwidgets-ucs fastcgi sss sssdb sssutils included-sss \ - geo included-geo \ - z bz2 lzo pcre gcrypt gnutls openssl krb5 sybase sybase-local sybase-new \ --ftds mysql orbacus freetype ftgl opengl mesa glut glew glew-mx \ -+ftds mysql orbacus odbc freetype ftgl opengl mesa glut glew glew-mx \ - bdb python perl jni sqlite3 icu boost boost-tag \ - sp expat sablot libxml libxslt libexslt xerces xalan zorba \ - oechem sge muparser hdf5 \ - gif jpeg tiff png xpm magic curl mimetic 3psw \ - local-lbsm ncbi-crypt connext \ --serial objects dbapi app ctools gui algo internal gbench" -+serial objects dbapi app ctools gui algo internal gbench x" - - x_with_list=`echo "$x_with_list" | sed 's/\([^ ][^ ]*\)/--with-\1 --without-\1/g'` - -@@ -2995,6 +2995,7 @@ - case "$x_arg" in - --with-extra-action= | --exec-prefix= | --with-projects= | --srcdir= \ - | --cache-file= | --build= | --host= | --target= | --with-runpath= \ -+ | --mandir= | --infodir= | --datadir= | --sysconfdir= | --localstatedir= \ - | --with-relative-runpath= | --x-includes= | --x-libraries= ) - { { echo "$as_me:$LINENO: error: $x_arg: requires value; use --help to show usage" >&5 - echo "$as_me: error: $x_arg: requires value; use --help to show usage" >&2;} -@@ -3007,6 +3008,7 @@ - | --with-universal=* | --with-tcheck=* \ - | --cache-file=* | --build=* | --host=* | --prefix=* | --exec-prefix=* \ - | --libdir=* | --bindir=* | --includedir=* | --srcdir=* \ -+ | --mandir=* | --infodir=* | --datadir=* | --sysconfdir=* | --localstatedir=* \ - | [A-Z]*=* \ - | --with-z=* | --with-bz2=* | --with-lzo=* \ - | --with-pcre=* \ -@@ -3201,6 +3203,17 @@ - *\ -O* | *\ -xO* ) skip_fast_flags=yes ;; - esac - fi -+if test -n "$with_projects"; then -+ case "$with_projects" in -+ /* ) abs_projects=$with_projects ;; -+ yes) abs_projects=$srcdir/projects ;; -+ * ) abs_projects=$srcdir/$with_projects ;; -+ esac -+ test -r "$abs_projects" || \ -+ { { echo "$as_me:$LINENO: error: unable to read requested projects file \"$abs_projects\"." >&5 -+echo "$as_me: error: unable to read requested projects file \"$abs_projects\"." >&2;} -+ { (exit 1); exit 1; }; } -+fi - - #### Always define this - -@@ -17878,68 +17891,6 @@ - fi - - --echo "$as_me:$LINENO: checking for std::is_sorted<> in <algorithm>" >&5 --echo $ECHO_N "checking for std::is_sorted<> in <algorithm>... $ECHO_C" >&6 --if test "${ncbi_cv_func_is_sorted+set}" = set; then -- echo $ECHO_N "(cached) $ECHO_C" >&6 --else -- cat >conftest.$ac_ext <<_ACEOF --/* confdefs.h. */ --_ACEOF --cat confdefs.h >>conftest.$ac_ext --cat >>conftest.$ac_ext <<_ACEOF --/* end confdefs.h. */ --#include <algorithm> --int --main () --{ --int a[2]; return std::is_sorted(a, a+2) ? 0 : 1; -- ; -- return 0; --} --_ACEOF --rm -f conftest.$ac_objext --if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 -- (eval $ac_compile) 2>conftest.er1 -- ac_status=$? -- grep -v '^ *+' conftest.er1 >conftest.err -- rm -f conftest.er1 -- cat conftest.err >&5 -- echo "$as_me:$LINENO: \$? = $ac_status" >&5 -- (exit $ac_status); } && -- { ac_try='test -z "$ac_cxx_werror_flag" -- || test ! -s conftest.err' -- { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 -- (eval $ac_try) 2>&5 -- ac_status=$? -- echo "$as_me:$LINENO: \$? = $ac_status" >&5 -- (exit $ac_status); }; } && -- { ac_try='test -s conftest.$ac_objext' -- { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 -- (eval $ac_try) 2>&5 -- ac_status=$? -- echo "$as_me:$LINENO: \$? = $ac_status" >&5 -- (exit $ac_status); }; }; then -- ncbi_cv_func_is_sorted=yes --else -- echo "$as_me: failed program was:" >&5 --sed 's/^/| /' conftest.$ac_ext >&5 -- --ncbi_cv_func_is_sorted=no --fi --rm -f conftest.err conftest.$ac_objext conftest.$ac_ext --fi --echo "$as_me:$LINENO: result: $ncbi_cv_func_is_sorted" >&5 --echo "${ECHO_T}$ncbi_cv_func_is_sorted" >&6 --if test "$ncbi_cv_func_is_sorted" = yes; then -- --cat >>confdefs.h <<\_ACEOF --#define HAVE_IS_SORTED 1 --_ACEOF -- --fi -- -- - - echo "$as_me:$LINENO: checking for SysV semaphores" >&5 - echo $ECHO_N "checking for SysV semaphores... $ECHO_C" >&6 -@@ -18550,7 +18501,7 @@ - echo $ECHO_N "(cached) $ECHO_C" >&6 - else - ncbi_cv_c_restrict=no -- for restrict in restrict __restrict__ __restrict; do -+ for restrict in __restrict__ __restrict restrict; do - test "$ncbi_cv_c_restrict" = "no" || break - cat >conftest.$ac_ext <<_ACEOF - /* confdefs.h. */ -@@ -18620,7 +18571,7 @@ - echo $ECHO_N "(cached) $ECHO_C" >&6 - else - ncbi_cv_cxx_restrict=no -- for restrict in restrict __restrict__ __restrict; do -+ for restrict in __restrict__ __restrict restrict; do - test "$ncbi_cv_cxx_restrict" = "no" || break - cat >conftest.$ac_ext <<_ACEOF - /* confdefs.h. */ -@@ -19046,67 +18997,6 @@ - _ACEOF - - fi -- --echo "$as_me:$LINENO: checking whether $CXX supports C++0x nullptr" >&5 --echo $ECHO_N "checking whether $CXX supports C++0x nullptr... $ECHO_C" >&6 --if test "${ncbi_cv_cxx_nullptr+set}" = set; then -- echo $ECHO_N "(cached) $ECHO_C" >&6 --else -- cat >conftest.$ac_ext <<_ACEOF --/* confdefs.h. */ --_ACEOF --cat confdefs.h >>conftest.$ac_ext --cat >>conftest.$ac_ext <<_ACEOF --/* end confdefs.h. */ -- --int --main () --{ --void * p = nullptr; -- ; -- return 0; --} --_ACEOF --rm -f conftest.$ac_objext --if { (eval echo "$as_me:$LINENO: \"$ac_compile\"") >&5 -- (eval $ac_compile) 2>conftest.er1 -- ac_status=$? -- grep -v '^ *+' conftest.er1 >conftest.err -- rm -f conftest.er1 -- cat conftest.err >&5 -- echo "$as_me:$LINENO: \$? = $ac_status" >&5 -- (exit $ac_status); } && -- { ac_try='test -z "$ac_cxx_werror_flag" -- || test ! -s conftest.err' -- { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 -- (eval $ac_try) 2>&5 -- ac_status=$? -- echo "$as_me:$LINENO: \$? = $ac_status" >&5 -- (exit $ac_status); }; } && -- { ac_try='test -s conftest.$ac_objext' -- { (eval echo "$as_me:$LINENO: \"$ac_try\"") >&5 -- (eval $ac_try) 2>&5 -- ac_status=$? -- echo "$as_me:$LINENO: \$? = $ac_status" >&5 -- (exit $ac_status); }; }; then -- ncbi_cv_cxx_nullptr=yes --else -- echo "$as_me: failed program was:" >&5 --sed 's/^/| /' conftest.$ac_ext >&5 -- --ncbi_cv_cxx_nullptr=no --fi --rm -f conftest.err conftest.$ac_objext conftest.$ac_ext --fi --echo "$as_me:$LINENO: result: $ncbi_cv_cxx_nullptr" >&5 --echo "${ECHO_T}$ncbi_cv_cxx_nullptr" >&6 --if test "$ncbi_cv_cxx_nullptr" = yes; then -- --cat >>confdefs.h <<\_ACEOF --#define HAVE_NULLPTR 1 --_ACEOF -- --fi - - ### Check for the availability of other packages - ### -------------------------------------------- diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-drop-STATIC-from-LIB.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-drop-STATIC-from-LIB.patch deleted file mode 100644 index fad02c38e..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-drop-STATIC-from-LIB.patch +++ /dev/null @@ -1,44 +0,0 @@ ---- ncbi_cxx--12_0_0/src/app/speedtest/Makefile.speedtest.app.ori 2014-06-26 16:46:27.000000000 +0200 -+++ ncbi_cxx--12_0_0/src/app/speedtest/Makefile.speedtest.app 2014-06-26 16:47:26.000000000 +0200 -@@ -9,7 +9,7 @@ - APP = speedtest - SRC = speedtest - LIB = prosplign xalgoalignutil xalgoseq xcleanup taxon1 submit $(BLAST_LIBS) \ -- xqueryparse xregexp $(PCRE_LIB) $(OBJMGR_LIBS:%=%$(STATIC)) -+ xqueryparse xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - - LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(PCRE_LIBS) $(ORIG_LIBS) - ---- ncbi_cxx--12_0_0/src/app/compart/Makefile.compart.app.ori 2014-06-26 16:47:53.000000000 +0200 -+++ ncbi_cxx--12_0_0/src/app/compart/Makefile.compart.app 2014-06-26 16:48:07.000000000 +0200 -@@ -7,7 +7,7 @@ - - LIB = xalgoalignutil xalgoalignsplign xalgoalignnw xalgoseq \ - taxon1 xalnmgr xqueryparse xregexp $(PCRE_LIB) \ -- $(BLAST_LIBS:%=%$(STATIC)) $(OBJMGR_LIBS:%=%$(STATIC)) -+ $(BLAST_LIBS) $(OBJMGR_LIBS) - - LIBS = $(PCRE_LIBS) $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - ---- ncbi_cxx--12_0_0/src/app/igblast/Makefile.igblastp.app.ori 2014-06-26 17:45:11.000000000 +0200 -+++ ncbi_cxx--12_0_0/src/app/igblast/Makefile.igblastp.app 2014-06-26 17:48:26.000000000 +0200 -@@ -3,7 +3,7 @@ - APP = igblastp - SRC = igblastp_app - LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS) --LIB = blast_app_util igblast $(LIB_:%=%$(STATIC)) -+LIB = blast_app_util igblast $(LIB_) - - # De-universalize Mac builds to work around a PPC toolchain limitation - CFLAGS = $(FAST_CFLAGS:ppc=i386) ---- ncbi_cxx--12_0_0/src/app/igblast/Makefile.igblastn.app.ori 2014-06-26 17:47:53.000000000 +0200 -+++ ncbi_cxx--12_0_0/src/app/igblast/Makefile.igblastn.app 2014-06-26 17:49:31.000000000 +0200 -@@ -3,7 +3,7 @@ - APP = igblastn - SRC = igblastn_app - LIB_ = $(BLAST_INPUT_LIBS) xalgoalignutil xqueryparse $(BLAST_LIBS) $(OBJMGR_LIBS) --LIB = blast_app_util igblast $(LIB_:%=%$(STATIC)) -+LIB = blast_app_util igblast $(LIB_) - - # De-universalize Mac builds to work around a PPC toolchain limitation - CFLAGS = $(FAST_CFLAGS:ppc=i386) diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-FreeTDS-upstream.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-FreeTDS-upstream.patch deleted file mode 100644 index fede70e51..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-FreeTDS-upstream.patch +++ /dev/null @@ -1,19 +0,0 @@ ---- src/app/agpconvert/Makefile.agpconvert.app.ori 2013-09-13 23:56:22.660032261 +0200 -+++ src/app/agpconvert/Makefile.agpconvert.app 2013-09-13 23:57:31.340032441 +0200 -@@ -6,13 +6,12 @@ - APP = agpconvert - SRC = agpconvert - --LIB = xalgoseq xobjedit $(OBJREAD_LIBS) taxon1 xalnmgr xobjutil submit \ -- ncbi_xdbapi_ftds $(FTDS_LIB) tables xregexp $(PCRE_LIB) $(OBJMGR_LIBS) --LIBS = $(FTDS_LIBS) $(CMPRS_LIBS) $(PCRE_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) -+LIB = $(OBJREAD_LIBS) taxon1 xregexp $(PCRE_LIB) $(OBJMGR_LIBS) -+LIBS = $(CMPRS_LIBS) $(PCRE_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - - CXXFLAGS = $(FAST_CXXFLAGS) - LDFLAGS = $(FAST_LDFLAGS) - --REQUIRES = objects algo -+REQUIRES = objects - - WATCHERS = xiangcha diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-creaders-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-creaders-linking.patch deleted file mode 100644 index 46c2e83fb..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-creaders-linking.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- src/objtools/alnmgr/demo/Makefile.alnmrg.app.ori 2013-09-13 23:51:34.340031508 +0200 -+++ src/objtools/alnmgr/demo/Makefile.alnmrg.app 2013-09-13 23:51:36.660031514 +0200 -@@ -5,7 +5,7 @@ - SRC = alnmrg - - LIB = xalnmgr $(OBJREAD_LIBS) ncbi_xloader_blastdb seqdb xobjutil submit blastdb \ -- tables $(OBJMGR_LIBS) -+ tables creaders $(OBJMGR_LIBS) - - LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(NETWORK_LIBS) $(ORIG_LIBS) - diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-install.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-install.patch deleted file mode 100644 index 97e845fdb..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-install.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- ncbi_cxx--12_0_0/src/build-system/Makefile.in.top.ori 2014-06-26 22:49:49.000000000 +0200 -+++ ncbi_cxx--12_0_0/src/build-system/Makefile.in.top 2014-06-26 22:50:57.000000000 +0200 -@@ -48,7 +48,7 @@ - for x in *.a; do ln -s "$$x" "`basename \"$$x\" .a`-static.a"; done - cd $(includedir0) && find * -name CVS -prune -o -print |\ - cpio -pd $(pincludedir) -- $(INSTALL) -m 644 $(incdir)/* $(pincludedir) -+ $(INSTALL) -m 644 $(incdir)/*.* $(pincludedir) - ## set up appropriate build and status directories somewhere under $(libdir)? - - install-gbench: diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-svn-URL-upstream.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-svn-URL-upstream.patch deleted file mode 100644 index 8bba91f1d..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-fix-svn-URL-upstream.patch +++ /dev/null @@ -1,10 +0,0 @@ ---- scripts/common/new_project.sh (revision 408264) -+++ scripts/common/new_project.sh (working copy) -@@ -6,7 +6,7 @@ - svn_revision=`echo '$Revision$' | sed "s%\\$[R]evision: *\\([^$][^$]*\\) \\$.*%\\1%"` - def_builddir="$NCBI/c++/Debug/build" - --repository_url='https://svn.ncbi.nlm.nih.gov/repos/toolkit' -+repository_url='http://anonsvn.ncbi.nlm.nih.gov/repos/v1' - tmp_app_checkout_dir='tmp_app_sample' - stem='sample/app' diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linkage-tuneups-addons.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linkage-tuneups-addons.patch deleted file mode 100644 index 553e41d29..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linkage-tuneups-addons.patch +++ /dev/null @@ -1,13 +0,0 @@ ---- ncbi_cxx--12_0_0/src/app/agpconvert/Makefile.agpconvert.app.ori (revision 439078) -+++ ncbi_cxx--12_0_0/src/app/agpconvert/Makefile.agpconvert.app (working copy) -@@ -7,8 +7,8 @@ - SRC = agpconvert - - LIB = xalgoseq xobjedit $(OBJREAD_LIBS) taxon1 xalnmgr xobjutil submit \ -- ncbi_xdbapi_ftds $(FTDS_LIB) tables xregexp $(PCRE_LIB) $(OBJMGR_LIBS) --LIBS = $(FTDS_LIBS) $(CMPRS_LIBS) $(PCRE_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) -+ tables xregexp $(PCRE_LIB) $(OBJMGR_LIBS) -+LIBS = $(CMPRS_LIBS) $(PCRE_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - - CXXFLAGS = $(FAST_CXXFLAGS) - LDFLAGS = $(FAST_LDFLAGS) diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linkage-tuneups.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linkage-tuneups.patch deleted file mode 100644 index 86e96b865..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-linkage-tuneups.patch +++ /dev/null @@ -1,421 +0,0 @@ -Index: src/algo/blast/format/Makefile.xblastformat.lib -=================================================================== ---- src/algo/blast/format/Makefile.xblastformat.lib (revision 439078) -+++ src/algo/blast/format/Makefile.xblastformat.lib (working copy) -@@ -7,6 +7,6 @@ - - CPPFLAGS = -DNCBI_MODULE=BLASTFORMAT $(ORIG_CPPFLAGS) - --DLL_LIB = align_format blastxml xhtml xcgi -+DLL_LIB = align_format xblast xnetblast blastxml xhtml xcgi - - WATCHERS = jianye zaretska madden camacho fongah2 -Index: src/app/compart/Makefile.compart.app -=================================================================== ---- src/app/compart/Makefile.compart.app (revision 439078) -+++ src/app/compart/Makefile.compart.app (working copy) -@@ -5,11 +5,11 @@ - APP = compart - SRC = compart - --LIB = xalgoalignutil xalgoalignsplign xalgoalignnw xqueryparse xalnmgr \ -- $(BLAST_LIBS:%=%$(STATIC)) \ -- $(OBJMGR_LIBS:%=%$(STATIC)) -+LIB = xalgoalignutil xalgoalignsplign xalgoalignnw xalgoseq \ -+ taxon1 xalnmgr xqueryparse xregexp $(PCRE_LIB) \ -+ $(BLAST_LIBS:%=%$(STATIC)) $(OBJMGR_LIBS:%=%$(STATIC)) - --LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) -+LIBS = $(PCRE_LIBS) $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - - CXXFLAGS = $(FAST_CXXFLAGS) - LDFLAGS = $(FAST_LDFLAGS) -Index: src/app/compart/Makefile.compartp.app -=================================================================== ---- src/app/compart/Makefile.compartp.app (revision 439078) -+++ src/app/compart/Makefile.compartp.app (working copy) -@@ -5,7 +5,8 @@ - APP = compartp - SRC = compartp - --LIB = prosplign xalgoalignutil $(BLAST_LIBS) xqueryparse $(OBJMGR_LIBS) -+LIB = prosplign xalgoalignutil xalgoseq taxon1 $(BLAST_LIBS) \ -+ xqueryparse xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - - LIBS = $(CMPRS_LIBS) $(PCRE_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - -Index: src/app/grid/util/Makefile.ncfetch.app -=================================================================== ---- src/app/grid/util/Makefile.ncfetch.app (revision 439078) -+++ src/app/grid/util/Makefile.ncfetch.app (working copy) -@@ -5,7 +5,7 @@ - APP = ncfetch.cgi - SRC = ncfetch - --LIB = xcgi xconnserv xconnect xutil xncbi -+LIB = xcgi xconnserv xthrserv xconnect xutil xncbi - LIBS = $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - - WATCHERS = kazimird -Index: src/app/hfilter/Makefile.hfilter.app -=================================================================== ---- src/app/hfilter/Makefile.hfilter.app (revision 439078) -+++ src/app/hfilter/Makefile.hfilter.app (working copy) -@@ -5,9 +5,10 @@ - APP = hfilter - SRC = hitfilter_app - --LIB = xalgoalignutil $(BLAST_LIBS) xqueryparse $(OBJMGR_LIBS) -+LIB = xalgoalignutil xalgoseq taxon1 $(BLAST_LIBS) xqueryparse \ -+ xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - --LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) -+LIBS = $(PCRE_LIBS) $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - - CXXFLAGS = $(FAST_CXXFLAGS) - LDFLAGS = $(FAST_LDFLAGS) -Index: src/app/speedtest/Makefile.speedtest.app -=================================================================== ---- src/app/speedtest/Makefile.speedtest.app (revision 439078) -+++ src/app/speedtest/Makefile.speedtest.app (working copy) -@@ -8,7 +8,7 @@ - - APP = speedtest - SRC = speedtest --LIB = prosplign xalgoalignutil xcleanup submit $(BLAST_LIBS) \ -+LIB = prosplign xalgoalignutil xalgoseq xcleanup taxon1 submit $(BLAST_LIBS) \ - xqueryparse xregexp $(PCRE_LIB) $(OBJMGR_LIBS:%=%$(STATIC)) - - LIBS = $(CMPRS_LIBS) $(DL_LIBS) $(PCRE_LIBS) $(ORIG_LIBS) -Index: src/app/splign/Makefile.splign.app -=================================================================== ---- src/app/splign/Makefile.splign.app (revision 439078) -+++ src/app/splign/Makefile.splign.app (working copy) -@@ -12,7 +12,7 @@ - LIB = xalgoalignsplign xalgoalignutil xalgoalignnw \ - $(BLAST_DB_DATA_LOADER_LIBS) \ - ncbi_xloader_lds2 lds2 sqlitewrapp \ -- xqueryparse xalgoseq $(PCRE_LIB) \ -+ xqueryparse xalgoseq taxon1 xregexp $(PCRE_LIB) \ - $(BLAST_LIBS:%=%$(STATIC)) submit \ - $(OBJMGR_LIBS:%=%$(STATIC)) - -Index: src/connect/services/test/Makefile.test_nsstorage.app -=================================================================== ---- src/connect/services/test/Makefile.test_nsstorage.app (revision 439078) -+++ src/connect/services/test/Makefile.test_nsstorage.app (working copy) -@@ -2,7 +2,7 @@ - - APP = test_nsstorage - SRC = test_nsstorage --LIB = xconnserv xconnect xutil xncbi -+LIB = xconnserv xthrserv xconnect xutil xncbi - - LIBS = $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - -Index: src/misc/hgvs/test/Makefile.hgvs2variation.app -=================================================================== ---- src/misc/hgvs/test/Makefile.hgvs2variation.app (revision 439078) -+++ src/misc/hgvs/test/Makefile.hgvs2variation.app (working copy) -@@ -6,7 +6,7 @@ - - CPPFLAGS = $(ORIG_CPPFLAGS) $(BOOST_INCLUDE) - --LIB_ = hgvs variation \ -+LIB_ = hgvs objcoords variation \ - entrez2cli entrez2 xregexp $(PCRE_LIB) xobjutil $(OBJMGR_LIBS) - LIB = $(LIB_:%=%$(STATIC)) - -Index: src/misc/hgvs/test/Makefile.test_hgvs_parser.app -=================================================================== ---- src/misc/hgvs/test/Makefile.test_hgvs_parser.app (revision 439078) -+++ src/misc/hgvs/test/Makefile.test_hgvs_parser.app (working copy) -@@ -5,7 +5,7 @@ - - CPPFLAGS = $(ORIG_CPPFLAGS) $(BOOST_INCLUDE) - --LIB_ = hgvs variation test_boost xregexp $(PCRE_LIB) xobjutil \ -+LIB_ = hgvs objcoords variation test_boost xregexp $(PCRE_LIB) xobjutil \ - entrez2cli entrez2 $(OBJMGR_LIBS) - - LIB = $(LIB_:%=%$(STATIC)) -Index: src/objects/biblio/Makefile.biblio.lib -=================================================================== ---- src/objects/biblio/Makefile.biblio.lib (revision 439078) -+++ src/objects/biblio/Makefile.biblio.lib (working copy) -@@ -1,2 +1,4 @@ - LIB = biblio - SRC = biblio__ biblio___ citation_base -+ -+DLL_LIB = general -Index: src/objects/blast/Makefile.blast.lib -=================================================================== ---- src/objects/blast/Makefile.blast.lib (revision 439078) -+++ src/objects/blast/Makefile.blast.lib (working copy) -@@ -1,4 +1,6 @@ - LIB = xnetblast - SRC = blast__ blast___ names - -+DLL_LIB = scoremat seqset -+ - WATCHERS = camacho -Index: src/objects/blast/Makefile.xnetblastcli.lib -=================================================================== ---- src/objects/blast/Makefile.xnetblastcli.lib (revision 439078) -+++ src/objects/blast/Makefile.xnetblastcli.lib (working copy) -@@ -2,3 +2,5 @@ - - LIB = xnetblastcli - SRC = blastclient blastclient_ -+ -+DLL_LIB = xnetblast xconnect -Index: src/objects/blastdb/Makefile.blastdb.lib -=================================================================== ---- src/objects/blastdb/Makefile.blastdb.lib (revision 439078) -+++ src/objects/blastdb/Makefile.blastdb.lib (working copy) -@@ -1,2 +1,4 @@ - LIB = blastdb - SRC = blastdb__ blastdb___ -+ -+DLL_LIB = seq -Index: src/objects/general/Makefile.general.lib -=================================================================== ---- src/objects/general/Makefile.general.lib (revision 439078) -+++ src/objects/general/Makefile.general.lib (working copy) -@@ -1,2 +1,4 @@ - LIB = general - SRC = general__ general___ uoconv -+ -+DLL_LIB = xser -Index: src/objects/medline/Makefile.medline.lib -=================================================================== ---- src/objects/medline/Makefile.medline.lib (revision 439078) -+++ src/objects/medline/Makefile.medline.lib (working copy) -@@ -1,2 +1,4 @@ - LIB = medline - SRC = medline__ medline___ -+ -+DLL_LIB = biblio general -Index: src/objects/pub/Makefile.pub.lib -=================================================================== ---- src/objects/pub/Makefile.pub.lib (revision 439078) -+++ src/objects/pub/Makefile.pub.lib (working copy) -@@ -1,2 +1,4 @@ - LIB = pub - SRC = pub__ pub___ -+ -+DLL_LIB = medline biblio -Index: src/objects/scoremat/Makefile.scoremat.lib -=================================================================== ---- src/objects/scoremat/Makefile.scoremat.lib (revision 439078) -+++ src/objects/scoremat/Makefile.scoremat.lib (working copy) -@@ -1,2 +1,4 @@ - LIB = scoremat - SRC = scoremat__ scoremat___ -+ -+DLL_LIB = seqset -Index: src/objects/seq/Makefile.seq.lib -=================================================================== ---- src/objects/seq/Makefile.seq.lib (revision 439078) -+++ src/objects/seq/Makefile.seq.lib (working copy) -@@ -13,3 +13,5 @@ - seq_loc_from_string seq_loc_reverse_complementer - - WATCHERS = vasilche grichenk -+ -+DLL_LIB = seqcode pub biblio general xser sequtil -Index: src/objects/seqset/Makefile.seqset.lib -=================================================================== ---- src/objects/seqset/Makefile.seqset.lib (revision 439078) -+++ src/objects/seqset/Makefile.seqset.lib (working copy) -@@ -1,2 +1,4 @@ - LIB = seqset - SRC = seqset__ seqset___ gb_release_file -+ -+DLL_LIB = xser -Index: src/objects/taxon1/Makefile.taxon1.lib -=================================================================== ---- src/objects/taxon1/Makefile.taxon1.lib (revision 439078) -+++ src/objects/taxon1/Makefile.taxon1.lib (working copy) -@@ -3,4 +3,6 @@ - LIB = taxon1 - SRC = taxon1__ taxon1___ taxon1 cache utils ctreecont - -+DLL_LIB = xconnect -+ - WATCHERS = domrach -Index: src/objmgr/util/Makefile.util.lib -=================================================================== ---- src/objmgr/util/Makefile.util.lib (revision 439078) -+++ src/objmgr/util/Makefile.util.lib (working copy) -@@ -8,5 +8,7 @@ - SRC = weight sequence feature seqtitle create_defline obj_sniff seq_loc_util seq_align_util - LIB = xobjutil - -+DLL_LIB = xobjmgr -+ - WATCHERS = ucko vasilche - -Index: src/objtools/blast/seqdb_reader/Makefile.seqdb.lib -=================================================================== ---- src/objtools/blast/seqdb_reader/Makefile.seqdb.lib (revision 439078) -+++ src/objtools/blast/seqdb_reader/Makefile.seqdb.lib (working copy) -@@ -29,4 +29,6 @@ - CXXFLAGS = $(FAST_CXXFLAGS) - LDFLAGS = $(FAST_LDFLAGS) - -+DLL_LIB = xobjmgr blastdb -+ - WATCHERS = maning camacho -Index: src/objtools/blast/services/Makefile.blast_services.lib -=================================================================== ---- src/objtools/blast/services/Makefile.blast_services.lib (revision 439078) -+++ src/objtools/blast/services/Makefile.blast_services.lib (working copy) -@@ -13,3 +13,4 @@ - CXXFLAGS = $(FAST_CXXFLAGS) - LDFLAGS = $(FAST_LDFLAGS) - -+DLL_LIB = xnetblastcli xconnect -Index: src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib -=================================================================== ---- src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib (revision 439078) -+++ src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb.lib (working copy) -@@ -7,4 +7,6 @@ - - ASN_DEP = blastdb seqset - -+DLL_LIB = seqdb -+ - WATCHERS = camacho -Index: src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib -=================================================================== ---- src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib (revision 439078) -+++ src/objtools/data_loaders/blastdb/Makefile.ncbi_xloader_blastdb_rmt.lib (working copy) -@@ -7,4 +7,6 @@ - - ASN_DEP = blastdb xnetblast - -+DLL_LIB = blast_services -+ - WATCHERS = camacho -Index: src/objtools/lds2/Makefile.lds2.lib -=================================================================== ---- src/objtools/lds2/Makefile.lds2.lib (revision 439078) -+++ src/objtools/lds2/Makefile.lds2.lib (working copy) -@@ -8,9 +8,9 @@ - SRC = lds2 lds2_db lds2_handlers - - # Dependencies for shared library --#DLL_LIB = sqlitewrapp -+DLL_LIB = sqlitewrapp $(COMPRESS_LIBS) - --LIBS = $(CMPRS_LIBS) $(ORIG_LIBS) -+LIBS = $(SQLITE3_LIBS) $(CMPRS_LIBS) $(ORIG_LIBS) - - CPPFLAGS = $(SQLITE3_INCLUDE) $(CMPRS_INCLUDE) $(ORIG_CPPFLAGS) - -Index: src/objtools/readers/Makefile.xobjread.lib -=================================================================== ---- src/objtools/readers/Makefile.xobjread.lib (revision 439078) -+++ src/objtools/readers/Makefile.xobjread.lib (working copy) -@@ -19,5 +19,6 @@ - best_feat_finder source_mod_parser fasta_exception - - --DLL_LIB = creaders -+DLL_LIB = seqset $(SEQ_LIBS) pub general creaders xutil - -+ -Index: src/sample/app/cgi/Makefile.cgi_session_sample.app -=================================================================== ---- src/sample/app/cgi/Makefile.cgi_session_sample.app (revision 439078) -+++ src/sample/app/cgi/Makefile.cgi_session_sample.app (working copy) -@@ -11,7 +11,7 @@ - # the lines reading "### BEGIN/END COPIED SETTINGS" in any way. - - ### BEGIN COPIED SETTINGS --LIB = xgridcgi xcgi xhtml xconnserv xconnect xutil xncbi -+LIB = xgridcgi xcgi xhtml xconnserv xthrserv xconnect xutil xncbi - - LIBS = $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - -Index: src/sample/app/netcache/Makefile.netcache_cgi_sample.app -=================================================================== ---- src/sample/app/netcache/Makefile.netcache_cgi_sample.app (revision 439078) -+++ src/sample/app/netcache/Makefile.netcache_cgi_sample.app (working copy) -@@ -4,7 +4,7 @@ - SRC = netcache_cgi_sample - - ### BEGIN COPIED SETTINGS --LIB = xconnserv xconnect xcgi xhtml xutil xncbi -+LIB = xconnserv xthrserv xconnect xcgi xhtml xutil xncbi - - LIBS = $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - ### END COPIED SETTINGS -Index: src/serial/Makefile.serial.lib -=================================================================== ---- src/serial/Makefile.serial.lib (revision 439078) -+++ src/serial/Makefile.serial.lib (working copy) -@@ -19,3 +19,5 @@ - LIB = xser - - WATCHERS = gouriano -+ -+DLL_LIB = xutil xncbi -Index: src/sra/data_loaders/bam/test/Makefile.test_bam_loader.app -=================================================================== ---- src/sra/data_loaders/bam/test/Makefile.test_bam_loader.app (revision 439078) -+++ src/sra/data_loaders/bam/test/Makefile.test_bam_loader.app (working copy) -@@ -7,7 +7,8 @@ - - CPPFLAGS = $(ORIG_CPPFLAGS) $(BOOST_INCLUDE) - --LIB = ncbi_xloader_bam bamread $(BAM_LIBS) xobjreadex xobjutil test_boost $(OBJMGR_LIBS) -+LIB = ncbi_xloader_bam bamread $(BAM_LIBS) \ -+ xobjreadex $(OBJREAD_LIBS) xobjutil test_boost $(OBJMGR_LIBS) - - LIBS = $(SRA_SDK_SYSLIBS) $(CMPRS_LIBS) $(NETWORK_LIBS) $(ORIG_LIBS) - -Index: src/sra/data_loaders/csra/test/Makefile.test_csra_loader.app -=================================================================== ---- src/sra/data_loaders/csra/test/Makefile.test_csra_loader.app (revision 439078) -+++ src/sra/data_loaders/csra/test/Makefile.test_csra_loader.app (working copy) -@@ -5,7 +5,8 @@ - - CPPFLAGS = $(ORIG_CPPFLAGS) $(BOOST_INCLUDE) - --LIB = ncbi_xloader_csra $(SRAREAD_LIBS) xobjreadex xobjutil test_boost $(OBJMGR_LIBS) -+LIB = ncbi_xloader_csra $(SRAREAD_LIBS) xobjreadex $(OBJREAD_LIBS) xobjutil \ -+ test_boost $(OBJMGR_LIBS) - - LIBS = $(SRA_SDK_SYSLIBS) $(CMPRS_LIBS) $(NETWORK_LIBS) $(ORIG_LIBS) - -Index: src/sra/readers/bam/test/Makefile.bam_test.app -=================================================================== ---- src/sra/readers/bam/test/Makefile.bam_test.app (revision 439078) -+++ src/sra/readers/bam/test/Makefile.bam_test.app (working copy) -@@ -9,7 +9,8 @@ - APP = bam_test - SRC = bam_test - --LIB = bamread xobjreadex xobjutil xobjsimple $(OBJMGR_LIBS) $(BAM_LIBS) -+LIB = bamread $(BAM_LIBS) xobjreadex $(OBJREAD_LIBS) xobjutil xobjsimple \ -+ $(OBJMGR_LIBS) - LIBS = $(SRA_SDK_SYSLIBS) $(CMPRS_LIBS) $(NETWORK_LIBS) $(ORIG_LIBS) - - REQUIRES = objects -Index: src/sra/sdk/libs/vfs/Makefile.vfs.lib -=================================================================== ---- src/sra/sdk/libs/vfs/Makefile.vfs.lib (revision 16076) -+++ src/sra/sdk/libs/vfs/Makefile.vfs.lib (working copy) -@@ -8,6 +8,9 @@ - CPPFLAGS = -I$(srcdir) $(SRA_INCLUDE) $(Z_INCLUDE) $(BZ2_INCLUDE) \ - $(SRA_INTERNAL_CPPFLAGS) -D_LIBRARY -DALWAYS_ADD_EXE $(ORIG_CPPFLAGS) - --DLL_LIB = srapath$(DLL) kurl$(DLL) krypto$(DLL) kfg$(DLL) kfs$(DLL) klib$(DLL) -+DLL_LIB = srapath$(FORCE_STATIC) kurl$(FORCE_STATIC) \ -+ krypto$(DLL) kfg$(DLL) kfs$(DLL) klib$(DLL) - -+LIBS = $(SRA_SDK_SYSLIBS) -+ - LIB_OR_DLL = both diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-more-patches.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-more-patches.patch deleted file mode 100644 index 449bbc5a9..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-more-patches.patch +++ /dev/null @@ -1,136 +0,0 @@ ---- ncbi_cxx--12_0_0/include/common/config/ncbiconf_msvc.h.ori 2013/09/30 13:46:04 59961 -+++ ncbi_cxx--12_0_0/include/common/config/ncbiconf_msvc.h 2013/09/30 14:10:44 59962 -@@ -62,10 +62,6 @@ - #define HAVE_SYS_TYPES_H 1 - #define HAVE_VSNPRINTF 1 - --#if _MSC_VER >= 1600 --# define HAVE_IS_SORTED 1 --#endif -- - #if _MSC_VER < 1500 - # define vsnprintf _vsnprintf - #endif -@@ -136,10 +132,6 @@ - - #endif - --#if _MSC_VER >= 1600 --# define HAVE_NULLPTR 1 --#endif -- - /* Windows XP and above */ - #define NCBI_WIN32_WINNT 0x0501 - #if !defined(_WIN32_WINNT) ---- ncbi_cxx--12_0_0/include/common/config/ncbiconf_xcode.h.ori 2013/09/30 13:46:04 59961 -+++ ncbi_cxx--12_0_0/include/common/config/ncbiconf_xcode.h 2013/09/30 14:10:44 59962 -@@ -258,9 +258,6 @@ - /* Define to 1 if you have `ios(_base)::register_callback'. */ - #define HAVE_IOS_REGISTER_CALLBACK 1 - --/* Define to 1 if <algorithm> supplies `std::is_sorted<>'. */ --/* #undef HAVE_IS_SORTED */ -- - /* Define to 1 if you have the `lchown' function. */ - /* #undef HAVE_LCHOWN */ - -@@ -595,9 +592,6 @@ - /* Define to 1 if wxWidgets is available. */ - /* #undef HAVE_WXWIDGETS */ - --/* Define to 1 if nullptr keyword is available. */ --/* #undef HAVE_NULLPTR */ -- - /* Define as const if the declaration of iconv() needs const. */ - #if MAC_OS_X_VERSION_MIN_REQUIRED >= 1050 /* MAC_OS_X_VERSION_10_5 */ - # define ICONV_CONST ---- ncbi_cxx--12_0_0/include/common/ncbiconf_impl.h.ori 2013/09/30 13:46:04 59961 -+++ ncbi_cxx--12_0_0/include/common/ncbiconf_impl.h 2013/09/30 14:10:44 59962 -@@ -115,6 +115,11 @@ - || defined(__GXX_EXPERIMENTAL_CPP0X__) - # define NCBI_HAVE_CXX11 1 - # endif -+# if defined(NCBI_HAVE_CXX11) \ -+ || (defined(NCBI_COMPILER_MSVC) && _MSC_VER >= 1600) -+# define HAVE_IS_SORTED 1 -+# define HAVE_NULLPTR 1 -+# endif - #endif - - #include <common/ncbi_skew_guard.h> ---- ncbi_cxx--12_0_0/src/build-system/config.h.in.ori 2013/09/30 13:46:04 59961 -+++ ncbi_cxx--12_0_0/src/build-system/config.h.in 2013/09/30 14:10:44 59962 -@@ -179,9 +179,6 @@ - /* Define to 1 if you have `ios(_base)::register_callback'. */ - #undef HAVE_IOS_REGISTER_CALLBACK - --/* Define to 1 if <algorithm> supplies `std::is_sorted<>'. */ --#undef HAVE_IS_SORTED -- - /* Define to 1 if you have the `lchown' function. */ - #undef HAVE_LCHOWN - -@@ -391,9 +388,6 @@ - /* Define to 1 if `min'/`max' templates are not implemented. */ - #undef HAVE_NO_MINMAX_TEMPLATE - --/* Define to 1 if your C++ compiler supports the C++0x `nullptr' keyword. */ --#undef HAVE_NULLPTR -- - /* Define to 1 if ODBC libraries are available. */ - #undef HAVE_ODBC - ---- ncbi_cxx--12_0_0/src/build-system/configure.ac.ori 2013/09/30 13:46:04 59961 -+++ ncbi_cxx--12_0_0/src/build-system/configure.ac 2013/09/30 14:10:44 59962 -@@ -3351,17 +3351,6 @@ - fi - - --AC_CACHE_CHECK([for std::is_sorted<> in <algorithm>], ncbi_cv_func_is_sorted, -- [AC_COMPILE_IFELSE([AC_LANG_PROGRAM( -- [[#include <algorithm>]], -- [[int a[2]; return std::is_sorted(a, a+2) ? 0 : 1;]])], -- [ncbi_cv_func_is_sorted=yes], [ncbi_cv_func_is_sorted=no])]) --if test "$ncbi_cv_func_is_sorted" = yes; then -- AC_DEFINE(HAVE_IS_SORTED, 1, -- [Define to 1 if <algorithm> supplies `std::is_sorted<>'.]) --fi -- -- - - AC_CACHE_CHECK([for SysV semaphores], ncbi_cv_sys_semaphores, - AC_LINK_IFELSE([AC_LANG_PROGRAM([#include <sys/types.h> -@@ -3498,7 +3487,7 @@ - AC_CACHE_CHECK([whether the C compiler supports C99 restrict], - ncbi_cv_c_restrict, - [ncbi_cv_c_restrict=no -- for restrict in restrict __restrict__ __restrict; do -+ for restrict in __restrict__ __restrict restrict; do - test "$ncbi_cv_c_restrict" = "no" || break - AC_COMPILE_IFELSE([AC_LANG_SOURCE([void f(int * $restrict p);])], - [ncbi_cv_c_restrict=$restrict], []) -@@ -3518,7 +3507,7 @@ - AC_CACHE_CHECK([whether the C++ compiler supports C99 restrict], - ncbi_cv_cxx_restrict, - [ncbi_cv_cxx_restrict=no -- for restrict in restrict __restrict__ __restrict; do -+ for restrict in __restrict__ __restrict restrict; do - test "$ncbi_cv_cxx_restrict" = "no" || break - AC_COMPILE_IFELSE([AC_LANG_SOURCE([void f(int * $restrict p);])], - [ncbi_cv_cxx_restrict=$restrict], []) -@@ -3623,14 +3612,6 @@ - unaligned addresses.]) - fi - --AC_CACHE_CHECK([whether $CXX supports C++0x nullptr], ncbi_cv_cxx_nullptr, -- [AC_COMPILE_IFELSE([AC_LANG_PROGRAM([], [[void * p = nullptr;]])], -- [ncbi_cv_cxx_nullptr=yes], [ncbi_cv_cxx_nullptr=no])]) --if test "$ncbi_cv_cxx_nullptr" = yes; then -- AC_DEFINE(HAVE_NULLPTR, 1, -- [Define to 1 if your C++ compiler supports the C++0x `nullptr' keyword.]) --fi -- - ### Check for the availability of other packages - ### -------------------------------------------- - - diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-never_build_test_boost.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-never_build_test_boost.patch deleted file mode 100644 index 68baea046..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-never_build_test_boost.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- ncbi_cxx--12_0_0/src/corelib/Makefile.in.ori 2016-12-01 20:28:33.239758102 +0100 -+++ ncbi_cxx--12_0_0/src/corelib/Makefile.in 2016-12-01 20:28:46.330110659 +0100 -@@ -7,7 +7,7 @@ - ################################# - - USR_PROJ = precompile --LIB_PROJ = corelib test_mt test_boost -+LIB_PROJ = corelib test_mt - SUB_PROJ = test - PROJ_TAG = core - diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-support-autoconf-2.60.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-support-autoconf-2.60.patch deleted file mode 100644 index 9047c3384..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-12.0.0-support-autoconf-2.60.patch +++ /dev/null @@ -1,296 +0,0 @@ ---- ncbi_cxx--12_0_0/src/build-system/aclocal.m4.ori 2014/05/05 12:38:59 62744 -+++ ncbi_cxx--12_0_0/src/build-system/aclocal.m4 2014/05/05 13:59:33 62745 -@@ -1,126 +1,44 @@ --# Hacked up in various ways, since Autoconf's version doesn't quite --# suit our (unusual) conventions. (Originally from status.m4) --m4_define([_AC_SRCPATHS], --[#ac_builddir=. # Useless! --ac_builddir=$builddir --dnl Base source directories on path to *input* file. --if test -n "$ac_file_in"; then -- ac_dir_in=`AS_DIRNAME(["$ac_file_in"])` -+# Autoconf's _AC_SRCDIRS (from status.m4; historically _AC_SRCPATHS) -+# doesn't quite suit the C++ Toolkit's conventions; tweak it accordingly. -+m4_copy([_AC_SRCDIRS], [NCBI_ORIG__AC_SRCDIRS]) -+m4_define([_AC_SRCDIRS], -+[# Base source directories on path to *input* file. -+if test -n "$ac_f"; then -+ ac_dir_in=`AS_DIRNAME(["$ac_f"])` - else - ac_dir_in=$1 - fi - --if test $ac_dir_in != .; then -- ac_dir_suffix=`echo $ac_dir_in | sed 's,^\.[[\\/]],,'` -- # A "../" for each directory in $ac_dir_suffix. -- ac_top_builddir=../`echo "$ac_dir_suffix" | sed 's,/[[^\\/]]*,../,g'` --else -- ac_dir_suffix= ac_top_builddir= --fi -+NCBI_ORIG__AC_SRCDIRS(["$ac_dir_in"]) - --case $srcdir in -- .) # No --srcdir option. We are building in place. -- ac_srcdir=. -- if test -z "$ac_top_builddir"; then -- ac_top_srcdir=. -- else -- ac_top_srcdir=`echo $ac_top_builddir | sed 's,/$,,'` -- fi ;; -- [[\\/]]* | ?:[[\\/]]* ) # Absolute path. -- ac_srcdir=$srcdir/$ac_dir_suffix; -- ac_top_srcdir=$srcdir ;; -- *) # Relative path. -- ac_srcdir=$ac_top_builddir$srcdir/$ac_dir_suffix -- ac_top_srcdir=$ac_top_builddir$srcdir ;; --esac --# Do not use `cd foo && pwd` to compute absolute paths, because --# the directories may not exist. --AS_SET_CATFILE([ac_abs_builddir], [$builddir], [$1]) --AS_SET_CATFILE([ac_abs_top_builddir], -- [$ac_abs_builddir], [${ac_top_builddir}.]) --AS_SET_CATFILE([ac_abs_top_srcdir], [$ac_dir_in], [$real_srcdir]) --AS_SET_CATFILE([ac_abs_srcdir], [$ac_abs_top_srcdir], [$ac_dir_suffix]) --])# _AC_SRCPATHS -- -- --# Copied from autoconf 2.59 (m4sh.m4), but rearranged to make bash a --# last resort due to issues with sourcing .bashrc. --m4_define([_AS_LINENO_PREPARE], --[_AS_LINENO_WORKS || { -- # Find who we are. Look in the path if we contain no path at all -- # relative or not. -- case $[0] in -- *[[\\/]]* ) as_myself=$[0] ;; -- *) _AS_PATH_WALK([], -- [test -r "$as_dir/$[0]" && as_myself=$as_dir/$[0] && break]) -- ;; -- esac -- # We did not find ourselves, most probably we were run as `sh COMMAND' -- # in which case we are not to be found in the path. -- if test "x$as_myself" = x; then -- as_myself=$[0] -- fi -- if test ! -f "$as_myself"; then -- AS_ERROR([cannot find myself; rerun with an absolute path]) -- fi -- case $CONFIG_SHELL in -- '') -- AS_UNSET(ZSH_VERSION) -- for as_base in sh ksh sh5 bash; do -- _AS_PATH_WALK([/bin$PATH_SEPARATOR/usr/bin$PATH_SEPARATOR$PATH], -- [case $as_dir in -- /*) -- if ("$as_dir/$as_base" -c \ -- 'test -z "$ZSH_VERSION" && { _AS_LINENO_WORKS; }') 2>/dev/null -- then -- AS_UNSET(BASH_ENV) -- AS_UNSET(ENV) -- CONFIG_SHELL=$as_dir/$as_base -- export CONFIG_SHELL -- exec "$CONFIG_SHELL" "$[0]" ${1+"$[@]"} -- fi;; -- esac -- done]);; -- esac -- -- # Create $as_me.lineno as a copy of $as_myself, but with $LINENO -- # uniformly replaced by the line number. The first 'sed' inserts a -- # line-number line before each line; the second 'sed' does the real -- # work. The second script uses 'N' to pair each line-number line -- # with the numbered line, and appends trailing '-' during -- # substitution so that $LINENO is not a special case at line end. -- # (Raja R Harinath suggested sed '=', and Paul Eggert wrote the -- # second 'sed' script. Blame Lee E. McMahon for sed's syntax. :-) -- sed '=' <$as_myself | -- sed ' -- N -- s,$,-, -- : loop -- s,^\([['$as_cr_digits']]*\)\(.*\)[[$]]LINENO\([[^'$as_cr_alnum'_]]\),\1\2\1\3, -- t loop -- s,-$,, -- s,^[['$as_cr_digits']]*\n,, -- ' >$as_me.lineno && -- chmod +x $as_me.lineno || -- AS_ERROR([cannot create $as_me.lineno; rerun with a POSIX shell]) -- -- # Don't try to exec as it changes $[0], causing all sort of problems -- # (the dirname of $[0] is not the place where we might find the -- # original and so on. Autoconf is especially sensible to this). -- . ./$as_me.lineno -- # Exit status is that of the last command. -- exit --} --])# _AS_LINENO_PREPARE -+ac_builddir=$builddir -+]) -+ -+ -+# _AS_DETECT_BETTER_SHELL and its helper _AS_RUN (from m4sh.m4; both -+# historically part of _AS_LINENO_PREPARE) also need tweaking, to make -+# bash a last resort due to issues with sourcing .bashrc while entirely -+# avoiding zsh, which passes itself off as ksh on some systems but runs -+# parent shells' exit handlers from subshells, resulting in premature -+# cleanup of temporary files (notably confdefs.h). -+m4_copy([_AS_DETECT_BETTER_SHELL], [NCBI_ORIG__AS_DETECT_BETTER_SHELL]) -+m4_copy([_AS_RUN], [NCBI_ORIG___AS_RUN]) -+ -+m4_define([_AS_DETECT_BETTER_SHELL], -+ [patsubst(m4_defn([NCBI_ORIG__AS_DETECT_BETTER_SHELL]), -+ [sh bash ksh sh5], [sh ksh sh5 bash])]) -+m4_define([_AS_RUN], -+[m4_divert_once([M4SH-SANITIZE], [AS_UNSET(ZSH_VERSION)])dnl -+NCBI_ORIG___AS_RUN([test -z "${ZSH_VERSION+set}" || exit $?; $1], [$2])]) - - - # One more hack: suppress PACKAGE_*, as we don't use them and some - # third-party libraries expose their corresponding settings, leading - # to preprocessor warnings. --m4_define([NCBI_ORIG_ACDU], m4_defn([AC_DEFINE_UNQUOTED])) -+m4_copy([AC_DEFINE_UNQUOTED], [NCBI_ORIG_AC_DEFINE_UNQUOTED]) - m4_define([AC_DEFINE_UNQUOTED], - [ifelse(m4_substr([$1], 0, 8), [PACKAGE_], [], -- [NCBI_ORIG_ACDU($@)])]) -+ [NCBI_ORIG_AC_DEFINE_UNQUOTED($@)])]) - - - AC_DEFUN(NCBI_FIX_DIR, -@@ -158,7 +76,7 @@ - AC_MSG_WARN([Proceeding without questions per --without-caution]) ;; - * ) - echo "$1 [[y/N]]" -- read answer -+ read answer <& AS_ORIGINAL_STDIN_FD - case "$answer" in - [[Yy]]* ) AC_MSG_WARN([Proceeding at your own risk...]) ;; - * ) AC_MSG_ERROR([Configuration has been canceled by user.]) ;; ---- ncbi_cxx--12_0_0/src/build-system/configure.ac.ori 2014/05/05 12:38:59 62744 -+++ ncbi_cxx--12_0_0/src/build-system/configure.ac 2014/05/05 13:59:33 62745 -@@ -38,7 +38,7 @@ - # - ############################################################################# - --AC_PREREQ(2.59) -+AC_PREREQ(2.60) - - dnl Early setup, most crucially for locking. The diversion magic lets - dnl this occur before AC_INIT, which already interferes with other -@@ -493,6 +493,10 @@ - [***** See also HTML documentation in ./doc/index.html *****]) - - -+AC_DIVERT_PUSH(PARSE_ARGS) -+dnl As of Autoconf 2.60, this needs to run too early for config.log, -+dnl to which AC_MSG_ERROR normally copies its output, to be available. -+m4_rename([AS_MESSAGE_LOG_FD], [NCBI_ORIG_ASMLFD]) - #### Check the passed arguments against the list of available ones - x_with_list="\ - debug max-debug symbols optimization profiling tcheck dll static static-exe \ -@@ -564,7 +568,7 @@ - | --with-muparser=* | --with-hdf5=* | --with-jni=* | --with-magic=* \ - | --x-includes=* | --x-libraries=* | --with-3psw=* \ - | --target=* | --with-runpath=* | --with-relative-runpath=* \ -- | --no-create | --no-recursion) -+ | --help | --no-create | --no-recursion) - ;; - - * ) -@@ -572,6 +576,8 @@ - ;; - esac - done -+m4_rename([NCBI_ORIG_ASMLFD], [AS_MESSAGE_LOG_FD]) -+AC_DIVERT_POP - - - if test "$with_gbench" = "yes" ; then -@@ -2176,7 +2182,7 @@ - fi - - AC_PATH_PROG(TOUCH, touch, [], /bin:/usr/bin:$PATH) --AC_PATH_PROG(GREP, grep) -+dnl AC_PATH_PROG(GREP, grep) - AC_PROG_EGREP - AC_MSG_CHECKING([how to run $EGREP quietly]) - if test -z "`echo foo | $EGREP -q fo+ 2>>config.log || echo $?`"; then ---- ncbi_cxx--12_0_0/include/common/config/ncbiconf_xcode.h.ori 2014/05/05 14:10:55 62749 -+++ ncbi_cxx--12_0_0/include/common/config/ncbiconf_xcode.h 2014/05/05 14:23:49 62750 -@@ -694,7 +694,7 @@ - /* Define to empty if `const' does not conform to ANSI C. */ - /* #undef const */ - --/* Define to `unsigned' if <sys/types.h> does not define. */ -+/* Define to `unsigned int' if <sys/types.h> does not define. */ - /* #undef size_t */ - - /* ---- ncbi_cxx--12_0_0/src/build-system/config.h.in.ori 2014/05/05 14:10:55 62749 -+++ ncbi_cxx--12_0_0/src/build-system/config.h.in 2014/05/05 14:23:49 62750 -@@ -802,37 +802,37 @@ - by a signal. */ - #undef SELECT_UPDATES_TIMEOUT - --/* The size of a `char', as computed by sizeof. */ -+/* The size of `char', as computed by sizeof. */ - #undef SIZEOF_CHAR - --/* The size of a `double', as computed by sizeof. */ -+/* The size of `double', as computed by sizeof. */ - #undef SIZEOF_DOUBLE - --/* The size of a `float', as computed by sizeof. */ -+/* The size of `float', as computed by sizeof. */ - #undef SIZEOF_FLOAT - --/* The size of a `int', as computed by sizeof. */ -+/* The size of `int', as computed by sizeof. */ - #undef SIZEOF_INT - --/* The size of a `long', as computed by sizeof. */ -+/* The size of `long', as computed by sizeof. */ - #undef SIZEOF_LONG - --/* The size of a `long double', as computed by sizeof. */ -+/* The size of `long double', as computed by sizeof. */ - #undef SIZEOF_LONG_DOUBLE - --/* The size of a `long long', as computed by sizeof. */ -+/* The size of `long long', as computed by sizeof. */ - #undef SIZEOF_LONG_LONG - --/* The size of a `short', as computed by sizeof. */ -+/* The size of `short', as computed by sizeof. */ - #undef SIZEOF_SHORT - --/* The size of a `size_t', as computed by sizeof. */ -+/* The size of `size_t', as computed by sizeof. */ - #undef SIZEOF_SIZE_T - --/* The size of a `void*', as computed by sizeof. */ -+/* The size of `void*', as computed by sizeof. */ - #undef SIZEOF_VOIDP - --/* The size of a `__int64', as computed by sizeof. */ -+/* The size of `__int64', as computed by sizeof. */ - #undef SIZEOF___INT64 - - /* Define to 1 if the stack grows down. */ -@@ -873,5 +873,5 @@ - /* Define to empty if `const' does not conform to ANSI C. */ - #undef const - --/* Define to `unsigned' if <sys/types.h> does not define. */ -+/* Define to `unsigned int' if <sys/types.h> does not define. */ - #undef size_t ---- ncbi_cxx--12_0_0/src/build-system/aclocal.m4.ori 2014/05/06 13:12:18 62759 -+++ ncbi_cxx--12_0_0/src/build-system/aclocal.m4 2014/05/06 13:42:48 62760 -@@ -11,6 +11,7 @@ - - NCBI_ORIG__AC_SRCDIRS(["$ac_dir_in"]) - -+AS_SET_CATFILE([ac_abs_top_srcdir], [$ac_dir_in], [$real_srcdir]) - ac_builddir=$builddir - ]) - - diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-configure.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-configure.patch deleted file mode 100644 index b2d887c92..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-configure.patch +++ /dev/null @@ -1,20 +0,0 @@ ---- ncbi_cxx--12_0_0/src/build-system/configure.ori 2014-06-25 23:47:05.000000000 +0200 -+++ ncbi_cxx--12_0_0/src/build-system/configure 2014-06-25 23:52:35.000000000 +0200 -@@ -3201,6 +3203,17 @@ - *\ -O* | *\ -xO* ) skip_fast_flags=yes ;; - esac - fi -+if test -n "$with_projects"; then -+ case "$with_projects" in -+ /* ) abs_projects=$with_projects ;; -+ yes) abs_projects=$srcdir/projects ;; -+ * ) abs_projects=$srcdir/$with_projects ;; -+ esac -+ test -r "$abs_projects" || \ -+ { { echo "$as_me:$LINENO: error: unable to read requested projects file \"$abs_projects\"." >&5 -+echo "$as_me: error: unable to read requested projects file \"$abs_projects\"." >&2;} -+ { (exit 1); exit 1; }; } -+fi - - #### Always define this - diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-annotwriter-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-annotwriter-linking.patch deleted file mode 100644 index c9428084d..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-annotwriter-linking.patch +++ /dev/null @@ -1,15 +0,0 @@ -Index: c++.18.0.0/src/app/annotwriter/Makefile.annotwriter.app -=================================================================== ---- c++.18.0.0/src/app/annotwriter/Makefile.annotwriter.app (revision 523253) -+++ c++.18.0.0/src/app/annotwriter/Makefile.annotwriter.app (working copy) -@@ -8,8 +8,8 @@ - - APP = annotwriter - SRC = annotwriter --LIB = xobjwrite variation_utils $(OBJREAD_LIBS) xalnmgr xobjutil \ -- gbseq entrez2cli entrez2 tables $(OBJMGR_LIBS) -+LIB = xobjwrite $(XFORMAT_LIBS) variation_utils $(OBJREAD_LIBS) xalnmgr \ -+ xobjutil entrez2cli entrez2 tables xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - - LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-blast_sample-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-blast_sample-linking.patch deleted file mode 100644 index 7a158dc5c..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-blast_sample-linking.patch +++ /dev/null @@ -1,26 +0,0 @@ -Index: c++.18.0.0/src/sample/app/blast/Makefile.blast_sample.app -=================================================================== ---- c++.18.0.0/src/sample/app/blast/Makefile.blast_sample.app (revision 523253) -+++ c++.18.0.0/src/sample/app/blast/Makefile.blast_sample.app (working copy) -@@ -12,7 +12,7 @@ - # the lines reading "### BEGIN/END COPIED SETTINGS" in any way. - - ### BEGIN COPIED SETTINGS --LIB_ = xobjsimple $(BLAST_LIBS) $(OBJMGR_LIBS) -+LIB_ = xobjsimple $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - LIB = $(LIB_:%=%$(STATIC)) - LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - -Index: c++.18.0.0/src/sample/app/blast/Makefile.vsrun_sample.app -=================================================================== ---- c++.18.0.0/src/sample/app/blast/Makefile.vsrun_sample.app (revision 523253) -+++ c++.18.0.0/src/sample/app/blast/Makefile.vsrun_sample.app (working copy) -@@ -12,7 +12,7 @@ - # the lines reading "### BEGIN/END COPIED SETTINGS" in any way. - - ### BEGIN COPIED SETTINGS --LIB_ = xobjsimple $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS) -+LIB_ = xobjsimple $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - LIB = $(LIB_:%=%$(STATIC)) - LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-compartp-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-compartp-linking.patch deleted file mode 100644 index 749c2e57f..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-compartp-linking.patch +++ /dev/null @@ -1,29 +0,0 @@ -Index: c++.18.0.0/src/app/compart/Makefile.compart.app -=================================================================== ---- c++.18.0.0/src/app/compart/Makefile.compart.app (revision 523253) -+++ c++.18.0.0/src/app/compart/Makefile.compart.app (working copy) -@@ -5,8 +5,8 @@ - APP = compart - SRC = compart - --LIB = xalgoalignsplign xalgoalignutil xalgoalignnw xqueryparse \ -- $(BLAST_LIBS:%=%$(STATIC)) \ -+LIB = xalgoalignsplign xalgoalignutil xalgoalignnw xalgoseq taxon1 \ -+ $(BLAST_LIBS:%=%$(STATIC)) xqueryparse xregexp $(PCRE_LIB) \ - $(OBJMGR_LIBS:%=%$(STATIC)) - - LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) -Index: c++.18.0.0/src/app/compart/Makefile.compartp.app -=================================================================== ---- c++.18.0.0/src/app/compart/Makefile.compartp.app (revision 523253) -+++ c++.18.0.0/src/app/compart/Makefile.compartp.app (working copy) -@@ -5,7 +5,8 @@ - APP = compartp - SRC = compartp - --LIB = prosplign xalgoalignutil $(BLAST_LIBS) xqueryparse $(OBJMGR_LIBS) -+LIB = prosplign xalgoalignutil xalgoseq taxon1 $(BLAST_LIBS) xqueryparse \ -+ xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - - LIBS = $(CMPRS_LIBS) $(PCRE_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-convert_seq-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-convert_seq-linking.patch deleted file mode 100644 index e495c9645..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-convert_seq-linking.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- ncbi_cxx--18_0_0/src/app/convert_seq/Makefile.convert_seq.app.ori 2017-03-23 19:24:31.534280319 +0100 -+++ ncbi_cxx--18_0_0/src/app/convert_seq/Makefile.convert_seq.app 2017-03-23 19:25:14.395360214 +0100 -@@ -2,7 +2,7 @@ - - APP = convert_seq - SRC = convert_seq --LIB = $(ncbi_xloader_wgs) $(SRAREAD_LIBS) xobjwrite \ -+LIB = $(ncbi_xloader_wgs) $(SRAREAD_LIBS) xobjwrite variation_utils \ - $(OBJREAD_LIBS) $(XFORMAT_LIBS) xalnmgr xobjutil tables xregexp \ - $(PCRE_LIB) $(OBJMGR_LIBS) - diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-hfilter-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-hfilter-linking.patch deleted file mode 100644 index 63bbcc45a..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-hfilter-linking.patch +++ /dev/null @@ -1,14 +0,0 @@ -Index: c++.18.0.0/src/app/hfilter/Makefile.hfilter.app -=================================================================== ---- c++.18.0.0/src/app/hfilter/Makefile.hfilter.app (revision 523253) -+++ c++.18.0.0/src/app/hfilter/Makefile.hfilter.app (working copy) -@@ -5,7 +5,8 @@ - APP = hfilter - SRC = hitfilter_app - --LIB = xalgoalignutil $(BLAST_LIBS) xqueryparse $(OBJMGR_LIBS) -+LIB = xalgoalignutil xalgoseq taxon1 $(BLAST_LIBS) \ -+ xqueryparse xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - - LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-igblast-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-igblast-linking.patch deleted file mode 100644 index ffd3f897f..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-igblast-linking.patch +++ /dev/null @@ -1,28 +0,0 @@ -Index: c++.18.0.0/src/app/igblast/Makefile.igblastn.app -=================================================================== ---- c++.18.0.0/src/app/igblast/Makefile.igblastn.app (revision 523253) -+++ c++.18.0.0/src/app/igblast/Makefile.igblastn.app (working copy) -@@ -2,7 +2,8 @@ - - APP = igblastn - SRC = igblastn_app --LIB_ = xalgoalignutil $(BLAST_INPUT_LIBS) xqueryparse $(BLAST_LIBS) $(OBJMGR_LIBS) -+LIB_ = xalgoalignutil $(BLAST_INPUT_LIBS) xqueryparse $(BLAST_LIBS) \ -+ xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - LIB = blast_app_util igblast $(LIB_:%=%$(STATIC)) - - # De-universalize Mac builds to work around a PPC toolchain limitation -Index: c++.18.0.0/src/app/igblast/Makefile.igblastp.app -=================================================================== ---- c++.18.0.0/src/app/igblast/Makefile.igblastp.app (revision 523253) -+++ c++.18.0.0/src/app/igblast/Makefile.igblastp.app (working copy) -@@ -2,7 +2,8 @@ - - APP = igblastp - SRC = igblastp_app --LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS) -+LIB_ = xalgoalignutil $(BLAST_INPUT_LIBS) xqueryparse $(BLAST_LIBS) \ -+ xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - LIB = blast_app_util igblast $(LIB_:%=%$(STATIC)) - - # De-universalize Mac builds to work around a PPC toolchain limitation diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-rmblastn-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-rmblastn-linking.patch deleted file mode 100644 index fce7263b2..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-rmblastn-linking.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- ncbi_cxx--18_0_0/src/app/rmblastn/Makefile.rmblastn.app.ori 2017-03-26 18:49:50.431994978 +0200 -+++ ncbi_cxx--18_0_0/src/app/rmblastn/Makefile.rmblastn.app 2017-03-26 18:50:11.222552131 +0200 -@@ -2,7 +2,7 @@ - - APP = rmblastn - SRC = rmblastn_app --LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS) -+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - LIB = blast_app_util $(LIB_:%=%$(STATIC)) - - # De-universalize Mac builds to work around a PPC toolchain limitation diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-table2asn-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-table2asn-linking.patch deleted file mode 100644 index 222cb2c06..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-table2asn-linking.patch +++ /dev/null @@ -1,13 +0,0 @@ ---- ncbi_cxx--18_0_0/src/app/table2asn/Makefile.table2asn.app.ori 2017-03-27 00:41:58.742206850 +0200 -+++ ncbi_cxx--18_0_0/src/app/table2asn/Makefile.table2asn.app 2017-03-27 00:43:13.142206236 +0200 -@@ -12,8 +12,8 @@ - - LIB = xdiscrepancy xalgophytree fastme prosplign xalgoalignutil xalgoseq xmlwrapp \ - xvalidate xobjwrite xobjreadex valerr biotree macro \ -- $(OBJEDIT_LIBS) $(XFORMAT_LIBS) $(BLAST_LIBS) id2cli \ -- xregexp $(PCRE_LIB) $(SRAREAD_LIBS) $(DATA_LOADERS_UTIL_LIB) $(OBJMGR_LIBS) -+ $(OBJEDIT_LIBS) $(XFORMAT_LIBS) $(BLAST_LIBS) taxon1 id2cli \ -+ xregexp $(PCRE_LIB) xqueryparse $(DATA_LOADERS_UTIL_LIB) $(OBJMGR_LIBS) - - LIBS = $(LIBXSLT_LIBS) $(DATA_LOADERS_UTIL_LIBS) $(LIBXML_LIBS) $(CMPRS_LIBS) $(PCRE_LIBS) \ - $(SRA_SDK_SYSLIBS) \ diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-tls-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-tls-linking.patch deleted file mode 100644 index 541dc2514..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-tls-linking.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- ncbi_cxx--18_0_0/src/app/tls/Makefile.tls.app.ori 2017-03-27 02:33:36.312151540 +0200 -+++ ncbi_cxx--18_0_0/src/app/tls/Makefile.tls.app 2017-03-27 02:34:19.372151184 +0200 -@@ -10,7 +10,7 @@ - SRC = tls - - LIB = $(OBJEDIT_LIBS) $(XFORMAT_LIBS) xalnmgr xobjutil \ -- xregexp $(PCRE_LIB) $(OBJMGR_LIBS) -+ xregexp $(PCRE_LIB) tables $(OBJMGR_LIBS) - - LIBS = $(PCRE_LIBS) \ - $(NETWORK_LIBS) $(CMPRS_LIBS) $(ORIG_LIBS) diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-vecscreen-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-vecscreen-linking.patch deleted file mode 100644 index 898e3a70b..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-app-vecscreen-linking.patch +++ /dev/null @@ -1,13 +0,0 @@ -Index: c++.18.0.0/src/app/vecscreen/Makefile.vecscreen.app -=================================================================== ---- c++.18.0.0/src/app/vecscreen/Makefile.vecscreen.app (revision 523253) -+++ c++.18.0.0/src/app/vecscreen/Makefile.vecscreen.app (working copy) -@@ -4,7 +4,7 @@ - - APP = vecscreen - SRC = vecscreen_app --LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS) -+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - LIB = $(LIB_:%=%$(STATIC)) - # FIXME: do we need blast_app_util - #LIB = blast_app_util $(LIB_:%=%$(STATIC)) diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-apps-blast-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-apps-blast-linking.patch deleted file mode 100644 index e9dd1f710..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-apps-blast-linking.patch +++ /dev/null @@ -1,130 +0,0 @@ -Index: c++.18.0.0/src/app/blast/Makefile.blast_formatter.app -=================================================================== ---- c++.18.0.0/src/app/blast/Makefile.blast_formatter.app (revision 523253) -+++ c++.18.0.0/src/app/blast/Makefile.blast_formatter.app (working copy) -@@ -2,7 +2,7 @@ - - APP = blast_formatter - SRC = blast_formatter --LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS) -+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - LIB = blast_app_util $(LIB_:%=%$(STATIC)) - - # De-universalize Mac builds to work around a PPC toolchain limitation -Index: c++.18.0.0/src/app/blast/Makefile.blastp.app -=================================================================== ---- c++.18.0.0/src/app/blast/Makefile.blastp.app (revision 523253) -+++ c++.18.0.0/src/app/blast/Makefile.blastp.app (working copy) -@@ -4,7 +4,7 @@ - - APP = blastp - SRC = blastp_app --LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS) -+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - LIB = blast_app_util $(LIB_:%=%$(STATIC)) - - # De-universalize Mac builds to work around a PPC toolchain limitation -Index: c++.18.0.0/src/app/blast/Makefile.blastx.app -=================================================================== ---- c++.18.0.0/src/app/blast/Makefile.blastx.app (revision 523253) -+++ c++.18.0.0/src/app/blast/Makefile.blastx.app (working copy) -@@ -4,7 +4,7 @@ - - APP = blastx - SRC = blastx_app --LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS) -+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - LIB = blast_app_util $(LIB_:%=%$(STATIC)) - - # De-universalize Mac builds to work around a PPC toolchain limitation -Index: c++.18.0.0/src/app/blast/Makefile.deltablast.app -=================================================================== ---- c++.18.0.0/src/app/blast/Makefile.deltablast.app (revision 523253) -+++ c++.18.0.0/src/app/blast/Makefile.deltablast.app (working copy) -@@ -1,7 +1,7 @@ - - APP = deltablast - SRC = deltablast_app --LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS) -+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - LIB = blast_app_util $(LIB_:%=%$(STATIC)) - - # De-universalize Mac builds to work around a PPC toolchain limitation -Index: c++.18.0.0/src/app/blast/Makefile.psiblast.app -=================================================================== ---- c++.18.0.0/src/app/blast/Makefile.psiblast.app (revision 523253) -+++ c++.18.0.0/src/app/blast/Makefile.psiblast.app (working copy) -@@ -2,7 +2,7 @@ - - APP = psiblast - SRC = psiblast_app --LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS) -+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - LIB = blast_app_util $(LIB_:%=%$(STATIC)) - - # De-universalize Mac builds to work around a PPC toolchain limitation -Index: c++.18.0.0/src/app/blast/Makefile.rpsblast.app -=================================================================== ---- c++.18.0.0/src/app/blast/Makefile.rpsblast.app (revision 523253) -+++ c++.18.0.0/src/app/blast/Makefile.rpsblast.app (working copy) -@@ -2,7 +2,7 @@ - - APP = rpsblast - SRC = rpsblast_app --LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS) -+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - LIB = blast_app_util $(LIB_:%=%$(STATIC)) - - # De-universalize Mac builds to work around a PPC toolchain limitation -Index: c++.18.0.0/src/app/blast/Makefile.rpstblastn.app -=================================================================== ---- c++.18.0.0/src/app/blast/Makefile.rpstblastn.app (revision 523253) -+++ c++.18.0.0/src/app/blast/Makefile.rpstblastn.app (working copy) -@@ -2,7 +2,7 @@ - - APP = rpstblastn - SRC = rpstblastn_app --LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS) -+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - LIB = blast_app_util $(LIB_:%=%$(STATIC)) - - # De-universalize Mac builds to work around a PPC toolchain limitation -Index: c++.18.0.0/src/app/blast/Makefile.seedtop.app -=================================================================== ---- c++.18.0.0/src/app/blast/Makefile.seedtop.app (revision 523253) -+++ c++.18.0.0/src/app/blast/Makefile.seedtop.app (working copy) -@@ -2,7 +2,7 @@ - - APP = seedtop - SRC = seedtop_app --LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS) -+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - LIB = blast_app_util $(LIB_:%=%$(STATIC)) - - # De-universalize Mac builds to work around a PPC toolchain limitation -Index: c++.18.0.0/src/app/blast/Makefile.tblastn.app -=================================================================== ---- c++.18.0.0/src/app/blast/Makefile.tblastn.app (revision 523253) -+++ c++.18.0.0/src/app/blast/Makefile.tblastn.app (working copy) -@@ -4,7 +4,7 @@ - - APP = tblastn - SRC = tblastn_app --LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS) -+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - LIB = blast_app_util $(LIB_:%=%$(STATIC)) - - # De-universalize Mac builds to work around a PPC toolchain limitation -Index: c++.18.0.0/src/app/blast/Makefile.tblastx.app -=================================================================== ---- c++.18.0.0/src/app/blast/Makefile.tblastx.app (revision 523253) -+++ c++.18.0.0/src/app/blast/Makefile.tblastx.app (working copy) -@@ -4,7 +4,7 @@ - - APP = tblastx - SRC = tblastx_app --LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) $(OBJMGR_LIBS) -+LIB_ = $(BLAST_INPUT_LIBS) $(BLAST_LIBS) xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - LIB = blast_app_util $(LIB_:%=%$(STATIC)) - - # De-universalize Mac builds to work around a PPC toolchain limitation diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-install.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-install.patch deleted file mode 100644 index 97e845fdb..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-install.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- ncbi_cxx--12_0_0/src/build-system/Makefile.in.top.ori 2014-06-26 22:49:49.000000000 +0200 -+++ ncbi_cxx--12_0_0/src/build-system/Makefile.in.top 2014-06-26 22:50:57.000000000 +0200 -@@ -48,7 +48,7 @@ - for x in *.a; do ln -s "$$x" "`basename \"$$x\" .a`-static.a"; done - cd $(includedir0) && find * -name CVS -prune -o -print |\ - cpio -pd $(pincludedir) -- $(INSTALL) -m 644 $(incdir)/* $(pincludedir) -+ $(INSTALL) -m 644 $(incdir)/*.* $(pincludedir) - ## set up appropriate build and status directories somewhere under $(libdir)? - - install-gbench: diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-ncfetch-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-ncfetch-linking.patch deleted file mode 100644 index aacb20a6c..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-ncfetch-linking.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- ncbi_cxx--18_0_0/src/app/grid/util/Makefile.ncfetch.app.ori 2017-03-23 21:12:52.028724998 +0100 -+++ ncbi_cxx--18_0_0/src/app/grid/util/Makefile.ncfetch.app 2017-03-23 21:13:30.079737366 +0100 -@@ -5,7 +5,7 @@ - APP = ncfetch.cgi - SRC = ncfetch - --LIB = xcgi xconnserv xconnect xutil xncbi -+LIB = xcgi xconnserv xthrserv xconnect xutil xncbi - LIBS = $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - - WATCHERS = sadyrovr diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-netcache_cgi_sample-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-netcache_cgi_sample-linking.patch deleted file mode 100644 index e074046cf..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-netcache_cgi_sample-linking.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- ncbi_cxx--18_0_0/src/sample/app/netcache/Makefile.netcache_cgi_sample.app.ori 2017-03-23 21:16:18.824226906 +0100 -+++ ncbi_cxx--18_0_0/src/sample/app/netcache/Makefile.netcache_cgi_sample.app 2017-03-23 21:16:50.085058615 +0100 -@@ -4,7 +4,7 @@ - SRC = netcache_cgi_sample - - ### BEGIN COPIED SETTINGS --LIB = xconnserv xconnect xcgi xhtml xutil xncbi -+LIB = xconnserv xthrserv xconnect xcgi xhtml xutil xncbi - - LIBS = $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - ### END COPIED SETTINGS diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-netstorage_gc-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-netstorage_gc-linking.patch deleted file mode 100644 index f237a86d8..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-netstorage_gc-linking.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- ncbi_cxx--18_0_0/src/app/netstorage/utils/Makefile.netstorage_gc.app.ori 2017-03-23 21:22:14.463688886 +0100 -+++ ncbi_cxx--18_0_0/src/app/netstorage/utils/Makefile.netstorage_gc.app 2017-03-23 21:22:48.854603873 +0100 -@@ -10,7 +10,7 @@ - REQUIRES = MT Linux - - --LIB = netstorage ncbi_xcache_netcache xconnserv \ -+LIB = netstorage ncbi_xcache_netcache xconnserv xthrserv \ - $(SDBAPI_LIB) xconnect connssl xutil xncbi - LIBS = $(SDBAPI_LIBS) $(NETWORK_LIBS) $(GNUTLS_LIBS) $(CMPRS_LIBS) $(DL_LIBS) $(ORIG_LIBS) - diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-sample-app-cgi-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-sample-app-cgi-linking.patch deleted file mode 100644 index c45d4ad96..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-sample-app-cgi-linking.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- ncbi_cxx--18_0_0/src/sample/app/cgi/Makefile.cgi_session_sample.app.ori 2017-03-22 23:52:58.984696074 +0100 -+++ ncbi_cxx--18_0_0/src/sample/app/cgi/Makefile.cgi_session_sample.app 2017-03-22 23:53:54.746258126 +0100 -@@ -11,7 +11,7 @@ - # the lines reading "### BEGIN/END COPIED SETTINGS" in any way. - - ### BEGIN COPIED SETTINGS --LIB = xgridcgi xcgi xhtml xconnserv xconnect xutil xncbi -+LIB = xgridcgi xcgi xhtml xconnserv xthrserv xconnect xutil xncbi - - LIBS = $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-speedtest-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-speedtest-linking.patch deleted file mode 100644 index 9435e8b6a..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-speedtest-linking.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- ncbi_cxx--18_0_0/src/app/speedtest/Makefile.speedtest.app.ori 2017-03-23 21:41:31.084603405 +0100 -+++ ncbi_cxx--18_0_0/src/app/speedtest/Makefile.speedtest.app 2017-03-23 21:45:47.601428174 +0100 -@@ -8,7 +8,7 @@ - - APP = speedtest - SRC = speedtest --LIB = prosplign xalgoalignutil xcleanup taxon3 valid valerr $(BLAST_LIBS) \ -+LIB = prosplign xalgoalignutil taxon1 xalgoseq xcleanup taxon3 valid valerr $(BLAST_LIBS) \ - xqueryparse xregexp $(PCRE_LIB) $(OBJMGR_LIBS:%=%$(STATIC)) - - LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(PCRE_LIBS) $(ORIG_LIBS) diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-splign-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-splign-linking.patch deleted file mode 100644 index 56f213f08..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-splign-linking.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- ncbi_cxx--18_0_0/src/app/splign/Makefile.splign.app.ori 2017-03-23 22:08:16.937327984 +0100 -+++ ncbi_cxx--18_0_0/src/app/splign/Makefile.splign.app 2017-03-23 22:09:19.208984755 +0100 -@@ -12,7 +12,7 @@ - LIB = xalgoalignsplign xalgoalignutil xalgoalignnw \ - $(BLAST_DB_DATA_LOADER_LIBS) \ - ncbi_xloader_lds2 lds2 sqlitewrapp \ -- xqueryparse xalgoseq $(PCRE_LIB) \ -+ xqueryparse xalgoseq taxon1 xregexp $(PCRE_LIB) \ - $(BLAST_LIBS:%=%$(STATIC)) \ - $(OBJMGR_LIBS:%=%$(STATIC)) - diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-srcchk-linking.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-srcchk-linking.patch deleted file mode 100644 index 49a4adb4e..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-srcchk-linking.patch +++ /dev/null @@ -1,15 +0,0 @@ -Index: c++.18.0.0/src/app/srcchk/Makefile.srcchk.app -=================================================================== ---- c++.18.0.0/src/app/srcchk/Makefile.srcchk.app (revision 523253) -+++ c++.18.0.0/src/app/srcchk/Makefile.srcchk.app (working copy) -@@ -8,8 +8,8 @@ - - APP = srcchk - SRC = srcchk --LIB = xobjwrite variation_utils $(OBJREAD_LIBS) xalnmgr xobjutil \ -- gbseq entrez2cli entrez2 tables $(OBJMGR_LIBS) -+LIB = xobjwrite $(XFORMAT_LIBS) variation_utils $(OBJREAD_LIBS) xalnmgr \ -+ xobjutil entrez2cli entrez2 tables xregexp $(PCRE_LIB) $(OBJMGR_LIBS) - - LIBS = $(CMPRS_LIBS) $(NETWORK_LIBS) $(DL_LIBS) $(ORIG_LIBS) - diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-undefined-lxncbi.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-undefined-lxncbi.patch deleted file mode 100644 index f0a27d85a..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-undefined-lxncbi.patch +++ /dev/null @@ -1,10 +0,0 @@ ---- work/ncbi_cxx--18_0_0/src/connect/Makefile.xthrserv.lib.ori 2017-03-17 22:33:51.569635396 +0100 -+++ ncbi_cxx--18_0_0/src/connect/Makefile.xthrserv.lib 2017-03-17 22:33:58.349811199 +0100 -@@ -4,6 +4,6 @@ - LIB = xthrserv - PROJ_TAG = core - LIBS = $(NETWORK_LIBS) --DLL_LIB = xutil xconnect -+DLL_LIB = xncbi xutil xconnect - - WATCHERS = vakatov diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-undefined-xobjread.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-undefined-xobjread.patch deleted file mode 100644 index 3c1cb0a9e..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-fix-undefined-xobjread.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- ncbi_cxx--18_0_0/src/app/asn2fasta/Makefile.asn2fasta.app.ori 2016-06-24 16:55:25.000000000 +0200 -+++ ncbi_cxx--18_0_0/src/app/asn2fasta/Makefile.asn2fasta.app 2017-03-21 14:07:31.070364301 +0100 -@@ -9,7 +9,7 @@ - APP = asn2fasta - SRC = asn2fasta - LIB = $(ncbi_xloader_wgs) $(SRAREAD_LIBS) \ -- xobjwrite xobjread $(XFORMAT_LIBS) xalnmgr xobjutil valerr xregexp \ -+ xobjwrite variation_utils $(OBJREAD_LIBS) $(XFORMAT_LIBS) xalnmgr xobjutil valerr xregexp \ - ncbi_xdbapi_ftds dbapi $(ncbi_xreader_pubseqos2) $(FTDS_LIB) \ - entrez2cli entrez2 tables $(OBJMGR_LIBS) $(PCRE_LIB) - diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-never_build_test_boost.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-never_build_test_boost.patch deleted file mode 100644 index 68baea046..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-never_build_test_boost.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- ncbi_cxx--12_0_0/src/corelib/Makefile.in.ori 2016-12-01 20:28:33.239758102 +0100 -+++ ncbi_cxx--12_0_0/src/corelib/Makefile.in 2016-12-01 20:28:46.330110659 +0100 -@@ -7,7 +7,7 @@ - ################################# - - USR_PROJ = precompile --LIB_PROJ = corelib test_mt test_boost -+LIB_PROJ = corelib test_mt - SUB_PROJ = test - PROJ_TAG = core - diff --git a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-remove-old-symlinks.patch b/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-remove-old-symlinks.patch deleted file mode 100644 index 098a9ad1e..000000000 --- a/sci-biology/ncbi-tools++/files/ncbi-tools++-18.0.0-remove-old-symlinks.patch +++ /dev/null @@ -1,10 +0,0 @@ ---- ncbi_cxx--18_0_0/src/dbapi/lang_bind/python/tests/Makefile.symlink.in.old 2017-03-26 19:01:58.101495278 +0200 -+++ ncbi_cxx--18_0_0/src/dbapi/lang_bind/python/tests/Makefile.symlink.in 2017-03-26 19:02:16.581990522 +0200 -@@ -13,6 +13,7 @@ - -a ! -d $(libdir)/64 ]; then \ - cd $(libdir) && $(LN_S) . 64; \ - fi -+ $(RM) $(LINK) - cd $(libdir) && $(LN_S) libpython_ncbi_dbapi$(loadable_ext) $(LINK) - - clean:; diff --git a/sci-biology/ncbi-tools++/files/report_project_settings_configure.ac.patch b/sci-biology/ncbi-tools++/files/report_project_settings_configure.ac.patch deleted file mode 100644 index 41240c330..000000000 --- a/sci-biology/ncbi-tools++/files/report_project_settings_configure.ac.patch +++ /dev/null @@ -1,64 +0,0 @@ ---- trunk/c++/src/build-system/configure.ac 2012/12/27 15:43:29 56694 -+++ trunk/c++/src/build-system/configure.ac 2013/01/03 03:16:14 56754 -@@ -605,7 +605,8 @@ - fi - - case "$with_projects" in -- "") if test -r projects; then -+ ""|yes) -+ if test -r projects; then - AC_MSG_NOTICE([using default projects file "projects".]) - with_projects=projects - AC_SUBST(PROJECTS, "\$(top_srcdir)/projects") -@@ -623,6 +624,16 @@ - * ) AC_SUBST(PROJECTS, "\$(top_srcdir)/$with_projects") ;; - esac - -+if test -n "$with_projects"; then -+ case "$with_projects" in -+ /* ) abs_projects=$with_projects ;; -+ yes) abs_projects=$srcdir/projects ;; -+ * ) abs_projects=$srcdir/$with_projects ;; -+ esac -+ test -r "$abs_projects" || \ -+ AC_MSG_ERROR([unable to read requested projects file "$abs_projects".]) -+fi -+ - # Check for custom optimization flags before potentially going with defaults. - skip_fast_flags=no - if test -z "${DEF_FAST_FLAGS}${FAST_CXXFLAGS}"; then -@@ -6379,7 +6390,7 @@ - sep=", " - fi - if test -n "$reason" -a "$with_internal" = "yes"; then -- if test -z "$with_projects" -o "$with_projects" = "no"; then -+ if test -z "$with_projects"; then - AC_MSG_ERROR([--with-internal: Cannot build INTERNAL projects: missing $reason]) - else - AC_MSG_WARN([--with-internal: Cannot build all INTERNAL projects: missing $reason]) -@@ -6982,11 +6993,9 @@ - else - cfm_flags='-remoteptb' - fi -- case "$with_projects" in -- yes ) cfm_flags="$cfm_flags -p projects" ;; -- no | '' ) ;; -- * ) cfm_flags="$cfm_flags -p $with_projects" ;; -- esac -+ if test -n "$with_projects"; then -+ cfm_flags="$cfm_flags -p $with_projects" -+ fi - if test "$with_configure_dialog" = yes; then - cfm_flags="$cfm_flags -cfg" - fi -@@ -7029,7 +7038,8 @@ - esac - - if test -n "$with_projects"; then -- build_proj="To build selected projects: cd $builddir && make all_p" -+ build_proj="To build selected projects (as listed in \"$with_projects\"): -+ cd $builddir && make all_p" - fi - - cat << EOCONF - diff --git a/sci-biology/ncbi-tools++/files/report_project_settings_configure.patch b/sci-biology/ncbi-tools++/files/report_project_settings_configure.patch deleted file mode 100644 index 0c1b2d227..000000000 --- a/sci-biology/ncbi-tools++/files/report_project_settings_configure.patch +++ /dev/null @@ -1,66 +0,0 @@ --- trunk/c++/src/build-system/configure 2012/12/27 15:43:29 56694 -+++ trunk/c++/src/build-system/configure 2013/01/03 03:16:14 56754 -@@ -3125,7 +3125,8 @@ - fi - - case "$with_projects" in -- "") if test -r projects; then -+ ""|yes) -+ if test -r projects; then - { echo "$as_me:$LINENO: using default projects file \"projects\"." >&5 - echo "$as_me: using default projects file \"projects\"." >&6;} - with_projects=projects -@@ -3151,6 +3152,18 @@ - ;; - esac - -+if test -n "$with_projects"; then -+ case "$with_projects" in -+ /* ) abs_projects=$with_projects ;; -+ yes) abs_projects=$srcdir/projects ;; -+ * ) abs_projects=$srcdir/$with_projects ;; -+ esac -+ test -r "$abs_projects" || \ -+ { { echo "$as_me:$LINENO: error: unable to read requested projects file \"$abs_projects\"." >&5 -+echo "$as_me: error: unable to read requested projects file \"$abs_projects\"." >&2;} -+ { (exit 1); exit 1; }; } -+fi -+ - # Check for custom optimization flags before potentially going with defaults. - skip_fast_flags=no - if test -z "${DEF_FAST_FLAGS}${FAST_CXXFLAGS}"; then -@@ -33825,7 +33838,7 @@ - sep=", " - fi - if test -n "$reason" -a "$with_internal" = "yes"; then -- if test -z "$with_projects" -o "$with_projects" = "no"; then -+ if test -z "$with_projects"; then - { { echo "$as_me:$LINENO: error: --with-internal: Cannot build INTERNAL projects: missing $reason" >&5 - echo "$as_me: error: --with-internal: Cannot build INTERNAL projects: missing $reason" >&2;} - { (exit 1); exit 1; }; } -@@ -36062,11 +36075,9 @@ - else - cfm_flags='-remoteptb' - fi -- case "$with_projects" in -- yes ) cfm_flags="$cfm_flags -p projects" ;; -- no | '' ) ;; -- * ) cfm_flags="$cfm_flags -p $with_projects" ;; -- esac -+ if test -n "$with_projects"; then -+ cfm_flags="$cfm_flags -p $with_projects" -+ fi - if test "$with_configure_dialog" = yes; then - cfm_flags="$cfm_flags -cfg" - fi -@@ -36110,7 +36121,8 @@ - esac - - if test -n "$with_projects"; then -- build_proj="To build selected projects: cd $builddir && make all_p" -+ build_proj="To build selected projects (as listed in \"$with_projects\"): -+ cd $builddir && make all_p" - fi - - cat << EOCONF - diff --git a/sci-biology/ncbi-tools++/files/respect_CXXFLAGS_configure.ac.patch b/sci-biology/ncbi-tools++/files/respect_CXXFLAGS_configure.ac.patch deleted file mode 100644 index 89dae23ad..000000000 --- a/sci-biology/ncbi-tools++/files/respect_CXXFLAGS_configure.ac.patch +++ /dev/null @@ -1,54 +0,0 @@ ---- trunk/c++/src/build-system/configure.ac 2012/12/21 15:12:14 56664 -+++ trunk/c++/src/build-system/configure.ac 2012/12/27 15:43:29 56694 -@@ -623,6 +623,13 @@ - * ) AC_SUBST(PROJECTS, "\$(top_srcdir)/$with_projects") ;; - esac - -+# Check for custom optimization flags before potentially going with defaults. -+skip_fast_flags=no -+if test -z "${DEF_FAST_FLAGS}${FAST_CXXFLAGS}"; then -+ case " $CFLAGS $CXXFLAGS" in -+ *\ -O* | *\ -xO* ) skip_fast_flags=yes ;; -+ esac -+fi - - #### Always define this - AC_DEFINE(NCBI_CXX_TOOLKIT, 1, [This is the NCBI C++ Toolkit.]) -@@ -1431,7 +1438,7 @@ - wsrx="[[$wschars]]" - - #### Flags to enable (potentially unsafe) extra optimization. --if test -z "$DEF_FAST_FLAGS" -o -z "$FAST_CXXFLAGS" ; then -+if test "$skip_fast_flags" = no -a -z "$DEF_FAST_FLAGS" ; then - case "$compiler:$compiler_version" in - GCC:2* | GCC:344 ) - # GCC 2.9x sometimes experiences internal errors at high optimization; -@@ -1502,8 +1509,6 @@ - DEF_FAST_FLAGS="-O" - ;; - esac --else -- DEF_FAST_FLAGS="-O" - fi - - : ${FAST_CFLAGS="$DEF_FAST_FLAGS"} -@@ -2608,9 +2613,15 @@ - CXXFLAGS="$CXXFLAGS -O" ; fi - if echo " $LDFLAGS " | grep -v "$optrx" >/dev/null ; then - LDFLAGS="$LDFLAGS -O" ; fi -- FAST_CFLAGS="$NOPT_CFLAGS $FAST_CFLAGS" -- FAST_CXXFLAGS="$NOPT_CXXFLAGS $FAST_CXXFLAGS" -- FAST_LDFLAGS="$NOPT_LDFLAGS $FAST_LDFLAGS" -+ if test "$skip_fast_flags" = yes ; then -+ FAST_CFLAGS="$CFLAGS" -+ FAST_CXXFLAGS="$CXXFLAGS" -+ FAST_LDFLAGS="$LDFLAGS" -+ else -+ FAST_CFLAGS="$NOPT_CFLAGS $FAST_CFLAGS" -+ FAST_CXXFLAGS="$NOPT_CXXFLAGS $FAST_CXXFLAGS" -+ FAST_LDFLAGS="$NOPT_LDFLAGS $FAST_LDFLAGS" -+ fi - fi - changequote([, ])dnl - fi - diff --git a/sci-biology/ncbi-tools++/files/respect_CXXFLAGS_configure.patch b/sci-biology/ncbi-tools++/files/respect_CXXFLAGS_configure.patch deleted file mode 100644 index 669b31722..000000000 --- a/sci-biology/ncbi-tools++/files/respect_CXXFLAGS_configure.patch +++ /dev/null @@ -1,53 +0,0 @@ ---- trunk/c++/src/build-system/configure 2012/12/21 15:12:14 56664 -+++ trunk/c++/src/build-system/configure 2012/12/27 15:43:29 56694 -@@ -3151,6 +3151,13 @@ - ;; - esac - -+# Check for custom optimization flags before potentially going with defaults. -+skip_fast_flags=no -+if test -z "${DEF_FAST_FLAGS}${FAST_CXXFLAGS}"; then -+ case " $CFLAGS $CXXFLAGS" in -+ *\ -O* | *\ -xO* ) skip_fast_flags=yes ;; -+ esac -+fi - - #### Always define this - -@@ -5715,7 +5722,7 @@ - wsrx="[$wschars]" - - #### Flags to enable (potentially unsafe) extra optimization. --if test -z "$DEF_FAST_FLAGS" -o -z "$FAST_CXXFLAGS" ; then -+if test "$skip_fast_flags" = no -a -z "$DEF_FAST_FLAGS" ; then - case "$compiler:$compiler_version" in - GCC:2* | GCC:344 ) - # GCC 2.9x sometimes experiences internal errors at high optimization; -@@ -5786,8 +5793,6 @@ - DEF_FAST_FLAGS="-O" - ;; - esac --else -- DEF_FAST_FLAGS="-O" - fi - - : ${FAST_CFLAGS="$DEF_FAST_FLAGS"} -@@ -8936,9 +8941,15 @@ - CXXFLAGS="$CXXFLAGS -O" ; fi - if echo " $LDFLAGS " | grep -v "$optrx" >/dev/null ; then - LDFLAGS="$LDFLAGS -O" ; fi -- FAST_CFLAGS="$NOPT_CFLAGS $FAST_CFLAGS" -- FAST_CXXFLAGS="$NOPT_CXXFLAGS $FAST_CXXFLAGS" -- FAST_LDFLAGS="$NOPT_LDFLAGS $FAST_LDFLAGS" -+ if test "$skip_fast_flags" = yes ; then -+ FAST_CFLAGS="$CFLAGS" -+ FAST_CXXFLAGS="$CXXFLAGS" -+ FAST_LDFLAGS="$LDFLAGS" -+ else -+ FAST_CFLAGS="$NOPT_CFLAGS $FAST_CFLAGS" -+ FAST_CXXFLAGS="$NOPT_CXXFLAGS $FAST_CXXFLAGS" -+ FAST_LDFLAGS="$NOPT_LDFLAGS $FAST_LDFLAGS" -+ fi - fi - fi - diff --git a/sci-biology/ncbi-tools++/metadata.xml b/sci-biology/ncbi-tools++/metadata.xml deleted file mode 100644 index fbf79d9b7..000000000 --- a/sci-biology/ncbi-tools++/metadata.xml +++ /dev/null @@ -1,19 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <use> - <flag name="boost">Undocumented USE</flag> - <flag name="cppunit">Undocumented USE</flag> - <flag name="freetype">Undocumented USE</flag> - <flag name="mesa">Undocumented USE</flag> - <flag name="muparser">Undocumented USE</flag> - <flag name="sablotron">Undocumented USE</flag> - <flag name="xerces">Undocumented USE</flag> - <flag name="xalan">Undocumented USE</flag> - <flag name="xslt">Undocumented USE</flag> - </use> -</pkgmetadata> diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild deleted file mode 100644 index 009085d15..000000000 --- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild +++ /dev/null @@ -1,364 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit toolchain-funcs - -MY_TAG="Jun_15_2010" -MY_Y="${MY_TAG/*_/}" -MY_PV="12_0_0" -MY_P="ncbi_cxx--${MY_PV}" -#ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools++/ARCHIVE/9_0_0/ncbi_cxx--9_0_0.tar.gz - -# for example sci-biology/ncbi-tools++-12.0.0 contains blastn-2.2.28+ -DESCRIPTION="NCBI C++ Toolkit, including NCBI BLAST+" -HOMEPAGE="https://ncbi.github.io/cxx-toolkit/" -SRC_URI=" - ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/${MY_PV}/ncbi_cxx--${MY_PV}.tar.gz" -# http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz" - -# should also install ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz -# see http://www.biostars.org/p/76551/ and http://blastedbio.blogspot.cz/2012/05/blast-tabular-missing-descriptions.html -LICENSE="public-domain" -SLOT="0" -IUSE=" - debug static-libs static threads pch - test wxwidgets odbc - berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype gif - glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png - sablotron sqlite tiff xerces xalan xml xpm xslt X" -#KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -KEYWORDS="~amd64" -RESTRICT="!test? ( test )" - -# sys-libs/db should be compiled with USE=cxx -# dev-libs/boost must have Boost.Test suite, probably dev-libs/boost[test] then? -DEPEND=" - <sys-devel/gcc-10:= - app-arch/cpio - berkdb? ( sys-libs/db:=[cxx(-)] ) - boost? ( dev-libs/boost[tools] ) - curl? ( net-misc/curl ) - sqlite? ( dev-db/sqlite:3 ) - mysql? ( virtual/mysql ) - fltk? ( x11-libs/fltk ) - opengl? ( virtual/opengl media-libs/glew:0= ) - mesa? ( media-libs/mesa[osmesa] ) - glut? ( media-libs/freeglut ) - freetype? ( media-libs/freetype ) - gnutls? ( net-libs/gnutls ) - cppunit? ( dev-util/cppunit ) - icu? ( dev-libs/icu ) - expat? ( dev-libs/expat ) - sablotron? ( app-text/sablotron ) - xml? ( dev-libs/libxml2 ) - xslt? ( dev-libs/libxslt ) - xerces? ( dev-libs/xerces-c ) - xalan? ( dev-libs/xalan-c ) - muparser? ( dev-cpp/muParser ) - hdf5? ( sci-libs/hdf5[cxx] ) - gif? ( media-libs/giflib ) - jpeg? ( media-libs/libjpeg-turbo:0= ) - png? ( media-libs/libpng:0= ) - tiff? ( media-libs/tiff:0= ) - xpm? ( x11-libs/libXpm ) - dev-libs/lzo - app-arch/bzip2 - dev-libs/libpcre" -# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge -# Intentionally omitted USE flags: -# ftds? ( dev-db/freetds ) # support for outside FreeTDS installations is currently broken. -# The default (heavily patched) embedded copy should work, or you can -# leave it off altogether -- the only public apps that make use of it are -# samples and tests, since NCBI's database servers are of course firewalled. - -# seems muParser is required, also glew is required. configure exits otherwise if these are explicitly passed to it (due to USE flag enabled) - -RDEPEND="${DEPEND}" - -S="${WORKDIR}/${MY_P}" - -PATCHES=( - "${FILESDIR}"/${P}-conf-opts.patch - "${FILESDIR}"/${P}-fix-svn-URL-upstream.patch - "${FILESDIR}"/${P}-linkage-tuneups.patch - "${FILESDIR}"/${P}-more-patches.patch - "${FILESDIR}"/${P}-linkage-tuneups-addons.patch - "${FILESDIR}"/${P}-configure.patch - "${FILESDIR}"/${P}-drop-STATIC-from-LIB.patch - "${FILESDIR}"/${P}-fix-install.patch - "${FILESDIR}"/${P}-bdb6.patch - "${FILESDIR}"/${P}-never_build_test_boost.patch # bug #579248 - ) - -src_prepare() { - default -# filter-ldflags -Wl,--as-needed -# append-ldflags -Wl,--no-undefined -# sed -i -e 's/-print-file-name=libstdc++.a//' \ -# -e '/sed/ s/\([gO]\[0-9\]\)\*/\1\\+/' \ -# src/build-system/configure || die -# epatch \ -# "${FILESDIR}"/${PN}-${PV#0.}-fix-order-of-libs.patch \ -# "${FILESDIR}"/curl-types.patch \ -# "${FILESDIR}"/malloc_initialize_upstream_fix.patch \ -# "${FILESDIR}"/respect_CXXFLAGS_configure.ac.patch \ -# "${FILESDIR}"/respect_CXXFLAGS_configure.patch \ -# "${FILESDIR}"/report_project_settings_configure.ac.patch \ -# "${FILESDIR}"/report_project_settings_configure.patch \ -# "${FILESDIR}"/make_install.patch - -# "${FILESDIR}"/${PN}-${PV#0.}-disable_test_compress.patch - -# "${FILESDIR}"/${PN}-${PV#0.}-gcc46.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-gcc47.patch \ -# "${WORKDIR}"/${PN}-${PV#0.}-asneeded.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-libpng15.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-glibc-214.patch - -# use prefix && append-ldflags -Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/${PN}" - -# The conf-opts.patch and as-needed.patch need to be adjusted for 12.0.0 line numbers -# "${FILESDIR}"/${P}-as-needed.patch -# "${FILESDIR}"/${P}-fix-creaders-linking.patch -# "${FILESDIR}"/${P}-fix-FreeTDS-upstream.patch -# ) - # "${FILESDIR}"/${P}-support-autoconf-2.60.patch - # make sure this one is the last one and contains the actual patches applied unless we can have autoconf-2.59 or 2.60 - # https://bugs.gentoo.org/show_bug.cgi?id=514706 - - tc-export CXX CC - - cd src/build-system || die -# eautoreconf - - # Temporarily disabling eautoconf because we patch configure via ${P}-support-autoconf-2.60.patch - # eautoconf # keep it disabled until we can ensure 2.59 is installed - # beware 12.0.0. and previous required autoconf-2.59, a patch for 12.0.0 brings autoconf-2.60 support -} - -# possibly place modified contents of ${W}/src/build-system/config.site.ncbi and {W}/src/build-system/config.site.ex into ${W}/src/build-system/config.site -src_configure() { - local myconf=() - #--without-optimization turn off optimization flags in non-debug mode - #--with-profiling build profiled versions of libs and apps - #--with-tcheck(=DIR) build for Intel Thread Checker (in DIR) - #--with-plugin-auto-load always enable the plugin manager by default - #--with-bundles build bundles in addition to dylibs on Mac OS X - #--with-bin-release build executables suitable for public release - # no dll and such - #--with-64 compile to 64-bit code - #--with-universal build universal binaries on Mac OS X - #--with-universal=CPUs build universal binaries targeting the given CPUs - #--without-exe do not build executables - #--with-relative-runpath=P specify an executable-relative DLL search path - #--with-hard-runpath hard-code runtime path, ignoring LD_LIBRARY_PATH - #--with-limited-linker don't attempt to build especially large projects - #--with-extra-action= script to call after the configuration is complete - #--with-autodep automatic generation of dependencies (GNU make) - #--with-fake-root=DIR appear to have been built under DIR - #--with-build-root-sfx=X add a user-specified suffix to the build dir name - #--without-execopy do not copy built executables to the BIN area - #--with-lib-rebuilds ensure that apps use up-to-date libraries - #--with-lib-rebuilds=ask ask whether to update each app's libraries - #--without-deactivation keep old copies of libraries that no longer build - #--without-makefile-auto-update do not auto-update generated makefiles - #--with-projects=FILE build projects listed in FILE by default - #--without-flat-makefile do not generate an all-encompassing flat makefile - #--with-configure-dialog allow interactive flat makefile project selection - #--with-saved-settings=F load configuration settings from the file F - #--with-check-tools=... use the specified tools for testing - #--with-ncbi-public ensure compatibility for all in-house platforms - #--with-sybase-local=DIR use local SYBASE install (DIR is optional) - #--with-sybase-new use newer SYBASE install (12.5 rather than 12.0) - #--without-sp do not use SP libraries - #--without-orbacus do not use ORBacus CORBA libraries - #--with-orbacus=DIR use ORBacus installation in DIR - #--with-jni(=JDK-DIR) build Java bindings (against the JDK in JDK-DIR) - #--with-sablot=DIR use Sablotron installation in DIR - #--without-sablot, do not use Sablotron - #--with-oechem=DIR use OpenEye OEChem installation in DIR - #--without-oechem do not use OEChem - #--with-sge=DIR use Sun Grid Engine installation in DIR - #--without-sge do not use Sun Grid Engine - #--with-magic=DIR use libmagic installation in DIR - #--without-magic do not use libmagic - #--without-local-lbsm turn off support for IPC with locally running LBSMD - #--without-ncbi-crypt use a dummy stubbed-out version of ncbi_crypt - #--without-connext do not build non-public CONNECT library extensions - #--without-serial do not build the serialization library and tools - #--without-objects do not generate/build serializeable objects from ASNs - #--without-dbapi do not build database connectivity libraries - #--without-app do not build standalone applications like ID1_FETCH - #--without-gui do not build most graphical projects - #--without-algo do not build CPU-intensive algorithms - #--without-internal do not build internal projects - #--with-gbench ensure that Genome Workbench can be built - #--without-gbench do not build Genome Workbench - myconf+=( - --with-dll - --with-lfs - --with-build-root="${S}"_build - --without-suffix - --without-hostspec - --without-version - --with-bincopy - --without-strip - --without-ccache - --without-distcc -# --with-ncbi-c - --without-ctools -# --with-sss -# --with-sssutils -# --with-sssdb -# --with-included-sss - --with-z="${EPREFIX}/usr" - --with-bz2="${EPREFIX}/usr" - --without-sybase - --with-autodep -# --with-3psw=std:netopt favor standard (system) builds of the above pkgs - # --without-downloaded-vdb is not available in 12.0.0 release yet - # preventing executing git to checkout during configure phase ncbi-vdb sources - # resulting in 'checking for ncbi-vdb... no' and - # '^PACKAGES:' - # '^ disabled: ... VDB' - # --without-downloaded-vdb - $(use_with debug) - $(use_with debug max-debug) - $(use_with debug symbols) - $(use_with static-libs static) - $(use_with static static-exe) - $(use_with threads mt) - $(use_with prefix runpath "${EPREFIX}/usr/$(get_libdir)/${PN}") - $(use_with test check) - $(use_with pch) - $(use_with lzo lzo "${EPREFIX}/usr") - $(use_with pcre pcre "${EPREFIX}/usr") - $(use_with gnutls gnutls "${EPREFIX}/usr") - $(use_with mysql mysql "${EPREFIX}/usr") - $(use_with muparser muparser "${EPREFIX}/usr") - $(usex fltk --with-fltk="${EPREFIX}/usr" "") - $(use_with opengl opengl "${EPREFIX}/usr") - $(use_with mesa mesa "${EPREFIX}/usr") - $(use_with opengl glut "${EPREFIX}/usr") - $(use_with opengl glew "${EPREFIX}/usr") - $(use_with opengl glew-mx) - $(use_with wxwidgets wxwidgets "${EPREFIX}/usr") - $(use_with wxwidgets wxwidgets-ucs) - $(use_with freetype freetype "${EPREFIX}/usr") - $(use_with fastcgi fastcgi "${EPREFIX}/usr") - $(use_with berkdb bdb "${EPREFIX}/usr") - $(usex odbc --with-odbc="${EPREFIX}/usr" "") - # is python2 - --without-python - $(use_with boost boost "${EPREFIX}/usr") - $(use_with sqlite sqlite3 "${EPREFIX}/usr") - $(use_with icu icu "${EPREFIX}/usr") - $(use_with expat expat "${EPREFIX}/usr") - $(use_with xml libxml "${EPREFIX}/usr") - $(use_with xml libxslt "${EPREFIX}/usr") - $(use_with xerces xerces "${EPREFIX}/usr") - $(use_with hdf5 hdf5 "${EPREFIX}/usr") - $(use_with xalan xalan "${EPREFIX}/usr") -# $(use_with gif gif "${EPREFIX}/usr") # prevent compilation failure in "ncbi-tools++-12.0.0/src/util/image/image_io_gif.cpp:351: error: 'QuantizeBuffer' was not declared in this scope" - --without-gif - $(use_with jpeg jpeg "${EPREFIX}/usr") - $(use_with tiff tiff "${EPREFIX}/usr") - $(use_with png png "${EPREFIX}/usr") - $(use_with xpm xpm "${EPREFIX}/usr") - $(use_with curl curl "${EPREFIX}/usr") -# $(use_with X x "${EPREFIX}/usr") -# $(use_with X x) # there is no --with-x option - ) - - # http://www.ncbi.nlm.nih.gov/books/NBK7167/ - use test || myconf+=( --with-projects="${FILESDIR}"/disable-testsuite-compilation.txt ) - - # TODO - # copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure - # otherwise your -O2 will be dropped in some subdirectories and replaced by e.g. -O9 - - einfo "bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}/usr" --libdir=/usr/lib64 ${myconf[@]}" - -# ECONF_SOURCE="src/build-system" \ -# econf \ - bash \ - ./src/build-system/configure \ - --srcdir="${S}" \ - --prefix="${EPREFIX}/usr" \ - --libdir=/usr/lib64 \ - --with-flat-makefile \ - ${myconf[@]} || die -#--without-debug \ -# --with-bin-release \ -# --with-bincopy \ -# --without-static \ -# --with-dll \ -# --with-mt \ -# --with-openmp \ -# --with-lfs \ -# --prefix="${ED}"/usr \ -# --libdir="${ED}"/usr/$(get_libdir)/"${PN}" \ -# ${myconf} LDFLAGS="-Wl,--no-as-needed" \ -# || die -# econf ${myconf[@]} -} - -src_compile() { - ## all_r would ignore the --with-projects contents and build more - ## emake all_r -C GCC*-Release*/build || die - ## all_p with compile only selected/required components - ##cd "${S}"_build &&\ - ##emake all_p -C GCC*-Release*/build || die "gcc-4.5.3 crashes at src/objects/valerr/ValidError.cpp:226:1: internal compiler error: Segmentation fault, right?" - #emake all_p -C "${S}"_build/build - - # - # Re: /usr/lib64/ncbi-tools++/libdbapi_driver.so: undefined reference to `ncbi::NcbiGetlineEOL(std::istream&, std::string&)' - # - # The next release should automatically address such underlinking, albeit - # only in --with-flat-makefile configurations. For now (12.0.0), you'll need to - # add or extend more DLL_LIB settings, to which end you may find the - # resources at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/ - # helpful. For instance, - # - # http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/dbapi_driver.html - # - # indicates that src/dbapi/driver/Makefile.dbapi_driver.lib should set - # - # DLL_LIB = xncbi - # - # (You can find the path to that makefile by examining - # .../status/.dbapi_driver.dep or .../build/Makefile.flat.) - # - # To take full advantage of --with-flat-makefile, you'll need the following (instead of 'emake all_p -C "${S}"_build/build') and call configure --with-flat-makefile: - emake -C "${S}"_build/build -f Makefile.flat - # - # >=gcc-5.3.0 is not supported, see also bug #579248#c8 - # configure: error: Do not know how to build MT-safe with compiler /usr/bin/x86_64-pc-linux-gnu-g++ 5.3.0 -} - -src_install() { - rm -rvf "${S}"_build/lib/ncbi || die - emake install prefix="${ED}/usr" libdir="${ED}/usr/$(get_libdir)/${PN}" - -# dobin "${S}"_build/bin/* -# dolib.so "${S}"_build/lib/*so* -# dolib.a "${S}"_build/lib/*.a -# doheader "${S}"_build/inc/* - - # File collisions with sci-biology/ncbi-tools - mv "${ED}"/usr/bin/asn2asn "${ED}"/usr/bin/asn2asn+ - mv "${ED}"/usr/bin/rpsblast "${ED}"/usr/bin/rpsblast+ - mv -f "${ED}"/usr/bin/test_regexp "${ED}"/usr/bin/test_regexp+ # drop the eventually mistakenly compiled binaries - mv "${ED}"/usr/bin/vecscreen "${ED}"/usr/bin/vecscreen+ - mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop+ - - echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}" > ${S}/99${PN} - doenvd "${S}/99${PN}" -} - -pkg_postinst() { - einfo 'Please run "source /etc/profile" before using this package in the current shell.' - einfo 'Documentation is at http://www.ncbi.nlm.nih.gov/books/NBK7167/' -} diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild deleted file mode 100644 index 604c9c638..000000000 --- a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild +++ /dev/null @@ -1,383 +0,0 @@ -# Copyright 1999-2022 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 toolchain-funcs - -MY_TAG="Jun_15_2010" -MY_Y="${MY_TAG/*_/}" -MY_PV="18_0_0" -MY_P="ncbi_cxx--${MY_PV}" -#ftp://ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools++/ARCHIVE/9_0_0/ncbi_cxx--9_0_0.tar.gz - -# for example sci-biology/ncbi-tools++-12.0.0 contains blastn-2.2.28+ -DESCRIPTION="NCBI C++ Toolkit, including NCBI BLAST+" -HOMEPAGE="https://ncbi.github.io/cxx-toolkit/" -SRC_URI=" - ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/2017/Jan_10_2017/ncbi_cxx--${MY_PV}.tar.gz" -# http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz" - -# should also install ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz -# see http://www.biostars.org/p/76551/ and http://blastedbio.blogspot.cz/2012/05/blast-tabular-missing-descriptions.html -LICENSE="public-domain" -SLOT="0" -IUSE=" - debug static-libs static threads pch - test wxwidgets odbc - berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype gif - glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python - sablotron sqlite tiff xerces xalan xml xpm xslt X" -KEYWORDS="~amd64 ~x86" -RESTRICT="!test? ( test )" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -# sys-libs/db should be compiled with USE=cxx -# dev-libs/boost must have Boost.Test suite, probably dev-libs/boost[test] then? -DEPEND=" - <sys-devel/gcc-10:= - app-arch/cpio - berkdb? ( sys-libs/db:=[cxx(-)] ) - boost? ( dev-libs/boost[tools] ) - curl? ( net-misc/curl ) - sqlite? ( dev-db/sqlite:3 ) - mysql? ( virtual/mysql ) - fltk? ( x11-libs/fltk ) - opengl? ( virtual/opengl media-libs/glew:0= ) - mesa? ( media-libs/mesa[osmesa] ) - glut? ( media-libs/freeglut ) - freetype? ( media-libs/freetype ) - gnutls? ( net-libs/gnutls ) - python? ( ${PYTHON_DEPS} ) - cppunit? ( dev-util/cppunit ) - icu? ( dev-libs/icu ) - expat? ( dev-libs/expat ) - sablotron? ( app-text/sablotron ) - xml? ( dev-libs/libxml2 ) - xslt? ( dev-libs/libxslt ) - xerces? ( dev-libs/xerces-c ) - xalan? ( dev-libs/xalan-c ) - muparser? ( dev-cpp/muParser ) - hdf5? ( sci-libs/hdf5[cxx] ) - gif? ( media-libs/giflib ) - jpeg? ( media-libs/libjpeg-turbo:0= ) - png? ( media-libs/libpng:0= ) - tiff? ( media-libs/tiff:0= ) - xpm? ( x11-libs/libXpm ) - dev-libs/lzo - app-arch/bzip2 - dev-libs/libpcre" -# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge -# Intentionally omitted USE flags: -# ftds? ( dev-db/freetds ) # support for outside FreeTDS installations is currently broken. -# The default (heavily patched) embedded copy should work, or you can -# leave it off altogether -- the only public apps that make use of it are -# samples and tests, since NCBI's database servers are of course firewalled. - -# seems muParser is required, also glew is required. configure exits otherwise if these are explicitly passed to it (due to USE flag enabled) - -RDEPEND="${DEPEND}" - -S="${WORKDIR}/${MY_P}" - -PATCHES=( - "${FILESDIR}"/${P}-configure.patch - "${FILESDIR}"/${P}-fix-install.patch - "${FILESDIR}"/${P}-never_build_test_boost.patch # bug #579248 - "${FILESDIR}"/${P}-fix-annotwriter-linking.patch - "${FILESDIR}"/${P}-fix-undefined-xobjread.patch - "${FILESDIR}"/${P}-fix-apps-blast-linking.patch - "${FILESDIR}"/${P}-fix-sample-app-cgi-linking.patch - "${FILESDIR}"/${P}-fix-app-compartp-linking.patch - "${FILESDIR}"/${P}-fix-app-convert_seq-linking.patch - "${FILESDIR}"/${P}-fix-app-hfilter-linking.patch - "${FILESDIR}"/${P}-fix-app-igblast-linking.patch - "${FILESDIR}"/${P}-fix-ncfetch-linking.patch - "${FILESDIR}"/${P}-fix-netcache_cgi_sample-linking.patch - "${FILESDIR}"/${P}-fix-netstorage_gc-linking.patch - "${FILESDIR}"/${P}-fix-speedtest-linking.patch - "${FILESDIR}"/${P}-fix-splign-linking.patch - "${FILESDIR}"/${P}-fix-srcchk-linking.patch - "${FILESDIR}"/${P}-fix-app-rmblastn-linking.patch - "${FILESDIR}"/${P}-remove-old-symlinks.patch - "${FILESDIR}"/${P}-fix-app-table2asn-linking.patch - "${FILESDIR}"/${P}-fix-app-tls-linking.patch - "${FILESDIR}"/${P}-fix-app-vecscreen-linking.patch - "${FILESDIR}"/${P}-fix-app-blast_sample-linking.patch - ) - -src_prepare() { - default -# filter-ldflags -Wl,--as-needed -# append-ldflags -Wl,--no-undefined -# sed -i -e 's/-print-file-name=libstdc++.a//' \ -# -e '/sed/ s/\([gO]\[0-9\]\)\*/\1\\+/' \ -# src/build-system/configure || die -# epatch \ -# "${FILESDIR}"/${PN}-${PV#0.}-fix-order-of-libs.patch \ -# "${FILESDIR}"/curl-types.patch \ -# "${FILESDIR}"/malloc_initialize_upstream_fix.patch \ -# "${FILESDIR}"/respect_CXXFLAGS_configure.ac.patch \ -# "${FILESDIR}"/respect_CXXFLAGS_configure.patch \ -# "${FILESDIR}"/report_project_settings_configure.ac.patch \ -# "${FILESDIR}"/report_project_settings_configure.patch \ -# "${FILESDIR}"/make_install.patch - -# "${FILESDIR}"/${PN}-${PV#0.}-disable_test_compress.patch - -# "${FILESDIR}"/${PN}-${PV#0.}-gcc46.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-gcc47.patch \ -# "${WORKDIR}"/${PN}-${PV#0.}-asneeded.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-libpng15.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-glibc-214.patch - -# use prefix && append-ldflags -Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/${PN}" - -# The conf-opts.patch and as-needed.patch need to be adjusted for 12.0.0 line numbers - #ncbi-tools++-18.0.0-fix-undefined-lxncbi.patch - # make sure this one is the last one and contains the actual patches applied unless we can have autoconf-2.59 or 2.60 - # https://bugs.gentoo.org/show_bug.cgi?id=514706 - - tc-export CXX CC - - cd src/build-system || die -# eautoreconf - - # Temporarily disabling eautoconf because we patch configure via ${P}-support-autoconf-2.60.patch - # eautoconf # keep it disabled until we can ensure 2.59 is installed - # beware 12.0.0. and previous required autoconf-2.59, a patch for 12.0.0 brings autoconf-2.60 support -} - -# possibly place modified contents of ${W}/src/build-system/config.site.ncbi and {W}/src/build-system/config.site.ex into ${W}/src/build-system/config.site -src_configure() { - local myconf=() - #--without-optimization turn off optimization flags in non-debug mode - #--with-profiling build profiled versions of libs and apps - #--with-tcheck(=DIR) build for Intel Thread Checker (in DIR) - #--with-plugin-auto-load always enable the plugin manager by default - #--with-bundles build bundles in addition to dylibs on Mac OS X - #--with-bin-release build executables suitable for public release - # no dll and such - #--with-64 compile to 64-bit code - #--with-universal build universal binaries on Mac OS X - #--with-universal=CPUs build universal binaries targeting the given CPUs - #--without-exe do not build executables - #--with-relative-runpath=P specify an executable-relative DLL search path - #--with-hard-runpath hard-code runtime path, ignoring LD_LIBRARY_PATH - #--with-limited-linker don't attempt to build especially large projects - #--with-extra-action= script to call after the configuration is complete - #--with-autodep automatic generation of dependencies (GNU make) - #--with-fake-root=DIR appear to have been built under DIR - #--with-build-root-sfx=X add a user-specified suffix to the build dir name - #--without-execopy do not copy built executables to the BIN area - #--with-lib-rebuilds ensure that apps use up-to-date libraries - #--with-lib-rebuilds=ask ask whether to update each app's libraries - #--without-deactivation keep old copies of libraries that no longer build - #--without-makefile-auto-update do not auto-update generated makefiles - #--with-projects=FILE build projects listed in FILE by default - #--without-flat-makefile do not generate an all-encompassing flat makefile - #--with-configure-dialog allow interactive flat makefile project selection - #--with-saved-settings=F load configuration settings from the file F - #--with-check-tools=... use the specified tools for testing - #--with-ncbi-public ensure compatibility for all in-house platforms - #--with-sybase-local=DIR use local SYBASE install (DIR is optional) - #--with-sybase-new use newer SYBASE install (12.5 rather than 12.0) - #--without-sp do not use SP libraries - #--without-orbacus do not use ORBacus CORBA libraries - #--with-orbacus=DIR use ORBacus installation in DIR - #--with-jni(=JDK-DIR) build Java bindings (against the JDK in JDK-DIR) - #--with-sablot=DIR use Sablotron installation in DIR - #--without-sablot, do not use Sablotron - #--with-oechem=DIR use OpenEye OEChem installation in DIR - #--without-oechem do not use OEChem - #--with-sge=DIR use Sun Grid Engine installation in DIR - #--without-sge do not use Sun Grid Engine - #--with-magic=DIR use libmagic installation in DIR - #--without-magic do not use libmagic - #--without-local-lbsm turn off support for IPC with locally running LBSMD - #--without-ncbi-crypt use a dummy stubbed-out version of ncbi_crypt - #--without-connext do not build non-public CONNECT library extensions - #--without-serial do not build the serialization library and tools - #--without-objects do not generate/build serializeable objects from ASNs - #--without-dbapi do not build database connectivity libraries - #--without-app do not build standalone applications like ID1_FETCH - #--without-gui do not build most graphical projects - #--without-algo do not build CPU-intensive algorithms - #--without-internal do not build internal projects - #--with-gbench ensure that Genome Workbench can be built - #--without-gbench do not build Genome Workbench - myconf+=( - --with-dll - --with-lfs - --with-build-root="${S}"_build - --without-suffix - --without-hostspec - --without-version - --with-bincopy - --without-strip - --without-ccache - --without-distcc -# --with-ncbi-c - --without-ctools -# --with-sss -# --with-sssutils -# --with-sssdb -# --with-included-sss - --with-z="${EPREFIX}/usr" - --with-bz2="${EPREFIX}/usr" - --without-sybase - --with-autodep -# --with-3psw=std:netopt favor standard (system) builds of the above pkgs - # --without-downloaded-vdb is not available in 12.0.0 release yet - # preventing executing git to checkout during configure phase ncbi-vdb sources - # resulting in 'checking for ncbi-vdb... no' and - # '^PACKAGES:' - # '^ disabled: ... VDB' - --without-downloaded-vdb - $(use_with debug) - $(use_with debug max-debug) - $(use_with debug symbols) - $(use_with static-libs static) - $(use_with static static-exe) - $(use_with threads mt) - $(use_with prefix runpath "${EPREFIX}/usr/$(get_libdir)/${PN}") - $(use_with test check) - $(use_with pch) - $(use_with lzo lzo "${EPREFIX}/usr") - $(use_with pcre pcre "${EPREFIX}/usr") - $(use_with gnutls gnutls "${EPREFIX}/usr") - $(use_with mysql mysql "${EPREFIX}/usr") - $(use_with muparser muparser "${EPREFIX}/usr") - $(usex fltk --with-fltk="${EPREFIX}/usr" "") - $(use_with opengl opengl "${EPREFIX}/usr") - $(use_with mesa mesa "${EPREFIX}/usr") - $(use_with opengl glut "${EPREFIX}/usr") - $(use_with opengl glew "${EPREFIX}/usr") - $(use_with opengl glew-mx) - $(use_with wxwidgets wxwidgets "${EPREFIX}/usr") - $(use_with wxwidgets wxwidgets-ucs) - $(use_with freetype freetype "${EPREFIX}/usr") - $(use_with fastcgi fastcgi "${EPREFIX}/usr") - $(use_with berkdb bdb "${EPREFIX}/usr") - $(usex odbc --with-odbc="${EPREFIX}/usr" "") - $(use_with python python "${EPREFIX}/usr") - $(use_with boost boost "${EPREFIX}/usr") - $(use_with sqlite sqlite3 "${EPREFIX}/usr") - $(use_with icu icu "${EPREFIX}/usr") - $(use_with expat expat "${EPREFIX}/usr") - $(use_with xml libxml "${EPREFIX}/usr") - $(use_with xml libxslt "${EPREFIX}/usr") - $(use_with xerces xerces "${EPREFIX}/usr") - $(use_with hdf5 hdf5 "${EPREFIX}/usr") - $(use_with xalan xalan "${EPREFIX}/usr") -# $(use_with gif gif "${EPREFIX}/usr") # prevent compilation failure in "ncbi-tools++-12.0.0/src/util/image/image_io_gif.cpp:351: error: 'QuantizeBuffer' was not declared in this scope" - --without-gif - $(use_with jpeg jpeg "${EPREFIX}/usr") - $(use_with tiff tiff "${EPREFIX}/usr") - $(use_with png png "${EPREFIX}/usr") - $(use_with xpm xpm "${EPREFIX}/usr") - $(use_with curl curl "${EPREFIX}/usr") -# $(use_with X x "${EPREFIX}/usr") -# $(use_with X x) # there is no --with-x option - ) - - # http://www.ncbi.nlm.nih.gov/books/NBK7167/ - use test || myconf+=( --with-projects="${FILESDIR}"/disable-testsuite-compilation.txt ) - - # TODO - # copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure - # otherwise your -O2 will be dropped in some subdirectories and replaced by e.g. -O9 - - einfo "bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}/usr" --libdir=/usr/lib64 ${myconf[@]}" - -# ECONF_SOURCE="src/build-system" \ -# econf \ - bash \ - ./src/build-system/configure \ - --srcdir="${S}" \ - --prefix="${EPREFIX}/usr" \ - --libdir=/usr/lib64 \ - --with-flat-makefile \ - ${myconf[@]} || die -#--without-debug \ -# --with-bin-release \ -# --with-bincopy \ -# --without-static \ -# --with-dll \ -# --with-mt \ -# --with-openmp \ -# --with-lfs \ -# --prefix="${ED}"/usr \ -# --libdir="${ED}"/usr/$(get_libdir)/"${PN}" \ -# ${myconf} LDFLAGS="-Wl,--no-as-needed" \ -# || die -# econf ${myconf[@]} -} - -src_compile() { - ## all_r would ignore the --with-projects contents and build more - ## emake all_r -C GCC*-Release*/build || die - ## all_p with compile only selected/required components - ##cd "${S}"_build &&\ - ##emake all_p -C GCC*-Release*/build || die "gcc-4.5.3 crashes at src/objects/valerr/ValidError.cpp:226:1: internal compiler error: Segmentation fault, right?" - #emake all_p -C "${S}"_build/build - - # - # Re: /usr/lib64/ncbi-tools++/libdbapi_driver.so: undefined reference to `ncbi::NcbiGetlineEOL(std::istream&, std::string&)' - # - # The next release should automatically address such underlinking, albeit - # only in --with-flat-makefile configurations. For now (12.0.0), you'll need to - # add or extend more DLL_LIB settings, to which end you may find the - # resources at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/ - # helpful. For instance, - # - # http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/dbapi_driver.html - # - # indicates that src/dbapi/driver/Makefile.dbapi_driver.lib should set - # - # DLL_LIB = xncbi - # - # (You can find the path to that makefile by examining - # .../status/.dbapi_driver.dep or .../build/Makefile.flat.) - # - # To take full advantage of --with-flat-makefile, you'll need the following (instead of 'emake all_p -C "${S}"_build/build') and call configure --with-flat-makefile: - emake -C "${S}"_build/build -f Makefile.flat - # - # >=gcc-5.3.0 is not supported, see also bug #579248#c8 - # configure: error: Do not know how to build MT-safe with compiler /usr/bin/x86_64-pc-linux-gnu-g++ 5.3.0 -} - -src_install() { - rm -rvf "${S}"_build/lib/ncbi || die - emake install prefix="${ED}/usr" libdir="${ED}/usr/$(get_libdir)/${PN}" - -# dobin "${S}"_build/bin/* -# dolib.so "${S}"_build/lib/*so* -# dolib.a "${S}"_build/lib/*.a -# doheader "${S}"_build/inc/* - - # File collisions with sci-biology/ncbi-tools - mv "${ED}"/usr/bin/asn2asn "${ED}"/usr/bin/asn2asn+ - mv "${ED}"/usr/bin/rpsblast "${ED}"/usr/bin/rpsblast+ - mv -f "${ED}"/usr/bin/test_regexp "${ED}"/usr/bin/test_regexp+ # drop the eventually mistakenly compiled binaries - mv "${ED}"/usr/bin/vecscreen "${ED}"/usr/bin/vecscreen+ - mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop+ - # - # idfetch collides with idfetch from ncbi-tools-2.2.26 - # Although the two idfetch implementations do deliberately have several - # options in common, the C++ version is not yet a full drop-in replacement - # for the C version (and will never entirely be, due to fundamental - # differences between the two toolkits' argument-parsing conventions). - mv "${ED}"/usr/bin/idfetch "${ED}"/usr/bin/idfetch+ # new in ncbi-tools++-18.0.0 - - echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}" > ${S}/99${PN} - doenvd "${S}/99${PN}" -} - -pkg_postinst() { - einfo 'Please run "source /etc/profile" before using this package in the current shell.' - einfo 'Documentation is at http://www.ncbi.nlm.nih.gov/books/NBK7167/' -} diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild deleted file mode 100644 index 4d0d6363e..000000000 --- a/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild +++ /dev/null @@ -1,388 +0,0 @@ -# Copyright 1999-2022 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 toolchain-funcs - -MY_TAG="Mar_28_2019" -MY_Y="${MY_TAG/*_/}" -MY_PV="22_0_0" -MY_P="ncbi_cxx--${MY_PV}" - -# for example sci-biology/ncbi-tools++-12.0.0 contains blastn-2.2.28+ -DESCRIPTION="NCBI C++ Toolkit, including NCBI BLAST+" -HOMEPAGE="https://ncbi.github.io/cxx-toolkit/" -# https://ncbi.github.io/cxx-toolkit/pages/release_notes -SRC_URI=" - ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/2019/${MY_TAG}/ncbi_cxx--${MY_PV}.tar.gz" -# http://dev.gentoo.org/~jlec/distfiles/${PN}-${PV#0.}-asneeded.patch.xz" - -# should also install ftp://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz -# see http://www.biostars.org/p/76551/ and http://blastedbio.blogspot.cz/2012/05/blast-tabular-missing-descriptions.html -LICENSE="public-domain" -SLOT="0" -IUSE=" - debug static-libs static threads pch - test wxwidgets odbc - berkdb boost bzip2 cppunit curl expat fastcgi fltk freetype gif - glut gnutls hdf5 icu jpeg lzo mesa mysql muparser opengl pcre png python - sablotron sqlite tiff xerces xalan xml xpm xslt X" -KEYWORDS="~amd64 ~x86" -RESTRICT="!test? ( test )" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -# sys-libs/db should be compiled with USE=cxx -# dev-libs/boost must have Boost.Test suite, probably dev-libs/boost[test] then? -DEPEND=" - <sys-devel/gcc-10:= - app-arch/cpio - berkdb? ( sys-libs/db:=[cxx(-)] ) - boost? ( dev-libs/boost[tools] ) - curl? ( net-misc/curl ) - sqlite? ( >=dev-db/sqlite-3.6.6:3 ) - mysql? ( virtual/mysql ) - fltk? ( x11-libs/fltk ) - opengl? ( virtual/opengl media-libs/glew:0= ) - mesa? ( media-libs/mesa[osmesa] ) - glut? ( media-libs/freeglut ) - freetype? ( media-libs/freetype ) - gnutls? ( net-libs/gnutls ) - python? ( ${PYTHON_DEPS} ) - cppunit? ( dev-util/cppunit ) - icu? ( dev-libs/icu ) - expat? ( dev-libs/expat ) - sablotron? ( app-text/sablotron ) - xml? ( dev-libs/libxml2 ) - xslt? ( >=dev-libs/libxslt-1.1.14 ) - xerces? ( dev-libs/xerces-c ) - xalan? ( dev-libs/xalan-c ) - muparser? ( dev-cpp/muParser ) - hdf5? ( sci-libs/hdf5[cxx] ) - gif? ( media-libs/giflib ) - jpeg? ( media-libs/libjpeg-turbo:0= ) - png? ( media-libs/libpng:0= ) - tiff? ( media-libs/tiff:0= ) - xpm? ( x11-libs/libXpm ) - >=dev-libs/lzo-2.0 - app-arch/bzip2 - dev-libs/libpcre" -# USE flags which should be added somehow: wxWindows wxWidgets SP ORBacus ODBC OEChem sge -# Intentionally omitted USE flags: -# ftds? ( dev-db/freetds ) # support for outside FreeTDS installations is currently broken. -# The default (heavily patched) embedded copy should work, or you can -# leave it off altogether -- the only public apps that make use of it are -# samples and tests, since NCBI's database servers are of course firewalled. - -# seems muParser is required, also glew is required. configure exits otherwise if these are explicitly passed to it (due to USE flag enabled) - -RDEPEND="${DEPEND}" - -S="${WORKDIR}/${MY_P}" - -src_prepare() { - default -# filter-ldflags -Wl,--as-needed -# append-ldflags -Wl,--no-undefined -# sed -i -e 's/-print-file-name=libstdc++.a//' \ -# -e '/sed/ s/\([gO]\[0-9\]\)\*/\1\\+/' \ -# src/build-system/configure || die -# epatch \ -# "${FILESDIR}"/${PN}-${PV#0.}-fix-order-of-libs.patch \ -# "${FILESDIR}"/curl-types.patch \ -# "${FILESDIR}"/malloc_initialize_upstream_fix.patch \ -# "${FILESDIR}"/respect_CXXFLAGS_configure.ac.patch \ -# "${FILESDIR}"/respect_CXXFLAGS_configure.patch \ -# "${FILESDIR}"/report_project_settings_configure.ac.patch \ -# "${FILESDIR}"/report_project_settings_configure.patch \ -# "${FILESDIR}"/make_install.patch - -# "${FILESDIR}"/${PN}-${PV#0.}-disable_test_compress.patch - -# "${FILESDIR}"/${PN}-${PV#0.}-gcc46.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-gcc47.patch \ -# "${WORKDIR}"/${PN}-${PV#0.}-asneeded.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-libpng15.patch \ -# "${FILESDIR}"/${PN}-${PV#0.}-glibc-214.patch - -# use prefix && append-ldflags -Wl,-rpath,"${EPREFIX}/usr/$(get_libdir)/${PN}" - -# The conf-opts.patch and as-needed.patch need to be adjusted for 12.0.0 line numbers -# local PATCHES=( -# "${FILESDIR}"/${P}-configure.patch -# "${FILESDIR}"/${P}-fix-install.patch -# "${FILESDIR}"/${P}-never_build_test_boost.patch # bug #579248 -# "${FILESDIR}"/${P}-fix-annotwriter-linking.patch -# "${FILESDIR}"/${P}-fix-undefined-xobjread.patch -# "${FILESDIR}"/${P}-fix-apps-blast-linking.patch -# "${FILESDIR}"/${P}-fix-sample-app-cgi-linking.patch -# "${FILESDIR}"/${P}-fix-app-compartp-linking.patch -# "${FILESDIR}"/${P}-fix-app-convert_seq-linking.patch -# "${FILESDIR}"/${P}-fix-app-hfilter-linking.patch -# "${FILESDIR}"/${P}-fix-app-igblast-linking.patch -# "${FILESDIR}"/${P}-fix-ncfetch-linking.patch -# "${FILESDIR}"/${P}-fix-netcache_cgi_sample-linking.patch -# "${FILESDIR}"/${P}-fix-netstorage_gc-linking.patch -# "${FILESDIR}"/${P}-fix-speedtest-linking.patch -# "${FILESDIR}"/${P}-fix-splign-linking.patch -# "${FILESDIR}"/${P}-fix-srcchk-linking.patch -# "${FILESDIR}"/${P}-fix-app-rmblastn-linking.patch -# "${FILESDIR}"/${P}-remove-old-symlinks.patch -# "${FILESDIR}"/${P}-fix-app-table2asn-linking.patch -# "${FILESDIR}"/${P}-fix-app-tls-linking.patch -# "${FILESDIR}"/${P}-fix-app-vecscreen-linking.patch -# "${FILESDIR}"/${P}-fix-app-blast_sample-linking.patch -# ) - #ncbi-tools++-18.0.0-fix-undefined-lxncbi.patch -# epatch ${PATCHES[@]} - # make sure this one is the last one and contains the actual patches applied unless we can have autoconf-2.59 or 2.60 - # https://bugs.gentoo.org/show_bug.cgi?id=514706 - - tc-export CXX CC - - cd src/build-system || die -# eautoreconf - - # Temporarily disabling eautoconf because we patch configure via ${P}-support-autoconf-2.60.patch - # eautoconf # keep it disabled until we can ensure 2.59 is installed - # beware 12.0.0. and previous required autoconf-2.59, a patch for 12.0.0 brings autoconf-2.60 support -} - -# possibly place modified contents of ${W}/src/build-system/config.site.ncbi and {W}/src/build-system/config.site.ex into ${W}/src/build-system/config.site -src_configure() { - local myconf=() - #--without-optimization turn off optimization flags in non-debug mode - #--with-profiling build profiled versions of libs and apps - #--with-tcheck(=DIR) build for Intel Thread Checker (in DIR) - #--with-plugin-auto-load always enable the plugin manager by default - #--with-bundles build bundles in addition to dylibs on Mac OS X - #--with-bin-release build executables suitable for public release - # no dll and such - #--with-64 compile to 64-bit code - #--with-universal build universal binaries on Mac OS X - #--with-universal=CPUs build universal binaries targeting the given CPUs - #--without-exe do not build executables - #--with-relative-runpath=P specify an executable-relative DLL search path - #--with-hard-runpath hard-code runtime path, ignoring LD_LIBRARY_PATH - #--with-limited-linker don't attempt to build especially large projects - #--with-extra-action= script to call after the configuration is complete - #--with-autodep automatic generation of dependencies (GNU make) - #--with-fake-root=DIR appear to have been built under DIR - #--with-build-root-sfx=X add a user-specified suffix to the build dir name - #--without-execopy do not copy built executables to the BIN area - #--with-lib-rebuilds ensure that apps use up-to-date libraries - #--with-lib-rebuilds=ask ask whether to update each app's libraries - #--without-deactivation keep old copies of libraries that no longer build - #--without-makefile-auto-update do not auto-update generated makefiles - #--with-projects=FILE build projects listed in FILE by default - #--without-flat-makefile do not generate an all-encompassing flat makefile - #--with-configure-dialog allow interactive flat makefile project selection - #--with-saved-settings=F load configuration settings from the file F - #--with-check-tools=... use the specified tools for testing - #--with-ncbi-public ensure compatibility for all in-house platforms - #--with-sybase-local=DIR use local SYBASE install (DIR is optional) - #--with-sybase-new use newer SYBASE install (12.5 rather than 12.0) - #--without-sp do not use SP libraries - #--without-orbacus do not use ORBacus CORBA libraries - #--with-orbacus=DIR use ORBacus installation in DIR - #--with-jni(=JDK-DIR) build Java bindings (against the JDK in JDK-DIR) - #--with-sablot=DIR use Sablotron installation in DIR - #--without-sablot, do not use Sablotron - #--with-oechem=DIR use OpenEye OEChem installation in DIR - #--without-oechem do not use OEChem - #--with-sge=DIR use Sun Grid Engine installation in DIR - #--without-sge do not use Sun Grid Engine - #--with-magic=DIR use libmagic installation in DIR - #--without-magic do not use libmagic - #--without-local-lbsm turn off support for IPC with locally running LBSMD - #--without-ncbi-crypt use a dummy stubbed-out version of ncbi_crypt - #--without-connext do not build non-public CONNECT library extensions - #--without-serial do not build the serialization library and tools - #--without-objects do not generate/build serializeable objects from ASNs - #--without-dbapi do not build database connectivity libraries - #--without-app do not build standalone applications like ID1_FETCH - #--without-gui do not build most graphical projects - #--without-algo do not build CPU-intensive algorithms - #--without-internal do not build internal projects - #--with-gbench ensure that Genome Workbench can be built - #--without-gbench do not build Genome Workbench - myconf+=( - --with-dll - --with-lfs - --with-build-root="${S}"_build - --without-suffix - --without-hostspec - --without-version - --with-bincopy - --without-strip - --without-ccache - --without-distcc -# --with-ncbi-c - --without-ctools -# --with-sss -# --with-sssutils -# --with-sssdb -# --with-included-sss - --with-z="${EPREFIX}/usr" - --with-bz2="${EPREFIX}/usr" - --without-sybase - --with-autodep -# --with-3psw=std:netopt favor standard (system) builds of the above pkgs - # --without-downloaded-vdb is not available in 12.0.0 release yet - # preventing executing git to checkout during configure phase ncbi-vdb sources - # resulting in 'checking for ncbi-vdb... no' and - # '^PACKAGES:' - # '^ disabled: ... VDB' - --without-downloaded-vdb - $(use_with debug) -# $(use_with debug max-debug) # broken in 22.0.0 as it triggers need for https://github.com/google/sanitizers/wiki/AddressSanitizer - $(use_with debug symbols) - $(use_with static-libs static) - $(use_with static static-exe) - $(use_with threads mt) - $(use_with prefix runpath "${EPREFIX}/usr/$(get_libdir)/${PN}") - $(use_with test check) - $(use_with pch) - $(use_with lzo lzo "${EPREFIX}/usr") - $(use_with pcre pcre "${EPREFIX}/usr") - $(use_with gnutls gnutls "${EPREFIX}/usr") - $(use_with mysql mysql "${EPREFIX}/usr") - $(use_with muparser muparser "${EPREFIX}/usr") - $(usex fltk --with-fltk="${EPREFIX}/usr" "") - $(use_with opengl opengl "${EPREFIX}/usr") - $(use_with mesa mesa "${EPREFIX}/usr") - $(use_with opengl glut "${EPREFIX}/usr") - $(use_with opengl glew "${EPREFIX}/usr") -# $(use_with opengl glew-mx) can't find this with any version of media-libs/glew installed: explicitly specified, but no usable version found. - $(use_with wxwidgets wxwidgets "${EPREFIX}/usr") - $(use_with wxwidgets wxwidgets-ucs) - $(use_with freetype freetype "${EPREFIX}/usr") - $(use_with fastcgi fastcgi "${EPREFIX}/usr") - $(use_with berkdb bdb "${EPREFIX}/usr") - $(usex odbc --with-odbc="${EPREFIX}/usr" "") - $(use_with python python "${EPREFIX}/usr") - $(use_with boost boost "${EPREFIX}/usr") - $(use_with sqlite sqlite3 "${EPREFIX}/usr") - $(use_with icu icu "${EPREFIX}/usr") - $(use_with expat expat "${EPREFIX}/usr") - $(use_with xml libxml "${EPREFIX}/usr") - $(use_with xml libxslt "${EPREFIX}/usr") - $(use_with xerces xerces "${EPREFIX}/usr") - $(use_with hdf5 hdf5 "${EPREFIX}/usr") - $(use_with xalan xalan "${EPREFIX}/usr") -# $(use_with gif gif "${EPREFIX}/usr") # prevent compilation failure in "ncbi-tools++-12.0.0/src/util/image/image_io_gif.cpp:351: error: 'QuantizeBuffer' was not declared in this scope" - --without-gif - $(use_with jpeg jpeg "${EPREFIX}/usr") - $(use_with tiff tiff "${EPREFIX}/usr") - $(use_with png png "${EPREFIX}/usr") - $(use_with xpm xpm "${EPREFIX}/usr") - $(use_with curl curl "${EPREFIX}/usr") -# $(use_with X x "${EPREFIX}/usr") -# $(use_with X x) # there is no --with-x option - ) - - # http://www.ncbi.nlm.nih.gov/books/NBK7167/ - use test || myconf+=( --with-projects="${FILESDIR}"/disable-testsuite-compilation.txt ) - - # TODO - # copy optimization -O options from CXXFLAGS to DEF_FAST_FLAGS and pass that also to configure - # otherwise your -O2 will be dropped in some subdirectories and replaced by e.g. -O9 - - einfo "LDFLAGS=-Wl,-rpath-link,"${S}"_build/lib bash ./src/build-system/configure --srcdir="${S}" --prefix="${EPREFIX}/usr" --libdir=/usr/lib64 ${myconf[@]}" - -# ECONF_SOURCE="src/build-system" \ -# econf \ - LDFLAGS=-Wl,-rpath-link,"${S}"_build/lib bash \ - ./src/build-system/configure \ - --srcdir="${S}" \ - --prefix="${EPREFIX}/usr" \ - --libdir=/usr/lib64 \ - --with-flat-makefile \ - ${myconf[@]} || die -#--without-debug \ -# --with-bin-release \ -# --with-bincopy \ -# --without-static \ -# --with-dll \ -# --with-mt \ -# --with-openmp \ -# --with-lfs \ -# --prefix="${ED}"/usr \ -# --libdir="${ED}"/usr/$(get_libdir)/"${PN}" \ -# ${myconf} LDFLAGS="-Wl,--no-as-needed" \ -# || die -# econf ${myconf[@]} -} - -src_compile() { - ## all_r would ignore the --with-projects contents and build more - ## emake all_r -C GCC*-Release*/build || die - ## all_p with compile only selected/required components - ##cd "${S}"_build &&\ - ##emake all_p -C GCC*-Release*/build || die "gcc-4.5.3 crashes at src/objects/valerr/ValidError.cpp:226:1: internal compiler error: Segmentation fault, right?" - #emake all_p -C "${S}"_build/build - - # - # Re: /usr/lib64/ncbi-tools++/libdbapi_driver.so: undefined reference to `ncbi::NcbiGetlineEOL(std::istream&, std::string&)' - # - # The next release should automatically address such underlinking, albeit - # only in --with-flat-makefile configurations. For now (12.0.0), you'll need to - # add or extend more DLL_LIB settings, to which end you may find the - # resources at http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/ - # helpful. For instance, - # - # http://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/depgraphs/dbapi_driver.html - # - # indicates that src/dbapi/driver/Makefile.dbapi_driver.lib should set - # - # DLL_LIB = xncbi - # - # (You can find the path to that makefile by examining - # .../status/.dbapi_driver.dep or .../build/Makefile.flat.) - # - # To take full advantage of --with-flat-makefile, you'll need the following (instead of 'emake all_p -C "${S}"_build/build') and call configure --with-flat-makefile: - LDFLAGS=-Wl,-rpath-link,"${S}"_build/lib emake -C "${S}"_build/build -f Makefile.flat - # - # >=gcc-5.3.0 is not supported, see also bug #579248#c8 - # configure: error: Do not know how to build MT-safe with compiler /usr/bin/x86_64-pc-linux-gnu-g++ 5.3.0 -} - -src_install() { - rm -rvf "${S}"_build/lib/ncbi || die - emake install prefix="${ED}/usr" libdir="${ED}/usr/$(get_libdir)/${PN}" - # - #if [ ! use static-libs -a ! use static ]; then - # rm -f "${ED}/usr/$(get_libdir)/${PN}"/*.a \ - # "${ED}/usr/$(get_libdir)/${PN}"/*-static.a || die - #fi - -# dobin "${S}"_build/bin/* -# dolib.so "${S}"_build/lib/*so* -# dolib.a "${S}"_build/lib/*.a -# doheader "${S}"_build/inc/* - - # File collisions with sci-biology/ncbi-tools - mv "${ED}"/usr/bin/asn2asn "${ED}"/usr/bin/asn2asn+ - mv "${ED}"/usr/bin/rpsblast "${ED}"/usr/bin/rpsblast+ - mv -f "${ED}"/usr/bin/test_regexp "${ED}"/usr/bin/test_regexp+ # drop the eventually mistakenly compiled binaries - mv "${ED}"/usr/bin/vecscreen "${ED}"/usr/bin/vecscreen+ - mv "${ED}"/usr/bin/seedtop "${ED}"/usr/bin/seedtop+ - # - # idfetch collides with idfetch from ncbi-tools-2.2.26 - # Although the two idfetch implementations do deliberately have several - # options in common, the C++ version is not yet a full drop-in replacement - # for the C version (and will never entirely be, due to fundamental - # differences between the two toolkits' argument-parsing conventions). - mv "${ED}"/usr/bin/idfetch "${ED}"/usr/bin/idfetch+ # new in ncbi-tools++-18.0.0 - - echo "LDPATH=${EPREFIX}/usr/$(get_libdir)/${PN}" > ${S}/99${PN} - doenvd "${S}/99${PN}" -} - -pkg_postinst() { - einfo 'Please run "source /etc/profile" before using this package in the current shell.' - einfo 'Documentation is at http://www.ncbi.nlm.nih.gov/books/NBK7167/' -} diff --git a/sci-biology/ncbi-vdb/ncbi-vdb-2.11.2.ebuild b/sci-biology/ncbi-vdb/ncbi-vdb-2.11.2.ebuild index 167e2a8c3..15f83b00c 100644 --- a/sci-biology/ncbi-vdb/ncbi-vdb-2.11.2.ebuild +++ b/sci-biology/ncbi-vdb/ncbi-vdb-2.11.2.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) inherit python-single-r1 DESCRIPTION=" NCBI SRA ( Sequence Read Archive )" diff --git a/sci-biology/neuroconv/Manifest b/sci-biology/neuroconv/Manifest new file mode 100644 index 000000000..35c461b92 --- /dev/null +++ b/sci-biology/neuroconv/Manifest @@ -0,0 +1 @@ +DIST neuroconv-0.4.8.gh.tar.gz 1020546 BLAKE2B 880d7c4bdce3faf3bc969c9a0fd4206e1fd9d57254e40aa1181cf2d8f48abd72491b8b66d8ccc1988a623f8b2a8be160f2575f59ea69080a8bb6ed501c389881 SHA512 d06a625823a71f21a5eac957e452ab80b6fb847fc5f8c8e68fb6c46360402c4bc338f7fc611537272e72c0b72555a2951c346d38aa89c8ac8b209921ea7af72d diff --git a/sci-biology/neuroconv/metadata.xml b/sci-biology/neuroconv/metadata.xml new file mode 100644 index 000000000..efd00647e --- /dev/null +++ b/sci-biology/neuroconv/metadata.xml @@ -0,0 +1,21 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>gentoo@chymera.eu</email> + <name>Horea Christian</name> + </maintainer> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <use> + <flag name="ecephys">Extracellular electrophysiology interfaces</flag> + <flag name="icephys">Intracellular electrophysiology interfaces</flag> + <flag name="ophys">Optical physiology interfaces</flag> + </use> + <upstream> + <remote-id type="github">catalystneuro/roiextractors</remote-id> + <remote-id type="pypi">roiextractors</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/neuroconv/neuroconv-0.4.8-r1.ebuild b/sci-biology/neuroconv/neuroconv-0.4.8-r1.ebuild new file mode 100644 index 000000000..b21c2fd8e --- /dev/null +++ b/sci-biology/neuroconv/neuroconv-0.4.8-r1.ebuild @@ -0,0 +1,66 @@ +# Copyright 2021-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 + +DESCRIPTION="Create NWB files from proprietary formats." +HOMEPAGE="https://github.com/catalystneuro/neuroconv" +SRC_URI="https://github.com/catalystneuro/neuroconv/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" +IUSE="+ecephys +icephys +ophys" + +RDEPEND=" + dev-python/docstring-parser[${PYTHON_USEDEP}] + dev-python/h5py[${PYTHON_USEDEP}] + dev-python/hdmf-zarr[${PYTHON_USEDEP}] + dev-python/hdmf[${PYTHON_USEDEP}] + dev-python/jsonschema[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/nwbinspector[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + dev-python/parse[${PYTHON_USEDEP}] + dev-python/psutil[${PYTHON_USEDEP}] + dev-python/pydantic[${PYTHON_USEDEP}] + dev-python/pynwb[${PYTHON_USEDEP}] + dev-python/pyyaml[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + dev-python/tqdm[${PYTHON_USEDEP}] + ecephys? ( + dev-python/spikeinterface[${PYTHON_USEDEP}] + ) + icephys? ( + dev-python/neo[${PYTHON_USEDEP}] + ) + ophys? ( + sci-biology/roiextractors[${PYTHON_USEDEP}] + ) +" +BDEPEND=" + test? ( + dev-python/parameterized[${PYTHON_USEDEP}] + ) +" + +distutils_enable_tests pytest + +# Reported upstream: +# https://github.com/catalystneuro/neuroconv/issues/785 +EPYTEST_DESELECT=( + tests/test_ecephys/test_mock_recording_interface.py::TestMockRecordingInterface::test_conversion_as_lone_interface +) + +python_test() { + # Additional tests require complex data getting infrastructure, ophys tests still have issues: + # https://github.com/catalystneuro/neuroconv/issues/305 + local my_tests=( "tests/test_minimal" ) + use ecephys && my_tests+=( "tests/test_ecephys" ) + #use ophys && my_tests+=( "tests/test_ophys" ) + epytest ${my_tests[*]// /|} +} diff --git a/sci-biology/nextclip/metadata.xml b/sci-biology/nextclip/metadata.xml index 138cb7705..b0874714e 100644 --- a/sci-biology/nextclip/metadata.xml +++ b/sci-biology/nextclip/metadata.xml @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">richardmleggett/nextclip</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/ngs/metadata.xml b/sci-biology/ngs/metadata.xml index 138cb7705..f165e6cbc 100644 --- a/sci-biology/ngs/metadata.xml +++ b/sci-biology/ngs/metadata.xml @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">ncbi/ngs</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/ngs/ngs-2.11.2.ebuild b/sci-biology/ngs/ngs-2.11.2.ebuild index 8675ae22a..0574c5076 100644 --- a/sci-biology/ngs/ngs-2.11.2.ebuild +++ b/sci-biology/ngs/ngs-2.11.2.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) inherit python-single-r1 java-pkg-2 DESCRIPTION="NGS Language Bindings " diff --git a/sci-biology/nilearn/Manifest b/sci-biology/nilearn/Manifest index 5dd197214..550ed1f0f 100644 --- a/sci-biology/nilearn/Manifest +++ b/sci-biology/nilearn/Manifest @@ -1,2 +1,2 @@ -DIST nilearn-0.8.1.tar.gz 11305317 BLAKE2B adefde80f5bce5ef115299326d212a7771a6ca1fc1ed7afc20fdd5b099882cfe37cc2d163807677450328916704d44e8f4044229b1470f764c75ee12d2e72b63 SHA512 4de95caa5c2080665e827310de28efb48a8b2e8161ac62f9e799984dbcd364f45ce486fcd21e9f30ef1fc41f48d2e41e477846acec5f89caf3cc1489373293d4 -DIST nilearn-0.9.1.tar.gz 11660100 BLAKE2B f2031b531faf2b7f77a6128ce2c41d4d8c4c9d5fab79df453ca127228f7ec4784b319107a9e9988b3d3a9ce87358d251e500a88dfb8226a6d4510ae5fe9f3a0c SHA512 f824fc563fd56b25508ee5803963fc98c2048fbab8823a6a6bde39e4b428a871588211649b4ce939f65173f6d4afd019e9fe1445b5cfdd00fba7823d9e23a571 +DIST nilearn-0.8.1.gh.tar.gz 11305317 BLAKE2B adefde80f5bce5ef115299326d212a7771a6ca1fc1ed7afc20fdd5b099882cfe37cc2d163807677450328916704d44e8f4044229b1470f764c75ee12d2e72b63 SHA512 4de95caa5c2080665e827310de28efb48a8b2e8161ac62f9e799984dbcd364f45ce486fcd21e9f30ef1fc41f48d2e41e477846acec5f89caf3cc1489373293d4 +DIST nilearn-0.9.1.gh.tar.gz 11660100 BLAKE2B f2031b531faf2b7f77a6128ce2c41d4d8c4c9d5fab79df453ca127228f7ec4784b319107a9e9988b3d3a9ce87358d251e500a88dfb8226a6d4510ae5fe9f3a0c SHA512 f824fc563fd56b25508ee5803963fc98c2048fbab8823a6a6bde39e4b428a871588211649b4ce939f65173f6d4afd019e9fe1445b5cfdd00fba7823d9e23a571 diff --git a/sci-biology/nilearn/files/0.4.1-bundled_joblib_test.patch b/sci-biology/nilearn/files/0.4.1-bundled_joblib_test.patch deleted file mode 100644 index e229d25fb..000000000 --- a/sci-biology/nilearn/files/0.4.1-bundled_joblib_test.patch +++ /dev/null @@ -1,39 +0,0 @@ ---- a/nilearn/input_data/tests/test_nifti_masker.py 2018-08-02 18:57:07.700111595 +0200 -+++ b/nilearn/input_data/tests/test_nifti_masker.py 2018-08-02 18:57:29.453556439 +0200 -@@ -219,36 +219,6 @@ - assert_raises(ValueError, masker.fit_transform, data_img) - - --def test_joblib_cache(): -- from sklearn.externals.joblib import hash, Memory -- mask = np.zeros((40, 40, 40)) -- mask[20, 20, 20] = 1 -- mask_img = Nifti1Image(mask, np.eye(4)) -- -- with testing.write_tmp_imgs(mask_img, create_files=True) as filename: -- masker = NiftiMasker(mask_img=filename) -- masker.fit() -- mask_hash = hash(masker.mask_img_) -- masker.mask_img_.get_data() -- assert_true(mask_hash == hash(masker.mask_img_)) -- -- # Test a tricky issue with memmapped joblib.memory that makes -- # imgs return by inverse_transform impossible to save -- cachedir = mkdtemp() -- try: -- masker.memory = Memory(cachedir=cachedir, mmap_mode='r', -- verbose=0) -- X = masker.transform(mask_img) -- # inverse_transform a first time, so that the result is cached -- out_img = masker.inverse_transform(X) -- out_img = masker.inverse_transform(X) -- out_img.to_filename(os.path.join(cachedir, 'test.nii')) -- finally: -- # enables to delete "filename" on windows -- del masker -- shutil.rmtree(cachedir, ignore_errors=True) -- -- - def test_mask_init_errors(): - # Errors that are caught in init - mask = NiftiMasker(mask_strategy='oops') diff --git a/sci-biology/nilearn/nilearn-0.8.1.ebuild b/sci-biology/nilearn/nilearn-0.8.1.ebuild index c73c9f519..3064c0ba5 100644 --- a/sci-biology/nilearn/nilearn-0.8.1.ebuild +++ b/sci-biology/nilearn/nilearn-0.8.1.ebuild @@ -1,15 +1,15 @@ -# Copyright 1999-2022 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 -PYTHON_COMPAT=( python3_{8..9} ) +PYTHON_COMPAT=( python3_{10..11} ) inherit distutils-r1 DESCRIPTION="Fast and easy statistical learning on NeuroImaging data" HOMEPAGE="http://nilearn.github.io/" -SRC_URI="https://github.com/nilearn/nilearn/archive/${PV}.tar.gz -> ${P}.tar.gz" +SRC_URI="https://github.com/nilearn/nilearn/archive/${PV}.tar.gz -> ${P}.gh.tar.gz" LICENSE="BSD" SLOT="0" diff --git a/sci-biology/nilearn/nilearn-0.9.1.ebuild b/sci-biology/nilearn/nilearn-0.9.1.ebuild index 7e3716791..425e79444 100644 --- a/sci-biology/nilearn/nilearn-0.9.1.ebuild +++ b/sci-biology/nilearn/nilearn-0.9.1.ebuild @@ -1,15 +1,15 @@ -# Copyright 1999-2022 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 -PYTHON_COMPAT=( python3_{8..9} ) +PYTHON_COMPAT=( python3_{10..11} ) inherit distutils-r1 DESCRIPTION="Fast and easy statistical learning on NeuroImaging data" HOMEPAGE="http://nilearn.github.io/" -SRC_URI="https://github.com/nilearn/nilearn/archive/${PV}.tar.gz -> ${P}.tar.gz" +SRC_URI="https://github.com/nilearn/nilearn/archive/${PV}.tar.gz -> ${P}.gh.tar.gz" LICENSE="BSD" SLOT="0" @@ -40,6 +40,7 @@ EPYTEST_IGNORE=( # Reported upstream: # https://github.com/nilearn/nilearn/issues/3232 EPYTEST_DESELECT=( + "nilearn/decoding/tests/test_decoder.py::test_decoder_dummy_classifier" "nilearn/interfaces/fmriprep/tests/test_load_confounds.py::test_nilearn_standardize[False-True-zscore]" "nilearn/interfaces/fmriprep/tests/test_load_confounds.py::test_nilearn_standardize[False-True-psc]" "nilearn/interfaces/fmriprep/tests/test_load_confounds.py::test_nilearn_standardize[True-True-zscore]" diff --git a/sci-biology/nitime/Manifest b/sci-biology/nitime/Manifest index 2ba87b1bb..4a9a85cc0 100644 --- a/sci-biology/nitime/Manifest +++ b/sci-biology/nitime/Manifest @@ -1 +1,2 @@ +DIST nitime-0.10.2.tar.gz 6231004 BLAKE2B 2214eb4fcb29567ebb4e819451bf7401ae6b467c0a2d196904c08bc44343e5c1ea840770f72d37df5e6642df455d895bfc9453b9389d8ef96cc88f3abc0d586e SHA512 c8c687f6c5e189e48bbe5cba4bbe3f19f34e6d087b43e3b0aa42d587f46081d3727867dbe07fa6d945381119086e12c98cdf12798055529a484152a4c04eae21 DIST nitime-0.9.tar.gz 6222979 BLAKE2B 45dbf34fd89b805f97ae5d4f88264f47ff88fa1f89b7ef05527477270bfa588a79fd1b356b2e7206919ed675936207accc02ad5b9a4be27e916a1dcf0561147e SHA512 cd8af7c3463143ac1765c472c1274915adfaf85508c334008c703ef72961e0a5e9ccbbd9321aaf62f7a58d9534934386baf1c7269a1d8f2d41b678707cd69406 diff --git a/sci-biology/nitime/metadata.xml b/sci-biology/nitime/metadata.xml index d504ea22c..606822ddb 100644 --- a/sci-biology/nitime/metadata.xml +++ b/sci-biology/nitime/metadata.xml @@ -10,10 +10,11 @@ <name>Gentoo Science Project</name> </maintainer> <longdescription lang="en"> -Nitime is a library for time-series analysis of data from neuroscience experiments -in both the time and spectral domains. -</longdescription> + Nitime is a library for time-series analysis of data from neuroscience experiments + in both the time and spectral domains. + </longdescription> <upstream> <remote-id type="github">nipy/nitime</remote-id> + <remote-id type="pypi">nitime</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/nitime/nitime-0.10.2.ebuild b/sci-biology/nitime/nitime-0.10.2.ebuild new file mode 100644 index 000000000..7e47d7288 --- /dev/null +++ b/sci-biology/nitime/nitime-0.10.2.ebuild @@ -0,0 +1,33 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) + +inherit distutils-r1 pypi + +DESCRIPTION="Time-series analysis of neuroscience data" +HOMEPAGE="http://nipy.org/nitime/index.html" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +COMMON_DEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/matplotlib[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + " +BDEPEND="${COMMON_DEPEND} + dev-python/cython[${PYTHON_USEDEP}] + " +RDEPEND=" + ${COMMON_DEPEND} + dev-python/networkx[${PYTHON_USEDEP}] + sci-libs/nibabel[${PYTHON_USEDEP}] + " + +distutils_enable_tests pytest +distutils_enable_sphinx doc diff --git a/sci-biology/nitime/nitime-0.9.ebuild b/sci-biology/nitime/nitime-0.9.ebuild index 90cb4ff6a..cae7fdfea 100644 --- a/sci-biology/nitime/nitime-0.9.ebuild +++ b/sci-biology/nitime/nitime-0.9.ebuild @@ -1,15 +1,14 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7,8,9} ) +PYTHON_COMPAT=( python3_{10..11} ) -inherit distutils-r1 virtualx +inherit distutils-r1 pypi virtualx DESCRIPTION="Time-series analysis of neuroscience data" HOMEPAGE="http://nipy.org/nitime/index.html" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" LICENSE="BSD" SLOT="0" diff --git a/sci-biology/nitime/nitime-9999.ebuild b/sci-biology/nitime/nitime-9999.ebuild index c46edf3c1..ee81c01dc 100644 --- a/sci-biology/nitime/nitime-9999.ebuild +++ b/sci-biology/nitime/nitime-9999.ebuild @@ -1,11 +1,12 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7,8,9} ) +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) -inherit distutils-r1 git-r3 virtualx +inherit distutils-r1 git-r3 DESCRIPTION="Time-series analysis of neuroscience data" HOMEPAGE="http://nipy.org/nitime/index.html" @@ -16,9 +17,6 @@ LICENSE="BSD" SLOT="0" KEYWORDS="" -# import file mismatch: -RESTRICT="test" - COMMON_DEPEND=" dev-python/numpy[${PYTHON_USEDEP}] dev-python/matplotlib[${PYTHON_USEDEP}] @@ -35,7 +33,3 @@ RDEPEND=" distutils_enable_tests pytest distutils_enable_sphinx doc - -python_test() { - virtx pytest -v || die -} diff --git a/sci-biology/ntCard/metadata.xml b/sci-biology/ntCard/metadata.xml index 138cb7705..fb03df79c 100644 --- a/sci-biology/ntCard/metadata.xml +++ b/sci-biology/ntCard/metadata.xml @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">bcgsc/ntCard</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/nwalign3/Manifest b/sci-biology/nwalign3/Manifest deleted file mode 100644 index 7a5302a6d..000000000 --- a/sci-biology/nwalign3/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST nwalign3-0.1.2.tar.gz 101141 BLAKE2B 9a7060db7362fa4a0b8b01f7f5131d1b168ce1f7bfe40ff7e3a6f3c09977c227e01f4da74915af62f73c9519d6137f42e345382fb3d591a70fbbdea6d2d8b3d4 SHA512 4e8bad31f8e648d7b4fc46bd34cd8404cc08fa9e188a74fc083e4e18b5615e4b2db77c78754ca2069e4158382483eb92d876049d68a6532e83f5df409ae36f93 diff --git a/sci-biology/nwalign3/metadata.xml b/sci-biology/nwalign3/metadata.xml deleted file mode 100644 index ad73a59be..000000000 --- a/sci-biology/nwalign3/metadata.xml +++ /dev/null @@ -1,15 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@gmail.com</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="pypi">nwalign</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/nwalign3/nwalign3-0.1.2.ebuild b/sci-biology/nwalign3/nwalign3-0.1.2.ebuild deleted file mode 100644 index 7c2b96bb6..000000000 --- a/sci-biology/nwalign3/nwalign3-0.1.2.ebuild +++ /dev/null @@ -1,22 +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} ) -DISTUTILS_USE_SETUPTOOLS=rdepend - -inherit distutils-r1 - -DESCRIPTION="Needleman-Wunsch global sequence alignment in python3" -HOMEPAGE="https://github.com/briney/nwalign3" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64" - -DEPEND=" - dev-python/numpy - dev-python/cython" -RDEPEND="${DEPEND}" diff --git a/sci-biology/open-ephys-gui/Manifest b/sci-biology/open-ephys-gui/Manifest index a2611bd74..5863b7945 100644 --- a/sci-biology/open-ephys-gui/Manifest +++ b/sci-biology/open-ephys-gui/Manifest @@ -1 +1,3 @@ DIST open-ephys-gui-0.5.5.tar.gz 63347783 BLAKE2B 8f3ab3c20e23dd4f613e2ed47dca1827ddbcc5e95be5ca12dfeefdc84611653d531d629b78049397fd4951d558f63531ea2265d13e629c8da793fc20090d1075 SHA512 b835a7f8bb3eeb08ec77f6d14f988d6278b2f5b1966fbf8bec55d429c9cee36050cf574dd78a2ebad4adc5c681bcec5b64dcfb1ec87e548c55e2bf1bff2eb2dc +DIST open-ephys-gui-0.6.1.tar.gz 44674639 BLAKE2B 10113418c41ccc62064bd8b993aab5402691259702c53c580e39371bd5034bc3b65babfa0adcaa7e2aadb8a86758e52cc4a86fee83db05614c849ed4c2b76ff4 SHA512 00ef7e5fd1242c84948e8eaf0479337365de21a28cb77252bf2baf806b186b9c8b7a424d756a4b6a883ecac48aefd6d2a532a8cadaa910e295b474d38056547e +DIST open-ephys-gui-0.6.4.tar.gz 44686737 BLAKE2B 839e33679cc14ffa9e2da99622e7a18f6c4f17d6a45a6c07b1136372126e2c05ad4804bc3bdf5412c7e74d00242d61d0a084574d619ea7acad4485a4aa150795 SHA512 5ac81076731d0b325ea9267d52c702c4fbb972a9c73ab156ccf9752b14cc842d7fdbca2ba292277c9127f124ca2fa73c555a51219bd3e1c95c63f40837f7eff2 diff --git a/sci-biology/open-ephys-gui/files/open-ephys-gui-0.6.1.patch b/sci-biology/open-ephys-gui/files/open-ephys-gui-0.6.1.patch new file mode 100644 index 000000000..0992f2241 --- /dev/null +++ b/sci-biology/open-ephys-gui/files/open-ephys-gui-0.6.1.patch @@ -0,0 +1,15 @@ +# Add 'Gentoo' build type + +--- ../CMakeLists.txt 2022-08-24 15:27:32.871426442 -0300 ++++ ../CMakeLists.txt 2022-08-24 15:31:03.438087613 -0300 +@@ -171,8 +171,8 @@ + target_compile_options(open-ephys PRIVATE -O0) #enable optimization for linux debug + elseif (${CMAKE_BUILD_TYPE} STREQUAL "Release") + target_compile_options(open-ephys PRIVATE -O3) #enable optimization for linux release +- else() +- message(FATAL_ERROR "Invalid build type") ++ # else() ++ # message(FATAL_ERROR "Invalid build type") + endif() + find_package(CURL REQUIRED) + find_package(PkgConfig REQUIRED) diff --git a/sci-biology/open-ephys-gui/files/open-ephys-gui-0.6.4.patch b/sci-biology/open-ephys-gui/files/open-ephys-gui-0.6.4.patch new file mode 100644 index 000000000..5c0c6526e --- /dev/null +++ b/sci-biology/open-ephys-gui/files/open-ephys-gui-0.6.4.patch @@ -0,0 +1,15 @@ +# Add 'Gentoo' build type + +--- ../CMakeLists.txt 2022-08-24 15:27:32.871426442 -0300 ++++ ../CMakeLists.txt 2022-08-24 15:31:03.438087613 -0300 +@@ -173,8 +173,8 @@ + target_compile_options(open-ephys PRIVATE -O0) #enable optimization for linux debug + elseif (${CMAKE_BUILD_TYPE} STREQUAL "Release") + target_compile_options(open-ephys PRIVATE -O3) #enable optimization for linux release +- else() +- message(FATAL_ERROR "Invalid build type") ++ # else() ++ # message(FATAL_ERROR "Invalid build type") + endif() + find_package(CURL REQUIRED) + find_package(PkgConfig REQUIRED) diff --git a/sci-biology/open-ephys-gui/files/open-ephys-gui-9999.patch b/sci-biology/open-ephys-gui/files/open-ephys-gui-9999.patch deleted file mode 100644 index 77e401639..000000000 --- a/sci-biology/open-ephys-gui/files/open-ephys-gui-9999.patch +++ /dev/null @@ -1,12 +0,0 @@ -# Add 'Gentoo' build type - ---- ../CMakeLists.txt 2019-12-02 22:29:24.021065669 -0300 -+++ ../CMakeLists.txt 2019-12-02 22:29:11.251065418 -0300 -@@ -123,6 +123,7 @@ - if(${CMAKE_BUILD_TYPE} STREQUAL "Debug") - - elseif (${CMAKE_BUILD_TYPE} STREQUAL "Release") -+ elseif (${CMAKE_BUILD_TYPE} STREQUAL "Gentoo") - else() - message(FATAL_ERROR "Invalid build type") - endif() diff --git a/sci-biology/open-ephys-gui/files/open-ephys-gui-99999999.patch b/sci-biology/open-ephys-gui/files/open-ephys-gui-99999999.patch deleted file mode 100644 index 77e401639..000000000 --- a/sci-biology/open-ephys-gui/files/open-ephys-gui-99999999.patch +++ /dev/null @@ -1,12 +0,0 @@ -# Add 'Gentoo' build type - ---- ../CMakeLists.txt 2019-12-02 22:29:24.021065669 -0300 -+++ ../CMakeLists.txt 2019-12-02 22:29:11.251065418 -0300 -@@ -123,6 +123,7 @@ - if(${CMAKE_BUILD_TYPE} STREQUAL "Debug") - - elseif (${CMAKE_BUILD_TYPE} STREQUAL "Release") -+ elseif (${CMAKE_BUILD_TYPE} STREQUAL "Gentoo") - else() - message(FATAL_ERROR "Invalid build type") - endif() diff --git a/sci-biology/open-ephys-gui/metadata.xml b/sci-biology/open-ephys-gui/metadata.xml index ed9bf87e3..2c9af77a9 100644 --- a/sci-biology/open-ephys-gui/metadata.xml +++ b/sci-biology/open-ephys-gui/metadata.xml @@ -5,6 +5,10 @@ <email>malfatti@disroot.org</email> <name>T Malfatti</name> </maintainer> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> <upstream> <remote-id type="github">open-ephys/plugin-GUI</remote-id> </upstream> diff --git a/sci-biology/open-ephys-gui/open-ephys-gui-0.6.1.ebuild b/sci-biology/open-ephys-gui/open-ephys-gui-0.6.1.ebuild new file mode 100644 index 000000000..fe6791a2d --- /dev/null +++ b/sci-biology/open-ephys-gui/open-ephys-gui-0.6.1.ebuild @@ -0,0 +1,83 @@ +# Copyright 2019-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 +inherit cmake udev + +DESCRIPTION="Processing, recording, and visualizing multichannel ephys data" +HOMEPAGE="https://open-ephys.org/gui/" +LICENSE="GPL-3" + +if [[ ${PV} == "9999" ]] ; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/open-ephys/plugin-GUI" + EGIT_BRANCH="main" + Suffix=${EGIT_BRANCH} + SubDir=${P} +elif [[ ${PV} == "99999999" ]] ; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/open-ephys/plugin-GUI" + EGIT_BRANCH="development" + Suffix=${EGIT_BRANCH} + SubDir=${P} +else + SRC_URI="https://github.com/open-ephys/plugin-GUI/archive/v${PV}.tar.gz -> ${P}.tar.gz" + Suffix=${PV} + SubDir="plugin-GUI-${PV}" + S="${WORKDIR}/${SubDir}" + KEYWORDS="~amd64 ~x86" +fi + +SLOT="${PV}" +IUSE="jack" + +DEPEND=" + dev-libs/openssl + media-libs/alsa-lib + media-libs/freeglut + media-libs/freetype + net-libs/webkit-gtk + net-misc/curl + x11-libs/libXrandr + x11-libs/libXcursor + x11-libs/libXinerama + jack? ( || ( media-sound/jack-audio-connection-kit media-sound/jack2 ) ) +" +RDEPEND="${DEPEND}" + +BUILD_DIR="${S}/Build" +PATCHES=( "${FILESDIR}"/${P}.patch ) + +QA_PREBUILT="opt/open-ephys-*/shared/*.so" +QA_PRESTRIPPED=" + opt/open-ephys-*/plugins/*.so + opt/open-ephys-*/open-ephys +" + +src_prepare() { + cmake_src_prepare + + if use jack; then + sed -i 's/JUCE_APP_VERSION=/JUCE_JACK=1\n JUCE_APP_VERSION=/' "${WORKDIR}/${SubDir}/CMakeLists.txt" || die "Sed failed!" + fi +} + +src_configure() { + local mycmakeargs=( -DCMAKE_SKIP_RPATH=ON ) + cmake_src_configure +} + +src_install() { + dodir opt/open-ephys-"${Suffix}"/ lib/udev/rules.d/ + cp -R "${BUILD_DIR}"/RelWithDebInfo/* "${ED}"/opt/open-ephys-"${Suffix}"/ || die + udev_newrules "${WORKDIR}"/"${SubDir}"/Resources/Scripts/40-open-ephys.rules 40-open-ephys-"${Suffix}".rules + dosym ../../opt/open-ephys-"${Suffix}"/open-ephys usr/bin/open-ephys-"${Suffix}" +} + +pkg_postinst() { + udev_reload +} + +pkg_postrm() { + udev_reload +} diff --git a/sci-biology/open-ephys-gui/open-ephys-gui-0.6.4.ebuild b/sci-biology/open-ephys-gui/open-ephys-gui-0.6.4.ebuild new file mode 100644 index 000000000..cae41e773 --- /dev/null +++ b/sci-biology/open-ephys-gui/open-ephys-gui-0.6.4.ebuild @@ -0,0 +1,83 @@ +# Copyright 2019-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 +inherit cmake udev + +DESCRIPTION="Processing, recording, and visualizing multichannel ephys data" +HOMEPAGE="https://open-ephys.org/gui/" +LICENSE="GPL-3" + +if [[ ${PV} == "9999" ]] ; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/open-ephys/plugin-GUI" + EGIT_BRANCH="main" + Suffix=${EGIT_BRANCH} + SubDir=${P} +elif [[ ${PV} == "99999999" ]] ; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/open-ephys/plugin-GUI" + EGIT_BRANCH="development" + Suffix=${EGIT_BRANCH} + SubDir=${P} +else + SRC_URI="https://github.com/open-ephys/plugin-GUI/archive/v${PV}.tar.gz -> ${P}.tar.gz" + Suffix=${PV} + SubDir="plugin-GUI-${PV}" + S="${WORKDIR}/${SubDir}" + KEYWORDS="~amd64 ~x86" +fi + +SLOT="${PV}" +IUSE="jack" + +DEPEND=" + dev-libs/openssl + media-libs/alsa-lib + media-libs/freeglut + media-libs/freetype + net-libs/webkit-gtk:4 + net-misc/curl + x11-libs/libXrandr + x11-libs/libXcursor + x11-libs/libXinerama + jack? ( || ( media-sound/jack-audio-connection-kit media-sound/jack2 ) ) +" +RDEPEND="${DEPEND}" + +BUILD_DIR="${S}/Build" +PATCHES=( "${FILESDIR}"/${P}.patch ) + +QA_PREBUILT="opt/open-ephys-*/shared/*.so" +QA_PRESTRIPPED=" + opt/open-ephys-*/plugins/*.so + opt/open-ephys-*/open-ephys +" + +src_prepare() { + cmake_src_prepare + + if use jack; then + sed -i 's/JUCE_APP_VERSION=/JUCE_JACK=1\n JUCE_APP_VERSION=/' "${WORKDIR}/${SubDir}/CMakeLists.txt" || die "Sed failed!" + fi +} + +src_configure() { + local mycmakeargs=( -DCMAKE_SKIP_RPATH=ON ) + cmake_src_configure +} + +src_install() { + dodir opt/open-ephys-"${Suffix}"/ lib/udev/rules.d/ + cp -R "${BUILD_DIR}"/RelWithDebInfo/* "${ED}"/opt/open-ephys-"${Suffix}"/ || die + udev_newrules "${WORKDIR}"/"${SubDir}"/Resources/Scripts/40-open-ephys.rules 40-open-ephys-"${Suffix}".rules + dosym ../../opt/open-ephys-"${Suffix}"/open-ephys usr/bin/open-ephys-"${Suffix}" +} + +pkg_postinst() { + udev_reload +} + +pkg_postrm() { + udev_reload +} diff --git a/sci-biology/open-ephys-gui/open-ephys-gui-9999.ebuild b/sci-biology/open-ephys-gui/open-ephys-gui-9999.ebuild index 1c2b20e24..2ab957f40 100644 --- a/sci-biology/open-ephys-gui/open-ephys-gui-9999.ebuild +++ b/sci-biology/open-ephys-gui/open-ephys-gui-9999.ebuild @@ -1,7 +1,7 @@ -# Copyright 2019-2021 Gentoo Authors +# Copyright 2019-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 inherit cmake udev DESCRIPTION="Processing, recording, and visualizing multichannel ephys data" @@ -11,7 +11,7 @@ LICENSE="GPL-3" if [[ ${PV} == "9999" ]] ; then inherit git-r3 EGIT_REPO_URI="https://github.com/open-ephys/plugin-GUI" - EGIT_BRANCH="master" + EGIT_BRANCH="main" Suffix=${EGIT_BRANCH} SubDir=${P} elif [[ ${PV} == "99999999" ]] ; then @@ -32,9 +32,12 @@ SLOT="${PV}" IUSE="jack" DEPEND=" + dev-libs/openssl media-libs/alsa-lib media-libs/freeglut media-libs/freetype + net-libs/webkit-gtk:4 + net-misc/curl x11-libs/libXrandr x11-libs/libXcursor x11-libs/libXinerama @@ -43,7 +46,7 @@ DEPEND=" RDEPEND="${DEPEND}" BUILD_DIR="${S}/Build" -PATCHES=( "${FILESDIR}"/${P}.patch ) +PATCHES=( "${FILESDIR}"/"${PN}"-0.6.4.patch ) QA_PREBUILT="opt/open-ephys-*/shared/*.so" QA_PRESTRIPPED=" @@ -66,7 +69,7 @@ src_configure() { src_install() { dodir opt/open-ephys-"${Suffix}"/ lib/udev/rules.d/ - cp -R "${BUILD_DIR}"/Gentoo/* "${ED}"/opt/open-ephys-"${Suffix}"/ + cp -R "${BUILD_DIR}"/RelWithDebInfo/* "${ED}"/opt/open-ephys-"${Suffix}"/ || die udev_newrules "${WORKDIR}"/"${SubDir}"/Resources/Scripts/40-open-ephys.rules 40-open-ephys-"${Suffix}".rules dosym ../../opt/open-ephys-"${Suffix}"/open-ephys usr/bin/open-ephys-"${Suffix}" } diff --git a/sci-biology/open-ephys-gui/open-ephys-gui-99999999.ebuild b/sci-biology/open-ephys-gui/open-ephys-gui-99999999.ebuild index 1c2b20e24..2ab957f40 100644 --- a/sci-biology/open-ephys-gui/open-ephys-gui-99999999.ebuild +++ b/sci-biology/open-ephys-gui/open-ephys-gui-99999999.ebuild @@ -1,7 +1,7 @@ -# Copyright 2019-2021 Gentoo Authors +# Copyright 2019-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 inherit cmake udev DESCRIPTION="Processing, recording, and visualizing multichannel ephys data" @@ -11,7 +11,7 @@ LICENSE="GPL-3" if [[ ${PV} == "9999" ]] ; then inherit git-r3 EGIT_REPO_URI="https://github.com/open-ephys/plugin-GUI" - EGIT_BRANCH="master" + EGIT_BRANCH="main" Suffix=${EGIT_BRANCH} SubDir=${P} elif [[ ${PV} == "99999999" ]] ; then @@ -32,9 +32,12 @@ SLOT="${PV}" IUSE="jack" DEPEND=" + dev-libs/openssl media-libs/alsa-lib media-libs/freeglut media-libs/freetype + net-libs/webkit-gtk:4 + net-misc/curl x11-libs/libXrandr x11-libs/libXcursor x11-libs/libXinerama @@ -43,7 +46,7 @@ DEPEND=" RDEPEND="${DEPEND}" BUILD_DIR="${S}/Build" -PATCHES=( "${FILESDIR}"/${P}.patch ) +PATCHES=( "${FILESDIR}"/"${PN}"-0.6.4.patch ) QA_PREBUILT="opt/open-ephys-*/shared/*.so" QA_PRESTRIPPED=" @@ -66,7 +69,7 @@ src_configure() { src_install() { dodir opt/open-ephys-"${Suffix}"/ lib/udev/rules.d/ - cp -R "${BUILD_DIR}"/Gentoo/* "${ED}"/opt/open-ephys-"${Suffix}"/ + cp -R "${BUILD_DIR}"/RelWithDebInfo/* "${ED}"/opt/open-ephys-"${Suffix}"/ || die udev_newrules "${WORKDIR}"/"${SubDir}"/Resources/Scripts/40-open-ephys.rules 40-open-ephys-"${Suffix}".rules dosym ../../opt/open-ephys-"${Suffix}"/open-ephys usr/bin/open-ephys-"${Suffix}" } diff --git a/sci-biology/opfvta_bidsdata/opfvta_bidsdata-2.0.ebuild b/sci-biology/opfvta_bidsdata/opfvta_bidsdata-2.0.ebuild index c43c10257..d21f85f8c 100644 --- a/sci-biology/opfvta_bidsdata/opfvta_bidsdata-2.0.ebuild +++ b/sci-biology/opfvta_bidsdata/opfvta_bidsdata-2.0.ebuild @@ -6,7 +6,7 @@ EAPI=7 inherit check-reqs DESCRIPTION="BIDS data files released with the OPFVTA publication" -HOMEPAGE="http://www.aic-fmi.ethz.ch/" +HOMEPAGE="http://chymera.eu/docs/focus/open-science/" SRC_URI=" https://zenodo.org/record/3575149/files/${P}.tar.xz " diff --git a/sci-biology/pbbam/Manifest b/sci-biology/pbbam/Manifest index c35432703..1bb2b2625 100644 --- a/sci-biology/pbbam/Manifest +++ b/sci-biology/pbbam/Manifest @@ -1 +1 @@ -DIST pbbam-1.8.1.tar.gz 11069936 BLAKE2B 6ef23c81f4cfbdb060bfc8355ca628024038466482a6cacb3dd162fa58ab1052702e482ab797a60160264fd2cc70fe116dd5385c6094560060adf6fe2cf74d10 SHA512 ea28b4683c72fafb2e459ac1f37a9be258ddc82e059ba9d8b094e8dd6e3a40d3f25d5edcc790c5bd274805190caf1123311199e30166bd4f3e815dcc77929387 +DIST pbbam-2.1.0.tar.gz 10405332 BLAKE2B c91122afcc8fae747fbf1e40274aeb7f2fbc5a02789945798899c6ae87ff01beaae994a80a356a71a788e8626ee5a3595537d8bd6468ac30a874733fa9e9d883 SHA512 5f606620d1a6eb7c31c36db4d6fd125e397c4b81d9f695dc8756535074ce98c4b05e04d86077ed33e0ba1e503e766b1b59e08bb73e8f8129af7789024f308094 diff --git a/sci-biology/pbbam/metadata.xml b/sci-biology/pbbam/metadata.xml index 138cb7705..e12f3579e 100644 --- a/sci-biology/pbbam/metadata.xml +++ b/sci-biology/pbbam/metadata.xml @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">PacificBiosciences/pbbam</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/pbbam/pbbam-1.8.1.ebuild b/sci-biology/pbbam/pbbam-2.1.0.ebuild index a114da0fc..a114da0fc 100644 --- a/sci-biology/pbbam/pbbam-1.8.1.ebuild +++ b/sci-biology/pbbam/pbbam-2.1.0.ebuild diff --git a/sci-biology/phusion2/Manifest b/sci-biology/phusion2/Manifest deleted file mode 100644 index fce8afa2a..000000000 --- a/sci-biology/phusion2/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST phusion2-3.0.tar.gz 136875 BLAKE2B 8338df1865ac8f684ba3a2a2fc15520fe167a1ace02e8f64db17f6acf07ea8cde2da18fd6f18a958e53b00dd02e7e8138305e2a762a84c6bf8d7cfbd2cb9b999 SHA512 a29e4102806d404a7bc78c1611d702f9c6415bc04ca518416632bf8d9d3e570324add907c43e627f645a5281b807ccf169908637121f66883c4e878080345eca diff --git a/sci-biology/phusion2/metadata.xml b/sci-biology/phusion2/metadata.xml deleted file mode 100644 index 0f267b755..000000000 --- a/sci-biology/phusion2/metadata.xml +++ /dev/null @@ -1,15 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">downloads</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/phusion2/phusion2-3.0.ebuild b/sci-biology/phusion2/phusion2-3.0.ebuild deleted file mode 100644 index 2ea281d41..000000000 --- a/sci-biology/phusion2/phusion2-3.0.ebuild +++ /dev/null @@ -1,37 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DESCRIPTION="Whole genome shotgun assembler using phrap (for Sanger-based reads)" -HOMEPAGE="https://sourceforge.net/projects/phusion2" -SRC_URI="https://downloads.sourceforge.net/project/${PN}/${P}.tar.gz" - -LICENSE="all-rights-reserved" # temporarily placed value -# from http://genome.cshlp.org/content/13/1/81.full -# Availability -# Phusion is undergoing a rewrite of the code to make this a portable package. It will be made available free of charge to academic sites, but requires licensing for commercial use. For more information please contact the authors. -SLOT="0" -KEYWORDS="~amd64" - -DEPEND="app-shells/tcsh - sys-cluster/openmpi" -RDEPEND="${DEPEND} - sci-biology/phrap - dev-lang/perl" - -# contains bundled ssaha -# file collision with sci-biology/shrimp on /usr/bin/fasta2fastq - -S="${WORKDIR}" - -src_prepare(){ - default - rm -f phusion2 *.o - sed -e 's/^CFLAGS =/# CFLAGS =/' -i Makefile || die -} - -src_install(){ - dobin ctgreads.pl phusion2 - dodoc how_to_make_mates -} diff --git a/sci-biology/polyphen/Manifest b/sci-biology/polyphen/Manifest deleted file mode 100644 index 6b1d95704..000000000 --- a/sci-biology/polyphen/Manifest +++ /dev/null @@ -1,3 +0,0 @@ -DIST mafft-7.221-without-extensions-src.tgz 376075 BLAKE2B effe24080d453bad8ff4cd424e8ea592e64e254233cbaa245cc71edbeba293edb24d039f9bde3f54c000a1b1f5d966317020a546d8fc78f63494066b207624a9 SHA512 f5a79621a784ef8b054e93be70aa0ada8a366951349b4e4f9e6a42c287502ba60ec0722c199da2874098c6b5c6b9449dfb5071914770a8364007b779a6a601a2 -DIST polyphen-2.2.2r405d.tar.gz 2205380 BLAKE2B 5cb863b8b1626bfa2da264bfebfe5fea3932d13eac5f74fd76932c310fa20cbdd33905d8faa7bb82739d3d0b2bdbaea94c1470a4f28c8df1fd5accee23faef26 SHA512 e2418b0e18aeb1ebeaa31a743901e89b8b5cd670357ed8d78d7d22f414b8f5e98e80124bbea9d7ebf2fdc7a6ef33f050b67683740c1e4a4d01ac7a75d33dbaac -DIST weka-3-6-12.zip 24335916 BLAKE2B fe9b9406fce1f8ad5b4338e7cf18d8a6cf1fbc19e335f5fd66197c1aa45fdaf25859a191a0d99d32e06e6f84a6d9f900817a9d574fe447a2be1a818855787f10 SHA512 4301e1c2a751e26ff8d860e24e54e71511276f8cb90020c935595aaaab547f8614381ca8087b83a670d13ef0ff3fa13084f4984b9249e16042703ef9f43c0bd1 diff --git a/sci-biology/polyphen/metadata.xml b/sci-biology/polyphen/metadata.xml deleted file mode 100644 index 138cb7705..000000000 --- a/sci-biology/polyphen/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>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/polyphen/polyphen-2.2.2.ebuild b/sci-biology/polyphen/polyphen-2.2.2.ebuild deleted file mode 100644 index 3100c6bbd..000000000 --- a/sci-biology/polyphen/polyphen-2.2.2.ebuild +++ /dev/null @@ -1,56 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DESCRIPTION="Predict effect of aminoacid substitution on human protein function" -HOMEPAGE="http://genetics.bwh.harvard.edu/pph2/dokuwiki/start" -SRC_URI=" - http://genetics.bwh.harvard.edu/pph2/dokuwiki/_media/polyphen-${PV}r405d.tar.gz - http://mafft.cbrc.jp/alignment/software/mafft-7.221-without-extensions-src.tgz - http://prdownloads.sourceforge.net/weka/weka-3-6-12.zip -" - -LICENSE="polyphen" # for non-commercial use only -SLOT="0" -KEYWORDS="~amd64" - -DEPEND=" - dev-perl/CGI - sci-biology/ncbi-blast+ -" -RDEPEND="${DEPEND}" -BDEPEND="app-arch/unzip" - -# 3.7GB -# ftp://genetics.bwh.harvard.edu/pph2/bundled/polyphen-2.2.2-databases-2011_12.tar.bz2 - -# 2.4GB -# ftp://genetics.bwh.harvard.edu/pph2/bundled/polyphen-2.2.2-alignments-mlc-2011_12.tar.bz2 - -# 895MB -# ftp://genetics.bwh.harvard.edu/pph2/bundled/polyphen-2.2.2-alignments-multiz-2009_10.tar.bz2 - -src_unpack() { - unpack "polyphen-${PV}r405d.tar.gz" - cp "${DISTDIR}/mafft-7.221-without-extensions-src.tgz" "${S}/src" || die - cp "${DISTDIR}/weka-3-6-12.zip" "${S}/src" || die -} - -src_configure() { - # non-standard configure script - ./configure -} - -src_compile() { - pushd src - emake -j1 - popd -} - -src_install() { - pushd src - default - popd - einstalldocs -} diff --git a/sci-biology/prokka/Manifest b/sci-biology/prokka/Manifest deleted file mode 100644 index e0285e5de..000000000 --- a/sci-biology/prokka/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST prokka-1.14.6.tar.gz 112621657 BLAKE2B 3188d0a9dc6c62fa375a007950eaf91a7ff3fe6d610e89daaa8f8f911dd0035ac976cd3a2f4a14719b5c5e7d9a5bf7fdae64f838d5c54101ca8818cb2d0fd2c0 SHA512 96cc7490072d68242d4444c0842af7618f7ac132d00b008b8c4c1056d45a1f6f25c0599e7b74cd0477794bd88d88897cf57276d29c979ff1104f79f5bbf7c447 diff --git a/sci-biology/prokka/metadata.xml b/sci-biology/prokka/metadata.xml deleted file mode 100644 index 138cb7705..000000000 --- a/sci-biology/prokka/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>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/prokka/prokka-1.14.6.ebuild b/sci-biology/prokka/prokka-1.14.6.ebuild deleted file mode 100644 index b56fd143f..000000000 --- a/sci-biology/prokka/prokka-1.14.6.ebuild +++ /dev/null @@ -1,36 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DESCRIPTION="Prokaryotic whole genome annotation pipeline" -HOMEPAGE="https://vicbioinformatics.com/software.prokka.shtml" -SRC_URI="https://github.com/tseemann/prokka/archive/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64" - -RDEPEND=" - sys-process/parallel - sci-biology/bioperl - sci-biology/prodigal - || ( sci-biology/ncbi-tools++ sci-biology/ncbi-blast+ ) - sci-biology/hmmer:* - sci-biology/infernal - sci-biology/exonerate - sci-biology/barrnap" -DEPEND="${RDEPEND}" -# sci-biology/minced -# >=sci-biolohy/hmmer-3.1 -# Aragorn -# >=RNAmmer-1.2 -# >=HMMmmer-2.0 (that is not sci-biology/hmmer) -# SignalP >= 3.0 -# sequin -# tbl2asn >= 23.0 from wget --mirror -nH -nd ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/linux64.tbl2asn.gz - -src_install() { - default - dobin bin/prokka -} diff --git a/sci-biology/proovread/Manifest b/sci-biology/proovread/Manifest deleted file mode 100644 index e6f75545a..000000000 --- a/sci-biology/proovread/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST proovread-2.14.1.tar.gz 21965507 BLAKE2B 5f9f3e6ae7f5b95a2cd9092f8ab8b53b70ac48733fe5f816fddd9b2e0957c3a8fe0bad74d317f780a628127e8a6674b238f9df9fb7908e705ff92ca7e21a8a4f SHA512 836c1da96fc90c24729d8e72610e48e6ccae5a9fc2d6fa94c32738537bbc95584c9d46b37659bbcf56cdc3c1412ca93b04c7c0a54a28a6e8cebeccd278a6f764 diff --git a/sci-biology/proovread/metadata.xml b/sci-biology/proovread/metadata.xml deleted file mode 100644 index 138cb7705..000000000 --- a/sci-biology/proovread/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>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/proovread/proovread-2.14.1.ebuild b/sci-biology/proovread/proovread-2.14.1.ebuild deleted file mode 100644 index be1d610b0..000000000 --- a/sci-biology/proovread/proovread-2.14.1.ebuild +++ /dev/null @@ -1,51 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit perl-functions - -DESCRIPTION="Error correct PacBio subreads using Illumina reads" -HOMEPAGE="https://github.com/BioInf-Wuerzburg/proovread" -if [ "$PV" == "9999" ]; then - inherit git-r3 - EGIT_REPO_URI="https://github.com/BioInf-Wuerzburg/proovread" -else - SRC_URI="https://github.com/BioInf-Wuerzburg/${PN}/releases/download/${P}/${P}.tar.gz" - KEYWORDS="~amd64 ~x86" -fi - -LICENSE="Artistic-2 GPL-3 blasr" -SLOT="0" - -# TODO: package shrimp and update blasr -# blasr requires new dep libblasr, which -# I cannot get to compile successfully -RDEPEND=" - >=dev-lang/perl-5.10 - dev-perl/Log-Log4perl - dev-perl/File-Which - >=sci-biology/ncbi-tools++-2.2.24 - >=sci-biology/samtools-1.1 -" -DEPEND="${RDEPEND}" - -src_install(){ - cd bin || die - dobin ChimeraToSeqFilter.pl dazz2sam ccseq bam2cns test_cfg.pl siamaera samfilter sam2cns proovread-flex proovread - cd ../util/bwa || die - dobin bwa-proovread # xa2multi.pl qualfa2fq.pl libbwa.a bwa.1 - cd ../../util/SeqFilter || die - dobin bin/SeqFilter - cd ../../util/SeqChunker || die - dobin bin/* - cd ../../lib || die - perl_domodule -r -C ${PN} * - cd ../util/blasr-1.3.1 || die - dobin blasr -} - -pkg_postinst(){ - einfo "Proovread uses its own, modified version of bwa as bwa-proovread" - einfo "with linked in libbwa.a. It also bundles shrimp2 and blasr" -} diff --git a/sci-biology/proovread/proovread-9999.ebuild b/sci-biology/proovread/proovread-9999.ebuild deleted file mode 100644 index be1d610b0..000000000 --- a/sci-biology/proovread/proovread-9999.ebuild +++ /dev/null @@ -1,51 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit perl-functions - -DESCRIPTION="Error correct PacBio subreads using Illumina reads" -HOMEPAGE="https://github.com/BioInf-Wuerzburg/proovread" -if [ "$PV" == "9999" ]; then - inherit git-r3 - EGIT_REPO_URI="https://github.com/BioInf-Wuerzburg/proovread" -else - SRC_URI="https://github.com/BioInf-Wuerzburg/${PN}/releases/download/${P}/${P}.tar.gz" - KEYWORDS="~amd64 ~x86" -fi - -LICENSE="Artistic-2 GPL-3 blasr" -SLOT="0" - -# TODO: package shrimp and update blasr -# blasr requires new dep libblasr, which -# I cannot get to compile successfully -RDEPEND=" - >=dev-lang/perl-5.10 - dev-perl/Log-Log4perl - dev-perl/File-Which - >=sci-biology/ncbi-tools++-2.2.24 - >=sci-biology/samtools-1.1 -" -DEPEND="${RDEPEND}" - -src_install(){ - cd bin || die - dobin ChimeraToSeqFilter.pl dazz2sam ccseq bam2cns test_cfg.pl siamaera samfilter sam2cns proovread-flex proovread - cd ../util/bwa || die - dobin bwa-proovread # xa2multi.pl qualfa2fq.pl libbwa.a bwa.1 - cd ../../util/SeqFilter || die - dobin bin/SeqFilter - cd ../../util/SeqChunker || die - dobin bin/* - cd ../../lib || die - perl_domodule -r -C ${PN} * - cd ../util/blasr-1.3.1 || die - dobin blasr -} - -pkg_postinst(){ - einfo "Proovread uses its own, modified version of bwa as bwa-proovread" - einfo "with linked in libbwa.a. It also bundles shrimp2 and blasr" -} diff --git a/sci-biology/pybedtools/Manifest b/sci-biology/pybedtools/Manifest index 8cfd1985e..a952ac4b8 100644 --- a/sci-biology/pybedtools/Manifest +++ b/sci-biology/pybedtools/Manifest @@ -1 +1,2 @@ DIST pybedtools-0.8.2.tar.gz 12496355 BLAKE2B f1ff67f524a5a51a6f6a5450bb72ecd6602fe41232c77a38838b9b4051c528abadaa65d561bbef69cb595624a7f2edee8b98927ca0e7a55d5352e56e17f81d64 SHA512 4534c0ff4eeebbe8e3b1f126563700e4ba2b212581a76106d89fa8c61e043974b76649bf68d0b78f45923d66eb63c44bc69994de1f5a42e5069a761a93b8acbe +DIST pybedtools-0.9.0.tar.gz 12497249 BLAKE2B f43c94a7dae773b2ca46c0105d4de57f4e93a095f168b67771a568b64bc088b517e160da27ef68d81fea3df75689cad1a3db2b25dda36a37ed688e4e426fe43a SHA512 aa0cca035d560bd4e4d39f6eac74e677e3bac3266af5b69ceca1c4878742220d576d0db9ebf9c8da490d24259b1153e9999a78d2a5c46f1acb544fa3dba73a18 diff --git a/sci-biology/pybedtools/pybedtools-0.8.2.ebuild b/sci-biology/pybedtools/pybedtools-0.8.2.ebuild index 95bee9be2..bc02bda6f 100644 --- a/sci-biology/pybedtools/pybedtools-0.8.2.ebuild +++ b/sci-biology/pybedtools/pybedtools-0.8.2.ebuild @@ -1,9 +1,10 @@ -# Copyright 1999-2022 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools inherit distutils-r1 @@ -15,9 +16,6 @@ LICENSE="MIT" SLOT="0" KEYWORDS="~amd64 ~x86" -# ModuleNotFoundError: No module named 'pybedtools.cbedtools' -RESTRICT="test" - RDEPEND=" sci-biology/bedtools sci-biology/pysam[${PYTHON_USEDEP}] @@ -34,3 +32,12 @@ BDEPEND="dev-python/cython[${PYTHON_USEDEP}]" # even if pybedtools is installed #distutils_enable_sphinx docs/source distutils_enable_tests pytest + +python_test() { + # Requires network + local EPYTEST_DESELECT=( + test/test_helpers.py::test_chromsizes + ) + cd "${T}" || die + epytest --pyargs pybedtools +} diff --git a/sci-biology/pybedtools/pybedtools-0.9.0.ebuild b/sci-biology/pybedtools/pybedtools-0.9.0.ebuild new file mode 100644 index 000000000..bc02bda6f --- /dev/null +++ b/sci-biology/pybedtools/pybedtools-0.9.0.ebuild @@ -0,0 +1,43 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools + +inherit distutils-r1 + +DESCRIPTION="Use BED and GFF files from python using BEDtools" +HOMEPAGE="https://daler.github.io/pybedtools" +SRC_URI="https://github.com/daler/pybedtools/archive/v${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +RDEPEND=" + sci-biology/bedtools + sci-biology/pysam[${PYTHON_USEDEP}] + dev-python/six[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + dev-python/matplotlib[${PYTHON_USEDEP}] +" + +BDEPEND="dev-python/cython[${PYTHON_USEDEP}]" + +# TODO: fix docs building +# ModuleNotFoundError: No module named 'pybedtools.cbedtools' +# even if pybedtools is installed +#distutils_enable_sphinx docs/source +distutils_enable_tests pytest + +python_test() { + # Requires network + local EPYTEST_DESELECT=( + test/test_helpers.py::test_chromsizes + ) + cd "${T}" || die + epytest --pyargs pybedtools +} diff --git a/sci-biology/pyfaidx/Manifest b/sci-biology/pyfaidx/Manifest index 7ce654125..0bb3b35f4 100644 --- a/sci-biology/pyfaidx/Manifest +++ b/sci-biology/pyfaidx/Manifest @@ -1 +1,2 @@ DIST pyfaidx-0.5.9.2.tar.gz 93438 BLAKE2B 3d3d225907f8bd04fdf4b20d608d02cd0e5a723f2a73df24b732992f139102e2a9042c37c5a73f762256fd007dd7e14bace910c0961e60870926c2ce1dca3ac3 SHA512 57b94421d6858fa2bd7b867b386d47d53d3afd75878b08e6e32fb7d8f4942f2a051e0123e6c4b4395abe656d639fa4f47afadbd8c4b2cbc001c5113cbbf96af4 +DIST pyfaidx-0.7.2.1.tar.gz 102951 BLAKE2B d8c76bb9f817a7f4a0f3aa58ef20344c1d5aa5e99a181f1171145264baab4603d772d7c37f8286654442ee0f6bf3b62f8d94d6e0495a65f54495e084403c0b92 SHA512 20833c2e11f942aa69b524170a0203ca4d035d058d1d8029c2fab50c4b60a4e947cbbdc0dc954e4ecdefbf07d095f861a86dbebdfdac4bdbecf65a691226e25c diff --git a/sci-biology/pyfaidx/metadata.xml b/sci-biology/pyfaidx/metadata.xml index fd0f24633..47cc39d79 100644 --- a/sci-biology/pyfaidx/metadata.xml +++ b/sci-biology/pyfaidx/metadata.xml @@ -11,5 +11,6 @@ </maintainer> <upstream> <remote-id type="pypi">pyfaidx</remote-id> + <remote-id type="github">mdshw5/pyfaidx</remote-id> </upstream> </pkgmetadata> diff --git a/sci-biology/pyfaidx/pyfaidx-0.5.9.2.ebuild b/sci-biology/pyfaidx/pyfaidx-0.5.9.2.ebuild index be1990514..bec223f6c 100644 --- a/sci-biology/pyfaidx/pyfaidx-0.5.9.2.ebuild +++ b/sci-biology/pyfaidx/pyfaidx-0.5.9.2.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2020 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7..9} ) +PYTHON_COMPAT=( python3_{10..11} ) DISTUTILS_USE_SETUPTOOLS=rdepend inherit distutils-r1 @@ -19,4 +19,4 @@ IUSE="" REPEND="dev-python/six[${PYTHON_USEDEP}]" -distutils_enable_tests nose +#distutils_enable_tests nose diff --git a/sci-biology/pyfaidx/pyfaidx-0.7.2.1.ebuild b/sci-biology/pyfaidx/pyfaidx-0.7.2.1.ebuild new file mode 100644 index 000000000..14f557869 --- /dev/null +++ b/sci-biology/pyfaidx/pyfaidx-0.7.2.1.ebuild @@ -0,0 +1,24 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools + +inherit distutils-r1 pypi + +DESCRIPTION="Efficient pythonic random access to fasta subsequences" +HOMEPAGE="https://pypi.python.org/pypi/pyfaidx https://github.com/mdshw5/pyfaidx" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" +# Test issues reported upstream: +# https://github.com/mdshw5/pyfaidx/issues/208 +RESTRICT="test" + +REPEND="dev-python/six[${PYTHON_USEDEP}]" + +distutils_enable_tests pytest diff --git a/sci-biology/pysamstats/Manifest b/sci-biology/pysamstats/Manifest deleted file mode 100644 index fb8a27ec1..000000000 --- a/sci-biology/pysamstats/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST pysamstats-1.1.2.tar.gz 251400 BLAKE2B 770a34d6f2c983aba78924dac2c42e26dd52113a2abd11dc6b7b416fc6c612104e263d3a62f869534f4ef2e06c4ce4c387d60575f7fb63c8f885f5ac05f9acde SHA512 d294aac0b8ed7144218d24209978e345bf89ba67c9786155c1826dd37c48fd820cda6467530d6b717ab4b84c6988fb65bec2ee679746c5782413babc45e600ef diff --git a/sci-biology/pysamstats/metadata.xml b/sci-biology/pysamstats/metadata.xml deleted file mode 100644 index cc923c1df..000000000 --- a/sci-biology/pysamstats/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="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="github">alimanfoo/pysamstats</remote-id> - <remote-id type="pypi">pysamstats</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/pysamstats/pysamstats-1.1.2.ebuild b/sci-biology/pysamstats/pysamstats-1.1.2.ebuild deleted file mode 100644 index 445ec2162..000000000 --- a/sci-biology/pysamstats/pysamstats-1.1.2.ebuild +++ /dev/null @@ -1,30 +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="Calculate stats against genome positions from SAM/BAM/CRAM file" -HOMEPAGE="https://github.com/alimanfoo/pysamstats - https://pypi.python.org/pypi/pysamstats" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -# TODO: fix this -# ModuleNotFoundError: No module named 'pysamstats.opt' -# happens even with the --install option -RESTRICT="test" - -BDEPEND="dev-python/cython[${PYTHON_USEDEP}]" -RDEPEND=" - dev-python/numpy[${PYTHON_USEDEP}] - sci-biology/pysam[${PYTHON_USEDEP}] -" - -distutils_enable_tests pytest diff --git a/sci-biology/quast/Manifest b/sci-biology/quast/Manifest deleted file mode 100644 index 200704ee2..000000000 --- a/sci-biology/quast/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST quast-5.0.2.tar.gz 34210765 BLAKE2B 6443e05586019bfe9b29feb2210194de69c7161fae4cbdadb7f16c72d03c3dbfd7f92c359b7d706786ae8fa42e0f59fc2263c5702f78a6b7b89ab6dbfafdc721 SHA512 eeb6f16435a1c8d1ed4c782b19b17557631d3cd129a4948da9355f71221ec1f6d12abe716557a239f736f94c36f1ced8922e5f8fec0b9bec5b447f8a354cda2b diff --git a/sci-biology/quast/metadata.xml b/sci-biology/quast/metadata.xml deleted file mode 100644 index c821b722e..000000000 --- a/sci-biology/quast/metadata.xml +++ /dev/null @@ -1,15 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">quast</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/quast/quast-5.0.2.ebuild b/sci-biology/quast/quast-5.0.2.ebuild deleted file mode 100644 index eb49a803b..000000000 --- a/sci-biology/quast/quast-5.0.2.ebuild +++ /dev/null @@ -1,23 +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="Compare quality of multiple genome assemblies to each other" -HOMEPAGE="http://bioinf.spbau.ru/QUAST" # no https -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -RDEPEND=" - dev-python/joblib[${PYTHON_USEDEP}] - dev-python/simplejson[${PYTHON_USEDEP}] -" - -distutils_enable_tests --install setup.py diff --git a/sci-biology/quicktree/metadata.xml b/sci-biology/quicktree/metadata.xml index 8417d1580..e3ce321ed 100644 --- a/sci-biology/quicktree/metadata.xml +++ b/sci-biology/quicktree/metadata.xml @@ -5,4 +5,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">khowe/quicktree</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/rat-brain-templates/metadata.xml b/sci-biology/rat-brain-templates/metadata.xml index ac271f806..5dacf4476 100644 --- a/sci-biology/rat-brain-templates/metadata.xml +++ b/sci-biology/rat-brain-templates/metadata.xml @@ -14,4 +14,7 @@ format oriented in the standard RAS space, with origin at bregma for use in magnetic resonance rat brain imaging. </longdescription> + <upstream> + <remote-id type="gitlab">FOS-FMI/rat-brain-templates_generator</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/rat-brain-templates/rat-brain-templates-0.2.ebuild b/sci-biology/rat-brain-templates/rat-brain-templates-0.2.ebuild index d41c14a11..cab3dec4f 100644 --- a/sci-biology/rat-brain-templates/rat-brain-templates-0.2.ebuild +++ b/sci-biology/rat-brain-templates/rat-brain-templates-0.2.ebuild @@ -7,7 +7,7 @@ inherit check-reqs DESCRIPTION="A collection of rat brain templates in NIfTI format" HOMEPAGE="https://gitlab.com/FOS-FMI/rat-brain-templates_generator" -SRC_URI="http://resources.chymera.eu/distfiles/${P}.tar.xz" +SRC_URI="https://resources.chymera.eu/distfiles/${P}.tar.xz" LICENSE="fairuse" SLOT="0" diff --git a/sci-biology/roche454ace2caf/Manifest b/sci-biology/roche454ace2caf/Manifest deleted file mode 100644 index 6711cecd3..000000000 --- a/sci-biology/roche454ace2caf/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST roche454ace2gap-2010-12-08.tgz 261317 BLAKE2B e00ba3b1d19c9856447c74d3943854e2c6556c14ef19a1abe73a6e0375b8e889c57b4c00beda2f9f9adf6cb76f6f89a12bfe9c9782b5668c0f883e914fa68204 SHA512 ce477ab88c45e947764d0dcb667f76de195db8f1ebc53ca6892f74017a79e231f77c458564a9ac682679bb6b486493ee6692157628401351de5a732894e5a732 diff --git a/sci-biology/roche454ace2caf/metadata.xml b/sci-biology/roche454ace2caf/metadata.xml deleted file mode 100644 index 138cb7705..000000000 --- a/sci-biology/roche454ace2caf/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/roche454ace2caf/roche454ace2caf-20100812.ebuild b/sci-biology/roche454ace2caf/roche454ace2caf-20100812.ebuild deleted file mode 100644 index a3c4eee39..000000000 --- a/sci-biology/roche454ace2caf/roche454ace2caf-20100812.ebuild +++ /dev/null @@ -1,28 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DESCRIPTION="ace to gap4 converter" -HOMEPAGE="https://genome.imb-jena.de/software/roche454ace2caf/" -SRC_URI="https://genome.imb-jena.de/software/roche454ace2caf/download/src/roche454ace2gap-2010-12-08.tgz" - -LICENSE="FLI-Jena" -SLOT="0" -KEYWORDS="~amd64" - -DEPEND="" -RDEPEND="${DEPEND} - sci-biology/align_to_scf - sci-biology/sff_dump - sci-biology/caftools - sci-biology/staden - dev-lang/perl - app-shells/ksh" - -S="${WORKDIR}/roche2gap" - -src_install(){ - dobin bin/*.pl bin/roche454ace2gap - einstalldocs -} diff --git a/sci-biology/roiextractors/Manifest b/sci-biology/roiextractors/Manifest new file mode 100644 index 000000000..4db78b7b8 --- /dev/null +++ b/sci-biology/roiextractors/Manifest @@ -0,0 +1 @@ +DIST roiextractors-0.5.1.gh.tar.gz 288765 BLAKE2B 5e1b1931f3da8c1157fc2668c203e3ea9812b94246b85e97848d25ff880b1b6d9433637b9847a28dc53c9d88746d1eaa472c7beffd2593d461a24f98eaddd997 SHA512 6f02decfca12f45c8e18ad9ee07931a5891a2099b046e56a7c415d179d93bc6b9a47a320e4ce500217b1f02abdbbdb59c7e85b4f0a773cbd44ba983f5b7595d6 diff --git a/sci-biology/roiextractors/metadata.xml b/sci-biology/roiextractors/metadata.xml new file mode 100644 index 000000000..000a44418 --- /dev/null +++ b/sci-biology/roiextractors/metadata.xml @@ -0,0 +1,16 @@ +<?xml version='1.0' encoding='UTF-8'?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>gentoo@chymera.eu</email> + <name>Horea Christian</name> + </maintainer> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <upstream> + <remote-id type="github">catalystneuro/roiextractors</remote-id> + <remote-id type="pypi">roiextractors</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-biology/roiextractors/roiextractors-0.5.1.ebuild b/sci-biology/roiextractors/roiextractors-0.5.1.ebuild new file mode 100644 index 000000000..1c2fba6ea --- /dev/null +++ b/sci-biology/roiextractors/roiextractors-0.5.1.ebuild @@ -0,0 +1,40 @@ +# Copyright 2021-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 + +DESCRIPTION="Optical imaging data handling from several file formats" +HOMEPAGE="https://github.com/catalystneuro/roiextractors" +SRC_URI="https://github.com/catalystneuro/roiextractors/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" +IUSE="" + +RDEPEND=" + dev-python/dill[${PYTHON_USEDEP}] + dev-python/h5py[${PYTHON_USEDEP}] + dev-python/lazy_ops[${PYTHON_USEDEP}] + dev-python/psutil[${PYTHON_USEDEP}] + dev-python/pynwb[${PYTHON_USEDEP}] + dev-python/pyyaml[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + dev-python/tqdm[${PYTHON_USEDEP}] +" +BDEPEND=" + test? ( + dev-python/parameterized[${PYTHON_USEDEP}] + dev-python/spikeinterface[${PYTHON_USEDEP}] + ) +" + +distutils_enable_tests pytest + +python_test() { + epytest tests/test_internals +} diff --git a/sci-biology/rtg-tools/Manifest b/sci-biology/rtg-tools/Manifest deleted file mode 100644 index 4e0799efc..000000000 --- a/sci-biology/rtg-tools/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST rtg-tools-3.12.tar.gz 32484461 BLAKE2B 3fcee1db9ddcb0d04c34d1252fdf3564aeb255bff36501d0e0bdbe5f6c7d3564581b7fd8aacc90c1a818787c03c3da5478590402cda3cb691be90e816a7ee048 SHA512 2ab7c2a2203e48c74983e89a72b2cf0053e8810a7442931868489f71af6db5f22ca119a5924e7e03bc0f524e41bddff0b20ee8e3c811a21f9168a6b3d6b92d89 diff --git a/sci-biology/rtg-tools/metadata.xml b/sci-biology/rtg-tools/metadata.xml deleted file mode 100644 index 138cb7705..000000000 --- a/sci-biology/rtg-tools/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/rtg-tools/rtg-tools-3.12.ebuild b/sci-biology/rtg-tools/rtg-tools-3.12.ebuild deleted file mode 100644 index a07f55539..000000000 --- a/sci-biology/rtg-tools/rtg-tools-3.12.ebuild +++ /dev/null @@ -1,63 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit java-pkg-2 java-ant-2 - -DESCRIPTION="Manipulate and analyze VCF files" -HOMEPAGE="https://github.com/RealTimeGenomics/rtg-tools" -SRC_URI="https://github.com/RealTimeGenomics/rtg-tools/archive/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="BSD-2" -SLOT="0" -KEYWORDS="~amd64" - -DEPEND=" - >=virtual/jdk-1.8:* - >=dev-java/ant-core-1.9 - dev-java/jython" -RDEPEND="${DEPEND} - >=virtual/jre-1.8:*" - -src_compile(){ - ant zip-nojre || die -} - -# "${S}"/lib/sam-2.9.1.jar -# "${S}"/lib/findbugs-annotations.jar -# "${S}"/lib/findbugs-jsr305.jar -# "${S}"/lib/velocity-tools-generic.jar -# "${S}"/lib/RPlot.jar -# "${S}"/lib/commons-collections-3.2.1.jar -# "${S}"/lib/velocity-1.7.jar -# "${S}"/lib/commons-compress-1.4.1.jar -# "${S}"/lib/commons-lang-2.4.jar -# "${S}"/lib/jumble-annotations.jar -# "${S}"/lib/sam-2.9.1-src.jar -# "${S}"/lib/gzipfix.jar -# "${S}"/buildLib/ant-contrib-1.0b3.jar -# "${S}"/buildLib/handlechecker.jar -# "${S}"/testLib/hamcrest-core-1.3.jar -# "${S}"/testLib/junit.jar -# "${S}"/testLib/spelling.jar - -src_install(){ - dobin installer/rtg - insinto /usr/share/"${PN}" - doins build/rtg-tools.jar - doins lib/gzipfix.jar - dodoc installer/resources/tools/RTGOperationsManual.pdf - doins -r installer/resources/tools/RTGOperationsManual - dodoc installer/resources/tools/scripts/README.txt - dodoc installer/ReleaseNotes.txt - # TODO - # extract more files from the generated rtg-tools-3.11-39691f9f-base.zip - # file or better the installer/resources/ source directory - # - # install installer/resources/common/scripts/rtg-bash-completion -} - -src_test(){ - ant runalltests || die -} diff --git a/sci-biology/ruffus/Manifest b/sci-biology/ruffus/Manifest deleted file mode 100644 index 41e7eb0b2..000000000 --- a/sci-biology/ruffus/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST ruffus-2.8.4.tar.gz 12147217 BLAKE2B 742fdb060d9c7bad6ee9ce9c602c72d205f3442bb8d33b7b455198bca2c84cbc275098f17e103650b18f70ab624cd6f491f6138d6d3906e4697dd010bedc93c7 SHA512 5f38ad4ca5aca007e63b59be6117af85618bc27e8d98cc3b32add82ac48766c37b3fb2633a28c98941397ab3154553ba57509b321d2c80d01c753ac189f092e7 diff --git a/sci-biology/ruffus/metadata.xml b/sci-biology/ruffus/metadata.xml deleted file mode 100644 index 1a91c19c5..000000000 --- a/sci-biology/ruffus/metadata.xml +++ /dev/null @@ -1,15 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="pypi">ruffus</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/ruffus/ruffus-2.8.4.ebuild b/sci-biology/ruffus/ruffus-2.8.4.ebuild deleted file mode 100644 index beda7db9a..000000000 --- a/sci-biology/ruffus/ruffus-2.8.4.ebuild +++ /dev/null @@ -1,26 +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="Python module to support computational pipelines" -HOMEPAGE="http://www.ruffus.org.uk" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -# TODO: why does this not work: Duplicate pipeline -RESTRICT="test" - -RDEPEND=" - media-gfx/graphviz -" - -distutils_enable_sphinx doc dev-python/sphinx_rtd_theme -distutils_enable_tests pytest diff --git a/sci-biology/salmon/Manifest b/sci-biology/salmon/Manifest deleted file mode 100644 index 37410d297..000000000 --- a/sci-biology/salmon/Manifest +++ /dev/null @@ -1,10 +0,0 @@ -DIST bwa-0.7.12.5.tar.gz 224584 BLAKE2B af273aa6751d73e82ce1891acdd42c7cbb0f332312157e1bcaf3f6175417f7358f1d73fd900ede7bddc4071b62f68ea8c79d1e0eb04f02ee618130bd0c33579f SHA512 c56a08c115fd15ca017f5ca5a2e053aef4df9fdf7b3a8f575646b2443cb38853dcd17e72588750dc0c8acdd7accca173d84894220d6cd06959ba0d994851f6c9 -DIST cereal-1.2.2.tar.gz 335759 BLAKE2B 6804b9aabb235a546758c70554502208f1b7b6bcab9b602fa075123335331f0522191a83027fdbac4ee947881c6866f24f48223a00b9490fca5ca961f3e4b260 SHA512 9567b2e19add9446b24f8afd122eea09ba6ecd1a090335cf0ab31fdc8f64c6c97daa3d9eaf0801c36a770737488e0eebf81d96d7b7a65deed30da6130f2d47eb -DIST libgff-1.1.tgz 79006 BLAKE2B 626a62614c4c52d823104eae78e4f04e0976eb43cd2ea7b820ac6549535771fb2ecccbcf4476a22f53a66b5d8bea4fd260c6d3cee864a2c1b264c6f223744dac SHA512 af797fdc753c21a61a817f0b57da55c523220a9c831a71b73328a49ec66b667a503f1fcbddab714826f802a4e2becf310265535276973e2978d5ad73525fa0bb -DIST libgff-salmon-1.6.0.tar.gz 102152 BLAKE2B 56bccaadf82fe51db4f6297177b3c49d7ab4fe858719e3a689834ef10b63dd0ffabba2424771865efab1bd226dccb3a104307ef406e3861e762426cfcc5de543 SHA512 c5e84fad659502134e90c45a0075e79fe1dcf84d08ec4820c337b898fae24c8fe3985cb5fb3e653a13d1756179730ff0cae53bb2c78fe37038f7bd9c7eae85e2 -DIST pufferfish-salmon-1.6.0.tar.gz 3119250 BLAKE2B f3db6506d003418fcaeeb78c114acc0dcd89d745d2433dcbf87dc8ff8dbec15299a799b469f6a07fd07f85afd925c85643c3791819413db3fc14de5686ae112f SHA512 82c1137a14ef7773101b35070b6a943213443d98e218118e6a5c2df1cab860ed9543bcac3b7408e0b7eeb74fe1997d521b4883515a964d03813bcea8b2bfaa8d -DIST salmon-0.10.2.tar.gz 10766806 BLAKE2B f9ba6f208a72a11f37c44a056e9b464f4bf018db88c13e67ce84fcdecee98d878046b2018b144dd48a152300f1ba0a178cf03c5c541b16358e210a5013fdfdce SHA512 828c3d5f3f8f42181bf4b563a49f789bdb82843cbdc9aec4555e7623642e2c663a2552ea7bfd1967cc4f8033e6f0678f8f6f82ce776bc2312bc0b4b8ab7ed19f -DIST salmon-0.10.2_RapMap.zip 1141708 BLAKE2B 397341693e0388093af8ffe620fa91941c584de0887a648d219a3f5662ffd6f9af22179f205bfb83927bc8913756b4d68cbc9179cbfb11f9b329c6aed32220a1 SHA512 8aa593feb61a45d25cc757f39b907e6e0cc108831bad69857268f3ac19614d76cf88de6d8679e52d3eea43bcf5b603bfd55135ececf39acb1700a23408fca573 -DIST salmon-1.6.0.tar.gz 7145603 BLAKE2B 5ffa9bd8cdd76232caaa736ffb959922b47f934217bd706417431f92c406f407529b5df67b13506df4365ce56676b70cf470466cdf616d097c96a8cd312d34d5 SHA512 580292b48165ba6db48db44d3e57e5020410f29a48b4015445c4c354e81989ff872e8874e2a7aab128362f178819330fbdc2a11089189bfbc8cd3058fc0eb4d6 -DIST spdlog-0.16.1.tar.gz 162408 BLAKE2B c90b94bac128f8b143d85522d224223b1361f7d552d9caa8b253e494dd72de56a2149cbd8d568eb4305224d7caf80d8067fbce606a1071bd94f74c43b3245782 SHA512 0ef741f2abcae7c925808b44bba7d2e55aa8bd3b07a77ab6e785068beb505cdbcd7835d7d103e8e96094235e262954969a176d9f4977e9d373f1bee8e2716ff2 -DIST staden-io_lib-1.14.8.tar.gz 2506985 BLAKE2B 0d64847d0958e0efc763e87bf0600e3af90d30b67c77908b2effa20b18ce43a0d5ad1b213747c46f9e9000a75c4f1260759b3c90cd632be821e039870a26eb4b SHA512 535c6701e61a1786ceb7b22905afe702d277e0383816fba82f69af553dd22ca497bf00766f9768fd9173621632483a02ea9919437e1786008b2236c1c2c8c69f diff --git a/sci-biology/salmon/files/salmon-0.10.2-no-boost-static.patch b/sci-biology/salmon/files/salmon-0.10.2-no-boost-static.patch deleted file mode 100644 index ac561d793..000000000 --- a/sci-biology/salmon/files/salmon-0.10.2-no-boost-static.patch +++ /dev/null @@ -1,18 +0,0 @@ ---- salmon-0.10.2/CMakeLists.txt 2018-06-25 10:51:47.179712781 +0200 -+++ salmon-0.10.2/CMakeLists.txt 2018-06-25 10:52:47.951289159 +0200 -@@ -213,15 +213,6 @@ - set (CMAKE_LIBRARY_PATH ${CUSTOM_BOOST_PATH}/lib ${CMAKE_LIBRARY_PATH}) - endif ( DEFINED CUSTOM_BOOST_PATH ) - --## --# We want static, multithreaded boost libraries --## --if(CONDA_BUILD) -- set (Boost_USE_STATIC_LIBS OFF) --else () -- set (Boost_USE_STATIC_LIBS ON) --endif(CONDA_BUILD) -- - set (Boost_USE_MULTITHREADED ON) - #set (Boost_USE_STATIC_RUNTIME OFF) - diff --git a/sci-biology/salmon/files/salmon-0.10.2_TestSalmonQuasi.cmake.patch b/sci-biology/salmon/files/salmon-0.10.2_TestSalmonQuasi.cmake.patch deleted file mode 100644 index 81edf96f5..000000000 --- a/sci-biology/salmon/files/salmon-0.10.2_TestSalmonQuasi.cmake.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- salmon-0.10.2/cmake/TestSalmonQuasi.cmake 2018-06-26 10:39:51.061971241 +0200 -+++ salmon-0.10.2/cmake/TestSalmonQuasi.cmake 2018-06-26 10:40:22.372822258 +0200 -@@ -5,7 +5,7 @@ - ) - - if (SALMON_QUASI_INDEX_RESULT) -- message(FATAL_ERROR "Error running ${SALMON_QUASI_INDEX_COMMAND}") -+ message(FATAL_ERROR "Error running ${SALMON_QUASI_INDEX_CMD}") - endif() - - set(SALMON_QUANT_COMMAND ${CMAKE_BINARY_DIR}/salmon quant -i sample_salmon_quasi_index -l IU -1 reads_1.fastq -2 reads_2.fastq -o sample_salmon_quasi_quant) diff --git a/sci-biology/salmon/files/salmon-0.10.2_fix_lib_dir.patch b/sci-biology/salmon/files/salmon-0.10.2_fix_lib_dir.patch deleted file mode 100644 index eb606c00c..000000000 --- a/sci-biology/salmon/files/salmon-0.10.2_fix_lib_dir.patch +++ /dev/null @@ -1,22 +0,0 @@ ---- salmon-0.10.2/src/CMakeLists.txt 2018-06-25 13:35:45.723519730 +0200 -+++ salmon-0.10.2/src/CMakeLists.txt 2018-06-25 13:44:01.326139539 +0200 -@@ -296,6 +296,8 @@ - ) - ENDIF(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT) - -+include(GNUInstallDirs) -+ - set(INSTALL_LIB_DIR lib ) - set(INSTALL_BIN_DIR bin ) - set(INSTALL_INCLUDE_DIR include ) -@@ -311,8 +313,8 @@ - - install(TARGETS salmon salmon_core - RUNTIME DESTINATION bin -- LIBRARY DESTINATION lib -- ARCHIVE DESTINATION lib -+ LIBRARY DESTINATION "${CMAKE_INSTALL_FULL_LIBDIR}" -+ ARCHIVE DESTINATION "${CMAKE_INSTALL_FULL_LIBDIR}" - ) - - add_custom_command(TARGET unitTests POST_BUILD diff --git a/sci-biology/salmon/files/salmon-0.10.2_fix_tests.patch b/sci-biology/salmon/files/salmon-0.10.2_fix_tests.patch deleted file mode 100644 index 0a95757a8..000000000 --- a/sci-biology/salmon/files/salmon-0.10.2_fix_tests.patch +++ /dev/null @@ -1,10 +0,0 @@ ---- salmon-0.10.2/src/CMakeLists.txt.ori 2018-06-26 10:34:29.293225671 +0200 -+++ salmon-0.10.2/src/CMakeLists.txt 2018-06-26 10:35:24.674730920 +0200 -@@ -335,6 +335,6 @@ - ) - - include(InstallRequiredSystemLibraries) --add_test( NAME unit_tests COMMAND ${CMAKE_COMMAND} -DTOPLEVEL_DIR=${CMAKE_INSTALL_PREFIX} -P ${GAT_SOURCE_DIR}/cmake/UnitTests.cmake ) -+add_test( NAME unit_tests COMMAND ${CMAKE_COMMAND} -DTOPLEVEL_DIR=${GAT_SOURCE_DIR} -P ${GAT_SOURCE_DIR}/cmake/UnitTests.cmake ) - add_test( NAME salmon_read_test_fmd COMMAND ${CMAKE_COMMAND} -DTOPLEVEL_DIR=${GAT_SOURCE_DIR} -P ${GAT_SOURCE_DIR}/cmake/TestSalmonFMD.cmake ) - add_test( NAME salmon_read_test_quasi COMMAND ${CMAKE_COMMAND} -DTOPLEVEL_DIR=${GAT_SOURCE_DIR} -P ${GAT_SOURCE_DIR}/cmake/TestSalmonQuasi.cmake ) diff --git a/sci-biology/salmon/files/salmon-0.10.2_remove_curl_call.patch b/sci-biology/salmon/files/salmon-0.10.2_remove_curl_call.patch deleted file mode 100644 index 8eddc6e3a..000000000 --- a/sci-biology/salmon/files/salmon-0.10.2_remove_curl_call.patch +++ /dev/null @@ -1,12 +0,0 @@ ---- salmon-9999/scripts/fetchRapMap.sh 2018-06-25 11:11:07.019798309 +0200 -+++ salmon-9999/scripts/fetchRapMap.sh 2018-06-25 11:12:25.131824486 +0200 -@@ -29,7 +29,8 @@ - EXPECTED_SHA256=c4ca27de299bee395b404d117d9d98ad9f0d6ee256ea1deb2890ea402893e688 - - mkdir -p ${EXTERNAL_DIR} --curl -k -L https://github.com/COMBINE-lab/RapMap/archive/${SVER}.zip -o ${EXTERNAL_DIR}/rapmap.zip -+# curl -k -L https://github.com/COMBINE-lab/RapMap/archive/${SVER}.zip -o ${EXTERNAL_DIR}/rapmap.zip -+cp ../../distdir/salmon-0.10.2_RapMap.zip ${EXTERNAL_DIR}/rapmap.zip - - hashcheck="" - if exists sha256sum; then diff --git a/sci-biology/salmon/files/salmon-0.10.2_remove_curl_calls.patch b/sci-biology/salmon/files/salmon-0.10.2_remove_curl_calls.patch deleted file mode 100644 index 438763960..000000000 --- a/sci-biology/salmon/files/salmon-0.10.2_remove_curl_calls.patch +++ /dev/null @@ -1,200 +0,0 @@ ---- salmon-0.10.2/CMakeLists.txt 2018-06-25 13:12:49.275828719 +0200 -+++ salmon-0.10.2/CMakeLists.txt 2018-06-25 13:12:38.945565690 +0200 -@@ -235,31 +235,7 @@ - - find_package (LibLZMA) - if (NOT LIBLZMA_FOUND) -- message ("Will attempt to fetch and build liblzma") -- message ("=======================================") --ExternalProject_Add(liblzma -- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external -- ## -- DOWNLOAD_COMMAND curl -k -L http://tukaani.org/xz/xz-5.2.2.tar.gz -o xz-5.2.2.tar.gz && -- ${SHASUM} 73df4d5d34f0468bd57d09f2d8af363e95ed6cc3a4a86129d2f2c366259902a2 xz-5.2.2.tar.gz && -- tar -xzvf xz-5.2.2.tar.gz -- #URL http://tukaani.org/xz/xz-5.2.2.tar.gz -- #URL_HASH SHA1=14663612422ab61386673be78fbb2556f50a1f08 -- ## -- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/xz-5.2.2 -- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install -- BUILD_IN_SOURCE TRUE -- CONFIGURE_COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/external/xz-5.2.2/configure --prefix=<INSTALL_DIR> CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} CFLAGS=${EXTRA_CMAKE_INCLUDE_FLAGS} CPPFLAGS=${EXTRA_CMAKE_INCLUDE_FLAGS} LDFLAGS=${EXTRA_CMAKE_LIBRARY_FLAGS} -- BUILD_COMMAND make ${QUIET_MAKE} -- INSTALL_COMMAND make ${QUIET_MAKE} install --) -- --# Tell cmake that the external project generated a library so we can --# add dependencies here instead of later --set (LIBLZMA_LIBRARIES ${GAT_SOURCE_DIR}/external/install/lib/liblzma.a) --set (LIBSTADEN_LDFLAGS "-L${GAT_SOURCE_DIR}/external/install/lib") --set (LIBSTADEN_CFLAGS "-I${GAT_SOURCE_DIR}/external/install/include") --set (FETCHED_LIBLZMA TRUE) -+ message (FATAL_ERROR "liblzma must be installed before configuration & building can proceed") - else() - message("Found liblzma library: ${LIBLZMA_LIBRARIES}") - message("===========================================") -@@ -267,28 +243,7 @@ - - find_package (BZip2) - if (NOT BZIP2_FOUND) -- message ("Will attempt to fetch and build libbz2") -- message ("=======================================") --ExternalProject_Add(libbz2 -- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external -- DOWNLOAD_COMMAND curl -k -L http://www.bzip.org/1.0.6/bzip2-1.0.6.tar.gz -o bzip2-1.0.6.tar.gz && -- ${SHASUM} a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd bzip2-1.0.6.tar.gz && -- tar -xzvf bzip2-1.0.6.tar.gz -- #URL http://www.bzip.org/1.0.6/bzip2-1.0.6.tar.gz -- #URL_HASH SHA1=3f89f861209ce81a6bab1fd1998c0ef311712002 -- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/bzip2-1.0.6 -- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install -- BUILD_IN_SOURCE TRUE -- CONFIGURE_COMMAND "" -- BUILD_COMMAND make ${QUIET_MAKE} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} -- INSTALL_COMMAND make ${QUIET_MAKE} install PREFIX=<INSTALL_DIR> --) --# Tell cmake that the external project generated a library so we can --# add dependencies here instead of later --set (BZIP2_LIBRARIES ${GAT_SOURCE_DIR}/external/install/lib/libbz2.a) --set (LIBSTADEN_LDFLAGS "-L${GAT_SOURCE_DIR}/external/install/lib -I${GAT_SOURCE_DIR}/external/install/include") --set (LIBSTADEN_CFLAGS "-I${GAT_SOURCE_DIR}/external/install/include") --set (FETCHED_LIBBZ2 TRUE) -+ message (FATAL_ERROR "libbz2 must be installed before configuration & building can proceed") - else() - message("Found libbz2 library: ${BZIP2_LIBRARIES}") - message("===========================================") -@@ -333,61 +288,15 @@ - # Either inform the user of how to obtain Boost, or, if they passed in the FETCH_BOOST - # option, go and grab it for them. - ## --if ((NOT Boost_FOUND) AND (NOT FETCH_BOOST)) -+if (NOT Boost_FOUND) - message(FATAL_ERROR - "Salmon cannot be compiled without Boost.\n" - "It is recommended to visit http://www.boost.org/ and install Boost according to those instructions.\n" - "This build system can also download and install a local version of boost for you (this takes a lot of time).\n" - "To fetch and build boost locally, call cmake with -DFETCH_BOOST=TRUE" - ) --elseif(FETCH_BOOST) -- ## Let the rest of the build process know we're going to be fetching boost -- set (BOOST_LIB_SUBSET --with-iostreams --with-atomic --with-chrono --with-container --with-date_time --with-exception -- --with-filesystem --with-graph --with-graph_parallel --with-math -- --with-program_options --with-system --with-thread -- --with-timer) -- set (BOOST_WILL_RECONFIGURE TRUE) -- set (FETCH_BOOST FALSE) -- message("Build system will fetch and build Boost") -- message("==================================================================") -- ExternalProject_Add(libboost -- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external -- DOWNLOAD_COMMAND curl -k -L http://downloads.sourceforge.net/project/boost/boost/1.66.0/boost_1_66_0.tar.gz -o boost_1_66_0.tar.gz && -- ${SHASUM} bd0df411efd9a585e5a2212275f8762079fed8842264954675a4fddc46cfcf60 boost_1_66_0.tar.gz && -- tar xzf boost_1_66_0.tar.gz -- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/boost_1_66_0 -- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install -- #PATCH_COMMAND patch -p2 < ${CMAKE_CURRENT_SOURCE_DIR}/external/boost156.patch -- CONFIGURE_COMMAND CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} ${CMAKE_CURRENT_SOURCE_DIR}/external/boost_1_66_0/bootstrap.sh ${BOOST_CONFIGURE_TOOLSET} ${BOOST_BUILD_LIBS} --prefix=<INSTALL_DIR> -- BUILD_COMMAND CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} ${CMAKE_CURRENT_SOURCE_DIR}/external/boost_1_66_0/b2 -d0 -j2 ${BOOST_LIB_SUBSET} toolset=${BOOST_TOOLSET} ${BOOST_EXTRA_FLAGS} cxxflags=${BOOST_CXX_FLAGS} link=static install -- BUILD_IN_SOURCE 1 -- INSTALL_COMMAND "" -- ) -- -- ## -- # After we've installed boost, -- ## -- SET( RECONFIG_FLAGS ${RECONFIG_FLAGS} -DBOOST_WILL_RECONFIGURE=FALSE -DBOOST_RECONFIGURE=TRUE -DFETCH_BOOST=FALSE) -- ExternalProject_Add_Step(libboost reconfigure -- COMMAND ${CMAKE_COMMAND} ${CMAKE_CURRENT_SOURCE_DIR} ${RECONFIG_FLAGS} -- DEPENDEES install -- ) -- set (FETCHED_BOOST TRUE) - endif() - --## --# If we're fetching boost and we need to have dummy paths for these variables --# so that CMake won't complain --## --if (BOOST_WILL_RECONFIGURE) -- message("Setting Temporary Boost paths") -- set(Boost_INCLUDE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install/include) -- set(Boost_INCLUDE_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/external/install/include) -- set(Boost_LIBRARY_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/external/install/lib) -- set(Boost_FOUND TRUE) --endif() -- -- - message("BOOST INCLUDE DIR = ${Boost_INCLUDE_DIR}") - message("BOOST INCLUDE DIRS = ${Boost_INCLUDE_DIRS}") - message("BOOST LIB DIR = ${Boost_LIBRARY_DIRS}") -@@ -422,9 +331,9 @@ - include(ExternalProject) - ExternalProject_Add(libcereal - DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external -- DOWNLOAD_COMMAND curl -k -L https://github.com/USCiLab/cereal/archive/v1.2.2.tar.gz -o cereal-v1.2.2.tar.gz && -- ${SHASUM} 1921f26d2e1daf9132da3c432e2fd02093ecaedf846e65d7679ddf868c7289c4 cereal-v1.2.2.tar.gz && -- tar -xzvf cereal-v1.2.2.tar.gz -+ DOWNLOAD_COMMAND cp ../../../distdir/cereal-1.2.2.tar.gz . && -+ ${SHASUM} 1921f26d2e1daf9132da3c432e2fd02093ecaedf846e65d7679ddf868c7289c4 cereal-1.2.2.tar.gz && -+ tar -xzvf cereal-1.2.2.tar.gz - - ## - #URL https://github.com/USCiLab/cereal/archive/v1.2.2.tar.gz -@@ -455,12 +364,12 @@ - ExternalProject_Add(libbwa - DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external - #URL https://github.com/COMBINE-lab/bwa/archive/0.7.12.3.tar.gz -- #DOWNLOAD_NAME bwa-master.tar.gz -- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/bwa/archive/v0.7.12.5.tar.gz -o bwa-master.tar.gz && -- ${SHASUM} 1ac5661d9e12e9017a47f0264201a75d9128f28dbd9a26952925f7745ddf6036 bwa-master.tar.gz && -- mkdir -p bwa-master && -- tar -xzvf bwa-master.tar.gz --strip-components=1 -C bwa-master -- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/bwa-master -+ #DOWNLOAD_NAME bwa-0.7.12.5.tar.gz -+ DOWNLOAD_COMMAND cp ../../../distdir/bwa-0.7.12.5.tar.gz . && -+ ${SHASUM} 1ac5661d9e12e9017a47f0264201a75d9128f28dbd9a26952925f7745ddf6036 bwa-0.7.12.5.tar.gz && -+ mkdir -p bwa-0.7.12.5 && -+ tar -xzvf bwa-0.7.12.5.tar.gz --strip-components=1 -C bwa-0.7.12.5 -+ SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/bwa-0.7.12.5 - INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install - CONFIGURE_COMMAND "" - BUILD_COMMAND sh -c "make ${QUIET_MAKE} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER}" -@@ -562,9 +471,9 @@ - message("==================================================================") - ExternalProject_Add(libgff - DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external -- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz -o libgff.tgz && -- ${SHASUM} 34597ecd3718e6d6e7a1dd4350220664be2c1cd992070d1218564a20d7aa5697 libgff.tgz && -- tar -xzvf libgff.tgz -+ DOWNLOAD_COMMAND cp ../../../distdir/libgff-1.1.tgz . && -+ ${SHASUM} 34597ecd3718e6d6e7a1dd4350220664be2c1cd992070d1218564a20d7aa5697 libgff-1.1.tgz && -+ tar -xzvf libgff-1.1.tgz - ## - #URL https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz - #DOWNLOAD_NAME libff.tgz -@@ -600,10 +509,10 @@ - message("==================================================================") - ExternalProject_Add(libstadenio - DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external -- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/staden-io_lib/archive/v1.14.8.1.tar.gz -o staden-io_lib-v1.14.8.tar.gz && -- ${SHASUM} f6f30eefa478cfb708f3109a35fb6ffa0e24951d9d971985df2cef5919dd0bc3 staden-io_lib-v1.14.8.tar.gz && -+ DOWNLOAD_COMMAND cp ../../../distdir/staden-io_lib-1.14.8.tar.gz . && -+ ${SHASUM} f6f30eefa478cfb708f3109a35fb6ffa0e24951d9d971985df2cef5919dd0bc3 staden-io_lib-1.14.8.tar.gz && - mkdir -p staden-io_lib-1.14.8 && -- tar -xzf staden-io_lib-v1.14.8.tar.gz --strip-components=1 -C staden-io_lib-1.14.8 && -+ tar -xzf staden-io_lib-1.14.8.tar.gz --strip-components=1 -C staden-io_lib-1.14.8 && - rm -fr staden-io_lib && - mv -f staden-io_lib-1.14.8 staden-io_lib - SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/staden-io_lib -@@ -620,9 +529,9 @@ - message("==================================================================") - ExternalProject_Add(libspdlog - DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external -- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/spdlog/archive/v0.16.1.tar.gz -o spdlog-v0.16.1.tar.gz && -- ${SHASUM} 733260e1fbdcf1b3dc307fc585e4476240026de8be28eb905731d2ab0942deae spdlog-v0.16.1.tar.gz && -- tar -xzf spdlog-v0.16.1.tar.gz -+ DOWNLOAD_COMMAND cp ../../../distdir/spdlog-0.16.1.tar.gz . && -+ ${SHASUM} 733260e1fbdcf1b3dc307fc585e4476240026de8be28eb905731d2ab0942deae spdlog-0.16.1.tar.gz && -+ tar -xzf spdlog-0.16.1.tar.gz - ## - #URL https://github.com/COMBINE-lab/spdlog/archive/v0.12.0.tar.gz - #DOWNLOAD_NAME spdlog-v0.12.0.tar.gz diff --git a/sci-biology/salmon/files/salmon-1.6.0-find-boost.patch b/sci-biology/salmon/files/salmon-1.6.0-find-boost.patch deleted file mode 100644 index 76ef25547..000000000 --- a/sci-biology/salmon/files/salmon-1.6.0-find-boost.patch +++ /dev/null @@ -1,116 +0,0 @@ -diff --git a/CMakeLists.txt b/CMakeLists.txt -index 1be02ab..48ffda2 100644 ---- a/CMakeLists.txt -+++ b/CMakeLists.txt -@@ -428,9 +428,9 @@ endif() - ## - # Set the latest version and look for what we need - ## --set(Boost_ADDITIONAL_VERSIONS "1.59.0" "1.60.0" "1.61.0" "1.62.0" "1.63.0" "1.64.0" "1.65.0" "1.66.0" "1.67.0" "1.68.0" "1.69.0" "1.70.0" "1.71.0") -+set(Boost_ADDITIONAL_VERSIONS "1.59.0" "1.60.0" "1.61.0" "1.62.0" "1.63.0" "1.64.0" "1.65.0" "1.66.0" "1.67.0" "1.68.0" "1.69.0" "1.70.0" "1.71.0" "1.77.0" "1.78.0") - if (NOT BOOST_RECONFIGURE) --find_package(Boost 1.59.0 COMPONENTS iostreams filesystem system timer chrono program_options) -+find_package(Boost 1.59.0 COMPONENTS ALL) - message("BOOST_INCLUDEDIR = ${BOOST_INCLUDEDIR}") - message("BOOST_LIBRARYDIR = ${BOOST_LIBRARYDIR}") - message("Boost_FOUND = ${Boost_FOUND}") -@@ -610,7 +610,7 @@ if (NOT CEREAL_FOUND) - endif() - - ## Try and find TBB first --find_package(TBB 2019.0 COMPONENTS tbb tbbmalloc tbbmalloc_proxy) -+find_package(TBB) - - ## NOTE: we actually require at least 2019 U4 or greater - ## since we are using tbb::global_control. However, they -@@ -618,12 +618,8 @@ find_package(TBB 2019.0 COMPONENTS tbb tbbmalloc tbbmalloc_proxy) - ## source. Check before release if we can bump to the 2020 - ## version (requires having tbb 2020 for OSX). - if (${TBB_FOUND}) -- if (${TBB_VERSION} VERSION_GREATER_EQUAL 2019.0) - message("FOUND SUITABLE TBB VERSION : ${TBB_VERSION}") - set(TBB_TARGET_EXISTED TRUE) -- else() -- set(TBB_TARGET_EXISTED FALSE) -- endif() - else() - set(TBB_TARGET_EXISTED FALSE) - endif() -@@ -750,10 +746,6 @@ if(NOT libgff_FOUND) - message("Build system will compile libgff") - message("==================================================================") - externalproject_add(libgff -- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external -- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/libgff/archive/v2.0.0.tar.gz -o libgff.tgz && -- ${SHASUM} 7656b19459a7ca7d2fd0fcec4f2e0fd0deec1b4f39c703a114e8f4c22d82a99c libgff.tgz && -- tar -xzvf libgff.tgz - ## - #URL https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz - #DOWNLOAD_NAME libff.tgz -diff --git a/cmake/Modules/FindTBB.cmake b/cmake/Modules/FindTBB.cmake -index c8b3eb5..b4c23da 100644 ---- a/cmake/Modules/FindTBB.cmake -+++ b/cmake/Modules/FindTBB.cmake -@@ -184,7 +184,6 @@ if(NOT TBB_FOUND) - ################################## - - if(TBB_INCLUDE_DIRS) -- file(READ "${TBB_INCLUDE_DIRS}/tbb/tbb_stddef.h" _tbb_version_file) - string(REGEX REPLACE ".*#define TBB_VERSION_MAJOR ([0-9]+).*" "\\1" - TBB_VERSION_MAJOR "${_tbb_version_file}") - string(REGEX REPLACE ".*#define TBB_VERSION_MINOR ([0-9]+).*" "\\1" -diff --git a/scripts/fetchPufferfish.sh b/scripts/fetchPufferfish.sh -index d32e131..1b5cbf2 100755 ---- a/scripts/fetchPufferfish.sh -+++ b/scripts/fetchPufferfish.sh -@@ -10,18 +10,6 @@ CURR_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd ) - EXTERNAL_DIR=${CURR_DIR}/../external - INSTALL_DIR=${CURR_DIR}/../external/install - --if [ -d ${EXTERNAL_DIR}/pufferfish ] ; then -- rm -fr ${EXTERNAL_DIR}/pufferfish --fi -- --if [ -d ${INSTALL_DIR}/include/pufferfish ] ; then -- rm -fr ${INSTALL_DIR}/include/pufferfish --fi -- --if [ -d ${INSTALL_DIR}/src/pufferfish ] ; then -- rm -fr ${INSTALL_DIR}/src/pufferfish --fi -- - SVER=salmon-v1.6.0 - #SVER=develop - #SVER=sketch-mode -@@ -29,31 +17,6 @@ SVER=salmon-v1.6.0 - EXPECTED_SHA256=f71b3c08f254200fcdc2eb8fe3dcca8a8e9489e79ef5952a4958d8b9979831dc - - mkdir -p ${EXTERNAL_DIR} --curl -k -L https://github.com/COMBINE-lab/pufferfish/archive/${SVER}.zip -o ${EXTERNAL_DIR}/pufferfish.zip -- --hashcheck="" --if exists sha256sum; then -- hashcheck="sha256sum" --elif exists shasum; then -- hashcheck="shasum -a256" --else -- unset hashcheck --fi -- --if [ -z "${hashcheck-}" ]; then -- echo "Couldn't find shasum command; can't verify contents of downloaded pufferfish"; --else -- if [[ $SVER != develop ]]; then -- echo "${EXPECTED_SHA256} ${EXTERNAL_DIR}/pufferfish.zip" | ${hashcheck} -c - || { echo "pufferfish.zip did not match expected SHA1! Exiting."; exit 1; } -- else -- echo "not testing sha since pulling from develop" -- fi --fi -- -- --rm -fr ${EXTERNAL_DIR}/pufferfish --unzip ${EXTERNAL_DIR}/pufferfish.zip -d ${EXTERNAL_DIR} --mv ${EXTERNAL_DIR}/pufferfish-${SVER} ${EXTERNAL_DIR}/pufferfish - - mkdir -p ${INSTALL_DIR}/include/pufferfish - diff --git a/sci-biology/salmon/metadata.xml b/sci-biology/salmon/metadata.xml deleted file mode 100644 index 1907254d6..000000000 --- a/sci-biology/salmon/metadata.xml +++ /dev/null @@ -1,15 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <maintainer type="person"> - <email>mschu.dev@gmail.com</email> - <name>Michael Schubert</name> - </maintainer> - <upstream> - <remote-id type="github">COMBINE-lab/salmon</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/salmon/salmon-0.10.2.ebuild b/sci-biology/salmon/salmon-0.10.2.ebuild deleted file mode 100644 index c3ef9e50a..000000000 --- a/sci-biology/salmon/salmon-0.10.2.ebuild +++ /dev/null @@ -1,73 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit cmake - -DESCRIPTION="Transcript-level quantification from RNA-seq reads using lightweight alignments" -HOMEPAGE="https://github.com/COMBINE-lab/salmon" -SRC_URI="https://github.com/COMBINE-lab/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz - https://github.com/COMBINE-lab/RapMap/archive/salmon-v0.10.2.zip -> ${P}_RapMap.zip - https://github.com/USCiLab/cereal/archive/v1.2.2.tar.gz -> cereal-1.2.2.tar.gz - https://github.com/COMBINE-lab/bwa/archive/v0.7.12.5.tar.gz -> bwa-0.7.12.5.tar.gz - https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz -> libgff-1.1.tgz - https://github.com/COMBINE-lab/staden-io_lib/archive/v1.14.8.1.tar.gz -> staden-io_lib-1.14.8.tar.gz - https://github.com/COMBINE-lab/spdlog/archive/v0.16.1.tar.gz -> spdlog-0.16.1.tar.gz" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -PATCHES=( "${FILESDIR}"/${P}-no-boost-static.patch - "${FILESDIR}"/salmon-0.10.2_remove_curl_call.patch - "${FILESDIR}"/salmon-0.10.2_remove_curl_calls.patch - "${FILESDIR}"/salmon-0.10.2_fix_lib_dir.patch - "${FILESDIR}"/salmon-0.10.2_fix_tests.patch - "${FILESDIR}"/salmon-0.10.2_TestSalmonQuasi.cmake.patch ) - -RDEPEND="${DEPEND}" -# budled copies of: -# sci-biology/bwa-0.7.12.5 -# sci-biology/jellyfish -# sci-biology/staden-1.14.8.1 -# sci-biology/gfftools -# -# libgff-1.1 from https://github.com/Kingsford-Group/libgff -# actually unreleased version from https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz -# https://github.com/Kingsford-Group/libgff/issues/1 -# -# dev-libs/spdlog-0.16.1 -# cereal-1.2.2 - -# see the many curl executions: -# salmon-0.10.2$ find . -type f | xargs grep curl 2>/dev/null -# -DEPEND=" - sys-libs/zlib - app-arch/bzip2 - app-arch/xz-utils - dev-libs/boost:0= - dev-libs/libdivsufsort - sci-biology/bwa - >=dev-libs/jemalloc-5.0.1 - >=dev-cpp/tbb-2018.20180312 -" -RDEPEND="${DEPEND}" -BDEPEND=" - net-misc/curl - app-arch/unzip -" - -src_prepare() { - # use system libs - sed -i \ - -e "s%\${GAT_SOURCE_DIR}/external/install/lib/libstaden-read.a%/usr/$(get_libdir)/libstaden-read.so%g" \ - -e "s%\${GAT_SOURCE_DIR}/external/install/lib/libdivsufsort.a%/usr/$(get_libdir)/libdivsufsort.so%g" \ - -e "s%\${GAT_SOURCE_DIR}/external/install/lib/libdivsufsort64.a%/usr/$(get_libdir)/libdivsufsort64.so%g" \ - -e "s%\${GAT_SOURCE_DIR}/external/install/lib/libbwa.a%/usr/$(get_libdir)/libbwa.so%g" \ - src/CMakeLists.txt || die - - cmake_src_prepare -} diff --git a/sci-biology/salmon/salmon-1.6.0.ebuild b/sci-biology/salmon/salmon-1.6.0.ebuild deleted file mode 100644 index 6c19ff58f..000000000 --- a/sci-biology/salmon/salmon-1.6.0.ebuild +++ /dev/null @@ -1,70 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -inherit cmake - -DESCRIPTION="Transcript-level quantification from RNA-seq reads using lightweight alignments" -HOMEPAGE="https://github.com/COMBINE-lab/salmon" -SRC_URI=" - https://github.com/COMBINE-lab/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz - https://github.com/COMBINE-lab/pufferfish/archive/salmon-v${PV}.tar.gz -> pufferfish-${P}.tar.gz - https://github.com/COMBINE-lab/libgff/archive/v2.0.0.tar.gz -> libgff-${P}.tar.gz -" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="~amd64" - -RDEPEND=" - dev-libs/boost:= - sys-libs/zlib -" - -DEPEND="${RDEPEND} - app-arch/bzip2 - app-arch/xz-utils - >=dev-libs/jemalloc-5.0.1 - >=dev-cpp/tbb-2018.20180312 - dev-libs/cereal - sci-libs/io_lib[static-libs] -" - -BDEPEND=" - app-arch/unzip - net-misc/curl -" - -PATCHES=( - "${FILESDIR}/${P}-find-boost.patch" -) - -src_unpack() { - default - mkdir -p "${S}/external/install/lib" || die - mv "${WORKDIR}/pufferfish-${PN}-v${PV}" "${S}/external/pufferfish" || die - mv "${WORKDIR}/libgff-2.0.0" "${S}/external/libgff-2.0.0" || die - ln -s "${EPREFIX}/usr/lib64/libtbb.so" "${S}/external/install/lib/libtbb.so" || die - ln -s "${EPREFIX}/usr/lib64/libtbbmalloc.so" "${S}/external/install/lib/libtbbmalloc.so" || die - ln -s "${EPREFIX}/usr/lib64/libtbbmalloc_proxy.so" "${S}/external/install/lib/libtbbmalloc_proxy.so" || die -} - -src_prepare() { - cmake_src_prepare - sed -e 's:tbb/mutex.h:oneapi/tbb/mutex.h:g' \ - -i external/pufferfish/external/twopaco/graphconstructor/vertexenumerator.h \ - -i external/pufferfish/external/twopaco/common/streamfastaparser.h || die -} - -src_configure() { - local mycmakeargs=( - -DFETCH_BOOST=FALSE - -DBOOST_INCLUDEDIR="${EPREFIX}/usr/include/boost" - -DBOOST_LIBRARYDIR="${EPREFIX}/usr/lib64" - -DBoost_ALL_FOUND=TRUE - -Dboost_headers_FOUND=TRUE - -DBoost_FOUND=TRUE - ) - cmake_src_configure -} diff --git a/sci-biology/samri/Manifest b/sci-biology/samri/Manifest index d683d1d3b..26d7dd5ed 100644 --- a/sci-biology/samri/Manifest +++ b/sci-biology/samri/Manifest @@ -1 +1,2 @@ -DIST samri-0.5.tar.gz 4117149 BLAKE2B 1767d6d07726431e43dad5f843eee04bd5111dde3174905b79b938aa94dbb340ca3f3d6316c6720bf01212b87c895df47c965738dff70ec1debbbd542bb77043 SHA512 94fb981adf78b2062e1beac8433bca34e3db90964f720918603e2b89d617b4dfe9f4bc1591b6953e060553ea0014ebca4db62aa0f5b264feb084bc785a48c367 +DIST samri-0.5.3.tar.gz 4122035 BLAKE2B 343dc6de7acf74b5fc169c1f07a4a7209483bee1d050021045a9582d13ea9ae2b8bd4dba0f7f876548e218863cd01bf6d12e571e2d83860366e88ceec7f8441c SHA512 fb9c98843477a35ec313d9284c1c23777af7c6c29fbaa3672b6aa7f7357a81ef874883e0f09f97f52a75febed11deb714343bdadc06708f3a5dcb12fea121a06 +DIST samri-0.5.4.tar.gz 4122057 BLAKE2B 3afdfe6198bc61697cac9ab80560d438d3c488b182d0da9b4a8321efca99d733c964bde000ef8a6a8b849df753f3369d8ea3ba984c8a9736fef466fe196dc003 SHA512 c783156b4eb66b146d039338381867d5683c2f90214d4451448da631609e1e0113f803851a04965b9e400ca5bc69910ec8cbaa1af4b023a89ded0ba6b38901b8 diff --git a/sci-biology/samri/samri-0.5.3.ebuild b/sci-biology/samri/samri-0.5.3.ebuild new file mode 100644 index 000000000..f632f83a8 --- /dev/null +++ b/sci-biology/samri/samri-0.5.3.ebuild @@ -0,0 +1,77 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools + +inherit distutils-r1 prefix + +DESCRIPTION="Small Animal Magnetic Resonance Imaging" +HOMEPAGE="https://github.com/IBT-FMI/SAMRI" +if [ "$PV" == "9999" ]; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/IBT-FMI/SAMRI.git" +else + SRC_URI="https://github.com/IBT-FMI/SAMRI/archive/${PV}.tar.gz -> ${P}.tar.gz" + KEYWORDS="~amd64" + S="${WORKDIR}/SAMRI-${PV}" +fi + +LICENSE="GPL-3" +SLOT="0" +IUSE="+atlases labbookdb" +REQUIRED_USE="test? ( atlases )" + +DEPEND=" + test? ( + sci-biology/samri_bidsdata + sci-biology/samri_bindata + ) + " +RDEPEND=" + dev-python/argh[${PYTHON_USEDEP}] + dev-python/joblib[${PYTHON_USEDEP}] + >=dev-python/matplotlib-2.0.2[${PYTHON_USEDEP}] + >=dev-python/numpy-1.13.3[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + dev-python/seaborn[${PYTHON_USEDEP}] + dev-python/statsmodels[${PYTHON_USEDEP}] + >=media-gfx/blender-2.83.4 + >=sci-biology/fsl-5.0.9 + sci-biology/bru2nii + atlases? ( sci-biology/mouse-brain-templates ) + labbookdb? ( sci-libs/labbookdb[${PYTHON_USEDEP}] ) + sci-libs/nibabel[${PYTHON_USEDEP}] + >=sci-libs/nipy-0.4.1[${PYTHON_USEDEP}] + >=sci-libs/nipype-1.0.0[${PYTHON_USEDEP}] + <sci-libs/pybids-0.10.2[${PYTHON_USEDEP}] + dev-python/scikit-image[${PYTHON_USEDEP}] + sci-biology/ants + sci-biology/afni + sci-biology/nilearn[${PYTHON_USEDEP}] +" + +distutils_enable_tests pytest +distutils_enable_sphinx doc/source dev-python/sphinxcontrib-napoleon + +src_prepare() { + distutils-r1_src_prepare + sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI \'/usr/ samri` || die + sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI /usr/ test_scripts.sh` || die + eprefixify $(grep -rl GENTOO_PORTAGE_EPREFIX samri/* test_scripts.sh) +} + +python_test() { + distutils_install_for_testing + export MPLBACKEND="agg" + export PATH=${TEST_DIR}/scripts:$PATH + export PYTHONIOENCODING=utf-8 + ./test_scripts.sh || die "Test scripts failed." + sed -i -e \ + "/def test_bru2bids():/i@pytest.mark.skip('Removed in full test suite, as this is already tested in `test_scripts.sh`')" \ + samri/pipelines/tests/test_repos.py || die + epytest -k "not longtime" +} diff --git a/sci-biology/samri/samri-0.5.4.ebuild b/sci-biology/samri/samri-0.5.4.ebuild new file mode 100644 index 000000000..f632f83a8 --- /dev/null +++ b/sci-biology/samri/samri-0.5.4.ebuild @@ -0,0 +1,77 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools + +inherit distutils-r1 prefix + +DESCRIPTION="Small Animal Magnetic Resonance Imaging" +HOMEPAGE="https://github.com/IBT-FMI/SAMRI" +if [ "$PV" == "9999" ]; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/IBT-FMI/SAMRI.git" +else + SRC_URI="https://github.com/IBT-FMI/SAMRI/archive/${PV}.tar.gz -> ${P}.tar.gz" + KEYWORDS="~amd64" + S="${WORKDIR}/SAMRI-${PV}" +fi + +LICENSE="GPL-3" +SLOT="0" +IUSE="+atlases labbookdb" +REQUIRED_USE="test? ( atlases )" + +DEPEND=" + test? ( + sci-biology/samri_bidsdata + sci-biology/samri_bindata + ) + " +RDEPEND=" + dev-python/argh[${PYTHON_USEDEP}] + dev-python/joblib[${PYTHON_USEDEP}] + >=dev-python/matplotlib-2.0.2[${PYTHON_USEDEP}] + >=dev-python/numpy-1.13.3[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + dev-python/seaborn[${PYTHON_USEDEP}] + dev-python/statsmodels[${PYTHON_USEDEP}] + >=media-gfx/blender-2.83.4 + >=sci-biology/fsl-5.0.9 + sci-biology/bru2nii + atlases? ( sci-biology/mouse-brain-templates ) + labbookdb? ( sci-libs/labbookdb[${PYTHON_USEDEP}] ) + sci-libs/nibabel[${PYTHON_USEDEP}] + >=sci-libs/nipy-0.4.1[${PYTHON_USEDEP}] + >=sci-libs/nipype-1.0.0[${PYTHON_USEDEP}] + <sci-libs/pybids-0.10.2[${PYTHON_USEDEP}] + dev-python/scikit-image[${PYTHON_USEDEP}] + sci-biology/ants + sci-biology/afni + sci-biology/nilearn[${PYTHON_USEDEP}] +" + +distutils_enable_tests pytest +distutils_enable_sphinx doc/source dev-python/sphinxcontrib-napoleon + +src_prepare() { + distutils-r1_src_prepare + sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI \'/usr/ samri` || die + sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI /usr/ test_scripts.sh` || die + eprefixify $(grep -rl GENTOO_PORTAGE_EPREFIX samri/* test_scripts.sh) +} + +python_test() { + distutils_install_for_testing + export MPLBACKEND="agg" + export PATH=${TEST_DIR}/scripts:$PATH + export PYTHONIOENCODING=utf-8 + ./test_scripts.sh || die "Test scripts failed." + sed -i -e \ + "/def test_bru2bids():/i@pytest.mark.skip('Removed in full test suite, as this is already tested in `test_scripts.sh`')" \ + samri/pipelines/tests/test_repos.py || die + epytest -k "not longtime" +} diff --git a/sci-biology/samri/samri-0.5.ebuild b/sci-biology/samri/samri-0.5.ebuild deleted file mode 100644 index 4cc90a0ef..000000000 --- a/sci-biology/samri/samri-0.5.ebuild +++ /dev/null @@ -1,71 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{8..9} ) - -inherit distutils-r1 prefix - -DESCRIPTION="Small Animal Magnetic Resonance Imaging" -HOMEPAGE="https://github.com/IBT-FMI/SAMRI" -SRC_URI="https://github.com/IBT-FMI/SAMRI/archive/${PV}.tar.gz -> ${P}.tar.gz" -S="${WORKDIR}/SAMRI-${PV}" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="~amd64" -IUSE="+atlases labbookdb" -REQUIRED_USE="test? ( atlases )" - -DEPEND=" - test? ( - sci-biology/samri_bidsdata - sci-biology/samri_bindata - ) - " -RDEPEND=" - dev-python/argh[${PYTHON_USEDEP}] - dev-python/joblib[${PYTHON_USEDEP}] - >=dev-python/matplotlib-2.0.2[${PYTHON_USEDEP}] - >=dev-python/numpy-1.13.3[${PYTHON_USEDEP}] - dev-python/pandas[${PYTHON_USEDEP}] - dev-python/scipy[${PYTHON_USEDEP}] - dev-python/seaborn[${PYTHON_USEDEP}] - dev-python/statsmodels[${PYTHON_USEDEP}] - >=media-gfx/blender-2.83.4 - >=sci-biology/fsl-5.0.9 - sci-biology/bru2nii - atlases? ( sci-biology/mouse-brain-templates ) - labbookdb? ( sci-libs/labbookdb[${PYTHON_USEDEP}] ) - sci-libs/nibabel[${PYTHON_USEDEP}] - >=sci-libs/nipy-0.4.1[${PYTHON_USEDEP}] - >=sci-libs/nipype-1.0.0[${PYTHON_USEDEP}] - <sci-libs/pybids-0.10.2[${PYTHON_USEDEP}] - sci-libs/scikit-image[${PYTHON_USEDEP}] - sci-biology/ants - sci-biology/afni - sci-biology/nilearn[${PYTHON_USEDEP}] -" - -distutils_enable_tests pytest -distutils_enable_sphinx doc/source dev-python/sphinxcontrib-napoleon - -src_prepare() { - distutils-r1_src_prepare - sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI \'/usr/ samri` || die - sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI /usr/ test_scripts.sh` || die - eprefixify $(grep -rl GENTOO_PORTAGE_EPREFIX samri/* test_scripts.sh) -} - -python_test() { - distutils_install_for_testing - export MPLBACKEND="agg" - export PATH=${TEST_DIR}/scripts:$PATH - export PYTHONIOENCODING=utf-8 - ./test_scripts.sh || die "Test scripts failed." - sed -i -e \ - "/def test_bru2bids():/i@pytest.mark.skip('Removed in full test suite, as this is already tested in `test_scripts.sh`')" \ - samri/pipelines/tests/test_repos.py || die - epytest -k "not longtime" -} diff --git a/sci-biology/samri/samri-9999.ebuild b/sci-biology/samri/samri-9999.ebuild new file mode 100644 index 000000000..f632f83a8 --- /dev/null +++ b/sci-biology/samri/samri-9999.ebuild @@ -0,0 +1,77 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools + +inherit distutils-r1 prefix + +DESCRIPTION="Small Animal Magnetic Resonance Imaging" +HOMEPAGE="https://github.com/IBT-FMI/SAMRI" +if [ "$PV" == "9999" ]; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/IBT-FMI/SAMRI.git" +else + SRC_URI="https://github.com/IBT-FMI/SAMRI/archive/${PV}.tar.gz -> ${P}.tar.gz" + KEYWORDS="~amd64" + S="${WORKDIR}/SAMRI-${PV}" +fi + +LICENSE="GPL-3" +SLOT="0" +IUSE="+atlases labbookdb" +REQUIRED_USE="test? ( atlases )" + +DEPEND=" + test? ( + sci-biology/samri_bidsdata + sci-biology/samri_bindata + ) + " +RDEPEND=" + dev-python/argh[${PYTHON_USEDEP}] + dev-python/joblib[${PYTHON_USEDEP}] + >=dev-python/matplotlib-2.0.2[${PYTHON_USEDEP}] + >=dev-python/numpy-1.13.3[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + dev-python/seaborn[${PYTHON_USEDEP}] + dev-python/statsmodels[${PYTHON_USEDEP}] + >=media-gfx/blender-2.83.4 + >=sci-biology/fsl-5.0.9 + sci-biology/bru2nii + atlases? ( sci-biology/mouse-brain-templates ) + labbookdb? ( sci-libs/labbookdb[${PYTHON_USEDEP}] ) + sci-libs/nibabel[${PYTHON_USEDEP}] + >=sci-libs/nipy-0.4.1[${PYTHON_USEDEP}] + >=sci-libs/nipype-1.0.0[${PYTHON_USEDEP}] + <sci-libs/pybids-0.10.2[${PYTHON_USEDEP}] + dev-python/scikit-image[${PYTHON_USEDEP}] + sci-biology/ants + sci-biology/afni + sci-biology/nilearn[${PYTHON_USEDEP}] +" + +distutils_enable_tests pytest +distutils_enable_sphinx doc/source dev-python/sphinxcontrib-napoleon + +src_prepare() { + distutils-r1_src_prepare + sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI \'/usr/ samri` || die + sed -i -e "s:/usr:@GENTOO_PORTAGE_EPREFIX@/usr:g" `grep -rlI /usr/ test_scripts.sh` || die + eprefixify $(grep -rl GENTOO_PORTAGE_EPREFIX samri/* test_scripts.sh) +} + +python_test() { + distutils_install_for_testing + export MPLBACKEND="agg" + export PATH=${TEST_DIR}/scripts:$PATH + export PYTHONIOENCODING=utf-8 + ./test_scripts.sh || die "Test scripts failed." + sed -i -e \ + "/def test_bru2bids():/i@pytest.mark.skip('Removed in full test suite, as this is already tested in `test_scripts.sh`')" \ + samri/pipelines/tests/test_repos.py || die + epytest -k "not longtime" +} diff --git a/sci-biology/screed/Manifest b/sci-biology/screed/Manifest deleted file mode 100644 index ff390a90d..000000000 --- a/sci-biology/screed/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST screed-1.0.4.tar.gz 121589 BLAKE2B 0d234e1b03247dca1515c7a6e03d297b75d708dfc6303124c28a0cd936704eb921d76560fd06956d190b8f8277ed301f27e776b6a3642209655d9218e32a3fe3 SHA512 6176029f7efa0319e4a7bf03727aad1729733859445fd0df51f39edfa660f44057e1849d487fe37c34289b023f1e85bc6f29b5f7ece189aea861637afd5fa516 diff --git a/sci-biology/screed/metadata.xml b/sci-biology/screed/metadata.xml deleted file mode 100644 index 297401f3d..000000000 --- a/sci-biology/screed/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="github">ged-lab/screed</remote-id> - <remote-id type="pypi">screed</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/screed/screed-1.0.4.ebuild b/sci-biology/screed/screed-1.0.4.ebuild deleted file mode 100644 index eab1748f4..000000000 --- a/sci-biology/screed/screed-1.0.4.ebuild +++ /dev/null @@ -1,26 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7,8,9} ) - -inherit distutils-r1 - -DESCRIPTION="Short read sequence utilities" -HOMEPAGE="https://pypi.python.org/pypi/screed https://github.com/ged-lab/screed/" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -SLOT="0" -LICENSE="BSD" -KEYWORDS="~amd64 ~x86" - -distutils_enable_tests --install pytest - -RDEPEND="dev-python/bz2file[${PYTHON_USEDEP}]" - -python_prepare_all() { - # do not depend on pytest-runner - sed -i "/pytest-runner/d" setup.py || die - distutils-r1_python_prepare_all -} diff --git a/sci-biology/seqtk/metadata.xml b/sci-biology/seqtk/metadata.xml index 138cb7705..a2d91d1c4 100644 --- a/sci-biology/seqtk/metadata.xml +++ b/sci-biology/seqtk/metadata.xml @@ -9,4 +9,7 @@ <email>sci-biology@gentoo.org</email> <name>Gentoo Biology Project</name> </maintainer> + <upstream> + <remote-id type="github">lh3/seqtk</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/signalp/Manifest b/sci-biology/signalp/Manifest deleted file mode 100644 index 4f4d96631..000000000 --- a/sci-biology/signalp/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST signalp-3.0.Linux.tar.Z 1216617 SHA256 260c2e5bd945b386e833a7b7326cff6d7332302868e99c0aeae306212047c0c2 diff --git a/sci-biology/signalp/metadata.xml b/sci-biology/signalp/metadata.xml deleted file mode 100644 index 8417d1580..000000000 --- a/sci-biology/signalp/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/signalp/signalp-3.0.ebuild b/sci-biology/signalp/signalp-3.0.ebuild deleted file mode 100644 index dcd83d920..000000000 --- a/sci-biology/signalp/signalp-3.0.ebuild +++ /dev/null @@ -1,46 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DESCRIPTION="Prediction of signal peptide cleavage sites in amino acid sequences" -HOMEPAGE="http://www.cbs.dtu.dk/services/SignalP/" -SRC_URI="${P}.Linux.tar.Z" - -LICENSE="signalp" -SLOT="0" -IUSE="gnuplot" -KEYWORDS="~amd64 ~x86" - -DEPEND="" -RDEPEND="gnuplot? ( - sci-visualization/gnuplot - media-libs/netpbm )" - -RESTRICT="fetch strip" - -pkg_nofetch() { - einfo "Please visit ${HOMEPAGE} and obtain the file" - einfo "\"${SRC_URI}\", then place it into your DISTDIR folder" -} - -src_prepare() { - default - sed -i -e '/SIGNALP=/ s/\/usr//' \ - -e '/TMPDIR=/ s/$SIGNALP//' "${S}/signalp" || die - sed -i 's/nawk/gawk/' "${S}"/bin/* || die -} - -src_install() { - dobin signalp - insinto /opt/${P} - doins -r bin hmm how mod syn* test - exeinto /opt/${P}/bin - doexe bin/* - exeinto /opt/${P}/hmm - doexe hmm/* - exeinto /opt/${P}/how - doexe how/* - doman signalp.1 - dodoc *readme -} diff --git a/sci-biology/snapgene-viewer/Manifest b/sci-biology/snapgene-viewer/Manifest new file mode 100644 index 000000000..2e6582002 --- /dev/null +++ b/sci-biology/snapgene-viewer/Manifest @@ -0,0 +1 @@ +DIST snapgene_7.0.3_linux.deb 129706720 BLAKE2B 539257921cc36c8770f5786e3af37502a6e958636ed32f861dcb2fd4621dfbac19d39c9a0772e0d08a532226f9b1875964bf657638917b52c606ff448a03b6f3 SHA512 b902d2bc229e697c4409b09b4f8e2a0ef6583a1958e7a38ef8321b453cdda687e33bc42adb14133d7320cc18791ec1b79409701efbfc5f6be0bbcce2f4e6e87f diff --git a/sci-biology/snapgene-viewer/metadata.xml b/sci-biology/snapgene-viewer/metadata.xml new file mode 100644 index 000000000..5c83ce208 --- /dev/null +++ b/sci-biology/snapgene-viewer/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>pacho@gentoo.org</email> + <name>Pacho Ramos</name> + </maintainer> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-biology/snapgene-viewer/snapgene-viewer-7.0.3.ebuild b/sci-biology/snapgene-viewer/snapgene-viewer-7.0.3.ebuild new file mode 100644 index 000000000..d117fbc14 --- /dev/null +++ b/sci-biology/snapgene-viewer/snapgene-viewer-7.0.3.ebuild @@ -0,0 +1,65 @@ +# Copyright 2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 +inherit unpacker wrapper xdg + +DESCRIPTION="Software for plasmid mapping, primer design, and restriction site analysis" +HOMEPAGE="https://www.snapgene.com/features" +SRC_URI="snapgene_${PV}_linux.deb" +SNAPGENE_DOWNLOAD="https://www.snapgene.com/local/targets/download.php?os=linux_deb&variant=paid&release=${PV}" +RESTRICT="fetch" + +LICENSE="GSL" +SLOT="0" +KEYWORDS="~amd64" + +DEPEND="" +# ldd /opt/gslbiotech/snapgene/snapgene +RDEPEND="${DEPEND} + app-arch/bzip2 + app-arch/xz-utils + app-crypt/qca[qt6] + dev-libs/openssl-compat:1.1.1 + dev-qt/qt5compat:6 + dev-qt/qtbase:6[concurrent,gui,network,opengl,sql,widgets,xml] + dev-qt/qtdeclarative:6 + dev-qt/qtpositioning:6 + dev-qt/qtwebchannel:6 + dev-qt/qtwebengine:6 + media-libs/libglvnd + media-libs/tiff-compat:4 + sci-libs/htslib:0/3 + sys-devel/gcc + sys-libs/glibc + sys-libs/libcxx[libcxxabi] + sys-libs/libunwind:0/8 + x11-libs/libX11 + x11-libs/libXau + x11-libs/libXdmcp + x11-libs/libxcb +" +BDEPEND=">=dev-util/patchelf-0.10" + +S="${WORKDIR}" +QA_PREBUILT="*" + +pkg_nofetch() { + elog "Please download ${SRC_URI} from" + elog "${SNAPGENE_DOWNLOAD}" + elog "and place it into your DISTDIR directory." +} + +src_install() { + patchelf --replace-needed libunwind.so.1 libunwind.so.8 \ + opt/gslbiotech/snapgene/snapgene || die + + mv usr/share/doc/snapgene usr/share/doc/${PF} || die + gzip -d usr/share/doc/${PF}/changelog.Debian.gz || die + + insinto / + doins -r * + + fperms +x /opt/gslbiotech/snapgene/snapgene{,.sh} + make_wrapper ${PN} ./snapgene.sh /opt/gslbiotech/snapgene/ +} diff --git a/sci-biology/spm/metadata.xml b/sci-biology/spm/metadata.xml index ae9640ffb..d888971d1 100644 --- a/sci-biology/spm/metadata.xml +++ b/sci-biology/spm/metadata.xml @@ -5,4 +5,7 @@ <email>sci@gentoo.org</email> <name>Gentoo Science Project</name> </maintainer> + <upstream> + <remote-id type="github">spm/spm12</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/sra-tools/files/libs_sra_Makefile.patch b/sci-biology/sra-tools/files/libs_sra_Makefile.patch deleted file mode 100644 index 44acc42b0..000000000 --- a/sci-biology/sra-tools/files/libs_sra_Makefile.patch +++ /dev/null @@ -1,77 +0,0 @@ -diff -u -w sra_sdk-2.1.9/work/sra_sdk-2.1.9/libs/sra/Makefile sra_sdk-2.1.9/work/sra_sdk-2.1.9/libs/sra/Makefile ---- sra_sdk-2.1.9/work/sra_sdk-2.1.9/libs/sra/Makefile 2011-12-02 21:30:12.000000000 +0100 -+++ sra_sdk-2.1.9/work/sra_sdk-2.1.9/libs/sra/Makefile 2012-02-06 18:38:45.000000000 +0100 -@@ -100,7 +100,7 @@ - $(addsuffix .$(LOBX),$(SRAPATH_SRC)) - - $(LIBDIR)/libsrapath.$(LIBX): $(SRAPATH_OBJ) -- $(LD) --slib -o $@ $^ -+ $(LD) --slib -o $(DESTDIR)$@ $^ - - libsrapath.vers.h: - @ true -@@ -138,10 +138,10 @@ - -dklib - - $(LIBDIR)/libsra-schema.$(SHLX): $(SRA_SCHEMA_OBJ) -- $(LD) --dlib --vers $(SRCDIR) -o $@ $^ $(SRA_SCHEMA_LIB) -+ $(LD) --dlib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(SRA_SCHEMA_LIB) - - $(LIBDIR)/libwsra-schema.$(SHLX): $(WSRA_SCHEMA_OBJ) -- $(LD) --dlib --vers $(SRCDIR) -o $@ $^ $(WSRA_SCHEMA_LIB) -+ $(LD) --dlib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(WSRA_SCHEMA_LIB) - - SRASCHEMA_SRC = \ - sraschema-stub -@@ -168,10 +168,10 @@ - $(addsuffix .$(LOBX),$(WSRASCHEMA_SRC)) - - $(LIBDIR)/libsraschema.$(LIBX): $(SRASCHEMA_OBJ) $(SRASCHEMA_DEPS) -- $(LD) --slib -o $@ $(SRASCHEMA_OBJ) $(SRA_SCHEMA_LIB) -+ $(LD) --slib -o $(DESTDIR)$@ $(SRASCHEMA_OBJ) $(SRA_SCHEMA_LIB) - - $(LIBDIR)/libwsraschema.$(LIBX): $(WSRASCHEMA_OBJ) $(WSRASCHEMA_DEPS) -- $(LD) --slib -o $@ $(WSRASCHEMA_OBJ) $(WSRA_SCHEMA_LIB) -+ $(LD) --slib -o $(DESTDIR)$@ $(WSRASCHEMA_OBJ) $(WSRA_SCHEMA_LIB) - - libsraschema_tag: - @ $(TOP)/build/tag-module.sh $(MODULE) libsraschema $(SRASCHEMA_OBJ) -@@ -205,10 +205,10 @@ - -dklib - - $(LIBDIR)/libsradb.$(SHLX): $(SRADB_OBJ) -- $(LD) --dlib --vers $(SRCDIR) -o $@ $^ $(SRADB_LIB) -+ $(LD) --dlib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(SRADB_LIB) - - $(LIBDIR)/libsradb.$(LIBX): $(SRADB_OBJ) -- $(LD) --slib --vers $(SRCDIR) -o $@ $^ $(SRADB_LIB) -+ $(LD) --slib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(SRADB_LIB) - - libsradb_tag: $(SRADB_TAGS) - @ $(TOP)/build/tag-module.sh $(MODULE) libsradb $(SRADB_OBJ) -@@ -236,10 +236,10 @@ - -dklib - - $(LIBDIR)/libwsradb.$(SHLX): $(WSRADB_OBJ) -- $(LD) --dlib --vers $(SRCDIR) -o $@ $^ $(WSRADB_LIB) -+ $(LD) --dlib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(WSRADB_LIB) - - $(LIBDIR)/libwsradb.$(LIBX): $(WSRADB_OBJ) -- $(LD) --slib --vers $(SRCDIR) -o $@ $^ $(WSRADB_LIB) -+ $(LD) --slib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(WSRADB_LIB) - - libwsradb_tag: $(WSRADB_TAGS) - @ $(TOP)/build/tag-module.sh $(MODULE) libwsradb $(WSRADB_OBJ) -@@ -266,10 +266,10 @@ - -dklib - - $(LIBDIR)/libsrareader.$(SHLX): $(SRAREADER_OBJ) -- $(LD) --dlib --vers $(SRCDIR) -o $@ $^ $(SRAREADER_LIB) -+ $(LD) --dlib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(SRAREADER_LIB) - - $(LIBDIR)/libsrareader.$(LIBX): $(SRAREADER_OBJ) -- $(LD) --slib --vers $(SRCDIR) -o $@ $^ $(SRAREADER_LIB) -+ $(LD) --slib --vers $(SRCDIR) -o $(DESTDIR)$@ $^ $(SRAREADER_LIB) - - libsrareader_tag: - @ $(TOP)/build/tag-module.sh $(MODULE) libsrareader $(SRAREADER_OBJ) diff --git a/sci-biology/sra-tools/files/sra_sdk-destdir.patch b/sci-biology/sra-tools/files/sra_sdk-destdir.patch deleted file mode 100644 index bf66c6e46..000000000 --- a/sci-biology/sra-tools/files/sra_sdk-destdir.patch +++ /dev/null @@ -1,76 +0,0 @@ -diff -r -u -w sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/Makefile.env sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/Makefile.env ---- sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/Makefile.env 2011-08-31 21:46:21.000000000 +0200 -+++ sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/Makefile.env 2012-02-06 02:02:38.000000000 +0100 -@@ -141,7 +141,7 @@ - - # create all required output directories - makedirs: -- @ mkdir -p $(addprefix $(TARGDIR)/,$(SUBDIRS) obj/$(MODULE)) $(NCBIDIR) -+ @ mkdir -p $(addprefix $(TARGDIR)/,$(SUBDIRS) obj/$(MODULE)) $(DESTDIR)/$(NCBIDIR) - - ifeq (win,$(OS)) - -diff -r -u -w sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/ld.linux.gcc.sh sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/ld.linux.gcc.sh ---- sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/ld.linux.gcc.sh 2010-12-28 22:46:39.000000000 +0100 -+++ sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/ld.linux.gcc.sh 2012-02-06 02:23:07.000000000 +0100 -@@ -38,10 +38,10 @@ - # versioned output - if [ "$VERS" = "" ] - then -- DLIB_CMD="$DLIB_CMD -o $TARG" -- EXE_CMD="$EXE_CMD -o $TARG" -+ DLIB_CMD="$DLIB_CMD -o $DESTDIR$TARG" -+ EXE_CMD="$EXE_CMD -o $TARG" - else - set-vers $(echo $VERS | tr '.' ' ') -- DLIB_CMD="$DLIB_CMD -o $OUTDIR/$NAME$DBGAP.so.$VERS -Wl,-soname,$NAME.so.$MAJ" -- EXE_CMD="$EXE_CMD -o $OUTDIR/$NAME$DBGAP.$VERS" -+ DLIB_CMD="$DLIB_CMD -o $DESTDIR$OUTDIR/$NAME$DBGAP.so.$VERS -Wl,-soname,$NAME.so.$MAJ" -+ EXE_CMD="$EXE_CMD -o $DESTDIR$OUTDIR/$NAME$DBGAP.$VERS" - fi -diff -r -u -w sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/ld.linux.ln.sh sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/ld.linux.ln.sh ---- sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/ld.linux.ln.sh 2010-12-28 22:46:39.000000000 +0100 -+++ sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/ld.linux.ln.sh 2012-02-06 02:34:46.000000000 +0100 -@@ -52,12 +52,12 @@ - - set-vers $(echo $VERS | tr '.' ' ') - --cd "$OUTDIR" || exit 5 -+cd $DESTDIR$OUTDIR || exit 5 - - # create link - create-link () - { -- rm -f "$2" -+ rm -f $DESTDIR"$2" - local CMD="ln -s $1 $2" - echo $CMD - $CMD ---- sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/ld.linux.slib.sh 2012-02-06 04:05:16.000000000 +0100 -+++ sra_sdk-2.1.9-/work/sra_sdk-2.1.9/build/ld.linux.slib.sh 2012-02-06 04:05:29.000000000 +0100 -@@ -77,7 +77,7 @@ - CMD="$CMD $TARG" - else - set-vers $(echo $VERS | tr '.' ' ') -- CMD="$CMD $OUTDIR/$NAME$DBGAP.a.$VERS" -+ CMD="$CMD $DESTDIR/$OUTDIR/$NAME$DBGAP.a.$VERS" - fi - - # tack on object files ---- sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/Makefile.gcc.ori 2012-02-06 04:24:39.000000000 +0100 -+++ sra_sdk-2.1.9/work/sra_sdk-2.1.9/build/Makefile.gcc 2012-02-06 04:22:57.000000000 +0100 -@@ -36,12 +36,12 @@ - LD = @ $(TOP)/build/ld.sh $(OS) $(ARCH) gcc \ - --build $(BUILD) --ldflags "$(LDFLAGS)" $(STATIC) \ - $(STATICSYSLIBS) $(CHECKSUM) --objx $(OBJX) --shlx $(SHLX) --libx $(LIBX) \ -- -MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(LIBDIR):$(ILIBDIR) -+ -MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(DESTDIR)$(LIBDIR):$(ILIBDIR) - - LP = @ $(TOP)/build/ld.sh $(OS) $(ARCH) g++ \ - --build $(BUILD) --ldflags "$(LDFLAGS)" $(STATIC) \ - $(STATICSYSLIBS) $(CHECKSUM) --objx $(OBJX) --shlx $(SHLX) --libx $(LIBX) \ -- -MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(LIBDIR):$(ILIBDIR) -+ -MD --srcdir $(SRCDIR) --bindir $(BINDIR) -L$(DESTDIR)$(LIBDIR):$(ILIBDIR) - - # tool options - WARN = -Wall -Wno-variadic-macros # -Wconversion diff --git a/sci-biology/sra-tools/files/tools_vdb-vcopy_Makefile.patch b/sci-biology/sra-tools/files/tools_vdb-vcopy_Makefile.patch deleted file mode 100644 index 738d67cbd..000000000 --- a/sci-biology/sra-tools/files/tools_vdb-vcopy_Makefile.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff -u -w sra_sdk-2.1.9/work/sra_sdk-2.1.9/tools/vdb-copy/Makefile sra_sdk-2.1.9/work/sra_sdk-2.1.9/tools/vdb-copy/Makefile ---- sra_sdk-2.1.9/work/sra_sdk-2.1.9/tools/vdb-copy/Makefile 2011-12-02 22:00:36.000000000 +0100 -+++ sra_sdk-2.1.9/work/sra_sdk-2.1.9/tools/vdb-copy/Makefile 2012-02-06 18:39:05.000000000 +0100 -@@ -89,7 +89,7 @@ - $(BINDIR)/vdb-copy: $(NCBIDIR)/vdb-copy.kfg - - $(NCBIDIR)/vdb-copy.kfg: $(SRCDIR)/vdb-copy.kfg -- cp $^ $@ -+ cp $^ $(DESTDIR)$@ - - VDB_COPY_SRC = \ - num-gen \ diff --git a/sci-biology/staden/Manifest b/sci-biology/staden/Manifest deleted file mode 100644 index 13f7d3536..000000000 --- a/sci-biology/staden/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST staden-2.0.0_beta11-src.tar.gz 4754651 BLAKE2B d55dcff2192a5f6c505d141960f624ad30afb358e481c438d285a267bb116f8e26e1b7d6562c222b4c7392729bacd14524ee9275ada5201b7d8bcefbd244112f SHA512 6f85cc3aa3b909431333a4998566b267f1d344b3160603604306caf41504cc36c05980790bf5a8f2b4a53f7aea2a369ffafbce163b41c3ea94605f7fee07a26a diff --git a/sci-biology/staden/files/staden-2.0.0_beta11-ldflags.patch b/sci-biology/staden/files/staden-2.0.0_beta11-ldflags.patch deleted file mode 100644 index 735feb315..000000000 --- a/sci-biology/staden/files/staden-2.0.0_beta11-ldflags.patch +++ /dev/null @@ -1,30 +0,0 @@ - abi/Makefile | 2 +- - alf/Makefile | 2 +- - 2 files changed, 2 insertions(+), 2 deletions(-) - -diff --git a/abi/Makefile b/abi/Makefile -index 3c1f8fb..58b4353 100644 ---- a/abi/Makefile -+++ b/abi/Makefile -@@ -23,7 +23,7 @@ getABISampleName: $(OBJSSN) - $(CLD) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(OBJSSN) $(LIBS) $(LIBSC) - - getABIdate: $(OBJSD) -- $(CLD) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(OBJSD) $(IOUTILS_LIB) $(MISC_LIB) $(LIBSC) -+ $(CLD) $(LDFLAGS) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(OBJSD) $(IOUTILS_LIB) $(MISC_LIB) $(LIBSC) - - getABIcomment: $(OBJSC) - $(CLD) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(OBJSC) $(LIBS) $(LIBSC) -diff --git a/alf/Makefile b/alf/Makefile -index 94b7480..ef41a26 100644 ---- a/alf/Makefile -+++ b/alf/Makefile -@@ -16,7 +16,7 @@ INCLUDES_E += $(MISC_INC) - ALFOBJ = alfsplit.o - - alfsplit: $(ALFOBJ) -- $(CLD) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(ALFOBJ) $(LIBSC) -+ $(CLD) $(LDFLAGS) $(LDEXEFLAG)$@$(EXE_SUFFIX) $(SUBSYSTEMCONSOLE) $(ALFOBJ) $(LIBSC) - - RSOBJ = $(ALFBIN)/2rs.o - diff --git a/sci-biology/staden/metadata.xml b/sci-biology/staden/metadata.xml deleted file mode 100644 index 1ed1820a4..000000000 --- a/sci-biology/staden/metadata.xml +++ /dev/null @@ -1,15 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">staden</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/staden/staden-2.0.0_beta11.ebuild b/sci-biology/staden/staden-2.0.0_beta11.ebuild deleted file mode 100644 index a0f91720b..000000000 --- a/sci-biology/staden/staden-2.0.0_beta11.ebuild +++ /dev/null @@ -1,76 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit flag-o-matic fortran-2 - -DESCRIPTION="DNA sequence assembly (gap4, gap5), editing and analysis tools (Spin)" -HOMEPAGE="https://sourceforge.net/projects/staden" -SRC_URI="https://downloads.sourceforge.net/staden/staden-${PV/_beta/b}-2016-src.tar.gz -> ${P}-src.tar.gz" - -LICENSE="staden" -SLOT="0" -KEYWORDS="~amd64" -IUSE="debug doc fortran png tcl tk X zlib" - -# either g77 or gfortran must be available -# edit src/mk/linux.mk accordingly -# -# this is a glibc-2.9 issue, see https://sourceforge.net/tracker/index.php?func=detail&aid=2629155&group_id=100316&atid=627058 -# -# -# - -DEPEND=" - app-arch/xz-utils - dev-lang/tk:0= - dev-tcltk/tklib - media-libs/libpng:0 - sci-biology/samtools:0 - >=sci-libs/io_lib-1.13.8 - sys-libs/zlib" -RDEPEND="${DEPEND} - >=dev-tcltk/iwidgets-4.0 - tcl? ( >=dev-tcltk/itcl-3.2 ) - tk? ( >=dev-tcltk/itk-3.2 ) - net-misc/curl - doc? ( sci-biology/staden_doc )" - -S="${WORKDIR}"/staden-${PV/_beta/b}-2016-src - -PATCHES=( - "${FILESDIR}/${P}-ldflags.patch" -) - -src_prepare() { - default - sed \ - -e 's:svnversion:false:' \ - -i configure.in || die -} - -src_configure(){ - use debug && append-cflags "-DCACHE_REF_DEBUG" - econf \ - $(use_enable X x) \ - $(use_enable amd64 64bit) \ - --with-tklib="/usr/$(get_libdir)/tklib" -} - -src_install() { - default - # install the LDPATH so that it appears in /etc/ld.so.conf after env-update - # subsequently, apps linked against /usr/lib/staden can be run because - # loader can find the library (I failed to use '-Wl,-rpath,/usr/lib/staden' - # somehow for gap2caf, for example - cat >> "${T}"/99staden <<- EOF - STADENROOT="${EPREFIX}"/usr/share/staden - LDPATH="${EPREFIX}/usr/$(get_libdir)/staden" - EOF - doenvd "${T}"/99staden -} - -pkg_postinst(){ - einfo "There is a tutorial at https://sourceforge.net/projects/staden/files/tutorials/1.1/course-1.1.tar.gz" -} diff --git a/sci-biology/staden_doc/Manifest b/sci-biology/staden_doc/Manifest deleted file mode 100644 index 108aad2fe..000000000 --- a/sci-biology/staden_doc/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST staden_doc-2.0.0b11-src.tar.gz 3184526 BLAKE2B cf67f702efd0743899b0f955434b815bdb695d28641069a4da981e5fe5de9091980b997e55d10897ff21fca1928f1afb787aa9a89d66ab658b14f8db9b35d110 SHA512 ca8aad2ab3ec660dbd8631bb65df95b10fa64e20d5d509925a03e277896ed8a2eebef89f6b170fe2acd0dd10e0075585620dd162b7b5c9153b248ee6dedd6ef1 diff --git a/sci-biology/staden_doc/metadata.xml b/sci-biology/staden_doc/metadata.xml deleted file mode 100644 index 1ed1820a4..000000000 --- a/sci-biology/staden_doc/metadata.xml +++ /dev/null @@ -1,15 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">staden</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-biology/staden_doc/staden_doc-2.0.0_beta11.ebuild b/sci-biology/staden_doc/staden_doc-2.0.0_beta11.ebuild deleted file mode 100644 index 5a70701b0..000000000 --- a/sci-biology/staden_doc/staden_doc-2.0.0_beta11.ebuild +++ /dev/null @@ -1,42 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DESCRIPTION="Documentation files for the staden package" -HOMEPAGE="https://sourceforge.net/projects/staden" -SRC_URI="https://sourceforge.net/projects/staden/files/staden/${PV/_beta/b}/staden_doc-${PV/_beta/b}-src.tar.gz" - -LICENSE="staden" -SLOT="0" -KEYWORDS="~amd64" - -DEPEND=" - dev-lang/perl - app-text/texlive - app-text/texi2html" -BDEPEND="app-editors/emacs" -RDEPEND="${DEPEND} ${BDEPEND}" - -S="${WORKDIR}"/staden_doc-${PV/_beta/b}-src - -# do not use texi2html-5 because it fails with: -# texi2html -menu -verbose -split_chapter -index_chars interface.htmlinfo -# Unknown option: index_char -# src_prepare(){ -# default -# # avoid running bundled texi2html code -# sed -e "s#./tools/texi2html#texi2html#" -i manual/Makefile || die -# } - -src_compile(){ - cd manual || die - emake -j1 spotless || die - cd .. || die - emake -j1 unix PAPER=A4 -} - -src_install(){ - emake -j1 install prefix="${D}"/usr - dodoc gkb547_gml.pdf -} diff --git a/sci-biology/tigmint/tigmint-1.2.4-r1.ebuild b/sci-biology/tigmint/tigmint-1.2.4-r1.ebuild index 84b582151..c5f630a96 100644 --- a/sci-biology/tigmint/tigmint-1.2.4-r1.ebuild +++ b/sci-biology/tigmint/tigmint-1.2.4-r1.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 -PYTHON_COMPAT=( python3_{8..9} ) +PYTHON_COMPAT=( python3_{10..10} ) DISTUTILS_USE_SETUPTOOLS=no inherit distutils-r1 diff --git a/sci-biology/tmhmm/Manifest b/sci-biology/tmhmm/Manifest deleted file mode 100644 index 875ce562e..000000000 --- a/sci-biology/tmhmm/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST tmhmm-2.0c.Linux.tar.gz 191561 SHA256 761a87ca82c174e0e6660c5065f257ef0b201fab98f934e1342291e4e673ca40 diff --git a/sci-biology/tmhmm/metadata.xml b/sci-biology/tmhmm/metadata.xml deleted file mode 100644 index 8417d1580..000000000 --- a/sci-biology/tmhmm/metadata.xml +++ /dev/null @@ -1,8 +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-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/tmhmm/tmhmm-2.0c.ebuild b/sci-biology/tmhmm/tmhmm-2.0c.ebuild deleted file mode 100644 index dc50101fa..000000000 --- a/sci-biology/tmhmm/tmhmm-2.0c.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 - -DESCRIPTION="Prediction of transmembrane helices in proteins" -HOMEPAGE="http://www.cbs.dtu.dk/services/TMHMM/" -SRC_URI="${P}.Linux.tar.gz" - -LICENSE="tmhmm" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -RESTRICT="fetch" - -S="TMHMM${PV}" - -pkg_nofetch() { - einfo "Please visit ${HOMEPAGE} and obtain the file" - einfo "\"${SRC_URI}\", then place it into your DISTDIR folder" -} - -src_prepare() { - default - sed -i '1 i #!/usr/bin/env perl' "${S}"/bin/tmhmm* || die - sed -i '1 a $opt_basedir = "/opt/tmhmm";' "${S}"/bin/tmhmm || die -} - -src_install() { - exeinto /opt/${PN}/bin - doexe bin/* - - insinto /opt/${PN}/lib - doins lib/* - - dosym ../${PN}/bin/tmhmm /opt/bin/tmhmm - - dodoc README TMHMM2.0.html -} diff --git a/sci-biology/trans-abyss/Manifest b/sci-biology/trans-abyss/Manifest deleted file mode 100644 index 9addb1899..000000000 --- a/sci-biology/trans-abyss/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST trans-abyss-2.0.1.tar.gz 359063 BLAKE2B 9b3f19b883e2616b05bc0677b9161e8c997596b288af7e570a83129549edd517a941f765d39dfb83638160e611df3f2acfc32eb944c7cca63c8350e77fb96246 SHA512 5362665a2758a76c579d8086f8904cf0e40c8dff0dfa1c82368b38af25e37f2f2852f60c3001db254e5f06400e9e2e7f6f6c301133b7806d47cee189f84a0f0f diff --git a/sci-biology/trans-abyss/metadata.xml b/sci-biology/trans-abyss/metadata.xml deleted file mode 100644 index 138cb7705..000000000 --- a/sci-biology/trans-abyss/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/trans-abyss/trans-abyss-2.0.1.ebuild b/sci-biology/trans-abyss/trans-abyss-2.0.1.ebuild deleted file mode 100644 index cf10dd3b9..000000000 --- a/sci-biology/trans-abyss/trans-abyss-2.0.1.ebuild +++ /dev/null @@ -1,35 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7,8,9} ) - -inherit python-r1 - -DESCRIPTION="Analyze and combine multiple assemblies from abyss" -HOMEPAGE="https://www.bcgsc.ca/resources/software/trans-abyss" -SRC_URI="https://github.com/bcgsc/transabyss/archive/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -DEPEND="${PYTHON_DEPS} - dev-lang/perl - dev-python/python-igraph[${PYTHON_USEDEP}] - sci-biology/abyss - sci-biology/blat -" -RDEPEND="${DEPEND}" - -S="${WORKDIR}/transabyss-${PV}" - -src_install() { - einstalldocs - python_foreach_impl python_domodule utilities - dobin transabyss - dobin transabyss-merge -} diff --git a/sci-biology/trim_galore/Manifest b/sci-biology/trim_galore/Manifest deleted file mode 100644 index d49ab113e..000000000 --- a/sci-biology/trim_galore/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST trim_galore-0.6.6.tar.gz 26829185 BLAKE2B b783d5b8fcf831c5b652cbfed82a42ad55e911aac1b16ac367d27ff6c07f298cd8fd797d4ac4b4213e7c9188ee02e7a2bab97799cc2c9eeba88244556b006832 SHA512 3714f89cee439cf2ef2c88c1f505507c00e426345ff59bdb48fadcc56fe78617d7641da9b6deb5f122fb1d41449fdc4b3f79ee336ec4bf240edbe071aeffc025 diff --git a/sci-biology/trim_galore/metadata.xml b/sci-biology/trim_galore/metadata.xml deleted file mode 100644 index 138cb7705..000000000 --- a/sci-biology/trim_galore/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/trim_galore/trim_galore-0.6.6.ebuild b/sci-biology/trim_galore/trim_galore-0.6.6.ebuild deleted file mode 100644 index c99dcfcc6..000000000 --- a/sci-biology/trim_galore/trim_galore-0.6.6.ebuild +++ /dev/null @@ -1,26 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DESCRIPTION="Perl wrapper around Cutadapt and FastQC to adapter and quality trimming" -HOMEPAGE="https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ https://github.com/FelixKrueger/TrimGalore" -SRC_URI="https://github.com/FelixKrueger/TrimGalore/archive/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="~amd64" - -DEPEND="" -RDEPEND=" - dev-lang/perl - sci-biology/cutadapt - sci-biology/fastqc - ${DEPEND}" - -S="${WORKDIR}/TrimGalore-${PV}" - -src_install(){ - dobin trim_galore - dodoc -r Docs -} diff --git a/sci-biology/ugene/metadata.xml b/sci-biology/ugene/metadata.xml index a3daeebd2..36e8936e5 100644 --- a/sci-biology/ugene/metadata.xml +++ b/sci-biology/ugene/metadata.xml @@ -9,4 +9,7 @@ <email>sci@gentoo.org</email> <name>Gentoo Science Project</name> </maintainer> + <upstream> + <remote-id type="github">ugeneunipro/ugene</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-biology/weblogo/Manifest b/sci-biology/weblogo/Manifest deleted file mode 100644 index 264bad9bd..000000000 --- a/sci-biology/weblogo/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST weblogo-3.7.5.tar.gz 817128 BLAKE2B f7619b6ea0c944fb21b8acdfc9593d6223e7d48ac9495c872c3bcadc0187249883b013e44bec70ce126d820abb6281b2e5ef5f04126e7a288c3f5a1026612ab0 SHA512 7fbf71854eee0bcebebe926f2c93653b0b8475462ed5b3dc951947cec67a37bee801d468f893932257f5bdca8c754264c3279695cdb3da747bd82e9353392c0b diff --git a/sci-biology/weblogo/metadata.xml b/sci-biology/weblogo/metadata.xml deleted file mode 100644 index 138cb7705..000000000 --- a/sci-biology/weblogo/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>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-biology/weblogo/weblogo-3.7.5.ebuild b/sci-biology/weblogo/weblogo-3.7.5.ebuild deleted file mode 100644 index a8db5bec5..000000000 --- a/sci-biology/weblogo/weblogo-3.7.5.ebuild +++ /dev/null @@ -1,33 +0,0 @@ -# Copyright 1999-2020 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="generate consensus sequence logo figures" -HOMEPAGE="http://weblogo.threeplusone.com/" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -RDEPEND=" - dev-python/scipy -" -BDEPEND=" - test? ( - app-text/ghostscript-gpl - dev-python/mypy - ) -" - -distutils_enable_tests pytest - -python_test() { - distutils_install_for_testing - pytest -vv || die "tests failed with ${EPYTHON}" -} diff --git a/sci-chemistry/chimera-bin/Manifest b/sci-chemistry/chimera-bin/Manifest deleted file mode 100644 index a3bee4f39..000000000 --- a/sci-chemistry/chimera-bin/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST chimera-1.14-linux_x86_64.bin 157644313 BLAKE2B 75dba07faa5cbd76b472318a50f8dc9dbedfccd9f2ff59769cb5517639d4381f025ecfc206a6c61bd1bfe49928d3bf9076e5506db2a7b700923663399657ac46 SHA512 2309305cff892e28b89d8281231c1546212143cc347885f83544a85f776733329ba6adc7dc748cb4453e31a6eb535b57487ecd34b1c1800ff222950e92109e85 -DIST chimera-1.15-linux_x86_64.bin 154069682 BLAKE2B 802f9e1b0182bf8b6ae38057145c25f2abfd2e71a3e4b7651a73130c8e11c9aee5e7eba230c2558821a95f33c6a4619897be355ee7ce3be0d319ded88a71b63f SHA512 7c4be169f22ab9557ac89087938a52b5c3d41d0971ff52e6ecf9c7dce41126f88a2c6f626e8b5c8876fe52fe36c94c55a61b515da7e7bdde17046546e75f4b97 diff --git a/sci-chemistry/chimera-bin/chimera-bin-1.14.ebuild b/sci-chemistry/chimera-bin/chimera-bin-1.14.ebuild deleted file mode 100644 index 7d5f9147a..000000000 --- a/sci-chemistry/chimera-bin/chimera-bin-1.14.ebuild +++ /dev/null @@ -1,96 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit desktop xdg - -DESCRIPTION="An extensible Molecular Modelling System" -HOMEPAGE="https://www.cgl.ucsf.edu/chimera/" -SRC_URI="chimera-${PV}-linux_x86_64.bin" - -SLOT="0" -LICENSE="chimera" -KEYWORDS="~amd64 ~x86" - -DEPEND="prefix? ( dev-util/patchelf )" -RDEPEND=" - dev-lang/tcl - dev-lang/tk - dev-libs/expat - dev-libs/libotf - dev-libs/openssl:0 - dev-libs/libpcre - sys-libs/zlib - media-libs/fontconfig - media-libs/freetype - media-libs/ftgl - media-libs/libpng - media-libs/tiff - sci-libs/hdf5 - sci-libs/xdrfile - sys-devel/gcc[openmp,fortran] - media-libs/libjpeg-turbo - virtual/glu - virtual/opengl - x11-libs/libX11 - x11-libs/libICE - x11-libs/libXext - x11-libs/libXft - x11-libs/libXmu - x11-libs/libXpm - x11-libs/libXrender - x11-libs/libSM - x11-libs/libXt - x11-libs/libGLw -" - -S="${WORKDIR}" - -RESTRICT="fetch mirror strip" - -QA_PREBUILT="opt/.*" - -pkg_nofetch() { - elog "Please visit" - elog "https://www.cgl.ucsf.edu/chimera/download.html" - elog "or" - elog "https://www.cgl.ucsf.edu/chimera/olddownload.html" - elog "and download ${A} into your DISTDIR" -} - -src_unpack() { - cp "${DISTDIR}"/${A} ${A}.zip - unzip ${A}.zip || die -} - -src_install() { - chmod +x ./chimera.bin - dodir /opt/ - ./chimera.bin -d foo || die - doicon foo/chimeraIcon.png - mv foo "${ED}/opt/${PN}" || die - - cat >> "${T}"/chimera <<- EOF - #!${EPREFX}/bin/bash - - export PATH="${EPREFIX}/opt/${PN}/bin:\${PATH}" - "${EPREFIX}/opt/${PN}/bin/chimera" \$@ - EOF - - exeinto /opt/bin/ - doexe "${T}"/chimera - - # point the symlink to the correct location - rm "${ED}/opt/chimera-bin/include/ft2build.h" - dosym ../../../usr/include/freetype2/ft2build.h opt/chimera-bin/include/ft2build.h - - make_desktop_entry "${EPREFIX}/opt/bin/chimera" Chimera chimeraIcon - - if use prefix; then - local i - for i in "${ED}"/opt/${PN}/bin/{tiffcp,povray,al2co} "${ED}"/opt/${PN}/lib/*.so; do - patchelf --set-rpath "${EPREFIX}/usr/lib:${EPREFIX}/opt/${PN}/lib" "${i}" || die - done - fi -} diff --git a/sci-chemistry/chimera-bin/chimera-bin-1.15.ebuild b/sci-chemistry/chimera-bin/chimera-bin-1.15.ebuild deleted file mode 100644 index 7d5f9147a..000000000 --- a/sci-chemistry/chimera-bin/chimera-bin-1.15.ebuild +++ /dev/null @@ -1,96 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit desktop xdg - -DESCRIPTION="An extensible Molecular Modelling System" -HOMEPAGE="https://www.cgl.ucsf.edu/chimera/" -SRC_URI="chimera-${PV}-linux_x86_64.bin" - -SLOT="0" -LICENSE="chimera" -KEYWORDS="~amd64 ~x86" - -DEPEND="prefix? ( dev-util/patchelf )" -RDEPEND=" - dev-lang/tcl - dev-lang/tk - dev-libs/expat - dev-libs/libotf - dev-libs/openssl:0 - dev-libs/libpcre - sys-libs/zlib - media-libs/fontconfig - media-libs/freetype - media-libs/ftgl - media-libs/libpng - media-libs/tiff - sci-libs/hdf5 - sci-libs/xdrfile - sys-devel/gcc[openmp,fortran] - media-libs/libjpeg-turbo - virtual/glu - virtual/opengl - x11-libs/libX11 - x11-libs/libICE - x11-libs/libXext - x11-libs/libXft - x11-libs/libXmu - x11-libs/libXpm - x11-libs/libXrender - x11-libs/libSM - x11-libs/libXt - x11-libs/libGLw -" - -S="${WORKDIR}" - -RESTRICT="fetch mirror strip" - -QA_PREBUILT="opt/.*" - -pkg_nofetch() { - elog "Please visit" - elog "https://www.cgl.ucsf.edu/chimera/download.html" - elog "or" - elog "https://www.cgl.ucsf.edu/chimera/olddownload.html" - elog "and download ${A} into your DISTDIR" -} - -src_unpack() { - cp "${DISTDIR}"/${A} ${A}.zip - unzip ${A}.zip || die -} - -src_install() { - chmod +x ./chimera.bin - dodir /opt/ - ./chimera.bin -d foo || die - doicon foo/chimeraIcon.png - mv foo "${ED}/opt/${PN}" || die - - cat >> "${T}"/chimera <<- EOF - #!${EPREFX}/bin/bash - - export PATH="${EPREFIX}/opt/${PN}/bin:\${PATH}" - "${EPREFIX}/opt/${PN}/bin/chimera" \$@ - EOF - - exeinto /opt/bin/ - doexe "${T}"/chimera - - # point the symlink to the correct location - rm "${ED}/opt/chimera-bin/include/ft2build.h" - dosym ../../../usr/include/freetype2/ft2build.h opt/chimera-bin/include/ft2build.h - - make_desktop_entry "${EPREFIX}/opt/bin/chimera" Chimera chimeraIcon - - if use prefix; then - local i - for i in "${ED}"/opt/${PN}/bin/{tiffcp,povray,al2co} "${ED}"/opt/${PN}/lib/*.so; do - patchelf --set-rpath "${EPREFIX}/usr/lib:${EPREFIX}/opt/${PN}/lib" "${i}" || die - done - fi -} diff --git a/sci-chemistry/chimera-bin/metadata.xml b/sci-chemistry/chimera-bin/metadata.xml deleted file mode 100644 index da36ecbfc..000000000 --- a/sci-chemistry/chimera-bin/metadata.xml +++ /dev/null @@ -1,8 +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-chemistry@gentoo.org</email> - <name>Gentoo Chemistry Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-chemistry/chimera/Manifest b/sci-chemistry/chimera/Manifest new file mode 100644 index 000000000..953fae5f9 --- /dev/null +++ b/sci-chemistry/chimera/Manifest @@ -0,0 +1,3 @@ +DIST Chimera512.png 68464 BLAKE2B 51797728b8b9421ab6e42e57bb60881a706d17eed09cbef57506f706b7ebab6511397f90834d15efaea5e86a22fc2ff9e55cf42c7a87d6166716444252d18f49 SHA512 6ed0dd8bd1b5a6b164f80acc1d7e1a91629513b147d37472e1831b657201a3f25c1c0c9a1b44bf565afaa4aa99469910d1ac307a45a80b9a12d0554e1812e2c5 +DIST chimera-1.17.1-linux_x86_64.bin 149832020 BLAKE2B 01e78d09a3373a3d927c93daa03d0c17473c18079afd989a29afaad5c56aa57bbfeb968bcef42eb50924e1cde67e939c92a545080c0e7b55549c30e43aae564d SHA512 f6df3ad320f09b3f8d918660a4a7596505c2a97ac0d60a4f6ef9c414851a90bb59ccba9728d5a71df93404b8c6ecf99ab9dca84befcfa10e60285f3a33e3c3bc +DIST chimera-1.17.3-linux_x86_64.bin 155528316 BLAKE2B 09caddbac9a518606b8065a19840fd2f5e3a57cbb529bea2e4b63cb83ecd91105c1de34dc3f1139382fc80f14e69b28c39152d9b15e16c39a08732ebcd374c51 SHA512 cfbf42dd3aa030db0619bf5750d08ba94acc53f54a890109d422a675394616afba9c85779e5d62bcd4ad83db4a7cfcf8190c2c42c84719c991061859c87288b7 diff --git a/sci-chemistry/chimera/chimera-1.17.1.ebuild b/sci-chemistry/chimera/chimera-1.17.1.ebuild new file mode 100644 index 000000000..919350ac9 --- /dev/null +++ b/sci-chemistry/chimera/chimera-1.17.1.ebuild @@ -0,0 +1,93 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 +inherit desktop xdg + +DESCRIPTION="Next generation molecular visualization program from RBVI" +HOMEPAGE="https://www.cgl.ucsf.edu/chimera/" +SRC_URI="chimera-${PV}-linux_x86_64.bin + fetch+http://svn.cgl.ucsf.edu/svn/chimera/trunk/icons/chimera/Chimera512.png" + +SLOT="0" +LICENSE="chimera" +KEYWORDS="~amd64 ~x86" + +RESTRICT="fetch mirror strip" +QA_PREBUILT="*" + +DEPEND="" +BDEPEND="" +RDEPEND=" + dev-lang/tcl + dev-lang/tk + dev-libs/expat + dev-libs/libotf + dev-libs/openssl:0 + dev-libs/libpcre + sys-libs/zlib + media-libs/fontconfig + media-libs/freetype + media-libs/ftgl + media-libs/libpng + media-libs/tiff + sci-libs/hdf5 + sys-devel/gcc[openmp,fortran] + media-libs/libjpeg-turbo + virtual/glu + virtual/opengl + x11-libs/libX11 + x11-libs/libICE + x11-libs/libXext + x11-libs/libXft + x11-libs/libXmu + x11-libs/libXpm + x11-libs/libXrender + x11-libs/libSM + x11-libs/libXt + x11-libs/libGLw + virtual/libcrypt:= +" + +S="${WORKDIR}" + +pkg_nofetch() { + elog "Please visit" + elog "https://www.cgl.ucsf.edu/chimera/download.html" + elog "and download chimera-${PV}-linux_x86_64.bin into your DISTDIR" +} + +src_unpack() { + cp "${DISTDIR}"/chimera-${PV}-linux_x86_64.bin chimera-${PV}-linux_x86_64.bin.zip + unzip chimera-${PV}-linux_x86_64.bin.zip || die +} + +src_install() { + chmod +x ./chimera.bin + dodir /opt/ + ./chimera.bin -d foo || die + newicon "${DISTDIR}"/Chimera512.png Chimera.png + make_desktop_entry "${EPREFIX}/opt/bin/chimera" Chimera Chimera + mv foo "${ED}/opt/${PN}" || die + + cat >> "${T}"/chimera <<- EOF + #!${EPREFX}/bin/bash + + export PATH="${EPREFIX}/opt/${PN}/bin:\${PATH}" + "${EPREFIX}/opt/${PN}/bin/chimera" \$@ + EOF + + exeinto /opt/bin/ + doexe "${T}"/chimera + + # point the symlink to the correct location + rm "${ED}/opt/chimera/include/ft2build.h" || die + dosym ../../../usr/include/freetype2/ft2build.h opt/chimera/include/ft2build.h + + if use prefix; then + local i + for i in "${ED}"/opt/${PN}/bin/{tiffcp,povray,al2co} "${ED}"/opt/${PN}/lib/*.so; do + patchelf --set-rpath "${EPREFIX}/usr/lib:${EPREFIX}/opt/${PN}/lib" "${i}" || die + done + fi +} diff --git a/sci-chemistry/chimera/chimera-1.17.3.ebuild b/sci-chemistry/chimera/chimera-1.17.3.ebuild new file mode 100644 index 000000000..4fdafd361 --- /dev/null +++ b/sci-chemistry/chimera/chimera-1.17.3.ebuild @@ -0,0 +1,93 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 +inherit desktop xdg + +DESCRIPTION="Next generation molecular visualization program from RBVI" +HOMEPAGE="https://www.cgl.ucsf.edu/chimera/" +SRC_URI="${P}-linux_x86_64.bin + mirror+https://dev.gentoo.org/~pacho/${PN}/Chimera512.png" + +SLOT="0" +LICENSE="chimera" +KEYWORDS="~amd64 ~x86" + +RESTRICT="fetch mirror strip" +QA_PREBUILT="*" + +DEPEND="" +BDEPEND="" +RDEPEND=" + dev-lang/tcl + dev-lang/tk + dev-libs/expat + dev-libs/libotf + dev-libs/openssl:0 + dev-libs/libpcre + sys-libs/zlib + media-libs/fontconfig + media-libs/freetype + media-libs/ftgl + media-libs/libpng + media-libs/tiff + sci-libs/hdf5 + sys-devel/gcc[openmp,fortran] + media-libs/libjpeg-turbo + virtual/glu + virtual/opengl + x11-libs/libX11 + x11-libs/libICE + x11-libs/libXext + x11-libs/libXft + x11-libs/libXmu + x11-libs/libXpm + x11-libs/libXrender + x11-libs/libSM + x11-libs/libXt + x11-libs/libGLw + virtual/libcrypt:= +" + +S="${WORKDIR}" + +pkg_nofetch() { + elog "Please visit" + elog "https://www.cgl.ucsf.edu/chimera/download.html" + elog "and download ${P}-linux_x86_64.bin into your DISTDIR" +} + +src_unpack() { + cp "${DISTDIR}"/${P}-linux_x86_64.bin ${P}-linux_x86_64.bin.zip + unzip ${P}-linux_x86_64.bin.zip || die +} + +src_install() { + chmod +x ./chimera.bin + dodir /opt/ + ./chimera.bin -d foo || die + newicon "${DISTDIR}"/Chimera512.png Chimera.png + make_desktop_entry "${EPREFIX}/opt/bin/chimera" Chimera Chimera + mv foo "${ED}/opt/${PN}" || die + + cat >> "${T}"/chimera <<- EOF + #!${EPREFX}/bin/bash + + export PATH="${EPREFIX}/opt/${PN}/bin:\${PATH}" + "${EPREFIX}/opt/${PN}/bin/chimera" \$@ + EOF + + exeinto /opt/bin/ + doexe "${T}"/chimera + + # point the symlink to the correct location + rm "${ED}/opt/chimera/include/ft2build.h" || die + dosym ../../../usr/include/freetype2/ft2build.h opt/chimera/include/ft2build.h + + if use prefix; then + local i + for i in "${ED}"/opt/${PN}/bin/{tiffcp,povray,al2co} "${ED}"/opt/${PN}/lib/*.so; do + patchelf --set-rpath "${EPREFIX}/usr/lib:${EPREFIX}/opt/${PN}/lib" "${i}" || die + done + fi +} diff --git a/sci-chemistry/chimera/metadata.xml b/sci-chemistry/chimera/metadata.xml new file mode 100644 index 000000000..5c83ce208 --- /dev/null +++ b/sci-chemistry/chimera/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>pacho@gentoo.org</email> + <name>Pacho Ramos</name> + </maintainer> + <maintainer type="project"> + <email>sci-chemistry@gentoo.org</email> + <name>Gentoo Chemistry Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-chemistry/concoord/Manifest b/sci-chemistry/concoord/Manifest index 5607cb51b..053b53267 100644 --- a/sci-chemistry/concoord/Manifest +++ b/sci-chemistry/concoord/Manifest @@ -1,4 +1,2 @@ -DIST concoord2.1_linux_i386.tgz 2948256 BLAKE2B 862de32d37a1680fbc3bdd7512127c2491e421ac63c716dc24ca43e58123ed3f1c00a6d4cb63f91a15d41a3ac0d885c08950de7896abc841167da65a99ce9d80 SHA512 2af10b14f24305dbea4ff12df86ca9bc5e8d2957873756b2f9b5ee57fc7b8db91a787ff09d70ce70a1c3d9278a142474c893250944aa3b8c83862311ed3e3cef -DIST concoord2.1_linux_x86_64.tgz 3352731 BLAKE2B d3ed53866053474378b22bb186822a46c01be4506f09930d26476814591d8c6474d7eff6797c1738c240c1cd8fc840849b9150f30c73aa8f826e246460313251 SHA512 cfb30d7d0950e5978ea0a908a0e607b675333e267ee7da6103ead1b27ceb4dedde42daef3f7027c47e40e01cd247f3e57c5fa13eb76c0f3ac7fa1868f5fb8bf5 DIST concoord_2.1.2_linux32.tgz 1193266 BLAKE2B 2adb51fdba074d608a2dc172556d5a0f37df2d8b7259b36da7d4330ded4a81f104b2c0ba1f18505141204d507f60b9bbfeffbc91eb2d129918fec9ad28ddde6c SHA512 d74f2fdbb6184f79d3c0770cfa01324dd52448f3a865f5fb379a51431024b843537b8de551aacd2b0117736f7cb2412379cf23e765716969c1ab3069e6e75ea2 DIST concoord_2.1.2_linux64.tgz 1431558 BLAKE2B 6e8d8d42bd629a79e86e84874590a66dc8b30269bda18fb75b91e3dcb84b4e8c36d61177e10282b0421f68d3828cd407f0d81f976f8aa32f28bd9dfb34506fd1 SHA512 e625e10ebe2e5ef6a84af3fe665e792d59ffed3df009f19d66ec0972bd88ec91167e3ec0eee9a72b1c35ba0a85ec70fa5420a7718b83e238b167ad31d95303cf diff --git a/sci-chemistry/concoord/concoord-2.1.ebuild b/sci-chemistry/concoord/concoord-2.1.ebuild deleted file mode 100644 index 2926f76c8..000000000 --- a/sci-chemistry/concoord/concoord-2.1.ebuild +++ /dev/null @@ -1,32 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DESCRIPTION="Protein conformations around a known structure based on geometric restrictions" -HOMEPAGE="https://www.mpibpc.mpg.de/groups/de_groot/concoord/concoord.html" -SRC_URI=" - amd64? ( https://www3.mpibpc.mpg.de/groups/de_groot/concoord/concoord2.1_linux_x86_64.tgz ) - x86? ( https://www3.mpibpc.mpg.de/groups/de_groot/concoord/concoord2.1_linux_i386.tgz )" - -SLOT="0" -KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux" -LICENSE="all-rights-reserved" - -QA_PREBUILT="opt/${PN}/bin/*" - -S="${WORKDIR}"/${PN}${PV} - -src_install() { - insinto /opt/${PN}/ - rm lib/*.a || die - doins -r lib - exeinto /opt/${PN}/bin - doexe bin/* - cat >> "${T}"/60${PN} <<- EOF - CONCOORDLIB="${EPREFIX}/opt/${PN}/lib" - CONCOORDBIN="${EPREFIX}/opt/${PN}/bin" - PATH="${EPREFIX}/opt/${PN}/bin" - EOF - doenvd "${T}"/60${PN} -} diff --git a/sci-chemistry/ctffind/Manifest b/sci-chemistry/ctffind/Manifest index 96d9b2769..103ece6da 100644 --- a/sci-chemistry/ctffind/Manifest +++ b/sci-chemistry/ctffind/Manifest @@ -1 +1,3 @@ +DIST ctffind-4.1.10.tar.gz 625495 BLAKE2B 29c16308005322f53de8e0e9e9c03bc4219f5499bdd303d08e6ee93debe022151fc6b4ea5a2dec3f5c155e26913ae678de98a9b8b37f10d391c284011399f36a SHA512 abaa94781a16b6a72d5ed461f89c1aa313540e4d982c75e81879df2e863bf3ff8ad9fb30d00df603bdc7b56565508e9caba31ef2af67a4a8b732df33b53ee4c6 +DIST ctffind-4.1.13.tar.gz 637267 BLAKE2B 89440d497c6cfe962fd6af14ebc78049ff7341f246bb794384337d7b69571e9123da2bb200f34bf6fdafd984e7f38a77ed1f11a2a4da30f1463b6cfdded0d247 SHA512 1523856b75431b1cdbc3d29336f7d59bf0e7ecee70573c79273a97661e75387aa78c91c3d337431a432e1b15760ca34ad2692832f2f57bdc37951d1bc03958eb DIST ctffind-4.1.14.tar.gz 662195 BLAKE2B cb81a971c74e8f2b38e87945aca9f34d4d9cf90770b149ddc5febaee9af4a7392e1d295b2146a14212ea7c820ebf51c5179811cd42875b8a0ef279f6a07e8642 SHA512 115d04ad1adce3f8a99b14e15844df8d6caa4b873faa24eed9d6999a48e88f5a35ffd0cffa6c50c38566cc0091e0de5baec4d0cc62719540a9cfe67bc7333d42 diff --git a/sci-chemistry/ctffind/ctffind-4.1.10.ebuild b/sci-chemistry/ctffind/ctffind-4.1.10.ebuild new file mode 100644 index 000000000..a69a36308 --- /dev/null +++ b/sci-chemistry/ctffind/ctffind-4.1.10.ebuild @@ -0,0 +1,37 @@ +# Copyright 2019-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +WX_GTK_VER="3.0-gtk3" +inherit wxwidgets + +DESCRIPTION="CTF estimation (ctffind, ctftilt)" +HOMEPAGE="https://grigoriefflab.umassmed.edu/" +SRC_URI="https://grigoriefflab.umassmed.edu/system/tdf?path=ctffind-${PV}.tar.gz&file=1&type=node&id=26 -> ${P}.tar.gz" + +LICENSE="Janelia-1.2" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +DEPEND=" + sci-libs/fftw:3.0 + media-libs/libjpeg-turbo + media-libs/tiff + x11-libs/wxGTK:* +" +RDEPEND="${DEPEND}" +BDEPEND=" + ${DEPEND} + virtual/pkgconfig" + +src_prepare() { + default + sed /pdb/d -i src/core/core_headers.h || die "removing pdb.h failed" + sed /water/d -i src/core/core_headers.h || die "removing water.h failed" +} + +src_configure() { + setup-wxwidgets + default +} diff --git a/sci-chemistry/ctffind/ctffind-4.1.13.ebuild b/sci-chemistry/ctffind/ctffind-4.1.13.ebuild new file mode 100644 index 000000000..a69a36308 --- /dev/null +++ b/sci-chemistry/ctffind/ctffind-4.1.13.ebuild @@ -0,0 +1,37 @@ +# Copyright 2019-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +WX_GTK_VER="3.0-gtk3" +inherit wxwidgets + +DESCRIPTION="CTF estimation (ctffind, ctftilt)" +HOMEPAGE="https://grigoriefflab.umassmed.edu/" +SRC_URI="https://grigoriefflab.umassmed.edu/system/tdf?path=ctffind-${PV}.tar.gz&file=1&type=node&id=26 -> ${P}.tar.gz" + +LICENSE="Janelia-1.2" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +DEPEND=" + sci-libs/fftw:3.0 + media-libs/libjpeg-turbo + media-libs/tiff + x11-libs/wxGTK:* +" +RDEPEND="${DEPEND}" +BDEPEND=" + ${DEPEND} + virtual/pkgconfig" + +src_prepare() { + default + sed /pdb/d -i src/core/core_headers.h || die "removing pdb.h failed" + sed /water/d -i src/core/core_headers.h || die "removing water.h failed" +} + +src_configure() { + setup-wxwidgets + default +} diff --git a/sci-chemistry/erkale/metadata.xml b/sci-chemistry/erkale/metadata.xml index eea62e858..996e48735 100644 --- a/sci-chemistry/erkale/metadata.xml +++ b/sci-chemistry/erkale/metadata.xml @@ -18,4 +18,7 @@ ground-state electron momentum densities and Compton profiles, and core (x-ray absorption and x-ray Raman scattering) and valence electron excitation spectra of atoms and molecules. </longdescription> + <upstream> + <remote-id type="github">susilehtola/erkale</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-chemistry/freeon/freeon-9999.ebuild b/sci-chemistry/freeon/freeon-9999.ebuild deleted file mode 100644 index e42a795f1..000000000 --- a/sci-chemistry/freeon/freeon-9999.ebuild +++ /dev/null @@ -1,26 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -FORTRAN_STANDARD=90 -PYTHON_COMPAT=( python3_{7,8,9} ) - -inherit cmake fortran-2 git-r3 python-any-r1 - -DESCRIPTION="An experimental suite of programs for linear scaling quantum chemistry" -HOMEPAGE="https://www.freeon.org" -EGIT_REPO_URI="https://github.com/FreeON/freeon.git" -EGIT_BRANCH="master" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="" - -RDEPEND=" - sci-libs/hdf5 - virtual/blas - virtual/lapack -" -DEPEND="${RDEPEND} - ${PYTHON_DEPS}" diff --git a/sci-chemistry/freeon/metadata.xml b/sci-chemistry/freeon/metadata.xml deleted file mode 100644 index 2fe5325ae..000000000 --- a/sci-chemistry/freeon/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>nicolasbock@gentoo.org</email> - <name>Nicolas Bock</name> - </maintainer> - <maintainer type="project"> - <email>sci-chemistry@gentoo.org</email> - <name>Gentoo Chemistry Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-chemistry/gamess/gamess-20180930.3-r1.ebuild b/sci-chemistry/gamess/gamess-20180930.3-r1.ebuild index 17fe76f76..173e3513e 100644 --- a/sci-chemistry/gamess/gamess-20180930.3-r1.ebuild +++ b/sci-chemistry/gamess/gamess-20180930.3-r1.ebuild @@ -272,7 +272,7 @@ src_compile() { ./compall || die "compall failed" # build the ddi TCP/IP socket stuff - cd ${S}/"ddi" + cd "${S}/ddi" ./compddi || die "compddi failed" # finally, link it all together diff --git a/sci-chemistry/ligplot+/Manifest b/sci-chemistry/ligplot+/Manifest deleted file mode 100644 index 996b438bb..000000000 --- a/sci-chemistry/ligplot+/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST LigPlus.zip 1937904 SHA256 5d47af05f1fb48b4c0a6dee4d8eacb0d2ffe90966b0419d954c9d0f7a6580b49 SHA512 fee1c9b54c895d26ebd81f283ab942b199db87d189a01f22aebf26d6ed90e801f53b64cf9abf870721a4b478e68bf390b0e1c9eb9b02a692a1011271611f7afd WHIRLPOOL d86822b5e4cd0bd429df912f3b60de11094a2e549841f59343c0435a329a5c1181e543e06af9eb760d3bbbc6a12414fc5477c87f192deb40304d7ce619b65f28 diff --git a/sci-chemistry/ligplot+/ligplot+-1.4.ebuild b/sci-chemistry/ligplot+/ligplot+-1.4.ebuild deleted file mode 100644 index 80963ed83..000000000 --- a/sci-chemistry/ligplot+/ligplot+-1.4.ebuild +++ /dev/null @@ -1,42 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit java-pkg-2 wrapper - -DESCRIPTION="GUI-based version of LIGPLOT" -HOMEPAGE="https://www.ebi.ac.uk/thornton-srv/software/LigPlus/" -SRC_URI="LigPlus.zip" - -SLOT="0" -LICENSE="ligplot+" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" - -RDEPEND="virtual/jre:*" -DEPEND="app-arch/unzip" - -RESTRICT="fetch" - -S="${WORKDIR}/LigPlus" - -QA_PREBUILT="opt/${PN}/.*" - -pkg_nofetch() { - elog "Please visit" - elog "http://www.ebi.ac.uk/thornton-srv/software/LigPlus/applicence.html" - elog "download ${A}" - elog "and save into your DISTDIR folder" -} - -src_prepare() { - default - rm -rf lib/*{win,mac} || die -} - -src_install() { - insinto /opt/${PN} - doins -r lib LigPlus.jar - - make_wrapper ${PN} "java -jar \"${EPREFIX}/opt/${PN}/LigPlus.jar\"" -} diff --git a/sci-chemistry/ligplot+/metadata.xml b/sci-chemistry/ligplot+/metadata.xml deleted file mode 100644 index da36ecbfc..000000000 --- a/sci-chemistry/ligplot+/metadata.xml +++ /dev/null @@ -1,8 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-chemistry@gentoo.org</email> - <name>Gentoo Chemistry Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-chemistry/mage/Manifest b/sci-chemistry/mage/Manifest deleted file mode 100644 index 72cb530fd..000000000 --- a/sci-chemistry/mage/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST mage.6.44.060606.src.tgz 726357 BLAKE2B e427bf0707b192653c6cafd392a6ceaf49ec45fcff5447c42b4dd7e0e75ff46bf78edd9b03260cfe0d465c6ae0c6b1ff6a6340fb4fdf34feec1dba13a971d3ca SHA512 dceb63cc9806690539d0838079c2b57d6e62164049ca178d158e9c7eae759988c28d7e911942fd50f1ea880e61b2e9d7a38cc64bc5c229a4e5d442357c1f9227 diff --git a/sci-chemistry/mage/files/6.44.060606-Makefile.patch b/sci-chemistry/mage/files/6.44.060606-Makefile.patch deleted file mode 100644 index df4fa4e1a..000000000 --- a/sci-chemistry/mage/files/6.44.060606-Makefile.patch +++ /dev/null @@ -1,29 +0,0 @@ -diff --git a/Makefile b/Makefile -index 62a2033..1722ba5 100644 ---- a/Makefile -+++ b/Makefile -@@ -11,7 +11,7 @@ - # and static compile fails for RH 7.2 and 7.3 - # - ifeq ($(MAKECMDGOALS),dynamic) --CFLAGS = -I/usr/X11R6/include #for RH7.3 -+CFLAGS += -I/usr/X11R6/include #for RH7.3 - # CFLAGS = -I/usr/X11R6/LessTif/Motif1.2/include/ #for RH7.1 - else #for RH8.0 - CFLAGS = -D_STATIC_ -@@ -80,13 +80,13 @@ static: $(OBJS) dlstubs.o - $(CC) -static -o mage $(OBJS) dlstubs.o $(LIBS) $(FIN) - - dynamic: $(OBJS) -- $(CC) -o mage $(OBJS) -L/usr/X11R6/lib $(LIBS) -ldl $(FIN) -+ $(CC) $(CFLAGS) $(LDFLAGS) -o mage $(OBJS) -L/usr/X11R6/lib $(LIBS) -ldl $(FIN) - # $(CC) -o mage $(OBJS) -L/usr/X11R6/LessTif/Motif1.2/lib $(LIBS) -ldl $(FIN) - # where RH7.1 needed explicit LessTif and could compile static - # RH7.3 fails static in all tried cases, but has Xm libraries implicit - - debug: $(OBJS) -- $(CC) -o mage $(OBJS) -L/usr/X11R6/lib $(LIBS) -ldl $(FIN) -+ $(CC) $(CFLAGS) $(LDFLAGS) -o mage $(OBJS) -L/usr/X11R6/lib $(LIBS) -ldl $(FIN) - - debugs: $(OBJS) dlstubs.o - $(CC) -static -o mage $(OBJS) dlstubs.o $(LIBS) $(FIN) diff --git a/sci-chemistry/mage/files/digest-mage-6.44.060606 b/sci-chemistry/mage/files/digest-mage-6.44.060606 deleted file mode 100644 index a73fa1c02..000000000 --- a/sci-chemistry/mage/files/digest-mage-6.44.060606 +++ /dev/null @@ -1,3 +0,0 @@ -MD5 aa49ae2cd466d718891391f593202f97 mage.6.44.060606.src.tgz 726357 -RMD160 08305d65dd61ed573c67e58975a611439235e9f5 mage.6.44.060606.src.tgz 726357 -SHA256 c812202138cfee6b6434c51206286d460e83a12828e694013ecb16f2d5e839b3 mage.6.44.060606.src.tgz 726357 diff --git a/sci-chemistry/mage/mage-6.44.060606.ebuild b/sci-chemistry/mage/mage-6.44.060606.ebuild deleted file mode 100644 index bffe9c21f..000000000 --- a/sci-chemistry/mage/mage-6.44.060606.ebuild +++ /dev/null @@ -1,35 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit toolchain-funcs - -MY_P="${PN}.${PV}" - -DESCRIPTION="Mage is a 3D vector display program which shows 'kinemage' graphics" -HOMEPAGE="http://kinemage.biochem.duke.edu/software/mage.php" -SRC_URI="http://kinemage.biochem.duke.edu/downloads/software/mage/${MY_P}.src.tgz" - -LICENSE="richardson" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -RDEPEND="sci-chemistry/prekin" -DEPEND="${RDEPEND}" - -S="${WORKDIR}/${MY_P}" - -PATCHES=( - "${FILESDIR}/${PV}-Makefile.patch" -) - -src_compile() { - emake \ - CC="$(tc-getCC)" \ - dynamic -} - -src_install() { - dobin "${S}"/mage -} diff --git a/sci-chemistry/mage/metadata.xml b/sci-chemistry/mage/metadata.xml deleted file mode 100644 index da36ecbfc..000000000 --- a/sci-chemistry/mage/metadata.xml +++ /dev/null @@ -1,8 +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-chemistry@gentoo.org</email> - <name>Gentoo Chemistry Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-chemistry/nmrpipe/Manifest b/sci-chemistry/nmrpipe/Manifest index 2da2b203c..c54650082 100644 --- a/sci-chemistry/nmrpipe/Manifest +++ b/sci-chemistry/nmrpipe/Manifest @@ -1,6 +1,6 @@ -DIST NMRPipeX-8.7.20200827.tZ 65154741 BLAKE2B c4eafa6496476046acf44e99063d18fed1e77bca1af749c92305f6c9b0ed5ec045f8fe611c34324eb03b1631be0bc68eb6fbf915fd2fdd02dfd41b6cfd6027b2 SHA512 0b84d655aa8b76e3b877e229e1f256403d1d714b7178bc39c4e213a238dc5614ff36fca8e36b285668eb0135134c975a108f447021c3442e9864554aadee8d00 -DIST binval-8.7.20200827.com 3745 BLAKE2B 18b99fb2286a94ce2d0c8d8792e4384c8042b7ce7c43a0aee189af3185db181fc9fc829d186684423f8360a2b681bfcf18d419f05c58352b32967117252465d7 SHA512 f857126b65d27436e471e8e45be049ef892a80272a7f0da97db81d6861f18024ced527da24ab0fdc8ef91c0ec66211ad72703d7ccdcd133babbc51eacfced9ba -DIST dyn-8.7.20200827.tZ 301148865 BLAKE2B 9706a163bdd2947e909a79333a4a50b58e09e7daa11d958dde805681e92ecff17204bd896bd4b1658a10fc2113ae4339e7f54636ebbb17d00845b95846023cd8 SHA512 2dd7dbbc6e4c0bceedfe7923e89095e6755e5f92b3a7635e70ef6a51570e88c4edf98387ccfd353b8450b46fe0aa6a56f3fe778a9492e85abfb0e4b15cdca1aa -DIST install-8.7.20200827.com 50940 BLAKE2B cc1e492549e3ab4377f607ab4e59ab1b344ece3ab0332cddc43c71b827e3224d77d4dec6101766e9f885db669f56a011fec8dbb2d512eb7e7c1ae665a1f6c829 SHA512 fdb8bcfa0f4ecac3f6690322db163695446b58a536411a503c80fe222b9995c395f0ba5e6b8933d7c1a8a4dca984ad2aa5c12aa8eef2fd985c7b18da431f5126 -DIST plugin.smile-8.7.20200827.tZ 77264061 BLAKE2B 04b464a00b2cf26ed309b4cb89b37f23dde38ffeedc848167fd1beeeed699c576fecf9fa3ba4bcfe5f597113c19d06e0bfd6210d24efdda9ee8b41d908295db3 SHA512 92c172fedf00fe31d68a532d9d40a63bd0e284b153a4b54d2b0d21a820ceba3b52e13e278c6f40a734e367e6f7b6b27bd470efcf6ef328c9017fad60a77361ac -DIST talos-8.7.20200827.tZ 209214741 BLAKE2B 63d84972c556d1fb5c5f5b4ab9b56e7eb5c48a9487d846dd09a3d6713a9228417431f40e965c4781c66b8c80655a2248eafec1b48163cc132e031382429f7092 SHA512 61d8cf81ae8dd316a7c68c1110ee4b12b36c0319ee89fbc4b0a2e67559527a57204ff270f008c25f000f17f0d893c6342d84af36b2af59088cfb255385899dcb +DIST NMRPipeX-8.7.20230206.tZ 100114853 BLAKE2B 6e0dda8ef3946ea2397f2a394529a2c20b09f4f6dc7f56205b17c35d0a0d09519f92899f0628070cf5f24aec41d71b54fc606f7d6a01f0ccb79f69fe59234b56 SHA512 0ec09385f0181af58a5ad1ba5335e32e1544d73b1322b2764b738474cbb96128158b6739684e0e008411c27bed831d58fd44953494c790bf20796cf82750792e +DIST binval-8.7.20230206.com 4004 BLAKE2B cf8d84c533431b6eeaa031285071abdd241a5774c4731a650084e312c2e3094c2a26e54432e8e9abb42280f2968dee276918659ba9e036587e799618d5dfb829 SHA512 ef47c209848a479e0c6f7f9a472279e6260cb56311e9571da22b474e520515abc64e75cc5dd7817bb629497e0a83c53a6f847904e08004e0b2d09ba035f688a9 +DIST dyn-8.7.20230206.tZ 301148865 BLAKE2B 11cdebd68efa2ed758309f27ba8fd57b6e659d9cdf98d3708c85f65b181eca42dc6fae832db13e9684e4f710d8f0ec7d60d7cc4d5dc698f730dcce317df0d56a SHA512 e5dc12af048f8f87c13c60c020df5ae47afaaa869852134563124bcc2f344176f1da452ce92169ed3cf2c7c4e505d6498bd60fb5ba1b3de489a9791e25f0354c +DIST install-8.7.20230206.com 50938 BLAKE2B ad8039df53d5069ed5b74be3d085fb0b11fda0a3b585d7992ed3634f383bb8b21c31c808befb9e917882392a0333da898a97d423c61cad49ac351f12fd8c4df4 SHA512 0b1aea3ab316dd29108cce60a4d1aa84835ab088389d6e46d8ee3c7bffb75d38506bac35f5e0c202dc9bf040e2e8418697126a3aa8dc6f256e3c75614b52a30c +DIST plugin.smile-8.7.20230206.tZ 73190777 BLAKE2B 94471d441a82a35feb9ce7c7fca52e343ea5ad4d8688dce09e23c9f6a76288de3a080cb587e4b44800d0c1401aebc0586753a83b4b6370030221519b2f34ba13 SHA512 511c39bbf3d9bd608cfb53a8720f26a1e201d3065e0109f8a11ee513ff0f160f3866099f88d359ec301cdfde05ef84b43a694846494bd4231bf4b401dd33e6b3 +DIST talos-8.7.20230206.tZ 209640635 BLAKE2B bb5fc9a925dbc5e553711a63177c69e8c01d4cdfacf4ec04960fe21d4996aeee35287686d89452dfc51f94712c1c42e9ab316073072f92f9576418ec282f9988 SHA512 3225f40dd4437e18d3dc8d3c1874df10b7257ee6f556cef8d2e77e90d64308799499aa70020b6c2b7152121c1124fac744e553b770097b544a9b888505250711 diff --git a/sci-chemistry/nmrpipe/nmrpipe-8.7.20200827.ebuild b/sci-chemistry/nmrpipe/nmrpipe-8.7.20200827.ebuild deleted file mode 100644 index 303f2c4a2..000000000 --- a/sci-chemistry/nmrpipe/nmrpipe-8.7.20200827.ebuild +++ /dev/null @@ -1,187 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -# Versioning is output of nmrPipe -help - -EAPI=7 - -inherit virtualx - -DESCRIPTION="Spectral visualisation, analysis and Fourier processing" -HOMEPAGE="https://www.ibbr.umd.edu/nmrpipe" -#SRC_URI=" -# NMRPipeX.tZ -# talos.tZ -# dyn.tZ -# binval.com -# install.com" -SRC_URI=" - https://www.ibbr.umd.edu/nmrpipe/install.com -> install-${PV}.com - https://www.ibbr.umd.edu/nmrpipe/binval.com -> binval-${PV}.com - https://www.ibbr.umd.edu/nmrpipe/NMRPipeX.tZ -> NMRPipeX-${PV}.tZ - https://www.ibbr.umd.edu/nmrpipe/plugin.smile.tZ -> plugin.smile-${PV}.tZ - https://www.ibbr.umd.edu/nmrpipe/talos.tZ -> talos-${PV}.tZ - https://www.ibbr.umd.edu/nmrpipe/dyn.tZ -> dyn-${PV}.tZ - " - -SLOT="0" -LICENSE="nmrpipe" -# Right now, precompiled executables are only available for Linux on the -# x86 architecture. The maintainer chose to keep the sources closed, but -# says he will gladly provide precompiled executables for other platforms -# if there are such requests. -KEYWORDS="~amd64 ~x86" - -RESTRICT="strip bindist mirror !test? ( test )" - -DEPEND="app-shells/tcsh" -RDEPEND="${DEPEND} - app-editors/nedit - dev-lang/tk - dev-tcltk/blt - media-fonts/font-sun-misc - sys-libs/ncurses-compat:5/5 - x11-apps/xset - x11-libs/xview-bin - !prefix? ( >=x11-libs/libX11-1.6.2 ) - prefix? ( dev-util/patchelf )" - -S="${WORKDIR}/NMR" - -NMRBASE="/opt/${PN}" -ENMRBASE="${EPREFIX}/${NMRBASE}" - -QA_PREBUILT="opt/.*" - -src_unpack() { - # The installation script will unpack the package. We just provide symlinks - # to the archive files, ... - for i in NMRPipeX-${PV}.tZ plugin.smile-${PV}.tZ talos-${PV}.tZ dyn-${PV}.tZ; do - ln -sf "${DISTDIR}"/${i} ${i/-${PV}/} || die - done - mkdir "${S}" && cd "${S}" || die - # ... copy the installation scripts ... - cp -L "${DISTDIR}"/install-${PV}.com install.com || die - cp -L "${DISTDIR}"/binval-${PV}.com binval.com || die - # ... and make the installation scripts executable. - chmod +x *.com || die - VIRTUALX_COMMAND="csh" - virtx \ - ./install.com \ - +type $(usex x86 linux9 linux212_64) \ - +src "${WORKDIR}" \ - +dest "${S}" \ - +nopost +nocshrc -} - -src_prepare() { - default - local bin i - - mv nmrbin.$(usex x86 linux9 linux212_64)/nmr{W,w}ish || die - - ebegin "Cleaning installation" - - # Remove some of the bundled applications and libraries; they are provided by Gentoo instead. - rm -rf nmrbin.linux*/{lib/*.timestamp,*timestamp,xv,gnuplot*,rasmol*,nc,nedit} \ - nmrbin.{linux,mac} nmruser format \ - $(usex x86 nmrbin.linux212_64 nmrbin.linux9) \ - || die "Failed to remove unnecessary libraries." - # As long as xview is not fixed for amd64 we do this - rm nmrbin.linux*/lib/{libxview.so*,libolgx.so*} || die - # Remove the initialisation script generated during the installation. - # It contains incorrect hardcoded paths; only the "nmrInit.com" script - # should be used. - rm -f com/nmrInit.linux*.com || die "Failed to remove broken init script." - # Remove installation log files. - rm -f README_NMRPIPE_USERS *.log install.com binval.com || die "Failed to remove installation log." - # Remove unused binaries - rm -f {talos*,spartaplus,promega}/bin/*{linux,mac,sgi6x,winxp} pdb/misc/addSeg || die - - # Some scripts are on the wrong place - cp -f nmrtxt/*.com com/ - rm -f {acme,com}/{nmrproc,fid,install}.com || die - eend - - ebegin "Fixing paths in scripts" - - # Set the correct path to NMRPipe in the auxiliary scripts. - for i in $(find com/ dynamo/surface/misc/ nmrtxt/ talos/misc talosplus/com -type f); do - sed -e "s%/u/delaglio%${ENMRBASE}%" -i ${i} || die \ - "Failed patching scripts." - done - sed -i "s:${WORKDIR}:${ENMRBASE}:g" com/font.com || die - - sed \ - -e "s:!/bin:!${EPREFIX}/bin:g" \ - -e "s:!/usr/bin:!${EPREFIX}/usr/bin:g" \ - -e "s:!/usr/local/bin:!${EPREFIX}/usr/bin:g" \ - -e "s: /bin: ${EPREFIX}/bin:g" \ - -e "s: /usr/bin: ${EPREFIX}/usr/bin:g" \ - -e "s: /usr/local/bin: ${EPREFIX}/usr/bin:g" \ - -i $(find "${S}" \( -name "*.tcl" -o -name "*.com" -o -name "*.ksh" \)) \ - {com/,nmrtxt/*.com,nmrtxt/nt/*.com,dynamo/tcl/,talos*/com/,dynamo/tcl/}* \ - nmrbin.linux*/{nmrDraw,xNotify} || die - eend - - if use prefix; then - sed \ - -e "s: sh : \"${EPREFIX}/bin/sh\" :g" \ - -e "s: csh : \"${EPREFIX}/bin/csh\" :g" \ - -e "s: bash : \"${EPREFIX}/bin/bash\" :g" \ - -e "s:appTerm -e:appTerm -e \"${EPREFIX}/bin/csh\":g" \ - -i com/* || die - - ebegin "Setting RPATH in binaries" - for bin in $(find nmrbin.linux*/ -type f -maxdepth 1); do - patchelf --set-rpath "${EPREFIX}/usr/lib/" ${bin} - done - eend $? - fi -} - -src_install() { - cat >> "${T}"/nmrWish <<- EOF - #!${EPREFIX}/bin/csh -f - setenv NMRBIN \${NMRBASE}/bin/ - setenv NMRLIB \${NMRBIN}/lib - setenv AUXLIB \${NMRBIN}/openwin/lib - setenv TCLPATH \${NMRBASE}/com - setenv TCL_LIBRARY \${NMRBASE}/nmrtcl/tcl8.4 - setenv TK_LIBRARY \${NMRBASE}/nmrtcl/tk8.4 - setenv BLT_LIBRARY \${NMRBASE}/nmrtcl/blt2.4 - setenv NMRPIPE_TCL_LIB \${NMRBASE}/nmrtcl/tcl8.4 - setenv NMRPIPE_TK_LIB \${NMRBASE}/nmrtcl/tk8.4 - setenv NMRPIPE_BLT_LIB \${NMRBASE}/nmrtcl/blt2.4 - - if (!(\$?LD_LIBRARY_PATH)) then - setenv LD_LIBRARY_PATH \${NMRLIB}:\${AUXLIB} - else - setenv LD_LIBRARY_PATH \${NMRLIB}:\${LD_LIBRARY_PATH}:\${AUXLIB} - endif - - nmrwish \$* - EOF - - sed \ - -e "s:/opt/nmrpipe:${EPREFIX}/opt/nmrpipe:g" \ - -e "s:@BINTYPE@:$(usex x86 linux9 linux212_64):g" \ - "${FILESDIR}"/env-${PN} \ - > "${T}"/env-${PN} || die - newenvd "${T}"/env-${PN} 40${PN} - - insinto ${NMRBASE} - doins -r * - - dosym nmrbin.linux* ${NMRBASE}/bin - - ebegin "Fixing permissions" - chmod 775 "${ED}"/${NMRBASE}/{talos*/bin/,sparta*/bin/,nmrbin.linux*/,com/,dynamo/tcl/,nmrtxt/*.com,talos*/com/,promega/bin/}* || die - eend - - exeinto ${NMRBASE}/nmrbin.$(usex x86 linux9 linux212_64) - doexe "${T}"/nmrWish - - insinto ${NMRBASE}/nmrtxt - doins "${FILESDIR}"/extract.M -} diff --git a/sci-chemistry/nmrpipe/nmrpipe-8.7.20230206.ebuild b/sci-chemistry/nmrpipe/nmrpipe-8.7.20230206.ebuild new file mode 100644 index 000000000..650c35305 --- /dev/null +++ b/sci-chemistry/nmrpipe/nmrpipe-8.7.20230206.ebuild @@ -0,0 +1,187 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +# Versioning is output of nmrPipe -help + +EAPI=8 + +inherit virtualx + +DESCRIPTION="Spectral visualisation, analysis and Fourier processing" +HOMEPAGE="https://www.ibbr.umd.edu/nmrpipe" +#SRC_URI=" +# NMRPipeX.tZ +# talos.tZ +# dyn.tZ +# binval.com +# install.com" +SRC_URI=" + https://www.ibbr.umd.edu/nmrpipe/install.com -> install-${PV}.com + https://www.ibbr.umd.edu/nmrpipe/binval.com -> binval-${PV}.com + https://www.ibbr.umd.edu/nmrpipe/NMRPipeX.tZ -> NMRPipeX-${PV}.tZ + https://www.ibbr.umd.edu/nmrpipe/plugin.smile.tZ -> plugin.smile-${PV}.tZ + https://www.ibbr.umd.edu/nmrpipe/talos.tZ -> talos-${PV}.tZ + https://www.ibbr.umd.edu/nmrpipe/dyn.tZ -> dyn-${PV}.tZ + " + +SLOT="0" +LICENSE="nmrpipe" +# Right now, precompiled executables are only available for Linux on the +# x86 architecture. The maintainer chose to keep the sources closed, but +# says he will gladly provide precompiled executables for other platforms +# if there are such requests. +KEYWORDS="~amd64 ~x86" + +RESTRICT="strip bindist mirror !test? ( test )" + +DEPEND="app-shells/tcsh" +RDEPEND="${DEPEND} + app-editors/nedit + dev-lang/tk + dev-tcltk/blt + media-fonts/font-sun-misc + sys-libs/ncurses-compat:5/5 + x11-apps/xset + x11-libs/xview-bin + !prefix? ( >=x11-libs/libX11-1.6.2 ) + prefix? ( dev-util/patchelf )" + +S="${WORKDIR}/NMR" + +NMRBASE="/opt/${PN}" +ENMRBASE="${EPREFIX}/${NMRBASE}" + +QA_PREBUILT="opt/.*" + +src_unpack() { + # The installation script will unpack the package. We just provide symlinks + # to the archive files, ... + for i in NMRPipeX-${PV}.tZ plugin.smile-${PV}.tZ talos-${PV}.tZ dyn-${PV}.tZ; do + ln -sf "${DISTDIR}"/${i} ${i/-${PV}/} || die + done + mkdir "${S}" && cd "${S}" || die + # ... copy the installation scripts ... + cp -L "${DISTDIR}"/install-${PV}.com install.com || die + cp -L "${DISTDIR}"/binval-${PV}.com binval.com || die + # ... and make the installation scripts executable. + chmod +x *.com || die + VIRTUALX_COMMAND="csh" + virtx \ + ./install.com \ + +type $(usex x86 linux9 linux212_64) \ + +src "${WORKDIR}" \ + +dest "${S}" \ + +nopost +nocshrc +} + +src_prepare() { + default + local bin i + + mv nmrbin.$(usex x86 linux9 linux212_64)/nmr{W,w}ish || die + + ebegin "Cleaning installation" + + # Remove some of the bundled applications and libraries; they are provided by Gentoo instead. + rm -rf nmrbin.linux*/{lib/*.timestamp,*timestamp,xv,gnuplot*,rasmol*,nc,nedit} \ + nmrbin.{linux,mac} nmruser format \ + $(usex x86 nmrbin.linux212_64 nmrbin.linux9) \ + || die "Failed to remove unnecessary libraries." + # As long as xview is not fixed for amd64 we do this + rm nmrbin.linux*/lib/{libxview.so*,libolgx.so*} || die + # Remove the initialisation script generated during the installation. + # It contains incorrect hardcoded paths; only the "nmrInit.com" script + # should be used. + rm -f com/nmrInit.linux*.com || die "Failed to remove broken init script." + # Remove installation log files. + rm -f README_NMRPIPE_USERS *.log install.com binval.com || die "Failed to remove installation log." + # Remove unused binaries + rm -f {talos*,spartaplus,promega}/bin/*{linux,mac,sgi6x,winxp} pdb/misc/addSeg || die + + # Some scripts are on the wrong place + cp -f nmrtxt/*.com com/ + rm -f {acme,com}/{nmrproc,fid,install}.com || die + eend + + ebegin "Fixing paths in scripts" + + # Set the correct path to NMRPipe in the auxiliary scripts. + for i in $(find com/ dynamo/surface/misc/ nmrtxt/ talos/misc talosplus/com -type f); do + sed -e "s%/u/delaglio%${ENMRBASE}%" -i ${i} || die \ + "Failed patching scripts." + done + sed -i "s:${WORKDIR}:${ENMRBASE}:g" com/font.com || die + + sed \ + -e "s:!/bin:!${EPREFIX}/bin:g" \ + -e "s:!/usr/bin:!${EPREFIX}/usr/bin:g" \ + -e "s:!/usr/local/bin:!${EPREFIX}/usr/bin:g" \ + -e "s: /bin: ${EPREFIX}/bin:g" \ + -e "s: /usr/bin: ${EPREFIX}/usr/bin:g" \ + -e "s: /usr/local/bin: ${EPREFIX}/usr/bin:g" \ + -i $(find "${S}" \( -name "*.tcl" -o -name "*.com" -o -name "*.ksh" \)) \ + {com/,nmrtxt/*.com,nmrtxt/nt/*.com,dynamo/tcl/,talos*/com/,dynamo/tcl/}* \ + nmrbin.linux*/{nmrDraw,xNotify} || die + eend + + if use prefix; then + sed \ + -e "s: sh : \"${EPREFIX}/bin/sh\" :g" \ + -e "s: csh : \"${EPREFIX}/bin/csh\" :g" \ + -e "s: bash : \"${EPREFIX}/bin/bash\" :g" \ + -e "s:appTerm -e:appTerm -e \"${EPREFIX}/bin/csh\":g" \ + -i com/* || die + + ebegin "Setting RPATH in binaries" + for bin in $(find nmrbin.linux*/ -type f -maxdepth 1); do + patchelf --set-rpath "${EPREFIX}/usr/lib/" ${bin} + done + eend $? + fi +} + +src_install() { + cat >> "${T}"/nmrWish <<- EOF + #!${EPREFIX}/bin/csh -f + setenv NMRBIN \${NMRBASE}/bin/ + setenv NMRLIB \${NMRBIN}/lib + setenv AUXLIB \${NMRBIN}/openwin/lib + setenv TCLPATH \${NMRBASE}/com + setenv TCL_LIBRARY \${NMRBASE}/nmrtcl/tcl8.4 + setenv TK_LIBRARY \${NMRBASE}/nmrtcl/tk8.4 + setenv BLT_LIBRARY \${NMRBASE}/nmrtcl/blt2.4 + setenv NMRPIPE_TCL_LIB \${NMRBASE}/nmrtcl/tcl8.4 + setenv NMRPIPE_TK_LIB \${NMRBASE}/nmrtcl/tk8.4 + setenv NMRPIPE_BLT_LIB \${NMRBASE}/nmrtcl/blt2.4 + + if (!(\$?LD_LIBRARY_PATH)) then + setenv LD_LIBRARY_PATH \${NMRLIB}:\${AUXLIB} + else + setenv LD_LIBRARY_PATH \${NMRLIB}:\${LD_LIBRARY_PATH}:\${AUXLIB} + endif + + nmrwish \$* + EOF + + sed \ + -e "s:/opt/nmrpipe:${EPREFIX}/opt/nmrpipe:g" \ + -e "s:@BINTYPE@:$(usex x86 linux9 linux212_64):g" \ + "${FILESDIR}"/env-${PN} \ + > "${T}"/env-${PN} || die + newenvd "${T}"/env-${PN} 40${PN} + + insinto ${NMRBASE} + doins -r * + + dosym nmrbin.linux* ${NMRBASE}/bin + + ebegin "Fixing permissions" + chmod 775 "${ED}"/${NMRBASE}/{talos*/bin/,sparta*/bin/,nmrbin.linux*/,com/,dynamo/tcl/,nmrtxt/*.com,talos*/com/,promega/bin/}* || die + eend + + exeinto ${NMRBASE}/nmrbin.$(usex x86 linux9 linux212_64) + doexe "${T}"/nmrWish + + insinto ${NMRBASE}/nmrtxt + doins "${FILESDIR}"/extract.M +} diff --git a/sci-chemistry/nmrview/Manifest b/sci-chemistry/nmrview/Manifest deleted file mode 100644 index c5cae1ddf..000000000 --- a/sci-chemistry/nmrview/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST nmrview5.2.2.lib.tar.gz 4097039 SHA256 96965ab68566b4d4b3873d53e0cf88f0bb5757d9d30dcabbbcb7e062008aac4e SHA512 6d5675a329371a63f16a0119cb71fcc8377a4a827c3d9e5eb3fc1dcef671ad28adc95ac19b99ffcc8431af5057715beda90c7d2853b65fe6c5aa40a272db6b16 WHIRLPOOL 8759f05384187c4146e7c7591fac72729c3ec808bed451c5fd53400e557b073250856e65ddb04fdf65f960af0d0a461afd9a8afcb542c28be9e78dc12a6e5cd2 -DIST nmrview5_2_2_01_linux.gz 963243 SHA256 ac60d882c6c1c9179f612e37e4257dbab819b5b4fbc215189441124815525b55 SHA512 99745586cde0927cb0942d3c5c2f4b9ef9d52f0c650325971526b9fa4d14bdd5fad89561805526f62e667d6ad9bc18e0929eb0a5d75a17e040bd3142d88c37cf WHIRLPOOL 1851ab48029443e294a4cb2b961c4b9bde1ef19e15e70208a163b374da3964e1573184856d9010c4181a7649d471333d71370db6326cba5429c1cee4e1c8f330 diff --git a/sci-chemistry/nmrview/files/README.Gentoo b/sci-chemistry/nmrview/files/README.Gentoo deleted file mode 100644 index fbb0fdf2f..000000000 --- a/sci-chemistry/nmrview/files/README.Gentoo +++ /dev/null @@ -1,17 +0,0 @@ -Using NMRView on Gentoo - -NMRView may be launched via the "nmrview "wrapper script installed in -"/usr/bin". The script will pass on all positional parameters to the NMRView -binary, so you may specify a start up script or a database to open on the -command line. - -If you want a convenient way to set up multiple configurations, you can use -shell aliases to redefine the "nmrview" command or to add new commands starting -nmrview with different startup scripts, databases, etc. The following example -alias declarations (for bash) could be put in "~/.bashrc" to redefine the -"nmrview" command to launch NMRView with a default startup file, and to add a -new command to launch the program with an alternative startup file and -application name. - -alias nmrview="nmrview -- -s ${HOME}/.nmrview/startup" -alias nmrview-dyn="nmrview -name nmrview-dyn -- -s ${HOME}/.nmrview/startup-dyn" diff --git a/sci-chemistry/nmrview/files/nmrview.sh b/sci-chemistry/nmrview/files/nmrview.sh deleted file mode 100644 index d879865e8..000000000 --- a/sci-chemistry/nmrview/files/nmrview.sh +++ /dev/null @@ -1,6 +0,0 @@ -#!/bin/bash - -export NMRVIEW5HOME="/opt/nmrview" -export TK_LIBRARY="/opt/nmrview/tk8.4" -export TCL_LIBRARY="/opt/nmrview/tcl8.4" -/opt/nmrview/nmrview5_2_2_01_linux diff --git a/sci-chemistry/nmrview/files/nmrview.sh-r1 b/sci-chemistry/nmrview/files/nmrview.sh-r1 deleted file mode 100644 index 9e122d0c5..000000000 --- a/sci-chemistry/nmrview/files/nmrview.sh-r1 +++ /dev/null @@ -1,6 +0,0 @@ -#!/bin/bash - -export NMRVIEW5HOME="/opt/nmrview" -export TK_LIBRARY="/opt/nmrview/tk8.4" -export TCL_LIBRARY="/opt/nmrview/tcl8.4" -/opt/nmrview/nmrview5_2_2_01_linux $@ diff --git a/sci-chemistry/nmrview/metadata.xml b/sci-chemistry/nmrview/metadata.xml deleted file mode 100644 index 79d42af98..000000000 --- a/sci-chemistry/nmrview/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>jlec@gentoo.org</email> - <name>Justin Lecher</name> - </maintainer> - <maintainer type="project"> - <email>sci-chemistry@gentoo.org</email> - <name>Gentoo Chemistry Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-chemistry/nmrview/nmrview-5.2.2-r3.ebuild b/sci-chemistry/nmrview/nmrview-5.2.2-r3.ebuild deleted file mode 100644 index 231d237bc..000000000 --- a/sci-chemistry/nmrview/nmrview-5.2.2-r3.ebuild +++ /dev/null @@ -1,57 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DESCRIPTION="Visualisation and analysis of processed NMR data" -HOMEPAGE="https://nmrfx.org/nmrfx/nmrviewj" -SRC_URI=" - ${PN}${PV}.lib.tar.gz - ${PN}${PV//./_}_01_linux.gz" - -SLOT="0" -LICENSE="all-rights-reserved" -KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux" - -RDEPEND="x11-libs/libX11" -DEPEND="" - -RESTRICT="fetch" - -S="${WORKDIR}" - -INSTDIR="/opt/nmrview" - -QA_PREBUILT="/opt/nmrview/nmrview5_2_2_01_linux" - -pkg_nofetch() { - einfo "Please visit:" - einfo "\t${HOMEPAGE}" - echo - einfo "Complete the registration process, then download the following files:" - einfo "\t${A}" - echo - einfo "Place the downloaded files in your distfiles directory" - echo -} - -src_install() { - insinto ${INSTDIR} - - sed \ - -e "s:/opt:${EPREFIX}/opt:g" \ - "${FILESDIR}"/${PN}.sh-r1 \ - > "${T}"/${PN} || die - - dobin "${T}"/${PN} - exeinto ${INSTDIR} - doexe ${PN}${PV//./_}_01_linux - - DIRS="help html images nvtcl nvtclC nvtclExt reslib star tcl8.4 tk8.4 tools" - doins -r ${DIRS} - - dodoc "${FILESDIR}"/README.Gentoo - doins README - dosym ${INSTDIR}/html /usr/share/doc/${PF}/html - dosym ${INSTDIR}/README /usr/share/doc/${PF}/README -} diff --git a/sci-chemistry/pymol-plugins-psico/Manifest b/sci-chemistry/pymol-plugins-psico/Manifest deleted file mode 100644 index 976149b88..000000000 --- a/sci-chemistry/pymol-plugins-psico/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST pymol-plugins-psico-3.4.tar.gz 88984 BLAKE2B 9ea006add8f24d41a8d9523fcb1bc6f5b9b98a93284da6db24e2faef69d713ed671d38aa2e424c4cf0400fbfb0b14ff06c0974f9abfdf9ffd5aa8db3dd311788 SHA512 846ae385751760c4760d044b71bbb6925abd0e91978390e7f2fa03618145ff9feef88df569b5bc7fd1398fdd44cdabe416efc21b46fee7b294283082096a1282 diff --git a/sci-chemistry/pymol-plugins-psico/metadata.xml b/sci-chemistry/pymol-plugins-psico/metadata.xml deleted file mode 100644 index 9d384241e..000000000 --- a/sci-chemistry/pymol-plugins-psico/metadata.xml +++ /dev/null @@ -1,14 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>jlec@gentoo.org</email> - </maintainer> - <maintainer type="project"> - <email>sci-chemistry@gentoo.org</email> - <name>Gentoo Chemistry Project</name> - </maintainer> - <upstream> - <remote-id type="github">speleo3/pymol-psico</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-chemistry/pymol-plugins-psico/pymol-plugins-psico-3.4-r1.ebuild b/sci-chemistry/pymol-plugins-psico/pymol-plugins-psico-3.4-r1.ebuild deleted file mode 100644 index 471e85be8..000000000 --- a/sci-chemistry/pymol-plugins-psico/pymol-plugins-psico-3.4-r1.ebuild +++ /dev/null @@ -1,27 +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} ) -DISTUTILS_USE_SETUPTOOLS=no - -inherit distutils-r1 optfeature - -DESCRIPTION="Pymol ScrIpt COllection" -HOMEPAGE="https://github.com/speleo3/pymol-psico/" -SRC_URI="https://github.com/speleo3/pymol-psico/archive/${PV}.tar.gz -> ${P}.tar.gz" - -SLOT="0" -KEYWORDS="~amd64 ~x86" -LICENSE="BSD-2" - -S="${WORKDIR}/pymol-psico-${PV}" - -RDEPEND=" - sci-chemistry/pymol[${PYTHON_USEDEP}] -" - -pkg_post_inst() { - optfeature sci-libs/mmtk "Normal modes via mmtk" -} diff --git a/sci-chemistry/relion/Manifest b/sci-chemistry/relion/Manifest index 6aa383614..75b932e28 100644 --- a/sci-chemistry/relion/Manifest +++ b/sci-chemistry/relion/Manifest @@ -1 +1,2 @@ -DIST relion-3.1.1.tar.gz 2340685 BLAKE2B 0e98db3af7ceb312111260d8af51225d9a6b82314f1f066fe52464b533e59f44f5487ba66110708d661506074be4d52eeb7e04d88344a939bbd33139a33f6dec SHA512 fddf6f8a3d63e4f73aa1f529e4fa8fa7da98d9226b6539530c83496b94793ceef27d013a2d902a794993ab994f8d6467569ea4b681b4dd948654acf482529b22 +DIST class_ranker_0.1.3_torch_1.0.1.pt.tar.gz 2190018 BLAKE2B 157d380693cb97f2f94aea5ee8b1c9b64c50cead45c65d8d95584b12a4901622df025e4bdfccfc9c87286a3d442ffc26ed2a89953b9361f59d7ae2852fcc3a6b SHA512 0e9d4046a9ba211c07abcc44d0b51c7d69805eb946ed96abdd1663760906188050d476268214b4e7a84f529f51226c39f40c3b418373437fae2f4bb24990f338 +DIST relion-4.0.0.tar.gz 3342593 BLAKE2B d2293531cdf3c5779a8f6beb5bc753931388f1c577faa89a927c6ccd72436db0d9a84fbe08b836601b466bc23e9df6500f9e87da1630adecd2b0cf0e245d63e6 SHA512 1e873868bc54a13a7cca74c4a623f5f2aeeec7bd2df04f74d0421127a9c9a3b40a56ebc5b04a9f4138cca1208417b05a30c38ae78106d53b92deeadbeeaf4209 diff --git a/sci-chemistry/relion/files/relion-4.0.0-build.patch b/sci-chemistry/relion/files/relion-4.0.0-build.patch new file mode 100644 index 000000000..d7cb7bf2e --- /dev/null +++ b/sci-chemistry/relion/files/relion-4.0.0-build.patch @@ -0,0 +1,39 @@ +From 138b9c71b41a3c8782c991053a28bfe074bffdd9 Mon Sep 17 00:00:00 2001 +From: Takanori Nakane <nakane.t@gmail.com> +Date: Fri, 28 Oct 2022 19:51:29 +0900 +Subject: [PATCH] Repaired the build failure reported in #826 (by + @prehensilecode and @acaprez) + +--- + src/apps/CMakeLists.txt | 16 ++++++++-------- + 1 file changed, 8 insertions(+), 8 deletions(-) + +diff --git a/src/apps/CMakeLists.txt b/src/apps/CMakeLists.txt +index 9870b735..30985aa7 100644 +--- a/src/apps/CMakeLists.txt ++++ b/src/apps/CMakeLists.txt +@@ -273,16 +273,16 @@ if (CUDA_FOUND) + + + +- file(GLOB REL_JAZ_CUDA_SRC "${CMAKE_SOURCE_DIR}/src/jaz/cuda/*.cu" "${CMAKE_SOURCE_DIR}/src/jaz/cuda/kernels/*.cu" ) ++ file(GLOB REL_JAZ_CUDA_SRC "${CMAKE_SOURCE_DIR}/src/jaz/cuda/*.cu") + cuda_add_library(relion_jaz_gpu_util ${REL_JAZ_CUDA_SRC}) + +- #list(APPEND EXTRA_LIBS "${CUDA_CUFFT_LIBRARIES}") +- #if(BUILD_SHARED_LIBS) +- # install (TARGETS relion_jaz_gpu_util LIBRARY DESTINATION lib) +- #else() +- # target_link_libraries(relion_jaz_gpu_util relion_lib) +- # target_link_libraries(relion_jaz_gpu_util ${CUDA_CUFFT_LIBRARIES}) +- #endif() ++ list(APPEND EXTRA_LIBS "${CUDA_CUFFT_LIBRARIES}") ++ if(BUILD_SHARED_LIBS) ++ install (TARGETS relion_jaz_gpu_util LIBRARY DESTINATION lib) ++ else() ++ target_link_libraries(relion_jaz_gpu_util relion_lib) ++ target_link_libraries(relion_jaz_gpu_util ${CUDA_CUFFT_LIBRARIES}) ++ endif() + + target_link_libraries(relion_lib relion_jaz_gpu_util ${CUDA_CUFFT_LIBRARIES}) + target_link_libraries(relion_lib relion_jaz_gpu_util ${CUDA_CUFFT_LIBRARIES} ${CUDA_curand_LIBRARY}) diff --git a/sci-chemistry/relion/metadata.xml b/sci-chemistry/relion/metadata.xml index cdabe7f2c..101a056b9 100644 --- a/sci-chemistry/relion/metadata.xml +++ b/sci-chemistry/relion/metadata.xml @@ -11,5 +11,9 @@ </maintainer> <use> <flag name="gui">Enable relion gui</flag> + <flag name="cuda">Enable CUDA support</flag> </use> + <upstream> + <remote-id type="github">3dem/relion</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-chemistry/relion/relion-3.1.1.ebuild b/sci-chemistry/relion/relion-3.1.1.ebuild deleted file mode 100644 index 39e4ab229..000000000 --- a/sci-chemistry/relion/relion-3.1.1.ebuild +++ /dev/null @@ -1,42 +0,0 @@ -# Copyright 2019-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit cmake - -DESCRIPTION="Image-processing software for cryo-electron microscopy" -HOMEPAGE="https://www3.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page" -SRC_URI="https://github.com/3dem/relion/archive/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64" -IUSE="+gui" - -DEPEND=" - gui? ( x11-libs/fltk ) - dev-cpp/tbb - sci-libs/fftw:3.0 - media-libs/tiff - virtual/mpi -" -RDEPEND=" - ${DEPEND} - sci-chemistry/ctffind -" -BDEPEND="${DEPEND}" - -src_configure() { - CMAKE_BUILD_TYPE=Release - mycmakeargs=( - -DBUILD_SHARED_LIBS=ON - -DALTCPU=$(usex !cuda) - -DFORCE_OWN_FFTW=OFF - -DFORCE_OWN_FLTK=OFF - -DFORCE_OWN_TBB=OFF - -DCUDA=OFF - -DGUI=$(usex gui) - ) - cmake_src_configure -} diff --git a/sci-chemistry/relion/relion-4.0.0.ebuild b/sci-chemistry/relion/relion-4.0.0.ebuild new file mode 100644 index 000000000..c6d7d90db --- /dev/null +++ b/sci-chemistry/relion/relion-4.0.0.ebuild @@ -0,0 +1,71 @@ +# Copyright 2019-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit cmake + +DESCRIPTION="Image-processing software for cryo-electron microscopy" +HOMEPAGE="https://www3.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page" + +if [[ ${PV} = *9999* ]]; then + EGIT_REPO_URI="https://github.com/3dem/relion.git" + [[ ${PV} = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="ver${PV:0:4}" + inherit git-r3 + SRC_URI="ftp://ftp.mrc-lmb.cam.ac.uk/pub/dari/class_ranker_0.1.3_torch_1.0.1.pt.tar.gz" +else + SRC_URI=" + https://github.com/3dem/relion/archive/${PV}.tar.gz -> ${P}.tar.gz + ftp://ftp.mrc-lmb.cam.ac.uk/pub/dari/class_ranker_0.1.3_torch_1.0.1.pt.tar.gz + " + KEYWORDS="~amd64" +fi + +LICENSE="GPL-2" +SLOT="0" +IUSE="+gui cuda" + +DEPEND=" + gui? ( x11-libs/fltk ) + cuda? ( dev-util/nvidia-cuda-toolkit ) + dev-cpp/tbb + sci-libs/fftw:3.0 + media-libs/tiff + virtual/mpi +" +RDEPEND=" + ${DEPEND} + sci-chemistry/ctffind +" +BDEPEND="${DEPEND}" + +PATCHES=( "${FILESDIR}/${PN}-4.0.0-build.patch" ) + +src_unpack() { + git-r3_src_unpack + default +} + +src_prepare() { + cmake_src_prepare + mkdir -p "${S}/external/torch_models/" + cp "${DISTDIR}/class_ranker_0.1.3_torch_1.0.1.pt.tar.gz" "${S}/external/torch_models/" + mkdir -p "${S}/external/torch_models/class_ranker/" + cp "${WORKDIR}/class_ranker_0.1.3_torch_1.0.1.pt" "${S}/external/torch_models/class_ranker/" + sed -e "s:{CMAKE_INSTALL_PREFIX}/lib:{CMAKE_INSTALL_PREFIX}/$(get_libdir):g" -i CMakeLists.txt || die + sed -e "s:LIBRARY DESTINATION lib:LIBRARY DESTINATION $(get_libdir):g" -i src/apps/CMakeLists.txt || die +} + +src_configure() { + CMAKE_BUILD_TYPE=Release + mycmakeargs=( + -DBUILD_SHARED_LIBS=ON + -DALTCPU=$(usex !cuda) + -DFORCE_OWN_FFTW=OFF + -DFORCE_OWN_FLTK=OFF + -DFORCE_OWN_TBB=OFF + -DCUDA=$(usex cuda) + -DGUI=$(usex gui) + ) + cmake_src_configure +} diff --git a/sci-chemistry/relion/relion-9999.ebuild b/sci-chemistry/relion/relion-9999.ebuild new file mode 100644 index 000000000..12e09d2fe --- /dev/null +++ b/sci-chemistry/relion/relion-9999.ebuild @@ -0,0 +1,69 @@ +# Copyright 2019-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit cmake + +DESCRIPTION="Image-processing software for cryo-electron microscopy" +HOMEPAGE="https://www3.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page" + +if [[ ${PV} = *9999* ]]; then + EGIT_REPO_URI="https://github.com/3dem/relion.git" + [[ ${PV} = 9999 ]] && EGIT_BRANCH="master" || EGIT_BRANCH="ver${PV:0:4}" + inherit git-r3 + SRC_URI="ftp://ftp.mrc-lmb.cam.ac.uk/pub/dari/class_ranker_0.1.3_torch_1.0.1.pt.tar.gz" +else + SRC_URI=" + https://github.com/3dem/relion/archive/${PV}.tar.gz -> ${P}.tar.gz + ftp://ftp.mrc-lmb.cam.ac.uk/pub/dari/class_ranker_0.1.3_torch_1.0.1.pt.tar.gz + " + KEYWORDS="~amd64" +fi + +LICENSE="GPL-2" +SLOT="0" +IUSE="+gui cuda" + +DEPEND=" + gui? ( x11-libs/fltk ) + cuda? ( dev-util/nvidia-cuda-toolkit ) + dev-cpp/tbb + sci-libs/fftw:3.0 + media-libs/tiff + virtual/mpi +" +RDEPEND=" + ${DEPEND} + sci-chemistry/ctffind +" +BDEPEND="${DEPEND}" + +src_unpack() { + git-r3_src_unpack + default +} + +src_prepare() { + cmake_src_prepare + mkdir -p "${S}/external/torch_models/" + cp "${DISTDIR}/class_ranker_0.1.3_torch_1.0.1.pt.tar.gz" "${S}/external/torch_models/" + mkdir -p "${S}/external/torch_models/class_ranker/" + cp "${WORKDIR}/class_ranker_0.1.3_torch_1.0.1.pt" "${S}/external/torch_models/class_ranker/" + sed -e "s:{CMAKE_INSTALL_PREFIX}/lib:{CMAKE_INSTALL_PREFIX}/$(get_libdir):g" -i CMakeLists.txt || die + sed -e "s:LIBRARY DESTINATION lib:LIBRARY DESTINATION $(get_libdir):g" -i src/apps/CMakeLists.txt || die +} + +src_configure() { + CMAKE_BUILD_TYPE=Release + mycmakeargs=( + -DBUILD_SHARED_LIBS=ON + -DALTCPU=$(usex !cuda) + -DFORCE_OWN_FFTW=OFF + -DFORCE_OWN_FLTK=OFF + -DFORCE_OWN_TBB=OFF + -DCUDA=$(usex cuda) + -DGUI=$(usex gui) + ) + cmake_src_configure +} diff --git a/sci-chemistry/rosetta-tools/Manifest b/sci-chemistry/rosetta-tools/Manifest deleted file mode 100644 index 912e8c895..000000000 --- a/sci-chemistry/rosetta-tools/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST BioTools-3.0.tgz 41121 SHA256 363689571fd131ba0e9b4fdbe239868c3a78b7104270f5b2d0285b0f96af4f9c diff --git a/sci-chemistry/rosetta-tools/metadata.xml b/sci-chemistry/rosetta-tools/metadata.xml deleted file mode 100644 index a5629e344..000000000 --- a/sci-chemistry/rosetta-tools/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="project"> - <email>sci-chemistry@gentoo.org</email> - <name>Gentoo Chemistry Project</name> - </maintainer> - <upstream> - <remote-id type="sourceforge">dylans-biotools</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-chemistry/rosetta-tools/rosetta-tools-3.0.ebuild b/sci-chemistry/rosetta-tools/rosetta-tools-3.0.ebuild deleted file mode 100644 index bbe5b2b8d..000000000 --- a/sci-chemistry/rosetta-tools/rosetta-tools-3.0.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 - -MY_PN="BioTools" -MY_P="${MY_PN}-${PV}" - -DESCRIPTION="Additional scripts for rosetta" -HOMEPAGE="http://www.rosettacommons.org/ http://dylans-biotools.sourceforge.net/" -SRC_URI="${MY_P}.tgz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -DEPEND="" -RDEPEND="dev-lang/perl" - -RESTRICT="fetch" - -S="${WORKDIR}/${MY_PN}" - -src_install() { - local x - for x in $(ls *.pl); do - newbin ${x} ${x%.pl} - done -} diff --git a/sci-electronics/minipro/Manifest b/sci-electronics/minipro/Manifest index 38ce85995..d37c88485 100644 --- a/sci-electronics/minipro/Manifest +++ b/sci-electronics/minipro/Manifest @@ -1 +1 @@ -DIST minipro-0.4.tar.gz 363052 BLAKE2B e6b07c05c1c2841fa862132d598781f3675df61cb41ac447e8dfb9677913126429f4f547afc757f2d32360ddbfc89850f3b234c13b381920d5f726f5fe163dd7 SHA512 cdbcb1a02b475874a32497b9a683a0b4734a16cc75d2b0336a5c5cd26a30b63ca4c115b3cfbe6448a8bb3be95aeb902c79ac256c45789d45abf9e01cda355eda +DIST minipro-0.5.tar.gz 388754 BLAKE2B c22110c269405e7b8ff81fd7c649c2b652bc39da84d92cf9a151da71a1c6d4a202baa6ae13a1fb789a04c8e57f3cc9a60403bcef82896320d95e2507c5960f01 SHA512 e2341213bc43ef53b106211d07a488a142083fe4b6dd6ced0f02595164ce2e0e47f6bdc0a6f6c63f19b9b9438c8f5ad173485953d8a29cb39f89272f8e70dc7c diff --git a/sci-electronics/minipro/files/minipro-0.5-makefile.patch b/sci-electronics/minipro/files/minipro-0.5-makefile.patch new file mode 100644 index 000000000..221643895 --- /dev/null +++ b/sci-electronics/minipro/files/minipro-0.5-makefile.patch @@ -0,0 +1,12 @@ +can't seem to override PREFIX at build time, so patch it +--- minipro-0.5/Makefile 2020-11-04 21:35:31.000000000 -0800 ++++ minipro-0.5/Makefile 2022-07-22 11:42:54.866390621 -0700 +@@ -9,7 +9,7 @@ + + # Normally minipro is installed to /usr/local. If you want to put it + # somewhere else, define that location here. +-PREFIX ?= /usr/local ++PREFIX ?= /usr + MANDIR ?= $(PREFIX)/share/man + + # Some older releases of MacOS need some extra library flags. diff --git a/sci-electronics/minipro/metadata.xml b/sci-electronics/minipro/metadata.xml index 430c9ea1b..438079e92 100644 --- a/sci-electronics/minipro/metadata.xml +++ b/sci-electronics/minipro/metadata.xml @@ -5,6 +5,13 @@ <email>sci-electronics@gentoo.org</email> <name>Gentoo Electronics Project</name> </maintainer> + <maintainer type="person"> + <email>scott@alfter.us</email> + <name>Scott Alfter</name> + </maintainer> + <longdescription lang="en"> + an open-source program for controlling the MiniPRO TL866xx series of chip programmers + </longdescription> <upstream> <remote-id type="github">vdudouyt/minipro</remote-id> </upstream> diff --git a/sci-electronics/minipro/minipro-0.4.ebuild b/sci-electronics/minipro/minipro-0.4.ebuild deleted file mode 100644 index ab75d6774..000000000 --- a/sci-electronics/minipro/minipro-0.4.ebuild +++ /dev/null @@ -1,24 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit bash-completion-r1 udev - -DESCRIPTION="A free and open TL866XX programmer" -HOMEPAGE="https://gitlab.com/DavidGriffith/minipro" -SRC_URI="https://gitlab.com/DavidGriffith/minipro/-/archive/${PV}/${P}.tar.gz" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="~amd64" - -RDEPEND="virtual/libusb:1" -DEPEND="${RDEPEND}" - -src_install() { - dobin minipro miniprohex - doman man/minipro.1 - udev_dorules udev/*.rules - dobashcomp bash_completion.d/minipro -} diff --git a/sci-electronics/minipro/minipro-0.5.ebuild b/sci-electronics/minipro/minipro-0.5.ebuild new file mode 100644 index 000000000..60854d55c --- /dev/null +++ b/sci-electronics/minipro/minipro-0.5.ebuild @@ -0,0 +1,27 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit udev + +DESCRIPTION="A free and open TL866XX programmer" +HOMEPAGE="https://gitlab.com/DavidGriffith/minipro" +SRC_URI="https://gitlab.com/DavidGriffith/minipro/-/archive/${PV}/${P}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND="virtual/libusb:1" +DEPEND="${RDEPEND}" + +PATCHES=( "${FILESDIR}/${P}-makefile.patch" ) + +pkg_postinst() { + udev_reload +} + +pkg_postrm() { + udev_reload +} diff --git a/sci-electronics/mpremote/Manifest b/sci-electronics/mpremote/Manifest new file mode 100644 index 000000000..1e55b52d3 --- /dev/null +++ b/sci-electronics/mpremote/Manifest @@ -0,0 +1,2 @@ +DIST mpremote-0.4.0.tar.gz 27266 BLAKE2B b31b6184d0f4fc5c525ea7d5d8d2722404e9ce82ce143ea9a14b8bdef28af3260514dd25ec756a0ac2507d5b206fa9d07ce67bd2228b1568d9495c9082bdace8 SHA512 580f0286d8973a93105a04c681428f798e0d72b4b75debbc43f8e49ea7a81da849987aeab795baff66c9cf40607fde27fb54b7b32ab311ae5e9fb3b8f8f976fc +DIST mpremote-1.22.0.tar.gz 24042 BLAKE2B 8bd6df4b9a46c10a93d42974a569adb42577d2783cb78b5b76ac6a6750f8219611ca49106ed91cb7f69910e3dfb28bb07a4522dbd721af0baac94d3e793c0576 SHA512 a3135e3be347370c967b7dc936f112e1ed5898288fa2dda4c485d216ebf432cb9706e539299d6769c1982ac02e456e9594ed2a7a86cbac2a1c7d08f2ff8a980b diff --git a/sci-electronics/mpremote/files/mpremote-1.22.0-requirements_txt.patch b/sci-electronics/mpremote/files/mpremote-1.22.0-requirements_txt.patch new file mode 100644 index 000000000..4d06c25aa --- /dev/null +++ b/sci-electronics/mpremote/files/mpremote-1.22.0-requirements_txt.patch @@ -0,0 +1,12 @@ +--- a/pyproject.toml 2020-02-01 19:00:00.000000000 -0500 ++++ b/pyproject.toml 2024-01-22 03:59:19.414593373 -0500 +@@ -33,9 +33,6 @@ + [project.scripts] + mpremote = "mpremote.main:main" + +-[tool.hatch.metadata.hooks.requirements_txt] +-files = ["requirements.txt"] +- + # This will be PEP-440 normalised into either: + # mpremote-X.Y.Z (on vX.Y.Z release tag) + # mpremote-X.Y.Zrc0 (on vX.Y.Z-preview tag, i.e. first commit in the cycle) diff --git a/sci-electronics/mpremote/metadata.xml b/sci-electronics/mpremote/metadata.xml new file mode 100644 index 000000000..820065154 --- /dev/null +++ b/sci-electronics/mpremote/metadata.xml @@ -0,0 +1,20 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci-electronics@gentoo.org</email> + <name>Gentoo Electronics Project</name> + </maintainer> + <maintainer type="person"> + <email>gentoo@chymera.eu</email> + <name>Horea Christian</name> + </maintainer> + <longdescription lang="en"> + This CLI tool provides an integrated set of utilities to remotely interact with + and automate a MicroPython device over a serial connection. + </longdescription> + <upstream> + <remote-id type="github">micropython/micropython</remote-id> + <remote-id type="pypi">mpremote</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-electronics/mpremote/mpremote-0.4.0.ebuild b/sci-electronics/mpremote/mpremote-0.4.0.ebuild new file mode 100644 index 000000000..80056b01e --- /dev/null +++ b/sci-electronics/mpremote/mpremote-0.4.0.ebuild @@ -0,0 +1,28 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +# Next release will move to hatchling: +# https://github.com/micropython/micropython/pull/10645 +#DISTUTILS_USE_PEP517=hatchling +DISTUTILS_USE_PEP517=setuptools + +inherit distutils-r1 pypi + +DESCRIPTION="MicroPython remote control" +HOMEPAGE="https://github.com/micropython/micropython/tree/master/tools/mpremote" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +RDEPEND=" + dev-python/pyserial[${PYTHON_USEDEP}] + dev-python/importlib-metadata[${PYTHON_USEDEP}] +" + +# The package might not have a test suite: +# https://github.com/orgs/micropython/discussions/11308 +#distutils_enable_tests pytest diff --git a/sci-electronics/mpremote/mpremote-1.22.0.ebuild b/sci-electronics/mpremote/mpremote-1.22.0.ebuild new file mode 100644 index 000000000..741478265 --- /dev/null +++ b/sci-electronics/mpremote/mpremote-1.22.0.ebuild @@ -0,0 +1,29 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..12} ) +DISTUTILS_USE_PEP517=hatchling + +inherit distutils-r1 pypi + +DESCRIPTION="MicroPython remote control" +HOMEPAGE="https://github.com/micropython/micropython/tree/master/tools/mpremote" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +RDEPEND=" + dev-python/pyserial[${PYTHON_USEDEP}] + dev-python/importlib-metadata[${PYTHON_USEDEP}] +" + +PATCHES=( + "${FILESDIR}/${P}-requirements_txt.patch" +) + +# The package might not have a test suite: +# https://github.com/orgs/micropython/discussions/11308 +#distutils_enable_tests pytest diff --git a/sci-libs/HDF5Plugin-Zstandard/HDF5Plugin-Zstandard-0_pre20201121-r1.ebuild b/sci-libs/HDF5Plugin-Zstandard/HDF5Plugin-Zstandard-0_pre20201121-r1.ebuild new file mode 100644 index 000000000..d1257f0ee --- /dev/null +++ b/sci-libs/HDF5Plugin-Zstandard/HDF5Plugin-Zstandard-0_pre20201121-r1.ebuild @@ -0,0 +1,27 @@ +# Copyright 2020-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +inherit cmake + +DESCRIPTION="ZSTD plugin for hdf5" +HOMEPAGE="https://github.com/aparamon/HDF5Plugin-Zstandard" +COMMIT="d5afdb5f04116d5c2d1a869dc9c7c0c72832b143" +SRC_URI="https://github.com/aparamon/HDF5Plugin-Zstandard/archive/${COMMIT}.tar.gz -> ${P}.tar.gz" + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +DEPEND="app-arch/zstd >=sci-libs/hdf5-1.12.2-r5" +RDEPEND="${DEPEND}" + +S=${WORKDIR}/${PN}-${COMMIT} + +src_configure() { + local mycmakeargs=( + -DPLUGIN_INSTALL_PATH="${EPREFIX}/usr/$(get_libdir)/hdf5/plugin" + ) + cmake_src_configure +} diff --git a/sci-libs/HDF5Plugin-Zstandard/HDF5Plugin-Zstandard-0_pre20201121.ebuild b/sci-libs/HDF5Plugin-Zstandard/HDF5Plugin-Zstandard-0_pre20201121.ebuild deleted file mode 100644 index a74996b46..000000000 --- a/sci-libs/HDF5Plugin-Zstandard/HDF5Plugin-Zstandard-0_pre20201121.ebuild +++ /dev/null @@ -1,27 +0,0 @@ -# Copyright 2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit cmake - -DESCRIPTION="ZSTD plugin for hdf5" -HOMEPAGE="https://github.com/aparamon/HDF5Plugin-Zstandard" -COMMIT="d5afdb5f04116d5c2d1a869dc9c7c0c72832b143" -SRC_URI="https://github.com/aparamon/HDF5Plugin-Zstandard/archive/${COMMIT}.tar.gz -> ${P}.tar.gz" - -LICENSE="Apache-2.0" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -DEPEND="app-arch/zstd >=sci-libs/hdf5-1.12.2-r2" -RDEPEND="${DEPEND}" - -S=${WORKDIR}/${PN}-${COMMIT} - -src_configure() { - local mycmakeargs=( - -DPLUGIN_INSTALL_PATH="${EPREFIX}/usr/$(get_libdir)/hdf5/plugin" - ) - cmake_src_configure -} diff --git a/sci-libs/HDF5Plugin-Zstandard/metadata.xml b/sci-libs/HDF5Plugin-Zstandard/metadata.xml index 753464ee5..a171606a6 100644 --- a/sci-libs/HDF5Plugin-Zstandard/metadata.xml +++ b/sci-libs/HDF5Plugin-Zstandard/metadata.xml @@ -5,4 +5,7 @@ <email>xgreenlandforwyy@gmail.com</email> <name>Yiyang Wu</name> </maintainer> + <upstream> + <remote-id type="github">aparamon/HDF5Plugin-Zstandard</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/arpack/Manifest b/sci-libs/arpack/Manifest deleted file mode 100644 index 730cdcfdd..000000000 --- a/sci-libs/arpack/Manifest +++ /dev/null @@ -1,3 +0,0 @@ -DIST arpack-3.8.0_p20220604.gh.tar.gz 1012341 BLAKE2B 30f71c334f3ce8b24bce309cdfa5869fa4781baa1935dbd7772936f1f135e4d6a3b576f9fece8ba9ff48f053bac1d1328c4f5f5545cacaa568e1ea5695013e2f SHA512 f31c7bd45a82a8a64e1d041ca18eac9c50dac0ebecf845ad5e57c70d1c12ab36ab0630db224897bfe6181c0fff9152f1dea7b3a6a2eb53bfda2f2a590ca8a37b -DIST arpack-tutorial.ps.gz 105599 BLAKE2B 99570e6a0cc1c020b9c271e8ce1cc224f69ff5333cc818c10b063dc8ffbaf66a9f5c6ede99541b4212286d422146b1c4e332eba7e1635c99efa0e4c2620f0630 SHA512 a7b8fefd1a572ed477ae208d49094c1c65c9368990d12de9b3528e33fed546c947659f74e54a810d04154b4a1b0f9a94bcba4db0cf59d379e20786a261066aa4 -DIST arpack-ug.ps.gz 248543 BLAKE2B ac010aef470060636fa00360636ba093f0d24d219fa927c79fb1726b798160eda74fa8b4be6c7dff94f5759efcf30afa99ad310e7959115e028738beb8aa125d SHA512 3349117fb10b07207ffbab2ffa31b406d026855ea4c16e8649b14c7d70bc94e11b5730672e34acd654817799136d4bd76569ac50ec78d787df5582d18ed61328 diff --git a/sci-libs/arpack/arpack-3.8.0_p20220604.ebuild b/sci-libs/arpack/arpack-3.8.0_p20220604.ebuild deleted file mode 100644 index b7a989641..000000000 --- a/sci-libs/arpack/arpack-3.8.0_p20220604.ebuild +++ /dev/null @@ -1,102 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -COMMIT="5eafea4328f1631eab28b1a20e757d1f0e21f8a6" -PYTHON_COMPAT=( python3_{8..10} ) - -inherit cmake flag-o-matic fortran-2 python-single-r1 - -DESCRIPTION="Arnoldi package library to solve large scale eigenvalue problems" -HOMEPAGE=" - https://www.caam.rice.edu/software/ARPACK/ - https://github.com/opencollab/arpack-ng -" -SRC_URI=" - https://github.com/opencollab/${PN}-ng/archive/${COMMIT}.tar.gz -> ${PF}.gh.tar.gz - doc? ( - http://www.caam.rice.edu/software/ARPACK/SRC/ug.ps.gz -> ${PN}-ug.ps.gz - http://www.caam.rice.edu/software/ARPACK/DOCS/tutorial.ps.gz -> ${PN}-tutorial.ps.gz - ) -" -S="${WORKDIR}/${PN}-ng-${COMMIT}" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~arm ~arm64 ~hppa ~ia64 ~ppc ~ppc64 ~riscv ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos" -IUSE="doc examples icb icbexmm int64 mpi python" - -RDEPEND=" - virtual/blas - virtual/lapack - - icbexmm? ( dev-cpp/eigen ) - mpi? ( virtual/mpi[fortran] ) - icb? ( virtual/mpi[cxx] ) - python? ( - ${PYTHON_DEPS} - $(python_gen_cond_dep 'dev-libs/boost:=[numpy,python,${PYTHON_USEDEP}]') - ) -" -DEPEND="${RDEPEND}" -BDEPEND="virtual/pkgconfig" - -REQUIRED_USE=" - icb? ( mpi ) - python? ( - ${PYTHON_REQUIRED_USE} - icbexmm - ) -" - -src_configure() { - append-fflags '-fallow-argument-mismatch' - - local mycmakeargs=( - -DBUILD_SHARED_LIBS=ON - -DEXAMPLES=$(usex examples) - -DICB=$(usex icb) - -DICBEXMM=$(usex icbexmm) - -DINTERFACE64=$(usex int64) - -DMPI=$(usex mpi) - -DPYTHON3=$(usex python) - ) - cmake_src_configure -} - -src_install() { - cmake_src_install - - dodoc DOCUMENTS/*.doc - newdoc DOCUMENTS/README README.doc - use doc && dodoc "${WORKDIR}"/*.ps - if use examples; then - for i in BAND COMPLEX NONSYM SIMPLE SVD SYM ; do - exeinto "/usr/libexec/${PN}/examples/${i}" - doexe "${BUILD_DIR}/EXAMPLES/${i}"/* - done - - if use mpi; then - exeinto "/usr/libexec/${PN}/examples/MPI" - doexe "${BUILD_DIR}"/PARPACK/EXAMPLES/MPI/* - fi - - if use python; then - docinto examples/pyarpack - dodoc "${BUILD_DIR}"/*.py - fi - docompress -x "/usr/share/doc/${PF}/examples" - fi - if use icbexmm; then - exeinto "/usr/libexec/${PN}/examples/MATRIX_MARKET" - doexe "${BUILD_DIR}/EXAMPLES/MATRIX_MARKET/arpackmm" - rm "${BUILD_DIR}/EXAMPLES/MATRIX_MARKET/arpackmm" || die - docinto examples - dodoc -r "${BUILD_DIR}/EXAMPLES/MATRIX_MARKET" - fi - if use python; then - python_domodule "${ED}/usr/$(get_libdir)/pyarpack" - rm -r "${ED}/usr/$(get_libdir)/pyarpack" || die - fi -} diff --git a/sci-libs/arpack/metadata.xml b/sci-libs/arpack/metadata.xml deleted file mode 100644 index 9cd539912..000000000 --- a/sci-libs/arpack/metadata.xml +++ /dev/null @@ -1,26 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "https://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 ARnoldi PACKage is a library of routines capable of solving large scale symmetric, - nonsymmetric, and generalized eigenproblems. The software is designed to compute a few - eigenvalues with user specified features such as those of largest real - part or largest magnitude. Storage requirements are on the order of - n*k locations. No auxiliary storage is required. A set of Schur basis - vectors for the desired k-dimensional eigen-space is computed which is - numerically orthogonal to working precision. Numerically accurate - eigenvectors are available on request. - </longdescription> - <upstream> - <remote-id type="github">opencollab/arpack-ng</remote-id> - </upstream> - <use> - <flag name="icb">Enable support for *[ae]upd_c with ISO_C_BINDING</flag> - <flag name="icbexmm">Enable support for matrix market example based on ICB</flag> - <flag name="int64">Use the 64-bit integer interface (ILP64)</flag> - </use> -</pkgmetadata> diff --git a/sci-libs/arrayfire/arrayfire-3.7.2.ebuild b/sci-libs/arrayfire/arrayfire-3.7.2.ebuild index eb8917457..5d2f3c7a4 100644 --- a/sci-libs/arrayfire/arrayfire-3.7.2.ebuild +++ b/sci-libs/arrayfire/arrayfire-3.7.2.ebuild @@ -44,7 +44,7 @@ RDEPEND=" " DEPEND="${RDEPEND}" BDEPEND=" - doc? ( app-doc/doxygen ) + doc? ( app-text/doxygen ) virtual/pkgconfig " diff --git a/sci-libs/arrayfire/arrayfire-3.7.3.ebuild b/sci-libs/arrayfire/arrayfire-3.7.3.ebuild index eb8917457..5d2f3c7a4 100644 --- a/sci-libs/arrayfire/arrayfire-3.7.3.ebuild +++ b/sci-libs/arrayfire/arrayfire-3.7.3.ebuild @@ -44,7 +44,7 @@ RDEPEND=" " DEPEND="${RDEPEND}" BDEPEND=" - doc? ( app-doc/doxygen ) + doc? ( app-text/doxygen ) virtual/pkgconfig " diff --git a/sci-libs/arrayfire/arrayfire-3.8.0.ebuild b/sci-libs/arrayfire/arrayfire-3.8.0.ebuild index eb8917457..5d2f3c7a4 100644 --- a/sci-libs/arrayfire/arrayfire-3.8.0.ebuild +++ b/sci-libs/arrayfire/arrayfire-3.8.0.ebuild @@ -44,7 +44,7 @@ RDEPEND=" " DEPEND="${RDEPEND}" BDEPEND=" - doc? ( app-doc/doxygen ) + doc? ( app-text/doxygen ) virtual/pkgconfig " diff --git a/sci-libs/asl/asl-0.1.7.ebuild b/sci-libs/asl/asl-0.1.7.ebuild index 50eaeea5d..cbfbde5c6 100644 --- a/sci-libs/asl/asl-0.1.7.ebuild +++ b/sci-libs/asl/asl-0.1.7.ebuild @@ -26,7 +26,7 @@ RDEPEND=" DEPEND="${RDEPEND} matlab? ( >=sci-libs/matio-1.5.2 ) " -BDEPEND="doc? ( app-doc/doxygen[dot] )" +BDEPEND="doc? ( app-text/doxygen[dot] )" S="${WORKDIR}/${MY_PN}-${PV}" diff --git a/sci-libs/asl/asl-9999.ebuild b/sci-libs/asl/asl-9999.ebuild index 82b464f7f..905c8813a 100644 --- a/sci-libs/asl/asl-9999.ebuild +++ b/sci-libs/asl/asl-9999.ebuild @@ -24,7 +24,7 @@ RDEPEND=" DEPEND="${RDEPEND} matlab? ( >=sci-libs/matio-1.5.2 ) " -BDEPEND="doc? ( app-doc/doxygen[dot] )" +BDEPEND="doc? ( app-text/doxygen[dot] )" src_prepare() { cmake_src_prepare diff --git a/sci-libs/bids-validator/bids-validator-1.4.4.ebuild b/sci-libs/bids-validator/bids-validator-1.4.4.ebuild index 00bf81571..a4f7f0340 100644 --- a/sci-libs/bids-validator/bids-validator-1.4.4.ebuild +++ b/sci-libs/bids-validator/bids-validator-1.4.4.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2020 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7..9} ) +PYTHON_COMPAT=( python3_{10..11} ) inherit distutils-r1 diff --git a/sci-libs/blis-amd/Manifest b/sci-libs/blis-amd/Manifest deleted file mode 100644 index 86192778f..000000000 --- a/sci-libs/blis-amd/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST blis-amd-2.2.tar.gz 9066754 BLAKE2B 9425a927b8dd37cc5a0843a0c5d7958906bcdbdd83b015d2428e2372e0cdc6206ed8ab9c4c0c6e6eccee091498b524061ffed8adcd9b0c857cc9c64446b3a19f SHA512 a7d58bda40c833b5388e0f7b316352cfcb186db535534682b647e2ca7b130518959b3c78043261e9f1f85f99a168bd20b919c6c2c184ee4f4d269da88d41a5d6 diff --git a/sci-libs/blis-amd/blis-amd-2.2.ebuild b/sci-libs/blis-amd/blis-amd-2.2.ebuild deleted file mode 100644 index eb6c16385..000000000 --- a/sci-libs/blis-amd/blis-amd-2.2.ebuild +++ /dev/null @@ -1,128 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7..9} ) -inherit fortran-2 python-any-r1 - -DESCRIPTION="AMD optimized BLAS-like Library Instantiation Software Framework" -HOMEPAGE="https://developer.amd.com/amd-aocl/" - -if [[ ${PV} == 9999 ]]; then - inherit git-r3 - EGIT_REPO_URI="https://github.com/amd/blis" -else - SRC_URI="https://github.com/amd/blis/archive/${PV}.tar.gz -> ${P}.tar.gz" - S="${WORKDIR}"/blis-"${PV}" - KEYWORDS="~amd64 ~arm ~arm64 ~ppc ~ppc64 ~x86" -fi - -LICENSE="BSD" -SLOT="0" -IUSE="64bit-index doc eselect-ldso openmp pthread static-libs" -REQUIRED_USE="?? ( openmp pthread ) ?? ( eselect-ldso 64bit-index )" - -RDEPEND+=" - >=app-eselect/eselect-blas-0.2 - !sci-libs/blis -" -DEPEND+="${RDEPEND} - ${PYTHON_DEPS} -" - -PATCHES=( - "${FILESDIR}"/${P}-blas_rpath.patch -) - -pkg_pretend() { - elog "It is very important that you set the BLIS_CONFNAME" - elog "variable when compiling blis as it tunes the" - elog "compilation to the specific CPU architecture." - elog "To look at valid BLIS_CONFNAMEs, look at directories in" - elog "\t https://github.com/amd/blis/tree/master/config" - elog "At the very least, it should be set to the ARCH of" - elog "the machine this will be run on, which gives a" - elog "performance increase of ~4-5x." -} - -src_configure() { - local myconf=( - --prefix="${BROOT}"/usr - --libdir="${BROOT}"/usr/$(get_libdir) - --enable-cblas - --enable-blas - --enable-arg-max-hack - --enable-verbose-make - --without-memkind - --enable-shared - $(use_enable static-libs static) - ) - - use 64bit-index && \ - myconf+=( - --int-size=64 - --blas-int-size=64 - ) - - # threading backend - openmp/pthreads/no - if use openmp; then - myconf+=( --enable-threading=openmp ) - elif use pthread; then - myconf+=( --enable-threading=pthreads ) - else - myconf+=( --enable-threading=no ) - fi - - # not an autotools configure script - ./configure "${myconf[@]}" \ - "${EXTRA_ECONF[@]}" \ - ${BLIS_CONFNAME:-generic} || die -} - -src_compile() { - SET_RPATH=no \ - DEB_LIBBLAS=libblas.so.3 \ - DEB_LIBCBLAS=libcblas.so.3 \ - default -} - -src_test() { - emake check -} - -src_install() { - default - use doc && dodoc README.md docs/*.md - - use eselect-ldso || return - - insinto /usr/$(get_libdir)/blas/blis-amd - doins lib/${BLIS_CONFNAME:-generic}/lib{c,}blas.so.3 - dosym libblas.so.3 usr/$(get_libdir)/blas/blis-amd/libblas.so - dosym libcblas.so.3 usr/$(get_libdir)/blas/blis-amd/libcblas.so -} - -pkg_postinst() { - use eselect-ldso || return - - local libdir=$(get_libdir) me="blis-amd" - - # check blas - elog "adding ${me}" - eselect blas add ${libdir} "${EROOT}"/usr/${libdir}/blas/${me} ${me} - elog "added ${me}" - local current_blas=$(eselect blas show ${libdir} | cut -d' ' -f2) - if [[ ${current_blas} == "${me}" || -z ${current_blas} ]]; then - eselect blas set ${libdir} ${me} - elog "Current eselect: BLAS/CBLAS ($libdir) -> [${current_blas}]." - else - elog "Current eselect: BLAS/CBLAS ($libdir) -> [${current_blas}]." - elog "To use blas [${me}] implementation, you have to issue (as root):" - elog "\t eselect blas set ${libdir} ${me}" - fi -} - -pkg_postrm() { - use eselect-ldso && eselect blas validate -} diff --git a/sci-libs/blis-amd/blis-amd-9999.ebuild b/sci-libs/blis-amd/blis-amd-9999.ebuild deleted file mode 100644 index 672277b36..000000000 --- a/sci-libs/blis-amd/blis-amd-9999.ebuild +++ /dev/null @@ -1,128 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7..9} ) -inherit fortran-2 python-any-r1 - -DESCRIPTION="AMD optimized BLAS-like Library Instantiation Software Framework" -HOMEPAGE="https://developer.amd.com/amd-aocl/" - -if [[ ${PV} == 9999 ]]; then - inherit git-r3 - EGIT_REPO_URI="https://github.com/amd/blis" -else - SRC_URI="https://github.com/amd/blis/archive/${PV}.tar.gz -> ${P}.tar.gz" - S="${WORKDIR}"/blis-"${PV}" - KEYWORDS="~amd64 ~arm ~arm64 ~ppc ~ppc64 ~x86" -fi - -LICENSE="BSD" -SLOT="0" -IUSE="64bit-index doc eselect-ldso openmp pthread static-libs" -REQUIRED_USE="?? ( openmp pthread ) ?? ( eselect-ldso 64bit-index )" - -RDEPEND+=" - >=app-eselect/eselect-blas-0.2 - !sci-libs/blis -" -DEPEND+="${RDEPEND} - ${PYTHON_DEPS} -" - -PATCHES=( - "${FILESDIR}"/${PN}-2.2-blas_rpath.patch -) - -pkg_pretend() { - elog "It is very important that you set the BLIS_CONFNAME" - elog "variable when compiling blis as it tunes the" - elog "compilation to the specific CPU architecture." - elog "To look at valid BLIS_CONFNAMEs, look at directories in" - elog "\t https://github.com/amd/blis/tree/master/config" - elog "At the very least, it should be set to the ARCH of" - elog "the machine this will be run on, which gives a" - elog "performance increase of ~4-5x." -} - -src_configure() { - local myconf=( - --prefix="${BROOT}"/usr - --libdir="${BROOT}"/usr/$(get_libdir) - --enable-cblas - --enable-blas - --enable-arg-max-hack - --enable-verbose-make - --without-memkind - --enable-shared - $(use_enable static-libs static) - ) - - use 64bit-index && \ - myconf+=( - --int-size=64 - --blas-int-size=64 - ) - - # threading backend - openmp/pthreads/no - if use openmp; then - myconf+=( --enable-threading=openmp ) - elif use pthread; then - myconf+=( --enable-threading=pthreads ) - else - myconf+=( --enable-threading=no ) - fi - - # not an autotools configure script - ./configure "${myconf[@]}" \ - "${EXTRA_ECONF[@]}" \ - ${BLIS_CONFNAME:-generic} || die -} - -src_compile() { - SET_RPATH=no \ - DEB_LIBBLAS=libblas.so.3 \ - DEB_LIBCBLAS=libcblas.so.3 \ - default -} - -src_test() { - emake check -} - -src_install() { - default - use doc && dodoc README.md docs/*.md - - use eselect-ldso || return - - insinto /usr/$(get_libdir)/blas/blis-amd - doins lib/${BLIS_CONFNAME:-generic}/lib{c,}blas.so.3 - dosym libblas.so.3 usr/$(get_libdir)/blas/blis-amd/libblas.so - dosym libcblas.so.3 usr/$(get_libdir)/blas/blis-amd/libcblas.so -} - -pkg_postinst() { - use eselect-ldso || return - - local libdir=$(get_libdir) me="blis-amd" - - # check blas - elog "adding ${me}" - eselect blas add ${libdir} "${EROOT}"/usr/${libdir}/blas/${me} ${me} - elog "added ${me}" - local current_blas=$(eselect blas show ${libdir} | cut -d' ' -f2) - if [[ ${current_blas} == "${me}" || -z ${current_blas} ]]; then - eselect blas set ${libdir} ${me} - elog "Current eselect: BLAS/CBLAS ($libdir) -> [${current_blas}]." - else - elog "Current eselect: BLAS/CBLAS ($libdir) -> [${current_blas}]." - elog "To use blas [${me}] implementation, you have to issue (as root):" - elog "\t eselect blas set ${libdir} ${me}" - fi -} - -pkg_postrm() { - use eselect-ldso && eselect blas validate -} diff --git a/sci-libs/blis-amd/files/blis-amd-2.2-blas_rpath.patch b/sci-libs/blis-amd/files/blis-amd-2.2-blas_rpath.patch deleted file mode 100644 index 90ab11d52..000000000 --- a/sci-libs/blis-amd/files/blis-amd-2.2-blas_rpath.patch +++ /dev/null @@ -1,46 +0,0 @@ -diff --git a/Makefile b/Makefile -index ea7a550..1b3a1d2 100644 ---- a/Makefile -+++ b/Makefile -@@ -689,6 +689,9 @@ else - endif - endif - -+ $(LINKER) $(SOFLAGS) -o $(BASE_LIB_PATH)/$(DEB_LIBBLAS) $? $(LDFLAGS) -Wl,--soname,$(DEB_LIBBLAS) -+ $(LINKER) $(SOFLAGS) -o $(BASE_LIB_PATH)/$(DEB_LIBCBLAS) $? $(LDFLAGS) -Wl,--soname,$(DEB_LIBCBLAS) -+ - # Local symlink for shared library. - # NOTE: We use a '.loc' suffix to avoid filename collisions in case this - # rule is executed concurrently with the install-lib-symlinks rule, which -diff --git a/common.mk b/common.mk -index e73a5d1..2aa8a23 100644 ---- a/common.mk -+++ b/common.mk -@@ -565,11 +565,14 @@ ifeq ($(MK_ENABLE_SHARED),yes) - ifeq ($(MK_ENABLE_STATIC),no) - LIBBLIS_L := $(LIBBLIS_SO) - LIBBLIS_LINK := $(LIBBLIS_SO_PATH) -+SET_RPATH ?= yes - ifeq ($(IS_WIN),no) -+ifeq ($(SET_RPATH),yes) - # For Linux and OS X: set rpath property of shared object. - LDFLAGS += -Wl,-rpath,$(BASE_LIB_PATH) - endif - endif -+endif - # On windows, use the shared library even if static is created. - ifeq ($(IS_WIN),yes) - LIBBLIS_L := $(LIBBLIS_SO) -diff --git a/configure b/configure -index 35d4f1d..93c2cd6 100755 ---- a/configure -+++ b/configure -@@ -3055,7 +3055,7 @@ main() - enable_aocl_zen='yes' - enable_aocl_zen_01=1 - else -- enable_aocl_zen = 'no'; -+ enable_aocl_zen='no'; - enable_aocl_zen_01=0; - fi - diff --git a/sci-libs/blis-amd/metadata.xml b/sci-libs/blis-amd/metadata.xml deleted file mode 100644 index 1a481192a..000000000 --- a/sci-libs/blis-amd/metadata.xml +++ /dev/null @@ -1,21 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>gentoo@aisha.cc</email> - <name>Aisha Tammy</name> - </maintainer> - <maintainer type="project"> - <email>sci@gentoo.org</email> - <name>Gentoo Science Project</name> - </maintainer> - <upstream> - <remote-id type="github">amd/libflame</remote-id> - </upstream> - <use> - <flag name="64bit-index">Enable 64bit array indexing, incompatible with runtime switching</flag> - <flag name="eselect-ldso">Enable runtime library switching by eselect and ld.so</flag> - <flag name="openmp">Use openmp threadding model</flag> - <flag name="pthread">Use pthread threadding model</flag> - </use> -</pkgmetadata> diff --git a/sci-libs/daal4py/Manifest b/sci-libs/daal4py/Manifest new file mode 100644 index 000000000..0d9bbdab2 --- /dev/null +++ b/sci-libs/daal4py/Manifest @@ -0,0 +1 @@ +DIST daal4py-2023.0.2.tar.gz 13864043 BLAKE2B dfc082a8b008553e0d20cf7a24417fecd510dd8e6b3286a57a633b1e3b79cecc87fc1189df6f4a3440d7ccb74077c54a9f6eaf58bfbb19181cb4b437b3e06ae6 SHA512 dd8c983365d4f32d2640caab17319970c86bfed5ad6852d15dce35ba66a3584c51b94fa5ef0d8073b917332ea18a8c9af95ef8da125edb47190f27e9b8cab424 diff --git a/sci-libs/daal4py/daal4py-2023.0.2.ebuild b/sci-libs/daal4py/daal4py-2023.0.2.ebuild new file mode 100644 index 000000000..f23e1c738 --- /dev/null +++ b/sci-libs/daal4py/daal4py-2023.0.2.ebuild @@ -0,0 +1,64 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 + +DESCRIPTION="Python API to the oneAPI Data Analytics Library" +HOMEPAGE="https://github.com/intel/scikit-learn-intelex" +SRC_URI="https://github.com/intel/scikit-learn-intelex/archive/${PV}.tar.gz -> ${P}.tar.gz" +S="${WORKDIR}/scikit-learn-intelex-${PV}" + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="~amd64" + +BDEPEND=" + dev-python/cython[${PYTHON_USEDEP}] + dev-python/pybind11[${PYTHON_USEDEP}] + dev-build/cmake + sys-devel/DPC++ + test? ( + sci-libs/scikit-learn[${PYTHON_USEDEP}] + sci-libs/scikit-learn-intelx[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + ) +" + +DEPEND=" + dev-python/jinja[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/dpctl[${PYTHON_USEDEP}] + sci-libs/oneDAL + virtual/mpi +" +RDEPEND="${DEPEND}" + +distutils_enable_tests pytest + +PATCHES=( + "${FILESDIR}/${PN}-2023.0.2-dont-use-entire-include.patch" +) + +python_prepare_all() { + # DPC++ compiler required for full functionality + export CC="${ESYSROOT}/usr/lib/llvm/intel/bin/clang" + export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++" + export DPCPPROOT="${ESYSROOT}/usr/lib/llvm/intel" + export CPLUS_INCLUDE_PATH="${ESYSROOT}/usr/lib/llvm/intel/include:${ESYSROOT}/usr/lib/llvm/intel/include/sycl:${ESYSROOT}/usr/lib/llvm/intel/include/sycl/CL/sycl" + export MPIROOT="${ESYSROOT}/usr" + export DALROOT="${ESYSROOT}/usr" + # Parallel build is broken + export MAKEOPTS="-j1" + + distutils-r1_python_prepare_all +} + +python_test() { + export PYTHONPATH="${BUILD_DIR}/install/usr/lib/${EPYTHON}/site-packages" + # We don't use epytest because it overwrites our PYTHONPATH + pytest -vv || die +} diff --git a/sci-libs/daal4py/files/daal4py-2023.0.2-dont-use-entire-include.patch b/sci-libs/daal4py/files/daal4py-2023.0.2-dont-use-entire-include.patch new file mode 100644 index 000000000..d26414105 --- /dev/null +++ b/sci-libs/daal4py/files/daal4py-2023.0.2-dont-use-entire-include.patch @@ -0,0 +1,104 @@ +diff --git a/generator/gen_daal4py.py b/generator/gen_daal4py.py +index 203c870..7fdac1e 100755 +--- a/generator/gen_daal4py.py ++++ b/generator/gen_daal4py.py +@@ -34,7 +34,7 @@ from .wrappers import (required, ignore, defaults, has_dist, ifaces, + enum_maps, enum_params, wrap_algo, result_to_compute) + from .wrapper_gen import wrapper_gen + from .format import mk_var +-from shutil import copytree, rmtree ++from shutil import copytree, copyfile, rmtree + from subprocess import call + + try: +@@ -1045,7 +1045,13 @@ def gen_daal4py(daalroot, outdir, version, warn_all=False, + head_path = jp("build", "include") + algo_path = jp(head_path, "algorithms") + rmtree(head_path, ignore_errors=True) +- copytree(orig_path, head_path) ++ copytree(jp(orig_path, 'services'), jp(head_path, 'services')) ++ copytree(jp(orig_path, 'oneapi', 'dal'), jp(head_path, 'oneapi', 'dal')) ++ copytree(jp(orig_path, 'data_management'), jp(head_path, 'data_management')) ++ copytree(jp(orig_path, 'algorithms'), jp(head_path, 'algorithms')) ++ copyfile(jp(orig_path, 'daal.h'), jp(head_path, 'daal.h')) ++ copyfile(jp(orig_path, 'daal_sycl.h'), jp(head_path, 'daal_sycl.h')) ++ copyfile(jp(orig_path, 'oneapi', 'dal.hpp'), jp(head_path, 'oneapi', 'dal.hpp')) + for (dirpath, dirnames, filenames) in os.walk(algo_path): + for filename in filenames: + call([shutil.which("clang-format"), "-i", jp(dirpath, filename)]) +diff --git a/scripts/build_backend.py b/scripts/build_backend.py +index dd314e4..ec1ec2c 100755 +--- a/scripts/build_backend.py ++++ b/scripts/build_backend.py +@@ -118,20 +118,12 @@ def custom_build_cmake_clib(iface, cxx=None, onedal_major_binary_version=1): + python_library_dir = win_python_path_lib if IS_WIN else get_config_var('LIBDIR')
+ numpy_include = np.get_include()
+
+- if iface == 'dpc':
+- if IS_WIN:
+- cxx = 'icx'
+- else:
+- cxx = 'icpx'
+- elif cxx is None:
+- raise RuntimeError('CXX compiler shall be specified')
+-
+ cmake_args = [
+ "cmake",
+ cmake_generator,
+ "-S" + builder_directory,
+ "-B" + abs_build_temp_path,
+- "-DCMAKE_CXX_COMPILER=" + cxx,
++ "-DCMAKE_CXX_COMPILER=" + os.environ.get('CXX'),
+ "-DCMAKE_INSTALL_PREFIX=" + install_directory,
+ "-DCMAKE_PREFIX_PATH=" + install_directory,
+ "-DIFACE=" + iface,
+@@ -140,7 +132,7 @@ def custom_build_cmake_clib(iface, cxx=None, onedal_major_binary_version=1): + "-DNUMPY_INCLUDE_DIRS=" + numpy_include,
+ "-DPYTHON_LIBRARY_DIR=" + python_library_dir,
+ "-DoneDAL_INCLUDE_DIRS=" + jp(os.environ['DALROOT'], 'include'),
+- "-DoneDAL_LIBRARY_DIR=" + jp(os.environ['DALROOT'], 'lib', 'intel64'),
++ "-DoneDAL_LIBRARY_DIR=" + jp(os.environ['DALROOT'], 'lib', 'lib64'),
+ "-Dpybind11_DIR=" + pybind11.get_cmake_dir(),
+ ]
+
+diff --git a/setup.py b/setup.py +index 8f56b48..36260ea 100644 +--- a/setup.py ++++ b/setup.py +@@ -48,13 +48,13 @@ if dal_root is None: + + if 'linux' in sys.platform: + IS_LIN = True +- lib_dir = jp(dal_root, 'lib', 'intel64') ++ lib_dir = jp(dal_root, 'lib', 'lib64') + elif sys.platform == 'darwin': + IS_MAC = True + lib_dir = jp(dal_root, 'lib') + elif sys.platform in ['win32', 'cygwin']: + IS_WIN = True +- lib_dir = jp(dal_root, 'lib', 'intel64') ++ lib_dir = jp(dal_root, 'lib', 'lib64') + else: + assert False, sys.platform + ' not supported' + +@@ -178,7 +178,8 @@ def get_build_options(): + 'icc', 'icpc', 'icl', 'dpcpp', 'icx', 'icpx'] + eca = ['-DPY_ARRAY_UNIQUE_SYMBOL=daal4py_array_API', + '-DD4P_VERSION="' + d4p_version + '"', '-DNPY_ALLOW_THREADS=1'] +- ela = [] ++ ela = os.environ.get('LDFLAGS').split(" ") ++ eca += os.environ.get('CFLAGS').split(" ") + + if using_intel and IS_WIN: + include_dir_plat.append( +@@ -311,8 +312,8 @@ def build_oneapi_backend(): + ela = ['-fsycl'] + ['-fsycl-device-code-split=per_kernel'] + ela + + return build_backend.build_cpp( +- cc=cc, +- cxx=cxx, ++ cc=os.environ.get('CC'), ++ cxx=os.environ.get('CXX'), + sources=['src/oneapi/oneapi_backend.cpp'], + targetname='oneapi_backend', + targetprefix='' if IS_WIN else 'lib', diff --git a/sci-libs/daal4py/metadata.xml b/sci-libs/daal4py/metadata.xml new file mode 100644 index 000000000..247707c87 --- /dev/null +++ b/sci-libs/daal4py/metadata.xml @@ -0,0 +1,11 @@ +<?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> + <upstream> + <remote-id type="github">intel/scikit-learn-intelex</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/etsf_io/etsf_io-1.0.4-r2.ebuild b/sci-libs/etsf_io/etsf_io-1.0.4-r2.ebuild index 5216809ec..3961e4951 100644 --- a/sci-libs/etsf_io/etsf_io-1.0.4-r2.ebuild +++ b/sci-libs/etsf_io/etsf_io-1.0.4-r2.ebuild @@ -7,7 +7,7 @@ inherit fortran-2 DESCRIPTION="A library of F90 routines to read/write the ETSF file format" HOMEPAGE="https://github.com/ElectronicStructureLibrary/libetsf_io" -SRC_URI="https://launchpad.net/etsf-io/1.0/${PV}/+download/${P}.tar.gz" +SRC_URI="https://launchpad.net/etsf-io/$(ver_cut 1-2)/${PV}/+download/${P}.tar.gz" LICENSE="LGPL-2" SLOT="0" diff --git a/sci-libs/etsf_io/metadata.xml b/sci-libs/etsf_io/metadata.xml index 5c8a3611e..d8e7a0e60 100644 --- a/sci-libs/etsf_io/metadata.xml +++ b/sci-libs/etsf_io/metadata.xml @@ -7,4 +7,8 @@ <use> <flag name="pic">Compile Position Independent Code</flag> </use> + <upstream> + <remote-id type="github">ElectronicStructureLibrary/libetsf_io</remote-id> + <remote-id type="launchpad">etsf-io</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/fast5/Manifest b/sci-libs/fast5/Manifest deleted file mode 100644 index 7ec4bcd49..000000000 --- a/sci-libs/fast5/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST fast5-0.6.5.tar.gz 93639 BLAKE2B 921bf57fa24faf24cfb56a5ee059e12afd8cbccbbb0039205dd27f739abc50f83452dd76726779d700fae93e23bf133aaf5cc42deb80c4ffeae36b89fc68cf9b SHA512 a587e112df36e3d0e151c8c7e01aeffe31294402c2743040c9567ff213f7ae93d6ea7d827a618c7a57fece038b8a53844dbf41fd226416b3fe8c1211bd9311c9 diff --git a/sci-libs/fast5/fast5-0.6.5.ebuild b/sci-libs/fast5/fast5-0.6.5.ebuild deleted file mode 100644 index cf06e1d8d..000000000 --- a/sci-libs/fast5/fast5-0.6.5.ebuild +++ /dev/null @@ -1,36 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7,8,9} ) - -DOCS_BUILDER="doxygen" -DOCS_DIR="${WORKDIR}/${P}" - -inherit distutils-r1 docs - -DESCRIPTION="C++ header-only library for reading Oxford Nanopore Fast5 files" -HOMEPAGE="https://github.com/mateidavid/fast5" -SRC_URI="https://github.com/mateidavid/fast5/archive/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -BDEPEND="sci-libs/hdf5 - dev-python/cython[${PYTHON_USEDEP}]" - -S="${WORKDIR}/${P}/python" - -python_compile() { - HDF5_DIR="${EPREFIX}"/usr HDF5_LIB_DIR="${EPREFIX}"/usr/$(get_libdir) distutils-r1_python_compile -} - -python_compile_all(){ - docs_compile -} - -python_install() { - HDF5_DIR="${EPREFIX}"/usr HDF5_LIB_DIR="${EPREFIX}"/usr/$(get_libdir) distutils-r1_python_install -} diff --git a/sci-libs/fast5/metadata.xml b/sci-libs/fast5/metadata.xml deleted file mode 100644 index 138cb7705..000000000 --- a/sci-libs/fast5/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>mmokrejs@fold.natur.cuni.cz</email> - <name>Martin Mokrejs</name> - </maintainer> - <maintainer type="project"> - <email>sci-biology@gentoo.org</email> - <name>Gentoo Biology Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-libs/flexiblas/Manifest b/sci-libs/flexiblas/Manifest deleted file mode 100644 index 90c0bcb3d..000000000 --- a/sci-libs/flexiblas/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST flexiblas-3.0.4.tar.gz 33597962 BLAKE2B d87190d7fbac70f93a5c4fa23cecd6ce75ef1886eb4f0758b4a9da8e9c3d271304e09c94ae53ad80206886ddc7084ff29e3c27b17d50cbcfa8225bcbe944bd48 SHA512 2f677244d4face8ca5ec8b304da55937e311040cc2bb9278fe28695c74f56e4b29810507a9cda0b30f289058f1f5a2bf0035258c39f69df516ee76c606b9f2a2 diff --git a/sci-libs/flexiblas/flexiblas-3.0.4.ebuild b/sci-libs/flexiblas/flexiblas-3.0.4.ebuild deleted file mode 100644 index 7a7e253d0..000000000 --- a/sci-libs/flexiblas/flexiblas-3.0.4.ebuild +++ /dev/null @@ -1,45 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7..9} ) -inherit cmake python-any-r1 - -DESCRIPTION="BLAS/LAPACK wrapper library for runtime switching of backends" -HOMEPAGE="https://www.mpi-magdeburg.mpg.de/projects/flexiblas" - -if [[ "${PV}" == *9999 ]]; then - inherit git-r3 - EGIT_REPO_URI="https://github.com/mpimd-csc/flexiblas" -else - SRC_URI="https://github.com/mpimd-csc/flexiblas/archive/v${PV}.tar.gz -> ${P}.tar.gz" - KEYWORDS="~amd64 ~x86" -fi - -LICENSE="GPL-3 MIT" -SLOT="0" -IUSE="test" -RESTRICT="!test? ( test )" - -BDEPEND=" - test? ( ${PYTHON_DEPS} ) -" - -src_configure() { - local mycmakeargs=( - -DTESTS=$(usex test) - -DEXAMPLES=OFF - -DCBLAS=ON - -DLAPACK=ON - -DBLAS_AUTO_DETECT=OFF - ) - cmake_src_configure -} - -src_install() { - cmake_src_install - dosym libflexiblas.so "/usr/$(get_libdir)/libblas.so" - dosym libflexiblas.so "/usr/$(get_libdir)/libcblas.so" - dosym libflexiblas.so "/usr/$(get_libdir)/liblapack.so" -} diff --git a/sci-libs/flexiblas/flexiblas-9999.ebuild b/sci-libs/flexiblas/flexiblas-9999.ebuild deleted file mode 100644 index 7a7e253d0..000000000 --- a/sci-libs/flexiblas/flexiblas-9999.ebuild +++ /dev/null @@ -1,45 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7..9} ) -inherit cmake python-any-r1 - -DESCRIPTION="BLAS/LAPACK wrapper library for runtime switching of backends" -HOMEPAGE="https://www.mpi-magdeburg.mpg.de/projects/flexiblas" - -if [[ "${PV}" == *9999 ]]; then - inherit git-r3 - EGIT_REPO_URI="https://github.com/mpimd-csc/flexiblas" -else - SRC_URI="https://github.com/mpimd-csc/flexiblas/archive/v${PV}.tar.gz -> ${P}.tar.gz" - KEYWORDS="~amd64 ~x86" -fi - -LICENSE="GPL-3 MIT" -SLOT="0" -IUSE="test" -RESTRICT="!test? ( test )" - -BDEPEND=" - test? ( ${PYTHON_DEPS} ) -" - -src_configure() { - local mycmakeargs=( - -DTESTS=$(usex test) - -DEXAMPLES=OFF - -DCBLAS=ON - -DLAPACK=ON - -DBLAS_AUTO_DETECT=OFF - ) - cmake_src_configure -} - -src_install() { - cmake_src_install - dosym libflexiblas.so "/usr/$(get_libdir)/libblas.so" - dosym libflexiblas.so "/usr/$(get_libdir)/libcblas.so" - dosym libflexiblas.so "/usr/$(get_libdir)/liblapack.so" -} diff --git a/sci-libs/flexiblas/metadata.xml b/sci-libs/flexiblas/metadata.xml deleted file mode 100644 index c37e14ea4..000000000 --- a/sci-libs/flexiblas/metadata.xml +++ /dev/null @@ -1,27 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>gentoo@aisha.cc</email> - <name>Aisha Tammy</name> - </maintainer> - <maintainer type="project"> - <email>sci@gentoo.org</email> - <name>Gentoo Science Project</name> - </maintainer> - <longdescription> - FlexiBLAS is a wrapper library that enables the - exchange of the BLAS, CBLAS and LAPACK implementations - used in an executable without recompiling or re-linking it. - FlexiBLAS provides a GNU Fortran compatible interface - to all functions and subroutines provided by the Netlib - reference implementations. As backends FlexiBLAS can employ - all BLAS and LAPACK implementations which consist of a - single shared library directly. Other variants like the - Intel MKL or ATLAS that use multiple files are integrated - by FlexiBLAS by wrapping all files into a single surrogate library. - </longdescription> - <upstream> - <remote-id type="github">mpimd-csc/flexiblas</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-libs/gdcm/Manifest b/sci-libs/gdcm/Manifest new file mode 100644 index 000000000..64b9caefd --- /dev/null +++ b/sci-libs/gdcm/Manifest @@ -0,0 +1,2 @@ +DIST gdcm-3.0.14.tar.bz2 2992355 BLAKE2B a97209a8bb6896095bfc59ac974b667386c8711f20118252567cf983f15165d259da7858ccfd6bfdfbb25194d7687c98512953b480913acec4bf6d176af7a005 SHA512 9c7d70723d288bf116a8b594c02dd965a4e80476e1c79a7c3cbd09584a229c83ad67f082c9b286305e3bb64150c8267ced06b5fb963adbeeb36e383f76612220 +DIST gdcmData.tar.gz 121157465 BLAKE2B 19b13efc2094d3e373f0f658f1120b1c83ea6da1be73fb392b815433725b4a6db2debb9ab7d9f2caa665637f152f70694cdf226c934850dfda344107050a14a6 SHA512 ddc67a7a0b41b2d6e1e03defb6fb8a06ceeb2e9dd9bb47dfa4f7283d79df7c1e52577b799c00e930719ae6cdda46bded9497a67b8241359f238f5366085ec9ee diff --git a/sci-libs/gdcm/files/gdcm-3.0.14-include-math-h.patch b/sci-libs/gdcm/files/gdcm-3.0.14-include-math-h.patch new file mode 100644 index 000000000..ba99c3547 --- /dev/null +++ b/sci-libs/gdcm/files/gdcm-3.0.14-include-math-h.patch @@ -0,0 +1,15 @@ +https://cgit.freebsd.org/ports/plain/devel/gdcm/files/patch-Utilities_VTK_vtkImageMapToWindowLevelColors2.cxx?id=8f5541298099b722e34632ca9ed388bda91064e7 + +- workaround for https://sourceforge.net/p/gdcm/bugs/536/ + +--- a/Utilities/VTK/vtkImageMapToWindowLevelColors2.cxx 2022-06-26 20:39:45 UTC ++++ b/Utilities/VTK/vtkImageMapToWindowLevelColors2.cxx +@@ -37,6 +37,8 @@ + #include "vtkScalarsToColors.h" + #include "vtkPointData.h" + ++#include <math.h> ++ + //vtkCxxRevisionMacro(vtkImageMapToWindowLevelColors2, "$Revision: 1.3 $") + vtkStandardNewMacro(vtkImageMapToWindowLevelColors2) + diff --git a/sci-libs/gdcm/files/gdcm_support_vtk9.patch b/sci-libs/gdcm/files/gdcm_support_vtk9.patch new file mode 100644 index 000000000..3818a82b5 --- /dev/null +++ b/sci-libs/gdcm/files/gdcm_support_vtk9.patch @@ -0,0 +1,70 @@ +--- a/Utilities/VTK/CMakeLists.txt ++++ b/Utilities/VTK/CMakeLists.txt +@@ -26,6 +26,11 @@ + ) + endif() + ++if( ${VTK_MAJOR_VERSION} GREATER_EQUAL 9 ) ++ set(VTK_INCLUDE_DIRS "${VTK_PREFIX_PATH}/include/vtk-${VTK_MAJOR_VERSION}.${VTK_MINOR_VERSION}") ++ include_directories(AFTER ${VTK_INCLUDE_DIRS}) ++endif() ++ + include(CheckCXXSourceCompiles) + set(CMAKE_REQUIRED_INCLUDES ${VTK_INCLUDE_DIRS}) + CHECK_CXX_SOURCE_COMPILES( +@@ -94,6 +99,10 @@ + endforeach() + endif() + ++if( ${VTK_MAJOR_VERSION} GREATER_EQUAL 9 ) ++ string(REGEX REPLACE "vtk([^;]+)" "VTK::\\1" vtkgdcm_LIBS "${vtkgdcm_LIBS}") ++endif() ++ + # Use wrapping hints for this project. + #set(VTK_WRAP_HINTS "${PROJECT_SOURCE_DIR}/hints") + +--- a/Utilities/VTK/Applications/CMakeLists.txt ++++ b/Utilities/VTK/Applications/CMakeLists.txt +@@ -25,6 +25,11 @@ + ) + endif() + ++set(vtk_ioxml vtkIOXML) ++if( ${VTK_MAJOR_VERSION} GREATER_EQUAL 9 ) ++ set(vtk_ioxml VTK::IOXML) ++endif() ++ + foreach(app ${GDCM_VTK_APPS}) + add_executable(${app} ${app}.cxx) + if(GDCM_EXECUTABLE_PROPERTIES) +@@ -42,7 +47,7 @@ + endif() + else() + # >= 6.0 +- target_link_libraries(${app} ${VTK_LIBRARIES} vtkIOXML) ++ target_link_libraries(${app} ${VTK_LIBRARIES} ${vtk_ioxml}) + endif() + if(WIN32 AND NOT CYGWIN) + target_link_libraries(${app} gdcmgetopt) +--- a/Utilities/VTK/vtkGDCMPolyDataWriter.cxx ++++ b/Utilities/VTK/vtkGDCMPolyDataWriter.cxx +@@ -496,6 +496,9 @@ + sqi = new SequenceOfItems; + + vtkIdType npts = 0; ++#if VTK_MAJOR_VERSION >= 9 ++ const ++#endif + vtkIdType *indx = 0; + double v[3]; + unsigned int cellnum = 0; +@@ -759,6 +762,9 @@ + vtkPoints *pts; + vtkCellArray *polys; + vtkIdType npts = 0; ++#if VTK_MAJOR_VERSION >= 9 ++ const ++#endif + vtkIdType *indx = 0; + pts = theData->GetPoints(); + polys = theData->GetPolys(); diff --git a/sci-libs/gdcm/gdcm-3.0.14.ebuild b/sci-libs/gdcm/gdcm-3.0.14.ebuild new file mode 100644 index 000000000..c1000fea9 --- /dev/null +++ b/sci-libs/gdcm/gdcm-3.0.14.ebuild @@ -0,0 +1,121 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_10 ) + +inherit cmake python-single-r1 + +DESCRIPTION="Cross-platform DICOM implementation" +HOMEPAGE="http://gdcm.sourceforge.net/" +SRC_URI="mirror://sourceforge/gdcm/${P}.tar.bz2 + test? ( mirror://sourceforge/gdcm/gdcmData.tar.gz )" # 3.0.14: .bz2 is broken, should be checked in next release + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="doc python test vtk" +RESTRICT="!test? ( test )" + +DEPEND=" + app-text/poppler:0=[cxx] + dev-libs/expat:0= + dev-libs/json-c:0= + dev-libs/libxml2:2= + dev-libs/openssl:0= + >=media-libs/charls-2.0.0:0= + >=media-libs/openjpeg-2.0.0:2= + sys-apps/util-linux:0= + sys-libs/zlib:0= + python? ( ${PYTHON_DEPS} ) + vtk? ( + sci-libs/vtk[rendering] + python? ( + sci-libs/vtk[python,${PYTHON_SINGLE_USEDEP}] + ) + ) +" +RDEPEND="${DEPEND}" +BDEPEND=" + dev-libs/libxslt + app-text/docbook-xsl-ns-stylesheets + doc? ( app-text/doxygen[dot] ) + python? ( + ${PYTHON_DEPS} + >=dev-lang/swig-3.0.7 + )" + +REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" + +PATCHES=( + "${FILESDIR}/gdcm_support_vtk9.patch" + "${FILESDIR}/gdcm-3.0.14-include-math-h.patch" +) + +pkg_setup() { + use python && python-single-r1_pkg_setup +} + +src_prepare() { + # drop unbundled libs + local -a DROPS=( gdcmcharls gdcmexpat gdcmopenjpeg gdcmuuid gdcmzlib getopt pvrg KWStyle Release ) + local x + for x in "${DROPS[@]}"; do + ebegin "Dropping bundled ${x#gdcm}" + rm -r "Utilities/${x}" || die + sed -i "s,^[ \t]*APPEND_COPYRIGHT(\\\${CMAKE_CURRENT_SOURCE_DIR}/${x}/,#&," "Utilities/CMakeLists.txt" || die + eend $? + done + find Utilities -mindepth 1 -maxdepth 1 '!' -name doxygen '!' -name VTK -type d \ + -exec ewarn "Using bundled" {} ';' || die + + # fix charls include case + sed -i 's:CharLS/charls\.h:charls/charls.h:' CMake/FindCharLS.cmake Utilities/gdcm_charls.h || die + sed -i 's:NAMES CharLS:NAMES charls:' CMake/FindCharLS.cmake || die + + # Use prefixed socket++ (to avoid potential conflicts) + sed -i '/target_link_libraries(/s/socketxx/gdcm&/' \ + Source/MessageExchangeDefinition/CMakeLists.txt \ + Applications/Cxx/CMakeLists.txt \ + || die + + cmake_src_prepare +} + +src_configure() { + local mycmakeargs=( + -DCMAKE_SKIP_RPATH=ON + -DGDCM_BUILD_SHARED_LIBS=ON + -DGDCM_DATA_ROOT="${WORKDIR}/gdcmData" + -DGDCM_INSTALL_LIB_DIR="$(get_libdir)" + -DGDCM_INSTALL_DOC_DIR="share/doc/${P}" + -DGDCM_INSTALL_PYTHONMODULE_DIR="lib/${EPYTHON}/site-packages" + -DGDCM_USE_SYSTEM_ZLIB=ON + -DGDCM_USE_SYSTEM_OPENSSL=ON + -DGDCM_USE_SYSTEM_UUID=ON + -DGDCM_USE_SYSTEM_EXPAT=ON + -DGDCM_USE_SYSTEM_JSON=ON + -DGDCM_USE_SYSTEM_PAPYRUS3=OFF + -DGDCM_USE_SYSTEM_SOCKETXX=OFF + -DSOCKETXX_NAMESPACE=GDCMSOCKETXX + -DGDCM_USE_SYSTEM_LJPEG=OFF + -DGDCM_USE_SYSTEM_OPENJPEG=ON + -DGDCM_USE_SYSTEM_CHARLS=ON + -DGDCM_USE_SYSTEM_POPPLER=ON + -DGDCM_USE_SYSTEM_LIBXML2=ON + -DGDCM_BUILD_TESTING=$(usex test) + -DGDCM_WRAP_PYTHON=$(usex python) + $(usex python "-DGDCM_DEFAULT_PYTHON_VERSION=${EPYTHON#python}" "") + -DGDCM_WRAP_PERL=OFF + -DGDCM_WRAP_PHP=OFF + -DGDCM_WRAP_JAVA=OFF + -DGDCM_WRAP_CSHARP=OFF + -DGDCM_DOCUMENTATION=$(usex doc) + $(usex doc "-DGDCM_PDF_DOCUMENTATION=OFF" "") + -DGDCM_BUILD_EXAMPLES=OFF + -DGDCM_BUILD_APPLICATIONS=ON + -DGDCM_USE_VTK=$(usex vtk) + ) + cmake_src_configure +} diff --git a/sci-libs/gdcm/metadata.xml b/sci-libs/gdcm/metadata.xml new file mode 100644 index 000000000..1845bf1bd --- /dev/null +++ b/sci-libs/gdcm/metadata.xml @@ -0,0 +1,14 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>fx.carton91@gmail.com</email> + <name>François-Xavier Carton</name> + </maintainer> + <use> + <flag name="vtk">Build <pkg>sci-libs/vtk</pkg> bridge</flag> + </use> + <upstream> + <remote-id type="sourceforge">gdcm</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/gvar/Manifest b/sci-libs/gvar/Manifest new file mode 100644 index 000000000..16bdf1de2 --- /dev/null +++ b/sci-libs/gvar/Manifest @@ -0,0 +1 @@ +DIST gvar-13.0.2.tar.gz 1001282 BLAKE2B 5c4032406e3d514351bac6f21b5353c8db4e2081efd26b758cce126cce4a3df350ac8086e89895c73ffc27367773a43354138e8598490cbe8f7bacdde216f0bd SHA512 541cb5cc44909cf44e9f808a08a959aa5e3e91c49356fb8865879a9dbb5fe6f3c4b46d88bc4f9346d9b83163c938dfd697e73b7b9a00815ed6dc383630795cb4 diff --git a/sci-libs/gvar/gvar-13.0.2.ebuild b/sci-libs/gvar/gvar-13.0.2.ebuild new file mode 100644 index 000000000..b9d9121e4 --- /dev/null +++ b/sci-libs/gvar/gvar-13.0.2.ebuild @@ -0,0 +1,22 @@ +EAPI=8 + +DISTUTILS_EXT=1 +PYTHON_COMPAT=( python3_{10..12} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 pypi + +DESCRIPTION="Gaussian random variables." +HOMEPAGE="https://github.com/gplepage/gvar" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~arm64" + +RDEPEND=" + >=dev-python/cython-0.17[${PYTHON_USEDEP}] + >=dev-python/numpy-1.16[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] +" +BDEPEND="${RDEPEND}" + +distutils_enable_tests unittest diff --git a/sci-libs/gvar/metadata.xml b/sci-libs/gvar/metadata.xml new file mode 100644 index 000000000..31346f0dd --- /dev/null +++ b/sci-libs/gvar/metadata.xml @@ -0,0 +1,19 @@ +<?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> + <maintainer type="person"> + <email>alexander@neuwirth-informatik.de</email> + <name>Alexander Puck Neuwirth</name> + </maintainer> + <longdescription lang="en"> + This package facilitates the creation and manipulation of arbitrarily complicated (correlated) multi-dimensional Gaussian random variables. The random variables are represented by a new data type (gvar.GVar) that can be used in arithmetic expressions and pure Python functions. Such expressions/functions create new Gaussian random variables while automatically tracking statistical correlations between the new and old variables. This data type is useful for simple error propagation, but also is heavily used by the Bayesian least-squares fitting module lsqfit.py to define priors and specify fit results, while accounting for correlations between all variables. + </longdescription> + <upstream> + <remote-id type="pypi">gvar</remote-id> + <remote-id type="github">gplepage/gvar</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/handyg/Manifest b/sci-libs/handyg/Manifest new file mode 100644 index 000000000..3487702bd --- /dev/null +++ b/sci-libs/handyg/Manifest @@ -0,0 +1 @@ +DIST handyg-v0.1.5.tar.gz 107946 BLAKE2B 338b0027f51fd8b329c1af4e6a0e76dda7b9a3d29a12cffcf60948c5800ee8e280ff97726359df483b60dc3d76a26c40bf21804113d318d83539828e54c4a1ff SHA512 f6f068e05c80c6dccf1c4c8a284da752d04d4fd3f15a78eee933227c6a93906fe794ef3ada359831a4098c00b0a7684af91e2f9cca2a06dd8d0381c1c20c59be diff --git a/sci-libs/handyg/files/handyg-0.1.5-so.patch b/sci-libs/handyg/files/handyg-0.1.5-so.patch new file mode 100644 index 000000000..48815780e --- /dev/null +++ b/sci-libs/handyg/files/handyg-0.1.5-so.patch @@ -0,0 +1,23 @@ +--- a/configure 2022-09-19 22:54:12.742507414 +0200 ++++ b/configure 2022-09-19 23:00:13.452378883 +0200 +@@ -839,7 +839,7 @@ + objects = \$(addprefix build/,\$(files)) + + +-all: libhandyg.a handyg.mod ${CONF_MPREP:+handyG} geval test ++all: libhandyg.a libhandyg.so handyg.mod ${CONF_MPREP:+handyG} geval test + + EOF + +@@ -868,6 +868,11 @@ + @echo "AR \$@" + @\$(AR) \$@ \$^ + ++libhandyg.so:\$(objects) ++ @echo "\$(FC) \$@" ++ \$(FC) \$(LFLAGS) -Wl,-soname,libhandyg.so -shared -o \$@ \$^ ++ ++ + handyg.mod: build/handyg.mod + cp \$< \$@ + diff --git a/sci-libs/handyg/handyg-0.1.5.ebuild b/sci-libs/handyg/handyg-0.1.5.ebuild new file mode 100644 index 000000000..97a18c08e --- /dev/null +++ b/sci-libs/handyg/handyg-0.1.5.ebuild @@ -0,0 +1,44 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit toolchain-funcs +MY_P=${PN}-v${PV} + +DESCRIPTION="Rapid numerical evaluation of generalised polylogarithms" +HOMEPAGE="https://gitlab.com/mule-tools/handyg" +SRC_URI="https://gitlab.com/mule-tools/${PN}/-/archive/v${PV}/${MY_P}.tar.gz" +S="${WORKDIR}/${MY_P}" + +LICENSE="GPL-3+" +SLOT="0" +KEYWORDS="~amd64" + +DEPEND="" +RDEPEND="${DEPEND}" +BDEPEND=" + virtual/fortran +" + +PATCHES=( + "${FILESDIR}/${P}-so.patch" +) + +src_configure() { + tc-export CC CXX FC AR + FFLAGS="${FFLAGS} -fPIC" LD="${FC}" ./configure --prefix="${EPREFIX}/usr" LDFLAGS="${LDFLAGS}" +} + +src_compile() { + # single thread force needed since fortan mods depend on each other + export MAKEOPTS=-j1 + emake all +} + +src_install() { + dolib.a libhandyg.a + dolib.so libhandyg.so + doheader handyg.mod + dobin geval +} diff --git a/sci-libs/handyg/metadata.xml b/sci-libs/handyg/metadata.xml new file mode 100644 index 000000000..bdee6992b --- /dev/null +++ b/sci-libs/handyg/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>alexander@neuwirth-informatik.de</email> + <name>Alexander Puck Neuwirth</name> + </maintainer> + <maintainer type="project"> + <email>sci-physics@gentoo.org</email> + <name>Gentoo Physics Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-libs/ipp/Manifest b/sci-libs/ipp/Manifest deleted file mode 100644 index 0007a0681..000000000 --- a/sci-libs/ipp/Manifest +++ /dev/null @@ -1,3 +0,0 @@ -DIST parallel_studio_xe_2018_update2_professional_edition.tgz 3877755304 BLAKE2B c8852df23abf080f482002a37af7781b3fbae3ecec448914ea5a237fa2b925073d1a3dc2dd94ba64002ff0f6c7e9b18b25fa7ada811a83b10344eb9b92cb37ff SHA512 a9b644b0305d83a9d0daa14d146cb3ce79949db55a410afe48d62259414e6256d9ef533a04bb50807103511db2016c4abcbbf769146854a25638f402a6d0f2be -DIST parallel_studio_xe_2019_update4_professional_edition.tgz 2629662464 BLAKE2B a5619f33535063ccd7310378504ca960aa8512527cef7e0884fae5570633c1823e50ff7135adbbc571b4d47e0b6fcc01afe8639e09feb50a7f289eeec3f61ca0 SHA512 d8f6780a3671f30a1bad5d3a9792062c73b31188dc31fbd38212e98abc593f1c8f64bb970a8a4fce9ce237afef18ed38adf8fd81aa73b63ec964224590d4a34d -DIST parallel_studio_xe_2020_update1_professional_edition.tgz 2783012958 BLAKE2B 975103ec4551a0e3bd84034ce771a5fc459d5de47f4247b5915b54d9c827e50e913f9054a103424b764f730190675d42b52a97e68551b34df6b3d8d9b922517a SHA512 00a3334bcdb8b30216ecb40fcfc709b27d043697606a53f522c90b05cf8598e1e60311d629ec17b6fe1016a7d2a27f4b428abddc9eba39badebfd8a9b53de404 diff --git a/sci-libs/ipp/ipp-18.0.2.199.ebuild b/sci-libs/ipp/ipp-18.0.2.199.ebuild deleted file mode 100644 index 5253840b9..000000000 --- a/sci-libs/ipp/ipp-18.0.2.199.ebuild +++ /dev/null @@ -1,43 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -INTEL_DIST_SKU=3235 -INTEL_DIST_PV=2018_update2_professional_edition - -inherit intel-sdp-r1 - -DESCRIPTION="Intel Integrated Performance Primitive library" -HOMEPAGE="http://software.intel.com/en-us/articles/intel-ipp/" - -IUSE="doc" -KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux" - -DEPEND="" -RDEPEND="~dev-libs/intel-common-${PV}[compiler]" - -CHECKREQS_DISK_BUILD=6500M - -INTEL_DIST_DAT_RPMS=( - "ipp-common-2018.2-199-2018.2-199.noarch.rpm" - "ipp-common-ps-2018.2-199-2018.2-199.noarch.rpm") -INTEL_DIST_AMD64_RPMS=( - "ipp-mt-2018.2-199-2018.2-199.x86_64.rpm" - "ipp-mt-devel-2018.2-199-2018.2-199.x86_64.rpm" - "ipp-st-2018.2-199-2018.2-199.x86_64.rpm" - "ipp-st-devel-2018.2-199-2018.2-199.x86_64.rpm" - "ipp-st-devel-ps-2018.2-199-2018.2-199.x86_64.rpm") -INTEL_DIST_X86_RPMS=( - "ipp-mt-32bit-2018.2-199-2018.2-199.x86_64.rpm" - "ipp-mt-devel-32bit-2018.2-199-2018.2-199.x86_64.rpm" - "ipp-st-32bit-2018.2-199-2018.2-199.x86_64.rpm" - "ipp-st-devel-32bit-2018.2-199-2018.2-199.x86_64.rpm" - "ipp-st-devel-ps-32bit-2018.2-199-2018.2-199.x86_64.rpm") - -pkg_setup() { - if use doc; then - INTEL_DIST_DAT_RPMS+=( - "ipp-doc-2018-2018.2-199.noarch.rpm") - fi -} diff --git a/sci-libs/ipp/ipp-19.0.4.243.ebuild b/sci-libs/ipp/ipp-19.0.4.243.ebuild deleted file mode 100644 index e42583e20..000000000 --- a/sci-libs/ipp/ipp-19.0.4.243.ebuild +++ /dev/null @@ -1,42 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -INTEL_DIST_PV=2019_update4_professional_edition - -inherit intel-sdp-r1 - -DESCRIPTION="Intel Integrated Performance Primitive library" -HOMEPAGE="http://software.intel.com/en-us/articles/intel-ipp/" - -IUSE="doc" -KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux" - -DEPEND="" -RDEPEND="~dev-libs/intel-common-${PV}[compiler]" - -CHECKREQS_DISK_BUILD=6500M - -INTEL_DIST_DAT_RPMS=( - "ipp-common-2019.4-243-2019.4-243.noarch.rpm" - "ipp-common-ps-2019.4-243-2019.4-243.noarch.rpm") -INTEL_DIST_AMD64_RPMS=( - "ipp-mt-2019.4-243-2019.4-243.x86_64.rpm" - "ipp-mt-devel-2019.4-243-2019.4-243.x86_64.rpm" - "ipp-st-2019.4-243-2019.4-243.x86_64.rpm" - "ipp-st-devel-2019.4-243-2019.4-243.x86_64.rpm" - "ipp-st-devel-ps-2019.4-243-2019.4-243.x86_64.rpm") -INTEL_DIST_X86_RPMS=( - "ipp-mt-32bit-2019.4-243-2019.4-243.x86_64.rpm" - "ipp-mt-devel-32bit-2019.4-243-2019.4-243.x86_64.rpm" - "ipp-st-32bit-2019.4-243-2019.4-243.x86_64.rpm" - "ipp-st-devel-32bit-2019.4-243-2019.4-243.x86_64.rpm" - "ipp-st-devel-ps-32bit-2019.4-243-2019.4-243.x86_64.rpm") - -pkg_setup() { - if use doc; then - INTEL_DIST_DAT_RPMS+=( - "ipp-doc-2019-2019.4-243.noarch.rpm") - fi -} diff --git a/sci-libs/ipp/ipp-2020.1.217.ebuild b/sci-libs/ipp/ipp-2020.1.217.ebuild deleted file mode 100644 index 2c0be6abf..000000000 --- a/sci-libs/ipp/ipp-2020.1.217.ebuild +++ /dev/null @@ -1,44 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -INTEL_DIST_PV=2020_update1_professional_edition - -inherit intel-sdp-r1 - -DESCRIPTION="Intel Integrated Performance Primitive library" -HOMEPAGE="http://software.intel.com/en-us/articles/intel-ipp/" - -IUSE="doc" -KEYWORDS="-* ~amd64 ~x86 ~amd64-linux ~x86-linux" - -DEPEND="" -RDEPEND="~dev-libs/intel-common-19.1.1.217[compiler]" - -CHECKREQS_DISK_BUILD=6500M - -MY_PV="$(ver_rs 2 '-')" # 2020.1-217 - -QA_PREBUILT="*" - -INTEL_DIST_DAT_RPMS=( - "ipp-common-${MY_PV}-${MY_PV}.noarch.rpm" - "ipp-common-ps-${MY_PV}-${MY_PV}.noarch.rpm") -INTEL_DIST_AMD64_RPMS=( - "ipp-mt-${MY_PV}-${MY_PV}.x86_64.rpm" - "ipp-mt-devel-${MY_PV}-${MY_PV}.x86_64.rpm" - "ipp-st-${MY_PV}-${MY_PV}.x86_64.rpm" - "ipp-st-devel-${MY_PV}-${MY_PV}.x86_64.rpm") -INTEL_DIST_X86_RPMS=( - "ipp-mt-32bit-${MY_PV}-${MY_PV}.x86_64.rpm" - "ipp-mt-devel-32bit-${MY_PV}-${MY_PV}.x86_64.rpm" - "ipp-st-32bit-${MY_PV}-${MY_PV}.x86_64.rpm" - "ipp-st-devel-32bit-${MY_PV}-${MY_PV}.x86_64.rpm") - -pkg_setup() { - if use doc; then - INTEL_DIST_DAT_RPMS+=( - "ipp-doc-2020-${MY_PV}.noarch.rpm") - fi -} diff --git a/sci-libs/ipp/metadata.xml b/sci-libs/ipp/metadata.xml deleted file mode 100644 index 7bd17909e..000000000 --- a/sci-libs/ipp/metadata.xml +++ /dev/null @@ -1,13 +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"> -Intel(R) Integrated Performance Primitives (Intel(R) IPP) is a -library of multi-core-ready, optimized software functions for -multimedia data processing, and communications applications. -</longdescription> -</pkgmetadata> diff --git a/sci-libs/itk/Manifest b/sci-libs/itk/Manifest index 31310f8b1..87328da27 100644 --- a/sci-libs/itk/Manifest +++ b/sci-libs/itk/Manifest @@ -1,10 +1,12 @@ -DIST ITKGenericLabelInterpolator-5.0.1.tar.gz 136432 BLAKE2B c367d5f29b3b3250f73d3b03b80b50a99607d895ebb83c3613b40ed665bce87b2731b2ecf471a5b77983db1f8894e486404662bb5787056f23de24c8ee897704 SHA512 6044aab4893d6c68c6190c5d81f460ea0dfc4683d33a03a5d56a8a0ae3b767edde530cdc8976e6777237cb1d172f66df044afe11c4cfc9148e5712cf9f3a11fc -DIST ITKGenericLabelInterpolator-5.1.0.tar.gz 140286 BLAKE2B 1c8efa033586368931d78fe4620ddd1449fcd15153b1585c716bce580df74a6fc990b3714677a81cdcedcd0e4626e4f155c522f6e7306e5be399d521213891b4 SHA512 7bf6310e8b0ea2356ae8ce0ddd0bc3a1516aa6bb5e3e8df9ed0114f1bb2b299d2edd046f27dbae364082afc63e225a3691c794c93d347ee564db617ea3fbf489 -DIST ITKGenericLabelInterpolator_test-5.0.1.zip 430662 BLAKE2B f46683bd1b3479ae6fc9ae63752810a1dda7940c67d4be8524edcb8b40ed384b331ac785ab752c3ed1570cce8d79af7de873820fdb76a11f2e4241ad7fd2d2c2 SHA512 435200a70ee8de30cc02b30d805697ebc61fb2792e6e7d8f5da923d2773ccd6adfdcec2ab953a6a043d624ebb01b9f7f30e2aad83a6442272f28104d357a7bde -DIST InsightData-5.0.1.tar.gz 290801718 BLAKE2B dcb7657cb1f8555365b2ec94e7f95c4feab13ba4d585fd70ec240e63e7a55cf48aadf091a63ba2263f1f8c10ce3935812655449bea275af3d2eeff3f2689ef46 SHA512 eb766c115049949937d6527937f1f49ef84304a71dc4924581a53173f45c4e5a0c5a0e180550e75ecd840314609580b9d1fe9b2358c5a87c82a2c6aff8e9f50e -DIST InsightData-5.1.0.tar.gz 292322103 BLAKE2B e55eddf06d72e87e68e7654c634f545923202467b710c75aa929cd040f37a9caa48ee262ca6465631961816af1cd854b9a046ff7e7ffed7731e428e092bc6020 SHA512 458c2959ba5e0745eee23e16ff7178230a7bae94d7dff065b3b38136e238becff96554693e3b2149d2307949c23a6c695c92676f8d44e6f7305dbb8bed48c9fa -DIST InsightToolkit-5.0.1.tar.gz 20627889 BLAKE2B 2bd53f64f18746a7d0226d4d97bc02529a1dd2c05fc2294b0c2a5adb3783a8e766b1d20e051a17f20b4e5855e7c5b4a18d5f177f239113bc64f1a0400ce6f04b SHA512 f36613ff72c513ded3d32504f71308a94fe75555cf9fd22b77485d1375601f6e1f1539cc5ac82a9e1e229bcf514a88ccb55122a7dfc74a6ae1b6604aa70bd814 -DIST InsightToolkit-5.1.0.tar.gz 20694338 BLAKE2B 6a14e2e00f6d68a1420cdeebabdef254d23c6ba6610828bb860cf4e27a87f0e1448cd222bf3bc02f6d32b4eb262d7ba032f4459ed05f59f8c95d80907e03571c SHA512 413b6ef549b59d8f507038130446ccb704794c6d0980d8ab631d1b1051cb91f399e77c26b69fab6a1e9b9bb4cc233d49996c3ee735cd4de065993d4379b4ed4c -DIST itk-5.1.0-test-a5e11ea71164ff78c65fcf259db01ea5db981a9d868e60045ff2bffca92984df1174bf984a1076e450f0d5d69b4f0191ed1a61465c220e2c91a893b5df150c0a 1017 BLAKE2B e6a3b734c3f4a23238dbb921c46297b491436e6c4b0b6d8992fe8fa3c813374f354495ca575d5d371ef49b7bcdc8b63d89a5e8d1ae608bce50fea0efc95ec60d SHA512 e69c77894cab5b295ec5edbecdf693525ec9a4673810b87cbc28646ea40888b7792b5707840069e277905c8b0014bd84ecea036836f87c3b16f388f544e34341 -DIST itk-5.1.0-test-bcdbb347f3704262d1f00be7179d6a0a6e68aed56c0653e8072ee5a94985c713bd229c935b1226a658af84fb7f1fffc2458c98364fc35303a2303b12f9f7ce2f 1018 BLAKE2B 50cad64ac0b674fe4dce36c732f8fababe13ec2893e22caa0b22274320fb4f6d70aec1e8b4f6ee5878ebc20b02c7300c877db911b77f82ac0cf2d6e3284f4ffa SHA512 27952af5d6243aa31c187280ea9ba82c434db3614b3db3b406fe8e5c7e4b7e333bc179d5d9956d5a17aa670a7aa7cfce037d37c4225125e703602e322d8ec68b -DIST itk-5.1.0-testingdata.tar.gz 2409232372 BLAKE2B 7eb1c3ca21558603d3aa915c2a17e9bb656867331dc48e7b514ece50a7eac3d24bdf01c8b0acc703566b598959780d6736b27d1516d932f949e3a5cfe6acd9e0 SHA512 8b451608cb3f75d3ba6a78fd23e79495948c2792a98d831e0f0c93745595df84d3c2a8d76389976f67ac7e7e1f5a44a18d201e51d2ee659cdb708ae28536df8f +DIST ITKAdaptiveDenoising-5.2.1.tar.gz 757851 BLAKE2B 3d94e1db6d2524adf7491e6e24308618b7b69e54184cbfe29a7084b55b8a337228a308233e0f0ab2cef04df9c8f42010a758e0071efdfd4905c28ca6399bfdfd SHA512 7e9c5a6681cd9777b33f11d1a1a5f6d8b1b6f7d2ec2d4d829398c78045b53b247bddea99e4a5450ba8d6666a31b5216ef6e07a2c874c5723af072e0d3c8cf9f4 +DIST ITKAdaptiveDenoising-5.3.0.tar.gz 757851 BLAKE2B 3d94e1db6d2524adf7491e6e24308618b7b69e54184cbfe29a7084b55b8a337228a308233e0f0ab2cef04df9c8f42010a758e0071efdfd4905c28ca6399bfdfd SHA512 7e9c5a6681cd9777b33f11d1a1a5f6d8b1b6f7d2ec2d4d829398c78045b53b247bddea99e4a5450ba8d6666a31b5216ef6e07a2c874c5723af072e0d3c8cf9f4 +DIST ITKGenericLabelInterpolator-1.2.0.tar.gz 137697 BLAKE2B f7bb877654e852f56f8eb1086f988ec3b71106b6528d5cf03734a3c3eb4ce5ac875b52081e0a1339ac237e1616b0516b8cc8efb4429ec0e5ef64ac5461a40836 SHA512 bc1fcd3c13cb182420bb4a5d2c9c789553f8b7b581fd7d0b7d687331e22c90d30efdd338bfbc22dfb8c97d3ab7209f761425c4d12755655d86d81ffb231d881c +DIST ITKGenericLabelInterpolator-5.2.1.tar.gz 140427 BLAKE2B b19703872926516d9d07acd4078d343e02f00a162d2cb8b6787d6210223be375a059e767cf9c32dd234e77ff51d1af5e08d9a9844c34e23a531938c7d3ded4a9 SHA512 69e53b281cd3f7c136ad9e7ded2c362e0d9e22dc2bd595f42abcefe2cf9ec4fa0f44192efc3d328290be4adaee1ebd74be3035b18147081cc8b8479a333cdea6 +DIST InsightData-5.2.1.tar.gz 293448802 BLAKE2B fd2bb012c0d96243d3543993a87e73c43be0626b0478959e36633f22c7e8d48a46d0f4d18fa3a8d952d4a705ca20594d92c07044000b8e1bc65390ce981af3e7 SHA512 93eae6bdf62ce29ea6dfb1dddedffe4046400a86074dd4d47e3ddcd7ff9ab10031363275cb7f9741add7c02343f1f3e6a41b0ec6533531f4a3a42607c51aa704 +DIST InsightData-5.3.0.tar.gz 366826437 BLAKE2B ae3cbb3f7a51d6b86717a073c0eb55c528baeff240f44413c25ce11319a7e0ef9ff073d1cb94d2d15d104687fe5b8e95d0d4286832dbb02993da8fe706fecb28 SHA512 3caf7d1d64543312d668ef1a6b8c879161a37deee5c980fbfeb14e299a296a2825ae48463bff915f50c98ec0ccdbef3e1aff7c4f52604a93c6028951f90a4757 +DIST InsightToolkit-5.2.1.tar.gz 20702482 BLAKE2B 06dc73a80b4999baff3fc75e225c8720d00927fd268bd0398bb0eea44679777b777836f307f02a2df3641a300e17c9c2ee9f77d2a87539bf8a6ed49ce341bf23 SHA512 6786e39cdf3d0c3a31abd1e23481e30f6dc9dac189ffe372dde3db688f2f57686a8beb321778327e1ff683ed844d41f1dee937b0ba542b2365e2195dfca398c7 +DIST InsightToolkit-5.3.0.tar.gz 21577835 BLAKE2B 7538b673cbe17ab23d6b70e2cb2486e6711df6a79d6806c641a10a8b624c4723ca5f562b97be814551c79c42dea772ac64ed7bc8fdf2d28f5a95cb6462e50638 SHA512 29359839c0fb13acd430410e6adadbecb4d9d8cb4871a0aba0ac67b539c235354a591655dd654f43daa5f035a33721671d665eee8a4a129a9d0d3419e2356e97 +DIST itk-5.2.1-testingdata.tar.gz 2411475710 BLAKE2B edb8ba9bea8bf890749aa46ab3fb29f7d3e25e0f8bb7da7d7cca8c6524f75778b823232536602ade763c025b8e0fe134a555e6fcf652b8d42cc08f08cbd0c29b SHA512 89b160dc5f7781e148aad065f539b80b9accb9ec384e424398287e62b42a88cff610afcf41622a6d3e4e12c1938e7403b3dae65fa13bfb40c29a6b2f90a02398 +DIST itk-5.3.0-testingdata.tar.gz 2569680868 BLAKE2B a358bdb3a9f6de883e9fe41129af88d7a476acc4839fd17075d484a441db40d7f1f2f247d07701817464de5c997b18066628921652630a5f110e238d3f2419ec SHA512 5fa0834c25d128c915b5bdaefb13574952e680fe52a5c99ced614737e52f57abce59510be764766ce43769ae5731c35c7d646cdf3e21f495aee14fbb7d1835b4 +DIST itk-test-a5e11ea71164ff78c65fcf259db01ea5db981a9d868e60045ff2bffca92984df1174bf984a1076e450f0d5d69b4f0191ed1a61465c220e2c91a893b5df150c0a 214819 BLAKE2B cd65212e72cb80eff54ee3f22d05b55036470684c582334fe94826a2d4ed49c840c50a214996f64f2bcd710e5973c2d46201ef31732fe847a43504379df62e25 SHA512 a5e11ea71164ff78c65fcf259db01ea5db981a9d868e60045ff2bffca92984df1174bf984a1076e450f0d5d69b4f0191ed1a61465c220e2c91a893b5df150c0a +DIST itk-test-bcdbb347f3704262d1f00be7179d6a0a6e68aed56c0653e8072ee5a94985c713bd229c935b1226a658af84fb7f1fffc2458c98364fc35303a2303b12f9f7ce2f 215417 BLAKE2B 318a6c55ba259a5af1e3e19cf859267caa0a612b05abfd9a83d9943902fd7edc25ec002707ed4ec85f7aebd4c5a82411942b5cfe2dc713c905a5bb5d1aa5ef23 SHA512 bcdbb347f3704262d1f00be7179d6a0a6e68aed56c0653e8072ee5a94985c713bd229c935b1226a658af84fb7f1fffc2458c98364fc35303a2303b12f9f7ce2f diff --git a/sci-libs/itk/files/0001-BUG-Wrap-TransformFileReader-TransformFileWriter.patch b/sci-libs/itk/files/0001-BUG-Wrap-TransformFileReader-TransformFileWriter.patch deleted file mode 100644 index 094ee3229..000000000 --- a/sci-libs/itk/files/0001-BUG-Wrap-TransformFileReader-TransformFileWriter.patch +++ /dev/null @@ -1,50 +0,0 @@ -From d069b7b94287dae15fcaf707775f5dd2bbebcc38 Mon Sep 17 00:00:00 2001 -From: Matt McCormick <matt.mccormick@kitware.com> -Date: Wed, 5 Feb 2014 15:52:34 -0500 -Subject: [PATCH 1/3] BUG: Wrap TransformFileReader, TransformFileWriter. - -Missing CMakeLists.txt in the wrapping directory. Need to explicitly include -the headers after "Template" was appended to the class name. - -Suggested-by: Sami Koho <sami.koho@gmail.com> - -Change-Id: I6f994bb18f37d5adf1d0f0311fa73506c41239a7 ---- - Modules/IO/TransformBase/wrapping/CMakeLists.txt | 3 +++ - Modules/IO/TransformBase/wrapping/itkTransformFileReader.wrap | 2 ++ - Modules/IO/TransformBase/wrapping/itkTransformFileWriter.wrap | 2 ++ - 3 files changed, 7 insertions(+) - create mode 100644 Modules/IO/TransformBase/wrapping/CMakeLists.txt - -diff --git a/Modules/IO/TransformBase/wrapping/CMakeLists.txt b/Modules/IO/TransformBase/wrapping/CMakeLists.txt -new file mode 100644 -index 0000000..6072567 ---- /dev/null -+++ b/Modules/IO/TransformBase/wrapping/CMakeLists.txt -@@ -0,0 +1,3 @@ -+itk_wrap_module(ITKIOTransformBase) -+itk_auto_load_submodules() -+itk_end_wrap_module() -diff --git a/Modules/IO/TransformBase/wrapping/itkTransformFileReader.wrap b/Modules/IO/TransformBase/wrapping/itkTransformFileReader.wrap -index 9b52fbc..662df9e 100644 ---- a/Modules/IO/TransformBase/wrapping/itkTransformFileReader.wrap -+++ b/Modules/IO/TransformBase/wrapping/itkTransformFileReader.wrap -@@ -1,3 +1,5 @@ -+set(WRAPPER_AUTO_INCLUDE_HEADERS OFF) -+itk_wrap_include("itkTransformFileReader.h") - itk_wrap_class("itk::TransformFileReaderTemplate" POINTER) - foreach(t ${WRAP_ITK_REAL}) - itk_wrap_template("${ITKM_${t}}" "${ITKT_${t}}") -diff --git a/Modules/IO/TransformBase/wrapping/itkTransformFileWriter.wrap b/Modules/IO/TransformBase/wrapping/itkTransformFileWriter.wrap -index 4f1ac4a..356aaf3 100644 ---- a/Modules/IO/TransformBase/wrapping/itkTransformFileWriter.wrap -+++ b/Modules/IO/TransformBase/wrapping/itkTransformFileWriter.wrap -@@ -1,3 +1,5 @@ -+set(WRAPPER_AUTO_INCLUDE_HEADERS OFF) -+itk_wrap_include("itkTransformFileWriter.h") - itk_wrap_class("itk::TransformFileWriterTemplate" POINTER) - foreach(t ${WRAP_ITK_REAL}) - itk_wrap_template("${ITKM_${t}}" "${ITKT_${t}}") --- -1.8.5.3 - diff --git a/sci-libs/itk/files/0002-COMP-Fixed-itkQuasiNewtonOptimizerv4-wrapping-warnin.patch b/sci-libs/itk/files/0002-COMP-Fixed-itkQuasiNewtonOptimizerv4-wrapping-warnin.patch deleted file mode 100644 index 4c74d5451..000000000 --- a/sci-libs/itk/files/0002-COMP-Fixed-itkQuasiNewtonOptimizerv4-wrapping-warnin.patch +++ /dev/null @@ -1,28 +0,0 @@ -From 66d2955fbe5528d9df216c639277d1d2686447e5 Mon Sep 17 00:00:00 2001 -From: Michka Popoff <michkapopoff@gmail.com> -Date: Fri, 7 Feb 2014 19:24:49 +0100 -Subject: [PATCH 2/3] COMP: Fixed itkQuasiNewtonOptimizerv4 wrapping warnings - -The warning : -/scratch/dashboards/Linux-x86_64-gcc4.4-WrapITK/ITK-build/Wrapping/Modules/ITKOptimizersv4/itkQuasiNewtonOptimizerv4.xml: warning(5): Unknown type type: itk::QuasiNewtonOptimizerv4 [typedef] -/scratch/dashboards/Linux-x86_64-gcc4.4-WrapITK/ITK-build/Wrapping/Modules/ITKOptimizersv4/itkQuasiNewtonOptimizerv4.xml: warning(4): ITK type not wrapped, or currently not known: itk::QuasiNewtonOptimizerv4Template< double > ---- - .../Numerics/Optimizersv4/wrapping/itkQuasiNewtonOptimizerv4.wrap | 8 +++++++- - 1 file changed, 7 insertions(+), 1 deletion(-) - -diff --git a/Modules/Numerics/Optimizersv4/wrapping/itkQuasiNewtonOptimizerv4.wrap b/Modules/Numerics/Optimizersv4/wrapping/itkQuasiNewtonOptimizerv4.wrap -index 4a43dd4..7eed11c 100644 ---- a/Modules/Numerics/Optimizersv4/wrapping/itkQuasiNewtonOptimizerv4.wrap -+++ b/Modules/Numerics/Optimizersv4/wrapping/itkQuasiNewtonOptimizerv4.wrap -@@ -1 +1,7 @@ --itk_wrap_simple_class("itk::QuasiNewtonOptimizerv4" POINTER) -+set(WRAPPER_AUTO_INCLUDE_HEADERS OFF) -+itk_wrap_include("itkQuasiNewtonOptimizerv4.h") -+itk_wrap_class("itk::QuasiNewtonOptimizerv4Template" POINTER) -+ foreach(t ${WRAP_ITK_REAL}) -+ itk_wrap_template("${ITKM_${t}}" "${ITKT_${t}}") -+ endforeach(t) -+itk_end_wrap_class() --- -1.8.5.3 - diff --git a/sci-libs/itk/files/0003-COMP-Fixed-itkGradientDescentOptimizerv4-wrapping-wa.patch b/sci-libs/itk/files/0003-COMP-Fixed-itkGradientDescentOptimizerv4-wrapping-wa.patch deleted file mode 100644 index d77345edf..000000000 --- a/sci-libs/itk/files/0003-COMP-Fixed-itkGradientDescentOptimizerv4-wrapping-wa.patch +++ /dev/null @@ -1,73 +0,0 @@ -From fced46ce8769b4edc7971ea0928045390b5c3f84 Mon Sep 17 00:00:00 2001 -From: Michka Popoff <michkapopoff@gmail.com> -Date: Mon, 10 Feb 2014 09:41:42 +0100 -Subject: [PATCH 3/3] COMP: Fixed itkGradientDescentOptimizerv4 wrapping - warnings - -I splitted the 3 wrapping calls in 3 separate files and fixed the wrapping. - -The warnings : -/home/kevin/kitware/ITK_Build/Wrapping/Modules/ITKOptimizersv4/itkGradientDescentOptimizerv4.xml: warning(5): Unknown type type: itk::GradientDescentOptimizerBasev4 [typedef] -/home/kevin/kitware/ITK_Build/Wrapping/Modules/ITKOptimizersv4/itkGradientDescentOptimizerv4.xml: warning(5): Unknown type type: itk::GradientDescentOptimizerv4 [typedef] -/home/kevin/kitware/ITK_Build/Wrapping/Modules/ITKOptimizersv4/itkGradientDescentOptimizerv4.xml: warning(5): Unknown type type: itk::ObjectToObjectOptimizerBase [typedef] -/home/kevin/kitware/ITK_Build/Wrapping/Modules/ITKOptimizersv4/itkGradientDescentOptimizerv4.xml: warning(4): ITK type not wrapped, or currently not known: itk::GradientDescentOptimizerBasev4Template< double > -/home/kevin/kitware/ITK_Build/Wrapping/Modules/ITKOptimizersv4/itkGradientDescentOptimizerv4.xml: warning(4): ITK type not wrapped, or currently not known: itk::GradientDescentOptimizerv4Template< double > -/home/kevin/kitware/ITK_Build/Wrapping/Modules/ITKOptimizersv4/itkGradientDescentOptimizerv4.xml: warning(4): ITK type not wrapped, or currently not known: itk::ObjectToObjectOptimizerBaseTemplate< double > - -Should also hopefully fix the new error on the dashboard I introduced by fixing the itkQuasiNewtonOptimizerv4 warnings (http://review.source.kitware.com/#/c/14317/) -/home/kevin/kitware/ITK_Build/Wrapping/Typedefs/itkQuasiNewtonOptimizerv4.i:87: Warning 401: Nothing known about base class 'itk::GradientDescentOptimizerv4Template< float >'. Ignored. -/home/kevin/kitware/ITK_Build/Wrapping/Typedefs/itkQuasiNewtonOptimizerv4.i:87: Warning 401: Maybe you forgot to instantiate 'itk::GradientDescentOptimizerv4Template< float >' using %template. - -Change-Id: I15b6af11690ed6efeaced68f73af5212ab5dc364 ---- - .../wrapping/itkGradientDescentOptimizerBasev4.wrap | 7 +++++++ - .../Optimizersv4/wrapping/itkGradientDescentOptimizerv4.wrap | 10 +++++++--- - .../Optimizersv4/wrapping/itkObjectToObjectOptimizerBase.wrap | 7 +++++++ - 3 files changed, 21 insertions(+), 3 deletions(-) - create mode 100644 Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerBasev4.wrap - create mode 100644 Modules/Numerics/Optimizersv4/wrapping/itkObjectToObjectOptimizerBase.wrap - -diff --git a/Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerBasev4.wrap b/Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerBasev4.wrap -new file mode 100644 -index 0000000..74f5a6c ---- /dev/null -+++ b/Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerBasev4.wrap -@@ -0,0 +1,7 @@ -+set(WRAPPER_AUTO_INCLUDE_HEADERS OFF) -+itk_wrap_include("itkGradientDescentOptimizerBasev4.h") -+itk_wrap_class("itk::GradientDescentOptimizerBasev4Template" POINTER) -+ foreach(t ${WRAP_ITK_REAL}) -+ itk_wrap_template("${ITKM_${t}}" "${ITKT_${t}}") -+ endforeach(t) -+itk_end_wrap_class() -diff --git a/Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerv4.wrap b/Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerv4.wrap -index d53a176..3236448 100644 ---- a/Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerv4.wrap -+++ b/Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerv4.wrap -@@ -1,3 +1,7 @@ --itk_wrap_simple_class("itk::ObjectToObjectOptimizerBase" POINTER) --itk_wrap_simple_class("itk::GradientDescentOptimizerBasev4" POINTER) --itk_wrap_simple_class("itk::GradientDescentOptimizerv4" POINTER) -+set(WRAPPER_AUTO_INCLUDE_HEADERS OFF) -+itk_wrap_include("itkGradientDescentOptimizerv4.h") -+itk_wrap_class("itk::GradientDescentOptimizerv4Template" POINTER) -+ foreach(t ${WRAP_ITK_REAL}) -+ itk_wrap_template("${ITKM_${t}}" "${ITKT_${t}}") -+ endforeach(t) -+itk_end_wrap_class() -diff --git a/Modules/Numerics/Optimizersv4/wrapping/itkObjectToObjectOptimizerBase.wrap b/Modules/Numerics/Optimizersv4/wrapping/itkObjectToObjectOptimizerBase.wrap -new file mode 100644 -index 0000000..61b2c44 ---- /dev/null -+++ b/Modules/Numerics/Optimizersv4/wrapping/itkObjectToObjectOptimizerBase.wrap -@@ -0,0 +1,7 @@ -+set(WRAPPER_AUTO_INCLUDE_HEADERS OFF) -+itk_wrap_include("itkObjectToObjectOptimizerBase.h") -+itk_wrap_class("itk::ObjectToObjectOptimizerBaseTemplate" POINTER) -+ foreach(t ${WRAP_ITK_REAL}) -+ itk_wrap_template("${ITKM_${t}}" "${ITKT_${t}}") -+ endforeach(t) -+itk_end_wrap_class() --- -1.8.5.3 - diff --git a/sci-libs/itk/files/0004-COMP-Warp-OptimizerParameterScalesEstimatorTemplate.patch b/sci-libs/itk/files/0004-COMP-Warp-OptimizerParameterScalesEstimatorTemplate.patch deleted file mode 100644 index 83b395626..000000000 --- a/sci-libs/itk/files/0004-COMP-Warp-OptimizerParameterScalesEstimatorTemplate.patch +++ /dev/null @@ -1,30 +0,0 @@ -Author: Matt McCormick <matt.mccormick@kitware.com> -Date: Thu Feb 6 10:26:49 2014 -0500 - - COMP: Wrap OptimizerParameterScalesEstimatorTemplate. - - The class name changed and it became templated. Fixes: - - /playpen/blowekamp/MacOSX-WrapITK/ITK-build/Wrapping/Modules/ITKOptimizersv4/itkOptimizerParameterScalesEstimator.xml: - warning(5): Unknown type type: itk::OptimizerParameterScalesEstimator - [typedef] - /playpen/blowekamp/MacOSX-WrapITK/ITK-build/Wrapping/Modules/ITKOptimizersv4/itkOptimizerParameterScalesEstimator.xml: - warning(4): ITK type not wrapped, or currently not known: - itk::OptimizerParameterScalesEstimatorTemplate< double > - - Change-Id: Ic6b4d6fba10d5d6c7b58de8d842bad6511e1ae7b - -diff --git a/Modules/Numerics/Optimizersv4/wrapping/itkOptimizerParameterScalesEstimator.wrap b/Modules/Numerics/Optimizersv4/wrapping/itkOptim -index efd6a8c..a647ee4 100644 ---- a/Modules/Numerics/Optimizersv4/wrapping/itkOptimizerParameterScalesEstimator.wrap -+++ b/Modules/Numerics/Optimizersv4/wrapping/itkOptimizerParameterScalesEstimator.wrap -@@ -1 +1,7 @@ --itk_wrap_simple_class("itk::OptimizerParameterScalesEstimator" POINTER) -+set(WRAPPER_AUTO_INCLUDE_HEADERS OFF) -+itk_wrap_include("itkOptimizerParameterScalesEstimator.h") -+itk_wrap_class("itk::OptimizerParameterScalesEstimatorTemplate" POINTER) -+ foreach(t ${WRAP_ITK_REAL}) -+ itk_wrap_template("${ITKM_${t}}" "${ITKT_${t}}") -+ endforeach(t) -+itk_end_wrap_class() - diff --git a/sci-libs/itk/files/0005-make-gdcm-helper-library-static.patch b/sci-libs/itk/files/0005-make-gdcm-helper-library-static.patch deleted file mode 100644 index d760ac7ba..000000000 --- a/sci-libs/itk/files/0005-make-gdcm-helper-library-static.patch +++ /dev/null @@ -1,11 +0,0 @@ -diff --git a/Modules/ThirdParty/GDCM/src/CMakeLists.txt b/Modules/ThirdParty/GDCM/src/CMakeLists.txt -index e98077c..70f4286 100644 ---- a/Modules/ThirdParty/GDCM/src/CMakeLists.txt -+++ b/Modules/ThirdParty/GDCM/src/CMakeLists.txt -@@ -1,5 +1,5 @@ - if(ITK_USE_SYSTEM_GDCM) -- add_library(ITKGDCM ITK-GDCM.cxx) -+ add_library(ITKGDCM STATIC ITK-GDCM.cxx) - target_link_libraries(ITKGDCM gdcmDICT gdcmMSFF) - itk_module_target(ITKGDCM) - return() diff --git a/sci-libs/itk/files/ITKModuleRemote.patch b/sci-libs/itk/files/ITKModuleRemote.patch deleted file mode 100644 index eb130159a..000000000 --- a/sci-libs/itk/files/ITKModuleRemote.patch +++ /dev/null @@ -1,45 +0,0 @@ -Disable automatic git clone attempt for modules: -https://github.com/InsightSoftwareConsortium/ITK/issues/1157 - ---- a/CMake/ITKModuleRemote.cmake 2019-08-13 18:10:33.385472767 +0200 -+++ b/CMake/ITKModuleRemote.cmake 2019-08-13 18:12:04.020198966 +0200 -@@ -165,39 +165,4 @@ - set(Module_${_name} ON CACHE FORCE "${_description}") - endif() - -- if(Module_${_name}) -- itk_download_attempt_check(Module_${_name}) -- include(CMakeParseArguments) -- cmake_parse_arguments(_fetch_options "" "GIT_REPOSITORY;GIT_TAG" "" ${ARGN}) -- find_package(Git) -- if(NOT GIT_EXECUTABLE) -- message(FATAL_ERROR "error: could not find git for clone of ${_name}") -- endif() -- execute_process( -- COMMAND "${GIT_EXECUTABLE}" --version -- OUTPUT_VARIABLE ov -- OUTPUT_STRIP_TRAILING_WHITESPACE -- ) -- string(REGEX REPLACE "^git version (.+)$" "\\1" _version "${ov}") -- if("${_version}" VERSION_LESS 1.6.6) -- message(FATAL_ERROR "Git version 1.6.6 or later is required.") -- endif() -- -- set(REMOTE_GIT_TAG "${_fetch_options_GIT_TAG}") -- -- if( DEFINED REMOTE_GIT_TAG_${_name} AND NOT "${REMOTE_GIT_TAG_${_name}}" STREQUAL "${_fetch_options_GIT_TAG}") -- set(REMOTE_GIT_TAG "${REMOTE_GIT_TAG_${_name}}") -- message(STATUS "NOTE: Using override 'REMOTE_GIT_TAG_${_name}=${REMOTE_GIT_TAG}'\n" -- " instead of value 'GIT_TAG=${_fetch_options_GIT_TAG}'\n" -- " specified in file ${ITK_SOURCE_DIR}/Modules/Remote/${_name}.remote.cmake'") -- endif() -- set(REMOTE_GIT_TAG_${_name} "${REMOTE_GIT_TAG}" CACHE STRING "Override default GIT_TAG value for remote module ${_name}") -- mark_as_advanced(REMOTE_GIT_TAG_${_name}) -- -- _fetch_with_git("${GIT_EXECUTABLE}" -- "${_fetch_options_GIT_REPOSITORY}" -- "${REMOTE_GIT_TAG}" -- "${ITK_SOURCE_DIR}/Modules/Remote/${_name}" -- ) -- endif() - endfunction() diff --git a/sci-libs/itk/files/itk-5.1.0-downloads.patch b/sci-libs/itk/files/itk-5.1.0-downloads.patch deleted file mode 100644 index 34fdb76d1..000000000 --- a/sci-libs/itk/files/itk-5.1.0-downloads.patch +++ /dev/null @@ -1,20 +0,0 @@ ---- a/CMake/ITKDownloadSetup.cmake 2020-07-30 19:03:10.330325423 -0400 -+++ b/CMake/ITKDownloadSetup.cmake 2020-07-30 19:03:10.330325423 -0400 -@@ -11,7 +11,7 @@ - - macro(itk_download_attempt_check _name) - if(ITK_FORBID_DOWNLOADS) -- message(SEND_ERROR "Attempted to download ${_name} when ITK_FORBID_DOWNLOADS is ON") -+ message(WARNING "Attempted to download ${_name} when ITK_FORBID_DOWNLOADS is ON") - endif() - endmacro() - ---- a/Modules/Remote/GenericLabelInterpolator.remote.cmake 2020-04-25 14:30:53.000000000 -0400 -+++ b/Modules/Remote/GenericLabelInterpolator.remote.cmake 2020-04-25 14:30:53.000000000 -0400 -@@ -44,6 +44,4 @@ - itk_fetch_module(GenericLabelInterpolator - "A generic interpolator for multi-label images." - MODULE_COMPLIANCE_LEVEL 2 -- GIT_REPOSITORY ${git_protocol}://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator.git -- GIT_TAG b95fe46c7f4fe8002af67c67e6fe4e1f087bf6b7 - ) diff --git a/sci-libs/itk/files/itk-5.1.0-include_limits.patch b/sci-libs/itk/files/itk-5.1.0-include_limits.patch deleted file mode 100644 index 9a8fae820..000000000 --- a/sci-libs/itk/files/itk-5.1.0-include_limits.patch +++ /dev/null @@ -1,10 +0,0 @@ ---- a/Modules/ThirdParty/GDCM/src/gdcm/Source/MediaStorageAndFileFormat/gdcmImageChangePhotometricInterpretation.h -+++ a/Modules/ThirdParty/GDCM/src/gdcm/Source/MediaStorageAndFileFormat/gdcmImageChangePhotometricInterpretation.h -@@ -16,6 +16,7 @@ - - #include "gdcmImageToImageFilter.h" - #include "gdcmPhotometricInterpretation.h" -+#include <limits> - - namespace gdcm - { diff --git a/sci-libs/itk/files/itk-5.2.1-fix-castxml-clang-attr-malloc.patch b/sci-libs/itk/files/itk-5.2.1-fix-castxml-clang-attr-malloc.patch new file mode 100644 index 000000000..05c9d5635 --- /dev/null +++ b/sci-libs/itk/files/itk-5.2.1-fix-castxml-clang-attr-malloc.patch @@ -0,0 +1,25 @@ +From: François-Xavier Carton <fx.carton91@gmail.com> +Date: Thu, 9 Jun 2022 14:56:22 +0200 +Subject: [PATCH] fix attr malloc error with recent glibc/gcc + +Recent GCC has support for __attribute__((__malloc__)) with arguments, but clang +does not. castxml uses clang internally. And recent glibc/gcc uses the attribute +with arguments. Mix all this, and you get: + +error: '__malloc__' attribute takes no arguments + +when compiling itk with python wrapping. + +To fix this, we add a define to castxml flags to remove the extra arguments. + +--- a/Wrapping/Generators/CastXML/CMakeLists.txt 2022-06-09 14:53:15.582352715 +0200 ++++ b/Wrapping/Generators/CastXML/CMakeLists.txt 2022-06-09 14:54:38.182351433 +0200 +@@ -237,7 +237,7 @@ + set(_castxml_cc ${_castxml_cc} "-D_HAS_TR1=0") + endif() + else() +- set(_castxml_cc --castxml-cc-gnu ( "${CMAKE_CXX_COMPILER}" ${_castxml_cc_flags} )) ++ set(_castxml_cc --castxml-cc-gnu ( "${CMAKE_CXX_COMPILER}" ${_castxml_cc_flags} -D__malloc__\(a,b\)=__malloc__ )) + endif() + set(_target) + if(CMAKE_CROSSCOMPILING) diff --git a/sci-libs/itk/files/itk-5.2.1-system-openjpeg.patch b/sci-libs/itk/files/itk-5.2.1-system-openjpeg.patch new file mode 100644 index 000000000..ad717f677 --- /dev/null +++ b/sci-libs/itk/files/itk-5.2.1-system-openjpeg.patch @@ -0,0 +1,558 @@ +--- a/Modules/ThirdParty/OpenJPEG/CMakeLists.txt ++++ b/Modules/ThirdParty/OpenJPEG/CMakeLists.txt +@@ -1,16 +1,32 @@ + project(ITKOpenJPEG) + set(ITKOpenJPEG_THIRD_PARTY 1) + +-set(ITKOpenJPEG_INCLUDE_DIRS +- ${ITKOpenJPEG_BINARY_DIR}/src/openjpeg +- ${ITKOpenJPEG_SOURCE_DIR}/src/openjpeg +- ) +-set(ITKOpenJPEG_LIBRARIES itkopenjpeg) ++option(ITK_USE_SYSTEM_OPENJPEG "Use system-installed openjpeg" ${ITK_USE_SYSTEM_LIBRARIES}) ++mark_as_advanced(ITK_USE_SYSTEM_OPENJPEG) ++ ++if(ITK_USE_SYSTEM_OPENJPEG) ++ find_package(OpenJPEG REQUIRED) ++ set(ITKOpenJPEG_INCLUDE_DIRS ++ ${ITKOpenJPEG_BINARY_DIR}/src ++ ) ++ set(ITKOpenJPEG_SYSTEM_INCLUDE_DIRS ++ ${OPENJPEG_INCLUDE_DIRS} ++ ) ++ set(ITKOpenJPEG_LIBRARIES "${OPENJPEG_LIBRARIES}") ++ set(ITKOpenJPEG_NO_SRC 1) ++else() ++ set(ITKOpenJPEG_INCLUDE_DIRS ++ ${ITKOpenJPEG_BINARY_DIR}/src/openjpeg ++ ${ITKOpenJPEG_SOURCE_DIR}/src/openjpeg ++ ) ++ set(ITKOpenJPEG_LIBRARIES itkopenjpeg) ++endif() ++ ++configure_file(src/itk_openjpeg.h.in src/itk_openjpeg.h) + set(ITK_LIBRARY_PROPERTIES WINDOWS_EXPORT_ALL_SYMBOLS FALSE) +- + itk_module_impl() + +-install(FILES ${ITKOpenJPEG_SOURCE_DIR}/src/itk_openjpeg.h ++install(FILES ${ITKOpenJPEG_BINARY_DIR}/src/itk_openjpeg.h + DESTINATION ${ITKOpenJPEG_INSTALL_INCLUDE_DIR} + COMPONENT Development + ) +diff --git a/Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h b/Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h.in +rename from Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h +rename to Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h.in +--- a/Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h ++++ b/Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h.in +@@ -25,6 +25,12 @@ + #ifndef itk_openjpeg_h + #define itk_openjpeg_h + +-#include <itkopenjpeg/openjpeg.h> ++/* Use the openjpeg library configured for ITK. */ ++#cmakedefine ITK_USE_SYSTEM_OPENJPEG ++#ifdef ITK_USE_SYSTEM_OPENJPEG ++# include <openjpeg.h> ++#else ++# include <itkopenjpeg/openjpeg.h> ++#endif + + #endif +--- a/Modules/IO/JPEG2000/src/itkJPEG2000ImageIO.cxx ++++ b/Modules/IO/JPEG2000/src/itkJPEG2000ImageIO.cxx +@@ -27,8 +27,6 @@ + extern "C" + { + #include "openjpeg.h" +-#include "j2k.h" +-#include "jp2.h" + } + + +@@ -139,11 +137,11 @@ + { + itkDebugMacro(<< "ReadImageInformation()"); + +- FILE * l_file = fopen(this->m_FileName.c_str(), "rb"); +- +- /* decompression parameters */ ++ /* set decoding parameters to default values */ ++ opj_set_default_decoder_parameters(&(this->m_Internal->m_DecompressionParameters)); + +- if (!l_file) ++ opj_stream_t * cio = opj_stream_create_default_file_stream(this->m_FileName.c_str(), true); ++ if (!cio) + { + itkExceptionMacro("JPEG2000ImageIO failed to open file for reading: " << this->GetFileName() << std::endl + << "Reason: " +@@ -151,10 +149,5 @@ + } + +- /* set decoding parameters to default values */ +- opj_set_default_decoder_parameters(&(this->m_Internal->m_DecompressionParameters)); +- +- opj_stream_t * cio = opj_stream_create_default_file_stream(l_file, true); +- + this->m_Internal->m_Dinfo = nullptr; /* handle to a decompressor */ + + opj_image_t * l_image = nullptr; +@@ -188,9 +181,8 @@ + + /* get a decoder handle */ +- this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_J2K); ++ this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_J2K); + if (!this->m_Internal->m_Dinfo) + { + opj_stream_destroy(cio); +- fclose(l_file); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " + << this->GetFileName() << std::endl +@@ -202,10 +194,9 @@ + { + /* JPEG 2000 compressed image data */ + /* get a decoder handle */ +- this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_JP2); ++ this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_JP2); + if (!this->m_Internal->m_Dinfo) + { + opj_stream_destroy(cio); +- fclose(l_file); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " + << this->GetFileName() << std::endl +@@ -217,10 +208,9 @@ + { + /* JPEG 2000, JPIP */ + /* get a decoder handle */ +- this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_JPT); ++ this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_JPT); + if (!this->m_Internal->m_Dinfo) + { + opj_stream_destroy(cio); +- fclose(l_file); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " + << this->GetFileName() << std::endl +@@ -230,7 +220,6 @@ + } + default: + opj_stream_destroy(cio); +- fclose(l_file); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " + << this->GetFileName() << std::endl + << "Reason: " +@@ -248,26 +237,8 @@ + } + +- // Image parameters - first tile +- OPJ_INT32 l_tile_x0; +- OPJ_INT32 l_tile_y0; +- +- // Image parameters - tile width, height and number of tiles +- OPJ_UINT32 l_tile_width; +- OPJ_UINT32 l_tile_height; +- OPJ_UINT32 l_nb_tiles_x; +- OPJ_UINT32 l_nb_tiles_y; +- + itkDebugMacro(<< "Trying to read header now..."); + +- bResult = opj_read_header(this->m_Internal->m_Dinfo, +- &l_image, +- &l_tile_x0, +- &l_tile_y0, +- &l_tile_width, +- &l_tile_height, +- &l_nb_tiles_x, +- &l_nb_tiles_y, +- cio); ++ bResult = opj_read_header(cio, this->m_Internal->m_Dinfo, &l_image); + + if (!bResult) + { +@@ -284,13 +255,21 @@ + } + +- this->m_Internal->m_TileStartX = l_tile_x0; +- this->m_Internal->m_TileStartY = l_tile_y0; ++ opj_codestream_info_v2_t* cp = opj_get_cstr_info(this->m_Internal->m_Dinfo); ++ if (!cp) ++ { ++ opj_stream_destroy(cio); ++ opj_image_destroy(l_image); ++ itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl ++ << "Reason: Error while reading image header"); ++ } ++ this->m_Internal->m_TileStartX = cp->tx0; ++ this->m_Internal->m_TileStartY = cp->ty0; + +- this->m_Internal->m_TileWidth = l_tile_width; +- this->m_Internal->m_TileHeight = l_tile_height; ++ this->m_Internal->m_TileWidth = cp->tdx; ++ this->m_Internal->m_TileHeight = cp->tdy; + +- this->m_Internal->m_NumberOfTilesInX = l_nb_tiles_x; +- this->m_Internal->m_NumberOfTilesInY = l_nb_tiles_y; ++ this->m_Internal->m_NumberOfTilesInX = cp->tw; ++ this->m_Internal->m_NumberOfTilesInY = cp->th; + + + itkDebugMacro(<< "Number of Components = " << l_image->numcomps); +@@ -307,6 +286,7 @@ + else + { + opj_stream_destroy(cio); ++ opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl + << "Reason: " + << "Unknown precision in file: " +@@ -320,6 +300,6 @@ + break; + case 3: +- if (l_image->color_space != CLRSPC_SRGB) ++ if (l_image->color_space != OPJ_CLRSPC_SRGB) + { + itkWarningMacro(<< "file does not specify color space, assuming sRGB"); + } +@@ -349,7 +329,6 @@ + + /* close the byte stream */ + opj_stream_destroy(cio); +- fclose(l_file); + + if (this->m_Internal->m_Dinfo) + { +@@ -368,16 +347,7 @@ + { + itkDebugMacro(<< "JPEG2000ImageIO::Read() Begin"); + +- FILE * l_file = fopen(this->m_FileName.c_str(), "rb"); +- +- if (!l_file) +- { +- itkExceptionMacro("JPEG2000ImageIO failed to open file for reading: " << this->GetFileName() << std::endl +- << "Reason: " +- << itksys::SystemTools::GetLastSystemError()); +- } +- +- opj_stream_t * l_stream = opj_stream_create_default_file_stream(l_file, true); ++ opj_stream_t * l_stream = opj_stream_create_default_file_stream(this->m_FileName.c_str(), true); + if (!l_stream) + { + itkExceptionMacro("JPEG2000ImageIO failed to read file: " +@@ -397,9 +367,10 @@ + { + /* JPEG-2000 codestream */ + /* get a decoder handle */ +- this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_J2K); ++ this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_J2K); + if (!this->m_Internal->m_Dinfo) + { ++ opj_stream_destroy(l_stream); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " + << this->GetFileName() << std::endl + << "Reason: opj_create_decompress(CODEC_J2K) returns nullptr"); +@@ -410,9 +381,10 @@ + { + /* JPEG 2000 compressed image data */ + /* get a decoder handle */ +- this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_JP2); ++ this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_JP2); + if (!this->m_Internal->m_Dinfo) + { ++ opj_stream_destroy(l_stream); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " + << this->GetFileName() << std::endl + << "Reason: opj_create_decompress(CODEC_JP2) returns nullptr"); +@@ -423,9 +395,10 @@ + { + /* JPEG 2000, JPIP */ + /* get a decoder handle */ +- this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_JPT); ++ this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_JPT); + if (!this->m_Internal->m_Dinfo) + { ++ opj_stream_destroy(l_stream); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " + << this->GetFileName() << std::endl + << "Reason: opj_create_decompress(CODEC_JPT) returns nullptr"); +@@ -433,7 +406,7 @@ + break; + } + default: +- fclose(l_file); ++ opj_stream_destroy(l_stream); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " + << this->GetFileName() << std::endl + << "Reason: " +@@ -445,32 +418,17 @@ + if (!opj_setup_decoder(this->m_Internal->m_Dinfo, &(this->m_Internal->m_DecompressionParameters))) + { ++ opj_stream_destroy(l_stream); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl + << "Reason: opj_setup_decoder returns false"); + } + +- OPJ_INT32 l_tile_x0, l_tile_y0; +- +- OPJ_UINT32 l_tile_width; +- OPJ_UINT32 l_tile_height; +- OPJ_UINT32 l_nb_tiles_x; +- OPJ_UINT32 l_nb_tiles_y; +- +- bool bResult = opj_read_header(this->m_Internal->m_Dinfo, +- &l_image, +- &l_tile_x0, +- &l_tile_y0, +- &l_tile_width, +- &l_tile_height, +- &l_nb_tiles_x, +- &l_nb_tiles_y, +- l_stream); ++ bool bResult = opj_read_header(l_stream, this->m_Internal->m_Dinfo, &l_image); + + if (!bResult) + { + opj_destroy_codec(this->m_Internal->m_Dinfo); + this->m_Internal->m_Dinfo = nullptr; + opj_stream_destroy(l_stream); +- fclose(l_file); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl + << "Reason: opj_read_header returns false"); + } +@@ -499,7 +457,7 @@ + itkDebugMacro(<< "p_end_x = " << p_end_x); + itkDebugMacro(<< "p_end_y = " << p_end_y); + +- bResult = opj_set_decode_area(this->m_Internal->m_Dinfo, p_start_x, p_start_y, p_end_x, p_end_y); ++ bResult = opj_set_decode_area(this->m_Internal->m_Dinfo, l_image, p_start_x, p_start_y, p_end_x, p_end_y); + + itkDebugMacro(<< "opj_set_decode_area() after"); + +@@ -509,6 +467,5 @@ + this->m_Internal->m_Dinfo = nullptr; + opj_stream_destroy(l_stream); +- fclose(l_file); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl + << "Reason: opj_set_decode_area returns false"); + } +@@ -525,13 +482,14 @@ + + OPJ_UINT32 l_max_data_size = 1000; + +- bool l_go_on = true; ++ OPJ_BOOL l_go_on = true; + + auto * l_data = (OPJ_BYTE *)malloc(1000); + + while (l_go_on) + { + bool tileHeaderRead = opj_read_tile_header(this->m_Internal->m_Dinfo, ++ l_stream, + &l_tile_index, + &l_data_size, + &l_current_tile_x0, +@@ -540,13 +498,11 @@ + &l_current_tile_y1, + &l_nb_comps, +- &l_go_on, +- l_stream); ++ &l_go_on); + + if (!tileHeaderRead) + { + free(l_data); + opj_stream_destroy(l_stream); +- fclose(l_file); + opj_destroy_codec(this->m_Internal->m_Dinfo); + opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl +@@ -571,7 +527,6 @@ + if (!l_data) + { + opj_stream_destroy(l_stream); +- fclose(l_file); + opj_destroy_codec(this->m_Internal->m_Dinfo); + opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl +@@ -590,7 +545,6 @@ + { + free(l_data); + opj_stream_destroy(l_stream); +- fclose(l_file); + opj_destroy_codec(this->m_Internal->m_Dinfo); + opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl +@@ -654,7 +608,6 @@ + { + free(l_data); + opj_stream_destroy(l_stream); +- fclose(l_file); + opj_destroy_codec(this->m_Internal->m_Dinfo); + opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl +@@ -667,13 +620,11 @@ + this->m_Internal->m_Dinfo = nullptr; + opj_stream_destroy(l_stream); +- fclose(l_file); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl + << "Reason: error whle reading image"); + } + + /* close the byte stream */ + opj_stream_destroy(l_stream); +- fclose(l_file); + + if (this->m_Internal->m_Dinfo) + { +@@ -775,6 +726,6 @@ + } + +- for (int i = 0; i < parameters.numpocs; i++) ++ for (OPJ_UINT32 i = 0; i < parameters.numpocs; i++) + { + if (parameters.POC[i].prg == -1) + { +@@ -840,13 +791,13 @@ + + parameters.numresolution = numberOfResolutions; + +- OPJ_COLOR_SPACE color_space = CLRSPC_GRAY; ++ OPJ_COLOR_SPACE color_space = OPJ_CLRSPC_GRAY; + opj_image_cmptparm_t cmptparms[3]; + + if (this->GetNumberOfComponents() == 3) + { + +- color_space = (this->GetPixelType() == IOPixelEnum::RGB) ? CLRSPC_SRGB : CLRSPC_UNSPECIFIED; ++ color_space = (this->GetPixelType() == IOPixelEnum::RGB) ? OPJ_CLRSPC_SRGB : OPJ_CLRSPC_UNSPECIFIED; + + /* initialize image components */ + memset(&cmptparms[0], 0, 3 * sizeof(opj_image_cmptparm_t)); +@@ -864,7 +815,7 @@ + + if (this->GetNumberOfComponents() == 1) + { +- color_space = CLRSPC_GRAY; ++ color_space = OPJ_CLRSPC_GRAY; + + /* initialize image components */ + memset(&cmptparms[0], 0, sizeof(opj_image_cmptparm_t)); +@@ -941,8 +892,9 @@ + if (extension == ".j2k") + { +- cinfo = opj_create_compress(CODEC_J2K); ++ cinfo = opj_create_compress(OPJ_CODEC_J2K); + if (!cinfo) + { ++ opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to write file: " + << this->GetFileName() << std::endl + << "Reason: opj_create_compress(CODEC_J2K) returns nullptr"); +@@ -950,9 +902,10 @@ + } + else if (extension == ".jp2") + { +- cinfo = opj_create_compress(CODEC_JP2); ++ cinfo = opj_create_compress(OPJ_CODEC_JP2); + if (!cinfo) + { ++ opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to write file: " + << this->GetFileName() << std::endl + << "Reason: opj_create_compress(CODEC_JP2) returns nullptr"); +@@ -960,9 +913,10 @@ + } + else if (extension == ".jpt") + { +- cinfo = opj_create_compress(CODEC_JPT); ++ cinfo = opj_create_compress(OPJ_CODEC_JPT); + if (!cinfo) + { ++ opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to write file: " + << this->GetFileName() << std::endl + << "Reason: opj_create_compress(CODEC_JPT) returns nullptr"); +@@ -970,6 +924,7 @@ + } + else + { ++ opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to write file: " << this->GetFileName() << std::endl + << "Reason: unknown encode format: " << extension); + } +@@ -985,23 +940,19 @@ + + if (!opj_setup_encoder(cinfo, ¶meters, l_image)) + { ++ opj_destroy_codec(cinfo); ++ opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to write file: " << this->GetFileName() << std::endl + << "Reason: opj_setup_encoder returns false"); + } + +- FILE * l_file = fopen(parameters.outfile, "wb"); +- if (!l_file) +- { +- itkExceptionMacro("JPEG2000ImageIO failed to open file for writing: " << this->GetFileName() << std::endl +- << "Reason: " +- << itksys::SystemTools::GetLastSystemError()); +- } +- + /* open a byte stream for writing */ + /* allocate memory for all tiles */ +- opj_stream_t * cio = opj_stream_create_default_file_stream(l_file, false); ++ opj_stream_t * cio = opj_stream_create_default_file_stream(parameters.outfile, false); + if (!cio) + { ++ opj_destroy_codec(cinfo); ++ opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to write file: " + << this->GetFileName() << std::endl + << "Reason: " +@@ -1017,7 +968,8 @@ + if (!bSuccess) + { + opj_stream_destroy(cio); +- fclose(l_file); ++ opj_destroy_codec(cinfo); ++ opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to write file: " << this->GetFileName() << std::endl + << "Reason: opj_start_compress returns false"); + } +@@ -1026,7 +978,8 @@ + if (!bSuccess) + { + opj_stream_destroy(cio); +- fclose(l_file); ++ opj_destroy_codec(cinfo); ++ opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to write file: " << this->GetFileName() << std::endl + << "Reason: opj_encode returns false"); + } +@@ -1035,14 +988,14 @@ + if (!bSuccess) + { + opj_stream_destroy(cio); +- fclose(l_file); ++ opj_destroy_codec(cinfo); ++ opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to write file: " << this->GetFileName() << std::endl + << "Reason: opj_end_compress returns false"); + } + + /* close and free the byte stream */ + opj_stream_destroy(cio); +- fclose(l_file); + + /* free remaining compression structures */ + opj_destroy_codec(cinfo); +--- a/Modules/Nonunit/Review/src/CMakeLists.txt ++++ b/Modules/Nonunit/Review/src/CMakeLists.txt +@@ -5,7 +5,7 @@ + + add_library(ITKReview ${ITKReview_SRC}) + itk_module_link_dependencies() +-target_link_libraries(ITKReview LINK_PUBLIC ${ITKTestKernel_LIBRARIES} ${ITKIOLSM_LIBRARIES} itkopenjpeg) ++target_link_libraries(ITKReview LINK_PUBLIC ${ITKTestKernel_LIBRARIES} ${ITKIOLSM_LIBRARIES} ${ITKOpenJPEG_LIBRARIES}) + itk_module_target(ITKReview) + + diff --git a/sci-libs/itk/files/itk-5.2.1-system-tiff-has-64.patch b/sci-libs/itk/files/itk-5.2.1-system-tiff-has-64.patch new file mode 100644 index 000000000..25c44db2c --- /dev/null +++ b/sci-libs/itk/files/itk-5.2.1-system-tiff-has-64.patch @@ -0,0 +1,18 @@ +From: François-Xavier Carton <fx.carton91@gmail.com> +Date: Wed, 8 Jun 2022 19:36:48 +0200 +Subject: [PATCH] system libtiff has INT64 + +Enabling this, otherwise using system libtiff leads to errors. In particular +tests fail because there is some IFD8 data but the itkTIFFDataSize function +returns 0 instead of 8, resulting in invalid mem access. + +--- a/Modules/ThirdParty/TIFF/src/itk_tiff.h.in.orig 2022-06-08 19:34:04.412431969 +0200 ++++ b/Modules/ThirdParty/TIFF/src/itk_tiff.h.in 2022-06-08 19:34:26.240431631 +0200 +@@ -34,6 +34,7 @@ + #cmakedefine ITK_TIFF_HAS_TIFFFieldReadCount + #cmakedefine ITK_TIFF_HAS_TIFFField + #ifdef ITK_USE_SYSTEM_TIFF ++# define TIFF_INT64_T int64_t + # include <tiffio.h> + #else + # include "itktiff/tiffio.h" diff --git a/sci-libs/itk/files/itk-5.2.1-upstream-fixes.patch b/sci-libs/itk/files/itk-5.2.1-upstream-fixes.patch new file mode 100644 index 000000000..2af8c4998 --- /dev/null +++ b/sci-libs/itk/files/itk-5.2.1-upstream-fixes.patch @@ -0,0 +1,309 @@ +https://github.com/InsightSoftwareConsortium/ITK/commit/2a7f5ed199926999b67f61a97c2c9a2595a11558.patch +https://github.com/InsightSoftwareConsortium/ITK/commit/0c31aa688e82a34e5430873bc6176740fd09ad75.patch +https://github.com/InsightSoftwareConsortium/ITK/commit/28325d921a9b8793e6aaefd612f53989f951d19c.patch +https://github.com/InsightSoftwareConsortium/ITK/commit/aafd1f9631d0fad60e1b6f53e049e95a50c48bd1.patch + +From 2a7f5ed199926999b67f61a97c2c9a2595a11558 Mon Sep 17 00:00:00 2001 +From: Niels Dekker <N.Dekker@lumc.nl> +Date: Thu, 24 Jun 2021 18:00:01 +0200 +Subject: [PATCH] COMP: Add missing `#include <iostream>` to Deprecated module + test + +Fixed a Visual C++ 2019 error, saying: + +> Deprecated\test\itkSimpleFastMutexLockTest.cxx(48,12): error C2039: 'cout': is not a member of 'std' +--- + .../Deprecated/test/itkSimpleFastMutexLockTest.cxx | 2 ++ + 1 file changed, 2 insertions(+) + +diff --git a/Modules/Compatibility/Deprecated/test/itkSimpleFastMutexLockTest.cxx b/Modules/Compatibility/Deprecated/test/itkSimpleFastMutexLockTest.cxx +index 11ad0c52700..60aa1c065b4 100644 +--- a/Modules/Compatibility/Deprecated/test/itkSimpleFastMutexLockTest.cxx ++++ b/Modules/Compatibility/Deprecated/test/itkSimpleFastMutexLockTest.cxx +@@ -19,6 +19,8 @@ + + #include "itkSimpleFastMutexLock.h" + ++#include <iostream> // For cout. ++ + + int + itkSimpleFastMutexLockTest(int, char *[]) +From 0c31aa688e82a34e5430873bc6176740fd09ad75 Mon Sep 17 00:00:00 2001 +From: Pablo Hernandez-Cerdan <pablo.hernandez.cerdan@outlook.com> +Date: Tue, 20 Apr 2021 17:21:21 +0200 +Subject: [PATCH] COMP: CastXML, ITKVtkGlue, include only when property exists + +Some targets (VTK libraries) didn't have the property INTERFACE_INCLUDE_DIRECTORIES + +```bash +CMake Error in Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt: + Found relative path while evaluating include directories of + "ITKVtkGluePython": + + "_vtk_lib_include_dirs-NOTFOUND" +``` + +Triggered when compiling Slicer with `Slicer_BUILD_ITKPython:BOOL=ON` +aka `ITK_WRAP_PYTHON:BOOL=ON`. + +Full error log with extra printing: + +```bash + +CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:3 (message): + ITKVtkGlue_VTK_LIBRARIES: + VTK::IOImage;VTK::ImagingSources;VTK::WrappingPythonCore;VTK::CommonCore;VTK::CommonDataModel;VTK::kwiml;VTK::CommonExecutionModel;VTK::RenderingOpenGL2;VTK::RenderingFreeType;VTK::InteractionStyle;VTK::InteractionWidgets + +CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message): + _vtk_lib_include_dirs: _vtk_lib_include_dirs-NOTFOUND + +CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message): + _vtk_lib_include_dirs: _vtk_lib_include_dirs-NOTFOUND + +CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message): + _vtk_lib_include_dirs: + build/VTK-build/Wrapping/PythonCore;build/VTK/Wrapping/PythonCore + +CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message): + _vtk_lib_include_dirs: _vtk_lib_include_dirs-NOTFOUND + +CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message): + _vtk_lib_include_dirs: _vtk_lib_include_dirs-NOTFOUND + +CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message): + _vtk_lib_include_dirs: + build/VTK-build/Utilities/KWIML;build/VTK/Utilities/KWIML + +CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message): + _vtk_lib_include_dirs: _vtk_lib_include_dirs-NOTFOUND + +CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message): + _vtk_lib_include_dirs: _vtk_lib_include_dirs-NOTFOUND + +CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message): + _vtk_lib_include_dirs: _vtk_lib_include_dirs-NOTFOUND + +CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message): + _vtk_lib_include_dirs: _vtk_lib_include_dirs-NOTFOUND + +CMake Warning at Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt:6 (message): + _vtk_lib_include_dirs: _vtk_lib_include_dirs-NOTFOUND + +-- ITKVtkGlue: Creating module. +-- ITKVtkGlue: Creating itkImageToVTKImageFilter submodule. +-- ITKVtkGlue: Creating itkVTKImageToImageFilter submodule. +-- ITKVtkGlue: Creating itkViewImage submodule. +-- MGHIO: Creating module. +-- MGHIO: Creating itkMGHImageIO submodule. +-- MorphologicalContourInterpolation: Creating module. +-- MorphologicalContourInterpolation: Creating itkMorphologicalContourInterpolator submodule. +-- ITKPyUtils: Creating module. +-- ITKPyUtils: Creating itkPyCommand submodule. +-- ITKPyUtils: Creating itkPyImageFilter submodule. +-- Configuring done +CMake Error: The following variables are used in this project, but they are set to NOTFOUND. +Please set them or make sure they are set and tested correctly in the CMake files: +_vtk_lib_include_dirs + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + used as include directory in directory build/ITK/Modules/Bridge/VtkGlue/wrapping + +CMake Error in Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt: + Found relative path while evaluating include directories of + "ITKVtkGluePython": + + "_vtk_lib_include_dirs-NOTFOUND" + +``` +--- + Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt | 4 +++- + 1 file changed, 3 insertions(+), 1 deletion(-) + +diff --git a/Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt b/Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt +index 3f3322957e1..2fd6a5af8f6 100644 +--- a/Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt ++++ b/Modules/Bridge/VtkGlue/wrapping/CMakeLists.txt +@@ -2,7 +2,9 @@ + if(NOT VTK_RENDERING_BACKEND STREQUAL "None") + foreach(_vtk_lib IN LISTS ITKVtkGlue_VTK_LIBRARIES) + get_target_property(_vtk_lib_include_dirs ${_vtk_lib} INTERFACE_INCLUDE_DIRECTORIES) +- include_directories(${_vtk_lib_include_dirs}) ++ if(_vtk_lib_include_dirs) ++ include_directories(${_vtk_lib_include_dirs}) ++ endif() + endforeach() + endif() + +From 28325d921a9b8793e6aaefd612f53989f951d19c Mon Sep 17 00:00:00 2001 +From: Butui Hu <hot123tea123@gmail.com> +Date: Mon, 1 Aug 2022 14:26:39 +0800 +Subject: [PATCH] COMP: use sysconfig.get_path as PEP 632 deprecate distutils + module + +--- + Wrapping/Generators/Python/CMakeLists.txt | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/Wrapping/Generators/Python/CMakeLists.txt b/Wrapping/Generators/Python/CMakeLists.txt +index fca3d999b87..3b7a1d37334 100644 +--- a/Wrapping/Generators/Python/CMakeLists.txt ++++ b/Wrapping/Generators/Python/CMakeLists.txt +@@ -36,7 +36,7 @@ file(MAKE_DIRECTORY ${WRAPPER_MASTER_INDEX_OUTPUT_DIR}/python) + ############################################################################### + # Configure Python wrapping installation + if(Python3_EXECUTABLE AND NOT PY_SITE_PACKAGES_PATH) +- set(python_check "try:\n import distutils.sysconfig\n print(distutils.sysconfig.get_python_lib(plat_specific=1, prefix=''))\nexcept:\n pass") ++ set(python_check "try:\n import sysconfig\n print(sysconfig.get_path('platlib'))\nexcept:\n pass") + file(WRITE ${CMAKE_CURRENT_BINARY_DIR}/detect_site_package_path.py ${python_check}) + execute_process(COMMAND "${Python3_EXECUTABLE}" "${CMAKE_CURRENT_BINARY_DIR}/detect_site_package_path.py" + OUTPUT_VARIABLE py_spp +From aafd1f9631d0fad60e1b6f53e049e95a50c48bd1 Mon Sep 17 00:00:00 2001 +From: Hans Johnson <hans-johnson@uiowa.edu> +Date: Wed, 15 Dec 2021 08:10:58 -0600 +Subject: [PATCH] COMP: Remove inclusion of .hxx files as headers + +The ability to include either .h or .hxx files as +header files required recursively reading the +.h files twice. The added complexity is +unnecessary, costly, and can confuse static +analysis tools that monitor header guardes (due +to reaching the maximum depth of recursion +limits for nested #ifdefs in checking). + +Co-authored-by: Simon Rit <simon.rit@creatis.insa-lyon.fr> +--- + CMake/ITKModuleHeaderTest.cmake | 3 +-- + Utilities/Maintenance/BuildHeaderTest.py | 4 ---- + 2 files changed, 1 insertion(+), 6 deletions(-) + +diff --git a/CMake/ITKModuleHeaderTest.cmake b/CMake/ITKModuleHeaderTest.cmake +index eb809d7e93d..82ad192a6f8 100644 +--- a/CMake/ITKModuleHeaderTest.cmake ++++ b/CMake/ITKModuleHeaderTest.cmake +@@ -36,8 +36,7 @@ macro( itk_module_headertest _name ) + # effected. + set( _include ${${_name}_SOURCE_DIR}/include ) + file( GLOB _h_files ${_include}/*.h ) +- file( GLOB _hxx_files ${_include}/*.hxx ) +- set( _header_files ${_h_files} ${_hxx_files} ) ++ set( _header_files ${_h_files} ) + list( LENGTH _h_files _num_headers ) + set( _outputs ${${_name}_BINARY_DIR}/test/${_name}HeaderTest1.cxx ) + set( _test_num 1 ) +diff --git a/Utilities/Maintenance/BuildHeaderTest.py b/Utilities/Maintenance/BuildHeaderTest.py +index 26a4b6ccb3f..f8ed9f7901e 100755 +--- a/Utilities/Maintenance/BuildHeaderTest.py ++++ b/Utilities/Maintenance/BuildHeaderTest.py +@@ -130,15 +130,11 @@ def main(): + else: + max_idx = added_header_idx + maximum_number_of_headers + for i in range(added_header_idx, max_idx): +- # Use the .hxx if possible. +- hxx_file = h_files[i][:-1] + "hxx" + # Files that include VTK headers need to link to VTK. + if h_files[i] in BANNED_HEADERS or h_files[i].lower().find("vtk") != -1: + to_include = ( + '// #include "' + h_files[i] + '" // Banned in BuildHeaderTest.py\n' + ) +- elif os.path.exists(os.path.join(module_source_path, "include", hxx_file)): +- to_include = '#include "' + hxx_file + '"\n' + else: + to_include = '#include "' + h_files[i] + '"\n' + diff --git a/sci-libs/itk/files/itk-5.3.0-system-openjpeg.patch b/sci-libs/itk/files/itk-5.3.0-system-openjpeg.patch new file mode 100644 index 000000000..27f139553 --- /dev/null +++ b/sci-libs/itk/files/itk-5.3.0-system-openjpeg.patch @@ -0,0 +1,550 @@ +--- a/Modules/ThirdParty/OpenJPEG/CMakeLists.txt ++++ b/Modules/ThirdParty/OpenJPEG/CMakeLists.txt +@@ -1,16 +1,32 @@ + project(ITKOpenJPEG) + set(ITKOpenJPEG_THIRD_PARTY 1) + +-set(ITKOpenJPEG_INCLUDE_DIRS +- ${ITKOpenJPEG_BINARY_DIR}/src/openjpeg +- ${ITKOpenJPEG_SOURCE_DIR}/src/openjpeg +- ) +-set(ITKOpenJPEG_LIBRARIES itkopenjpeg) ++option(ITK_USE_SYSTEM_OPENJPEG "Use system-installed openjpeg" ${ITK_USE_SYSTEM_LIBRARIES}) ++mark_as_advanced(ITK_USE_SYSTEM_OPENJPEG) ++ ++if(ITK_USE_SYSTEM_OPENJPEG) ++ find_package(OpenJPEG REQUIRED) ++ set(ITKOpenJPEG_INCLUDE_DIRS ++ ${ITKOpenJPEG_BINARY_DIR}/src ++ ) ++ set(ITKOpenJPEG_SYSTEM_INCLUDE_DIRS ++ ${OPENJPEG_INCLUDE_DIRS} ++ ) ++ set(ITKOpenJPEG_LIBRARIES "${OPENJPEG_LIBRARIES}") ++ set(ITKOpenJPEG_NO_SRC 1) ++else() ++ set(ITKOpenJPEG_INCLUDE_DIRS ++ ${ITKOpenJPEG_BINARY_DIR}/src/openjpeg ++ ${ITKOpenJPEG_SOURCE_DIR}/src/openjpeg ++ ) ++ set(ITKOpenJPEG_LIBRARIES itkopenjpeg) ++endif() ++ ++configure_file(src/itk_openjpeg.h.in src/itk_openjpeg.h) + set(ITK_LIBRARY_PROPERTIES WINDOWS_EXPORT_ALL_SYMBOLS FALSE) +- + itk_module_impl() + +-install(FILES ${ITKOpenJPEG_SOURCE_DIR}/src/itk_openjpeg.h ++install(FILES ${ITKOpenJPEG_BINARY_DIR}/src/itk_openjpeg.h + DESTINATION ${ITKOpenJPEG_INSTALL_INCLUDE_DIR} + COMPONENT Development + ) +diff --git a/Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h b/Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h.in +rename from Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h +rename to Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h.in +--- a/Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h ++++ b/Modules/ThirdParty/OpenJPEG/src/itk_openjpeg.h.in +@@ -25,6 +25,12 @@ + #ifndef itk_openjpeg_h + #define itk_openjpeg_h + +-#include <itkopenjpeg/openjpeg.h> ++/* Use the openjpeg library configured for ITK. */ ++#cmakedefine ITK_USE_SYSTEM_OPENJPEG ++#ifdef ITK_USE_SYSTEM_OPENJPEG ++# include <openjpeg.h> ++#else ++# include <itkopenjpeg/openjpeg.h> ++#endif + + #endif +--- a/Modules/IO/JPEG2000/src/itkJPEG2000ImageIO.cxx ++++ b/Modules/IO/JPEG2000/src/itkJPEG2000ImageIO.cxx +@@ -27,8 +27,6 @@ + extern "C" + { + #include "openjpeg.h" +-#include "j2k.h" +-#include "jp2.h" + } + + +@@ -139,11 +137,11 @@ + { + itkDebugMacro(<< "ReadImageInformation()"); + +- FILE * l_file = fopen(this->m_FileName.c_str(), "rb"); +- +- /* decompression parameters */ ++ /* set decoding parameters to default values */ ++ opj_set_default_decoder_parameters(&(this->m_Internal->m_DecompressionParameters)); + +- if (!l_file) ++ opj_stream_t * cio = opj_stream_create_default_file_stream(this->m_FileName.c_str(), true); ++ if (!cio) + { + itkExceptionMacro("JPEG2000ImageIO failed to open file for reading: " << this->GetFileName() << std::endl + << "Reason: " +@@ -151,10 +149,5 @@ + } + +- /* set decoding parameters to default values */ +- opj_set_default_decoder_parameters(&(this->m_Internal->m_DecompressionParameters)); +- +- opj_stream_t * cio = opj_stream_create_default_file_stream(l_file, true); +- + this->m_Internal->m_Dinfo = nullptr; /* handle to a decompressor */ + + opj_image_t * l_image = nullptr; +@@ -188,9 +181,8 @@ + + /* get a decoder handle */ +- this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_J2K); ++ this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_J2K); + if (!this->m_Internal->m_Dinfo) + { + opj_stream_destroy(cio); +- fclose(l_file); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " + << this->GetFileName() << std::endl +@@ -202,10 +194,9 @@ + { + /* JPEG 2000 compressed image data */ + /* get a decoder handle */ +- this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_JP2); ++ this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_JP2); + if (!this->m_Internal->m_Dinfo) + { + opj_stream_destroy(cio); +- fclose(l_file); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " + << this->GetFileName() << std::endl +@@ -217,10 +208,9 @@ + { + /* JPEG 2000, JPIP */ + /* get a decoder handle */ +- this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_JPT); ++ this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_JPT); + if (!this->m_Internal->m_Dinfo) + { + opj_stream_destroy(cio); +- fclose(l_file); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " + << this->GetFileName() << std::endl +@@ -230,7 +220,6 @@ + } + default: + opj_stream_destroy(cio); +- fclose(l_file); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " + << this->GetFileName() << std::endl + << "Reason: " +@@ -248,26 +237,8 @@ + } + +- // Image parameters - first tile +- OPJ_INT32 l_tile_x0; +- OPJ_INT32 l_tile_y0; +- +- // Image parameters - tile width, height and number of tiles +- OPJ_UINT32 l_tile_width; +- OPJ_UINT32 l_tile_height; +- OPJ_UINT32 l_nb_tiles_x; +- OPJ_UINT32 l_nb_tiles_y; +- + itkDebugMacro(<< "Trying to read header now..."); + +- bResult = opj_read_header(this->m_Internal->m_Dinfo, +- &l_image, +- &l_tile_x0, +- &l_tile_y0, +- &l_tile_width, +- &l_tile_height, +- &l_nb_tiles_x, +- &l_nb_tiles_y, +- cio); ++ bResult = opj_read_header(cio, this->m_Internal->m_Dinfo, &l_image); + + if (!bResult) + { +@@ -284,13 +255,21 @@ + } + +- this->m_Internal->m_TileStartX = l_tile_x0; +- this->m_Internal->m_TileStartY = l_tile_y0; ++ opj_codestream_info_v2_t* cp = opj_get_cstr_info(this->m_Internal->m_Dinfo); ++ if (!cp) ++ { ++ opj_stream_destroy(cio); ++ opj_image_destroy(l_image); ++ itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl ++ << "Reason: Error while reading image header"); ++ } ++ this->m_Internal->m_TileStartX = cp->tx0; ++ this->m_Internal->m_TileStartY = cp->ty0; + +- this->m_Internal->m_TileWidth = l_tile_width; +- this->m_Internal->m_TileHeight = l_tile_height; ++ this->m_Internal->m_TileWidth = cp->tdx; ++ this->m_Internal->m_TileHeight = cp->tdy; + +- this->m_Internal->m_NumberOfTilesInX = l_nb_tiles_x; +- this->m_Internal->m_NumberOfTilesInY = l_nb_tiles_y; ++ this->m_Internal->m_NumberOfTilesInX = cp->tw; ++ this->m_Internal->m_NumberOfTilesInY = cp->th; + + + itkDebugMacro(<< "Number of Components = " << l_image->numcomps); +@@ -307,6 +286,7 @@ + else + { + opj_stream_destroy(cio); ++ opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl + << "Reason: " + << "Unknown precision in file: " +@@ -320,6 +300,6 @@ + break; + case 3: +- if (l_image->color_space != CLRSPC_SRGB) ++ if (l_image->color_space != OPJ_CLRSPC_SRGB) + { + itkWarningMacro(<< "file does not specify color space, assuming sRGB"); + } +@@ -349,7 +329,6 @@ + + /* close the byte stream */ + opj_stream_destroy(cio); +- fclose(l_file); + + if (this->m_Internal->m_Dinfo) + { +@@ -368,16 +347,7 @@ + { + itkDebugMacro(<< "JPEG2000ImageIO::Read() Begin"); + +- FILE * l_file = fopen(this->m_FileName.c_str(), "rb"); +- +- if (!l_file) +- { +- itkExceptionMacro("JPEG2000ImageIO failed to open file for reading: " << this->GetFileName() << std::endl +- << "Reason: " +- << itksys::SystemTools::GetLastSystemError()); +- } +- +- opj_stream_t * l_stream = opj_stream_create_default_file_stream(l_file, true); ++ opj_stream_t * l_stream = opj_stream_create_default_file_stream(this->m_FileName.c_str(), true); + if (!l_stream) + { + itkExceptionMacro("JPEG2000ImageIO failed to read file: " +@@ -397,9 +367,10 @@ + { + /* JPEG-2000 codestream */ + /* get a decoder handle */ +- this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_J2K); ++ this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_J2K); + if (!this->m_Internal->m_Dinfo) + { ++ opj_stream_destroy(l_stream); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " + << this->GetFileName() << std::endl + << "Reason: opj_create_decompress(CODEC_J2K) returns nullptr"); +@@ -410,9 +381,10 @@ + { + /* JPEG 2000 compressed image data */ + /* get a decoder handle */ +- this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_JP2); ++ this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_JP2); + if (!this->m_Internal->m_Dinfo) + { ++ opj_stream_destroy(l_stream); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " + << this->GetFileName() << std::endl + << "Reason: opj_create_decompress(CODEC_JP2) returns nullptr"); +@@ -423,9 +395,10 @@ + { + /* JPEG 2000, JPIP */ + /* get a decoder handle */ +- this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_JPT); ++ this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_JPT); + if (!this->m_Internal->m_Dinfo) + { ++ opj_stream_destroy(l_stream); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " + << this->GetFileName() << std::endl + << "Reason: opj_create_decompress(CODEC_JPT) returns nullptr"); +@@ -433,7 +406,7 @@ + break; + } + default: +- fclose(l_file); ++ opj_stream_destroy(l_stream); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " + << this->GetFileName() << std::endl + << "Reason: " +@@ -445,32 +418,17 @@ + if (!opj_setup_decoder(this->m_Internal->m_Dinfo, &(this->m_Internal->m_DecompressionParameters))) + { ++ opj_stream_destroy(l_stream); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl + << "Reason: opj_setup_decoder returns false"); + } + +- OPJ_INT32 l_tile_x0, l_tile_y0; +- +- OPJ_UINT32 l_tile_width; +- OPJ_UINT32 l_tile_height; +- OPJ_UINT32 l_nb_tiles_x; +- OPJ_UINT32 l_nb_tiles_y; +- +- bool bResult = opj_read_header(this->m_Internal->m_Dinfo, +- &l_image, +- &l_tile_x0, +- &l_tile_y0, +- &l_tile_width, +- &l_tile_height, +- &l_nb_tiles_x, +- &l_nb_tiles_y, +- l_stream); ++ bool bResult = opj_read_header(l_stream, this->m_Internal->m_Dinfo, &l_image); + + if (!bResult) + { + opj_destroy_codec(this->m_Internal->m_Dinfo); + this->m_Internal->m_Dinfo = nullptr; + opj_stream_destroy(l_stream); +- fclose(l_file); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl + << "Reason: opj_read_header returns false"); + } +@@ -499,7 +457,7 @@ + itkDebugMacro(<< "p_end_x = " << p_end_x); + itkDebugMacro(<< "p_end_y = " << p_end_y); + +- bResult = opj_set_decode_area(this->m_Internal->m_Dinfo, p_start_x, p_start_y, p_end_x, p_end_y); ++ bResult = opj_set_decode_area(this->m_Internal->m_Dinfo, l_image, p_start_x, p_start_y, p_end_x, p_end_y); + + itkDebugMacro(<< "opj_set_decode_area() after"); + +@@ -509,6 +467,5 @@ + this->m_Internal->m_Dinfo = nullptr; + opj_stream_destroy(l_stream); +- fclose(l_file); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl + << "Reason: opj_set_decode_area returns false"); + } +@@ -525,13 +482,14 @@ + + OPJ_UINT32 l_max_data_size = 1000; + +- bool l_go_on = true; ++ OPJ_BOOL l_go_on = true; + + auto * l_data = (OPJ_BYTE *)malloc(1000); + + while (l_go_on) + { + bool tileHeaderRead = opj_read_tile_header(this->m_Internal->m_Dinfo, ++ l_stream, + &l_tile_index, + &l_data_size, + &l_current_tile_x0, +@@ -540,13 +498,11 @@ + &l_current_tile_y1, + &l_nb_comps, +- &l_go_on, +- l_stream); ++ &l_go_on); + + if (!tileHeaderRead) + { + free(l_data); + opj_stream_destroy(l_stream); +- fclose(l_file); + opj_destroy_codec(this->m_Internal->m_Dinfo); + opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl +@@ -571,7 +527,6 @@ + if (!l_data) + { + opj_stream_destroy(l_stream); +- fclose(l_file); + opj_destroy_codec(this->m_Internal->m_Dinfo); + opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl +@@ -590,7 +545,6 @@ + { + free(l_data); + opj_stream_destroy(l_stream); +- fclose(l_file); + opj_destroy_codec(this->m_Internal->m_Dinfo); + opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl +@@ -654,7 +608,6 @@ + { + free(l_data); + opj_stream_destroy(l_stream); +- fclose(l_file); + opj_destroy_codec(this->m_Internal->m_Dinfo); + opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl +@@ -667,13 +620,11 @@ + this->m_Internal->m_Dinfo = nullptr; + opj_stream_destroy(l_stream); +- fclose(l_file); + itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl + << "Reason: error whle reading image"); + } + + /* close the byte stream */ + opj_stream_destroy(l_stream); +- fclose(l_file); + + if (this->m_Internal->m_Dinfo) + { +@@ -840,13 +791,13 @@ + + parameters.numresolution = numberOfResolutions; + +- OPJ_COLOR_SPACE color_space = CLRSPC_GRAY; ++ OPJ_COLOR_SPACE color_space = OPJ_CLRSPC_GRAY; + opj_image_cmptparm_t cmptparms[3]; + + if (this->GetNumberOfComponents() == 3) + { + +- color_space = (this->GetPixelType() == IOPixelEnum::RGB) ? CLRSPC_SRGB : CLRSPC_UNSPECIFIED; ++ color_space = (this->GetPixelType() == IOPixelEnum::RGB) ? OPJ_CLRSPC_SRGB : OPJ_CLRSPC_UNSPECIFIED; + + /* initialize image components */ + memset(&cmptparms[0], 0, 3 * sizeof(opj_image_cmptparm_t)); +@@ -864,7 +815,7 @@ + + if (this->GetNumberOfComponents() == 1) + { +- color_space = CLRSPC_GRAY; ++ color_space = OPJ_CLRSPC_GRAY; + + /* initialize image components */ + memset(&cmptparms[0], 0, sizeof(opj_image_cmptparm_t)); +@@ -941,8 +892,9 @@ + if (extension == ".j2k") + { +- cinfo = opj_create_compress(CODEC_J2K); ++ cinfo = opj_create_compress(OPJ_CODEC_J2K); + if (!cinfo) + { ++ opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to write file: " + << this->GetFileName() << std::endl + << "Reason: opj_create_compress(CODEC_J2K) returns nullptr"); +@@ -950,9 +902,10 @@ + } + else if (extension == ".jp2") + { +- cinfo = opj_create_compress(CODEC_JP2); ++ cinfo = opj_create_compress(OPJ_CODEC_JP2); + if (!cinfo) + { ++ opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to write file: " + << this->GetFileName() << std::endl + << "Reason: opj_create_compress(CODEC_JP2) returns nullptr"); +@@ -960,9 +913,10 @@ + } + else if (extension == ".jpt") + { +- cinfo = opj_create_compress(CODEC_JPT); ++ cinfo = opj_create_compress(OPJ_CODEC_JPT); + if (!cinfo) + { ++ opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to write file: " + << this->GetFileName() << std::endl + << "Reason: opj_create_compress(CODEC_JPT) returns nullptr"); +@@ -970,6 +924,7 @@ + } + else + { ++ opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to write file: " << this->GetFileName() << std::endl + << "Reason: unknown encode format: " << extension); + } +@@ -985,23 +940,19 @@ + + if (!opj_setup_encoder(cinfo, ¶meters, l_image)) + { ++ opj_destroy_codec(cinfo); ++ opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to write file: " << this->GetFileName() << std::endl + << "Reason: opj_setup_encoder returns false"); + } + +- FILE * l_file = fopen(parameters.outfile, "wb"); +- if (!l_file) +- { +- itkExceptionMacro("JPEG2000ImageIO failed to open file for writing: " << this->GetFileName() << std::endl +- << "Reason: " +- << itksys::SystemTools::GetLastSystemError()); +- } +- + /* open a byte stream for writing */ + /* allocate memory for all tiles */ +- opj_stream_t * cio = opj_stream_create_default_file_stream(l_file, false); ++ opj_stream_t * cio = opj_stream_create_default_file_stream(parameters.outfile, false); + if (!cio) + { ++ opj_destroy_codec(cinfo); ++ opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to write file: " + << this->GetFileName() << std::endl + << "Reason: " +@@ -1017,7 +968,8 @@ + if (!bSuccess) + { + opj_stream_destroy(cio); +- fclose(l_file); ++ opj_destroy_codec(cinfo); ++ opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to write file: " << this->GetFileName() << std::endl + << "Reason: opj_start_compress returns false"); + } +@@ -1026,7 +978,8 @@ + if (!bSuccess) + { + opj_stream_destroy(cio); +- fclose(l_file); ++ opj_destroy_codec(cinfo); ++ opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to write file: " << this->GetFileName() << std::endl + << "Reason: opj_encode returns false"); + } +@@ -1035,14 +988,14 @@ + if (!bSuccess) + { + opj_stream_destroy(cio); +- fclose(l_file); ++ opj_destroy_codec(cinfo); ++ opj_image_destroy(l_image); + itkExceptionMacro("JPEG2000ImageIO failed to write file: " << this->GetFileName() << std::endl + << "Reason: opj_end_compress returns false"); + } + + /* close and free the byte stream */ + opj_stream_destroy(cio); +- fclose(l_file); + + /* free remaining compression structures */ + opj_destroy_codec(cinfo); +--- a/Modules/Nonunit/Review/src/CMakeLists.txt ++++ b/Modules/Nonunit/Review/src/CMakeLists.txt +@@ -5,7 +5,7 @@ + + add_library(ITKReview ${ITKReview_SRC}) + itk_module_link_dependencies() +-target_link_libraries(ITKReview LINK_PUBLIC ${ITKTestKernel_LIBRARIES} ${ITKIOLSM_LIBRARIES} itkopenjpeg) ++target_link_libraries(ITKReview LINK_PUBLIC ${ITKTestKernel_LIBRARIES} ${ITKIOLSM_LIBRARIES} ${ITKOpenJPEG_LIBRARIES}) + itk_module_target(ITKReview) + + diff --git a/sci-libs/itk/files/itk-5.3.0-uint8.patch b/sci-libs/itk/files/itk-5.3.0-uint8.patch new file mode 100644 index 000000000..724314574 --- /dev/null +++ b/sci-libs/itk/files/itk-5.3.0-uint8.patch @@ -0,0 +1,10 @@ +--- a/Modules/Filtering/MathematicalMorphology/include/itkMathematicalMorphologyEnums.h ++++ b/Modules/Filtering/MathematicalMorphology/include/itkMathematicalMorphologyEnums.h +@@ -20,6 +20,7 @@ + + #include <iostream> + #include "ITKMathematicalMorphologyExport.h" ++#include <cstdint> + + + namespace itk diff --git a/sci-libs/itk/files/nrrdio-linking.patch b/sci-libs/itk/files/nrrdio-linking.patch deleted file mode 100644 index a549650d2..000000000 --- a/sci-libs/itk/files/nrrdio-linking.patch +++ /dev/null @@ -1,15 +0,0 @@ -Description: Link libITKNrrdIO with -lm (needed for sqrt) -Author: Steve Robbins <smr@debian.org> -Forwarded: no - ---- insighttoolkit4-4.5.0.orig/Modules/ThirdParty/NrrdIO/src/NrrdIO/CMakeLists.txt -+++ insighttoolkit4-4.5.0/Modules/ThirdParty/NrrdIO/src/NrrdIO/CMakeLists.txt -@@ -64,7 +64,7 @@ - ADD_DEFINITIONS(-DTEEM_ZLIB=1) - - ADD_LIBRARY(ITKNrrdIO ${nrrdio_SRCS} ) --TARGET_LINK_LIBRARIES(ITKNrrdIO ${ITKZLIB_LIBRARIES}) -+TARGET_LINK_LIBRARIES(ITKNrrdIO ${ITKZLIB_LIBRARIES} -lm) - - IF(ITK_LIBRARY_PROPERTIES) - SET_TARGET_PROPERTIES(ITKNrrdIO PROPERTIES ${ITK_LIBRARY_PROPERTIES}) diff --git a/sci-libs/itk/files/tests.patch b/sci-libs/itk/files/tests.patch deleted file mode 100644 index c24714e4d..000000000 --- a/sci-libs/itk/files/tests.patch +++ /dev/null @@ -1,41 +0,0 @@ -Known to fail by upstream: -https://github.com/InsightSoftwareConsortium/ITK/issues/1212#issuecomment-527998115 - ---- a/Modules/Bridge/VtkGlue/test/CMakeLists.txt 2019-09-09 00:45:14.736032139 +0200 -+++ b/Modules/Bridge/VtkGlue/test/CMakeLists.txt 2019-09-09 00:49:42.183935497 +0200 -@@ -7,8 +7,6 @@ - if(NOT VTK_RENDERING_BACKEND STREQUAL "None") - list(APPEND ITKVtkGlueTests - itkVtkMedianFilterTest.cxx -- itkVtkConnectedComponentImageFilterTest.cxx -- QuickViewTest.cxx - # ### runViewImage ### - # No test generated. Use it for view images (2D or 3D) with: - # ITKVtkGlueTestDriver runViewImage image_file -@@ -40,26 +38,3 @@ - NAME itkVTKImageToImageFilterTest - COMMAND ITKVtkGlueTestDriver - itkVTKImageToImageFilterTest) -- --if(NOT VTK_RENDERING_BACKEND STREQUAL "None") -- itk_add_test( -- NAME itkVtkMedianImageFilterTest -- COMMAND ITKVtkGlueTestDriver -- itkVtkMedianFilterTest DATA{${ITK_DATA_ROOT}/Input/cthead1.png} 2) -- set_property(TEST itkVtkMedianImageFilterTest APPEND PROPERTY LABELS REQUIRES_DISPLAY) -- -- itk_add_test( -- NAME QuickViewTest -- COMMAND ITKVtkGlueTestDriver -- --compare DATA{Baseline/QuickViewTest.png,:} -- ${ITK_TEST_OUTPUT_DIR}/QuickViewTest0.png -- --compareNumberOfPixelsTolerance 1500 -- QuickViewTest DATA{${ITK_DATA_ROOT}/Input/peppers.png} ${ITK_TEST_OUTPUT_DIR}) -- set_property(TEST QuickViewTest APPEND PROPERTY LABELS REQUIRES_DISPLAY) -- -- itk_add_test( -- NAME itkVtkConnectedComponentImageFilterTest -- COMMAND ITKVtkGlueTestDriver -- itkVtkConnectedComponentImageFilterTest DATA{${ITK_DATA_ROOT}/Input/cthead1.png}) -- set_property(TEST itkVtkConnectedComponentImageFilterTest APPEND PROPERTY LABELS REQUIRES_DISPLAY) --endif() diff --git a/sci-libs/itk/itk-5.0.1.ebuild b/sci-libs/itk/itk-5.0.1.ebuild deleted file mode 100644 index bf9f0f021..000000000 --- a/sci-libs/itk/itk-5.0.1.ebuild +++ /dev/null @@ -1,178 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7,8,9} ) - -inherit cmake python-single-r1 - -MY_PN="InsightToolkit" -MY_P="${MY_PN}-${PV}" -GLI_HASH="187ab99b7d42718c99e5017f0acd3900d7469bd1" -GLI_TEST_HASH="57b5d5de8d777f10f269445a" - -DESCRIPTION="NLM Insight Segmentation and Registration Toolkit" -HOMEPAGE="http://www.itk.org" -SRC_URI=" - https://github.com/InsightSoftwareConsortium/ITK/releases/download/v${PV}/${MY_P}.tar.gz - https://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator/archive/${GLI_HASH}.tar.gz -> ITKGenericLabelInterpolator-${PV}.tar.gz - test? ( - https://data.kitware.com/api/v1/folder/${GLI_TEST_HASH}/download -> ITKGenericLabelInterpolator_test-${PV}.zip - https://github.com/InsightSoftwareConsortium/ITK/releases/download/v${PV}/InsightData-${PV}.tar.gz - ) - " - -LICENSE="Apache-2.0" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="debug doc examples fftw python review test vtkglue" -RESTRICT="!test? ( test )" -# python will not work, this is a know issue upstream: -# https://github.com/InsightSoftwareConsortium/ITK/issues/1229 -# https://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator/issues/10 - -RDEPEND=" - dev-libs/double-conversion:0= - media-libs/openjpeg:2 - media-libs/libpng:0= - media-libs/tiff:0= - sci-libs/dcmtk:0= - sci-libs/hdf5:0=[cxx] - sys-libs/zlib:0= - media-libs/libjpeg-turbo:0= - fftw? ( sci-libs/fftw:3.0= ) - vtkglue? ( sci-libs/vtk:0=[rendering,python?] ) - python? ( ${PYTHON_DEPS} ) -" -DEPEND="${RDEPEND} - sys-apps/coreutils - python? ( - >=dev-lang/swig-2.0:0 - dev-cpp/castxml - ) - doc? ( app-doc/doxygen ) -" -BDEPEND="app-arch/unzip" - -REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" - -S="${WORKDIR}/${MY_P}" - -PATCHES=( - "${FILESDIR}"/ITKModuleRemote.patch - "${FILESDIR}"/tests.patch -) - -pkg_pretend() { - if [[ -z ${ITK_COMPUTER_MEMORY_SIZE} ]]; then - elog "To tune ITK to make the best use of working memory you can set" - elog " ITK_COMPUTER_MEMORY_SIZE=XX" - elog "in make.conf, default is 1 (unit is GB)" - fi - if use python && [[ -z ${ITK_WRAP_DIMS} ]]; then - elog "For Python language bindings, you can define the dimensions" - elog "you want to create bindings for by setting" - elog " ITK_WRAP_DIMS=X;Y;Z..." - elog "in make.conf, default is 2;3 for 2D and 3D data" - fi -} - -src_prepare() { - sed -i -e "s/find_package(OpenJPEG 2.0.0/find_package(OpenJPEG/g"\ - Modules/ThirdParty/GDCM/src/gdcm/CMakeLists.txt - ln -sr ../ITKGenericLabelInterpolator-* Modules/Remote/ITKGenericLabelInterpolator || die - if use test; then - for filename in ../GenericLabelInterpolator/test/*/*mha; do - MD5=$(md5sum $filename) || die - MD5=${MD5% *} || die - cp "$filename" ".ExternalData/MD5/${MD5}" || die - done - fi - cmake_src_prepare -} - -src_configure() { - local mycmakeargs=( - -DBUILD_SHARED_LIBS=ON - -DGDCM_USE_SYSTEM_OPENJPEG=ON - -DITK_FORBID_DOWNLOADS:BOOL=OFF - -DITK_USE_SYSTEM_DCMTK=ON - -DITK_USE_SYSTEM_DOUBLECONVERSION=ON - -DITK_USE_SYSTEM_CASTXML=ON - -DITK_USE_SYSTEM_HDF5=ON - -DITK_USE_SYSTEM_JPEG=ON - -DITK_USE_SYSTEM_PNG=ON - -DITK_USE_SYSTEM_SWIG=ON - -DITK_USE_SYSTEM_TIFF=ON - -DITK_USE_SYSTEM_ZLIB=ON - -DITK_USE_KWSTYLE=OFF - -DITK_BUILD_DEFAULT_MODULES=ON - -DITK_COMPUTER_MEMORY_SIZE="${ITK_COMPUTER_MEMORY_SIZE:-1}" - -DWRAP_ITK_JAVA=OFF - -DWRAP_ITK_TCL=OFF - -Ddouble-conversion_INCLUDE_DIRS="${EPREFIX}/usr/include/double-conversion" - -DExternalData_OBJECT_STORES="${WORKDIR}/InsightToolkit-${PV}/.ExternalData" - -DModule_GenericLabelInterpolator:BOOL=ON - -DModule_ITKReview:BOOL=ON - -DBUILD_TESTING="$(usex test ON OFF)" - -DBUILD_EXAMPLES="$(usex examples ON OFF)" - -DITK_USE_REVIEW="$(usex review ON OFF)" - -DITK_BUILD_DOCUMENTATION="$(usex doc ON OFF)" - -DITK_INSTALL_LIBRARY_DIR=$(get_libdir) - ) - if use fftw; then - mycmakeargs+=( - -DUSE_FFTWD=ON - -DUSE_FFTWF=ON - -DUSE_SYSTEM_FFTW=ON - -DITK_WRAP_double=ON - -DITK_WRAP_vector_double=ON - -DITK_WRAP_covariant_vector_double=ON - -DITK_WRAP_complex_double=ON - ) - fi - if use vtkglue; then - mycmakeargs+=( - -DModule_ITKVtkGlue=ON - ) - fi - if use python; then - mycmakeargs+=( - -DITK_WRAP_PYTHON=ON - -DITK_WRAP_DIMS="${ITK_WRAP_DIMS:-2;3}" - ) - else - mycmakeargs+=( - -DITK_WRAP_PYTHON=OFF - ) - fi - cmake_src_configure -} - -src_install() { - cmake_src_install - - if use examples; then - docinto examples - docompress -x /usr/share/doc/${PF}/examples - dodoc -r "${S}"/Examples/* - fi - - echo "ITK_DATA_ROOT=${EPREFIX}/usr/share/${PN}/data" > ${T}/40${PN} - local ldpath="${EPREFIX}/usr/$(get_libdir)/InsightToolkit" - if use python; then - echo "PYTHONPATH=${EPREFIX}/usr/$(get_libdir)/InsightToolkit/WrapITK/Python" >> "${T}"/40${PN} - ldpath="${ldpath}:${EPREFIX}/usr/$(get_libdir)/InsightToolkit/WrapITK/lib" - fi - echo "LDPATH=${ldpath}" >> "${T}"/40${PN} - doenvd "${T}"/40${PN} - - if use doc; then - cd "${WORKDIR}"/html || die - rm *.md5 || die "Failed to remove superfluous hashes" - einfo "Installing API docs. This may take some time." - docinto api-docs - dodoc -r * - fi -} diff --git a/sci-libs/itk/itk-5.1.0.ebuild b/sci-libs/itk/itk-5.1.0.ebuild deleted file mode 100644 index 3f6c759ec..000000000 --- a/sci-libs/itk/itk-5.1.0.ebuild +++ /dev/null @@ -1,191 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7,8,9} ) - -inherit cmake python-single-r1 - -MY_PN="InsightToolkit" -MY_P="${MY_PN}-${PV}" -GLI_HASH="a02cbeaf28cb3d28ac66b9ac651073530eb6ab78" -TEST_HASH="0eb202e23ae81be123b1b26cf31a9ba743824700" -declare -a GLI_TEST_HASHES=( - "a5e11ea71164ff78c65fcf259db01ea5db981a9d868e60045ff2bffca92984df1174bf984a1076e450f0d5d69b4f0191ed1a61465c220e2c91a893b5df150c0a" - "bcdbb347f3704262d1f00be7179d6a0a6e68aed56c0653e8072ee5a94985c713bd229c935b1226a658af84fb7f1fffc2458c98364fc35303a2303b12f9f7ce2f" -) - -GLI_TEST_SRC="" -for i in "${GLI_TEST_HASHES[@]}"; do - GLI_TEST_SRC+="https://data.kitware.com/api/v1/file/hashsum/sha512/${i} -> ${P}-test-${i} " -done - -DESCRIPTION="NLM Insight Segmentation and Registration Toolkit" -HOMEPAGE="http://www.itk.org" -SRC_URI=" - https://github.com/InsightSoftwareConsortium/ITK/releases/download/v${PV}/${MY_P}.tar.gz - https://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator/archive/${GLI_HASH}.tar.gz -> ITKGenericLabelInterpolator-${PV}.tar.gz - test? ( - https://github.com/InsightSoftwareConsortium/ITK/releases/download/v${PV}/InsightData-${PV}.tar.gz - https://github.com/InsightSoftwareConsortium/ITKTestingData/archive/${TEST_HASH}.tar.gz -> ${P}-testingdata.tar.gz - ${GLI_TEST_SRC} - ) - " - -LICENSE="Apache-2.0" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="debug doc examples fftw itkv4-compat python review test vtkglue" -RESTRICT="!test? ( test )" -# python will not work, this is a know issue upstream: -# https://github.com/InsightSoftwareConsortium/ITK/issues/2005 -# https://github.com/InsightSoftwareConsortium/ITK/issues/1229 -# https://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator/issues/10 - -RDEPEND=" - dev-libs/double-conversion:0= - media-libs/openjpeg:2 - media-libs/libpng:0= - media-libs/tiff:0=[jpeg] - sci-libs/dcmtk:0= - sci-libs/hdf5:0=[cxx] - sys-libs/zlib:0= - media-libs/libjpeg-turbo:0= - fftw? ( sci-libs/fftw:3.0= ) - vtkglue? ( sci-libs/vtk:0=[rendering,python?] ) - python? ( ${PYTHON_DEPS} ) -" -DEPEND="${RDEPEND} - sys-apps/coreutils - python? ( - >=dev-lang/swig-2.0:0 - dev-cpp/castxml - ) - doc? ( app-doc/doxygen ) -" - -REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" - -S="${WORKDIR}/${MY_P}" - -PATCHES=( - "${FILESDIR}"/tests.patch - "${FILESDIR}"/${P}-downloads.patch - "${FILESDIR}"/${P}-include_limits.patch -) - -pkg_pretend() { - if [[ -z ${ITK_COMPUTER_MEMORY_SIZE} ]]; then - elog "To tune ITK to make the best use of working memory you can set" - elog " ITK_COMPUTER_MEMORY_SIZE=XX" - elog "in make.conf, default is 1 (unit is GB)" - fi - if use python && [[ -z ${ITK_WRAP_DIMS} ]]; then - elog "For Python language bindings, you can define the dimensions" - elog "you want to create bindings for by setting" - elog " ITK_WRAP_DIMS=X;Y;Z..." - elog "in make.conf, default is 2;3 for 2D and 3D data" - fi -} - -src_prepare() { - sed -i -e "s/find_package(OpenJPEG 2.0.0/find_package(OpenJPEG/g"\ - Modules/ThirdParty/GDCM/src/gdcm/CMakeLists.txt - ln -sr ../ITKGenericLabelInterpolator-* Modules/External/ITKGenericLabelInterpolator || die - cmake_src_prepare - if use test; then - cp -rf "../ITKTestingData-${TEST_HASH}/"* ".ExternalData/" || die - mv "../ITKTestingData-${TEST_HASH}" "${BUILD_DIR}/.ExternalData" || die - for i in "${GLI_TEST_HASHES[@]}"; do - cp "${DISTDIR}/${i}" ".ExternalData/SHA512/" || die - cp "${DISTDIR}/${i}" "${BUILD_DIR}/.ExternalData/SHA512/" || die - done - fi -} - -src_configure() { - local mycmakeargs=( - -DITK_BUILD_DOCUMENTATION="$(usex doc ON OFF)" - -DBUILD_EXAMPLES="$(usex examples ON OFF)" - -DBUILD_SHARED_LIBS=ON - -DBUILD_TESTING="$(usex test ON OFF)" - -Ddouble-conversion_INCLUDE_DIRS="${EPREFIX}/usr/include/double-conversion" - -DExternalData_OBJECT_STORES="${WORKDIR}/InsightToolkit-${PV}/.ExternalData" - -DGDCM_USE_SYSTEM_OPENJPEG=ON - -DITK_FORBID_DOWNLOADS:BOOL=ON - -DITK_INSTALL_LIBRARY_DIR=$(get_libdir) - -DITK_USE_REVIEW="$(usex review ON OFF)" - -DITK_USE_SYSTEM_DCMTK=ON - -DITK_USE_SYSTEM_DOUBLECONVERSION=ON - -DITK_USE_SYSTEM_CASTXML=ON - -DITK_USE_SYSTEM_HDF5=ON - -DITK_USE_SYSTEM_JPEG=ON - -DITK_USE_SYSTEM_PNG=ON - -DITK_USE_SYSTEM_SWIG=ON - -DITK_USE_SYSTEM_TIFF=ON - -DITK_USE_SYSTEM_ZLIB=ON - -DITK_USE_KWSTYLE=OFF - -DITK_BUILD_DEFAULT_MODULES=ON - -DITK_COMPUTER_MEMORY_SIZE="${ITK_COMPUTER_MEMORY_SIZE:-1}" - -DModule_GenericLabelInterpolator:BOOL=ON - -DModule_ITKReview:BOOL=ON - -DWRAP_ITK_JAVA=OFF - -DWRAP_ITK_TCL=OFF - -DITKV4_COMPATIBILITY:BOOL=$(usex itkv4-compat) - ) - if use fftw; then - mycmakeargs+=( - -DUSE_FFTWD=ON - -DUSE_FFTWF=ON - -DUSE_SYSTEM_FFTW=ON - -DITK_WRAP_double=ON - -DITK_WRAP_vector_double=ON - -DITK_WRAP_covariant_vector_double=ON - -DITK_WRAP_complex_double=ON - ) - fi - if use vtkglue; then - mycmakeargs+=( - -DModule_ITKVtkGlue=ON - ) - fi - if use python; then - mycmakeargs+=( - -DITK_WRAP_PYTHON=ON - -DITK_WRAP_DIMS="${ITK_WRAP_DIMS:-2;3}" - ) - else - mycmakeargs+=( - -DITK_WRAP_PYTHON=OFF - ) - fi - cmake_src_configure -} - -src_install() { - cmake_src_install - - if use examples; then - docinto examples - docompress -x /usr/share/doc/${PF}/examples - dodoc -r "${S}"/Examples/* - fi - - echo "ITK_DATA_ROOT=${EPREFIX}/usr/share/${PN}/data" > ${T}/40${PN} - local ldpath="${EPREFIX}/usr/$(get_libdir)/InsightToolkit" - if use python; then - echo "PYTHONPATH=${EPREFIX}/usr/$(get_libdir)/InsightToolkit/WrapITK/Python" >> "${T}"/40${PN} - ldpath="${ldpath}:${EPREFIX}/usr/$(get_libdir)/InsightToolkit/WrapITK/lib" - fi - echo "LDPATH=${ldpath}" >> "${T}"/40${PN} - doenvd "${T}"/40${PN} - - if use doc; then - cd "${WORKDIR}"/html || die - rm *.md5 || die "Failed to remove superfluous hashes" - einfo "Installing API docs. This may take some time." - docinto api-docs - dodoc -r * - fi -} diff --git a/sci-libs/itk/itk-5.2.1-r2.ebuild b/sci-libs/itk/itk-5.2.1-r2.ebuild new file mode 100644 index 000000000..0b1f25860 --- /dev/null +++ b/sci-libs/itk/itk-5.2.1-r2.ebuild @@ -0,0 +1,250 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +VIRTUALX_REQUIRED="manual" + +inherit cmake python-single-r1 virtualx + +MY_PN="InsightToolkit" +MY_P="${MY_PN}-${PV}" +GLI_HASH="89da9305f5750d3990ca9fd35ecc5ce0b39c71a6" +IAD_HASH="24825c8d246e941334f47968553f0ae388851f0c" +TEST_HASH="7ab9d41ad5b42ccbe8adcaf0b24416d439a264d0" +declare -a GLI_TEST_HASHES=( + "a5e11ea71164ff78c65fcf259db01ea5db981a9d868e60045ff2bffca92984df1174bf984a1076e450f0d5d69b4f0191ed1a61465c220e2c91a893b5df150c0a" + "bcdbb347f3704262d1f00be7179d6a0a6e68aed56c0653e8072ee5a94985c713bd229c935b1226a658af84fb7f1fffc2458c98364fc35303a2303b12f9f7ce2f" +) + +GLI_TEST_SRC="" +for i in "${GLI_TEST_HASHES[@]}"; do + GLI_TEST_SRC+="https://data.kitware.com/api/v1/file/hashsum/sha512/${i}/download -> ${PN}-test-${i} " +done + +DESCRIPTION="NLM Insight Segmentation and Registration Toolkit" +HOMEPAGE="https://itk.org" +SRC_URI=" + https://github.com/InsightSoftwareConsortium/ITK/releases/download/v${PV}/${MY_P}.tar.gz + https://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator/archive/${GLI_HASH}.tar.gz -> ITKGenericLabelInterpolator-${PV}.tar.gz + https://github.com/ntustison/ITKAdaptiveDenoising/archive/${IAD_HASH}.tar.gz -> ITKAdaptiveDenoising-${PV}.tar.gz + test? ( + https://github.com/InsightSoftwareConsortium/ITK/releases/download/v${PV}/InsightData-${PV}.tar.gz + https://github.com/InsightSoftwareConsortium/ITKTestingData/archive/${TEST_HASH}.tar.gz -> ${P}-testingdata.tar.gz + ${GLI_TEST_SRC} + ) + " + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="debug doc examples fftw itkv4-compat python review test vtkglue" +REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" + +RESTRICT="!test? ( test )" + +RDEPEND=" + dev-cpp/eigen:3 + dev-libs/double-conversion:0= + dev-libs/expat:0= + media-libs/openjpeg:2 + media-libs/libpng:0= + media-libs/tiff:0=[jpeg] + sci-libs/dcmtk:0= + sci-libs/hdf5:0=[cxx] + sci-libs/gdcm:0= + sys-libs/zlib:0= + media-libs/libjpeg-turbo:0= + fftw? ( sci-libs/fftw:3.0= ) + vtkglue? ( + sci-libs/vtk:0=[rendering] + python? ( + sci-libs/vtk:0=[python,${PYTHON_SINGLE_USEDEP}] + ) + ) + python? ( ${PYTHON_DEPS} ) +" +DEPEND="${RDEPEND} + sys-apps/coreutils + python? ( + >=dev-lang/swig-2.0:0 + dev-libs/castxml + ) + doc? ( app-text/doxygen ) +" +BDEPEND=" + test? ( + vtkglue? ( ${VIRTUALX_DEPEND} ) + python? ( + $(python_gen_cond_dep 'dev-python/numpy[${PYTHON_USEDEP}]') + ) + ) +" + +S="${WORKDIR}/${MY_P}" + +PATCHES=( + "${FILESDIR}/${P}-upstream-fixes.patch" + "${FILESDIR}/${P}-system-tiff-has-64.patch" + "${FILESDIR}/${P}-fix-castxml-clang-attr-malloc.patch" + "${FILESDIR}/${P}-system-openjpeg.patch" +) + +pkg_pretend() { + if [[ -z ${ITK_COMPUTER_MEMORY_SIZE} ]]; then + elog "To tune ITK to make the best use of working memory you can set" + elog " ITK_COMPUTER_MEMORY_SIZE=XX" + elog "in make.conf, default is 1 (unit is GB)" + fi + if use python && [[ -z ${ITK_WRAP_DIMS} ]]; then + elog "For Python language bindings, you can define the dimensions" + elog "you want to create bindings for by setting" + elog " ITK_WRAP_DIMS=X;Y;Z..." + elog "in make.conf, default is 2;3 for 2D and 3D data" + fi +} + +src_prepare() { + # drop bundled libs + local -a DROPS=( + DoubleConversion/src/double-conversion + Eigen3/src/itkeigen + Expat/src/expat + GDCM/src/gdcm + JPEG/src/itkjpeg + HDF5/src/itkhdf5 + OpenJPEG/src/openjpeg + PNG/src/itkpng + TIFF/src/itktiff + ZLIB/src/itkzlib + ) + local x + for x in "${DROPS[@]}"; do + ebegin "Dropping bundled ${x%%/*}" + rm -r "Modules/ThirdParty/${x}" || die + eend $? + done + { + find Modules/ThirdParty -mindepth 2 -maxdepth 2 -type d -name src -printf '%P\n' + printf '%s\n' "${DROPS[@]}" | sed 's,/[^/]*$,,' + } | sort | uniq -u | xargs -n 1 ewarn "Using bundled" || die + + # Remote modules + ln -sr "../ITKGenericLabelInterpolator-${GLI_HASH}" Modules/External/ITKGenericLabelInterpolator || die + ln -sr "../ITKAdaptiveDenoising-${IAD_HASH}" Modules/External/ITKAdaptiveDenoising || die + + cmake_src_prepare + + if use test; then + cp -rf "../ITKTestingData-${TEST_HASH}/"* ".ExternalData/" || die + mv "../ITKTestingData-${TEST_HASH}" "${BUILD_DIR}/.ExternalData" || die + for i in "${GLI_TEST_HASHES[@]}"; do + cp "${DISTDIR}/${PN}-test-${i}" ".ExternalData/SHA512/${i}" || die + cp "${DISTDIR}/${PN}-test-${i}" "${BUILD_DIR}/.ExternalData/SHA512/${i}" || die + done + fi +} + +src_configure() { + local mycmakeargs=( + -DITK_BUILD_DOCUMENTATION="$(usex doc ON OFF)" + -DITK_INSTALL_DOC_DIR="share/doc/${P}" + -DBUILD_EXAMPLES="$(usex examples ON OFF)" + -DBUILD_SHARED_LIBS=ON + -DBUILD_TESTING="$(usex test ON OFF)" + -Ddouble-conversion_INCLUDE_DIRS="${EPREFIX}/usr/include/double-conversion" + -DExternalData_OBJECT_STORES="${WORKDIR}/InsightToolkit-${PV}/.ExternalData" + -DGDCM_USE_SYSTEM_OPENJPEG=ON + -DITK_FORBID_DOWNLOADS:BOOL=ON + -DITK_INSTALL_LIBRARY_DIR=$(get_libdir) + -DITK_USE_REVIEW="$(usex review ON OFF)" + -DITK_USE_SYSTEM_DCMTK=ON + -DITK_USE_SYSTEM_DOUBLECONVERSION=ON + -DITK_USE_SYSTEM_CASTXML=ON + -DITK_USE_SYSTEM_EIGEN=ON + -DITK_USE_SYSTEM_EXPAT=ON + -DITK_USE_SYSTEM_GDCM=ON + -DITK_USE_SYSTEM_HDF5=ON + -DITK_USE_SYSTEM_JPEG=ON + -DITK_USE_SYSTEM_OPENJPEG=ON + -DITK_USE_SYSTEM_PNG=ON + -DITK_USE_SYSTEM_SWIG=ON + -DITK_USE_SYSTEM_TIFF=ON + -DITK_USE_SYSTEM_ZLIB=ON + -DITK_USE_KWSTYLE=OFF + -DITK_BUILD_DEFAULT_MODULES=ON + -DITK_COMPUTER_MEMORY_SIZE="${ITK_COMPUTER_MEMORY_SIZE:-1}" + -DModule_AdaptiveDenoising:BOOL=ON + -DModule_GenericLabelInterpolator:BOOL=ON + -DModule_ITKReview:BOOL=ON + -DWRAP_ITK_JAVA=OFF + -DWRAP_ITK_TCL=OFF + -DITKV4_COMPATIBILITY:BOOL=$(usex itkv4-compat) + ) + if use fftw; then + mycmakeargs+=( + -DUSE_FFTWD=ON + -DUSE_FFTWF=ON + -DUSE_SYSTEM_FFTW=ON + -DITK_WRAP_double=ON + -DITK_WRAP_vector_double=ON + -DITK_WRAP_covariant_vector_double=ON + -DITK_WRAP_complex_double=ON + ) + fi + if use vtkglue; then + mycmakeargs+=( + -DModule_ITKVtkGlue=ON + ) + fi + if use python; then + mycmakeargs+=( + -DITK_WRAP_PYTHON=ON + -DPython3_EXECUTABLE="${PYTHON}" + -DITK_WRAP_DIMS="${ITK_WRAP_DIMS:-2;3}" + ) + else + mycmakeargs+=( + -DITK_WRAP_PYTHON=OFF + ) + fi + cmake_src_configure +} + +src_install() { + cmake_src_install + + if use examples; then + docinto examples + docompress -x /usr/share/doc/${PF}/examples + dodoc -r "${S}"/Examples/* + fi + + echo "ITK_DATA_ROOT=${EPREFIX}/usr/share/${PN}/data" > ${T}/40${PN} || die + local ldpath="${EPREFIX}/usr/$(get_libdir)/InsightToolkit" + if use python; then + echo "PYTHONPATH=${EPREFIX}/usr/$(get_libdir)/InsightToolkit/WrapITK/Python" >> "${T}"/40${PN} || die + ldpath="${ldpath}:${EPREFIX}/usr/$(get_libdir)/InsightToolkit/WrapITK/lib" + fi + echo "LDPATH=${ldpath}" >> "${T}"/40${PN} || die + doenvd "${T}"/40${PN} + + if use doc; then + cd "${WORKDIR}"/html || die + rm *.md5 || die "Failed to remove superfluous hashes" + einfo "Installing API docs. This may take some time." + docinto api-docs + dodoc -r * + fi + + use python && python_optimize +} + +src_test() { + if use vtkglue; then + virtx cmake_src_test + else + cmake_src_test + fi +} diff --git a/sci-libs/itk/itk-5.3.0-r1.ebuild b/sci-libs/itk/itk-5.3.0-r1.ebuild new file mode 100644 index 000000000..b2c3af801 --- /dev/null +++ b/sci-libs/itk/itk-5.3.0-r1.ebuild @@ -0,0 +1,269 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +VIRTUALX_REQUIRED="manual" + +inherit cmake python-single-r1 virtualx + +MY_PN="InsightToolkit" +MY_P="${MY_PN}-${PV}" +GLI_V="1.2.0" +IAD_HASH="24825c8d246e941334f47968553f0ae388851f0c" +TEST_HASH="bb6d3b9a932333901465c75417fe8859124f5fed" +declare -a GLI_TEST_HASHES=( + "a5e11ea71164ff78c65fcf259db01ea5db981a9d868e60045ff2bffca92984df1174bf984a1076e450f0d5d69b4f0191ed1a61465c220e2c91a893b5df150c0a" + "bcdbb347f3704262d1f00be7179d6a0a6e68aed56c0653e8072ee5a94985c713bd229c935b1226a658af84fb7f1fffc2458c98364fc35303a2303b12f9f7ce2f" +) + +GLI_TEST_SRC="" +for i in "${GLI_TEST_HASHES[@]}"; do + GLI_TEST_SRC+="https://data.kitware.com/api/v1/file/hashsum/sha512/${i}/download -> ${PN}-test-${i} " +done + +DESCRIPTION="NLM Insight Segmentation and Registration Toolkit" +HOMEPAGE="https://itk.org" +SRC_URI=" + https://github.com/InsightSoftwareConsortium/ITK/releases/download/v${PV}/${MY_P}.tar.gz + https://github.com/InsightSoftwareConsortium/ITKGenericLabelInterpolator/archive/refs/tags/v${GLI_V}.tar.gz -> ITKGenericLabelInterpolator-${GLI_V}.tar.gz + https://github.com/ntustison/ITKAdaptiveDenoising/archive/${IAD_HASH}.tar.gz -> ITKAdaptiveDenoising-${PV}.tar.gz + test? ( + https://github.com/InsightSoftwareConsortium/ITK/releases/download/v${PV}/InsightData-${PV}.tar.gz + https://github.com/InsightSoftwareConsortium/ITKTestingData/archive/${TEST_HASH}.tar.gz -> ${P}-testingdata.tar.gz + ${GLI_TEST_SRC} + ) + " + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="debug doc examples fftw itkv4-compat python review test vtkglue" +REQUIRED_USE="python? ( ${PYTHON_REQUIRED_USE} )" + +RESTRICT="!test? ( test )" + +RDEPEND=" + dev-cpp/eigen:3 + dev-libs/double-conversion:0= + dev-libs/expat:0= + dev-libs/icu:0= + media-libs/libjpeg-turbo:0= + media-libs/libpng:0= + media-libs/openjpeg:2 + media-libs/tiff:0=[jpeg] + sci-libs/dcmtk:0= + sci-libs/gdcm:0= + sci-libs/hdf5:0=[cxx] + sys-libs/zlib-ng + fftw? ( sci-libs/fftw:3.0=[threads] ) + vtkglue? ( + sci-libs/vtk:0=[rendering] + python? ( + sci-libs/vtk:0=[python,${PYTHON_SINGLE_USEDEP}] + ) + ) + python? ( ${PYTHON_DEPS} ) +" +# Might also need: +# dev-libs/kwsys::guru +# kwiml +# minc +# metaio +# niftilib +# sci-lib/vxl::science +DEPEND="${RDEPEND} + sys-apps/coreutils + python? ( + >=dev-lang/swig-2.0:0 + dev-libs/castxml + ) + doc? ( app-text/doxygen ) +" +BDEPEND=" + test? ( + vtkglue? ( ${VIRTUALX_DEPEND} ) + python? ( + $(python_gen_cond_dep 'dev-python/numpy[${PYTHON_USEDEP}]') + ) + ) +" + +S="${WORKDIR}/${MY_P}" + +# uint patch applied by upstream for next release. +PATCHES=( + "${FILESDIR}/${PN}-5.2.1-system-tiff-has-64.patch" + "${FILESDIR}/${PN}-5.3.0-system-openjpeg.patch" + "${FILESDIR}/${PN}-5.3.0-uint8.patch" +) + +pkg_pretend() { + if [[ -z ${ITK_COMPUTER_MEMORY_SIZE} ]]; then + elog "To tune ITK to make the best use of working memory you can set" + elog " ITK_COMPUTER_MEMORY_SIZE=XX" + elog "in make.conf, default is 1 (unit is GB)" + fi + if use python && [[ -z ${ITK_WRAP_DIMS} ]]; then + elog "For Python language bindings, you can define the dimensions" + elog "you want to create bindings for by setting" + elog " ITK_WRAP_DIMS=X;Y;Z..." + elog "in make.conf, default is 2;3 for 2D and 3D data" + fi +} + +src_prepare() { + # drop bundled libs + local -a DROPS=( + DoubleConversion/src/double-conversion + Eigen3/src/itkeigen + Expat/src/expat + GDCM/src/gdcm + JPEG/src/itkjpeg + HDF5/src/itkhdf5 + OpenJPEG/src/openjpeg + PNG/src/itkpng + TIFF/src/itktiff + ZLIB/src/itkzlib-ng + ) + local x + for x in "${DROPS[@]}"; do + ebegin "Dropping bundled ${x%%/*}" + rm -r "Modules/ThirdParty/${x}" || die + eend $? + done + { + find Modules/ThirdParty -mindepth 2 -maxdepth 2 -type d -name src -printf '%P\n' + printf '%s\n' "${DROPS[@]}" | sed 's,/[^/]*$,,' + } | sort | uniq -u | xargs -n 1 ewarn "Using bundled" || die + + # Remote modules + ln -sr "../ITKGenericLabelInterpolator-${GLI_V}" Modules/External/ITKGenericLabelInterpolator || die + ln -sr "../ITKAdaptiveDenoising-${IAD_HASH}" Modules/External/ITKAdaptiveDenoising || die + + cmake_src_prepare + + if use test; then + cp -rf "../ITKTestingData-${TEST_HASH}/"* ".ExternalData/" || die + mv "../ITKTestingData-${TEST_HASH}" "${BUILD_DIR}/.ExternalData" || die + for i in "${GLI_TEST_HASHES[@]}"; do + cp "${DISTDIR}/${PN}-test-${i}" ".ExternalData/SHA512/${i}" || die + cp "${DISTDIR}/${PN}-test-${i}" "${BUILD_DIR}/.ExternalData/SHA512/${i}" || die + done + fi +} + +src_configure() { + local mycmakeargs=( + -DITK_BUILD_DOCUMENTATION="$(usex doc ON OFF)" + -DITK_INSTALL_DOC_DIR="share/doc/${P}" + -DBUILD_EXAMPLES="$(usex examples ON OFF)" + -DBUILD_SHARED_LIBS=ON + -DBUILD_TESTING="$(usex test ON OFF)" + -Ddouble-conversion_INCLUDE_DIRS="${EPREFIX}/usr/include/double-conversion" + -DExternalData_OBJECT_STORES="${WORKDIR}/InsightToolkit-${PV}/.ExternalData" + -DGDCM_USE_SYSTEM_OPENJPEG=ON + -DITK_FORBID_DOWNLOADS:BOOL=ON + -DITK_INSTALL_LIBRARY_DIR=$(get_libdir) + -DITK_USE_REVIEW="$(usex review ON OFF)" + -DITK_USE_SYSTEM_ICU=ON + -DITK_USE_SYSTEM_DCMTK=ON + -DITK_USE_SYSTEM_DOUBLECONVERSION=ON + -DITK_USE_SYSTEM_CASTXML=ON + -DITK_USE_SYSTEM_EIGEN=ON + -DITK_USE_SYSTEM_EXPAT=ON + -DITK_USE_SYSTEM_GDCM=ON + -DITK_USE_SYSTEM_HDF5=ON + -DITK_USE_SYSTEM_JPEG=ON + -DITK_USE_SYSTEM_OPENJPEG=ON + -DITK_USE_SYSTEM_PNG=ON + -DITK_USE_SYSTEM_SWIG=ON + -DITK_USE_SYSTEM_TIFF=ON + -DITK_USE_SYSTEM_ZLIB=ON + -DITK_USE_KWSTYLE=OFF + -DITK_BUILD_DEFAULT_MODULES=ON + -DITK_COMPUTER_MEMORY_SIZE="${ITK_COMPUTER_MEMORY_SIZE:-1}" + -DModule_AdaptiveDenoising:BOOL=ON + -DModule_GenericLabelInterpolator:BOOL=ON + -DModule_ITKReview:BOOL=ON + -DWRAP_ITK_JAVA=OFF + -DWRAP_ITK_TCL=OFF + -DITKV4_COMPATIBILITY:BOOL=$(usex itkv4-compat) + ) + if use fftw; then + mycmakeargs+=( + -DITK_USE_FFTWD:BOOL=ON + -DITK_USE_FFTWF:BOOL=ON + -DITK_USE_SYSTEM_FFTW:BOOL=ON + -DITK_WRAP_double=ON + -DITK_WRAP_vector_double=ON + -DITK_WRAP_covariant_vector_double=ON + -DITK_WRAP_complex_double=ON + ) + else + mycmakeargs+=( + -DITK_USE_FFTWD:BOOL=OFF + -DITK_USE_FFTWF:BOOL=OFF + -DITK_USE_SYSTEM_FFTW:BOOL=OFF + -DITK_WRAP_double=OFF + -DITK_WRAP_vector_double=OFF + -DITK_WRAP_covariant_vector_double=OFF + -DITK_WRAP_complex_double=OFF + ) + fi + if use vtkglue; then + mycmakeargs+=( + -DModule_ITKVtkGlue=ON + ) + fi + if use python; then + mycmakeargs+=( + -DITK_WRAP_PYTHON=ON + -DPython3_EXECUTABLE="${PYTHON}" + -DITK_WRAP_DIMS="${ITK_WRAP_DIMS:-2;3}" + ) + else + mycmakeargs+=( + -DITK_WRAP_PYTHON=OFF + ) + fi + cmake_src_configure +} + +src_install() { + cmake_src_install + + if use examples; then + docinto examples + docompress -x /usr/share/doc/${PF}/examples + dodoc -r "${S}"/Examples/* + fi + + echo "ITK_DATA_ROOT=${EPREFIX}/usr/share/${PN}/data" > ${T}/40${PN} || die + local ldpath="${EPREFIX}/usr/$(get_libdir)/InsightToolkit" + if use python; then + echo "PYTHONPATH=${EPREFIX}/usr/$(get_libdir)/InsightToolkit/WrapITK/Python" >> "${T}"/40${PN} || die + ldpath="${ldpath}:${EPREFIX}/usr/$(get_libdir)/InsightToolkit/WrapITK/lib" + fi + echo "LDPATH=${ldpath}" >> "${T}"/40${PN} || die + doenvd "${T}"/40${PN} + + if use doc; then + cd "${WORKDIR}"/html || die + rm *.md5 || die "Failed to remove superfluous hashes" + einfo "Installing API docs. This may take some time." + docinto api-docs + dodoc -r * + fi + + use python && python_optimize +} + +src_test() { + if use vtkglue; then + virtx cmake_src_test + else + cmake_src_test + fi +} diff --git a/sci-libs/itk/metadata.xml b/sci-libs/itk/metadata.xml index c41202e23..5da2678ec 100644 --- a/sci-libs/itk/metadata.xml +++ b/sci-libs/itk/metadata.xml @@ -19,6 +19,7 @@ <flag name="vtkglue">PLEASE FIX MY DESCRIPTION</flag> </use> <upstream> + <remote-id type="github">InsightSoftwareConsortium/ITK</remote-id> <remote-id type="sourceforge">itk</remote-id> </upstream> </pkgmetadata> diff --git a/sci-libs/labbookdb/labbookdb-0.1.ebuild b/sci-libs/labbookdb/labbookdb-0.1.ebuild index 4da4106a2..57c90a390 100644 --- a/sci-libs/labbookdb/labbookdb-0.1.ebuild +++ b/sci-libs/labbookdb/labbookdb-0.1.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7..9} ) +PYTHON_COMPAT=( python3_{10..11} ) inherit distutils-r1 diff --git a/sci-libs/lib2bit/files/lib2bit-0.2.1_respect_DESTDIR.patch b/sci-libs/lib2bit/files/lib2bit-0.2.1_respect_DESTDIR.patch deleted file mode 100644 index 0f64b325f..000000000 --- a/sci-libs/lib2bit/files/lib2bit-0.2.1_respect_DESTDIR.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- lib2bit-0.2.1/Makefile.ori 2017-03-31 22:09:48.387098439 +0200 -+++ lib2bit-0.2.1/Makefile 2017-03-31 22:10:29.889020564 +0200 -@@ -8,7 +8,7 @@ - LDLIBS = - INCLUDES = - --prefix = /usr/local -+prefix = $(DESTDIR)/usr/local - includedir = $(prefix)/include - libdir = $(exec_prefix)/lib - diff --git a/sci-libs/mlpack/Manifest b/sci-libs/mlpack/Manifest deleted file mode 100644 index 827319a78..000000000 --- a/sci-libs/mlpack/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST mlpack-3.4.1.tar.gz 5782241 BLAKE2B d5a1050489c61a934330a0f3d1142e7949f7fdd9c31f679d7963208fc8aaea8fd8c0eb7e45920c3799712cb059808c75098e31b913557ec3c2af2f1d32e561f0 SHA512 53de83c2ca36829a0ae952357b25bee44bf85d01c2414848fe2c5f09ebe4732bd0a1d3c72de202646345fa66964fbc3247ddeb6a327e87459c036a215fe55fc2 -DIST mlpack-3.4.2.tar.gz 5782921 BLAKE2B d775124462357b489f91f6ef75f5f908d9a9234082c48223f19a728ab9e41cb6576fca9b4b59415d3096471f4ab2d2970296387954977652169a447b8e036263 SHA512 05a66b73cba8d83f630b0999023913e7a4a3214632930ff3c598d964d52bcae4eab113018eecf385130c0e7e9c16c25380b31dd62a2e0ecf419b4bf3856b34b0 diff --git a/sci-libs/mlpack/metadata.xml b/sci-libs/mlpack/metadata.xml deleted file mode 100644 index f587c48a7..000000000 --- a/sci-libs/mlpack/metadata.xml +++ /dev/null @@ -1,27 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>gentoo@aisha.cc</email> - <name>Aisha Tammy</name> - </maintainer> - <maintainer type="project"> - <email>sci@gentoo.org</email> - <name>Gentoo Science Project</name> - </maintainer> - <longdescription lang="en"> - mlpack is a C++ machine learning library with emphasis on - scalability, speed, and ease-of-use. Its aim is to make machine - learning possible for novice users by means of a simple, consistent - API, while simultaneously exploiting C++ language features to - provide maximum performance and maximum flexibility for expert - users. - </longdescription> - <use> - <flag name="arma-debug">build with armadillo dbug symbols</flag> - <flag name="go">build go bindings</flag> - <flag name="julia">build julia bindings</flag> - <flag name="matlab">build matlab bindings</flag> - <flag name="R">build R bindings</flag> - </use> -</pkgmetadata> diff --git a/sci-libs/mlpack/mlpack-3.4.1.ebuild b/sci-libs/mlpack/mlpack-3.4.1.ebuild deleted file mode 100644 index d03dd9ab1..000000000 --- a/sci-libs/mlpack/mlpack-3.4.1.ebuild +++ /dev/null @@ -1,112 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7..9} ) - -inherit cmake python-single-r1 - -DESCRIPTION="scalable C++ machine learning library" -HOMEPAGE="https://www.mlpack.org/" -SRC_URI="https://www.mlpack.org/files/${P}.tar.gz" - -LICENSE="LGPL-3" -SLOT="0" -KEYWORDS="~amd64" -IUSE+="arma-debug debug doc go julia matlab openmp profile R test" -REQUIRED_USE="${PYTHON_REQUIRED_USE} arma-debug? ( debug )" -RESTRICT="!test? ( test )" - -CDEPEND=" - ${PYTHON_DEPS} - julia? ( || ( - dev-lang/julia - dev-lang/julia-bin:* - ) - ) - go? ( dev-lang/go ) - R? ( dev-lang/R ) -" - -RDEPEND=" - ${CDEPEND} - $(python_gen_cond_dep ' - dev-libs/boost[${PYTHON_USEDEP}] - dev-libs/libxml2[${PYTHON_USEDEP}] - ') - dev-python/pandas - dev-python/cython - dev-python/numpy - dev-libs/stb - >=sci-libs/armadillo-8.4.0[arpack,blas,lapack] - sci-libs/ensmallen -" -DEPEND="${RDEPEND}" -BDEPEND=" - ${CDEPEND} - app-text/txt2man - virtual/pkgconfig - doc? ( - app-doc/doxygen - dev-libs/mathjax - ) - test? ( $( python_gen_cond_dep ' - dev-python/pytest[${PYTHON_USEDEP}] - ') - ) -" - -pkg_setup() { - elog "If you want to build matlab bindings then you" - elog "need to make sure that matlab has been installed" - elog "prior to building this package and it is available" - elog "in the standard locations to be found by" - elog "CMake, library finders, header includes and other" - elog "trinkets that are used while compiling." - elog "Matlab will not be entertained as a first class" - elog "citizen until we have enough personnel" - - python-single-r1_pkg_setup -} - -src_prepare() { - sed -i \ - -e "s:share/doc/mlpack:share/doc/${PF}:" \ - -e 's/-O3//g' \ - CMakeLists.txt || die - cmake_src_prepare -} - -src_configure() { - local mycmakeargs=( - -DDISABLE_DOWNLOADS=ON - -DDOWNLOAD_ENSMALLEN=OFF - -DDOWNLOAD_STB_IMAGE=OFF - -DBUILD_WITH_COVERAGE=OFF - -DBUILD_PYTHON_BINDINGS=ON - -DBUILD_SHARED_LIBS=ON - -DBUILD_CLI_EXECUTABLES=ON - -DTEST_VERBOSE=$(usex test) - -DBUILD_TESTS=$(usex test) - -DDEBUG=$(usex debug) - -DPROFILE=$(usex profile) - -DARMA_EXTRA_DEBUG=$(usex arma-debug) - -DUSE_OPENMP=$(usex openmp) - -DMATLAB_BINDINGS=$(usex matlab) - -DBUILD_GO_SHLIB=$(usex go) - -DBUILD_JULIA_BINDINGS=$(usex julia) - -DBUILD_GO_BINDINGS=$(usex go) - -DBUILD_R_BINDINGS=$(usex R) - -DBUILD_MARKDOWN_BINDINGS=$(usex doc) - -DMATHJAX=$(usex doc) - ${EXTRA_ECONF[@]} - ) - cmake_src_configure -} - -src_install() { - cmake_src_install - - python_optimize -} diff --git a/sci-libs/mlpack/mlpack-3.4.2.ebuild b/sci-libs/mlpack/mlpack-3.4.2.ebuild deleted file mode 100644 index bfc7231e1..000000000 --- a/sci-libs/mlpack/mlpack-3.4.2.ebuild +++ /dev/null @@ -1,118 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7..9} ) - -inherit cmake python-single-r1 - -DESCRIPTION="scalable C++ machine learning library" -HOMEPAGE="https://www.mlpack.org/" -SRC_URI="https://www.mlpack.org/files/${P}.tar.gz" - -LICENSE="LGPL-3" -SLOT="0" -KEYWORDS="~amd64" -IUSE+="arma-debug debug doc go julia matlab openmp profile R test" -REQUIRED_USE="${PYTHON_REQUIRED_USE} arma-debug? ( debug )" -RESTRICT="!test? ( test )" - -CDEPEND=" - ${PYTHON_DEPS} - julia? ( || ( - dev-lang/julia - dev-lang/julia-bin:* - ) - ) - go? ( dev-lang/go ) - R? ( dev-lang/R ) -" - -RDEPEND=" - ${CDEPEND} - $(python_gen_cond_dep ' - dev-libs/boost[${PYTHON_USEDEP}] - dev-libs/libxml2[${PYTHON_USEDEP}] - dev-python/pandas[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/cython[${PYTHON_USEDEP}] - ') - dev-libs/stb - >=sci-libs/armadillo-8.4.0[arpack,blas,lapack] - sci-libs/ensmallen -" -DEPEND="${RDEPEND}" -BDEPEND=" - ${CDEPEND} - app-text/txt2man - virtual/pkgconfig - doc? ( - app-doc/doxygen - dev-libs/mathjax - ) - $(python_gen_cond_dep ' - dev-python/cython[${PYTHON_USEDEP}] - ') - test? ( $( python_gen_cond_dep ' - dev-python/pytest[${PYTHON_USEDEP}] - ') - ) -" - -pkg_setup() { - elog "If you want to build matlab bindings then you" - elog "need to make sure that matlab has been installed" - elog "prior to building this package and it is available" - elog "in the standard locations to be found by" - elog "CMake, library finders, header includes and other" - elog "trinkets that are used while compiling." - elog "Matlab will not be entertained as a first class" - elog "citizen until we have enough personnel" - - python-single-r1_pkg_setup -} - -src_prepare() { - sed -i \ - -e "s:share/doc/mlpack:share/doc/${PF}:" \ - -e 's/-O3//g' \ - CMakeLists.txt || die - # drop dep on pytest-runner - sed -i -e "/setup_requires/d" \ - src/mlpack/bindings/python/setup.py.in || die - cmake_src_prepare -} - -src_configure() { - local mycmakeargs=( - -DDISABLE_DOWNLOADS=ON - -DDOWNLOAD_ENSMALLEN=OFF - -DDOWNLOAD_STB_IMAGE=OFF - -DBUILD_WITH_COVERAGE=OFF - -DBUILD_PYTHON_BINDINGS=ON - -DBUILD_SHARED_LIBS=ON - -DBUILD_CLI_EXECUTABLES=ON - -DTEST_VERBOSE=$(usex test) - -DBUILD_TESTS=$(usex test) - -DDEBUG=$(usex debug) - -DPROFILE=$(usex profile) - -DARMA_EXTRA_DEBUG=$(usex arma-debug) - -DUSE_OPENMP=$(usex openmp) - -DMATLAB_BINDINGS=$(usex matlab) - -DBUILD_GO_SHLIB=$(usex go) - -DBUILD_JULIA_BINDINGS=$(usex julia) - -DBUILD_GO_BINDINGS=$(usex go) - -DBUILD_R_BINDINGS=$(usex R) - -DBUILD_MARKDOWN_BINDINGS=$(usex doc) - -DMATHJAX=$(usex doc) - ${EXTRA_ECONF[@]} - ) - cmake_src_configure -} - -src_install() { - cmake_src_install - - python_optimize -} diff --git a/sci-libs/mpfun90/Manifest b/sci-libs/mpfun90/Manifest new file mode 100644 index 000000000..56d64f14c --- /dev/null +++ b/sci-libs/mpfun90/Manifest @@ -0,0 +1 @@ +DIST 2023-02-26.tar.gz 66883 BLAKE2B 3b93099977b614e0d9a16df76f7f3c1eda9b76905664db3f0dc0ad0bd00b503105649aeb4c960d7293e7d536e3a902dbe8cb62f89be3bce655e9bae963097f35 SHA512 7280ecba6cb95f15cea91ea95f5cf21b69f76a490a3c92bef40cf8a1dfadd651cb93480bddddd684d0f18144db65cdb1590964df11d37a9f35eaeeb94f369d63 diff --git a/sci-libs/mpfun90/metadata.xml b/sci-libs/mpfun90/metadata.xml new file mode 100644 index 000000000..e3eb0d9c1 --- /dev/null +++ b/sci-libs/mpfun90/metadata.xml @@ -0,0 +1,18 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>alexander@neuwirth-informatik.de</email> + <name>Alexander Puck Neuwirth</name> + </maintainer> + <maintainer type="project"> + <email>sci-physics@gentoo.org</email> + <name>Gentoo Physics Project</name> + </maintainer> + <longdescription lang="en"> + This package permits one to perform floating-point computations (real and complex) to arbitrarily high numeric precision + </longdescription> + <upstream> + <remote-id type="github">APN-Pucky/mpfun90</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/mpfun90/mpfun90-2023.02.26.ebuild b/sci-libs/mpfun90/mpfun90-2023.02.26.ebuild new file mode 100644 index 000000000..4f885fa2c --- /dev/null +++ b/sci-libs/mpfun90/mpfun90-2023.02.26.ebuild @@ -0,0 +1,29 @@ +# Copyright 2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit toolchain-funcs fortran-2 + +DESCRIPTION="High-Precision Software" +HOMEPAGE=" + https://www.davidhbailey.com/dhbsoftware/ + https://github.com/APN-Pucky/mpfun90 +" +MY_PV=$(ver_rs 1- '-') +SRC_URI="https://github.com/APN-Pucky/mpfun90/archive/refs/tags/${MY_PV}.tar.gz" +S="${WORKDIR}/mpfun90-${MY_PV}" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" + +src_compile() { + emake -j1 dynamic +} + +src_install() { + doheader *.mod + dolib.so libmpfun90.so + dolib.a libmpfun90.a +} diff --git a/sci-libs/nexus/nexus-4.4.3_p20200126.ebuild b/sci-libs/nexus/nexus-4.4.3_p20200126.ebuild index b19a65fbe..58d8264cf 100644 --- a/sci-libs/nexus/nexus-4.4.3_p20200126.ebuild +++ b/sci-libs/nexus/nexus-4.4.3_p20200126.ebuild @@ -29,7 +29,7 @@ RDEPEND=" " DEPEND="${RDEPEND}" BDEPEND=" - app-doc/doxygen[dot] + app-text/doxygen[dot] " pkg_setup() { diff --git a/sci-libs/nibabel/Manifest b/sci-libs/nibabel/Manifest index 31eb1f65e..d50b1b3b7 100644 --- a/sci-libs/nibabel/Manifest +++ b/sci-libs/nibabel/Manifest @@ -1,3 +1,2 @@ -DIST nibabel-2.5.1.tar.gz 4281663 BLAKE2B 361f1118d850a76fb8d2aa3ac6ebf0da711cf8df93aa6e2689201f3e713f35e028442ef00f69ce7a4a96d3c376b4966d0b76a087005123101f743b4d6074d3b2 SHA512 49de1a42113e64a56336e02f3143588b574c7b063b10b892ee125048451be701955e505bd1d51183327e2ee221f8364005fdd9fa7d256343113ab6ca1994820d -DIST nibabel-3.0.2.tar.gz 4336181 BLAKE2B b95ea57f28265eab627caea71f65c8ad1b0f868d40d80efb68f2dbb1e81f7d4f10b2da21d33f803abcd9441f3afe2c861f96828f8701f3981e4b7a4b2f97308e SHA512 51a10a72ade0382e43a006a0b9453b0c00f962a1c0d32c7a9da6ce3b9c95db05cd3bd672389d514107768b688a8315cba2e34d52bc845db3ca3e7912a1a0a8ac -DIST nibabel-3.2.1.tar.gz 4442534 BLAKE2B 5a76275c0c3746bbe094789350f4f6d9dc17e332915c9f567660138c44ba50672415272d21d7b0834c77f4f9660950bda8c684f7664d58f0e5784b782384cb2f SHA512 5c5d95313f4b22462ba67c23d52dd34ed5d690c72a3137b21ac0bdbc4d20aa4f0c1d87d23c675f8c2f6e4335dc51fb9ab788ac8c63be56eec8ab8657ed95a6d7 +DIST nibabel-5.0.0.tar.gz 4480342 BLAKE2B ef5c8fcd27fda60ae85fb657b360453a3b6ae58ea2b8e4eb55bfeb4bdecf6aa94cf1594d0b90a3187f6f3bad32fa9c721bba0827ec0966f799e5b59720778956 SHA512 5f27c03518c47856ecb33b878e9969ea33c7ebb717e6f4f9d89d9fdf415459e47675353051cdb824efea4e6a819759e0bf61cf49caa7212411c63423a77ed0d4 +DIST nibabel-5.1.0.tar.gz 4522882 BLAKE2B 62ffd86e14f66ab57bcfa127e9d0da0b46a04224739b61493080848305295f25136b51bc6fae69c0ec653b4185a28a1b5c323573588abc02f6ebb7372808b8fe SHA512 a07b4c2742ac3af8c0a87a0fa0562ed55c1377fb2067a7813fa2482cab4fc407f013b13b541dd863fa9620c644058296040487aeaba0b26818ff783b2dc2474e diff --git a/sci-libs/nibabel/nibabel-2.5.1.ebuild b/sci-libs/nibabel/nibabel-2.5.1.ebuild deleted file mode 100644 index 3316b84d5..000000000 --- a/sci-libs/nibabel/nibabel-2.5.1.ebuild +++ /dev/null @@ -1,42 +0,0 @@ -# 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="Access a cacophony of neuro-imaging file formats" -HOMEPAGE="https://nipy.org/nibabel/" -SRC_URI="https://github.com/nipy/nibabel/archive/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="dicom doc test" -RESTRICT="!test? ( test )" - -RDEPEND=" - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/scipy[${PYTHON_USEDEP}] - dev-python/mock[${PYTHON_USEDEP}] - dicom? ( - sci-libs/pydicom - dev-python/pillow[${PYTHON_USEDEP}] - ) -" -DEPEND=" - dev-python/setuptools[${PYTHON_USEDEP}] - test? ( - ${RDEPEND} - dev-python/nose[${PYTHON_USEDEP}] - ) - doc? ( dev-python/sphinx[${PYTHON_USEDEP}] ) -" - -python_test() { - cd "${BUILD_DIR}" || die - echo "backend: Agg" > matplotlibrc - MPLCONFIGDIR=. nosetests || die -} diff --git a/sci-libs/nibabel/nibabel-3.0.2.ebuild b/sci-libs/nibabel/nibabel-3.0.2.ebuild deleted file mode 100644 index 3316b84d5..000000000 --- a/sci-libs/nibabel/nibabel-3.0.2.ebuild +++ /dev/null @@ -1,42 +0,0 @@ -# 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="Access a cacophony of neuro-imaging file formats" -HOMEPAGE="https://nipy.org/nibabel/" -SRC_URI="https://github.com/nipy/nibabel/archive/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="dicom doc test" -RESTRICT="!test? ( test )" - -RDEPEND=" - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/scipy[${PYTHON_USEDEP}] - dev-python/mock[${PYTHON_USEDEP}] - dicom? ( - sci-libs/pydicom - dev-python/pillow[${PYTHON_USEDEP}] - ) -" -DEPEND=" - dev-python/setuptools[${PYTHON_USEDEP}] - test? ( - ${RDEPEND} - dev-python/nose[${PYTHON_USEDEP}] - ) - doc? ( dev-python/sphinx[${PYTHON_USEDEP}] ) -" - -python_test() { - cd "${BUILD_DIR}" || die - echo "backend: Agg" > matplotlibrc - MPLCONFIGDIR=. nosetests || die -} diff --git a/sci-libs/nibabel/nibabel-3.2.1.ebuild b/sci-libs/nibabel/nibabel-3.2.1.ebuild deleted file mode 100644 index d469867f9..000000000 --- a/sci-libs/nibabel/nibabel-3.2.1.ebuild +++ /dev/null @@ -1,36 +0,0 @@ -# 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="Access a cacophony of neuro-imaging file formats" -HOMEPAGE="https://nipy.org/nibabel/" -SRC_URI="https://github.com/nipy/nibabel/archive/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="dicom" - -RDEPEND=" - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/packaging[${PYTHON_USEDEP}] - dev-python/scipy[${PYTHON_USEDEP}] - dev-python/mock[${PYTHON_USEDEP}] - dicom? ( - sci-libs/pydicom - dev-python/pillow[${PYTHON_USEDEP}] - ) -" - -BDEPEND="test? ( - dev-python/pytest-doctestplus[${PYTHON_USEDEP}] -)" - -distutils_enable_sphinx doc/source dev-python/texext dev-python/numpydoc dev-python/matplotlib -distutils_enable_tests pytest diff --git a/sci-libs/nibabel/nibabel-5.0.0.ebuild b/sci-libs/nibabel/nibabel-5.0.0.ebuild new file mode 100644 index 000000000..0fec805b1 --- /dev/null +++ b/sci-libs/nibabel/nibabel-5.0.0.ebuild @@ -0,0 +1,35 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=hatchling + +inherit distutils-r1 + +DESCRIPTION="Access a cacophony of neuro-imaging file formats" +HOMEPAGE="https://nipy.org/nibabel/" +SRC_URI="https://github.com/nipy/nibabel/archive/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="dicom" + +RDEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/packaging[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + dicom? ( + dev-python/pillow[${PYTHON_USEDEP}] + sci-libs/pydicom + ) +" + +BDEPEND="test? ( + dev-python/pytest-httpserver[${PYTHON_USEDEP}] +)" + +distutils_enable_sphinx doc/source dev-python/texext dev-python/numpydoc dev-python/matplotlib +distutils_enable_tests pytest diff --git a/sci-libs/nibabel/nibabel-5.1.0.ebuild b/sci-libs/nibabel/nibabel-5.1.0.ebuild new file mode 100644 index 000000000..0fec805b1 --- /dev/null +++ b/sci-libs/nibabel/nibabel-5.1.0.ebuild @@ -0,0 +1,35 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=hatchling + +inherit distutils-r1 + +DESCRIPTION="Access a cacophony of neuro-imaging file formats" +HOMEPAGE="https://nipy.org/nibabel/" +SRC_URI="https://github.com/nipy/nibabel/archive/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="dicom" + +RDEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/packaging[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + dicom? ( + dev-python/pillow[${PYTHON_USEDEP}] + sci-libs/pydicom + ) +" + +BDEPEND="test? ( + dev-python/pytest-httpserver[${PYTHON_USEDEP}] +)" + +distutils_enable_sphinx doc/source dev-python/texext dev-python/numpydoc dev-python/matplotlib +distutils_enable_tests pytest diff --git a/sci-libs/nibabel/nibabel-9999.ebuild b/sci-libs/nibabel/nibabel-9999.ebuild deleted file mode 100644 index 283ad8804..000000000 --- a/sci-libs/nibabel/nibabel-9999.ebuild +++ /dev/null @@ -1,37 +0,0 @@ -# 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 git-r3 - -DESCRIPTION="Access a cacophony of neuro-imaging file formats" -HOMEPAGE="https://nipy.org/nibabel/" -SRC_URI="" -EGIT_REPO_URI="https://github.com/nipy/nibabel.git" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="" -IUSE="dicom" - -RDEPEND=" - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/packaging[${PYTHON_USEDEP}] - dev-python/scipy[${PYTHON_USEDEP}] - dev-python/mock[${PYTHON_USEDEP}] - dicom? ( - sci-libs/pydicom - dev-python/pillow[${PYTHON_USEDEP}] - ) -" - -BDEPEND="test? ( - dev-python/pytest-doctestplus[${PYTHON_USEDEP}] -)" - -distutils_enable_sphinx doc/source dev-python/texext dev-python/numpydoc dev-python/matplotlib -distutils_enable_tests pytest diff --git a/sci-libs/nipy/Manifest b/sci-libs/nipy/Manifest index d9bac81b5..9444a9dd3 100644 --- a/sci-libs/nipy/Manifest +++ b/sci-libs/nipy/Manifest @@ -1 +1 @@ -DIST nipy-0.4.2.tar.gz 2403688 BLAKE2B 883377356787652450bb5a8090be48708144c9d11473232248d48e8bc36eb292cdd672ae30b337de6fb8c5e593a772489908c9575c2f97a8dbd82a8e4d6ad0df SHA512 730654e422c9fd15c0abf7ce0e0cb5e9569788527a35e9cc6deb71e2384b0ed2dbbf82f9eafe9cd739647bb1dc3a3d43606d0244fae5accd0896f1fc5bb3a8cc +DIST nipy-0.6.0.gh.tar.gz 1650342 BLAKE2B 5f375e23fb2d895cfb4320b8ec92cefcf902f3768b6b8dc2ba26b4db30168eb4a29d38be1241e2ae5ae9d87013beb64427c8aca1ac2adaa92d083c700dc0453a SHA512 a59485ccd677c443b9d1e2358c3b3d523ddfa9f390c180661e9afaf3b69943e1b1670c44410954e1bba11c88b9ca20e9e586392804b5c99e9f58b5b68df4641f diff --git a/sci-libs/nipy/metadata.xml b/sci-libs/nipy/metadata.xml index 327dd23d3..30440d9a2 100644 --- a/sci-libs/nipy/metadata.xml +++ b/sci-libs/nipy/metadata.xml @@ -11,5 +11,6 @@ </maintainer> <upstream> <remote-id type="pypi">nipy</remote-id> + <remote-id type="github">nipy/nipy</remote-id> </upstream> </pkgmetadata> diff --git a/sci-libs/nipy/nipy-0.4.2.ebuild b/sci-libs/nipy/nipy-0.4.2.ebuild deleted file mode 100644 index c20d904f5..000000000 --- a/sci-libs/nipy/nipy-0.4.2.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 - -PYTHON_COMPAT=( python3_{7..9} ) - -inherit distutils-r1 flag-o-matic - -DESCRIPTION="Neuroimaging tools for Python" -HOMEPAGE="https://nipy.org/" -SRC_URI="https://github.com/${PN}/${PN}/archive/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -RDEPEND=" - dev-python/prov[${PYTHON_USEDEP}] - dev-python/scipy[${PYTHON_USEDEP}] - dev-python/sympy[${PYTHON_USEDEP}] - >=sci-libs/nibabel-1.2[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - " - -DEPEND=" - ${RDEPEND} - dev-python/setuptools[${PYTHON_USEDEP}] - " - -python_prepare_all() { - distutils-r1_python_prepare_all - # bug #397605 - [[ ${CHOST} == *-darwin* ]] \ - && append-ldflags -bundle "-undefined dynamic_lookup" \ - || append-ldflags -shared - - # nipy uses the horrible numpy.distutils automagic -} - -python_test() { - distutils-r1_install_for_testing - cp nipy/testing/*.nii.gz "${BUILD_DIR}/lib/nipy/testing/" - cp nipy/modalities/fmri/tests/*.{mat,npz,txt} "${BUILD_DIR}/lib/nipy/modalities/fmri/tests/" - cp nipy/algorithms/statistics/models/tests/test_data.bin "${BUILD_DIR}/lib/nipy/algorithms/statistics/models/tests" - cp nipy/labs/spatial_models/tests/some_blobs.nii "${BUILD_DIR}/lib/nipy/labs/spatial_models/tests/some_blobs.nii" - mkdir "${BUILD_DIR}/lib/nipy/algorithms/diagnostics/tests/data/" - cp nipy/algorithms/diagnostics/tests/data/tsdiff_results.mat "${BUILD_DIR}/lib/nipy/algorithms/diagnostics/tests/data/" - cd "${BUILD_DIR}" || die - echo "backend : agg" > matplotlibrc - nosetests || die -} diff --git a/sci-libs/nipy/nipy-0.6.0.ebuild b/sci-libs/nipy/nipy-0.6.0.ebuild new file mode 100644 index 000000000..8f8ea83e8 --- /dev/null +++ b/sci-libs/nipy/nipy-0.6.0.ebuild @@ -0,0 +1,37 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=meson-python +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_EXT=1 + +inherit distutils-r1 + +DESCRIPTION="Neuroimaging tools for Python" +HOMEPAGE="https://nipy.org/" +SRC_URI="https://github.com/nipy/nipy/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="" +# Test data unavailable: +# https://github.com/nipy/nipy/issues/561#event-11866547632 +RESTRICT="test" + +RDEPEND=" + dev-python/scipy[${PYTHON_USEDEP}] + dev-python/sympy[${PYTHON_USEDEP}] + sci-libs/nibabel[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + " +DEPEND="" + +distutils_enable_tests pytest + +python_test() { + rm -rf nipy || die + epytest +} diff --git a/sci-libs/nipy/nipy-9999.ebuild b/sci-libs/nipy/nipy-9999.ebuild deleted file mode 100644 index 7acc9a234..000000000 --- a/sci-libs/nipy/nipy-9999.ebuild +++ /dev/null @@ -1,54 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7..9} ) - -inherit distutils-r1 flag-o-matic git-r3 - -DESCRIPTION="Neuroimaging tools for Python" -HOMEPAGE="https://nipy.org/" -SRC_URI="" -EGIT_REPO_URI="https://github.com/nipy/nipy" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="" -IUSE="" - -RDEPEND=" - dev-python/prov[${PYTHON_USEDEP}] - dev-python/scipy[${PYTHON_USEDEP}] - dev-python/sympy[${PYTHON_USEDEP}] - >=sci-libs/nibabel-1.2[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - " - -DEPEND=" - ${RDEPEND} - dev-python/setuptools[${PYTHON_USEDEP}] - " - -python_prepare_all() { - distutils-r1_python_prepare_all - # bug #397605 - [[ ${CHOST} == *-darwin* ]] \ - && append-ldflags -bundle "-undefined dynamic_lookup" \ - || append-ldflags -shared - - # nipy uses the horrible numpy.distutils automagic -} - -python_test() { - distutils-r1_install_for_testing - cp nipy/testing/*.nii.gz "${BUILD_DIR}/lib/nipy/testing/" - cp nipy/modalities/fmri/tests/*.{mat,npz,txt} "${BUILD_DIR}/lib/nipy/modalities/fmri/tests/" - cp nipy/algorithms/statistics/models/tests/test_data.bin "${BUILD_DIR}/lib/nipy/algorithms/statistics/models/tests" - cp nipy/labs/spatial_models/tests/some_blobs.nii "${BUILD_DIR}/lib/nipy/labs/spatial_models/tests/some_blobs.nii" - mkdir "${BUILD_DIR}/lib/nipy/algorithms/diagnostics/tests/data/" - cp nipy/algorithms/diagnostics/tests/data/tsdiff_results.mat "${BUILD_DIR}/lib/nipy/algorithms/diagnostics/tests/data/" - cd "${BUILD_DIR}" || die - echo "backend : agg" > matplotlibrc - nosetests || die -} diff --git a/sci-libs/nipype/Manifest b/sci-libs/nipype/Manifest index a3c77d4ff..6c9059e1c 100644 --- a/sci-libs/nipype/Manifest +++ b/sci-libs/nipype/Manifest @@ -1 +1,2 @@ -DIST nipype-1.5.0.tar.gz 2735317 BLAKE2B d618714b15defde52325bac32a80449846b448d1c141a21f9d950976c8c89624d714dbab10b4cd99fe20d4eb99ceb4095ebc6ddc567f57b3803e2c16ffda155a SHA512 eb11096a090855278c3e76ffe9643ab4de046a017511ba51f59448fd8cf9d67a4f6c552acbbbdd38065cfb456c24fd21299cf698fa05c5be507524622f28ac85 +DIST nipype-1.8.4.tar.gz 2914433 BLAKE2B c25b82c22641f6df2b57c8a07fd318034bb4fe4eaa1037baebc1ffc03d3e1add347d9f0c94139144fc17043a5c97926c88b40755f19794cc71366d76ba339698 SHA512 8949226accd7c158b6a3ec92389a11760a9b306098ccb8ef50844efbddb4e6a9108bb6a32ec7b0402c4ea56881a3548b052fe7f5e757d2771aea5b2eebc9377b +DIST nipype-1.8.6.tar.gz 2921102 BLAKE2B 79a2131b8265f1b0a3a8d2fa6ff56cbbc2d393c79099178cf036d82357a971a72f024b132d7b4d7d4af85165f562192b6cc5cfc9e797105bdc009734e8a89033 SHA512 23140beb02f4c3807d9d0291bde41ce8c1b06e48dc94001b007f193caaa89428387d1528fa20ae328d2c4a781024c9acf07f7be9ce507ecb2f1daf338c092eec diff --git a/sci-libs/nipype/files/nipype-1.5.0-collections.patch b/sci-libs/nipype/files/nipype-1.5.0-collections.patch new file mode 100644 index 000000000..e784ba48b --- /dev/null +++ b/sci-libs/nipype/files/nipype-1.5.0-collections.patch @@ -0,0 +1,28 @@ +--- a/nipype/interfaces/base/traits_extension.py 2020-06-03 11:08:30.000000000 -0400 ++++ b/nipype/interfaces/base/traits_extension.py 2022-07-11 14:09:31.847784312 -0400 +@@ -19,7 +19,10 @@ + (usually by Robert Kern). + + """ +-from collections import Sequence ++try: ++ from collections import Sequence ++except ImportError: ++ from collections.abc import Sequence + + # perform all external trait imports here + from traits import __version__ as traits_version +--- a/nipype/utils/misc.py 2020-06-03 11:08:30.000000000 -0400 ++++ b/nipype/utils/misc.py 2020-06-03 14:08:57.951408897 -0400 +@@ -6,7 +6,10 @@ + import os + import sys + import re +-from collections import Iterator ++try: ++ from collections import Iterator ++except ImportError: ++ from collections.abc import Iterator + from warnings import warn + + from distutils.version import LooseVersion diff --git a/sci-libs/nipype/files/nipype-1.8.4-dependency_compatibility.patch b/sci-libs/nipype/files/nipype-1.8.4-dependency_compatibility.patch new file mode 100644 index 000000000..9811139e7 --- /dev/null +++ b/sci-libs/nipype/files/nipype-1.8.4-dependency_compatibility.patch @@ -0,0 +1,575 @@ +From a31870d0f9dc0e774f1cf9d18351586f78ecb252 Mon Sep 17 00:00:00 2001 +From: Chris Markiewicz <effigies@gmail.com> +Date: Sat, 28 Jan 2023 08:11:54 -0500 +Subject: [PATCH 1/9] FIX: Set dtypes for integer test images + +NiBabel 4 began warning that int64 images would error, and NiBabel 5 +began erroring if not passed an explicit dtype or header. + +We don't need int64 images, just set some sensible dtypes. +--- + nipype/algorithms/tests/test_ErrorMap.py | 2 +- + nipype/algorithms/tests/test_TSNR.py | 3 ++- + nipype/algorithms/tests/test_metrics.py | 2 +- + 3 files changed, 4 insertions(+), 3 deletions(-) + +diff --git a/nipype/algorithms/tests/test_ErrorMap.py b/nipype/algorithms/tests/test_ErrorMap.py +index 98f05d8e17..adac507bad 100644 +--- a/nipype/algorithms/tests/test_ErrorMap.py ++++ b/nipype/algorithms/tests/test_ErrorMap.py +@@ -17,7 +17,7 @@ def test_errormap(tmpdir): + volume1 = np.array([[[2.0, 8.0], [1.0, 2.0]], [[1.0, 9.0], [0.0, 3.0]]]) + # Alan Turing's birthday + volume2 = np.array([[[0.0, 7.0], [2.0, 3.0]], [[1.0, 9.0], [1.0, 2.0]]]) +- mask = np.array([[[1, 0], [0, 1]], [[1, 0], [0, 1]]]) ++ mask = np.array([[[1, 0], [0, 1]], [[1, 0], [0, 1]]], dtype=np.uint8) + + img1 = nb.Nifti1Image(volume1, np.eye(4)) + img2 = nb.Nifti1Image(volume2, np.eye(4)) +diff --git a/nipype/algorithms/tests/test_TSNR.py b/nipype/algorithms/tests/test_TSNR.py +index 26c1019b63..320bec8ab2 100644 +--- a/nipype/algorithms/tests/test_TSNR.py ++++ b/nipype/algorithms/tests/test_TSNR.py +@@ -131,5 +131,6 @@ def assert_unchanged(self, expected_ranges): + [ + [[[2, 4, 3, 9, 1], [3, 6, 4, 7, 4]], [[8, 3, 4, 6, 2], [4, 0, 4, 4, 2]]], + [[[9, 7, 5, 5, 7], [7, 8, 4, 8, 4]], [[0, 4, 7, 1, 7], [6, 8, 8, 8, 7]]], +- ] ++ ], ++ dtype=np.int16, + ) +diff --git a/nipype/algorithms/tests/test_metrics.py b/nipype/algorithms/tests/test_metrics.py +index ad7502992e..3652fc2ce5 100644 +--- a/nipype/algorithms/tests/test_metrics.py ++++ b/nipype/algorithms/tests/test_metrics.py +@@ -45,7 +45,7 @@ def test_fuzzy_overlap(tmpdir): + + # Just considering the mask, the central pixel + # that raised the index now is left aside. +- data = np.zeros((3, 3, 3), dtype=int) ++ data = np.zeros((3, 3, 3), dtype=np.uint8) + data[0, 0, 0] = 1 + data[2, 2, 2] = 1 + nb.Nifti1Image(data, np.eye(4)).to_filename("mask.nii.gz") + +From 443492e82f3b197ad739cb244912ced652853a8d Mon Sep 17 00:00:00 2001 +From: Chris Markiewicz <effigies@gmail.com> +Date: Sat, 28 Jan 2023 08:43:07 -0500 +Subject: [PATCH 2/9] FIX: Coerce depidx to lil_matrix + +--- + nipype/pipeline/plugins/base.py | 18 +++++++++++++----- + 1 file changed, 13 insertions(+), 5 deletions(-) + +diff --git a/nipype/pipeline/plugins/base.py b/nipype/pipeline/plugins/base.py +index a927b24686..3d600dda55 100644 +--- a/nipype/pipeline/plugins/base.py ++++ b/nipype/pipeline/plugins/base.py +@@ -21,6 +21,18 @@ + logger = logging.getLogger("nipype.workflow") + + ++def _graph_to_lil_matrix(graph, nodelist): ++ """Provide a sparse linked list matrix across various NetworkX versions""" ++ import scipy.sparse as ssp ++ ++ try: ++ from networkx import to_scipy_sparse_array ++ except ImportError: # NetworkX < 2.7 ++ from networkx import to_scipy_sparse_matrix as to_scipy_sparse_array ++ ++ return ssp.lil_matrix(to_scipy_sparse_array(graph, nodelist=nodelist, format="lil")) ++ ++ + class PluginBase(object): + """Base class for plugins.""" + +@@ -431,12 +443,8 @@ def _task_finished_cb(self, jobid, cached=False): + + def _generate_dependency_list(self, graph): + """Generates a dependency list for a list of graphs.""" +- import networkx as nx +- + self.procs, _ = topological_sort(graph) +- self.depidx = nx.to_scipy_sparse_matrix( +- graph, nodelist=self.procs, format="lil" +- ) ++ self.depidx = _graph_to_lil_matrix(graph, nodelist=self.procs) + self.refidx = self.depidx.astype(int) + self.proc_done = np.zeros(len(self.procs), dtype=bool) + self.proc_pending = np.zeros(len(self.procs), dtype=bool) + +From 34ef6c2ff89f327fcf2951b792ef38b6d56f8c4e Mon Sep 17 00:00:00 2001 +From: Chris Markiewicz <effigies@gmail.com> +Date: Sat, 28 Jan 2023 11:57:54 -0500 +Subject: [PATCH 3/9] FIX: Accept "str" in dipy type (includes "string") + +--- + nipype/interfaces/dipy/base.py | 6 +++--- + 1 file changed, 3 insertions(+), 3 deletions(-) + +diff --git a/nipype/interfaces/dipy/base.py b/nipype/interfaces/dipy/base.py +index d8a1c0fbf5..161ed33227 100644 +--- a/nipype/interfaces/dipy/base.py ++++ b/nipype/interfaces/dipy/base.py +@@ -110,7 +110,7 @@ def convert_to_traits_type(dipy_type, is_file=False): + """Convert DIPY type to Traits type.""" + dipy_type = dipy_type.lower() + is_mandatory = bool("optional" not in dipy_type) +- if "variable" in dipy_type and "string" in dipy_type: ++ if "variable" in dipy_type and "str" in dipy_type: + return traits.ListStr, is_mandatory + elif "variable" in dipy_type and "int" in dipy_type: + return traits.ListInt, is_mandatory +@@ -120,9 +120,9 @@ def convert_to_traits_type(dipy_type, is_file=False): + return traits.ListBool, is_mandatory + elif "variable" in dipy_type and "complex" in dipy_type: + return traits.ListComplex, is_mandatory +- elif "string" in dipy_type and not is_file: ++ elif "str" in dipy_type and not is_file: + return traits.Str, is_mandatory +- elif "string" in dipy_type and is_file: ++ elif "str" in dipy_type and is_file: + return File, is_mandatory + elif "int" in dipy_type: + return traits.Int, is_mandatory + +From 83c8cf86d6bbb0dc04aa58dbe5119fd864342d9c Mon Sep 17 00:00:00 2001 +From: Chris Markiewicz <effigies@gmail.com> +Date: Sat, 28 Jan 2023 11:55:34 -0500 +Subject: [PATCH 4/9] MNT: Update requirements from info.py + +--- + requirements.txt | 6 +++--- + 1 file changed, 3 insertions(+), 3 deletions(-) + +diff --git a/requirements.txt b/requirements.txt +index afec34ebfd..331e2c5def 100644 +--- a/requirements.txt ++++ b/requirements.txt +@@ -2,8 +2,7 @@ + click>=6.6.0 + networkx>=2.0 + nibabel>=2.1.0 +-numpy>=1.13 ; python_version < "3.7" +-numpy>=1.15.3 ; python_version >= "3.7" ++numpy>=1.17 + packaging + prov>=1.5.2 + pydot>=1.2.3 +@@ -11,6 +10,7 @@ python-dateutil>=2.2 + rdflib>=5.0.0 + scipy>=0.14 + simplejson>=3.8.0 +-traits>=4.6,!=5.0 ++traits>=4.6,<6.4,!=5.0 + filelock>=3.0.0 + etelemetry>=0.2.0 ++looseversion + +From 24c55a6f48aa658320ff35283b6f91ec38b13a40 Mon Sep 17 00:00:00 2001 +From: Horea Christian <chr@chymera.eu> +Date: Thu, 26 Jan 2023 02:28:33 -0500 +Subject: [PATCH 5/9] Writing pickles directly as networkx no longer ships + write_gpickle + +--- + nipype/interfaces/cmtk/cmtk.py | 12 ++++++++---- + nipype/interfaces/cmtk/nbs.py | 7 +++++-- + nipype/interfaces/cmtk/nx.py | 12 ++++++++---- + nipype/interfaces/cmtk/tests/test_nbs.py | 4 +++- + 4 files changed, 24 insertions(+), 11 deletions(-) + +diff --git a/nipype/interfaces/cmtk/cmtk.py b/nipype/interfaces/cmtk/cmtk.py +index 8775a8517e..8df7a1c5ad 100644 +--- a/nipype/interfaces/cmtk/cmtk.py ++++ b/nipype/interfaces/cmtk/cmtk.py +@@ -226,7 +226,8 @@ def cmat( + # Add node information from specified parcellation scheme + path, name, ext = split_filename(resolution_network_file) + if ext == ".pck": +- gp = nx.read_gpickle(resolution_network_file) ++ with open(resolution_network_file, 'rb') as f: ++ gp = pickle.load(f) + elif ext == ".graphml": + gp = nx.read_graphml(resolution_network_file) + else: +@@ -379,7 +380,8 @@ def cmat( + fibdev.add_edge(u, v, weight=di["fiber_length_std"]) + + iflogger.info("Writing network as %s", matrix_name) +- nx.write_gpickle(G, op.abspath(matrix_name)) ++ with open(op.abspath(matrix_name), 'wb') as f: ++ pickle.dump(G, f, pickle.HIGHEST_PROTOCOL) + + numfib_mlab = nx.to_numpy_matrix(numfib, dtype=int) + numfib_dict = {"number_of_fibers": numfib_mlab} +@@ -394,7 +396,8 @@ def cmat( + path, name, ext = split_filename(matrix_name) + intersection_matrix_name = op.abspath(name + "_intersections") + ext + iflogger.info("Writing intersection network as %s", intersection_matrix_name) +- nx.write_gpickle(I, intersection_matrix_name) ++ with open(intersection_matrix_name, 'wb') as f: ++ pickle.dump(I, f, pickle.HIGHEST_PROTOCOL) + + path, name, ext = split_filename(matrix_mat_name) + if not ext == ".mat": +@@ -1070,7 +1073,8 @@ def create_nodes(roi_file, resolution_network_file, out_filename): + ) + ) + G.nodes[int(u)]["dn_position"] = tuple([xyz[0], xyz[2], -xyz[1]]) +- nx.write_gpickle(G, out_filename) ++ with open(out_filename, 'wb') as f: ++ pickle.dump(G, f, pickle.HIGHEST_PROTOCOL) + return out_filename + + +diff --git a/nipype/interfaces/cmtk/nbs.py b/nipype/interfaces/cmtk/nbs.py +index 4e1db9ffb7..57d63897c7 100644 +--- a/nipype/interfaces/cmtk/nbs.py ++++ b/nipype/interfaces/cmtk/nbs.py +@@ -6,6 +6,7 @@ + + import numpy as np + import networkx as nx ++import pickle + + from ... import logging + from ..base import ( +@@ -172,12 +173,14 @@ def _run_interface(self, runtime): + + path = op.abspath("NBS_Result_" + details) + iflogger.info(path) +- nx.write_gpickle(nbsgraph, path) ++ with open(path, 'wb') as f: ++ pickle.dump(nbsgraph, f, pickle.HIGHEST_PROTOCOL) + iflogger.info("Saving output NBS edge network as %s", path) + + pval_path = op.abspath("NBS_P_vals_" + details) + iflogger.info(pval_path) +- nx.write_gpickle(nbs_pval_graph, pval_path) ++ with open(pval_path, 'wb') as f: ++ pickle.dump(nbs_pval_graph, f, pickle.HIGHEST_PROTOCOL) + iflogger.info("Saving output p-value network as %s", pval_path) + return runtime + +diff --git a/nipype/interfaces/cmtk/nx.py b/nipype/interfaces/cmtk/nx.py +index aaf4bece39..a662eb65c6 100644 +--- a/nipype/interfaces/cmtk/nx.py ++++ b/nipype/interfaces/cmtk/nx.py +@@ -200,7 +200,8 @@ def average_networks(in_files, ntwk_res_file, group_id): + + # Writes the networks and returns the name + network_name = group_id + "_average.pck" +- nx.write_gpickle(avg_ntwk, op.abspath(network_name)) ++ with open(op.abspath(network_name), 'wb') as f: ++ pickle.dump(avg_ntwk, f, pickle.HIGHEST_PROTOCOL) + iflogger.info("Saving average network as %s", op.abspath(network_name)) + avg_ntwk = fix_keys_for_gexf(avg_ntwk) + network_name = group_id + "_average.gexf" +@@ -483,7 +484,8 @@ def _run_interface(self, runtime): + for key in list(node_measures.keys()): + newntwk = add_node_data(node_measures[key], ntwk) + out_file = op.abspath(self._gen_outfilename(key, "pck")) +- nx.write_gpickle(newntwk, out_file) ++ with open(out_file, 'wb') as f: ++ pickle.dump(newntwk, f, pickle.HIGHEST_PROTOCOL) + nodentwks.append(out_file) + if isdefined(self.inputs.out_node_metrics_matlab): + node_out_file = op.abspath(self.inputs.out_node_metrics_matlab) +@@ -497,7 +499,8 @@ def _run_interface(self, runtime): + for key in list(edge_measures.keys()): + newntwk = add_edge_data(edge_measures[key], ntwk) + out_file = op.abspath(self._gen_outfilename(key, "pck")) +- nx.write_gpickle(newntwk, out_file) ++ with open(out_file, 'wb') as f: ++ pickle.dump(newntwk, f, pickle.HIGHEST_PROTOCOL) + edgentwks.append(out_file) + if isdefined(self.inputs.out_edge_metrics_matlab): + edge_out_file = op.abspath(self.inputs.out_edge_metrics_matlab) +@@ -521,7 +524,8 @@ def _run_interface(self, runtime): + out_file = op.abspath( + self._gen_outfilename(self.inputs.out_k_crust, "pck") + ) +- nx.write_gpickle(ntwk_measures[key], out_file) ++ with open(out_file, 'wb') as f: ++ pickle.dump(ntwk_measures[key], f, pickle.HIGHEST_PROTOCOL) + kntwks.append(out_file) + gpickled.extend(kntwks) + +diff --git a/nipype/interfaces/cmtk/tests/test_nbs.py b/nipype/interfaces/cmtk/tests/test_nbs.py +index 46da939f1a..7a60b407a4 100644 +--- a/nipype/interfaces/cmtk/tests/test_nbs.py ++++ b/nipype/interfaces/cmtk/tests/test_nbs.py +@@ -2,6 +2,7 @@ + from ....utils.misc import package_check + import numpy as np + import networkx as nx ++import pickle + import pytest + + have_cv = True +@@ -20,7 +21,8 @@ def creating_graphs(tmpdir): + G = nx.from_numpy_matrix(graph) + out_file = tmpdir.strpath + graphnames[idx] + ".pck" + # Save as pck file +- nx.write_gpickle(G, out_file) ++ with open(out_file, 'wb') as f: ++ pickle.dump(G, f, pickle.HIGHEST_PROTOCOL) + graphlist.append(out_file) + return graphlist + + +From b9a8e2000be9ce30a94aca85453d5cf4e32e10ec Mon Sep 17 00:00:00 2001 +From: Horea Christian <chr@chymera.eu> +Date: Thu, 26 Jan 2023 02:03:39 -0500 +Subject: [PATCH 6/9] updating networkx from_numpy_{matrix,array} + +--- + nipype/interfaces/cmtk/cmtk.py | 2 +- + nipype/interfaces/cmtk/nbs.py | 4 ++-- + nipype/interfaces/cmtk/tests/test_nbs.py | 2 +- + 3 files changed, 4 insertions(+), 4 deletions(-) + +diff --git a/nipype/interfaces/cmtk/cmtk.py b/nipype/interfaces/cmtk/cmtk.py +index 8df7a1c5ad..fc730b1166 100644 +--- a/nipype/interfaces/cmtk/cmtk.py ++++ b/nipype/interfaces/cmtk/cmtk.py +@@ -264,7 +264,7 @@ def cmat( + ) + intersection_matrix = np.matrix(intersection_matrix) + I = G.copy() +- H = nx.from_numpy_matrix(np.matrix(intersection_matrix)) ++ H = nx.from_numpy_array(np.matrix(intersection_matrix)) + H = nx.relabel_nodes(H, lambda x: x + 1) # relabel nodes so they start at 1 + I.add_weighted_edges_from( + ((u, v, d["weight"]) for u, v, d in H.edges(data=True)) +diff --git a/nipype/interfaces/cmtk/nbs.py b/nipype/interfaces/cmtk/nbs.py +index 57d63897c7..b0a8b5df33 100644 +--- a/nipype/interfaces/cmtk/nbs.py ++++ b/nipype/interfaces/cmtk/nbs.py +@@ -150,8 +150,8 @@ def _run_interface(self, runtime): + pADJ[x, y] = PVAL[idx] + + # Create networkx graphs from the adjacency matrix +- nbsgraph = nx.from_numpy_matrix(ADJ) +- nbs_pval_graph = nx.from_numpy_matrix(pADJ) ++ nbsgraph = nx.from_numpy_array(ADJ) ++ nbs_pval_graph = nx.from_numpy_array(pADJ) + + # Relabel nodes because they should not start at zero for our convention + nbsgraph = nx.relabel_nodes(nbsgraph, lambda x: x + 1) +diff --git a/nipype/interfaces/cmtk/tests/test_nbs.py b/nipype/interfaces/cmtk/tests/test_nbs.py +index 7a60b407a4..6323546c1e 100644 +--- a/nipype/interfaces/cmtk/tests/test_nbs.py ++++ b/nipype/interfaces/cmtk/tests/test_nbs.py +@@ -18,7 +18,7 @@ def creating_graphs(tmpdir): + graphnames = ["name" + str(i) for i in range(6)] + for idx, name in enumerate(graphnames): + graph = np.random.rand(10, 10) +- G = nx.from_numpy_matrix(graph) ++ G = nx.from_numpy_array(graph) + out_file = tmpdir.strpath + graphnames[idx] + ".pck" + # Save as pck file + with open(out_file, 'wb') as f: + +From 7aa7c5968cf28afed9aca658bca28470afbfeb9f Mon Sep 17 00:00:00 2001 +From: Chris Markiewicz <effigies@gmail.com> +Date: Sat, 28 Jan 2023 12:45:17 -0500 +Subject: [PATCH 7/9] FIX: Purge nx.to_numpy_matrix + +--- + nipype/interfaces/cmtk/cmtk.py | 8 ++++---- + nipype/interfaces/cmtk/nbs.py | 2 +- + 2 files changed, 5 insertions(+), 5 deletions(-) + +diff --git a/nipype/interfaces/cmtk/cmtk.py b/nipype/interfaces/cmtk/cmtk.py +index fc730b1166..00c134fc37 100644 +--- a/nipype/interfaces/cmtk/cmtk.py ++++ b/nipype/interfaces/cmtk/cmtk.py +@@ -383,13 +383,13 @@ def cmat( + with open(op.abspath(matrix_name), 'wb') as f: + pickle.dump(G, f, pickle.HIGHEST_PROTOCOL) + +- numfib_mlab = nx.to_numpy_matrix(numfib, dtype=int) ++ numfib_mlab = nx.to_numpy_array(numfib, dtype=int) + numfib_dict = {"number_of_fibers": numfib_mlab} +- fibmean_mlab = nx.to_numpy_matrix(fibmean, dtype=np.float64) ++ fibmean_mlab = nx.to_numpy_array(fibmean, dtype=np.float64) + fibmean_dict = {"mean_fiber_length": fibmean_mlab} +- fibmedian_mlab = nx.to_numpy_matrix(fibmedian, dtype=np.float64) ++ fibmedian_mlab = nx.to_numpy_array(fibmedian, dtype=np.float64) + fibmedian_dict = {"median_fiber_length": fibmedian_mlab} +- fibdev_mlab = nx.to_numpy_matrix(fibdev, dtype=np.float64) ++ fibdev_mlab = nx.to_numpy_array(fibdev, dtype=np.float64) + fibdev_dict = {"fiber_length_std": fibdev_mlab} + + if intersections: +diff --git a/nipype/interfaces/cmtk/nbs.py b/nipype/interfaces/cmtk/nbs.py +index b0a8b5df33..2560ed8e3c 100644 +--- a/nipype/interfaces/cmtk/nbs.py ++++ b/nipype/interfaces/cmtk/nbs.py +@@ -40,7 +40,7 @@ def ntwks_to_matrices(in_files, edge_key): + raise KeyError( + "the graph edges do not have {} attribute".format(edge_key) + ) +- matrix[:, :, idx] = nx.to_numpy_matrix(graph) # Retrieve the matrix ++ matrix[:, :, idx] = nx.to_numpy_array(graph) # Retrieve the matrix + return matrix + + + +From f20035c303a88fba3e207ac60388397665bb97be Mon Sep 17 00:00:00 2001 +From: Chris Markiewicz <effigies@gmail.com> +Date: Sat, 28 Jan 2023 12:45:38 -0500 +Subject: [PATCH 8/9] FIX: Purge nx.read_gpickle + +--- + nipype/interfaces/cmtk/convert.py | 9 ++++++++- + nipype/interfaces/cmtk/nbs.py | 11 ++++++++--- + nipype/interfaces/cmtk/nx.py | 11 ++++++++--- + 3 files changed, 24 insertions(+), 7 deletions(-) + +diff --git a/nipype/interfaces/cmtk/convert.py b/nipype/interfaces/cmtk/convert.py +index 321a40fbba..a45daddcd6 100644 +--- a/nipype/interfaces/cmtk/convert.py ++++ b/nipype/interfaces/cmtk/convert.py +@@ -18,6 +18,13 @@ + from .base import CFFBaseInterface, have_cfflib + + ++def _read_pickle(fname): ++ import pickle ++ ++ with open(fname, 'rb') as f: ++ return pickle.load(f) ++ ++ + class CFFConverterInputSpec(BaseInterfaceInputSpec): + graphml_networks = InputMultiPath( + File(exists=True), desc="list of graphML networks" +@@ -135,7 +142,7 @@ def _run_interface(self, runtime): + unpickled = [] + for ntwk in self.inputs.gpickled_networks: + _, ntwk_name, _ = split_filename(ntwk) +- unpickled = nx.read_gpickle(ntwk) ++ unpickled = _read_pickle(ntwk) + cnet = cf.CNetwork(name=ntwk_name) + cnet.set_with_nxgraph(unpickled) + a.add_connectome_network(cnet) +diff --git a/nipype/interfaces/cmtk/nbs.py b/nipype/interfaces/cmtk/nbs.py +index 2560ed8e3c..a2bd42abee 100644 +--- a/nipype/interfaces/cmtk/nbs.py ++++ b/nipype/interfaces/cmtk/nbs.py +@@ -24,13 +24,18 @@ + iflogger = logging.getLogger("nipype.interface") + + ++def _read_pickle(fname): ++ with open(fname, 'rb') as f: ++ return pickle.load(f) ++ ++ + def ntwks_to_matrices(in_files, edge_key): +- first = nx.read_gpickle(in_files[0]) ++ first = _read_pickle(in_files[0]) + files = len(in_files) + nodes = len(first.nodes()) + matrix = np.zeros((nodes, nodes, files)) + for idx, name in enumerate(in_files): +- graph = nx.read_gpickle(name) ++ graph = _read_pickle(name) + for u, v, d in graph.edges(data=True): + try: + graph[u][v]["weight"] = d[ +@@ -162,7 +167,7 @@ def _run_interface(self, runtime): + else: + node_ntwk_name = self.inputs.in_group1[0] + +- node_network = nx.read_gpickle(node_ntwk_name) ++ node_network = _read_pickle(node_ntwk_name) + iflogger.info( + "Populating node dictionaries with attributes from %s", node_ntwk_name + ) +diff --git a/nipype/interfaces/cmtk/nx.py b/nipype/interfaces/cmtk/nx.py +index a662eb65c6..991ca89dcf 100644 +--- a/nipype/interfaces/cmtk/nx.py ++++ b/nipype/interfaces/cmtk/nx.py +@@ -24,11 +24,16 @@ + iflogger = logging.getLogger("nipype.interface") + + ++def _read_pickle(fname): ++ with open(fname, 'rb') as f: ++ return pickle.load(f) ++ ++ + def read_unknown_ntwk(ntwk): + if not isinstance(ntwk, nx.classes.graph.Graph): + _, _, ext = split_filename(ntwk) + if ext == ".pck": +- ntwk = nx.read_gpickle(ntwk) ++ ntwk = _read_pickle(ntwk) + elif ext == ".graphml": + ntwk = nx.read_graphml(ntwk) + return ntwk +@@ -121,7 +126,7 @@ def average_networks(in_files, ntwk_res_file, group_id): + counting_ntwk = ntwk.copy() + # Sums all the relevant variables + for index, subject in enumerate(in_files): +- tmp = nx.read_gpickle(subject) ++ tmp = _read_pickle(subject) + iflogger.info("File %s has %i edges", subject, tmp.number_of_edges()) + edges = list(tmp.edges()) + for edge in edges: +@@ -461,7 +466,7 @@ def _run_interface(self, runtime): + edgentwks = list() + kntwks = list() + matlab = list() +- ntwk = nx.read_gpickle(self.inputs.in_file) ++ ntwk = _read_pickle(self.inputs.in_file) + + # Each block computes, writes, and saves a measure + # The names are then added to the output .pck file list + +From f6bf0af19c044709de5be79a4488dcfd4d08f305 Mon Sep 17 00:00:00 2001 +From: Chris Markiewicz <effigies@gmail.com> +Date: Sat, 28 Jan 2023 13:23:33 -0500 +Subject: [PATCH 9/9] FIX: Add dtypes to nilearn interface/tests + +--- + nipype/interfaces/nilearn.py | 2 +- + nipype/interfaces/tests/test_nilearn.py | 5 +++-- + 2 files changed, 4 insertions(+), 3 deletions(-) + +diff --git a/nipype/interfaces/nilearn.py b/nipype/interfaces/nilearn.py +index 053902e2bd..95494e7f5f 100644 +--- a/nipype/interfaces/nilearn.py ++++ b/nipype/interfaces/nilearn.py +@@ -155,7 +155,7 @@ def _process_inputs(self): + if self.inputs.include_global: + global_label_data = label_data.dataobj.sum(axis=3) # sum across all regions + global_label_data = ( +- np.rint(global_label_data).astype(int).clip(0, 1) ++ np.rint(global_label_data).clip(0, 1).astype('u1') + ) # binarize + global_label_data = self._4d(global_label_data, label_data.affine) + global_masker = nl.NiftiLabelsMasker( +diff --git a/nipype/interfaces/tests/test_nilearn.py b/nipype/interfaces/tests/test_nilearn.py +index 2066c00768..4f94bbb87b 100644 +--- a/nipype/interfaces/tests/test_nilearn.py ++++ b/nipype/interfaces/tests/test_nilearn.py +@@ -184,10 +184,11 @@ def assert_expected_output(self, labels, wanted): + [[2, -2, -1, -2, -5], [3, 0, 3, -5, -2]], + [[-4, -2, -2, 1, -2], [3, 1, 4, -3, -2]], + ], +- ] ++ ], ++ np.int16, + ) + +- fake_label_data = np.array([[[1, 0], [3, 1]], [[2, 0], [1, 3]]]) ++ fake_label_data = np.array([[[1, 0], [3, 1]], [[2, 0], [1, 3]]], np.uint8) + + fake_equiv_4d_label_data = np.array( + [ diff --git a/sci-libs/nipype/files/nipype-1.8.4-no_etelemetry.patch b/sci-libs/nipype/files/nipype-1.8.4-no_etelemetry.patch new file mode 100644 index 000000000..b5c223422 --- /dev/null +++ b/sci-libs/nipype/files/nipype-1.8.4-no_etelemetry.patch @@ -0,0 +1,50 @@ +diff --git a/nipype/__init__.py b/nipype/__init__.py +index 06084e823..2e42dcbce 100644 +--- a/nipype/__init__.py ++++ b/nipype/__init__.py +@@ -73,23 +73,6 @@ from .interfaces import ( + ) + + +-def check_latest_version(raise_exception=False): +- """ +- Check for the latest version of the library. +- +- Parameters +- ---------- +- raise_exception: bool +- Raise a RuntimeError if a bad version is being used +- """ +- import etelemetry +- +- logger = logging.getLogger("nipype.utils") +- return etelemetry.check_available_version( +- "nipy/nipype", __version__, logger, raise_exception +- ) +- +- + # Run telemetry on import for interactive sessions, such as IPython, Jupyter notebooks, Python REPL + if config.getboolean("execution", "check_version"): + import __main__ +@@ -98,4 +81,4 @@ if config.getboolean("execution", "check_version"): + from .interfaces.base import BaseInterface + + if BaseInterface._etelemetry_version_data is None: +- BaseInterface._etelemetry_version_data = check_latest_version() or "n/a" ++ BaseInterface._etelemetry_version_data = "n/a" +diff --git a/nipype/interfaces/base/core.py b/nipype/interfaces/base/core.py +index c8099be63..f7770dbfc 100644 +--- a/nipype/interfaces/base/core.py ++++ b/nipype/interfaces/base/core.py +@@ -183,10 +183,9 @@ class BaseInterface(Interface): + config.getboolean("execution", "check_version") + and "NIPYPE_NO_ET" not in os.environ + ): +- from ... import check_latest_version + + if BaseInterface._etelemetry_version_data is None: +- BaseInterface._etelemetry_version_data = check_latest_version() or "n/a" ++ BaseInterface._etelemetry_version_data = "n/a" + + if not self.input_spec: + raise Exception("No input_spec in class: %s" % self.__class__.__name__) diff --git a/sci-libs/nipype/nipype-1.5.0.ebuild b/sci-libs/nipype/nipype-1.5.0.ebuild deleted file mode 100644 index 35792adbc..000000000 --- a/sci-libs/nipype/nipype-1.5.0.ebuild +++ /dev/null @@ -1,90 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7..9} ) -PYTHON_REQ_USE="threads(+),sqlite" - -inherit distutils-r1 - -DESCRIPTION="Neuroimaging in Python: Pipelines and Interfaces" -HOMEPAGE="http://nipy.sourceforge.net/nipype/" -SRC_URI="https://github.com/nipy/nipype/archive/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="test" -RESTRICT="!test? ( test )" - -DEPEND=" - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/prov[${PYTHON_USEDEP}] - sci-libs/nibabel[${PYTHON_USEDEP}] - test? ( - dev-python/mock[${PYTHON_USEDEP}] - dev-python/pytest[${PYTHON_USEDEP}] - ${RDEPEND} - ) -" -# Dependency disabled as upstream test configuration which requires it fails -#dev-python/pytest-xdist[${PYTHON_USEDEP}] - -RDEPEND=" - >=dev-python/click-6.6[${PYTHON_USEDEP}] - dev-python/filelock[${PYTHON_USEDEP}] - dev-python/networkx[${PYTHON_USEDEP}] - dev-python/packaging[${PYTHON_USEDEP}] - dev-python/pydot[${PYTHON_USEDEP}] - dev-python/pydotplus[${PYTHON_USEDEP}] - dev-python/python-dateutil[${PYTHON_USEDEP}] - >=dev-python/rdflib-5.0.0[${PYTHON_USEDEP}] - dev-python/scipy[${PYTHON_USEDEP}] - dev-python/simplejson[${PYTHON_USEDEP}] - dev-python/traits[${PYTHON_USEDEP}] -" - -PATCHES=( - "${FILESDIR}/${P}"-version_check.patch -) - -src_prepare() { - # Remove etelemetry - sed -i '/"etelemetry/d' nipype/info.py || die - - # Mark failing tests - sed -i \ - -e "/def test_no_et(tmp_path):/i@pytest.mark.skip('Known to fail by upstream: https://github.com/nipy/nipype/issues/3196#issuecomment-606003186')" \ - nipype/tests/test_nipype.py || die - sed -i \ - -e "/def test_fslversion():/i@pytest.mark.skip('Known to fail by upstream: https://github.com/nipy/nipype/issues/3196#issuecomment-605997462')" \ - nipype/interfaces/fsl/tests/test_base.py || die - default -} - -python_install_all() { - distutils-r1_python_install_all - doenvd "${FILESDIR}/98nipype" -} - -python_test() { - # Setting environment variable to disable etelemetry version check: - # https://github.com/nipy/nipype/issues/3196#issuecomment-605980044 - NIPYPE_NO_ET=1 pytest -vv\ - || die - # Upstream test configuration fails - #-c nipype/pytest.ini\ - #--doctest-modules nipype\ - #--cov nipype\ - #--cov-config .coveragerc\ - #--cov-report xml:cov.xml\ -} - -pkg_postinst() { - echo - einfo "Please run the following commands if you" - einfo "intend to use nipype from an existing shell:" - einfo "source /etc/profile" - echo -} diff --git a/sci-libs/nipype/nipype-1.8.4-r1.ebuild b/sci-libs/nipype/nipype-1.8.4-r1.ebuild new file mode 100644 index 000000000..7c2e801ff --- /dev/null +++ b/sci-libs/nipype/nipype-1.8.4-r1.ebuild @@ -0,0 +1,94 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) +PYTHON_REQ_USE="threads(+),sqlite" + +inherit distutils-r1 + +DESCRIPTION="Neuroimaging in Python: Pipelines and Interfaces" +HOMEPAGE="https://nipype.readthedocs.io/" +SRC_URI="https://github.com/nipy/nipype/archive/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" +IUSE="test" +RESTRICT="!test? ( test )" + +DEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/prov[${PYTHON_USEDEP}] + sci-libs/nibabel[${PYTHON_USEDEP}] + test? ( + dev-python/mock[${PYTHON_USEDEP}] + dev-python/pytest[${PYTHON_USEDEP}] + ${RDEPEND} + ) +" + +RDEPEND=" + dev-python/click[${PYTHON_USEDEP}] + dev-python/filelock[${PYTHON_USEDEP}] + dev-python/looseversion[${PYTHON_USEDEP}] + dev-python/networkx[${PYTHON_USEDEP}] + dev-python/packaging[${PYTHON_USEDEP}] + dev-python/pydot[${PYTHON_USEDEP}] + dev-python/python-dateutil[${PYTHON_USEDEP}] + dev-python/rdflib[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + dev-python/simplejson[${PYTHON_USEDEP}] + <dev-python/traits-6.4.0[${PYTHON_USEDEP}] +" + +PATCHES=( + "${FILESDIR}/${PN}-1.8.4-dependency_compatibility.patch" +) + +src_prepare() { + # Remove etelemetry + sed -i '/"etelemetry/d' nipype/info.py requirements.txt || die + + # Mark failing tests + sed -i \ + -e "/def test_no_et(tmp_path):/i@pytest.mark.skip('Known to fail by upstream: https://github.com/nipy/nipype/issues/3196#issuecomment-606003186')" \ + nipype/tests/test_nipype.py || die + sed -i \ + -e "/def test_fslversion():/i@pytest.mark.skip('Known to fail by upstream: https://github.com/nipy/nipype/issues/3196#issuecomment-605997462')" \ + nipype/interfaces/fsl/tests/test_base.py || die + default +} + +python_install_all() { + distutils-r1_python_install_all + doenvd "${FILESDIR}/98nipype" +} + +# Reported upstream: +# https://github.com/nipy/nipype/issues/3540 +EPYTEST_DESELECT=( + nipype/interfaces/tests/test_io.py::test_s3datagrabber_communication +) + +python_test() { + # Setting environment variable to disable etelemetry version check: + # https://github.com/nipy/nipype/issues/3196#issuecomment-605980044 + NIPYPE_NO_ET=1 epytest + # Upstream test configuration fails + #-c nipype/pytest.ini\ + #--doctest-modules nipype\ + #--cov nipype\ + #--cov-config .coveragerc\ + #--cov-report xml:cov.xml\ +} + +pkg_postinst() { + echo + einfo "Please run the following commands if you" + einfo "intend to use nipype from an existing shell:" + einfo "source /etc/profile" + echo +} diff --git a/sci-libs/nipype/nipype-1.8.4-r2.ebuild b/sci-libs/nipype/nipype-1.8.4-r2.ebuild new file mode 100644 index 000000000..4c3da70b3 --- /dev/null +++ b/sci-libs/nipype/nipype-1.8.4-r2.ebuild @@ -0,0 +1,96 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) +PYTHON_REQ_USE="threads(+),sqlite" + +inherit distutils-r1 + +DESCRIPTION="Neuroimaging in Python: Pipelines and Interfaces" +HOMEPAGE="https://nipype.readthedocs.io/" +SRC_URI="https://github.com/nipy/nipype/archive/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="test" +RESTRICT="!test? ( test )" + +DEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/prov[${PYTHON_USEDEP}] + sci-libs/nibabel[${PYTHON_USEDEP}] + test? ( + dev-python/mock[${PYTHON_USEDEP}] + dev-python/pytest[${PYTHON_USEDEP}] + ${RDEPEND} + ) +" + +RDEPEND=" + dev-python/click[${PYTHON_USEDEP}] + dev-python/filelock[${PYTHON_USEDEP}] + dev-python/looseversion[${PYTHON_USEDEP}] + dev-python/networkx[${PYTHON_USEDEP}] + dev-python/packaging[${PYTHON_USEDEP}] + dev-python/pydot[${PYTHON_USEDEP}] + dev-python/python-dateutil[${PYTHON_USEDEP}] + dev-python/rdflib[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + dev-python/simplejson[${PYTHON_USEDEP}] + <dev-python/traits-6.4.0[${PYTHON_USEDEP}] +" + +PATCHES=( + "${FILESDIR}/${PN}-1.8.4-dependency_compatibility.patch" + "${FILESDIR}/${PN}-1.8.4-no_etelemetry.patch" +) + +src_prepare() { + # Remove etelemetry + # Doing this separately since the file is affected by another patch. + sed -i '/"etelemetry/d' nipype/info.py requirements.txt || die + + # Mark failing tests + sed -i \ + -e "/def test_no_et(tmp_path):/i@pytest.mark.skip('Known to fail by upstream: https://github.com/nipy/nipype/issues/3196#issuecomment-606003186')" \ + nipype/tests/test_nipype.py || die + sed -i \ + -e "/def test_fslversion():/i@pytest.mark.skip('Known to fail by upstream: https://github.com/nipy/nipype/issues/3196#issuecomment-605997462')" \ + nipype/interfaces/fsl/tests/test_base.py || die + default +} + +python_install_all() { + distutils-r1_python_install_all + doenvd "${FILESDIR}/98nipype" +} + +# Reported upstream: +# https://github.com/nipy/nipype/issues/3540 +EPYTEST_DESELECT=( + nipype/interfaces/tests/test_io.py::test_s3datagrabber_communication +) + +python_test() { + # Setting environment variable to disable etelemetry version check: + # https://github.com/nipy/nipype/issues/3196#issuecomment-605980044 + NIPYPE_NO_ET=1 epytest + # Upstream test configuration fails + #-c nipype/pytest.ini\ + #--doctest-modules nipype\ + #--cov nipype\ + #--cov-config .coveragerc\ + #--cov-report xml:cov.xml\ +} + +pkg_postinst() { + echo + einfo "Please run the following commands if you" + einfo "intend to use nipype from an existing shell:" + einfo "source /etc/profile" + echo +} diff --git a/sci-libs/nipype/nipype-1.8.6.ebuild b/sci-libs/nipype/nipype-1.8.6.ebuild new file mode 100644 index 000000000..88bc23395 --- /dev/null +++ b/sci-libs/nipype/nipype-1.8.6.ebuild @@ -0,0 +1,97 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..11} ) +PYTHON_REQ_USE="threads(+),sqlite" + +inherit distutils-r1 + +DESCRIPTION="Neuroimaging in Python: Pipelines and Interfaces" +HOMEPAGE="https://nipype.readthedocs.io/" +SRC_URI="https://github.com/nipy/nipype/archive/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="test" +# Tests fail with numpy import error: +# https://github.com/nipy/nipype/issues/3626 +RESTRICT="test" + +DEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/prov[${PYTHON_USEDEP}] + sci-libs/nibabel[${PYTHON_USEDEP}] + test? ( + dev-python/mock[${PYTHON_USEDEP}] + dev-python/pytest[${PYTHON_USEDEP}] + ${RDEPEND} + ) +" + +RDEPEND=" + dev-python/click[${PYTHON_USEDEP}] + dev-python/filelock[${PYTHON_USEDEP}] + dev-python/looseversion[${PYTHON_USEDEP}] + dev-python/networkx[${PYTHON_USEDEP}] + dev-python/packaging[${PYTHON_USEDEP}] + dev-python/pydot[${PYTHON_USEDEP}] + dev-python/python-dateutil[${PYTHON_USEDEP}] + dev-python/rdflib[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + dev-python/simplejson[${PYTHON_USEDEP}] + <dev-python/traits-6.4.0[${PYTHON_USEDEP}] +" + +PATCHES=( + "${FILESDIR}/${PN}-1.8.4-no_etelemetry.patch" +) + +src_prepare() { + # Remove etelemetry + # Doing this separately since the file is affected by another patch. + sed -i '/"etelemetry/d' nipype/info.py requirements.txt || die + + # Mark failing tests + sed -i \ + -e "/def test_no_et(tmp_path):/i@pytest.mark.skip('Known to fail by upstream: https://github.com/nipy/nipype/issues/3196#issuecomment-606003186')" \ + nipype/tests/test_nipype.py || die + sed -i \ + -e "/def test_fslversion():/i@pytest.mark.skip('Known to fail by upstream: https://github.com/nipy/nipype/issues/3196#issuecomment-605997462')" \ + nipype/interfaces/fsl/tests/test_base.py || die + default +} + +python_install_all() { + distutils-r1_python_install_all + doenvd "${FILESDIR}/98nipype" +} + +# Reported upstream: +# https://github.com/nipy/nipype/issues/3540 +EPYTEST_DESELECT=( + nipype/interfaces/tests/test_io.py::test_s3datagrabber_communication +) + +python_test() { + # Setting environment variable to disable etelemetry version check: + # https://github.com/nipy/nipype/issues/3196#issuecomment-605980044 + NIPYPE_NO_ET=1 epytest + # Upstream test configuration fails + #-c nipype/pytest.ini\ + #--doctest-modules nipype\ + #--cov nipype\ + #--cov-config .coveragerc\ + #--cov-report xml:cov.xml\ +} + +pkg_postinst() { + echo + einfo "Please run the following commands if you" + einfo "intend to use nipype from an existing shell:" + einfo "source /etc/profile" + echo +} diff --git a/sci-libs/oneDAL/Manifest b/sci-libs/oneDAL/Manifest new file mode 100644 index 000000000..4ea34591f --- /dev/null +++ b/sci-libs/oneDAL/Manifest @@ -0,0 +1,4 @@ +DIST mklfpk_lnx_20221214.tgz 88817211 BLAKE2B 3416ce8fe8c768c0d8598536d23f68aafe9e47590d854ce19e8ac79108aa5f10a2fd2fdbf7c96aec9f083ef8ad3ae7a1515e5f5b0e565f0c1686cc5fc0eeb02d SHA512 c0a0beb56c3f41deff9b587d116e7cd366ff31b393a78d4ad608ef620d5b503bc80b720eb61b9355c8d5547a3a566f223d5deb3421c97498fbff90997d8d7e62 +DIST mklgpufpk_lnx_20221214.tgz 15283052 BLAKE2B 54137083613cef5114cd95cade61e58456a0858bd46ecc9fe2294ba06d5bd405bbb1259b16f9003ba466a91cfa0b3801dc8485338fd11d612f09811741ff25a2 SHA512 2cf035133269ac24fa7d39aecaa673d21a65b772d86179a04fec20e4d6e1ad20122ae8ce262f2814ad768272258c512e6fedf0ab978ed687ba54949bb7b6b3b5 +DIST oneDAL-2023.0.1.tar.gz 61208026 BLAKE2B 2a9509fe59808ee1211b39b2ae0da34b37ba73e747316fdb407112611bbba1b808d451f5aef0afc9552178839adaae71bbe80c2fdeea39a23048674f87b159c1 SHA512 58e9aacc5c09bae67d5bdc6477b7e5d6f0c696513e532d778ae427314e35f629c6c3b8d94f382638ab736786f4ae965dcbdf2e25ab018efc863ee21000116894 +DIST oneDAL-2023.2.1.tar.gz 50938584 BLAKE2B c14bbdc7a1d4faf5266f47a0849a1a9403824c6824ca392f5bafc5fe7c9e6abd6448647cb73d1ffd9cec8b347bba2ca3d58d86306af185896a0a5880132e593a SHA512 d412bd8f353a017929b31411ff2788fada04ceee9cb4f6d98828e5bb10a50a28dc4d73f89da0a0db21baf1cb4accebfb647198331748f95a6af9299c4977d5b7 diff --git a/sci-libs/oneDAL/files/oneDAL-2021.7.1_p20221207-fix-compile.patch b/sci-libs/oneDAL/files/oneDAL-2021.7.1_p20221207-fix-compile.patch new file mode 100644 index 000000000..553e742ab --- /dev/null +++ b/sci-libs/oneDAL/files/oneDAL-2021.7.1_p20221207-fix-compile.patch @@ -0,0 +1,164 @@ +diff --git a/dev/bazel/deps/onedal.bzl b/dev/bazel/deps/onedal.bzl +index f0f7662..6b9d11f 100644 +--- a/dev/bazel/deps/onedal.bzl ++++ b/dev/bazel/deps/onedal.bzl +@@ -21,18 +21,12 @@ onedal_repo = repos.prebuilt_libs_repo_rule( + "include", + ], + libs = [ +- # Static +- "lib/intel64/libonedal_core.a", +- "lib/intel64/libonedal_thread.a", +- "lib/intel64/libonedal.a", +- "lib/intel64/libonedal_dpc.a", +- "lib/intel64/libonedal_sycl.a", +- + # Dynamic + "lib/intel64/libonedal_core.so", + "lib/intel64/libonedal_thread.so", + "lib/intel64/libonedal.so", + "lib/intel64/libonedal_dpc.so", ++ "lib/intel64/libonedal_sycl.so", + ], + build_template = "@onedal//dev/bazel/deps:onedal.tpl.BUILD", + ) +diff --git a/dev/bazel/deps/onedal.tpl.BUILD b/dev/bazel/deps/onedal.tpl.BUILD +index 60be678..0f7990e 100644 +--- a/dev/bazel/deps/onedal.tpl.BUILD ++++ b/dev/bazel/deps/onedal.tpl.BUILD +@@ -9,62 +9,17 @@ cc_library( + includes = [ "include" ], + ) + +-cc_library( +- name = "core_static", +- srcs = [ +- "lib/intel64/libonedal_core.a", +- ], +- deps = [ +- ":headers", +- # TODO: Currently vml_ipp lib depends on TBB, but it shouldn't +- # Remove TBB from deps once problem with vml_ipp is resolved +- "@tbb//:tbb_binary", +- ], +-) +- +-cc_library( +- name = "thread_static", +- srcs = [ +- "lib/intel64/libonedal_thread.a", +- ], +- deps = [ +- ":headers", +- "@tbb//:tbb_binary", +- "@tbb//:tbbmalloc_binary", +- ], +-) + + cc_library( + name = "onedal_sycl", + srcs = [ +- "lib/intel64/libonedal_sycl.a", +- ], +- deps = [ +- ":headers", +- ], +-) +- +-cc_library( +- name = "onedal_static", +- srcs = [ +- "lib/intel64/libonedal.a", ++ "lib/intel64/libonedal_sycl.so", + ], + deps = [ + ":headers", + ], + ) + +-cc_library( +- name = "onedal_static_dpc", +- srcs = [ +- "lib/intel64/libonedal_dpc.a", +- ], +- deps = [ +- ":headers", +- ":onedal_sycl", +- ], +-) +- + cc_library( + name = "core_dynamic", + srcs = [ +diff --git a/dev/make/cmplr.dpcpp.mk b/dev/make/cmplr.dpcpp.mk +index 2ac2ed9..bd0e182 100644 +--- a/dev/make/cmplr.dpcpp.mk ++++ b/dev/make/cmplr.dpcpp.mk +@@ -28,13 +28,13 @@ CORE.SERV.COMPILER.dpcpp = generic + -Zl.dpcpp = + -DEBC.dpcpp = -g + +-COMPILER.lnx.dpcpp = icpx -fsycl $(if $(IA_is_ia32),-m32,-m64) -stdlib=libstdc++ -fgnu-runtime -fwrapv \ +- -Werror -Wreturn-type -fsycl-device-code-split=per_kernel +-COMPILER.win.dpcpp = icx -fsycl $(if $(MSVC_RT_is_release),-MD, -MDd /debug:none) -nologo -WX \ ++COMPILER.lnx.dpcpp = $(CXX) $(CXXFLAGS) -fsycl $(if $(IA_is_ia32),-m32,-m64) -stdlib=libstdc++ -fgnu-runtime -fwrapv \ ++ -Wreturn-type -fsycl-device-code-split=per_kernel ++COMPILER.win.dpcpp = $(CC) $(CFLAGS) -fsycl $(if $(MSVC_RT_is_release),-MD, -MDd /debug:none) -nologo -WX \ + -Wno-deprecated-declarations -fsycl-device-code-split=per_kernel + +-link.dynamic.lnx.dpcpp = icpx -fsycl $(if $(IA_is_ia32),-m32,-m64) -fsycl-device-code-split=per_kernel +-link.dynamic.win.dpcpp = icx -fsycl $(if $(IA_is_ia32),-m32,-m64) -fsycl-device-code-split=per_kernel ++link.dynamic.lnx.dpcpp = $(CXX) $(LDFLAGS) -fsycl $(if $(IA_is_ia32),-m32,-m64) -fsycl-device-code-split=per_kernel ++link.dynamic.win.dpcpp = $(CC) $(LDFLAGS) -fsycl $(if $(IA_is_ia32),-m32,-m64) -fsycl-device-code-split=per_kernel + + pedantic.opts.lnx.dpcpp = -pedantic \ + -Wall \ +diff --git a/dev/make/cmplr.icx.mk b/dev/make/cmplr.icx.mk +index 28ce293..7c478b0 100644 +--- a/dev/make/cmplr.icx.mk ++++ b/dev/make/cmplr.icx.mk +@@ -24,14 +24,14 @@ CMPLRDIRSUFF.icx = _icx + + CORE.SERV.COMPILER.icx = generic + +--Zl.icx = -no-intel-lib=libirc ++-Zl.icx = + -DEBC.icx = -g + +-COMPILER.lnx.icx = icpx $(if $(IA_is_ia32),-m32,-m64) \ +- -Werror -Wreturn-type ++COMPILER.lnx.icx = $(CXX) $(CXXFLAGS) $(if $(IA_is_ia32),-m32,-m64) \ ++ -Wreturn-type + + +-link.dynamic.lnx.icx = icpx $(if $(IA_is_ia32),-m32,-m64) ++link.dynamic.lnx.icx = $(CXX) $(LDFLAGS) $(if $(IA_is_ia32),-m32,-m64) + + pedantic.opts.icx = -pedantic \ + -Wall \ +diff --git a/makefile b/makefile +index 9c51bad..20aaff5 100644 +--- a/makefile ++++ b/makefile +@@ -219,7 +219,7 @@ TBBDIR.2 := $(if $(TBBDIR.2),$(TBBDIR.2),$(error Can`t find TBB neither in $(DIR + + TBBDIR.include := $(if $(TBBDIR),$(TBBDIR)/include/tbb $(TBBDIR)/include) + +-TBBDIR.libia.prefix := $(TBBDIR.2)/lib ++TBBDIR.libia.prefix := $(TBBDIR.2)/lib64 + + TBBDIR.libia.win.vc1 := $(if $(OS_is_win),$(if $(wildcard $(call frompf1,$(TBBDIR.libia.prefix))/$(_IA)/vc_mt),$(TBBDIR.libia.prefix)/$(_IA)/vc_mt,$(if $(wildcard $(call frompf1,$(TBBDIR.libia.prefix))/$(_IA)/vc14),$(TBBDIR.libia.prefix)/$(_IA)/vc14))) + TBBDIR.libia.win.vc2 := $(if $(OS_is_win),$(if $(TBBDIR.libia.win.vc1),,$(firstword $(filter $(call topf,$$TBBROOT)%,$(subst ;,$(space),$(call topf,$$LIB)))))) +@@ -227,10 +227,10 @@ TBBDIR.libia.win.vc22 := $(if $(OS_is_win),$(if $(TBBDIR.libia.win.vc2),$(wildca + + TBBDIR.libia.win:= $(if $(OS_is_win),$(if $(TBBDIR.libia.win.vc22),$(TBBDIR.libia.win.vc2),$(if $(TBBDIR.libia.win.vc1),$(TBBDIR.libia.win.vc1),$(error Can`t find TBB libs nether in $(call frompf,$(TBBDIR.libia.prefix))/$(_IA)/vc_mt not in $(firstword $(filter $(TBBROOT)%,$(subst ;,$(space),$(LIB)))).)))) + +-TBBDIR.libia.lnx.gcc1 := $(if $(OS_is_lnx),$(if $(wildcard $(TBBDIR.libia.prefix)/$(_IA)/gcc4.8/*),$(TBBDIR.libia.prefix)/$(_IA)/gcc4.8)) ++TBBDIR.libia.lnx.gcc1 := $(if $(OS_is_lnx),$(if $(wildcard $(TBBDIR.libia.prefix)/*),$(TBBDIR.libia.prefix))) + TBBDIR.libia.lnx.gcc2 := $(if $(OS_is_lnx),$(if $(TBBDIR.libia.lnx.gcc1),,$(firstword $(filter $(TBBROOT)%,$(subst :,$(space),$(LD_LIBRARY_PATH)))))) + TBBDIR.libia.lnx.gcc22 := $(if $(OS_is_lnx),$(if $(TBBDIR.libia.lnx.gcc2),$(wildcard $(TBBDIR.libia.lnx.gcc2)/libtbb.so))) +-TBBDIR.libia.lnx := $(if $(OS_is_lnx),$(if $(TBBDIR.libia.lnx.gcc22),$(TBBDIR.libia.lnx.gcc2),$(if $(TBBDIR.libia.lnx.gcc1),$(TBBDIR.libia.lnx.gcc1),$(error Can`t find TBB runtimes nether in $(TBBDIR.libia.prefix)/$(_IA)/gcc4.8 not in $(firstword $(filter $(TBBROOT)%,$(subst :,$(space),$(LD_LIBRARY_PATH)))).)))) ++TBBDIR.libia.lnx := $(if $(OS_is_lnx),$(if $(TBBDIR.libia.lnx.gcc22),$(TBBDIR.libia.lnx.gcc2),$(if $(TBBDIR.libia.lnx.gcc1),$(TBBDIR.libia.lnx.gcc1),$(error Can`t find TBB runtimes nether in $(TBBDIR.libia.prefix) not in $(firstword $(filter $(TBBROOT)%,$(subst :,$(space),$(LD_LIBRARY_PATH)))).)))) + + TBBDIR.libia.mac.clang1 := $(if $(OS_is_mac),$(if $(wildcard $(TBBDIR.libia.prefix)/*),$(TBBDIR.libia.prefix))) + TBBDIR.libia.mac.clang2 := $(if $(OS_is_mac),$(if $(TBBDIR.libia.mac.clang1),,$(firstword $(filter $(TBBROOT)%,$(subst :,$(space),$(LIBRARY_PATH)))))) diff --git a/sci-libs/oneDAL/files/oneDAL-2023.2.1-fix-compile.patch b/sci-libs/oneDAL/files/oneDAL-2023.2.1-fix-compile.patch new file mode 100644 index 000000000..50731570d --- /dev/null +++ b/sci-libs/oneDAL/files/oneDAL-2023.2.1-fix-compile.patch @@ -0,0 +1,162 @@ +diff --git a/dev/bazel/deps/onedal.bzl b/dev/bazel/deps/onedal.bzl +index f0f7662c0..6b9d11ff2 100644 +--- a/dev/bazel/deps/onedal.bzl ++++ b/dev/bazel/deps/onedal.bzl +@@ -21,18 +21,12 @@ onedal_repo = repos.prebuilt_libs_repo_rule( + "include", + ], + libs = [ +- # Static +- "lib/intel64/libonedal_core.a", +- "lib/intel64/libonedal_thread.a", +- "lib/intel64/libonedal.a", +- "lib/intel64/libonedal_dpc.a", +- "lib/intel64/libonedal_sycl.a", +- + # Dynamic + "lib/intel64/libonedal_core.so", + "lib/intel64/libonedal_thread.so", + "lib/intel64/libonedal.so", + "lib/intel64/libonedal_dpc.so", ++ "lib/intel64/libonedal_sycl.so", + ], + build_template = "@onedal//dev/bazel/deps:onedal.tpl.BUILD", + ) +diff --git a/dev/bazel/deps/onedal.tpl.BUILD b/dev/bazel/deps/onedal.tpl.BUILD +index 60be67856..0f7990ef5 100644 +--- a/dev/bazel/deps/onedal.tpl.BUILD ++++ b/dev/bazel/deps/onedal.tpl.BUILD +@@ -9,62 +9,17 @@ cc_library( + includes = [ "include" ], + ) + +-cc_library( +- name = "core_static", +- srcs = [ +- "lib/intel64/libonedal_core.a", +- ], +- deps = [ +- ":headers", +- # TODO: Currently vml_ipp lib depends on TBB, but it shouldn't +- # Remove TBB from deps once problem with vml_ipp is resolved +- "@tbb//:tbb_binary", +- ], +-) +- +-cc_library( +- name = "thread_static", +- srcs = [ +- "lib/intel64/libonedal_thread.a", +- ], +- deps = [ +- ":headers", +- "@tbb//:tbb_binary", +- "@tbb//:tbbmalloc_binary", +- ], +-) + + cc_library( + name = "onedal_sycl", + srcs = [ +- "lib/intel64/libonedal_sycl.a", +- ], +- deps = [ +- ":headers", +- ], +-) +- +-cc_library( +- name = "onedal_static", +- srcs = [ +- "lib/intel64/libonedal.a", ++ "lib/intel64/libonedal_sycl.so", + ], + deps = [ + ":headers", + ], + ) + +-cc_library( +- name = "onedal_static_dpc", +- srcs = [ +- "lib/intel64/libonedal_dpc.a", +- ], +- deps = [ +- ":headers", +- ":onedal_sycl", +- ], +-) +- + cc_library( + name = "core_dynamic", + srcs = [ +diff --git a/dev/make/cmplr.dpcpp.mk b/dev/make/cmplr.dpcpp.mk +index 2a78043b7..b431e1255 100644 +--- a/dev/make/cmplr.dpcpp.mk ++++ b/dev/make/cmplr.dpcpp.mk +@@ -28,13 +28,13 @@ CORE.SERV.COMPILER.dpcpp = generic + -Zl.dpcpp = + -DEBC.dpcpp = -g + +-COMPILER.lnx.dpcpp = icpx -fsycl -m64 -stdlib=libstdc++ -fgnu-runtime -fwrapv \ ++COMPILER.lnx.dpcpp = $(CXX) $(CXXFLAGS) -fsycl -m64 -stdlib=libstdc++ -fgnu-runtime -fwrapv \ + -Werror -Wreturn-type -fsycl-device-code-split=per_kernel +-COMPILER.win.dpcpp = icx -fsycl $(if $(MSVC_RT_is_release),-MD, -MDd /debug:none) -nologo -WX \ ++COMPILER.win.dpcpp = $(CC) $(CFLAGS) -fsycl $(if $(MSVC_RT_is_release),-MD, -MDd /debug:none) -nologo -WX \ + -Wno-deprecated-declarations -fsycl-device-code-split=per_kernel + +-link.dynamic.lnx.dpcpp = icpx -fsycl -m64 -fsycl-device-code-split=per_kernel +-link.dynamic.win.dpcpp = icx -fsycl -m64 -fsycl-device-code-split=per_kernel ++link.dynamic.lnx.dpcpp = $(CXX) $(LDFLAGS) -fsycl -m64 -fsycl-device-code-split=per_kernel ++link.dynamic.win.dpcpp = $(CC) $(LDFLAGS) -fsycl -m64 -fsycl-device-code-split=per_kernel + + pedantic.opts.lnx.dpcpp = -pedantic \ + -Wall \ +diff --git a/dev/make/cmplr.icx.mk b/dev/make/cmplr.icx.mk +index cbcde1a7e..61ef3583c 100644 +--- a/dev/make/cmplr.icx.mk ++++ b/dev/make/cmplr.icx.mk +@@ -24,14 +24,14 @@ CMPLRDIRSUFF.icx = _icx + + CORE.SERV.COMPILER.icx = generic + +--Zl.icx = -no-intel-lib=libirc ++-Zl.icx = + -DEBC.icx = -g + +-COMPILER.lnx.icx = icpx -m64 \ ++COMPILER.lnx.icx = $(CXX) $(CXXFLAGS) -m64 \ + -Werror -Wreturn-type + + +-link.dynamic.lnx.icx = icpx -m64 ++link.dynamic.lnx.icx = $(CXX) $(LDFLAGS) -m64 + + pedantic.opts.icx = -pedantic \ + -Wall \ +diff --git a/makefile b/makefile +index 525e52728..db864e9cb 100644 +--- a/makefile ++++ b/makefile +@@ -215,7 +215,7 @@ TBBDIR.2 := $(if $(TBBDIR.2),$(TBBDIR.2),$(error Can`t find TBB neither in $(DIR + + TBBDIR.include := $(if $(TBBDIR),$(TBBDIR)/include/tbb $(TBBDIR)/include) + +-TBBDIR.libia.prefix := $(TBBDIR.2)/lib ++TBBDIR.libia.prefix := $(TBBDIR.2)/lib64 + + TBBDIR.libia.win.vc1 := $(if $(OS_is_win),$(if $(wildcard $(call frompf1,$(TBBDIR.libia.prefix))/$(_IA)/vc_mt),$(TBBDIR.libia.prefix)/$(_IA)/vc_mt,$(if $(wildcard $(call frompf1,$(TBBDIR.libia.prefix))/$(_IA)/vc14),$(TBBDIR.libia.prefix)/$(_IA)/vc14))) + TBBDIR.libia.win.vc2 := $(if $(OS_is_win),$(if $(TBBDIR.libia.win.vc1),,$(firstword $(filter $(call topf,$$TBBROOT)%,$(subst ;,$(space),$(call topf,$$LIB)))))) +@@ -223,10 +223,10 @@ TBBDIR.libia.win.vc22 := $(if $(OS_is_win),$(if $(TBBDIR.libia.win.vc2),$(wildca + + TBBDIR.libia.win:= $(if $(OS_is_win),$(if $(TBBDIR.libia.win.vc22),$(TBBDIR.libia.win.vc2),$(if $(TBBDIR.libia.win.vc1),$(TBBDIR.libia.win.vc1),$(error Can`t find TBB libs nether in $(call frompf,$(TBBDIR.libia.prefix))/$(_IA)/vc_mt not in $(firstword $(filter $(TBBROOT)%,$(subst ;,$(space),$(LIB)))).)))) + +-TBBDIR.libia.lnx.gcc1 := $(if $(OS_is_lnx),$(if $(wildcard $(TBBDIR.libia.prefix)/$(_IA)/gcc4.8/*),$(TBBDIR.libia.prefix)/$(_IA)/gcc4.8)) ++TBBDIR.libia.lnx.gcc1 := $(if $(OS_is_lnx),$(if $(wildcard $(TBBDIR.libia.prefix)/*),$(TBBDIR.libia.prefix))) + TBBDIR.libia.lnx.gcc2 := $(if $(OS_is_lnx),$(if $(TBBDIR.libia.lnx.gcc1),,$(firstword $(filter $(TBBROOT)%,$(subst :,$(space),$(LD_LIBRARY_PATH)))))) + TBBDIR.libia.lnx.gcc22 := $(if $(OS_is_lnx),$(if $(TBBDIR.libia.lnx.gcc2),$(wildcard $(TBBDIR.libia.lnx.gcc2)/libtbb.so))) +-TBBDIR.libia.lnx := $(if $(OS_is_lnx),$(if $(TBBDIR.libia.lnx.gcc22),$(TBBDIR.libia.lnx.gcc2),$(if $(TBBDIR.libia.lnx.gcc1),$(TBBDIR.libia.lnx.gcc1),$(error Can`t find TBB runtimes nether in $(TBBDIR.libia.prefix)/$(_IA)/gcc4.8 not in $(firstword $(filter $(TBBROOT)%,$(subst :,$(space),$(LD_LIBRARY_PATH)))).)))) ++TBBDIR.libia.lnx := $(if $(OS_is_lnx),$(if $(TBBDIR.libia.lnx.gcc22),$(TBBDIR.libia.lnx.gcc2),$(if $(TBBDIR.libia.lnx.gcc1),$(TBBDIR.libia.lnx.gcc1),$(error Can`t find TBB runtimes nether in $(TBBDIR.libia.prefix) not in $(firstword $(filter $(TBBROOT)%,$(subst :,$(space),$(LD_LIBRARY_PATH)))).)))) + + TBBDIR.libia.mac.clang1 := $(if $(OS_is_mac),$(if $(wildcard $(TBBDIR.libia.prefix)/*),$(TBBDIR.libia.prefix))) + TBBDIR.libia.mac.clang2 := $(if $(OS_is_mac),$(if $(TBBDIR.libia.mac.clang1),,$(firstword $(filter $(TBBROOT)%,$(subst :,$(space),$(LIBRARY_PATH)))))) diff --git a/sci-libs/oneDAL/metadata.xml b/sci-libs/oneDAL/metadata.xml new file mode 100644 index 000000000..2793ac235 --- /dev/null +++ b/sci-libs/oneDAL/metadata.xml @@ -0,0 +1,11 @@ +<?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> + <upstream> + <remote-id type="github">oneapi-src/oneDAL</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/oneDAL/oneDAL-2023.0.1.ebuild b/sci-libs/oneDAL/oneDAL-2023.0.1.ebuild new file mode 100644 index 000000000..589a74960 --- /dev/null +++ b/sci-libs/oneDAL/oneDAL-2023.0.1.ebuild @@ -0,0 +1,85 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +inherit python-any-r1 java-pkg-2 + +MKLFPK_VER="20221214" +MKLGPUFPK_VER="20221214" + +DESCRIPTION="oneAPI Data Analytics Library" +HOMEPAGE="https://github.com/oneapi-src/oneDAL" +# Secondary urls extracted from dev/download_micromkl.sh +SRC_URI=" + https://github.com/oneapi-src/oneDAL/archive/${PV}.tar.gz -> ${P}.tar.gz + https://github.com/oneapi-src/oneDAL/releases/download/Dependencies/mklgpufpk_lnx_${MKLGPUFPK_VER}.tgz + https://github.com/oneapi-src/oneDAL/releases/download/Dependencies/mklfpk_lnx_${MKLFPK_VER}.tgz +" + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="~amd64" + +BDEPEND="sys-devel/DPC++" + +RDEPEND=" + dev-cpp/tbb:= + dev-libs/opencl-icd-loader + virtual/jdk:17 +" +DEPEND=" + ${DEPEND} + ${PYTHON_DEPS} +" + +PATCHES=( + "${FILESDIR}/${PN}-2021.7.1_p20221207-fix-compile.patch" +) + +pkg_setup() { + python-any-r1_pkg_setup + java-pkg-2_pkg_setup +} + +src_unpack() { + unpack "${P}.tar.gz" + mkdir -p "${S}/__deps/mklfpk/" "${S}/__deps/mklgpufpk/lnx" || die + cd "${S}/__deps/mklfpk/" || die + unpack "mklfpk_lnx_${MKLFPK_VER}.tgz" + cd "${S}/__deps/mklgpufpk/lnx" || die + unpack "mklgpufpk_lnx_${MKLGPUFPK_VER}.tgz" +} + +src_prepare() { + # DPC++ compiler required for full functionality + export CC="${ESYSROOT}/usr/lib/llvm/intel/bin/clang" + export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++" + export TBBROOT="${ESYSROOT}/usr" + export CPLUS_INCLUDE_PATH="./cpp/daal/include:${ESYSROOT}/usr/lib/llvm/intel/include" + export JAVA_HOME="${ESYSROOT}/usr/lib64/openjdk-17/" + export PATH="${JAVA_HOME}/bin:${PATH}" + export CPATH="${JAVA_HOME}/include:${JAVA_HOME}/include/linux:${CPATH}" + + default +} + +src_compile() { + emake PLAT=lnx32e COMPILER=icx daal oneapi +} + +src_install() { + einstalldocs + cd __release_lnx_icx/daal/latest || die + docinto examples + dodoc -r examples/* + docinto samples + dodoc -r samples/* + doheader -r include/* + dolib.so lib/intel64/*.so* + dolib.a lib/intel64/*.a* + insinto /usr/share/pkgconfig + doins -r lib/pkgconfig/* + java-pkg_dojar lib/*.jar +} diff --git a/sci-libs/oneDAL/oneDAL-2023.2.1.ebuild b/sci-libs/oneDAL/oneDAL-2023.2.1.ebuild new file mode 100644 index 000000000..9007f7a51 --- /dev/null +++ b/sci-libs/oneDAL/oneDAL-2023.2.1.ebuild @@ -0,0 +1,85 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +inherit python-any-r1 java-pkg-2 + +MKLFPK_VER="20221214" +MKLGPUFPK_VER="20221214" + +DESCRIPTION="oneAPI Data Analytics Library" +HOMEPAGE="https://github.com/oneapi-src/oneDAL" +# Secondary urls extracted from dev/download_micromkl.sh +SRC_URI=" + https://github.com/oneapi-src/oneDAL/archive/${PV}.tar.gz -> ${P}.tar.gz + https://github.com/oneapi-src/oneDAL/releases/download/Dependencies/mklgpufpk_lnx_${MKLGPUFPK_VER}.tgz + https://github.com/oneapi-src/oneDAL/releases/download/Dependencies/mklfpk_lnx_${MKLFPK_VER}.tgz +" + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="~amd64" + +BDEPEND="sys-devel/DPC++" + +RDEPEND=" + dev-cpp/tbb:= + dev-libs/opencl-icd-loader + virtual/jdk:17 +" +DEPEND=" + ${DEPEND} + ${PYTHON_DEPS} +" + +PATCHES=( + "${FILESDIR}/${PN}-2023.2.1-fix-compile.patch" +) + +pkg_setup() { + python-any-r1_pkg_setup + java-pkg-2_pkg_setup +} + +src_unpack() { + unpack "${P}.tar.gz" + mkdir -p "${S}/__deps/mklfpk/" "${S}/__deps/mklgpufpk/lnx" || die + cd "${S}/__deps/mklfpk/" || die + unpack "mklfpk_lnx_${MKLFPK_VER}.tgz" + cd "${S}/__deps/mklgpufpk/lnx" || die + unpack "mklgpufpk_lnx_${MKLGPUFPK_VER}.tgz" +} + +src_prepare() { + # DPC++ compiler required for full functionality + export CC="${ESYSROOT}/usr/lib/llvm/intel/bin/clang" + export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++" + export TBBROOT="${ESYSROOT}/usr" + export CPLUS_INCLUDE_PATH="./cpp/daal/include:${ESYSROOT}/usr/lib/llvm/intel/include" + export JAVA_HOME="${ESYSROOT}/usr/lib64/openjdk-17/" + export PATH="${JAVA_HOME}/bin:${PATH}" + export CPATH="${JAVA_HOME}/include:${JAVA_HOME}/include/linux:${CPATH}" + + default +} + +src_compile() { + emake PLAT=lnx32e COMPILER=icx daal oneapi +} + +src_install() { + einstalldocs + cd __release_lnx_icx/daal/latest || die + docinto examples + dodoc -r examples/* + docinto samples + dodoc -r samples/* + doheader -r include/* + dolib.so lib/intel64/*.so* + dolib.a lib/intel64/*.a* + insinto /usr/share/pkgconfig + doins -r lib/pkgconfig/* + java-pkg_dojar lib/*.jar +} diff --git a/sci-libs/oneMKL/Manifest b/sci-libs/oneMKL/Manifest new file mode 100644 index 000000000..9999712a5 --- /dev/null +++ b/sci-libs/oneMKL/Manifest @@ -0,0 +1,2 @@ +DIST oneMKL-0.2_p20221201.tar.gz 958514 BLAKE2B 14fe7ca0095440f90ae74f9480be1693677c405071d123b10044d3ce09c7e2f8cb42f262ecfe617ba7d68efdf506ccd6aa31c52e376ff3bd1789f4923597b2b5 SHA512 e474f3d37aa58978aba417073f466507c91e428477c7a4b6f52206584e4ba6c307df7157b5b6e6e9b82e8bd1d9b6537eebef569fe8170cf053f6d1d87d2c1176 +DIST oneMKL-0.2_p20230221.tar.gz 983270 BLAKE2B 73f399301989938c78620dfd833cc895050e253d5880d4b7b6a416438179ac3299278f7dfef8198ba81aa55c33e95bb37d62c523345aa5d876177ca482cbaab7 SHA512 b502b0511613927e74e0d40186c0d91864f12bd23880eb029876a30b89cf1d495f0af9bfefe0278ee102b6d0bb7f698b50a3280ad53b33a9ebce32ec5ce84e85 diff --git a/sci-libs/oneMKL/files/oneMKL-0.2_p20221201-find-lapacke.patch b/sci-libs/oneMKL/files/oneMKL-0.2_p20221201-find-lapacke.patch new file mode 100644 index 000000000..2c2fc1367 --- /dev/null +++ b/sci-libs/oneMKL/files/oneMKL-0.2_p20221201-find-lapacke.patch @@ -0,0 +1,22 @@ +diff --git a/cmake/FindLAPACKE.cmake b/cmake/FindLAPACKE.cmake +index 42a5b7d..080108a 100644 +--- a/cmake/FindLAPACKE.cmake ++++ b/cmake/FindLAPACKE.cmake +@@ -19,13 +19,13 @@ + + include_guard() + +-find_library(LAPACKE64_file NAMES lapacke64.dll.lib lapacke64.lib lapacke64 HINTS ${REF_LAPACK_ROOT} PATH_SUFFIXES lib lib64) ++find_library(LAPACKE64_file NAMES lapacke64.dll.lib lapacke64.lib lapacke HINTS ${REF_LAPACK_ROOT} PATH_SUFFIXES lib lib64) + find_package_handle_standard_args(LAPACKE REQUIRED_VARS LAPACKE64_file) +-find_library(LAPACK64_file NAMES lapack64.dll.lib lapack64.lib lapack64 HINTS ${REF_LAPACK_ROOT} PATH_SUFFIXES lib lib64) ++find_library(LAPACK64_file NAMES lapack64.dll.lib lapack64.lib lapack HINTS ${REF_LAPACK_ROOT} PATH_SUFFIXES lib lib64) + find_package_handle_standard_args(LAPACKE REQUIRED_VARS LAPACK64_file) +-find_library(CBLAS64_file NAMES cblas64.dll.lib cblas64.lib cblas64 HINTS ${REF_LAPACK_ROOT} PATH_SUFFIXES lib lib64) ++find_library(CBLAS64_file NAMES cblas64.dll.lib cblas64.lib cblas HINTS ${REF_LAPACK_ROOT} PATH_SUFFIXES lib lib64) + find_package_handle_standard_args(LAPACKE REQUIRED_VARS CBLAS64_file) +-find_library(BLAS64_file NAMES blas64.dll.lib blas64.lib blas64 HINTS ${REF_LAPACK_ROOT} PATH_SUFFIXES lib lib64) ++find_library(BLAS64_file NAMES blas64.dll.lib blas64.lib blas HINTS ${REF_LAPACK_ROOT} PATH_SUFFIXES lib lib64) + find_package_handle_standard_args(LAPACKE REQUIRED_VARS BLAS64_file) + + get_filename_component(LAPACKE64_LIB_DIR ${LAPACKE64_file} DIRECTORY) diff --git a/sci-libs/oneMKL/metadata.xml b/sci-libs/oneMKL/metadata.xml new file mode 100644 index 000000000..77e2dd702 --- /dev/null +++ b/sci-libs/oneMKL/metadata.xml @@ -0,0 +1,11 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <upstream> + <remote-id type="github">oneapi-src/oneMKL</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/oneMKL/oneMKL-0.2_p20221201.ebuild b/sci-libs/oneMKL/oneMKL-0.2_p20221201.ebuild new file mode 100644 index 000000000..35d773397 --- /dev/null +++ b/sci-libs/oneMKL/oneMKL-0.2_p20221201.ebuild @@ -0,0 +1,59 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit cmake + +COMMIT="f4866ab2648cd7cff4a047b91be5f94ff7b73ba1" + +DESCRIPTION="oneAPI Math Kernel Library Interfaces " +HOMEPAGE="https://github.com/oneapi-src/oneMKL" +SRC_URI="https://github.com/oneapi-src/oneMKL/archive/${COMMIT}.tar.gz -> ${P}.tar.gz" +S="${WORKDIR}/${PN}-${COMMIT}" + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="~amd64" + +IUSE="test" +# Tests don't compile properly +# RESTRICT="!test? ( test )" +RESTRICT="test" + +BDEPEND="sys-devel/DPC++" + +DEPEND=" + dev-cpp/tbb:= + sci-libs/lapack[lapacke] + sci-libs/mkl +" +RDEPEND="${DEPEND}" + +PATCHES=( + "${FILESDIR}/${P}-find-lapacke.patch" +) + +src_prepare() { + # DPC++ compiler required for full functionality + export CC="${ESYSROOT}/usr/lib/llvm/intel/bin/clang" + export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++" + + cmake_src_prepare +} + +src_configure() { + local mycmakeargs=( + -DCMAKE_CXX_COMPILER="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++" + -DCMAKE_C_COMPILER="${ESYSROOT}/usr/lib/llvm/intel/bin/clang" + -DMKL_ROOT="${ESYSROOT}/opt/intel/oneapi/mkl/latest" + -DBUILD_FUNCTIONAL_TESTS="$(usex test)" + ) + cmake_src_configure +} + +src_install() { + cmake_src_install + # Move into the correct libdid + mv "${ED}/usr/lib" "${ED}/usr/$(get_libdir)" || die +} diff --git a/sci-libs/oneMKL/oneMKL-0.2_p20230221.ebuild b/sci-libs/oneMKL/oneMKL-0.2_p20230221.ebuild new file mode 100644 index 000000000..896ed4566 --- /dev/null +++ b/sci-libs/oneMKL/oneMKL-0.2_p20230221.ebuild @@ -0,0 +1,59 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit cmake + +COMMIT="793c771c60f5105c12eaf59e1534eeb21d1cfe4a" + +DESCRIPTION="oneAPI Math Kernel Library Interfaces " +HOMEPAGE="https://github.com/oneapi-src/oneMKL" +SRC_URI="https://github.com/oneapi-src/oneMKL/archive/${COMMIT}.tar.gz -> ${P}.tar.gz" +S="${WORKDIR}/${PN}-${COMMIT}" + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="~amd64" + +IUSE="test" +# Tests don't compile properly +# RESTRICT="!test? ( test )" +RESTRICT="test" + +BDEPEND="sys-devel/DPC++" + +DEPEND=" + dev-cpp/tbb:= + sci-libs/lapack[lapacke] + sci-libs/mkl +" +RDEPEND="${DEPEND}" + +PATCHES=( + "${FILESDIR}/${PN}-0.2_p20221201-find-lapacke.patch" +) + +src_prepare() { + # DPC++ compiler required for full functionality + export CC="${ESYSROOT}/usr/lib/llvm/intel/bin/clang" + export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++" + + cmake_src_prepare +} + +src_configure() { + local mycmakeargs=( + -DCMAKE_CXX_COMPILER="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++" + -DCMAKE_C_COMPILER="${ESYSROOT}/usr/lib/llvm/intel/bin/clang" + -DMKL_ROOT="${ESYSROOT}/opt/intel/oneapi/mkl/latest" + -DBUILD_FUNCTIONAL_TESTS="$(usex test)" + ) + cmake_src_configure +} + +src_install() { + cmake_src_install + # Move into the correct libdir + mv "${ED}/usr/lib" "${ED}/usr/$(get_libdir)" || die +} diff --git a/sci-libs/pybids/Manifest b/sci-libs/pybids/Manifest index 28c1b4626..fc1863ad9 100644 --- a/sci-libs/pybids/Manifest +++ b/sci-libs/pybids/Manifest @@ -1,4 +1,3 @@ DIST pybids-0.10.2.tar.gz 3013772 BLAKE2B 70255fbca7a7d5a51efa454ee20d30a9527703d6028a965b51da883aa10f8b63d180f72fd127e12b27249c3f388825a9bb2ba4604680c57f3a512ec7093c01c4 SHA512 c90b7e471d73b070e86452ca5d03639d0263e74c3c79386b52ed2c5fc49576f985bc923f2327882ee56bc4691631105c831ebe40f78aade5b9943be83909ba16 -DIST pybids-0.11.1.tar.gz 3026079 BLAKE2B 9ca7d1299a074f4b7ae51e7d6ff29a55664b6c32c85511913fb69459bd66a0c09b63dddfef2c433c5cccf47c4e358720cbd101f85e7794e22a9935bd6a36ac65 SHA512 bcc1cc3a06b6921e8336990e83e820439c217cfdce6aee3b4b93f2c1ee04acf0bf9009fa2fc80fd50cd59bd9b1a2a3ceb934589b5fd590612de386e91e4f7340 DIST pybids-0.12.4.tar.gz 3031862 BLAKE2B de9d1ba0a0eb400da1de44189f4920a8d1f003dba1c47b18e339d593c68b5a80c340a9acc5267dbfbf730a59aad004035568a1f8b0de30dbab9c211b11790fbd SHA512 1f2f3a784a1e3f0e74919c6ada2ae0365ab89315d724f0a6b6b38a0416c1e6f7e938966b2dda80f090ef2bbf84ce0bcf0bb214a652743432b1d193d9569eb7b1 DIST pybids-0.6.5.tar.gz 2915557 BLAKE2B d7765b872917bbffcd2706488d7c789976be5bbb1eb5d112cb0b7bcedb483236643f8bf7c177f4a64a44a4d50787a4df1d39fbec8e826bfffd2e2e6f891b3ef3 SHA512 9eef42f00440dddf0147d91f90e07db81f9f95a650f0e47c04304771173ca8691cdb366bd0df1d752c0444f102a4aa010c2343ba75df96528cceb9a98f9d8a0e diff --git a/sci-libs/pybids/pybids-0.10.2.ebuild b/sci-libs/pybids/pybids-0.10.2.ebuild index 062cad939..5f2776855 100644 --- a/sci-libs/pybids/pybids-0.10.2.ebuild +++ b/sci-libs/pybids/pybids-0.10.2.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2020 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7..9} ) +PYTHON_COMPAT=( python3_{10..11} ) inherit distutils-r1 @@ -29,12 +29,4 @@ RDEPEND=" dev-python/scipy[${PYTHON_USEDEP}] " -#RESTRICT="test" -# Fails because fixtures are called directly -# https://github.com/bids-standard/pybids/issues/289#issuecomment-476853673 - -python_test() { - #rm bids/tests/test_config.py || die - distutils_install_for_testing - pytest -vv || die -} +distutils_enable_tests pytest diff --git a/sci-libs/pybids/pybids-0.11.1.ebuild b/sci-libs/pybids/pybids-0.11.1.ebuild deleted file mode 100644 index 062cad939..000000000 --- a/sci-libs/pybids/pybids-0.11.1.ebuild +++ /dev/null @@ -1,40 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7..9} ) - -inherit distutils-r1 - -DESCRIPTION="Python package to access BIDS datasets" -HOMEPAGE="https://github.com/INCF/pybids" -SRC_URI="https://github.com/INCF/pybids/archive/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64" -IUSE="test" -RESTRICT="!test? ( test )" - -DEPEND="" -RDEPEND=" - dev-python/num2words[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/pandas[${PYTHON_USEDEP}] - dev-python/patsy[${PYTHON_USEDEP}] - dev-python/sqlalchemy[${PYTHON_USEDEP}] - sci-libs/bids-validator[${PYTHON_USEDEP}] - sci-libs/nibabel[${PYTHON_USEDEP}] - dev-python/scipy[${PYTHON_USEDEP}] - " - -#RESTRICT="test" -# Fails because fixtures are called directly -# https://github.com/bids-standard/pybids/issues/289#issuecomment-476853673 - -python_test() { - #rm bids/tests/test_config.py || die - distutils_install_for_testing - pytest -vv || die -} diff --git a/sci-libs/pybids/pybids-0.12.4.ebuild b/sci-libs/pybids/pybids-0.12.4.ebuild index 40a8adc17..7860d69c9 100644 --- a/sci-libs/pybids/pybids-0.12.4.ebuild +++ b/sci-libs/pybids/pybids-0.12.4.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7..9} ) +PYTHON_COMPAT=( python3_{10..11} ) DISTUTILS_USE_SETUPTOOLS=rdepend inherit distutils-r1 @@ -16,9 +16,7 @@ LICENSE="MIT" SLOT="0" KEYWORDS="~amd64" -BDEPEND="dev-python/versioneer[${PYTHON_USEDEP}] - test? ( dev-python/mock[${PYTHON_USEDEP}] ) -" +BDEPEND="test? ( dev-python/mock[${PYTHON_USEDEP}] )" RDEPEND=" dev-python/click[${PYTHON_USEDEP}] @@ -32,4 +30,4 @@ RDEPEND=" dev-python/scipy[${PYTHON_USEDEP}] " -distutils_enable_tests --install pytest +distutils_enable_tests pytest diff --git a/sci-libs/pybids/pybids-0.6.5.ebuild b/sci-libs/pybids/pybids-0.6.5.ebuild index 521ef9947..6103c3191 100644 --- a/sci-libs/pybids/pybids-0.6.5.ebuild +++ b/sci-libs/pybids/pybids-0.6.5.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2020 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7..9} ) +PYTHON_COMPAT=( python3_{10..11} ) inherit distutils-r1 diff --git a/sci-libs/pydicom/Manifest b/sci-libs/pydicom/Manifest index b49bf81e1..b5e5f2a75 100644 --- a/sci-libs/pydicom/Manifest +++ b/sci-libs/pydicom/Manifest @@ -1,3 +1,2 @@ -DIST pydicom-1.1.0.tar.gz 6724086 BLAKE2B efdcdd722bc877b9b9cf137ecd2a3fa6fb2b7da022bdab49f03dbcdb5a3e3dc8bc24b6b0d8eb9ab946934ec182c13ec1df671461c357476f543afb6f435f604c SHA512 ffca9eb4333d29accea1d6e5a5b4c3c0bd0f8c12fdf00c5c84d83769db621e8f348c9200dff1dc1cd6016cbf5d76b00f08c3b112ba653433a84ce31ad1ab33d5 -DIST pydicom-1.4.2.tar.gz 35237997 BLAKE2B 0b4db847150153519cc7d805a9a7b9c5c4d9ed46496bd561a24e5ede1cd3b5f176581a9741aba65c31cdd0533fb6a33905cc21003f0237c7cd7e603ef672c67a SHA512 8fc0a2e5f0a8578b98d49b749912cca98d51bdcae2b3bd5759e03e13cd2a2d4f45ce0e2a22d80526abfa5f428a4a71b5fad2c9f36bafc4f3fa2866cd687ac015 DIST pydicom-2.2.2.tar.gz 2149674 BLAKE2B d109975c6ac0081a02c534bb014040ca767968d276fb841a0000ab4f7b4884ab604276b7092f8cc699d24d0429426cf5be3225ae56b8b8ebdad89cf541ab065a SHA512 5f1829d445c462884debb75328f59471dea4da51701835a3a97a1c22c1c0b75730e0688558cb76ef3f7a4b29f350028190a515d73f88968a7fda09ed414ec145 +DIST pydicom-2.3.1.tar.gz 2164956 BLAKE2B ffdf14c582a7a783ae963008de9d8d9dd54c6d6889f10ebb767ff87abf00ab36406ea3dbab50304bcf1902af745b871b9dc1702d8824fb9ed163d1d909e88ac5 SHA512 bf2856b8afa13f6477a37abdc7d723337f532746705832b0eb01cfcf468f318ec4b74af5aade3b8629d050947a87e87fb39aca965ff98d0a348170a900d7dd57 diff --git a/sci-libs/pydicom/pydicom-1.1.0.ebuild b/sci-libs/pydicom/pydicom-1.1.0.ebuild deleted file mode 100644 index 523da2654..000000000 --- a/sci-libs/pydicom/pydicom-1.1.0.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_{7,8,9} ) - -inherit distutils-r1 - -DESCRIPTION="A pure python package for parsing DICOM files" -HOMEPAGE="http://www.pydicom.org/" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="test" - -# Upstream bug: https://github.com/pydicom/pydicom/issues/663 -RESTRICT="test" - -DEPEND="test? ( dev-python/pytest[${PYTHON_USEDEP}] )" - -python_test() { - distutils-r1_install_for_testing - py.test --cov=pydicom -r sx --pyargs pydicom --verbose || die -} diff --git a/sci-libs/pydicom/pydicom-1.4.2.ebuild b/sci-libs/pydicom/pydicom-1.4.2.ebuild deleted file mode 100644 index f02b71a97..000000000 --- a/sci-libs/pydicom/pydicom-1.4.2.ebuild +++ /dev/null @@ -1,26 +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 distutils-r1 - -DESCRIPTION="A pure python package for parsing DICOM files" -HOMEPAGE="http://www.pydicom.org/" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="test" - -RESTRICT="!test? ( test )" - -DEPEND="test? ( dev-python/pytest[${PYTHON_USEDEP}] )" - -python_test() { - distutils-r1_install_for_testing - py.test -r sx --pyargs pydicom --verbose || die -} diff --git a/sci-libs/pydicom/pydicom-2.2.2.ebuild b/sci-libs/pydicom/pydicom-2.2.2.ebuild index f36be3a78..69cbed0c7 100644 --- a/sci-libs/pydicom/pydicom-2.2.2.ebuild +++ b/sci-libs/pydicom/pydicom-2.2.2.ebuild @@ -1,27 +1,28 @@ -# Copyright 1999-2022 Gentoo Authors +# Copyright 1999-2023 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 -PYTHON_COMPAT=( python3_{7..10} ) +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..12} ) -inherit distutils-r1 +inherit distutils-r1 pypi DESCRIPTION="A pure python package for parsing DICOM files" -HOMEPAGE="http://www.pydicom.org/" -SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz" +HOMEPAGE="https://pydicom.github.io/pydicom/dev/" LICENSE="MIT" SLOT="0" KEYWORDS="~amd64 ~x86" IUSE="test" -# Upstream bug: https://github.com/pydicom/pydicom/issues/663 +# Reported upstream: +# https://github.com/pydicom/pydicom/issues/1800 RESTRICT="test" DEPEND="test? ( dev-python/pytest[${PYTHON_USEDEP}] )" python_test() { distutils-r1_install_for_testing - py.test --cov=pydicom -r sx --pyargs pydicom --verbose || die + py.test -r sx --pyargs pydicom --verbose || die } diff --git a/sci-libs/pydicom/pydicom-2.3.1.ebuild b/sci-libs/pydicom/pydicom-2.3.1.ebuild new file mode 100644 index 000000000..69cbed0c7 --- /dev/null +++ b/sci-libs/pydicom/pydicom-2.3.1.ebuild @@ -0,0 +1,28 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..12} ) + +inherit distutils-r1 pypi + +DESCRIPTION="A pure python package for parsing DICOM files" +HOMEPAGE="https://pydicom.github.io/pydicom/dev/" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="test" + +# Reported upstream: +# https://github.com/pydicom/pydicom/issues/1800 +RESTRICT="test" + +DEPEND="test? ( dev-python/pytest[${PYTHON_USEDEP}] )" + +python_test() { + distutils-r1_install_for_testing + py.test -r sx --pyargs pydicom --verbose || die +} diff --git a/sci-libs/rdkit/rdkit-2021.09.4.ebuild b/sci-libs/rdkit/rdkit-2021.09.4.ebuild index a9b1258c9..a1621ea79 100644 --- a/sci-libs/rdkit/rdkit-2021.09.4.ebuild +++ b/sci-libs/rdkit/rdkit-2021.09.4.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) inherit cmake python-single-r1 diff --git a/sci-libs/scikit-learn-intelx/Manifest b/sci-libs/scikit-learn-intelx/Manifest new file mode 100644 index 000000000..d14b31510 --- /dev/null +++ b/sci-libs/scikit-learn-intelx/Manifest @@ -0,0 +1 @@ +DIST scikit-learn-intelx-2023.0.2.tar.gz 13864043 BLAKE2B dfc082a8b008553e0d20cf7a24417fecd510dd8e6b3286a57a633b1e3b79cecc87fc1189df6f4a3440d7ccb74077c54a9f6eaf58bfbb19181cb4b437b3e06ae6 SHA512 dd8c983365d4f32d2640caab17319970c86bfed5ad6852d15dce35ba66a3584c51b94fa5ef0d8073b917332ea18a8c9af95ef8da125edb47190f27e9b8cab424 diff --git a/sci-libs/scikit-learn-intelx/metadata.xml b/sci-libs/scikit-learn-intelx/metadata.xml new file mode 100644 index 000000000..247707c87 --- /dev/null +++ b/sci-libs/scikit-learn-intelx/metadata.xml @@ -0,0 +1,11 @@ +<?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> + <upstream> + <remote-id type="github">intel/scikit-learn-intelex</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/scikit-learn-intelx/scikit-learn-intelx-2023.0.2.ebuild b/sci-libs/scikit-learn-intelx/scikit-learn-intelx-2023.0.2.ebuild new file mode 100644 index 000000000..29288cbcf --- /dev/null +++ b/sci-libs/scikit-learn-intelx/scikit-learn-intelx-2023.0.2.ebuild @@ -0,0 +1,49 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 + +DESCRIPTION="Seamless way to speed up your Scikit-learn application" +HOMEPAGE="https://github.com/intel/scikit-learn-intelex" +SRC_URI="https://github.com/intel/scikit-learn-intelex/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz" +S="${WORKDIR}/scikit-learn-intelex-${PV}" + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="~amd64" + +DEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + sci-libs/daal4py[${PYTHON_USEDEP}] + sci-libs/scikit-learn[${PYTHON_USEDEP}] +" +RDEPEND="${DEPEND}" + +distutils_enable_tests pytest + +python_prepare_all() { + # DPC++ compiler required for full functionality + export CC="${ESYSROOT}/usr/lib/llvm/intel/bin/clang" + export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++" + export DPCPPROOT="${ESYSROOT}/usr/lib/llvm/intel" + export CPLUS_INCLUDE_PATH="${ESYSROOT}/usr/lib/llvm/intel/include:${ESYSROOT}/usr/lib/llvm/intel/include/sycl" + export MPIROOT="${ESYSROOT}/usr" + export DALROOT="${ESYSROOT}/usr" + + # remove the daal4py setup files, and rename skleanex setup files + rm setup.py setup.cfg || die + mv setup_sklearnex.cfg setup.cfg || die + mv setup_sklearnex.py setup.py || die + + distutils-r1_python_prepare_all +} + +python_test() { + export PYTHONPATH="${BUILD_DIR}/install/usr/lib/${EPYTHON}/site-packages" + # We don't use epytest because it overwrites our PYTHONPATH + pytest -vv || die +} diff --git a/sci-libs/scikits_video/Manifest b/sci-libs/scikits_video/Manifest deleted file mode 100644 index d18395f99..000000000 --- a/sci-libs/scikits_video/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST scikits_video-1.1.11_p20200115.tar.gz 32060067 BLAKE2B 2f2c14ed89638f46b3c7e27b5d7562429a17f86982442f66015392173dcda89fa3ef810e4529dca9f4dccdb59287f12af2d897411124e4d15abb6197e7d13fc5 SHA512 ca3c4eaf343075934d83c540ff11cb4f2e611838bcbfd9f06efb69b00875ffc77dac1f0f32978d554a7cb126c8d689013fb103b61cda39b7d4d9f85c81542b2d diff --git a/sci-libs/scikits_video/metadata.xml b/sci-libs/scikits_video/metadata.xml deleted file mode 100644 index 186bb5c9c..000000000 --- a/sci-libs/scikits_video/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"> - Scikit-video is designed for easy video processing using Python. It is - modeled in the spirit of other successful scikits such as scikit-learn - and scikit-image. This project aims to provide an all-in-one solution to - make video algorithms easy to access for students, engineers, - instructors, and researchers. - </longdescription> - <upstream> - <remote-id type="pypi">scikit-video</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-libs/scikits_video/scikits_video-1.1.11_p20200115.ebuild b/sci-libs/scikits_video/scikits_video-1.1.11_p20200115.ebuild deleted file mode 100644 index bb8efaa24..000000000 --- a/sci-libs/scikits_video/scikits_video-1.1.11_p20200115.ebuild +++ /dev/null @@ -1,32 +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 - -MY_PN="scikit-video" -MY_HASH="87c7113a84b50679d9853ba81ba34b557f516b05" - -DESCRIPTION="Video processing in Python" -HOMEPAGE="https://scikit-image.org/" -SRC_URI="https://github.com/scikit-video/scikit-video/archive/${MY_HASH}.tar.gz -> ${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -RDEPEND=" - media-video/ffmpeg - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/scipy[${PYTHON_USEDEP}] - dev-python/pillow[${PYTHON_USEDEP}] - sci-libs/scikit-learn[${PYTHON_USEDEP}] - media-video/mediainfo -" - -S="${WORKDIR}/${MY_PN}-${MY_HASH}" - -distutils_enable_tests pytest diff --git a/sci-libs/simpleitk/simpleitk-1.2.4.ebuild b/sci-libs/simpleitk/simpleitk-1.2.4.ebuild index 8a3bf5f5a..26e0c688d 100644 --- a/sci-libs/simpleitk/simpleitk-1.2.4.ebuild +++ b/sci-libs/simpleitk/simpleitk-1.2.4.ebuild @@ -1,9 +1,9 @@ -# Copyright 1999-2021 Gentoo Authors +# Copyright 1999-2022 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=7 +EAPI=8 -PYTHON_COMPAT=( python3_{7..9} ) +PYTHON_COMPAT=( python3_10 ) LUA_COMPAT=( lua5-{1..3} ) inherit lua-single cmake python-single-r1 diff --git a/sci-libs/spams-python/Manifest b/sci-libs/spams-python/Manifest deleted file mode 100644 index d58c9e869..000000000 --- a/sci-libs/spams-python/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST spams-python-2.6.2.tar.gz 315332 BLAKE2B 1aa972a65c2f69de859391b98a28972ebbd30f166ea3d44083933f746e119105d45d6ee5adff99064dc396f5522c31e5dd4055210c82e93c1217a06bf4bce2f2 SHA512 dec2ce2abe5abeb78bf470952c5f854501bf9ea21019dda1de66683f813153e78cc9b87b5376e91ac74beedb4d13854cc053e54e97bfded4177728c540812a9f diff --git a/sci-libs/spams-python/metadata.xml b/sci-libs/spams-python/metadata.xml deleted file mode 100644 index 4cb1814dc..000000000 --- a/sci-libs/spams-python/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>gentoo@chymera.eu</email> - <name>Horea Christian</name> - </maintainer> - <maintainer type="project"> - <email>sci@gentoo.org</email> - <name>Gentoo Science Project</name> - </maintainer> - <longdescription lang="en"> - SPAMS (SPArse Modeling Software) is an optimization toolbox for solving - various sparse estimation problems, such as: Dictionary learning and - matrix factorization (NMF, sparse PCA, ...); solving sparse decomposition - problems with LARS, coordinate descent, OMP, SOMP, proximal methods; and - Solving structured sparse decomposition problems (l1/l2, l1/linf, sparse - group lasso, tree-structured regularization, structured sparsity with - overlapping groups,...). - </longdescription> - <upstream> - <remote-id type="github">samuelstjean/spams-python</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-libs/spams-python/spams-python-2.6.2.ebuild b/sci-libs/spams-python/spams-python-2.6.2.ebuild deleted file mode 100644 index 99b1e6370..000000000 --- a/sci-libs/spams-python/spams-python-2.6.2.ebuild +++ /dev/null @@ -1,60 +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 toolchain-funcs - -DESCRIPTION="Optimization toolbox for solving various sparse estimation problems" -HOMEPAGE="http://spams-devel.gforge.inria.fr/index.html" -SRC_URI="https://github.com/samuelstjean/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="GPL-3" -SLOT="0" -KEYWORDS="~amd64" - -DEPEND=" - dev-python/distro[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/pillow[${PYTHON_USEDEP}] - sci-libs/openblas - virtual/lapack - " -RDEPEND="${DEPEND} - dev-python/scipy[${PYTHON_USEDEP}] - " - -pc_libdir() { - $(tc-getPKG_CONFIG) --libs-only-L $@ | \ - sed -e 's/^-L//' -e 's/[ ]*-L/:/g' -e 's/[ ]*$//' -e 's|^,||' -} - -pc_libs() { - $(tc-getPKG_CONFIG) --libs-only-l $@ | \ - sed -e 's/[ ]-l*\(pthread\|m\)\([ ]\|$\)//g' \ - -e 's/^-l//' -e 's/[ ]*-l/,/g' -e 's/[ ]*$//' \ - | tr ',' '\n' | sort -u | tr '\n' ',' | sed -e 's|,$||' -} -pkg_pretend() { - [[ ${MERGE_TYPE} != binary ]] && tc-check-openmp -} - -pkg_setup() { - [[ ${MERGE_TYPE} != binary ]] && tc-check-openmp -} - -python_prepare_all() { - local libdir="${EPREFIX}"/usr/$(get_libdir) - MY_LAPACK=$(pc_libs lapack) - MY_BLAS=$(pc_libs blas) - MY_LIBDIRS="$(pc_libdir blas lapack)'${libdir}'" - sed -i -e "s/'blas', 'lapack'/'${MY_BLAS}', '${MY_LAPACK}'/g" setup.py || die - sed -i -e "s|libdirs = \[\]|libdirs = [${MY_LIBDIRS}]|g" setup.py || die - distutils-r1_python_prepare_all -} - -python_test() { - ${EPYTHON} test_spams.py -} diff --git a/sci-libs/spyking-circus/metadata.xml b/sci-libs/spyking-circus/metadata.xml index 844f386de..89a208f6f 100644 --- a/sci-libs/spyking-circus/metadata.xml +++ b/sci-libs/spyking-circus/metadata.xml @@ -16,4 +16,7 @@ on datasets coming from in vitro retina with 252 electrodes MEA, from in vivo hippocampus with tetrodes, and in vivo and in vitro cortex data. </longdescription> + <upstream> + <remote-id type="github">spyking-circus/spyking-circus</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/spyking-circus/spyking-circus-1.1.0.ebuild b/sci-libs/spyking-circus/spyking-circus-1.1.0.ebuild index 3d7feaaf0..9b9233020 100644 --- a/sci-libs/spyking-circus/spyking-circus-1.1.0.ebuild +++ b/sci-libs/spyking-circus/spyking-circus-1.1.0.ebuild @@ -3,7 +3,7 @@ EAPI=8 -PYTHON_COMPAT=( python3_{8..10} ) +PYTHON_COMPAT=( python3_10 ) inherit distutils-r1 @@ -13,7 +13,7 @@ SRC_URI="https://github.com/spyking-circus/spyking-circus/archive/${PV}.tar.gz - LICENSE="CeCILL-2" SLOT="0" -KEYWORDS="~amd64 ~x86" +KEYWORDS="~amd64" # Wants to run mpirun (and fails) RESTRICT="test" @@ -27,7 +27,7 @@ RDEPEND=" >=dev-python/mpi4py-3.0.0[${PYTHON_USEDEP}] >=dev-python/numpy-1.17.4[${PYTHON_USEDEP}] >=dev-python/psutil-5.6.7[${PYTHON_USEDEP}] - >=dev-python/statsmodels-0.10.1[${PYTHON_USEDEP}] + dev-python/statsmodels[${PYTHON_USEDEP}] >=dev-python/tqdm-4.40.0[${PYTHON_USEDEP}] >=dev-python/scipy-1.3.1[${PYTHON_USEDEP}] " diff --git a/sci-libs/torchvision/Manifest b/sci-libs/torchvision/Manifest index 8e703b008..7cf5fa956 100644 --- a/sci-libs/torchvision/Manifest +++ b/sci-libs/torchvision/Manifest @@ -1 +1,2 @@ -DIST torchvision-0.11.2.tar.gz 9361872 BLAKE2B a3086b1ac8a05ab1f8dac13c5ee15f75274a96cebb72b48b525ac9721c961c67d742878efa7ef4c245a885904ea88d2c2dde311df8ef710563c3656c2629b644 SHA512 11891d19c1a17d27fbcc95b576a7bba7d2d2b96673661bc8488505aded9c70e7ee09229732d42eac4a590e11fb8f0066fb5a2d9f5b7fa95265f54d533ffc1359 +DIST torchvision-0.14.1.tar.gz 9265179 BLAKE2B 0708635b00ac7c2cf4e54799f1190f01f3240f53233695819f691313b8a369b8922520e2f3cf96184bab671877b5826b84e0936d9ca5b58004d6e2a098c6cbbf SHA512 08fb1e35da1c3f1d0446ef879d9b6a7ae839a5137c3b5b46ef8111c2ae890299e2b555d1bd3b3d61f96b8778b831d8f895487cf8a4e36e371fcd4b8acda67d1f +DIST torchvision-0.17.1.tar.gz 13091686 BLAKE2B db25faab565412f2892ca4cf8d13c459b8045aaab83009a686a93272f0b3e3e8c0da930f1d7b0682e0adc7a600195b035ca19f71fd15a26f77b349206e3ed324 SHA512 c9ef5704a337a43c1ab3a5865b2a20d09d07a9b5eeda66c7aa1e1931772bad9acee822bb400cf627960a84ace01188cd32e95f0e709eb392bf9028d36cfc50be diff --git a/sci-libs/torchvision/files/torchvision-0.17.1-ffmpeg-6.patch b/sci-libs/torchvision/files/torchvision-0.17.1-ffmpeg-6.patch new file mode 100644 index 000000000..7a3637f3a --- /dev/null +++ b/sci-libs/torchvision/files/torchvision-0.17.1-ffmpeg-6.patch @@ -0,0 +1,36 @@ +From 86620bd84b872b76db0acafec167949dca03a29e Mon Sep 17 00:00:00 2001 +From: =?UTF-8?q?Zolt=C3=A1n=20B=C3=B6sz=C3=B6rm=C3=A9nyi?= + <zboszor@gmail.com> +Date: Tue, 7 Nov 2023 10:43:11 +0100 +Subject: [PATCH] Fix build with ffmpeg 6.0 +MIME-Version: 1.0 +Content-Type: text/plain; charset=UTF-8 +Content-Transfer-Encoding: 8bit + +Signed-off-by: Zoltán Böszörményi <zboszor@gmail.com> +--- + torchvision/csrc/io/decoder/stream.cpp | 11 ++--------- + 1 file changed, 2 insertions(+), 9 deletions(-) + +diff --git a/torchvision/csrc/io/decoder/stream.cpp b/torchvision/csrc/io/decoder/stream.cpp +index 0d625ef211c..8c914050587 100644 +--- a/torchvision/csrc/io/decoder/stream.cpp ++++ b/torchvision/csrc/io/decoder/stream.cpp +@@ -63,15 +63,8 @@ int Stream::openCodec(std::vector<DecoderMetadata>* metadata, int num_threads) { + codecCtx_->thread_count = num_threads; + } else { + // otherwise set sensible defaults +- // with the special case for the different MPEG4 codecs +- // that don't have threading context functions +- if (codecCtx_->codec->capabilities & AV_CODEC_CAP_INTRA_ONLY) { +- codecCtx_->thread_type = FF_THREAD_FRAME; +- codecCtx_->thread_count = 2; +- } else { +- codecCtx_->thread_count = 8; +- codecCtx_->thread_type = FF_THREAD_SLICE; +- } ++ codecCtx_->thread_count = 8; ++ codecCtx_->thread_type = FF_THREAD_SLICE; + } + + int ret; diff --git a/sci-libs/torchvision/metadata.xml b/sci-libs/torchvision/metadata.xml index ad3ef354b..9c4ddaefd 100644 --- a/sci-libs/torchvision/metadata.xml +++ b/sci-libs/torchvision/metadata.xml @@ -1,11 +1,11 @@ <?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> - <use> - <flag name="cuda">Enable CUDA support if enabled in PyTorch</flag> - </use> + <maintainer type="person"> + <email>jpizarrocallejas@gmail.com</email> + <name>Jorge Pizarro Callejas</name> + </maintainer> + <upstream> + <remote-id type="github">pytorch/vision</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-libs/torchvision/torchvision-0.11.2.ebuild b/sci-libs/torchvision/torchvision-0.11.2.ebuild deleted file mode 100644 index 6df2cbc01..000000000 --- a/sci-libs/torchvision/torchvision-0.11.2.ebuild +++ /dev/null @@ -1,47 +0,0 @@ -# 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="Datasets, transforms and models to specific to computer vision" -HOMEPAGE="https://github.com/pytorch/vision" -SRC_URI="https://github.com/pytorch/vision/archive/v${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64" -IUSE="cuda" - -RDEPEND=" - dev-python/av[${PYTHON_USEDEP}] - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/pillow[${PYTHON_USEDEP}] - dev-python/six[${PYTHON_USEDEP}] - dev-python/tqdm[${PYTHON_USEDEP}] - dev-python/scipy[${PYTHON_USEDEP}] - sci-libs/pytorch[${PYTHON_USEDEP}] - media-video/ffmpeg - dev-qt/qtcore:5 -" -DEPEND="${RDEPEND}" -BDEPEND=" - test? ( - $(python_gen_cond_dep ' - dev-python/mock[${PYTHON_USEDEP}] - ') - )" - -S="${WORKDIR}/vision-${PV}" - -distutils_enable_tests pytest - -pkg_setup() { - if use cuda; then - export FORCE_CUDA=1 - export TORCH_CUDA_ARCH_LIST="3.5;3.7;5.0;5.2;5.3;6.0;6.0+PTX;6.1;6.1+PTX;6.2;6.2+PTX;7.0;7.0+PTX;7.2;7.2+PTX;7.5;7.5+PTX" - fi -} diff --git a/sci-libs/torchvision/torchvision-0.14.1.ebuild b/sci-libs/torchvision/torchvision-0.14.1.ebuild new file mode 100644 index 000000000..7f40fe556 --- /dev/null +++ b/sci-libs/torchvision/torchvision-0.14.1.ebuild @@ -0,0 +1,40 @@ +# Copyright 2020-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_10 ) +DISTUTILS_SINGLE_IMPL=1 +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 + +DESCRIPTION="Datasets, transforms and models to specific to computer vision" +HOMEPAGE="https://github.com/pytorch/vision" +SRC_URI="https://github.com/pytorch/vision/archive/v${PV}.tar.gz -> ${P}.tar.gz" +S="${WORKDIR}/vision-${PV}" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + $(python_gen_cond_dep ' + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/typing-extensions[${PYTHON_USEDEP}] + dev-python/pillow[${PYTHON_USEDEP}] + dev-python/requests[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + ') + sci-libs/pytorch[${PYTHON_SINGLE_USEDEP}] + media-video/ffmpeg + dev-qt/qtcore:5 +" +DEPEND="${RDEPEND}" +BDEPEND=" + test? ( + $(python_gen_cond_dep ' + dev-python/mock[${PYTHON_USEDEP}] + ') + )" + +distutils_enable_tests pytest diff --git a/sci-libs/torchvision/torchvision-0.17.1.ebuild b/sci-libs/torchvision/torchvision-0.17.1.ebuild new file mode 100644 index 000000000..e0c72684c --- /dev/null +++ b/sci-libs/torchvision/torchvision-0.17.1.ebuild @@ -0,0 +1,45 @@ +# Copyright 2020-2024 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..12} ) +DISTUTILS_SINGLE_IMPL=1 +DISTUTILS_USE_PEP517=setuptools +DISTUTILS_EXT=1 +inherit distutils-r1 multiprocessing + +DESCRIPTION="Datasets, transforms and models to specific to computer vision" +HOMEPAGE="https://github.com/pytorch/vision" +SRC_URI="https://github.com/pytorch/vision/archive/v${PV}.tar.gz -> ${P}.tar.gz" +S="${WORKDIR}/vision-${PV}" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" +RESTRICT="test" + +RDEPEND=" + $(python_gen_cond_dep ' + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/typing-extensions[${PYTHON_USEDEP}] + dev-python/pillow[${PYTHON_USEDEP}] + dev-python/requests[${PYTHON_USEDEP}] + dev-python/scipy[${PYTHON_USEDEP}] + ') + sci-libs/pytorch[${PYTHON_SINGLE_USEDEP}] + media-video/ffmpeg:= +" +DEPEND="${RDEPEND}" + +PATCHES=( "${FILESDIR}/${PN}-0.17.1-ffmpeg-6.patch" ) + +src_compile() +{ + export MAX_JOBS="$(makeopts_jobs)" # Let ninja respect MAKEOPTS + + # Ensure some ext_module sources are compiled before linking + export MAKEOPTS="-j1" + + distutils-r1_src_compile +} diff --git a/sci-libs/vegas/Manifest b/sci-libs/vegas/Manifest new file mode 100644 index 000000000..c636ac4c2 --- /dev/null +++ b/sci-libs/vegas/Manifest @@ -0,0 +1 @@ +DIST vegas-6.0.1.tar.gz 1535565 BLAKE2B 3cd30387e9369ce7efe62e1f5838f87c73bb93e1690c131602a8e0b77a6671e9d9cadb6b909e1f9ba548cd4a32cb09bd6d1d50bfaf536b7c3fbd269c4595ed04 SHA512 ead47a9f194846d704e229d62163233a7b063dab504e665d620f59be5c9abe2b31facf14cad612b102d4bf64d60d9f6f53c0b4bca0ba78d1e62cbd9bda77e0b1 diff --git a/sci-libs/vegas/metadata.xml b/sci-libs/vegas/metadata.xml new file mode 100644 index 000000000..8ae183900 --- /dev/null +++ b/sci-libs/vegas/metadata.xml @@ -0,0 +1,19 @@ +<?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> + <maintainer type="person"> + <email>alexander@neuwirth-informatik.de</email> + <name>Alexander Puck Neuwirth</name> + </maintainer> + <longdescription lang="en"> + The vegas package is for evaluating multidimensional integrals using an improved version of the adaptive Monte Carlo vegas algorithm (G. P. Lepage, J. Comput. Phys. 27(1978) 192). + </longdescription> + <upstream> + <remote-id type="pypi">vegas</remote-id> + <remote-id type="github">gplepage/vegas</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-libs/vegas/vegas-6.0.1.ebuild b/sci-libs/vegas/vegas-6.0.1.ebuild new file mode 100644 index 000000000..7654563e4 --- /dev/null +++ b/sci-libs/vegas/vegas-6.0.1.ebuild @@ -0,0 +1,24 @@ +EAPI=8 + +DISTUTILS_EXT=1 +PYTHON_COMPAT=( python3_{10..12} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 pypi + +DESCRIPTION="Adaptive multidimensional Monte Carlo integration." +HOMEPAGE="https://github.com/gplepage/vegas" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~arm64" + +RDEPEND=" + >=dev-python/numpy-1.16[${PYTHON_USEDEP}] + >=sci-libs/gvar-13.0.2[${PYTHON_USEDEP}] +" +DEPEND="${RDEPEND}" +BDEPEND=" + >=dev-python/cython-0.17[${PYTHON_USEDEP}] +" + +distutils_enable_tests unittest diff --git a/sci-libs/vxl/metadata.xml b/sci-libs/vxl/metadata.xml index 22feba67c..f7d43af09 100644 --- a/sci-libs/vxl/metadata.xml +++ b/sci-libs/vxl/metadata.xml @@ -13,5 +13,6 @@ written in ANSI/ISO C++ and is designed to be portable over many platforms. </longdescription> <upstream> <remote-id type="sourceforge">vxl</remote-id> + <remote-id type="github">vxl/vxl</remote-id> </upstream> </pkgmetadata> diff --git a/sci-libs/wannier90/files/wannier90-1.1-0001.patch b/sci-libs/wannier90/files/wannier90-1.1-0001.patch deleted file mode 100644 index e68c5f4fe..000000000 --- a/sci-libs/wannier90/files/wannier90-1.1-0001.patch +++ /dev/null @@ -1,16 +0,0 @@ -diff -urN wannier90-1.1.old/src/wannier_lib.F90 wannier90-1.1.new/src/wannier_lib.F90 ---- wannier90-1.1.old/src/wannier_lib.F90 2007-12-20 10:58:37.000000000 +0100 -+++ wannier90-1.1.new/src/wannier_lib.F90 2008-04-28 17:27:19.000000000 +0200 -@@ -166,6 +166,12 @@ - exclude_bands_loc(1:num_exclude_bands) = exclude_bands(1:num_exclude_bands) - end if - -+ if (postproc_setup) then -+ call kmesh_write() -+ write(stdout,'(1x,a25,f11.3,a)') 'Time to write kmesh ',io_time(),' (sec)' -+ write(stdout,'(/a)') ' '//trim(seedname)//'.nnkp written.' -+ endif -+ - - call kmesh_dealloc() - call param_dealloc() diff --git a/sci-libs/wannier90/files/wannier90-1.1-0002.patch b/sci-libs/wannier90/files/wannier90-1.1-0002.patch deleted file mode 100644 index 391a34ca2..000000000 --- a/sci-libs/wannier90/files/wannier90-1.1-0002.patch +++ /dev/null @@ -1,105 +0,0 @@ -diff -urN wannier90-1.1.old/src/disentangle.F90 wannier90-1.1.new/src/disentangle.F90 ---- wannier90-1.1.old/src/disentangle.F90 2009-03-07 15:44:11.000000000 +0100 -+++ wannier90-1.1.new/src/disentangle.F90 2009-03-07 15:48:05.000000000 +0100 -@@ -1784,9 +1784,9 @@ - ! [BIG ITERATION LOOP (iter)] - - if (.not.dis_converged) then -- write(stdout,'(/5x,a)') '<<< Warning: Maximum number of disentanglement & -- &iterations reached >>>' -- write(stdout,'(10x,a)') '<<< Disentanglement convergence criteria not satisfied >>>' -+ write(stdout,'(/5x,a)') & -+ '<<< Warning: Maximum number of disentanglement iterations reached >>>' -+ write(stdout,'(10x,a)') '<<< Disentanglement convergence criteria not satisfied >>>' - endif - - if (icompflag.eq.1) then -@@ -2551,8 +2551,8 @@ - ! [BIG ITERATION LOOP (iter)] - - if (.not.dis_converged) then -- write(stdout,'(/5x,a)') '<<< Warning: Maximum number of disentanglement & -- &iterations reached >>>' -+ write(stdout,'(/5x,a)') & -+ '<<< Warning: Maximum number of disentanglement iterations reached >>>' - write(stdout,'(10x,a)') '<<< Disentanglement convergence criteria not satisfied >>>' - endif - -diff -urN wannier90-1.1.old/src/overlap.F90 wannier90-1.1.new/src/overlap.F90 ---- wannier90-1.1.old/src/overlap.F90 2009-03-07 15:44:11.000000000 +0100 -+++ wannier90-1.1.new/src/overlap.F90 2009-03-07 15:48:36.000000000 +0100 -@@ -141,8 +141,8 @@ - nn_found=.true. - nn=inn - else -- call io_error('Error reading '//trim(seedname)//'.mmn.& -- & More than one matching nearest neighbour found') -+ call io_error('Error reading '//trim(seedname)// & -+ '.mmn. More than one matching nearest neighbour found') - endif - endif - end do -diff -urN wannier90-1.1.old/src/parameters.F90 wannier90-1.1.new/src/parameters.F90 ---- wannier90-1.1.old/src/parameters.F90 2009-03-07 15:44:11.000000000 +0100 -+++ wannier90-1.1.new/src/parameters.F90 2009-03-07 15:50:46.000000000 +0100 -@@ -1054,8 +1054,9 @@ - write(stdout,'(1x,a)') '+----------------------------------------------------------------------------+' - do nsp=1,num_species - do nat=1,atoms_species_num(nsp) -- write(stdout,'(1x,a1,1x,a2,1x,i3,3F10.5,3x,a1,1x,3F10.5,4x,a1)') '|',atoms_symbol(nsp),nat,atoms_pos_frac(:,nat,nsp),& -- '|',atoms_pos_cart(:,nat,nsp)*lenconfac,'|' -+ write(stdout,'(1x,a1,1x,a2,1x,i3,3F10.5,3x,a1,1x,3F10.5,4x,a1)') & -+& '|',atoms_symbol(nsp),nat,atoms_pos_frac(:,nat,nsp),& -+& '|',atoms_pos_cart(:,nat,nsp)*lenconfac,'|' - end do - end do - write(stdout,'(1x,a)') '*----------------------------------------------------------------------------*' -@@ -1073,8 +1074,8 @@ - write(stdout,'(1x,a)') '| Frac. Coord. l mr r z-axis x-axis Z/a |' - write(stdout,'(1x,a)') '+----------------------------------------------------------------------------+' - do nsp=1,num_proj -- write(stdout,'(1x,a1,3(1x,f5.2),1x,i2,1x,i2,1x,i2,3(1x,f6.3),3(1x,f6.3),& -- & 2x,f4.1,1x,a1)') '|',proj_site(1,nsp),proj_site(2,nsp),& -+ write(stdout,'(1x,a1,3(1x,f5.2),1x,i2,1x,i2,1x,i2,3(1x,f6.3),3(1x,f6.3),2x,f4.1,1x,a1)')& -+& '|',proj_site(1,nsp),proj_site(2,nsp),& - proj_site(3,nsp),proj_l(nsp), proj_m(nsp),proj_radial(nsp),& - proj_z(1,nsp),proj_z(2,nsp),proj_z(3,nsp),proj_x(1,nsp),& - proj_x(2,nsp),proj_x(3,nsp),proj_zona(nsp),'|' -@@ -2738,8 +2739,8 @@ - dummy=utility_strip(in_data(line)) - dummy=adjustl(dummy) - pos1=index(dummy,':') -- if(pos1==0) call io_error('param_read_projection: malformed projection & -- &definition: '//trim(dummy)) -+ if(pos1==0) & -+ call io_error('param_read_projection: malformed projection definition: '//trim(dummy)) - sites=0 - ctemp=dummy(:pos1-1) - ! Read the atomic site -@@ -2980,11 +2981,11 @@ - endif - end if - if(sites==-1) then -- if(counter+sum(ang_states) > num_proj) call io_error('param_get_projection: & -- &too many projections defined') -+ if(counter+sum(ang_states) > num_proj) & -+ call io_error('param_get_projection: too many projections defined') - else -- if(counter+sites*sum(ang_states) > num_proj) call io_error('param_get_projection:& -- & too many projections defined') -+ if(counter+sites*sum(ang_states) > num_proj) & -+ call io_error('param_get_projection: too many projections defined') - end if - ! - if(sites==-1) then -@@ -3025,8 +3026,8 @@ - - ! check there are enough projections and add random projections if required - if (.not. lpartrandom) then -- if (counter.ne.num_proj) call io_error('param_get_projections:& -- & Fewer projections defined than the number of Wannier functions requested') -+ if (counter.ne.num_proj) call io_error(& -+ 'param_get_projections: Fewer projections defined than the number of Wannier functions requested') - else - call random_seed() - do loop=counter+1,num_proj diff --git a/sci-libs/wannier90/files/wannier90-2.0.1.1-runtest.patch b/sci-libs/wannier90/files/wannier90-2.0.1.1-runtest.patch deleted file mode 100644 index c9656ac31..000000000 --- a/sci-libs/wannier90/files/wannier90-2.0.1.1-runtest.patch +++ /dev/null @@ -1,12 +0,0 @@ -diff -Naurp wannier90-2.0.1.1.orig/tests/run_test.pl wannier90-2.0.1.1/tests/run_test.pl ---- wannier90-2.0.1.1.orig/tests/run_test.pl 2016-02-08 11:51:52.000000000 +0000 -+++ wannier90-2.0.1.1/tests/run_test.pl 2017-01-05 12:10:29.584850729 +0000 -@@ -2,7 +2,7 @@ - # - use Cwd; - my $cwd = cwd(); --$wanex="../wannier90.x" ; -+$wanex="../src/wannier90.x" ; - $wanex=$cwd."/".$wanex ; - print " Running test set of inputs\n"; - @tests_found = <./test*>; diff --git a/sci-libs/wannier90/metadata.xml b/sci-libs/wannier90/metadata.xml index a7ac8e977..273952673 100644 --- a/sci-libs/wannier90/metadata.xml +++ b/sci-libs/wannier90/metadata.xml @@ -18,5 +18,6 @@ <upstream> <doc>http://www.wannier.org/</doc> <remote-id type="launchpad">wannier90</remote-id> + <remote-id type="github">wannier-developers/wannier90</remote-id> </upstream> </pkgmetadata> diff --git a/sci-libs/xblas/Manifest b/sci-libs/xblas/Manifest deleted file mode 100644 index 4919da836..000000000 --- a/sci-libs/xblas/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST xblas-1.0.248.tar.gz 2087424 BLAKE2B 47f446f95f033260baec4053f4d761eda54e753bd39477cdf0636f3b68f1a3748f6c48aa32eaa693a486a8bb92b259b2742e42a2663fa1b3a75de1d3ff93daac SHA512 4a3c3a6aea0e12a5620ba1c4d328ca9f20764da4871b2bac48c21366c25afed31daa3a3ef291973159b890b2bbf033bdc14503634637b50ff4514f425b4356ad diff --git a/sci-libs/xblas/metadata.xml b/sci-libs/xblas/metadata.xml deleted file mode 100644 index 11b4b52f7..000000000 --- a/sci-libs/xblas/metadata.xml +++ /dev/null @@ -1,17 +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 XBLAS library of routines is part of a reference implementation for -the Dense and Banded Basic Linear Algebra Subroutines, along with their -Extended and Mixed Precision versions, as documented in Chapters 2 and 4 -of the new BLAS Standard. -</longdescription> - <use> - <flag name="int64">Build the 64 bits integer library</flag> - </use> -</pkgmetadata> diff --git a/sci-libs/xblas/xblas-1.0.248-r1.ebuild b/sci-libs/xblas/xblas-1.0.248-r1.ebuild deleted file mode 100644 index a5b0c8cf4..000000000 --- a/sci-libs/xblas/xblas-1.0.248-r1.ebuild +++ /dev/null @@ -1,110 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -NUMERIC_MODULE_NAME="xblas" -FORTRAN_NEEDED=fortran - -inherit fortran-2 numeric numeric-int64-multibuild multilib toolchain-funcs - -DESCRIPTION="Extra Precise Basic Linear Algebra Subroutines" -HOMEPAGE="https://www.netlib.org/xblas/" -SRC_URI="https://www.netlib.org/xblas/${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" -IUSE="doc fortran static-libs" - -RDEPEND="" -DEPEND="${RDEPEND} - sys-devel/m4" - -static_to_shared() { - local libstatic=${1}; shift - local libname=$(basename ${libstatic%.a}) - local soname=${libname}$(get_libname $(ver_cut 1-2)) - local libdir=$(dirname ${libstatic}) - - einfo "Making ${soname} from ${libstatic}" - if [[ ${CHOST} == *-darwin* ]] ; then - ${LINK:-$(tc-getCC)} ${LDFLAGS} \ - -dynamiclib -install_name "${EPREFIX}"/usr/lib/"${soname}" \ - -Wl,-all_load -Wl,${libstatic} \ - "$@" -o ${libdir}/${soname} || die "${soname} failed" - else - ${LINK:-$(tc-getCC)} ${LDFLAGS} \ - -shared -Wl,-soname=${soname} \ - -Wl,--whole-archive ${libstatic} -Wl,--no-whole-archive \ - "$@" -o ${libdir}/${soname} || die "${soname} failed" - [[ ${#PV} -gt 1 ]] && \ - ln -s ${soname} ${libdir}/${libname}$(get_libname $(ver_cut 0-1)) || die - ln -s ${soname} ${libdir}/${libname}$(get_libname) || die - fi -} - -pkg_setup() { - use fortran && fortran-2_pkg_setup -} - -src_prepare() { - default - numeric-int64-multibuild_copy_sources -} - -src_configure() { - xblas_configure() { - export FCFLAGS="${FCFLAGS} $(get_abi_CFLAGS) $(numeric-int64_get_fortran_int64_abi_fflags)" - econf $(use_enable fortran) - } - numeric-int64-multibuild_foreach_all_abi_variants run_in_build_dir xblas_configure -} - -src_compile() { - xblas_src_compile() { - local profname=$(numeric-int64_get_module_name) - local libname="${profname//-/_}" - # default target builds and runs tests - split - # build first static libs because of fPIC afterwards - # and we link tests with shared ones - if use static-libs; then - emake makefiles - emake lib XBLASLIB=lib${libname}_nonpic.a - emake clean - fi - sed -i \ - -e 's:\(CFLAGS.*\).*:\1 -fPIC:' \ - make.inc || die - emake makefiles - emake lib XBLASLIB=lib${libname}.a - static_to_shared lib${libname}.a - } - numeric-int64-multibuild_foreach_all_abi_variants run_in_build_dir xblas_src_compile -} - -src_test() { - numeric-int64-multibuild_foreach_all_abi_variants run_in_build_dir emake tests -} - -src_install() { - xblas_src_install() { - local profname=$(numeric-int64_get_module_name) - local libname="${profname//-/_}" - if numeric-int64_is_static_build; then - use static-libs && newlib.a lib${libname}_nonpic.a lib${libname}.a - else - dolib.so lib${libname}$(get_libname)* - - create_pkgconfig \ - --name ${profname} \ - --libs "-L\${libdir} -l${libname}" \ - --cflags "-I\${includedir} $(numeric-int64_get_fortran_int64_abi_fflags)" \ - ${profname} - fi - } - numeric-int64-multibuild_foreach_all_abi_variants run_in_build_dir xblas_src_install - - dodoc README README.devel - use doc && dodoc doc/report.ps -} diff --git a/sci-libs/xraylib/Manifest b/sci-libs/xraylib/Manifest deleted file mode 100644 index 9ca464e07..000000000 --- a/sci-libs/xraylib/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST xraylib-4.0.0.tar.gz 7844625 BLAKE2B 3db521e15147d9bae4ce8aa08c488460a57233143df2b71518fddffdcf14de34b44ffde0262ad44bcddd39fa067badc304d341d841e0beedee99d36a46cd364f SHA512 ce5cc0d628d397921e10a812251c21a159f529165589b9408fa43112024cd44f3c7fe710a4f1fc51778645850896a23ea32fddbda21ebeebf9e53eefaf1e5b29 diff --git a/sci-libs/xraylib/metadata.xml b/sci-libs/xraylib/metadata.xml deleted file mode 100644 index a7d2f91fb..000000000 --- a/sci-libs/xraylib/metadata.xml +++ /dev/null @@ -1,42 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>cjk34@cam.ac.uk</email> - </maintainer> - <maintainer type="project"> - <email>sci@gentoo.org</email> - <name>Gentoo Science Project</name> - </maintainer> - <longdescription lang="en"> -Quantitative estimate of elemental composition by spectroscopic and imaging -techniques using X-ray fluorescence requires the availability of accurate data -of X-ray interaction with matter. Although a wide number of computer codes -and data sets are reported in literature, none of them is presented in the -form of freely available library functions which can be easily included in -software applications for X-ray fluorescence. This work presents a compilation -of data sets from different published works and an xraylib interface in the -form of callable functions. Although the target applications are on X-ray -fluorescence, cross sections of interactions like photoionization, coherent -scattering and Compton scattering, as well as form factors and anomalous -scattering functions, are also available. - -xraylib provides access to some of the most respected databases of physical -data in the field of x-rays. The core of xraylib is a library, written in ANSI -C, containing over 40 functions to be used to retrieve data from these -databases. This C library can be directly linked with any program written in -C, C++ or Objective-C. Furthermore, the xraylib package contains bindings to -several popular programming languages: Fortran 2003, Perl, Python, Java, IDL, -Lua and .NET, as well as a command-line utility which can be used as a -pocket-calculator. Although not officially supported, xraylib has been -reported to be useable from within Matlab and LabView. - -Reference: T. Schoonjans, A. Brunetti, B. Golosio, M. Sanchez del Rio, -V. A. Solé, C. Ferrero and L. Vincze, "The xraylib library for X-ray--matter -interactions. Recent developments", Spectrochimica Acta B 66 (2011) 776-784 -( doi: http://dx.doi.org/10.1016/j.sab.2011.09.011 ) -</longdescription> - <upstream> - <remote-id type="github">tschoonj/xraylib</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-libs/xraylib/xraylib-4.0.0.ebuild b/sci-libs/xraylib/xraylib-4.0.0.ebuild deleted file mode 100644 index 6dfde6dae..000000000 --- a/sci-libs/xraylib/xraylib-4.0.0.ebuild +++ /dev/null @@ -1,96 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -AUTOTOOLS_AUTORECONF=true -FORTRAN_NEEDED=fortran -FORTRAN_STANDARD=2003 -PYTHON_COMPAT=( python3_{7,8,9} ) # python 3 supported by github master -LUA_COMPAT=( lua5-{1..3} ) -USE_RUBY="ruby27 ruby30" - -inherit python-single-r1 lua-single ruby-single java-pkg-opt-2 fortran-2 - -DESCRIPTION="X-ray matter interaction cross sections for X-ray fluorescence library" -HOMEPAGE="https://github.com/tschoonj/xraylib" -SRC_URI="http://lvserver.ugent.be/xraylib/${P}.tar.gz" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64" - -#IUSE="examples fortran java lua perl python" -# jave now uses the gradle build system which is not supported by portage -IUSE="examples fortran lua perl php python ruby" - -REQUIRED_USE=" - python? ( ${PYTHON_REQUIRED_USE} ) - lua? ( ${LUA_REQUIRED_USE} ) -" - -RDEPEND=" - lua? ( ${LUA_DEPS} ) - perl? ( dev-lang/perl ) - php? ( <dev-lang/php-8:* ) - python? ( - ${PYTHON_DEPS} - $(python_gen_cond_dep \ - 'dev-python/numpy[${PYTHON_USEDEP}]' - ) - ) - ruby? ( ${RUBY_DEPS} ) -" # java? ( >=virtual/jre-1.7:* ) - -DEPEND="${RDEPEND}" -# java? ( >=virtual/jdk-1.7:* ) - -DOCS=( AUTHORS Changelog README TODO ) - -pkg_setup() { - fortran-2_pkg_setup - java-pkg-opt-2_pkg_setup - use python && python-single-r1_pkg_setup -} - -src_configure() { - econf \ - --disable-idl \ - $(use_enable fortran fortran2003) \ - $(use_enable lua) \ - $(use_enable perl) \ - $(use_enable perl perl-integration) \ - $(use_enable php) \ - $(use_enable php php-integration) \ - $(use_enable python) \ - $(use_enable python python-integration) \ - $(use_enable python python-numpy) \ - $(use_enable ruby) \ - $(use_enable ruby ruby-integration) \ - # $(use_enable java) -} - -src_test() { - # see https://github.com/tschoonj/xraylib/issues/11 - emake -j1 check -} - -src_install() { - default - use python && python_optimize - - if use examples; then - docinto /usr/share/doc/${PF}/examples - dodoc example/*.c example/*.cpp - use fortran && dodoc example/*.f90 - use lua && dodoc example/*.lua - use perl && dodoc example/*.pl - use php && dodoc example/*.php - use python && dodoc example/*.py - use ruby && dodoc example/*.rb - # use java && dodoc example/*.java - docompress -x /usr/share/doc/${PF}/examples # Don't compress examples - fi - - # use java && java-pkg_regso /usr/share/xraylib/java/libxraylib.so -} diff --git a/sci-mathematics/acl2/Manifest b/sci-mathematics/acl2/Manifest deleted file mode 100644 index b824d2c10..000000000 --- a/sci-mathematics/acl2/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST acl2-8.3.tar.gz 116808616 BLAKE2B 77bba8c91231c2ae6ebae34ceeec9939101862156bfda4be2a0e3389f51cfdc183004d9cb3b27511a7494a9ead8ced5016f648a1712ab468c781dd8f8feca822 SHA512 92b59d1b31ce8d980bf043d02d4ee6ae36c69b3c2cc7be106e4d8f46e660a813e42f6e41a0903159ce65e9332dccb770cbd69472602889724f8ba724bfa301e2 -DIST acl2-8.4.tar.gz 202242463 BLAKE2B 887273910c7913d08455e5053a4c4d065743e0ba247f94f994a3400f27c97f8fce07debb145dbf26287c8b72e9335d995fcbc49f7085e17384b38035d260c8b8 SHA512 5a38271ffa9f9aad79d2aaf575144a58cf1b926b9ba3f9fb34af927862c95f6f683e870c9b453b2527abe8bdcd5603c6b5ad4c50b70c407606db78e0a79545bb diff --git a/sci-mathematics/acl2/acl2-8.3-r1.ebuild b/sci-mathematics/acl2/acl2-8.3-r1.ebuild deleted file mode 100644 index d0bb4eade..000000000 --- a/sci-mathematics/acl2/acl2-8.3-r1.ebuild +++ /dev/null @@ -1,86 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -inherit elisp-common - -DESCRIPTION="Industrial strength theorem prover" -HOMEPAGE="https://www.cs.utexas.edu/users/moore/acl2/" -SRC_URI="https://github.com/acl2/acl2/archive/${PV}/${P}.tar.gz" - -SLOT="0" -LICENSE="BSD" -KEYWORDS="~amd64 ~x86" -IUSE="books doc emacs" - -BDEPEND=" - dev-lisp/sbcl - emacs? ( >=app-editors/emacs-23.1:* ) -" -DEPEND=" - dev-lisp/sbcl:= - books? ( dev-lang/perl ) - doc? ( dev-lang/perl ) -" -RDEPEND="${DEPEND}" - -PATCHES=( "${FILESDIR}"/${PN}-use_make_variable.patch ) - -src_prepare() { - find . -type f -name "*.bak" -delete - find . -type f -name "*.orig" -delete - # Remove sparc binary inadvertently included in upstream - rm books/workshops/2003/schmaltz-al-sammane-et-al/support/acl2link || die - default -} - -src_compile() { - emake LISP="sbcl --noinform --noprint \ - --no-sysinit --no-userinit --disable-debugger" - - if use books; then - emake "ACL2=${S}/saved_acl2" basic - fi - - if use doc; then - emake "ACL2=${S}/saved_acl2" DOC - fi - - if use emacs; then - elisp-compile emacs/*.el - fi -} - -src_install() { - local SAVED_NAME=saved_acl2 - sed -e "s:${S}:/usr/share/acl2:g" -i ${SAVED_NAME} || die - dobin ${SAVED_NAME} - - insinto /usr/share/acl2 - doins ${SAVED_NAME}.core - if use books; then - sed -e "/5/a export ACL2_SYSTEM_BOOKS=/usr/share/acl2/books/" \ - -i ${SAVED_NAME} || die - doins -r books - fi - - DOCS=( books/README.md ) - if use doc; then - HTML_DOCS=( doc/HTML/. ) - fi - einstalldocs - - if use emacs; then - elisp-install ${PN} emacs/*{.el,elc} - doins TAGS - fi -} - -pkg_postinst() { - use emacs && elisp-site-regen -} - -pkg_postrm() { - use emacs && elisp-site-regen -} diff --git a/sci-mathematics/acl2/acl2-8.3-r2.ebuild b/sci-mathematics/acl2/acl2-8.3-r2.ebuild deleted file mode 100644 index 03cd890b4..000000000 --- a/sci-mathematics/acl2/acl2-8.3-r2.ebuild +++ /dev/null @@ -1,89 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -inherit elisp-common - -DESCRIPTION="Industrial strength theorem prover" -HOMEPAGE="https://www.cs.utexas.edu/users/moore/acl2/" -SRC_URI="https://github.com/acl2/acl2/archive/${PV}/${P}.tar.gz" - -SLOT="0" -LICENSE="BSD" -KEYWORDS="~amd64 ~x86" -IUSE="books doc emacs" - -BDEPEND=" - dev-lisp/sbcl - emacs? ( >=app-editors/emacs-23.1:* ) -" -DEPEND=" - dev-lisp/sbcl:= - books? ( dev-lang/perl ) - doc? ( dev-lang/perl ) -" -RDEPEND="${DEPEND}" - -PATCHES=( "${FILESDIR}"/${PN}-use_make_variable.patch ) - -src_prepare() { - find . -type f -name "*.bak" -delete - find . -type f -name "*.orig" -delete - # Remove sparc binary inadvertently included in upstream - rm books/workshops/2003/schmaltz-al-sammane-et-al/support/acl2link || die - default -} - -src_compile() { - emake LISP="sbcl --noinform --noprint \ - --no-sysinit --no-userinit --disable-debugger" - - if use books; then - emake "ACL2=${S}/saved_acl2" basic - fi - - if use doc; then - emake "ACL2=${S}/saved_acl2" DOC - fi - - if use emacs; then - elisp-compile emacs/*.el - fi -} - -src_install() { - local SAVED_NAME=saved_acl2 - sed -e "s:${S}:/usr/share/acl2:g" -i ${SAVED_NAME} || die - if use books; then - sed -e "5iexport ACL2_SYSTEM_BOOKS=/usr/share/acl2/books/" \ - -i ${SAVED_NAME} || die - fi - dobin ${SAVED_NAME} - - insinto /usr/share/acl2 - doins ${SAVED_NAME}.core - - if use books; then - doins -r books - fi - - DOCS=( books/README.md ) - if use doc; then - HTML_DOCS=( doc/HTML/. ) - fi - einstalldocs - - if use emacs; then - elisp-install ${PN} emacs/*{.el,elc} - doins TAGS - fi -} - -pkg_postinst() { - use emacs && elisp-site-regen -} - -pkg_postrm() { - use emacs && elisp-site-regen -} diff --git a/sci-mathematics/acl2/acl2-8.4-r1.ebuild b/sci-mathematics/acl2/acl2-8.4-r1.ebuild deleted file mode 100644 index cb1098877..000000000 --- a/sci-mathematics/acl2/acl2-8.4-r1.ebuild +++ /dev/null @@ -1,89 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -inherit elisp-common - -DESCRIPTION="Industrial strength theorem prover" -HOMEPAGE="https://www.cs.utexas.edu/users/moore/acl2/" -SRC_URI="https://github.com/acl2/acl2/archive/${PV}/${P}.tar.gz" - -SLOT="0" -LICENSE="BSD" -KEYWORDS="~amd64 ~x86" -IUSE="books doc emacs" - -BDEPEND=" - >=dev-lisp/sbcl-1.5.2 - emacs? ( >=app-editors/emacs-23.1:* ) -" -DEPEND=" - dev-lisp/sbcl:= - books? ( dev-lang/perl ) - doc? ( dev-lang/perl ) -" -RDEPEND="${DEPEND}" - -PATCHES=( "${FILESDIR}"/${PN}-use_make_variable.patch ) - -src_prepare() { - find . -type f -name "*.bak" -delete - find . -type f -name "*.orig" -delete - # Remove sparc binary inadvertently included in upstream - rm books/workshops/2003/schmaltz-al-sammane-et-al/support/acl2link || die - default -} - -src_compile() { - emake LISP="sbcl --noinform --noprint \ - --no-sysinit --no-userinit --disable-debugger" - - if use books; then - emake "ACL2=${S}/saved_acl2" basic - fi - - if use doc; then - emake "ACL2=${S}/saved_acl2" DOC - fi - - if use emacs; then - elisp-compile emacs/*.el - fi -} - -src_install() { - local SAVED_NAME=saved_acl2 - sed -e "s:${S}:/usr/share/acl2:g" -i ${SAVED_NAME} || die - if use books; then - sed -e "5iexport ACL2_SYSTEM_BOOKS=/usr/share/acl2/books/" \ - -i ${SAVED_NAME} || die - fi - dobin ${SAVED_NAME} - - insinto /usr/share/acl2 - doins ${SAVED_NAME}.core - - if use books; then - doins -r books - fi - - DOCS=( books/README.md ) - if use doc; then - HTML_DOCS=( doc/HTML/. ) - fi - einstalldocs - - if use emacs; then - elisp-install ${PN} emacs/*{.el,elc} - doins TAGS - fi -} - -pkg_postinst() { - use emacs && elisp-site-regen -} - -pkg_postrm() { - use emacs && elisp-site-regen -} diff --git a/sci-mathematics/acl2/acl2-8.4.ebuild b/sci-mathematics/acl2/acl2-8.4.ebuild deleted file mode 100644 index dfc3967ed..000000000 --- a/sci-mathematics/acl2/acl2-8.4.ebuild +++ /dev/null @@ -1,86 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -inherit elisp-common - -DESCRIPTION="Industrial strength theorem prover" -HOMEPAGE="https://www.cs.utexas.edu/users/moore/acl2/" -SRC_URI="https://github.com/acl2/acl2/archive/${PV}/${P}.tar.gz" - -SLOT="0" -LICENSE="BSD" -KEYWORDS="~amd64 ~x86" -IUSE="books doc emacs" - -BDEPEND=" - >=dev-lisp/sbcl-1.5.2 - emacs? ( >=app-editors/emacs-23.1:* ) -" -DEPEND=" - dev-lisp/sbcl:= - books? ( dev-lang/perl ) - doc? ( dev-lang/perl ) -" -RDEPEND="${DEPEND}" - -PATCHES=( "${FILESDIR}"/${PN}-use_make_variable.patch ) - -src_prepare() { - find . -type f -name "*.bak" -delete - find . -type f -name "*.orig" -delete - # Remove sparc binary inadvertently included in upstream - rm books/workshops/2003/schmaltz-al-sammane-et-al/support/acl2link || die - default -} - -src_compile() { - emake LISP="sbcl --noinform --noprint \ - --no-sysinit --no-userinit --disable-debugger" - - if use books; then - emake "ACL2=${S}/saved_acl2" basic - fi - - if use doc; then - emake "ACL2=${S}/saved_acl2" DOC - fi - - if use emacs; then - elisp-compile emacs/*.el - fi -} - -src_install() { - local SAVED_NAME=saved_acl2 - sed -e "s:${S}:/usr/share/acl2:g" -i ${SAVED_NAME} || die - dobin ${SAVED_NAME} - - insinto /usr/share/acl2 - doins ${SAVED_NAME}.core - if use books; then - sed -e "/5/a export ACL2_SYSTEM_BOOKS=/usr/share/acl2/books/" \ - -i ${SAVED_NAME} || die - doins -r books - fi - - DOCS=( books/README.md ) - if use doc; then - HTML_DOCS=( doc/HTML/. ) - fi - einstalldocs - - if use emacs; then - elisp-install ${PN} emacs/*{.el,elc} - doins TAGS - fi -} - -pkg_postinst() { - use emacs && elisp-site-regen -} - -pkg_postrm() { - use emacs && elisp-site-regen -} diff --git a/sci-mathematics/acl2/files/acl2-use_make_variable.patch b/sci-mathematics/acl2/files/acl2-use_make_variable.patch deleted file mode 100644 index 32e0f05da..000000000 --- a/sci-mathematics/acl2/files/acl2-use_make_variable.patch +++ /dev/null @@ -1,13 +0,0 @@ -use make variable to avoid QA issue: "make[1]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule" - ---- a/GNUmakefile -+++ b/GNUmakefile -@@ -576,7 +576,7 @@ doc/home-page.html: doc/home-page.lisp - # xdoc::save that populates doc/manual/ (not under books/). - acl2-manual: check-books - rm -rf doc/manual books/system/doc/acl2-manual.cert -- cd books ; make USE_QUICKLISP=1 system/doc/acl2-manual.cert -+ cd books ; $(MAKE) USE_QUICKLISP=1 system/doc/acl2-manual.cert - rm -rf doc/manual/download/* - - # WARNING: The dependency list just below isn't complete, since it diff --git a/sci-mathematics/acl2/metadata.xml b/sci-mathematics/acl2/metadata.xml deleted file mode 100644 index b3d826757..000000000 --- a/sci-mathematics/acl2/metadata.xml +++ /dev/null @@ -1,25 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>dongxuli2011@gmail.com</email> - <name>Dongxu Li</name> - <description>Industrial strength theorem prover</description> - </maintainer> - <maintainer type="project"> - <email>sci-mathematics@gentoo.org</email> - <name>Gentoo Mathematics Project</name> - </maintainer> - <longdescription> - ACL2 is both a programming language in which you can model computer systems and - a tool to help you prove properties of those models. ACL2 is part of the - Boyer-Moore family of provers, for which its authors have received the 2005 ACM - Software System Award. - </longdescription> - <use> - <flag name="books">build community books, the canonical collection of open-source libraries</flag> - </use> - <upstream> - <remote-id type="github">acl2/acl2</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-mathematics/cipi/cipi-1.0-r1.ebuild b/sci-mathematics/cipi/cipi-1.0-r1.ebuild new file mode 100644 index 000000000..6cd189e33 --- /dev/null +++ b/sci-mathematics/cipi/cipi-1.0-r1.ebuild @@ -0,0 +1,51 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit cmake flag-o-matic + +DESCRIPTION="Computing information projections iteratively" +HOMEPAGE="https://github.com/tom111/cipi" +SRC_URI="https://github.com/tom111/cipi/archive/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +IUSE="doc" + +DEPEND=" + dev-libs/boost:= + doc? ( virtual/latex-base )" +RDEPEND="${DEPEND}" + +DOCS="AUTHORS README" + +CMAKE_IN_SOURCE_BUILD="yes" + +PATCHES=( + "${FILESDIR}/${P}-boost.patch" +) + +src_prepare() { + cmake_src_prepare + append-ldflags -Wl,--copy-dt-needed-entries +} + +src_configure() { + mycmakeargs=( + -DENABLE_DOC=$(usex doc ON OFF) + ) + + cmake_src_configure +} + +pkg_postinst() { + elog + elog "The sample PARAM file has been installed to /usr/share/${PN}-${PV}" + elog + if use doc; then + elog "A pdf manual has been installed to /usr/share/${PN}-${PV}" + fi +} diff --git a/sci-mathematics/cipi/cipi-1.0.ebuild b/sci-mathematics/cipi/cipi-1.0.ebuild index 2dae2c71a..33d744c7c 100644 --- a/sci-mathematics/cipi/cipi-1.0.ebuild +++ b/sci-mathematics/cipi/cipi-1.0.ebuild @@ -7,7 +7,7 @@ inherit cmake flag-o-matic DESCRIPTION="Computing information projections iteratively" HOMEPAGE="https://github.com/tom111/cipi" -SRC_URI="https://github.com/tom111/cipi/archive/1.0.tar.gz -> ${P}.tar.gz" +SRC_URI="https://github.com/tom111/cipi/archive/${PV}.tar.gz -> ${P}.tar.gz" LICENSE="GPL-3" SLOT="0" diff --git a/sci-mathematics/cipi/files/cipi-1.0-boost.patch b/sci-mathematics/cipi/files/cipi-1.0-boost.patch new file mode 100644 index 000000000..66aa9fd3f --- /dev/null +++ b/sci-mathematics/cipi/files/cipi-1.0-boost.patch @@ -0,0 +1,11 @@ +--- a/src/CMakeLists.txt 2024-02-16 21:36:58.808186061 +0100 ++++ b/src/CMakeLists.txt 2024-02-16 21:36:55.288131610 +0100 +@@ -8,7 +8,7 @@ + Message("Boost found" ${Boost_LIBRARY_DIR}) + INCLUDE_DIRECTORIES(${Boost_INCLUDE_DIR}) + #MESSAGE("Boost was found" ${Boost_INCLUDE_DIR}) +- TARGET_LINK_LIBRARIES (cipi boost_thread-mt) ++ TARGET_LINK_LIBRARIES (cipi boost_thread) + ENDIF (Boost_FOUND) + + INSTALL(PROGRAMS cipi DESTINATION bin) diff --git a/sci-mathematics/flocq/Manifest b/sci-mathematics/flocq/Manifest deleted file mode 100644 index 21dee2252..000000000 --- a/sci-mathematics/flocq/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST flocq-3.4.0.tar.gz 453124 BLAKE2B 0c3e7f7fe18f9722e341a62b8770ebe94a9195fc6e47a2beb6493ed976e8fac6da6eecae23a77d394a6b3dee89897f2fc918307130e7e8d3b1d08f2eb175c87e SHA512 26be9e6d0d30f0035f898c3cfd973ca954195af2068b1fc1ddcffe6ea81d9c3d8b9d72fad1ae75a816f67942bb4bef269bf9739e95ecf6cc17aecdbe1fcaf7a0 diff --git a/sci-mathematics/flocq/flocq-3.4.0-r1.ebuild b/sci-mathematics/flocq/flocq-3.4.0-r1.ebuild deleted file mode 100644 index f0e6c73a8..000000000 --- a/sci-mathematics/flocq/flocq-3.4.0-r1.ebuild +++ /dev/null @@ -1,37 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -inherit multiprocessing - -DESCRIPTION="A floating-point formalization for the Coq system" -HOMEPAGE="http://flocq.gforge.inria.fr/" -SRC_URI="https://gforge.inria.fr/frs/download.php/file/38385/${P}.tar.gz" - -LICENSE="LGPL-3" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -DEPEND=">=sci-mathematics/coq-8.7" -RDEPEND="${DEPEND}" - -src_prepare() { - default - sed -i Remakefile.in \ - -e "s:mkdir -p @libdir@:mkdir -p \${DESTDIR}@libdir@:g" \ - -e "s:cp \$f @libdir@:cp \$f \${DESTDIR}@libdir@:g" -} - -src_configure() { - econf --libdir="`coqc -where`/user-contrib/Flocq" -} - -src_compile() { - ./remake --jobs=$(makeopts_jobs) || die "emake failed" -} - -src_install() { - DESTDIR="${D}" ./remake install || die - einstalldocs -} diff --git a/sci-mathematics/flocq/metadata.xml b/sci-mathematics/flocq/metadata.xml deleted file mode 100644 index de5ba354b..000000000 --- a/sci-mathematics/flocq/metadata.xml +++ /dev/null @@ -1,14 +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-mathematics@gentoo.org</email> - <name>Gentoo Mathematics Project</name> - </maintainer> - <longdescription> -Flocq (Floats for Coq) is a floating-point formalization for the Coq -system. It provides a comprehensive library of theorems on a multi-radix -multi-precision arithmetic. It also supports efficient numerical -computations inside Coq. -</longdescription> -</pkgmetadata> diff --git a/sci-mathematics/frama-c/files/ocamlgraph185_compat.patch b/sci-mathematics/frama-c/files/ocamlgraph185_compat.patch deleted file mode 100644 index 798d17fd3..000000000 --- a/sci-mathematics/frama-c/files/ocamlgraph185_compat.patch +++ /dev/null @@ -1,254 +0,0 @@ -From: Mehdi Dogguy <mehdi@debian.org> -Date: Sun, 27 Apr 2014 13:46:16 +0200 -Subject: Port to OCamlgraph 1.8.5 - ---- - src/impact/reason_graph.ml | 2 +- - src/kernel/stmts_graph.ml | 10 +++++----- - src/logic/property_status.ml | 8 ++++---- - src/misc/service_graph.ml | 4 ++-- - src/pdg_types/pdgTypes.ml | 6 +++--- - src/postdominators/print.ml | 2 +- - src/semantic_callgraph/register.ml | 4 ++-- - src/slicing/printSlice.ml | 10 +++++----- - src/syntactic_callgraph/register.ml | 4 ++-- - src/wp/cil2cfg.ml | 12 ++++++------ - 10 files changed, 31 insertions(+), 31 deletions(-) - -diff --git a/src/impact/reason_graph.ml b/src/impact/reason_graph.ml -index eabacb0..ce19b4a 100644 ---- a/src/impact/reason_graph.ml -+++ b/src/impact/reason_graph.ml -@@ -139,7 +139,7 @@ module Printer (X: AdditionalInfo) = struct - - let graph_attributes _ = [`Label "Impact graph"] - -- let default_vertex_attributes _g = [`Style [`Filled]; `Shape `Box] -+ let default_vertex_attributes _g = [`Style `Filled; `Shape `Box] - let default_edge_attributes _g = [] - - let vertex_attributes v = -diff --git a/src/kernel/stmts_graph.ml b/src/kernel/stmts_graph.ml -index a8fe121..16059c3 100644 ---- a/src/kernel/stmts_graph.ml -+++ b/src/kernel/stmts_graph.ml -@@ -157,12 +157,12 @@ module TP = struct - - let vertex_attributes s = - match s.skind with -- | Loop _ -> [`Color 0xFF0000; `Style [`Filled]] -- | If _ -> [`Color 0x00FF00; `Style [`Filled]; `Shape `Diamond] -- | Return _ -> [`Color 0x0000FF; `Style [`Filled]] -+ | Loop _ -> [`Color 0xFF0000; `Style `Filled] -+ | If _ -> [`Color 0x00FF00; `Style `Filled; `Shape `Diamond] -+ | Return _ -> [`Color 0x0000FF; `Style `Filled] - | Block _ -> [`Shape `Box; `Fontsize 8] -- | Goto _ -> [`Shape `Diamond; `Color 0x00FFFF ; `Style [`Filled]] -- | Instr (Skip _) -> [`Color 0x00FFFF ; `Style [`Filled]] -+ | Goto _ -> [`Shape `Diamond; `Color 0x00FFFF ; `Style `Filled] -+ | Instr (Skip _) -> [`Color 0x00FFFF ; `Style `Filled] - | _ -> [] - let default_vertex_attributes _ = [] - -diff --git a/src/logic/property_status.ml b/src/logic/property_status.ml -index f7c278d..47485f6 100644 ---- a/src/logic/property_status.ml -+++ b/src/logic/property_status.ml -@@ -1481,12 +1481,12 @@ module Consolidation_graph = struct - let s = get_status p in - let color = status_color p s in - let style = match s with -- | Never_tried -> [`Style [`Bold]; `Width 0.8 ] -- | _ -> [`Style [`Filled]] -+ | Never_tried -> [`Style `Bold; `Width 0.8 ] -+ | _ -> [`Style `Filled] - in - style @ [ label v; `Color color; `Shape `Box ] - | Emitter _ as v -> -- [ label v; `Shape `Diamond; `Color 0xb0c4de; `Style [`Filled] ] -+ [ label v; `Shape `Diamond; `Color 0xb0c4de; `Style `Filled ] - | Tuning_parameter _ as v -> - [ label v; (*`Style `Dotted;*) `Color 0xb0c4de; ] - (*| Correctness_parameter _ (*as v*) -> assert false (*[ label v; `Color 0xb0c4de ]*)*) -@@ -1495,7 +1495,7 @@ module Consolidation_graph = struct - | None -> [] - | Some s -> - let c = emitted_status_color s in -- [ `Color c; `Fontcolor c; `Style [`Bold] ] -+ [ `Color c; `Fontcolor c; `Style `Bold ] - - let default_vertex_attributes _ = [] - let default_edge_attributes _ = [] -diff --git a/src/misc/service_graph.ml b/src/misc/service_graph.ml -index 4f866c5..d158028 100644 ---- a/src/misc/service_graph.ml -+++ b/src/misc/service_graph.ml -@@ -289,7 +289,7 @@ Src root:%s in %s (is_root:%b) Dst:%s in %s (is_root:%b) [2d case]" - color e - else - match CallG.E.label e with -- | Inter_services -> [ `Style [`Invis] ] -+ | Inter_services -> [ `Style `Invis ] - | Inter_functions | Both -> color e - - let default_edge_attributes _ = [] -@@ -303,7 +303,7 @@ Src root:%s in %s (is_root:%b) Dst:%s in %s (is_root:%b) [2d case]" - sg_attributes = - [ `Label ("S " ^ cs); - `Color (Extlib.number_to_color id); -- `Style [`Bold] ] } -+ `Style `Bold ] } - - end - -diff --git a/src/pdg_types/pdgTypes.ml b/src/pdg_types/pdgTypes.ml -index 05754e4..74cdebf 100644 ---- a/src/pdg_types/pdgTypes.ml -+++ b/src/pdg_types/pdgTypes.ml -@@ -626,7 +626,7 @@ module Pdg = struct - - let graph_attributes _ = [`Rankdir `TopToBottom ] - -- let default_vertex_attributes _ = [`Style [`Filled]] -+ let default_vertex_attributes _ = [`Style `Filled] - let vertex_name v = string_of_int (Node.id v) - - let vertex_attributes v = -@@ -711,13 +711,13 @@ module Pdg = struct - if Dpd.is_ctrl d then (`Arrowtail `Odot)::attrib else attrib - in - let attrib = -- if Dpd.is_addr d then (`Style [`Dotted])::attrib else attrib -+ if Dpd.is_addr d then (`Style `Dotted)::attrib else attrib - in - attrib - - let get_subgraph v = - let mk_subgraph name attrib = -- let attrib = (`Style [`Filled]) :: attrib in -+ let attrib = (`Style `Filled) :: attrib in - Some { Graph.Graphviz.DotAttributes.sg_name= name; - sg_parent = None; - sg_attributes = attrib } -diff --git a/src/postdominators/print.ml b/src/postdominators/print.ml -index f2e3a25..15f4ff2 100644 ---- a/src/postdominators/print.ml -+++ b/src/postdominators/print.ml -@@ -63,7 +63,7 @@ module Printer = struct - - let graph_attributes (title, _) = [`Label title] - -- let default_vertex_attributes _g = [`Style [`Filled]] -+ let default_vertex_attributes _g = [`Style `Filled] - let default_edge_attributes _g = [] - - let vertex_attributes (s, has_postdom) = -diff --git a/src/semantic_callgraph/register.ml b/src/semantic_callgraph/register.ml -index 1c79dcc..071f061 100644 ---- a/src/semantic_callgraph/register.ml -+++ b/src/semantic_callgraph/register.ml -@@ -102,8 +102,8 @@ module Service = - let name = Kernel_function.get_name - let attributes v = - [ `Style -- [if Kernel_function.is_definition v then `Bold -- else `Dotted] ] -+ (if Kernel_function.is_definition v then `Bold -+ else `Dotted) ] - let entry_point () = - try Some (fst (Globals.entry_point ())) - with Globals.No_such_entry_point _ -> None -diff --git a/src/slicing/printSlice.ml b/src/slicing/printSlice.ml -index c5363f9..211e0bb 100644 ---- a/src/slicing/printSlice.ml -+++ b/src/slicing/printSlice.ml -@@ -227,7 +227,7 @@ module PrintProject = struct - - let graph_attributes (name, _) = [`Label name] - -- let default_vertex_attributes _ = [`Style [`Filled]] -+ let default_vertex_attributes _ = [`Style `Filled] - - let vertex_name v = match v with - | Src fi -> SlicingMacros.fi_name fi -@@ -280,16 +280,16 @@ module PrintProject = struct - - let edge_attributes (e, call) = - let attrib = match e with -- | (Src _, Src _) -> [`Style [`Invis]] -- | (OptSliceCallers _, _) -> [`Style [`Invis]] -- | (_, OptSliceCallers _) -> [`Style [`Invis]] -+ | (Src _, Src _) -> [`Style `Invis] -+ | (OptSliceCallers _, _) -> [`Style `Invis] -+ | (_, OptSliceCallers _) -> [`Style `Invis] - | _ -> [] - in match call with None -> attrib - | Some call -> (`Label (string_of_int call.sid)):: attrib - - let get_subgraph v = - let mk_subgraph name attrib = -- let attrib = (*(`Label name) ::*) (`Style [`Filled]) :: attrib in -+ let attrib = (*(`Label name) ::*) (`Style `Filled) :: attrib in - Some { Graph.Graphviz.DotAttributes.sg_name= name; - sg_parent = None; - sg_attributes = attrib } -diff --git a/src/syntactic_callgraph/register.ml b/src/syntactic_callgraph/register.ml -index d4669c4..d41980e 100644 ---- a/src/syntactic_callgraph/register.ml -+++ b/src/syntactic_callgraph/register.ml -@@ -37,8 +37,8 @@ module Service = - let name v = nodeName v.cnInfo - let attributes v = - [ match v.cnInfo with -- | NIVar (_,b) when not !b -> `Style [`Dotted] -- | _ -> `Style [`Bold] ] -+ | NIVar (_,b) when not !b -> `Style `Dotted -+ | _ -> `Style `Bold ] - let equal v1 v2 = id v1 = id v2 - let compare v1 v2 = - let i1 = id v1 in -diff --git a/src/wp/cil2cfg.ml b/src/wp/cil2cfg.ml -index 6d8cf09..ba5f410 100644 ---- a/src/wp/cil2cfg.ml -+++ b/src/wp/cil2cfg.ml -@@ -1278,9 +1278,9 @@ module Printer (PE : sig val edge_txt : edge -> string end) = struct - | Vstart | Vend | Vexit -> [`Color 0x0000FF; `Shape `Doublecircle] - | VfctIn | VfctOut -> [`Color 0x0000FF; `Shape `Box] - | VblkIn _ | VblkOut _ -> [`Shape `Box] -- | Vloop _ | Vloop2 _ -> [`Color 0xFF0000; `Style [`Filled]] -+ | Vloop _ | Vloop2 _ -> [`Color 0xFF0000; `Style `Filled] - | Vtest _ | Vswitch _ -> -- [`Color 0x00FF00; `Style [`Filled]; `Shape `Diamond] -+ [`Color 0x00FF00; `Style `Filled; `Shape `Diamond] - | Vcall _ | Vstmt _ -> [] - in (`Label (String.escaped label))::attr - -@@ -1290,15 +1290,15 @@ module Printer (PE : sig val edge_txt : edge -> string end) = struct - let attr = [] in - let attr = (`Label (String.escaped (PE.edge_txt e)))::attr in - let attr = -- if is_back_edge e then (`Constraint false)::(`Style [`Bold])::attr -+ if is_back_edge e then (`Constraint false)::(`Style `Bold)::attr - else attr - in - let attr = match (edge_type e) with - | Ethen | EbackThen -> (`Color 0x00FF00)::attr - | Eelse | EbackElse -> (`Color 0xFF0000)::attr -- | Ecase [] -> (`Color 0x0000FF)::(`Style [`Dashed])::attr -+ | Ecase [] -> (`Color 0x0000FF)::(`Style `Dashed)::attr - | Ecase _ -> (`Color 0x0000FF)::attr -- | Enext -> (`Style [`Dotted])::attr -+ | Enext -> (`Style `Dotted)::attr - | Eback -> attr (* see is_back_edge above *) - | Enone -> attr - in -@@ -1308,7 +1308,7 @@ module Printer (PE : sig val edge_txt : edge -> string end) = struct - - let get_subgraph v = - let mk_subgraph name attrib = -- let attrib = (`Style [`Filled]) :: attrib in -+ let attrib = (`Style `Filled) :: attrib in - Some { Graph.Graphviz.DotAttributes.sg_name= name; - sg_parent = None; - sg_attributes = attrib } --- diff --git a/sci-mathematics/frama-c/frama-c-22.0.ebuild b/sci-mathematics/frama-c/frama-c-22.0.ebuild index a64c05e82..aaf815f4f 100644 --- a/sci-mathematics/frama-c/frama-c-22.0.ebuild +++ b/sci-mathematics/frama-c/frama-c-22.0.ebuild @@ -20,7 +20,7 @@ RESTRICT="strip" DEPEND=" >=dev-lang/ocaml-3.12.1[ocamlopt?] - >=dev-ml/ocamlgraph-1.8.5[gtk(-)?,ocamlopt?] + >=dev-ml/ocamlgraph-1.8.5[ocamlopt?] dev-ml/zarith dev-ml/yojson sci-mathematics/coq diff --git a/sci-mathematics/freefem++/Manifest b/sci-mathematics/freefem++/Manifest index da96d35bc..cde77c554 100644 --- a/sci-mathematics/freefem++/Manifest +++ b/sci-mathematics/freefem++/Manifest @@ -1,2 +1 @@ DIST freefem++-4.10.tar.gz 12607380 BLAKE2B 2adcbcb48555c218bdec087b52b955fef7d2b8c0b17045be64d8acf9cde0910dd9c1a1856c046582e3d3e3024848db284cf8262f2e7c9a2e46024768f0dbad7a SHA512 768e8657884e92cd32f08ea82b3f384ed1522d1a693c6de95281fe1bf49e61d084d7d4d5c6c31f70a05ed95ba7cc0af75979242225466d06c2173176e862995e -DIST freefem++-4.7.1.tar.gz 12522562 BLAKE2B a94cc91406486cf4acbd9d544ecdb3f9744d8e4172d84ee6c5bbad4aa8db04bd958e574f98537ec652deb2b1d74adb8d125138f6092030363cdf74c86c6f8a07 SHA512 e42b29f9aa4edf1e4a170425a304996d291b0c3127d75267d421d0f2ff757cdc64fb9b177e38f4e183edc6f256430c39880fea307698417721605b72f6d3c2d0 diff --git a/sci-mathematics/freefem++/freefem++-4.7.1.ebuild b/sci-mathematics/freefem++/freefem++-4.7.1.ebuild deleted file mode 100644 index 6d55116fd..000000000 --- a/sci-mathematics/freefem++/freefem++-4.7.1.ebuild +++ /dev/null @@ -1,102 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit autotools toolchain-funcs - -MY_PV="$(ver_rs 2 -)" - -DESCRIPTION="Solve PDEs using FEM on 2d and 3d domains" -HOMEPAGE="https://freefem.org/" -SRC_URI="https://github.com/FreeFem/FreeFem-sources/archive/v4.7-1.tar.gz -> ${P}.tar.gz" - -LICENSE="LGPL-2.1" -SLOT="0" -KEYWORDS="~amd64" -IUSE="examples mpi opengl X" - -RDEPEND=" - sci-libs/fftw:3.0 - virtual/cblas - virtual/lapack - sci-libs/umfpack - sci-libs/arpack - sci-libs/hdf5[cxx] - mpi? ( virtual/mpi ) - opengl? ( - media-libs/freeglut - virtual/opengl - ) - X? ( - media-fonts/font-misc-misc - x11-libs/libX11 - x11-libs/libXext - x11-libs/libXpm - x11-libs/libXxf86vm - )" - -DEPEND="${RDEPEND}" -BDEPEND="virtual/pkgconfig" - -S="${WORKDIR}/FreeFem-sources-${MY_PV}" - -src_prepare() { - default - - eautoreconf -} - -src_configure() { - local myconf - - if use mpi; then - myconf="${myconf} --with-mpi=/usr/bin/mpi" - else - myconf="--without-mpi" - fi - - econf \ - --disable-download \ - --disable-optim \ - --enable-generic \ - --with-blas="$($(tc-getPKG_CONFIG) --libs blas)" \ - --with-lapack="$($(tc-getPKG_CONFIG) --libs lapack)" \ - $(use_enable opengl) \ - ${myconf} -} - -src_test() { - if use mpi; then - # This may depend on the used MPI implementation. It is needed - # with mpich2, but should not be needed with lam-mpi or mpich - # (if the system is configured correctly). - ewarn "Please check that your MPI root ring is on before running" - ewarn "the test phase. Failing to start it before that phase may" - ewarn "result in a failing emerge." - epause - fi - emake -j1 check -} - -src_install() { - default - - if use examples; then - einfo "Installing examples..." - - # Remove compiled examples: - emake clean - - einfo "Some of the installed examples assumes that the user has write" - einfo "permissions in the working directory and other will look for" - einfo "data files in the working directory. For this reason in order to" - einfo "run the examples it's better to temporary copy them somewhere" - einfo "in the user folder. For example to run the tutorial examples" - einfo "it's better to copy the entire examples++-tutorial folder into" - einfo "the user directory." - - rm -f examples*/Makefile* || die - doins -r examples* - fi -} diff --git a/sci-mathematics/freefem++/metadata.xml b/sci-mathematics/freefem++/metadata.xml index a605d78d7..5cee338ce 100644 --- a/sci-mathematics/freefem++/metadata.xml +++ b/sci-mathematics/freefem++/metadata.xml @@ -10,4 +10,7 @@ FreeFem++ is an implementation of a language dedicated to the finite element method. It enables you to solve Partial Differential Equations (PDE) easily. </longdescription> + <upstream> + <remote-id type="github">FreeFem/FreeFem-sources</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-mathematics/gap/Manifest b/sci-mathematics/gap/Manifest deleted file mode 100644 index b64b9f6e7..000000000 --- a/sci-mathematics/gap/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -DIST gap-4.11.0-core-packages.tar.gz 53096715 BLAKE2B 1cfec307efe95a91869e9bf4d3947dd9010a26a0cbe2c317eafb5f5402068f00f8f1518e995c92a7827e9a0fa387fc8db5dc6dd2f6cc5a1b24df1754c1e96c7f SHA512 e4ac9ffd7c33121af46ec3f255634c47efb8445429b570a8ad3c8784688f7e966d48c8f74aa50d039608974bd93e05bf61497df02e4b42f5577651c88c3884d4 -DIST gap-4.11.0-core.tar.bz2 13467788 BLAKE2B a0e1415bb2a6725f4ef6283e4823e1c1cd4d9813f981f5e6d02554fe2ae3ad05793320239e70d6412a4d4722da436bacd4fe127c79b9ec891ccbdfa3cd7c2d12 SHA512 94d5451e76ddcea33a5f83b1082f9b5d0ecb83f30491bdf510338f1eecea9faa868312cb682b5dd08c2b71c03cd3ca3f837df98fb96e52c8b89ab2443402ee49 diff --git a/sci-mathematics/gap/files/gap-4.11.0-autoconf.patch b/sci-mathematics/gap/files/gap-4.11.0-autoconf.patch deleted file mode 100644 index b220f3ada..000000000 --- a/sci-mathematics/gap/files/gap-4.11.0-autoconf.patch +++ /dev/null @@ -1,86 +0,0 @@ -diff --git a/configure.ac b/configure.ac -index 938fcd3..b3b2340 100644 ---- a/configure.ac -+++ b/configure.ac -@@ -6,6 +6,7 @@ AC_INIT([GAP], [4.dev], [support@gap-system.org], [gap], [https://www.gap-system - - AC_CONFIG_SRCDIR([src/gap.c]) - AC_CONFIG_AUX_DIR([cnf]) -+AC_CONFIG_MACRO_DIR([m4]) - - AC_CONFIG_HEADERS([gen/config.h:src/config.h.in]) - AC_CONFIG_COMMANDS([gen/stamp-h], [echo timestamp > gen/stamp-h]) -@@ -207,29 +208,41 @@ dnl User setting: Debug mode (off by default) - dnl - AC_ARG_ENABLE([debug], - [AS_HELP_STRING([--enable-debug], [enable debug mode])], -- [AC_DEFINE([GAP_KERNEL_DEBUG], [1], [define if building in debug mode]) -- AC_DEFINE([GAP_PRINT_BACKTRACE], [1], [to enable backtraces upon crashes])], -+ [], - [enable_debug=no] - ) - AC_MSG_CHECKING([whether to enable debug mode]) - AC_MSG_RESULT([$enable_debug]) - -+AS_IF([test "x$enable_debug" != "xno"], -+ [AC_DEFINE([GAP_KERNEL_DEBUG], [1], [define if building in debug mode]) -+ AC_DEFINE([GAP_PRINT_BACKTRACE], [1], [to enable backtraces upon crashes])], -+) -+ - AC_ARG_ENABLE([memory-checking], - [AS_HELP_STRING([--enable-memory-checking], [enable memory checking])], -- [AC_DEFINE([GAP_MEM_CHECK], [1], [define if building with memory checking])], -+ [], - [enable_memory_checking=no] - ) - AC_MSG_CHECKING([whether to enable memory checking]) - AC_MSG_RESULT([$enable_memory_checking]) - -+AS_IF([test "x$enable_memory_checking" != "xno"], -+ [AC_DEFINE([GAP_MEM_CHECK], [1], [define if building with memory checking])] -+) -+ - AC_ARG_ENABLE([valgrind], - [AS_HELP_STRING([--enable-valgrind], [enable valgrind extensions to GASMAN])], -- [AC_DEFINE([GAP_MEMORY_CANARY], [1], [define if building with valgrind extensions])], -+ [], - [enable_valgrind=no] - ) - AC_MSG_CHECKING([whether to enable valgrind extensions to GASMAN]) - AC_MSG_RESULT([$enable_valgrind]) - -+AS_IF([test "x$enable_valgrind" != "xno"], -+ [AC_DEFINE([GAP_MEMORY_CANARY], [1], [define if building with valgrind extensions])] -+) -+ - if test "x$enable_valgrind" != "xno" -a "x$enable_memory_checking" != "xno"; then - AC_MSG_ERROR([--enable-valgrind and --enable-memory-checking cannot be used at the same time]) - fi -@@ -549,10 +562,9 @@ AS_IF([test "x$with_gc" = xboehm], - # - # As a side benefit, users do not have to worry about installing dependencies. - -- BUILD_LIBATOMIC_OPS=yes -- LIBATOMIC_OPS_CPPFLAGS='-I${abs_builddir}/extern/install/libatomic_ops/include' -- LIBATOMIC_OPS_LDFLAGS='${abs_builddir}/extern/install/libatomic_ops/lib/libatomic_ops.la' -- LIBATOMIC_OPS_LIBS= -+ BUILD_LIBATOMIC_OPS=no -+ #PKG_CHECK_MODULES([LIBATOMIC_OPS], [atomic_ops]) -+ - AC_SUBST([BUILD_LIBATOMIC_OPS]) - AC_SUBST([LIBATOMIC_OPS_CPPFLAGS]) - AC_SUBST([LIBATOMIC_OPS_LDFLAGS]) -@@ -561,11 +573,8 @@ AS_IF([test "x$with_gc" = xboehm], - ATOMIC_OPS_CFLAGS=$LIBATOMIC_OPS_CPPFLAGS - ATOMIC_OPS_LIBS=$LIBATOMIC_OPS_LDFLAGS - -- -- BUILD_BOEHM_GC=yes -- BOEHM_GC_CPPFLAGS='-I${abs_builddir}/extern/install/gc/include' -- BOEHM_GC_LDFLAGS='${abs_builddir}/extern/install/gc/lib/libgc.la' -- BOEHM_GC_LIBS= -+ BUILD_BOEHM_GC=no -+ #PKG_CHECK_MODULES([BOEHM_GC], [bdw-gc]) - AC_SUBST([BUILD_BOEHM_GC]) - AC_SUBST([BOEHM_GC_CPPFLAGS]) - AC_SUBST([BOEHM_GC_LDFLAGS]) diff --git a/sci-mathematics/gap/gap-4.11.0.ebuild b/sci-mathematics/gap/gap-4.11.0.ebuild deleted file mode 100644 index d94a02143..000000000 --- a/sci-mathematics/gap/gap-4.11.0.ebuild +++ /dev/null @@ -1,140 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7..9} ) -inherit autotools python-any-r1 - -DESCRIPTION="Computational discrete algebra system - minimal GAP core system" -HOMEPAGE="https://www.gap-system.org/" -SRC_URI="https://github.com/gap-system/gap/releases/download/v${PV}/gap-${PV}-core.tar.bz2 - https://github.com/gap-system/gap/releases/download/v${PV}/packages-required-v${PV}.tar.gz -> ${P}-core-packages.tar.gz -" - -SLOT="0" -LICENSE="GPL-2" -KEYWORDS="~amd64" -# broken HPC and boehm -IUSE="boehm debug hpc julia julia-gc memcheck valgrind" -REQUIRED_USE="valgrind? ( memcheck ) julia-gc? ( julia ) hpc? ( boehm )" - -RDEPEND+=" - dev-libs/gmp - net-libs/zeromq - sci-libs/cddlib - sys-libs/readline - sys-libs/zlib - julia? ( || ( - dev-lang/julia - dev-lang/julia-bin:* - ) ) - valgrind? ( dev-util/valgrind ) -" -DEPEND+="${RDEPEND}" -BDEPEND+="${PYTHON_DEPS}" - -PATCHES=( "${FILESDIR}"/${PN}-4.11.0-autoconf.patch ) - -pkg_setup() { - if use valgrind; then - elog "If you enable the use of valgrind duing building" - elog "be sure that you have enabled the proper flags" - elog "in gcc to support it:" - elog "https://wiki.gentoo.org/wiki/Debugging#Valgrind" - fi -} - -src_unpack() { - default - mkdir -p "${S}"/pkg || die - mv "${WORKDIR}"/{GAPDoc*,primgrp*,SmallGrp*,transgrp*} "${S}"/pkg || die -} - -src_prepare() { - default - eautoreconf -f -i - - # use GNUmakefile - rm Makefile || die - - # make sure of no external gmp/zlib being build - # gap uses bundled libatomic_ops and boehm-gc - rm -rf extern || die - - # this test takes TOO long - rm tst/teststandard/opers/AutomorphismGroup.tst || die -} - -src_configure() { - addwrite /proc/self - local myconf=( - --enable-shared - --disable-static - --with-gmp - --with-zlib - --with-readline - --enable-popcnt - $(use_enable memcheck memory-checking) - $(use_enable valgrind) - $(use_enable hpc hpcgap) - $(use_enable debug) - $(use_with julia) - ) - # garbage collector settings - if use boehm; then - myconf+=( --with-gc=boehm ) - elif use julia-gc; then - myconf+=( --with-gc=julia ) - else - myconf+=( --with-gc=gasman ) - fi - - # only supporting amd64 builds - econf ${myconf[@]} ABI=64 -} - -src_test() { - emake testinstall testlibgap -} - -src_install() { - # upstream has no install function - # we try to simulate on as best as we can - - dodoc README{,.buildsys,.hpcgap}.md \ - CHANGES.md CITATION - - sed -e "s:^abs_top_builddir=.*$:abs_top_builddir=\"${EPREFIX}/usr/share/gap\":" \ - -e "s:^abs_top_srcdir=.*$:abs_top_srcdir=\"${EPREFIX}/usr/share/gap\":" \ - -i gac || die - dobin gac - - exeinto /usr/share/gap/ - doexe gap - - cat <<-EOF > gap.sh || die - #!/bin/sh - exec "${EPREFIX}"/usr/share/gap/gap -l "${EPREFIX}"/usr/share/gap "\$@" - EOF - newbin gap.sh gap - - dolib.so .libs/libgap.so* - - dodir /usr/include/gap - cp -a src/*.h gen/*.h "${ED}"/usr/include/gap || die - if use hpc; then - dodir /usr/include/gap/hpc - cp -a src/hpc/*.h "${ED}"/usr/include/gap/hpc || die - fi - - cp -a doc grp lib libtool pkg "${ED}"/usr/share/gap || die - - sed -e "s:${S}:${EPREFIX}/usr/share/gap:g" -i sysinfo.gap - insinto /usr/share/gap - doins sysinfo.gap* - - # remove objects and static lib files - find "${ED}" \( -name "*.o" -o -name "*.a" -o -name "*.la" \) \ - -delete || die -} diff --git a/sci-mathematics/gap/metadata.xml b/sci-mathematics/gap/metadata.xml deleted file mode 100644 index f1f953b82..000000000 --- a/sci-mathematics/gap/metadata.xml +++ /dev/null @@ -1,30 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="person"> - <email>gentoo@aisha.cc</email> - <name>Aisha Tammy</name> - </maintainer> - <maintainer type="project"> - <email>sci-mathematics@gentoo.org</email> - <name>Gentoo Mathematics Project</name> - </maintainer> - <longdescription lang="en"> - Groups, Algorithms, Programming is a system for computational - discrete algebra, with particular emphasis on Computational Group - Theory. GAP provides a programming language, a library of thousands - of functions implementing algebraic algorithms written in the GAP - language as well as large data libraries of algebraic objects. GAP - is used in research and teaching for studying groups and their - representations, rings, vector spaces, algebras, combinatorial - structures, and more. - </longdescription> - <use> - <flag name="boehm">Use <pkg>dev-libs/boehm-gc</pkg> as garbage collector</flag> - <flag name="hpc">Build gap with multithreading and parallel process support</flag> - <flag name="julia">Build julia bindings</flag> - <flag name="julia-gc">Use the julia garbage collector</flag> - <flag name="memcheck">Enable memory checking</flag> - <flag name="valgrind">Build symbols to be used by valgrind</flag> - </use> -</pkgmetadata> diff --git a/sci-mathematics/gappa/Manifest b/sci-mathematics/gappa/Manifest deleted file mode 100644 index 132e4af1c..000000000 --- a/sci-mathematics/gappa/Manifest +++ /dev/null @@ -1,2 +0,0 @@ -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 deleted file mode 100644 index 58ce7ffe7..000000000 --- a/sci-mathematics/gappa/gappa-1.3.5.ebuild +++ /dev/null @@ -1,44 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -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/${P}.tar.gz" - -LICENSE="|| ( CeCILL-2 GPL-2 )" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="doc" - -RDEPEND=" - dev-libs/gmp:0= - dev-libs/mpfr:0= - dev-libs/boost -" -DEPEND="${RDEPEND} - doc? ( app-doc/doxygen )" - -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" -} - -src_compile() { - # Only accept number of parrellel jobs because remake does not understand --load-average - ./remake -d -j$(makeopts_jobs) || die "emake failed" - if use doc; then - ./remake doc/html/index.html - fi -} - -src_install() { - DESTDIR="${D}" ./remake install - einstalldocs - use doc && dodoc -r doc/html/* -} diff --git a/sci-mathematics/gappa/gappa-1.4.0.ebuild b/sci-mathematics/gappa/gappa-1.4.0.ebuild deleted file mode 100644 index 7395c8ea3..000000000 --- a/sci-mathematics/gappa/gappa-1.4.0.ebuild +++ /dev/null @@ -1,42 +0,0 @@ -# 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-mathematics/gappa/metadata.xml b/sci-mathematics/gappa/metadata.xml deleted file mode 100644 index 448d16798..000000000 --- a/sci-mathematics/gappa/metadata.xml +++ /dev/null @@ -1,15 +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-mathematics@gentoo.org</email> - <name>Gentoo Mathematics Project</name> - </maintainer> - <longdescription> -Gappa is a tool intended to help verifying and formally proving -properties on numerical programs dealing with floating-point or -fixed-point arithmetic. It has been used to write robust floating-point -filters for CGAL and it is used to certify elementary functions in -CRlibm. -</longdescription> -</pkgmetadata> diff --git a/sci-mathematics/gappalib-coq/Manifest b/sci-mathematics/gappalib-coq/Manifest deleted file mode 100644 index aaea09aac..000000000 --- a/sci-mathematics/gappalib-coq/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST gappalib-coq-1.4.6.tar.gz 114284 BLAKE2B 2c1b38b324786f20d7503d1c2243b95b7f8b090068563120669de37ef6cd5dc4fa479b5f3e0559372f4d1fdafa833619191c73780adad45056972108a32e1d1e SHA512 bb9c431d320d9c66998ec02ba7d459ee3f00cb7b16f89e57f3d7eb4b89cd3c9254e98e3906a8dfac31f73e5a32918ad12eaeaf7504750d3bfdce878913b745d3 diff --git a/sci-mathematics/gappalib-coq/gappalib-coq-1.4.6.ebuild b/sci-mathematics/gappalib-coq/gappalib-coq-1.4.6.ebuild deleted file mode 100644 index 82b02933c..000000000 --- a/sci-mathematics/gappalib-coq/gappalib-coq-1.4.6.ebuild +++ /dev/null @@ -1,35 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DESCRIPTION="Allows the certificates Gappa generates to be imported by the Coq" -HOMEPAGE="http://gappa.gforge.inria.fr/" -SRC_URI="https://gforge.inria.fr/frs/download.php/file/38386/${P}.tar.gz" - -LICENSE="LGPL-2" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -DEPEND=" - >=sci-mathematics/gappa-1.3.2 - >=sci-mathematics/coq-8.8 - >=sci-mathematics/flocq-3.0 -" -RDEPEND="${DEPEND}" - -src_prepare() { - default - sed -i Remakefile.in \ - -e "s:mkdir -p @libdir@:mkdir -p \${DESTDIR}@libdir@:g" \ - -e "s:cp \$(OBJS) \$(MLTARGETS) @libdir@:cp \$(OBJS) \$(MLTARGETS) \${DESTDIR}@libdir@:g" -} - -src_compile() { - ./remake || die "emake failed" -} - -src_install() { - DESTDIR="${D}" ./remake install || die "emake install failed" - einstalldocs -} diff --git a/sci-mathematics/gappalib-coq/metadata.xml b/sci-mathematics/gappalib-coq/metadata.xml deleted file mode 100644 index 182ed0520..000000000 --- a/sci-mathematics/gappalib-coq/metadata.xml +++ /dev/null @@ -1,13 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-mathematics@gentoo.org</email> - <name>Gentoo Mathematics Project</name> - </maintainer> - <longdescription> -While Gappa is intended to be used directly, it can also act as a -backend prover for the Why software verification plateform or as an -automatic tactic for the Coq proof assistant. -</longdescription> -</pkgmetadata> diff --git a/sci-mathematics/lie/lie-2.2.2.ebuild b/sci-mathematics/lie/lie-2.2.2.ebuild index 9577bf240..173e0715e 100644 --- a/sci-mathematics/lie/lie-2.2.2.ebuild +++ b/sci-mathematics/lie/lie-2.2.2.ebuild @@ -21,7 +21,7 @@ RDEPEND=" sys-libs/ncurses:= " DEPEND="${RDEPEND}" -BDEPEND="${RDEPEND} +BDEPEND=" sys-devel/bison " diff --git a/sci-mathematics/ltl2ba/Manifest b/sci-mathematics/ltl2ba/Manifest index 4d6528d6b..659c1c6e6 100644 --- a/sci-mathematics/ltl2ba/Manifest +++ b/sci-mathematics/ltl2ba/Manifest @@ -1 +1,3 @@ DIST ltl2ba-1.1.tar.gz 29629 BLAKE2B 06ba7f7b5e3c6b72d2f0ea3b991346c803669e24d66dc38e311109ee08ed6dcc72bfd9f2ebe0f8864b0f80f010a4438029f4f5dbbf0087469ca2d07cdfce6b3f SHA512 8d010e2bb59fa5d682a56a50133865da938fd3bfcde6386184880eec6989bc1b694d6af9146b4b708cefdcdbcf98248f87074b8c973ea8cab65d658b394ccf69 +DIST ltl2ba-1.2.tar.gz 33026 BLAKE2B f19359e33d4eeb4dde75425ed03d940c08f46dd265b1b9c6773807e7dca67fd44f694f685d4153ca786118e336fab736104a865c5d0e9883390fca694f72b492 SHA512 148ffb1b4dbe134b69c6e946a4a9f1a95a809bf36ef3533117eedeceb721dd4c8a3238bbda2de5782a79b7aee70e33adf6ff193917441092a1ccb4e56a53a655 +DIST ltl2ba-1.3.tar.gz 38265 BLAKE2B bd74d9b9e22589ac00fbaa15f745dd6371894f68b50f85507694648274d9391ad3a90cdf1ee6c342abbceb04d0e2eb5d71473d43969b469a933517cfcd1e16c1 SHA512 1bcef13d98879c083dc907939c652e694802ed91c33a5d90bbeb6fc22d6265a0b153932c5fb3f8557aad30582322c16d0be822bf4208f40faf9384b367a84aa6 diff --git a/sci-mathematics/ltl2ba/ltl2ba-1.2.ebuild b/sci-mathematics/ltl2ba/ltl2ba-1.2.ebuild new file mode 100644 index 000000000..0678dcf8e --- /dev/null +++ b/sci-mathematics/ltl2ba/ltl2ba-1.2.ebuild @@ -0,0 +1,31 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit flag-o-matic + +DESCRIPTION="Fast LTL to Buechi Automata Translation" +HOMEPAGE="http://www.lsv.ens-cachan.fr/~gastin/ltl2ba" +SRC_URI="http://www.lsv.ens-cachan.fr/~gastin/${PN}/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +src_prepare() { + default + sed -i Makefile \ + -e "s/CC=gcc/#CC=gcc/g" \ + -e "s/CFLAGS= -O3 -ansi -DNXT/CFLAGS+= -ansi -DNXT/g" || die +} + +src_configure() { + append-cflags -fcommon + default +} + +src_install() { + dobin ltl2ba + dodoc README +} diff --git a/sci-mathematics/ltl2ba/ltl2ba-1.3.ebuild b/sci-mathematics/ltl2ba/ltl2ba-1.3.ebuild new file mode 100644 index 000000000..0678dcf8e --- /dev/null +++ b/sci-mathematics/ltl2ba/ltl2ba-1.3.ebuild @@ -0,0 +1,31 @@ +# Copyright 1999-2015 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit flag-o-matic + +DESCRIPTION="Fast LTL to Buechi Automata Translation" +HOMEPAGE="http://www.lsv.ens-cachan.fr/~gastin/ltl2ba" +SRC_URI="http://www.lsv.ens-cachan.fr/~gastin/${PN}/${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +src_prepare() { + default + sed -i Makefile \ + -e "s/CC=gcc/#CC=gcc/g" \ + -e "s/CFLAGS= -O3 -ansi -DNXT/CFLAGS+= -ansi -DNXT/g" || die +} + +src_configure() { + append-cflags -fcommon + default +} + +src_install() { + dobin ltl2ba + dodoc README +} diff --git a/sci-mathematics/netgen/Manifest b/sci-mathematics/netgen/Manifest deleted file mode 100644 index 32cbc28b8..000000000 --- a/sci-mathematics/netgen/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST netgen-6.2.2105.tar.gz 3372181 BLAKE2B 73ce8aff6e73a6a0ab79b0511c6c32c41240b9b6a743b8132cf27565b3c9f68820ad8337a9e761a37b74ffd7623a0321495a31dd868986ab4b90ff0dde66e9a8 SHA512 ed2727b7779af1ba564b0a7d9cc52fad5d3dccd478dcb71a4a77c7b9768a17eedfb6bfc2555f839cf592a7fc4ded5057f0e649239582e3d366d37ccfd030f4e9 diff --git a/sci-mathematics/netgen/files/netgen-6.2.2105-find-tk.patch b/sci-mathematics/netgen/files/netgen-6.2.2105-find-tk.patch deleted file mode 100644 index c638d83a7..000000000 --- a/sci-mathematics/netgen/files/netgen-6.2.2105-find-tk.patch +++ /dev/null @@ -1,35 +0,0 @@ -diff --git a/CMakeLists.txt b/CMakeLists.txt -index dcc24af..24f444e 100644 ---- a/CMakeLists.txt -+++ b/CMakeLists.txt -@@ -246,7 +246,8 @@ if (USE_GUI) - - add_definitions(-DTCL -DOPENGL -DUSE_TOGL_2) - include_directories(${TCL_INCLUDE_PATH}) -- include_directories(${TK_INCLUDE_PATH}) -+ include_directories(${TK_INCLUDE_PATH}/generic) -+ include_directories(${TK_INCLUDE_PATH}/unix) - set(LIBTOGL togl) - - if(WIN32) -@@ -268,7 +269,7 @@ else() - endif() - - if (USE_PYTHON) -- add_subdirectory(external_dependencies/pybind11) -+ find_package(pybind11) - find_path(PYBIND_INCLUDE_DIR pybind11/pybind11.h HINTS ${PYTHON_INCLUDE_DIR}) - if( PYBIND_INCLUDE_DIR ) - message(STATUS "Found Pybind11: ${PYBIND_INCLUDE_DIR}") -diff --git a/cmake/SuperBuild.cmake b/cmake/SuperBuild.cmake -index c24b631..2354a09 100644 ---- a/cmake/SuperBuild.cmake -+++ b/cmake/SuperBuild.cmake -@@ -39,7 +39,6 @@ endif(NOT WIN32) - ####################################################################### - if (USE_PYTHON) - find_path(PYBIND_INCLUDE_DIR pybind11/pybind11.h PATHS ${CMAKE_CURRENT_SOURCE_DIR}/external_dependencies/pybind11/include NO_DEFAULT_PATH) -- set(NG_INSTALL_PYBIND ON) - if( NOT PYBIND_INCLUDE_DIR ) - # if the pybind submodule is missing, try to initialize and update all submodules - execute_process(COMMAND git submodule update --init --recursive WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}) diff --git a/sci-mathematics/netgen/files/netgen.desktop b/sci-mathematics/netgen/files/netgen.desktop deleted file mode 100644 index 714ba53c4..000000000 --- a/sci-mathematics/netgen/files/netgen.desktop +++ /dev/null @@ -1,8 +0,0 @@ -[Desktop Entry] -Name=Netgen -Comment=3D modeling, Mesh generation. -Exec=/usr/bin/netgen -Icon=netgen -Terminal=false -Type=Application -Categories=Graphics; diff --git a/sci-mathematics/netgen/files/netgen.png b/sci-mathematics/netgen/files/netgen.png Binary files differdeleted file mode 100644 index cb2fd8466..000000000 --- a/sci-mathematics/netgen/files/netgen.png +++ /dev/null diff --git a/sci-mathematics/netgen/metadata.xml b/sci-mathematics/netgen/metadata.xml deleted file mode 100644 index cb94caeca..000000000 --- a/sci-mathematics/netgen/metadata.xml +++ /dev/null @@ -1,14 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> -<pkgmetadata> - <maintainer type="project"> - <email>sci-mathematics@gentoo.org</email> - <name>Gentoo Mathematics Project</name> - </maintainer> - <use> - <flag name="opencascade"> Enable OpenCASCADE support</flag> - </use> - <upstream> - <remote-id type="github">NGSolve/netgen</remote-id> - </upstream> -</pkgmetadata> diff --git a/sci-mathematics/netgen/netgen-6.2.2105.ebuild b/sci-mathematics/netgen/netgen-6.2.2105.ebuild deleted file mode 100644 index ed85bcb69..000000000 --- a/sci-mathematics/netgen/netgen-6.2.2105.ebuild +++ /dev/null @@ -1,102 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{8..10} ) -inherit cmake desktop python-single-r1 xdg - -DESCRIPTION="Automatic 3d tetrahedral mesh generator" -HOMEPAGE="https://ngsolve.org/ https://github.com/NGSolve/netgen" -SRC_URI="https://github.com/NGSolve/netgen/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz" - -SLOT="0" -LICENSE="LGPL-2.1" -KEYWORDS="~amd64 ~x86" - -IUSE="ffmpeg jpeg mpi opencascade openmp python +gui" -REQUIRED_USE="${PYTHON_REQUIRED_USE}" - -DEPEND=" - dev-lang/tcl:0/8.6 - dev-lang/tk:0/8.6 - dev-tcltk/tix - dev-tcltk/togl:0 - gui? ( - virtual/opengl - x11-libs/libX11 - x11-libs/libXmu - ) - python? ( - ${PYTHON_DEPS} - $(python_gen_cond_dep ' - dev-python/pybind11[${PYTHON_USEDEP}] - dev-python/pybind11-stubgen[${PYTHON_USEDEP}] - ' - ) - mpi? ( - $(python_gen_cond_dep 'dev-python/mpi4py[${PYTHON_USEDEP}]' ) - ) - ) - opencascade? ( sci-libs/opencascade:* ) - ffmpeg? ( media-video/ffmpeg ) - jpeg? ( media-libs/libjpeg-turbo:0= ) - mpi? ( virtual/mpi sci-libs/parmetis opencascade? ( sci-libs/hdf5[mpi] ) ) -" -RDEPEND="${DEPEND}" -BDEPEND="dev-vcs/git" - -PATCHES=( "${FILESDIR}/${P}-find-tk.patch" ) - -src_prepare() { - # https://github.com/NGSolve/netgen/issues/72 - git init -q || die - git config --global user.email "you@example.com" || die - git config --global user.name "Your Name" || die - git add . || die - git commit -qm 'init' || die - git tag "${PV}" || die - - cmake_src_prepare -} - -src_configure() { - local mycmakeargs=( - -DUSE_MPI="$(usex mpi)" - -DUSE_JPEG="$(usex jpeg)" - -DUSE_MPEG="$(usex ffmpeg)" - -DUSE_GUI="$(usex gui)" - -DUSE_OCC="$(usex opencascade)" - -DUSE_PYTHON="$(usex python)" - -DTK_INCLUDE_PATH="/usr/$(get_libdir)/tk8.6/include" - -DNG_INSTALL_DIR_LIB="$(get_libdir)" - -DINSTALL_PROFILES=ON - -DUSE_INTERNAL_TCL=OFF - ) - if use python; then - mycmakeargs+=( - -DPYBIND_INCLUDE_DIR="/usr/lib/${EPYTHON}/site-packages/pybind11/include/" - -DNG_INSTALL_PYBIND=OFF - ) - fi - if use mpi && use python; then - mycmakeargs+=( -DUSE_MPI4PY=ON ) - else - mycmakeargs+=( -DUSE_MPI4PY=OFF ) - fi - cmake_src_configure -} - -src_install() { - cmake_src_install - local NETGENDIR="/usr/share/netgen" - - echo -e "NETGENDIR=${NETGENDIR} \nLDPATH=/usr/$(get_libdir)/Togl2.0" > ./99netgen - doenvd 99netgen - - mv "${D}"/usr/bin/{*.tcl,*.ocf} "${D}${NETGENDIR}" || die - - # Install icon and .desktop for menu entry - doicon "${FILESDIR}"/${PN}.png - domenu "${FILESDIR}"/${PN}.desktop -} diff --git a/sci-mathematics/pulp/Manifest b/sci-mathematics/pulp/Manifest index 8a93a1b47..abe10a827 100644 --- a/sci-mathematics/pulp/Manifest +++ b/sci-mathematics/pulp/Manifest @@ -1 +1 @@ -DIST pulp-2.4.tar.gz 54307777 BLAKE2B 6be924cb8cfbf49cf754791cdc7d6cf3c16559af776b52bcba3697aeca1228a148f8643a899653fbc18cfa3525aa73967ff835fb19c91cd57013cbe001281852 SHA512 e534660ac2b04833a4305fd2e7eb121bbb136d67379b0df662a5e5b47397ca72c43c568a9ae142877ef67a15af14990d455ea1d6c74ad5cdad5912e883fe6fb3 +DIST pulp-2.7.0.gh.tar.gz 28000854 BLAKE2B d2ec0f2e795ffc93051189e236ddefc92c1e0fbfc825f8bd32b6f8569c1e0ec290acaa418e93768587238ff25c3ae9a4d27457c7e5eb0635fc919ebb80b3de3b SHA512 be89eaeaac81cb79f6533b8764283f1f4ba85570f7626db6fa3e760124a26dcc1ee3ff3b293c67de2ed48083fe611ae0ca93db83da801456a34fe7cff816ba61 diff --git a/sci-mathematics/pulp/metadata.xml b/sci-mathematics/pulp/metadata.xml index ce584d233..c86c3b501 100644 --- a/sci-mathematics/pulp/metadata.xml +++ b/sci-mathematics/pulp/metadata.xml @@ -7,5 +7,6 @@ </maintainer> <upstream> <remote-id type="pypi">PuLP</remote-id> + <remote-id type="github">coin-or/pulp</remote-id> </upstream> </pkgmetadata> diff --git a/sci-mathematics/pulp/pulp-2.4.ebuild b/sci-mathematics/pulp/pulp-2.4.ebuild deleted file mode 100644 index 1833c45a9..000000000 --- a/sci-mathematics/pulp/pulp-2.4.ebuild +++ /dev/null @@ -1,23 +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} ) -DISTUTILS_USE_SETUPTOOLS=rdepend - -inherit distutils-r1 - -DESCRIPTION="Create MPS/LP files, call solvers, and present results" -HOMEPAGE="https://coin-or.github.io/pulp/" -SRC_URI="https://github.com/coin-or/${PN}/archive/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="BSD-2" -KEYWORDS="~amd64 ~x86" -SLOT="0" - -RDEPEND="dev-python/amply[${PYTHON_USEDEP}]" - -distutils_enable_tests setup.py -# ToDo: package theme -#distutils_enable_sphinx doc/source dev-python/sphinx_glpi_theme diff --git a/sci-mathematics/pulp/pulp-2.7.0.ebuild b/sci-mathematics/pulp/pulp-2.7.0.ebuild new file mode 100644 index 000000000..641a91622 --- /dev/null +++ b/sci-mathematics/pulp/pulp-2.7.0.ebuild @@ -0,0 +1,21 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools + +inherit distutils-r1 + +DESCRIPTION="Create MPS/LP files, call solvers, and present results" +HOMEPAGE="https://coin-or.github.io/pulp/" +SRC_URI="https://github.com/coin-or/${PN}/archive/${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="BSD-2" +KEYWORDS="~amd64 ~x86" +SLOT="0" + +distutils_enable_tests setup.py +# ToDo: package theme +#distutils_enable_sphinx doc/source dev-python/sphinx_glpi_theme diff --git a/sci-mathematics/ripser/metadata.xml b/sci-mathematics/ripser/metadata.xml index fbef5ab11..05f38b851 100644 --- a/sci-mathematics/ripser/metadata.xml +++ b/sci-mathematics/ripser/metadata.xml @@ -1,16 +1,19 @@ <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> - <maintainer type="person"> - <email>gentoo@aisha.cc</email> - <name>Aisha Tammy</name> - </maintainer> - <maintainer type="project"> - <email>sci@gentoo.org</email> - <name>Gentoo Science Project</name> - </maintainer> - <use> - <flag name="progress">print progress of calculations in console</flag> - <flag name="sparsehash">use google sparsehash for storage</flag> - </use> + <maintainer type="person"> + <email>gentoo@aisha.cc</email> + <name>Aisha Tammy</name> + </maintainer> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <use> + <flag name="progress">print progress of calculations in console</flag> + <flag name="sparsehash">use google sparsehash for storage</flag> + </use> + <upstream> + <remote-id type="github">Ripser/ripser</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-mathematics/scilab-bin/Manifest b/sci-mathematics/scilab-bin/Manifest index d4c0e32f7..6029dc30e 100644 --- a/sci-mathematics/scilab-bin/Manifest +++ b/sci-mathematics/scilab-bin/Manifest @@ -1 +1,2 @@ +DIST scilab-2023.1.0.bin.x86_64-linux-gnu.tar.xz 182801620 BLAKE2B 19847145a8d70550afa77591854aa651ee5fe23f9998eee21c11acdd4112397fb5e2e82c6bc7edbc2f808048f70905dc0df37db00c43b5794bf304e9a0807ca4 SHA512 af0f71d270513f283ac732e2004094854a117ce4550c5ab579eda5c5ec52bde76a8fa5dd7649db84d68d43124524342f2fdc5f1ba269a60a3930c578ef3391f8 DIST scilab-6.1.1.bin.linux-x86_64.tar.gz 215840619 BLAKE2B dcfb88f2488cf26371c5beee1e905a33e4c6fc343bb490bb43a73334960f0c13df7d372841949a46d7dc5b6c0a404e6648828104717274518a8ff905a0ae15ad SHA512 ed386e01869cfac3d12881ddb4ae0258bb02e1d4a919a82405dbedce77406c04269883b6e1456dbad52551217307a7baebbb355a699168b77810263f5e357895 diff --git a/sci-mathematics/scilab-bin/scilab-bin-2023.1.0.ebuild b/sci-mathematics/scilab-bin/scilab-bin-2023.1.0.ebuild new file mode 100644 index 000000000..83d189b8a --- /dev/null +++ b/sci-mathematics/scilab-bin/scilab-bin-2023.1.0.ebuild @@ -0,0 +1,78 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit xdg + +MY_PN="${PN//-bin}" +MY_P="${MY_PN}-${PV}" + +DESCRIPTION="Scientific software package for numerical computations" +HOMEPAGE="https://www.scilab.org/" +SRC_URI="https://www.scilab.org/download/${PV}/${MY_P}.bin.x86_64-linux-gnu.tar.xz" +S="${WORKDIR}/${P//-bin}" + +LICENSE="GPL-2 Apache-2.0 sun-bcla-jhall jing MPL-1.0 MIT" +SLOT="0" +KEYWORDS="-* ~amd64" + +# Bundled dependencies not packaged in ::gentoo +# sci-libs/hdf5[cxx]:0/9 +# libgluegen.so (in ::sci) +# libjogl_desktop.so (in ::sci) +# libOpenXLSX.so (in ::sci) +# +# Bundled dependencies in ::gentoo +# dev-lang/tcl +# dev-libs/openssl:0/1.1 +# dev-libs/newt +# dev-libs/libpcre +# net-misc/curl +# sci-libs/amd +# sci-libs/arpack +# sci-libs/camd +# sci-libs/ccolamd +# sci-libs/cholmod +# sci-libs/colamd +# sci-libs/fftw:3.0/3 +# sci-libs/lapack +# sci-libs/matio +# sci-libs/openblas +# sci-libs/umfpack + +RDEPEND=" + sys-libs/ncurses-compat + virtual/jre:1.8 +" + +QA_PREBUILT=( "opt/${MY_PN}/*" ) + +src_prepare() { + default + local SCILAB_HOME="/opt/${MY_PN}" + # fix the .pc file to reflect the dirs where we are installing stuff + sed -i -e "/^prefix=/c prefix=${SCILAB_HOME}" lib/pkgconfig/scilab.pc || die + + # move appdata to metainfo + mv share/appdata share/metainfo || die +} + +src_install() { + local SCILAB_HOME="/opt/${MY_PN}" + dodir "${SCILAB_HOME}" + + # make convenience symlinks in PATH + for file in bin/*; do + dosym "../${MY_PN}/${file}" "/opt/${file}" + done + + # copy all the things + cp -r "${S}/"* "${ED}/${SCILAB_HOME}" || die + + # move out dekstop, icons etc + dodir /usr/share + mv "${ED}/${SCILAB_HOME}/share/"{metainfo,applications,icons,locale,mime} "${ED}/usr/share/" || die + dodir /usr/lib64/pkgconfig + mv "${ED}/${SCILAB_HOME}/lib/pkgconfig/scilab.pc" "${ED}/usr/lib64/pkgconfig/" || die +} diff --git a/sci-misc/elmer-fem/elmer-fem-9.0-r1.ebuild b/sci-misc/elmer-fem/elmer-fem-9.0-r1.ebuild deleted file mode 100644 index 6d810ed14..000000000 --- a/sci-misc/elmer-fem/elmer-fem-9.0-r1.ebuild +++ /dev/null @@ -1,76 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -FORTRAN_STANDARD=90 - -inherit fortran-2 flag-o-matic cmake - -ELMER_ROOT="elmerfem" -MY_PN=${PN/elmer-/} - -DESCRIPTION="Finite element programs, libraries, and visualization tools" -HOMEPAGE="https://www.csc.fi/web/elmer https://www.elmerfem.org/blog/" -SRC_URI="https://github.com/ElmerCSC/elmerfem/archive/release-${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -IUSE="ice gui matc mumps mpi post test" -RESTRICT="!test? ( test )" - -RDEPEND=" - virtual/blas - virtual/lapack - sci-libs/arpack - mumps? ( sci-libs/mumps ) - mpi? ( sys-cluster/openmpi ) - post? ( - dev-lang/tcl:0= - dev-lang/tk:0= - ) - gui? ( x11-libs/qwt:6 ) -" -DEPEND="${RDEPEND}" -# Note this seems to only configure correctly with the elmer version of umfpack -# But this doesn't stop it from compiling / working without it - -PATCHES=( - "${FILESDIR}/${PN}-DCRComplexSolve-compile-error.patch" - "${FILESDIR}/${PN}-ElmerIce-compile.patch" -) - -S="${WORKDIR}/elmerfem-release-${PV}" - -src_prepare() { - cmake_src_prepare - sed -i '/#include <QPainter>/a #include <QPainterPath>' ElmerGUI/Application/twod/renderarea.cpp || die - test-flag-FC -fallow-argument-mismatch && append-fflags -fallow-argument-mismatch - test-flag-FC -fallow-invalid-boz && append-fflags -fallow-invalid-boz - # TODO: fix the tests, fails in compile phase: multiple rules to make target - rm -r fem/tests/* || die - touch fem/tests/CMakeLists.txt || die -} - -src_configure() { - local mycmakeargs=( - -DMPI_Fortran_COMPILE_FLAGS="$FCFLAGS" - -DCMAKE_Fortran_FLAGS="$FCFLAGS" - -DELMER_INSTALL_LIB_DIR="/usr/$(get_libdir)/elmersolver" - -DWITH_MPI="$(usex mpi)" - -DWITH_OpenMP="$(usex mpi)" - -DWITH_MATC="$(usex matc)" - -DWITH_Mumps="$(usex mumps)" - -DWITH_ElmerIce="$(usex ice)" - -DWITH_ELMERPOST="$(usex post)" - -DWITH_ELMERGUI="$(usex gui)" - -DWITH_QT5="$(usex gui)" - -DWITH_QWT="$(usex gui)" - -DQWT_INCLUDE_DIR="/usr/include/qwt6" - -DQWT_LIBRARY="/usr/$(get_libdir)/libqwt6-qt5.so" - -DBUILD_TESTING="$(usex test)" - ) - cmake_src_configure -} diff --git a/sci-misc/elmer-fem/elmer-fem-9.0-r2.ebuild b/sci-misc/elmer-fem/elmer-fem-9.0-r2.ebuild new file mode 100644 index 000000000..82e1c796f --- /dev/null +++ b/sci-misc/elmer-fem/elmer-fem-9.0-r2.ebuild @@ -0,0 +1,78 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +FORTRAN_STANDARD=90 + +inherit fortran-2 flag-o-matic cmake + +ELMER_ROOT="elmerfem" +MY_PN=${PN/elmer-/} + +DESCRIPTION="Finite element programs, libraries, and visualization tools" +HOMEPAGE="https://www.csc.fi/web/elmer https://www.elmerfem.org/blog/" +SRC_URI="https://github.com/ElmerCSC/elmerfem/archive/release-${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +IUSE="ice gui matc mumps mpi post test" +RESTRICT="!test? ( test )" + +RDEPEND=" + virtual/blas + virtual/lapack + sci-libs/arpack + mumps? ( sci-libs/mumps ) + mpi? ( sys-cluster/openmpi ) + post? ( + dev-lang/tcl:0= + dev-lang/tk:0= + ) + gui? ( x11-libs/qwt:6 ) +" +DEPEND="${RDEPEND}" +# Note this seems to only configure correctly with the elmer version of umfpack +# But this doesn't stop it from compiling / working without it + +PATCHES=( + "${FILESDIR}/${PN}-DCRComplexSolve-compile-error.patch" + "${FILESDIR}/${PN}-ElmerIce-compile.patch" + "${FILESDIR}/${PN}-rpath.patch" + "${FILESDIR}/${P}-qwt-6.2.patch" +) + +S="${WORKDIR}/elmerfem-release-${PV}" + +src_prepare() { + cmake_src_prepare + sed -i '/#include <QPainter>/a #include <QPainterPath>' ElmerGUI/Application/twod/renderarea.cpp || die + test-flag-FC -fallow-argument-mismatch && append-fflags -fallow-argument-mismatch + test-flag-FC -fallow-invalid-boz && append-fflags -fallow-invalid-boz + # TODO: fix the tests, fails in compile phase: multiple rules to make target + rm -r fem/tests/* || die + touch fem/tests/CMakeLists.txt || die +} + +src_configure() { + local mycmakeargs=( + -DMPI_Fortran_COMPILE_FLAGS="$FCFLAGS" + -DCMAKE_Fortran_FLAGS="$FCFLAGS" + -DELMER_INSTALL_LIB_DIR="/usr/$(get_libdir)/elmersolver" + -DWITH_MPI="$(usex mpi)" + -DWITH_OpenMP="$(usex mpi)" + -DWITH_MATC="$(usex matc)" + -DWITH_Mumps="$(usex mumps)" + -DWITH_ElmerIce="$(usex ice)" + -DWITH_ELMERPOST="$(usex post)" + -DWITH_ELMERGUI="$(usex gui)" + -DWITH_QT5="$(usex gui)" + -DWITH_QWT="$(usex gui)" + -DQWT_INCLUDE_DIR="/usr/include/qwt6" + -DQWT_LIBRARY="/usr/$(get_libdir)/libqwt6-qt5.so" + -DBUILD_TESTING="$(usex test)" + ) + cmake_src_configure +} diff --git a/sci-misc/elmer-fem/files/elmer-fem-9.0-qwt-6.2.patch b/sci-misc/elmer-fem/files/elmer-fem-9.0-qwt-6.2.patch new file mode 100644 index 000000000..13eaf1c5f --- /dev/null +++ b/sci-misc/elmer-fem/files/elmer-fem-9.0-qwt-6.2.patch @@ -0,0 +1,35 @@ +From 48e9430ccb858ca5bda28b967a0c84b51e2404b2 Mon Sep 17 00:00:00 2001 +From: "E. Albiter" <ealbiter@gmail.com> +Date: Fri, 15 Oct 2021 13:12:48 -0500 +Subject: [PATCH] Compatibility with Qwt 6.2. Fix for #293 + +--- + ElmerGUI/Application/src/convergenceview.h | 8 ++++---- + 1 file changed, 4 insertions(+), 4 deletions(-) + +diff --git a/ElmerGUI/Application/src/convergenceview.h b/ElmerGUI/Application/src/convergenceview.h +index 377b644b99..4259eb730e 100755 +--- a/ElmerGUI/Application/src/convergenceview.h ++++ b/ElmerGUI/Application/src/convergenceview.h +@@ -51,8 +51,8 @@ + #include <qwt_plot_curve.h>
+ #include <qwt_plot_grid.h>
+ #include <qwt_legend.h>
+-/*#include <qwt_data.h> <-- deprecated in Qwt6, using qwt_compat.h instead*/
+-#include <qwt_compat.h>
++/*#include <qwt_data.h> <-- deprecated in Qwt6, using qwt_compat.h instead
++#include <qwt_compat.h> <-- Removed in Qwt 6.2 */
+ #include <qwt_text.h>
+ #include <qwt_scale_engine.h>
+
+@@ -76,8 +76,8 @@ class CurveData +
+ private:
+ int d_count;
+- QwtArray<double> d_x;
+- QwtArray<double> d_y;
++ QVector<double> d_x;
++ QVector<double> d_y;
+ };
+
+ class Curve
diff --git a/sci-misc/elmer-fem/files/elmer-fem-rpath.patch b/sci-misc/elmer-fem/files/elmer-fem-rpath.patch new file mode 100644 index 000000000..27249fef9 --- /dev/null +++ b/sci-misc/elmer-fem/files/elmer-fem-rpath.patch @@ -0,0 +1,11 @@ +--- a/CMakeLists.txt.orig 2022-08-24 21:50:59.940905698 -0500 ++++ b/CMakeLists.txt 2022-08-24 21:51:08.610804464 -0500 +@@ -479,7 +479,7 @@ + + # Set up rpaths to point ELMER_INSTALL_LIB_DIR + IF(${CMAKE_SYSTEM_NAME} MATCHES "Linux") +- SET(ELMERSOLVER_RPATH_STRING "\$ORIGIN/../${ELMER_INSTALL_LIB_DIR}") ++ SET(ELMERSOLVER_RPATH_STRING "${ELMER_INSTALL_LIB_DIR}") + SET(ELMERLIB_RPATH_STRING "\$ORIGIN/") + ELSEIF(APPLE) + SET(ELMERSOLVER_RPATH_STRING "@loader_path/../${ELMER_INSTALL_LIB_DIR}") diff --git a/sci-misc/elmer-fem/metadata.xml b/sci-misc/elmer-fem/metadata.xml index feab34b47..37464c70a 100644 --- a/sci-misc/elmer-fem/metadata.xml +++ b/sci-misc/elmer-fem/metadata.xml @@ -7,6 +7,7 @@ </maintainer> <upstream> <remote-id type="sourceforge">svn</remote-id> + <remote-id type="github">ElmerCSC/elmerfem</remote-id> </upstream> <use> <flag name="gui">Build the ElmerGUI</flag> diff --git a/sci-misc/jwnl/jwnl-1.4_rc2.ebuild b/sci-misc/jwnl/jwnl-1.4_rc2.ebuild index ee4be9427..c6ab40229 100644 --- a/sci-misc/jwnl/jwnl-1.4_rc2.ebuild +++ b/sci-misc/jwnl/jwnl-1.4_rc2.ebuild @@ -3,7 +3,7 @@ EAPI=7 -inherit java-pkg-2 java-utils-2 +inherit java-pkg-2 MY_P=${PN}${PV//.} diff --git a/sci-misc/openfst/Manifest b/sci-misc/openfst/Manifest index 3f2abd738..f89088f0a 100644 --- a/sci-misc/openfst/Manifest +++ b/sci-misc/openfst/Manifest @@ -1 +1 @@ -DIST openfst-1.8.1.tar.gz 1333532 BLAKE2B 5cc6d222a91c774edde869246fc8ae27ce1975632ac17d3b28236e63c65b6d7f637c1e88c54378b63ef66d59a29acc528a4c3ccc66ec3d7e20100f990cb1d67c SHA512 4c350a3f47de33d134536ac70a906cabf7d3641527c6823d378c4dd8651082dd9246343a233ad7c4c25a42905315441a6528e3e3c3730bfd17da320098e94b59 +DIST openfst-1.8.2.tar.gz 1342793 BLAKE2B bae3ff40e1234a5c2a9bbd642ba5a7e29b0ecef2e304b2a952d1ebb354c3fb4d772dfdf85710fcd4940e01798ac4064226377e59f1a3f46b2331219e1bd3f8cf SHA512 ca7f9f19e24141e1f1d0bbabf43795e6e278bce3887c14261d9ce204a0e01b1588eaf982755a9105247510a19f67da2f566e9b14b1d869497148f95b55606d5c diff --git a/sci-misc/openfst/files/kaldi-openfst-1.4.1.patch b/sci-misc/openfst/files/kaldi-openfst-1.4.1.patch deleted file mode 100644 index 140ea4e24..000000000 --- a/sci-misc/openfst/files/kaldi-openfst-1.4.1.patch +++ /dev/null @@ -1,269 +0,0 @@ -diff -crB openfst-1.4.1.orig/src/include/fst/lock.h openfst-1.4.1/src/include/fst/lock.h -*** openfst-1.4.1.orig/src/include/fst/lock.h 2012-04-25 19:43:47.000000000 -0400 ---- openfst-1.4.1/src/include/fst/lock.h 2015-02-28 14:12:29.009385600 -0400 -*************** -*** 78,85 **** - RefCounter() : count_(1) {} - - int count() const { return count_; } -! int Incr() const { return ++count_; } -! int Decr() const { return --count_; } - - private: - mutable int count_; ---- 78,93 ---- - RefCounter() : count_(1) {} - - int count() const { return count_; } -! -! // below lines are modifications of openfst for multi-thrads support, -! // from tools/extras/openfst_gcc41up.patch, applied by tools/Makefile, -! // applicable to gcc 4.1 or above -! // int Incr() const { return ++count_; } -! // int Decr() const { return --count_; } -! -! int Incr() const { return __sync_add_and_fetch(&count_, 1); } -! int Decr() const { return __sync_sub_and_fetch(&count_, 1); } -! // end modifications - - private: - mutable int count_; -diff -crB openfst-1.4.1.orig/src/include/fst/minimize.h openfst-1.4.1/src/include/fst/minimize.h -*** openfst-1.4.1.orig/src/include/fst/minimize.h 2014-04-29 18:15:17.000000000 -0400 ---- openfst-1.4.1/src/include/fst/minimize.h 2015-02-28 14:11:39.270566070 -0400 -*************** -*** 134,140 **** - typedef typename A::Weight Weight; - typedef ReverseArc<A> RevA; - -! CyclicMinimizer(const ExpandedFst<A>& fst) { - Initialize(fst); - Compute(fst); - } ---- 134,147 ---- - typedef typename A::Weight Weight; - typedef ReverseArc<A> RevA; - -! CyclicMinimizer(const ExpandedFst<A>& fst): -! // tell the Partition data-member to expect multiple repeated -! // calls to SplitOn with the same element if we are non-deterministic. -! P_(fst.Properties(kIDeterministic, true) == 0) { -! if(fst.Properties(kIDeterministic, true) == 0) -! CHECK(Weight::Properties() & kIdempotent); // this minimization -! // algorithm for non-deterministic FSTs can only work with idempotent -! // semirings. - Initialize(fst); - Compute(fst); - } -*************** -*** 315,321 **** - typedef typename A::StateId ClassId; - typedef typename A::Weight Weight; - -! AcyclicMinimizer(const ExpandedFst<A>& fst) { - Initialize(fst); - Refine(fst); - } ---- 322,334 ---- - typedef typename A::StateId ClassId; - typedef typename A::Weight Weight; - -! AcyclicMinimizer(const ExpandedFst<A>& fst): -! // tell the Partition data-member to expect multiple repeated -! // calls to SplitOn with the same element if we are non-deterministic. -! partition_(fst.Properties(kIDeterministic, true) == 0) { -! if(fst.Properties(kIDeterministic, true) == 0) -! CHECK(Weight::Properties() & kIdempotent); // minimization for -! // non-deterministic FSTs can only work with idempotent semirings. - Initialize(fst); - Refine(fst); - } -*************** -*** 531,543 **** - void Minimize(MutableFst<A>* fst, - MutableFst<A>* sfst = 0, - float delta = kDelta) { -! uint64 props = fst->Properties(kAcceptor | kIDeterministic| -! kWeighted | kUnweighted, true); -! if (!(props & kIDeterministic)) { -! FSTERROR() << "FST is not deterministic"; -! fst->SetProperties(kError, kError); -! return; -! } - - if (!(props & kAcceptor)) { // weighted transducer - VectorFst< GallicArc<A, GALLIC_LEFT> > gfst; ---- 544,550 ---- - void Minimize(MutableFst<A>* fst, - MutableFst<A>* sfst = 0, - float delta = kDelta) { -! uint64 props = fst->Properties(kAcceptor | kWeighted | kUnweighted, true); - - if (!(props & kAcceptor)) { // weighted transducer - VectorFst< GallicArc<A, GALLIC_LEFT> > gfst; -diff -crB openfst-1.4.1.orig/src/include/fst/partition.h openfst-1.4.1/src/include/fst/partition.h -*** openfst-1.4.1.orig/src/include/fst/partition.h 2014-04-29 18:15:17.000000000 -0400 ---- openfst-1.4.1/src/include/fst/partition.h 2015-02-28 14:11:39.271566087 -0400 -*************** -*** 43,50 **** - friend class PartitionIterator<T>; - - struct Element { -! Element() : value(0), next(0), prev(0) {} -! Element(T v) : value(v), next(0), prev(0) {} - - T value; - Element* next; ---- 43,50 ---- - friend class PartitionIterator<T>; - - struct Element { -! Element() : value(0), next(0), prev(0) {} -! Element(T v) : value(v), next(0), prev(0) {} - - T value; - Element* next; -*************** -*** 52,60 **** - }; - - public: -! Partition() {} - -! Partition(T num_states) { - Initialize(num_states); - } - ---- 52,62 ---- - }; - - public: -! Partition(bool allow_repeated_split): -! allow_repeated_split_(allow_repeated_split) {} - -! Partition(bool allow_repeated_split, T num_states): -! allow_repeated_split_(allow_repeated_split) { - Initialize(num_states); - } - -*************** -*** 137,152 **** - if (class_size_[class_id] == 1) return; - - // first time class is split -! if (split_size_[class_id] == 0) - visited_classes_.push_back(class_id); -! - // increment size of split (set of element at head of chain) - split_size_[class_id]++; -! - // update split point -! if (class_split_[class_id] == 0) -! class_split_[class_id] = classes_[class_id]; -! if (class_split_[class_id] == elements_[element_id]) - class_split_[class_id] = elements_[element_id]->next; - - // move to head of chain in same class ---- 139,154 ---- - if (class_size_[class_id] == 1) return; - - // first time class is split -! if (split_size_[class_id] == 0) { - visited_classes_.push_back(class_id); -! class_split_[class_id] = classes_[class_id]; -! } - // increment size of split (set of element at head of chain) - split_size_[class_id]++; -! - // update split point -! if (class_split_[class_id] != 0 -! && class_split_[class_id] == elements_[element_id]) - class_split_[class_id] = elements_[element_id]->next; - - // move to head of chain in same class -*************** -*** 157,165 **** - // class indices of the newly created class. Returns the new_class id - // or -1 if no new class was created. - T SplitRefine(T class_id) { - // only split if necessary -! if (class_size_[class_id] == split_size_[class_id]) { -! class_split_[class_id] = 0; - split_size_[class_id] = 0; - return -1; - } else { ---- 159,169 ---- - // class indices of the newly created class. Returns the new_class id - // or -1 if no new class was created. - T SplitRefine(T class_id) { -+ -+ Element* split_el = class_split_[class_id]; - // only split if necessary -! //if (class_size_[class_id] == split_size_[class_id]) { -! if(split_el == NULL) { // we split on everything... - split_size_[class_id] = 0; - return -1; - } else { -*************** -*** 163,180 **** - split_size_[class_id] = 0; - return -1; - } else { -- - T new_class = AddClass(); - size_t remainder = class_size_[class_id] - split_size_[class_id]; - if (remainder < split_size_[class_id]) { // add smaller -- Element* split_el = class_split_[class_id]; - classes_[new_class] = split_el; -- class_size_[class_id] = split_size_[class_id]; -- class_size_[new_class] = remainder; - split_el->prev->next = 0; - split_el->prev = 0; - } else { -- Element* split_el = class_split_[class_id]; - classes_[new_class] = classes_[class_id]; - class_size_[class_id] = remainder; - class_size_[new_class] = split_size_[class_id]; ---- 167,189 ---- - split_size_[class_id] = 0; - return -1; - } else { - T new_class = AddClass(); -+ -+ if(allow_repeated_split_) { // split_size_ is possibly -+ // inaccurate, so work it out exactly. -+ size_t split_count; Element *e; -+ for(split_count=0,e=classes_[class_id]; -+ e != split_el; split_count++, e=e->next); -+ split_size_[class_id] = split_count; -+ } - size_t remainder = class_size_[class_id] - split_size_[class_id]; - if (remainder < split_size_[class_id]) { // add smaller - classes_[new_class] = split_el; - split_el->prev->next = 0; - split_el->prev = 0; -+ class_size_[class_id] = split_size_[class_id]; -+ class_size_[new_class] = remainder; - } else { - classes_[new_class] = classes_[class_id]; - class_size_[class_id] = remainder; - class_size_[new_class] = split_size_[class_id]; -*************** -*** 245,254 **** ---- 254,269 ---- - vector<T> class_size_; - - // size of split for each class -+ // in the nondeterministic case, split_size_ is actually an upper -+ // bound on the size of split for each class. - vector<T> split_size_; - - // set of visited classes to be used in split refine - vector<T> visited_classes_; -+ -+ // true if input fst was deterministic: we can make -+ // certain assumptions in this case that speed up the algorithm. -+ bool allow_repeated_split_; - }; - - diff --git a/sci-misc/openfst/files/kaldi.patch b/sci-misc/openfst/files/kaldi.patch deleted file mode 100644 index 3a3854eff..000000000 --- a/sci-misc/openfst/files/kaldi.patch +++ /dev/null @@ -1,599 +0,0 @@ -diff -crB openfst-1.3.4.orig/src/include/fst/interval-set.h openfst-1.3.4/src/include/fst/interval-set.h -*** openfst-1.3.4.orig/src/include/fst/interval-set.h 2013-01-24 06:36:23.000000000 +0400 ---- openfst-1.3.4/src/include/fst/interval-set.h 2013-11-21 15:59:08.541136087 +0400 -*************** -*** 37,74 **** - class IntervalSet { - public: - struct Interval { -! T begin; -! T end; - -! Interval() : begin(-1), end(-1) {} - -! Interval(T b, T e) : begin(b), end(e) {} - - bool operator<(const Interval &i) const { -! return begin < i.begin || (begin == i.begin && end > i.end); - } - - bool operator==(const Interval &i) const { -! return begin == i.begin && end == i.end; - } - - bool operator!=(const Interval &i) const { -! return begin != i.begin || end != i.end; - } - - istream &Read(istream &strm) { - T n; - ReadType(strm, &n); -! begin = n; - ReadType(strm, &n); -! end = n; - return strm; - } - - ostream &Write(ostream &strm) const { -! T n = begin; - WriteType(strm, n); -! n = end; - WriteType(strm, n); - return strm; - } ---- 37,74 ---- - class IntervalSet { - public: - struct Interval { -! T begin_; -! T end_; - -! Interval() : begin_(-1), end_(-1) {} - -! Interval(T b, T e) : begin_(b), end_(e) {} - - bool operator<(const Interval &i) const { -! return begin_ < i.begin_ || (begin_ == i.begin_ && end_ > i.end_); - } - - bool operator==(const Interval &i) const { -! return begin_ == i.begin_ && end_ == i.end_; - } - - bool operator!=(const Interval &i) const { -! return begin_ != i.begin_ || end_ != i.end_; - } - - istream &Read(istream &strm) { - T n; - ReadType(strm, &n); -! begin_ = n; - ReadType(strm, &n); -! end_ = n; - return strm; - } - - ostream &Write(ostream &strm) const { -! T n = begin_; - WriteType(strm, n); -! n = end_; - WriteType(strm, n); - return strm; - } -*************** -*** 108,114 **** - lower_bound(intervals_.begin(), intervals_.end(), interval); - if (lb == intervals_.begin()) - return false; -! return (--lb)->end > value; - } - - // Requires intervals be normalized. ---- 108,114 ---- - lower_bound(intervals_.begin(), intervals_.end(), interval); - if (lb == intervals_.begin()) - return false; -! return (--lb)->end_ > value; - } - - // Requires intervals be normalized. -*************** -*** 123,129 **** - - bool Singleton() const { - return intervals_.size() == 1 && -! intervals_[0].begin + 1 == intervals_[0].end; - } - - ---- 123,129 ---- - - bool Singleton() const { - return intervals_.size() == 1 && -! intervals_[0].begin_ + 1 == intervals_[0].end_; - } - - -*************** -*** 178,194 **** - T size = 0; - for (T i = 0; i < intervals_.size(); ++i) { - Interval &inti = intervals_[i]; -! if (inti.begin == inti.end) - continue; - for (T j = i + 1; j < intervals_.size(); ++j) { - Interval &intj = intervals_[j]; -! if (intj.begin > inti.end) - break; -! if (intj.end > inti.end) -! inti.end = intj.end; - ++i; - } -! count_ += inti.end - inti.begin; - intervals_[size++] = inti; - } - intervals_.resize(size); ---- 178,194 ---- - T size = 0; - for (T i = 0; i < intervals_.size(); ++i) { - Interval &inti = intervals_[i]; -! if (inti.begin_ == inti.end_) - continue; - for (T j = i + 1; j < intervals_.size(); ++j) { - Interval &intj = intervals_[j]; -! if (intj.begin_ > inti.end_) - break; -! if (intj.end_ > inti.end_) -! inti.end_ = intj.end_; - ++i; - } -! count_ += inti.end_ - inti.begin_; - intervals_[size++] = inti; - } - intervals_.resize(size); -*************** -*** 208,224 **** - oset->count_ = 0; - - while (it1 != intervals_.end() && it2 != iintervals->end()) { -! if (it1->end <= it2->begin) { - ++it1; -! } else if (it2->end <= it1->begin) { - ++it2; - } else { - Interval interval; -! interval.begin = max(it1->begin, it2->begin); -! interval.end = min(it1->end, it2->end); - ointervals->push_back(interval); -! oset->count_ += interval.end - interval.begin; -! if (it1->end < it2->end) - ++it1; - else - ++it2; ---- 208,224 ---- - oset->count_ = 0; - - while (it1 != intervals_.end() && it2 != iintervals->end()) { -! if (it1->end_ <= it2->begin_) { - ++it1; -! } else if (it2->end_ <= it1->begin_) { - ++it2; - } else { - Interval interval; -! interval.begin_ = max(it1->begin_, it2->begin_); -! interval.end_ = min(it1->end_, it2->end_); - ointervals->push_back(interval); -! oset->count_ += interval.end_ - interval.begin_; -! if (it1->end_ < it2->end_) - ++it1; - else - ++it2; -*************** -*** 235,255 **** - oset->count_ = 0; - - Interval interval; -! interval.begin = 0; - for (typename vector<Interval>::const_iterator it = intervals_.begin(); - it != intervals_.end(); - ++it) { -! interval.end = min(it->begin, maxval); -! if (interval.begin < interval.end) { - ointervals->push_back(interval); -! oset->count_ += interval.end - interval.begin; - } -! interval.begin = it->end; - } -! interval.end = maxval; -! if (interval.begin < interval.end) { - ointervals->push_back(interval); -! oset->count_ += interval.end - interval.begin; - } - } - ---- 235,255 ---- - oset->count_ = 0; - - Interval interval; -! interval.begin_ = 0; - for (typename vector<Interval>::const_iterator it = intervals_.begin(); - it != intervals_.end(); - ++it) { -! interval.end_ = min(it->begin_, maxval); -! if (interval.begin_ < interval.end_) { - ointervals->push_back(interval); -! oset->count_ += interval.end_ - interval.begin_; - } -! interval.begin_ = it->end_; - } -! interval.end_ = maxval; -! if (interval.begin_ < interval.end_) { - ointervals->push_back(interval); -! oset->count_ += interval.end_ - interval.begin_; - } - } - -*************** -*** 263,269 **** - oset->count_ = 0; - } else { - IntervalSet<T> cset; -! iset.Complement(intervals_.back().end, &cset); - Intersect(cset, oset); - } - } ---- 263,269 ---- - oset->count_ = 0; - } else { - IntervalSet<T> cset; -! iset.Complement(intervals_.back().end_, &cset); - Intersect(cset, oset); - } - } -*************** -*** 277,285 **** - typename vector<Interval>::const_iterator it2 = intervals->begin(); - - while (it1 != intervals_.end() && it2 != intervals->end()) { -! if (it1->end <= it2->begin) { - ++it1; -! } else if (it2->end <= it1->begin) { - ++it2; - } else { - return true; ---- 277,285 ---- - typename vector<Interval>::const_iterator it2 = intervals->begin(); - - while (it1 != intervals_.end() && it2 != intervals->end()) { -! if (it1->end_ <= it2->begin_) { - ++it1; -! } else if (it2->end_ <= it1->begin_) { - ++it2; - } else { - return true; -*************** -*** 300,320 **** - bool overlap = false; // point in both intervals_ and intervals - - while (it1 != intervals_.end() && it2 != intervals->end()) { -! if (it1->end <= it2->begin) { // no overlap - it1 first - only1 = true; - ++it1; -! } else if (it2->end <= it1->begin) { // no overlap - it2 first - only2 = true; - ++it2; -! } else if (it2->begin == it1->begin && it2->end == it1->end) { // equals - overlap = true; - ++it1; - ++it2; -! } else if (it2->begin <= it1->begin && it2->end >= it1->end) { // 1 c 2 - only2 = true; - overlap = true; - ++it1; -! } else if (it1->begin <= it2->begin && it1->end >= it2->end) { // 2 c 1 - only1 = true; - overlap = true; - ++it2; ---- 300,320 ---- - bool overlap = false; // point in both intervals_ and intervals - - while (it1 != intervals_.end() && it2 != intervals->end()) { -! if (it1->end_ <= it2->begin_) { // no overlap - it1 first - only1 = true; - ++it1; -! } else if (it2->end_ <= it1->begin_) { // no overlap - it2 first - only2 = true; - ++it2; -! } else if (it2->begin_ == it1->begin_ && it2->end_ == it1->end_) { // equals - overlap = true; - ++it1; - ++it2; -! } else if (it2->begin_ <= it1->begin_ && it2->end_ >= it1->end_) { // 1 c 2 - only2 = true; - overlap = true; - ++it1; -! } else if (it1->begin_ <= it2->begin_ && it1->end_ >= it2->end_) { // 2 c 1 - only1 = true; - overlap = true; - ++it2; -*************** -*** 346,356 **** - typename vector<Interval>::const_iterator it2 = intervals->begin(); - - while (it1 != intervals_.end() && it2 != intervals->end()) { -! if (it1->end <= it2->begin) { // no overlap - it1 first - ++it1; -! } else if (it2->begin < it1->begin || it2->end > it1->end) { // no C - return false; -! } else if (it2->end == it1->end) { - ++it1; - ++it2; - } else { ---- 346,356 ---- - typename vector<Interval>::const_iterator it2 = intervals->begin(); - - while (it1 != intervals_.end() && it2 != intervals->end()) { -! if (it1->end_ <= it2->begin_) { // no overlap - it1 first - ++it1; -! } else if (it2->begin_ < it1->begin_ || it2->end_ > it1->end_) { // no C - return false; -! } else if (it2->end_ == it1->end_) { - ++it1; - ++it2; - } else { -*************** -*** 370,376 **** - ++it) { - if (it != intervals->begin()) - strm << ","; -! strm << "[" << it->begin << "," << it->end << ")"; - } - strm << "}"; - return strm; ---- 370,376 ---- - ++it) { - if (it != intervals->begin()) - strm << ","; -! strm << "[" << it->begin_ << "," << it->end_ << ")"; - } - strm << "}"; - return strm; -diff -crB openfst-1.3.4.orig/src/include/fst/minimize.h openfst-1.3.4/src/include/fst/minimize.h -*** openfst-1.3.4.orig/src/include/fst/minimize.h 2013-01-24 06:36:23.000000000 +0400 ---- openfst-1.3.4/src/include/fst/minimize.h 2013-11-21 15:59:08.539136087 +0400 -*************** -*** 134,140 **** - typedef typename A::Weight Weight; - typedef ReverseArc<A> RevA; - -! CyclicMinimizer(const ExpandedFst<A>& fst) { - Initialize(fst); - Compute(fst); - } ---- 134,147 ---- - typedef typename A::Weight Weight; - typedef ReverseArc<A> RevA; - -! CyclicMinimizer(const ExpandedFst<A>& fst): -! // tell the Partition data-member to expect multiple repeated -! // calls to SplitOn with the same element if we are non-deterministic. -! P_(fst.Properties(kIDeterministic, true) == 0) { -! if(fst.Properties(kIDeterministic, true) == 0) -! CHECK(Weight::Properties() & kIdempotent); // this minimization -! // algorithm for non-deterministic FSTs can only work with idempotent -! // semirings. - Initialize(fst); - Compute(fst); - } -*************** -*** 315,321 **** - typedef typename A::StateId ClassId; - typedef typename A::Weight Weight; - -! AcyclicMinimizer(const ExpandedFst<A>& fst) { - Initialize(fst); - Refine(fst); - } ---- 322,334 ---- - typedef typename A::StateId ClassId; - typedef typename A::Weight Weight; - -! AcyclicMinimizer(const ExpandedFst<A>& fst): -! // tell the Partition data-member to expect multiple repeated -! // calls to SplitOn with the same element if we are non-deterministic. -! partition_(fst.Properties(kIDeterministic, true) == 0) { -! if(fst.Properties(kIDeterministic, true) == 0) -! CHECK(Weight::Properties() & kIdempotent); // minimization for -! // non-deterministic FSTs can only work with idempotent semirings. - Initialize(fst); - Refine(fst); - } -*************** -*** 531,543 **** - void Minimize(MutableFst<A>* fst, - MutableFst<A>* sfst = 0, - float delta = kDelta) { -! uint64 props = fst->Properties(kAcceptor | kIDeterministic| -! kWeighted | kUnweighted, true); -! if (!(props & kIDeterministic)) { -! FSTERROR() << "FST is not deterministic"; -! fst->SetProperties(kError, kError); -! return; -! } - - if (!(props & kAcceptor)) { // weighted transducer - VectorFst< GallicArc<A, STRING_LEFT> > gfst; ---- 544,550 ---- - void Minimize(MutableFst<A>* fst, - MutableFst<A>* sfst = 0, - float delta = kDelta) { -! uint64 props = fst->Properties(kAcceptor | kWeighted | kUnweighted, true); - - if (!(props & kAcceptor)) { // weighted transducer - VectorFst< GallicArc<A, STRING_LEFT> > gfst; -diff -crB openfst-1.3.4.orig/src/include/fst/partition.h openfst-1.3.4/src/include/fst/partition.h -*** openfst-1.3.4.orig/src/include/fst/partition.h 2013-01-24 06:36:23.000000000 +0400 ---- openfst-1.3.4/src/include/fst/partition.h 2013-11-21 15:59:08.539136087 +0400 -*************** -*** 43,50 **** - friend class PartitionIterator<T>; - - struct Element { -! Element() : value(0), next(0), prev(0) {} -! Element(T v) : value(v), next(0), prev(0) {} - - T value; - Element* next; ---- 43,50 ---- - friend class PartitionIterator<T>; - - struct Element { -! Element() : value(0), next(0), prev(0) {} -! Element(T v) : value(v), next(0), prev(0) {} - - T value; - Element* next; -*************** -*** 52,60 **** - }; - - public: -! Partition() {} - -! Partition(T num_states) { - Initialize(num_states); - } - ---- 52,62 ---- - }; - - public: -! Partition(bool allow_repeated_split): -! allow_repeated_split_(allow_repeated_split) {} - -! Partition(bool allow_repeated_split, T num_states): -! allow_repeated_split_(allow_repeated_split) { - Initialize(num_states); - } - -*************** -*** 137,152 **** - if (class_size_[class_id] == 1) return; - - // first time class is split -! if (split_size_[class_id] == 0) - visited_classes_.push_back(class_id); -! - // increment size of split (set of element at head of chain) - split_size_[class_id]++; -! - // update split point -! if (class_split_[class_id] == 0) -! class_split_[class_id] = classes_[class_id]; -! if (class_split_[class_id] == elements_[element_id]) - class_split_[class_id] = elements_[element_id]->next; - - // move to head of chain in same class ---- 139,154 ---- - if (class_size_[class_id] == 1) return; - - // first time class is split -! if (split_size_[class_id] == 0) { - visited_classes_.push_back(class_id); -! class_split_[class_id] = classes_[class_id]; -! } - // increment size of split (set of element at head of chain) - split_size_[class_id]++; -! - // update split point -! if (class_split_[class_id] != 0 -! && class_split_[class_id] == elements_[element_id]) - class_split_[class_id] = elements_[element_id]->next; - - // move to head of chain in same class -*************** -*** 157,165 **** - // class indices of the newly created class. Returns the new_class id - // or -1 if no new class was created. - T SplitRefine(T class_id) { - // only split if necessary -! if (class_size_[class_id] == split_size_[class_id]) { -! class_split_[class_id] = 0; - split_size_[class_id] = 0; - return -1; - } else { ---- 159,169 ---- - // class indices of the newly created class. Returns the new_class id - // or -1 if no new class was created. - T SplitRefine(T class_id) { -+ -+ Element* split_el = class_split_[class_id]; - // only split if necessary -! //if (class_size_[class_id] == split_size_[class_id]) { -! if(split_el == NULL) { // we split on everything... - split_size_[class_id] = 0; - return -1; - } else { -*************** -*** 163,180 **** - split_size_[class_id] = 0; - return -1; - } else { -- - T new_class = AddClass(); - size_t remainder = class_size_[class_id] - split_size_[class_id]; - if (remainder < split_size_[class_id]) { // add smaller -- Element* split_el = class_split_[class_id]; - classes_[new_class] = split_el; -- class_size_[class_id] = split_size_[class_id]; -- class_size_[new_class] = remainder; - split_el->prev->next = 0; - split_el->prev = 0; - } else { -- Element* split_el = class_split_[class_id]; - classes_[new_class] = classes_[class_id]; - class_size_[class_id] = remainder; - class_size_[new_class] = split_size_[class_id]; ---- 167,189 ---- - split_size_[class_id] = 0; - return -1; - } else { - T new_class = AddClass(); -+ -+ if(allow_repeated_split_) { // split_size_ is possibly -+ // inaccurate, so work it out exactly. -+ size_t split_count; Element *e; -+ for(split_count=0,e=classes_[class_id]; -+ e != split_el; split_count++, e=e->next); -+ split_size_[class_id] = split_count; -+ } - size_t remainder = class_size_[class_id] - split_size_[class_id]; - if (remainder < split_size_[class_id]) { // add smaller - classes_[new_class] = split_el; - split_el->prev->next = 0; - split_el->prev = 0; -+ class_size_[class_id] = split_size_[class_id]; -+ class_size_[new_class] = remainder; - } else { - classes_[new_class] = classes_[class_id]; - class_size_[class_id] = remainder; - class_size_[new_class] = split_size_[class_id]; -*************** -*** 245,254 **** ---- 254,269 ---- - vector<T> class_size_; - - // size of split for each class -+ // in the nondeterministic case, split_size_ is actually an upper -+ // bound on the size of split for each class. - vector<T> split_size_; - - // set of visited classes to be used in split refine - vector<T> visited_classes_; -+ -+ // true if input fst was deterministic: we can make -+ // certain assumptions in this case that speed up the algorithm. -+ bool allow_repeated_split_; - }; - - diff --git a/sci-misc/openfst/files/openfst-20080422_beta-gcc-4.3.patch b/sci-misc/openfst/files/openfst-20080422_beta-gcc-4.3.patch deleted file mode 100644 index 8eb3116d0..000000000 --- a/sci-misc/openfst/files/openfst-20080422_beta-gcc-4.3.patch +++ /dev/null @@ -1,83 +0,0 @@ -diff -Naur -Naur OpenFst/fst/bin/main.cc OpenFst-nu/fst/bin/main.cc ---- OpenFst/fst/bin/main.cc 2008-03-17 17:42:00.000000000 +0200 -+++ OpenFst-nu/fst/bin/main.cc 2008-10-20 16:30:36.000000000 +0300 -@@ -18,6 +18,8 @@ - // Classes and functions for registering and invoking Fst main - // functions that support multiple and extensible arc types. - -+#include <cstring> -+#include <climits> - #include <iostream> - - #include "fst/bin/main.h" -diff -Naur -Naur OpenFst/fst/bin/Makefile OpenFst-nu/fst/bin/Makefile ---- OpenFst/fst/bin/Makefile 2008-03-17 17:42:00.000000000 +0200 -+++ OpenFst-nu/fst/bin/Makefile 2008-10-20 16:31:12.000000000 +0300 -@@ -15,7 +15,7 @@ - FSTLIBMAIN=libfstmain.$(LIBTYPE) - LIBS=-lfstmain -lfst -lm -lpthread -ldl - CC=g++ --OPT=-O2 -+OPT=-O2 -fPIC - CFLAGS=-I../.. $(OPT) -DFST_DL - LDLFLAGS=-Wl,-L$(LIBDIR),-L$(BINDIR) - LDRFLAGS=-Wl,-rpath,$(LIBDIR),-rpath,$(BINDIR) # empty on macosx -diff -Naur -Naur OpenFst/fst/lib/compat.h OpenFst-nu/fst/lib/compat.h ---- OpenFst/fst/lib/compat.h 2008-03-17 17:41:56.000000000 +0200 -+++ OpenFst-nu/fst/lib/compat.h 2008-10-20 16:25:49.000000000 +0300 -@@ -27,7 +27,7 @@ - #include <map> - #include <string> - #include <vector> -- -+#include <cstring> - #include <ext/hash_map> - #include <fcntl.h> - #include <pthread.h> -diff -Naur -Naur OpenFst/fst/lib/Makefile OpenFst-nu/fst/lib/Makefile ---- OpenFst/fst/lib/Makefile 2008-03-17 17:41:56.000000000 +0200 -+++ OpenFst-nu/fst/lib/Makefile 2008-10-20 16:23:05.000000000 +0300 -@@ -2,7 +2,7 @@ - SRCS=fst.cc properties.cc symbol-table.cc compat.cc - OBJS=fst.o properties.o symbol-table.o compat.o - CC=g++ --OPT=-O2 -+OPT=-fPIC -O2 - CFLAGS=$(OPT) -I../.. -DFST_DL - LIBTYPE=so # "dylib" on macosx - SOFLAGS=-shared # "-dynamiclib -flat_namespace -undefined suppress" on macosx -diff -Naur -Naur OpenFst/fst/lib/randgen.h OpenFst-nu/fst/lib/randgen.h ---- OpenFst/fst/lib/randgen.h 2008-03-17 17:41:56.000000000 +0200 -+++ OpenFst-nu/fst/lib/randgen.h 2008-10-20 16:44:33.000000000 +0300 -@@ -23,6 +23,7 @@ - #include <cmath> - #include <cstdlib> - #include <ctime> -+#include <climits> - - #include "fst/lib/mutable-fst.h" - -diff -Naur -Naur OpenFst/fst/lib/symbol-table.cc OpenFst-nu/fst/lib/symbol-table.cc ---- OpenFst/fst/lib/symbol-table.cc 2008-03-17 17:41:56.000000000 +0200 -+++ OpenFst-nu/fst/lib/symbol-table.cc 2008-10-20 16:21:16.000000000 +0300 -@@ -17,6 +17,8 @@ - // \file - // Classes to provide symbol-to-integer and integer-to-symbol mappings. - -+#include <cstring> -+ - #include "fst/lib/symbol-table.h" - #include "fst/lib/util.h" - -diff -Naur -Naur OpenFst/fst/lib/vector-fst.h OpenFst-nu/fst/lib/vector-fst.h ---- OpenFst/fst/lib/vector-fst.h 2008-03-17 17:41:56.000000000 +0200 -+++ OpenFst-nu/fst/lib/vector-fst.h 2008-10-20 16:21:25.000000000 +0300 -@@ -21,6 +21,8 @@ - #ifndef FST_LIB_VECTOR_FST_H__ - #define FST_LIB_VECTOR_FST_H__ - -+#include <cstring> -+ - #include "fst/lib/mutable-fst.h" - #include "fst/lib/test-properties.h" - diff --git a/sci-misc/openfst/metadata.xml b/sci-misc/openfst/metadata.xml index 2d4fb61e6..8b44b5491 100644 --- a/sci-misc/openfst/metadata.xml +++ b/sci-misc/openfst/metadata.xml @@ -4,4 +4,8 @@ <maintainer type="person"> <email>flammie@gentoo.org</email> </maintainer> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> </pkgmetadata> diff --git a/sci-misc/openfst/openfst-1.8.1.ebuild b/sci-misc/openfst/openfst-1.8.1.ebuild deleted file mode 100644 index 16c275e8e..000000000 --- a/sci-misc/openfst/openfst-1.8.1.ebuild +++ /dev/null @@ -1,30 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DESCRIPTION="Finite State Transducer tools by Google et al" -HOMEPAGE="http://www.openfst.org" -SRC_URI="http://www.openfst.org/twiki/pub/FST/FstDownload/${P}.tar.gz" - -LICENSE="Apache-2.0" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -src_configure() { - local myeconfargs=( - --enable-compact-fsts - --enable-compress - --enable-const-fsts - --enable-far - --enable-linear-fsts - --enable-lookahead-fsts - --enable-mpdt - --enable-ngram-fsts - --enable-pdt - --enable-special - --enable-bin - --enable-grm - ) - econf ${myeconfargs[@]} -} diff --git a/sci-misc/openfst/openfst-1.8.2.ebuild b/sci-misc/openfst/openfst-1.8.2.ebuild new file mode 100644 index 000000000..923a36f64 --- /dev/null +++ b/sci-misc/openfst/openfst-1.8.2.ebuild @@ -0,0 +1,30 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DESCRIPTION="Finite State Transducer tools by Google et al" +HOMEPAGE="http://www.openfst.org" +SRC_URI="http://www.openfst.org/twiki/pub/FST/FstDownload/${P}.tar.gz" + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +src_configure() { + local myeconfargs=( + --enable-compact-fsts + --enable-compress + --enable-const-fsts + --enable-far + --enable-linear-fsts + --enable-lookahead-fsts + --enable-mpdt + --enable-ngram-fsts + --enable-pdt + --enable-special + --enable-bin + --enable-grm + ) + econf ${myeconfargs[@]} +} diff --git a/sci-misc/pqdump/Manifest b/sci-misc/pqdump/Manifest new file mode 100644 index 000000000..f738c3ede --- /dev/null +++ b/sci-misc/pqdump/Manifest @@ -0,0 +1,119 @@ +DIST adler-1.0.2.crate 12778 BLAKE2B a1dc17786adae945ac09d3525e609ed944e6465690787bbb831a1b9d53793cba1989793d0a5606d5d23ee20d36457923d451b1b3530c9ec7072a487aa3e55bbd SHA512 7ab190d31890fc05b0b55d8e2c6527a505e06793d5496be0b3831e0513412f9ba97f8148f6f68ed0770fa9cd980a5092d885e058becf1d5506b7c74b82674aa1 +DIST ahash-0.8.3.crate 42416 BLAKE2B 84836a4e33451012ff32c1a1a90500d87eb7ce649b60dff4eecfb0d25b9782a186376c154673c3121b154ff4616016d1718dfd687b88f4772c2c89eeb2f119b6 SHA512 cf2d2f1201ac0969cf4e2a0c47090bee971b2287ac44b5e091c90a9eced03cf6ff56d7900cc0f529d4acedc30bd400261c15e50efabdd1731f79951b449af53e +DIST alloc-no-stdlib-2.0.4.crate 10105 BLAKE2B afa0bfeb7df1d742edb412dca4c22957fc21c2a1be21c64c58503d4b943c06e3163d0f3c90525b25323b8dc38e6c64136ec4f9608758c5c6f3bd07c2c033ee74 SHA512 6518856fa524ee0fe8e04cf133c11028efcf2f6a28f3a70e401566a4eb343c954dba34aec2a02c0d0359757dfb5dcf48279610646215eea190d699708d838904 +DIST alloc-stdlib-0.2.2.crate 6693 BLAKE2B a22faf3482e416664f2e104f5f45c4e6d116a42b890216b80102e266f7a3a3accd2933aeca71650a4c4626e3d9da76b6488ffc9ea2ae4229cdfbf1ce9ca6c7cf SHA512 9c4169052ad460af2be6f2a128056661b2f26da0122877f13fcd4f4f3e2e9537783cb2b2bec47af43569629639aa8ad507ab010833982e5d942f5b26cfd46c14 +DIST android-tzdata-0.1.1.crate 7674 BLAKE2B 4385a4875aadaacd5284a9ca7d1bf8a7bf14bf8925d1563d52fbabacc3af2c1ea08bfcf77106f3648f4fa052ac295158a21e7a0131d31eb9aecd99ea4ba20055 SHA512 4294024c21ddd0090c42c8eedf708d40d917f55ad5a4cb7aa3e64cfb6551b6df60f2e36bc08620c1d2fc8c7ba7207411518ee5c8635f60ed8ad9efdd458a2077 +DIST android_system_properties-0.1.5.crate 5243 BLAKE2B 86f68ec3bdabf8c6ec47881d794970f08a9eefc7417fc8a2bf4fe9faf9bdd2a2024a94adb0cbf96673409f5fbbd4d0111a1ac371339e7a90a277b6cd5003524e SHA512 b09f51339f9772c0e2e4241b36cf51573c6b96b19ffc1fbbc94b1c1d1d2fdfe8eac3134af54174a675ab05d18ef4f6bcb2c7fcc20114bbeef6e17e3692202191 +DIST anstream-0.5.0.crate 19646 BLAKE2B 770dc99092e1c48ad5c1658e83abff3b8c9e0915e360048bfe0fe04faf61991e01e88ca4adca23533bf11fe078066e351778661128d69381756688341022f29d SHA512 8e285cc8f92708cf9482e7b4dc84dd891e5ec0bd8c57894c6bb368eede1127b7b903adb4c40b37287e3644535cc60c92662951c2c8fb5b92e10f49ff5374d359 +DIST anstyle-1.0.2.crate 13983 BLAKE2B 4274b101d1cab2b62f9bb7637dab35f4b16e8c08a080355a2ea53e2b7b353ff230aa77fb3a244e0d6ff0dcd27abe5895eb306c630aa0822d0c608f041d4abfea SHA512 09220abfc844192ca698589897845752e02666b4ecd6529af4cde9f260ef36694e6e631c7503fc0e438ac72c88c419043b78399385cb248e789e86404503935a +DIST anstyle-parse-0.2.1.crate 24802 BLAKE2B 6304a56c6a9fbaf1bb4d1d177b2315684345dc9d71c35836f9544145364f8d6eb56e25c03076690c594ab7db5914501acb569f6c136952e59c93179ced527fb2 SHA512 5c8fc7d88ffc3a6e78340ffe0f3c2d72e865512030ade4509de9c673eba955c536bb1873dac11f6ba11cc8367fb30c67451ed65d19f81507c9e917c702bfd176 +DIST anstyle-query-1.0.0.crate 8620 BLAKE2B 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b46085e324a6fb90ef4f6198154e2f45d58b91302f07b0e7ec3394183e1981d8e25c2d617425bb656756988cac57fdee15d6de3510e6e0b3ea1fe450ff06b8df SHA512 e312842abd713b5dd750ae92dbac297136291bef22b95572b52141c7d991f9d8bc84dc605f30c062a9cdd42d610ba5eb2f8e1ce3a8489f4ba816fca5eca7e5d8 +DIST brotli-decompressor-2.3.4.crate 192085 BLAKE2B 8ae8a47410215cbae102bbf19aa87f05e8739d6fe31e8eaff25948b1b4138ffed36e699947be30faf0b48891a010c10aafa835065cbd9a31f0c2628564a02359 SHA512 2698f1d9fc33ae37efc4587a448255320c864d1bba498ead93c5e28167ef696bcb5ddec9d4292b5fde93c3acddb7e99b453d6507780d0034e325bd20e5222c62 +DIST bumpalo-3.13.0.crate 82114 BLAKE2B 62a930b165e853aeeb40558079f570c75ed13ff5e8436d99309dc6252aa28ae69d327c4b438913d6c7543bc156f2714f0c1e80d759ea0d44babe24ef0f268ac0 SHA512 419368d6ca37474c2867751fe5706d0c747326bebce323d571cfc07ee0f022d8e8a7ef5692091b0fa804995b081998dafc55da19a53e51135a767bc0afdb9605 +DIST byteorder-1.4.3.crate 22512 BLAKE2B d39c546ba7346df315297fc53da4bfc77ecb1f38567ddb788549ee31cae2719a8bc0b7d1f1705abb3cff033aa57af004987d90748f5a31765273b3223a011c0d SHA512 8c8000eb8ecf40351c9ce36a3a8acd7a02f81786d1b11aab85adfeffa0f2267ed74df29b2ca5d1d38128484d1d3cad2b673aa0d0441dcd0620dfd3934bb888fa +DIST bytes-1.4.0.crate 58080 BLAKE2B 99a9d343424e04649bd209bf2a6c3a089a6cc9fdb799968f8c3a711189328e4499df2e09cc6a2a8ce05d2cc668149b364cf30cb3b09e96e21d50a39519c2f49f SHA512 502c63b9fdcd36ed28ede55a63cd359dc7b28658ecd43020511d17d48d7c34e45aa8ff7e4b17770f12197451040c2b724fe68d2aa3ab4f81c9171d052f2aa000 +DIST cc-1.0.83.crate 68343 BLAKE2B 33245b33fa845ea2f36da36e3830ec835f937e4319865b357ee9d5ea29a0f9f8392eadb38bf1d95e3c15ed201e561acaa87aedcef744f8db3dabff87a96c7f02 SHA512 742a248c3a7547bb220a0b9c97b67a831fab9b4ac21daa08c85a3966b9fe576088def33e16132fcabec9a2828a6fc437088bb045bfc98b2cea829df6742565a7 +DIST cfg-if-1.0.0.crate 7934 BLAKE2B e99a5589c11d79d77a4537b34ce0a45d37b981c123b79b807cea836c89fc3926d693458893baca2882448d3d44e3f64e06141f6d916b748daa10b8cc1ae16d1b SHA512 0fb16a8882fd30e86b62c5143b1cb18ab564e84e75bd1f28fd12f24ffdc4a42e0d2e012a99abb606c12efe3c11061ff5bf8e24ab053e550ae083f7d90f6576ff +DIST chrono-0.4.26.crate 191501 BLAKE2B eae49ee247607995c28463b8c3e2119497141e69d19a756c408f2b72d94bea39397ea2d0d3cd2ccbf1348ef973dd8bae6d29a0d0590e8dd34633f365a9170adb SHA512 2b66faf4d8374cfb0485710ceb2c9c1ce63aa6f9670e405a0810af4aca01c57d8dcd198a1f4cad498d5efd89e00003ba1b4f0bab599422af4f9bd6fb74494c47 +DIST clap-4.4.0.crate 54523 BLAKE2B 0292f888fc6426d4e79fbc82fe382be091c222371d2920cfca93cce9a16b3781d7d9bdddb1be62c4593a18d1bc0be0424139ef26745cb26e2ffbe33e684e30df SHA512 359d61374fe40f00a3b3af0e2962e80829cdd34f91b05c7c2347cf58568913037acda79409e44b25f7529901def008c0da0acf5837f784acc45d14936172f2eb +DIST clap_builder-4.4.0.crate 162489 BLAKE2B 0856a43db80c074ee98477a5a83260b56c8fbf73b00855e0120969fb643211955403045c7354878d4774d81df2e3035b9aa361172cd5286adf164565391f6d8b SHA512 2a79dda8d5dc4a0fc7d43f714d003096bacbb6a2c58f5085732f1a9b73d5f8f6346f4d9195a2e5a8d683cc206d59e54e400c9c748c0bc7abb176f6ed62bb3c33 +DIST clap_derive-4.4.0.crate 29055 BLAKE2B 1cc5364e48025c21dbf72808270ae6c9c1d130307a5e8047335ffc2bb6153a98e55967d11a04fbe2fcb8afb4cca230ec0f637dfb5023309270e62b145bf73ab4 SHA512 4c8fc71e2480a93b98c723a1282e68047acace1474fdbd1f6cf76fd6fe95d1564d0929a336da4eed090da0f119f029d087d38e95c05f0f078158c755eabb01a0 +DIST clap_lex-0.5.1.crate 11793 BLAKE2B 8e3d2dc120401fdd0cf0bf069119c8b7eafa13e5f682c56499062fc09acc05f443caafa6fca791ea53e693a83de69e98fd0488726a4170db037c37118ce0edf1 SHA512 ea5e49e9a8536093f7de89be30add7c3d880b232b0ce393b0429fd4402db2518036998689817bdfd472b6400224fd3c42fec1b5f8538dc433c31dadeb6281e80 +DIST colorchoice-1.0.0.crate 6857 BLAKE2B a0818be1299717461ffc1bcfb6fc53a0b3b645aa8c45fb72e045cf2d876fa207948610e58d6a837aad24838ea9616e80b0558ca3eae03fdf9bc4c03a8e5ba52f SHA512 53363f2889cd8e8a3b3ed10c48356896c0daa72f3c12c9c7804707ab0dbc07c0e34ef52fa4f0fb1647311ce5913168c1bf62c2407ff86a33f765a9e6fccad551 +DIST comfy-table-7.0.1.crate 72831 BLAKE2B af07dc0551c133dc8d8e29375055eb7092c93f02c9ba62e4cf67e66eb3678e34161da2394efdbcd4554037feb51dc2209e1bcb4e2fc8de1840a1cb68121fd48d SHA512 4ce73693e659ad12fed827b7b6e6e2260577f25eb41849dc66375e032fcd0dcf9928aca6101fb3f4327100e6c0875ca91ac7d9d17572ae0d5cd09c0e27c42d55 +DIST const-random-0.1.15.crate 6699 BLAKE2B 2580963485d51a910a23d4d5723a0a1da66788328d4988f39f9ef50d89625f8d07707eac7caee2dae803772b1b6e93961dfe9471ca8b821eca377e27a79ad600 SHA512 efda06434f62ad74eca1a8768de065367a6e2466b98fade93a6714834b71092c9009219f92969da233b329bc4bcf630944fbf666bc5fb852aacd4dfddc881c40 +DIST const-random-macro-0.1.15.crate 6680 BLAKE2B 597bfb60bcf1e9007abf0f81e4d9f2a328622a8379b91898826f8409ec72345cccaab8bab9aad850d47d19f3cfb4f669aad24f142dd4679849e1248428fb2874 SHA512 2dfc7248fab80463df8e848855dc91e82810cb302e047ac6a5c4afd6140784b86203f3a9f30559079d26b6f29fa3974b367ec4aa78b9d00f1d79339703163d9d +DIST core-foundation-sys-0.8.4.crate 17725 BLAKE2B 8afe47838dc91c8848c0d6a96a604149e5f0762228dbc10c17b85e4e9cd2c3928712bd0b28e1071f5fd6fd76d4ef972cb86c6c929246fb6e84577776933a8ac7 SHA512 15da472316d6decc213e4e5f08ecd22a108ebefe427b890741de4f9199614f19123e64329da76de5e8b4c9ff74ffc31738fd929acc1460fc757b4aa1fd3fdbb6 +DIST crc32fast-1.3.2.crate 38661 BLAKE2B ce3762b03d24d5367d89738991c060f4b3af7840e0a7ac7fc17d01ed438caf964bbaefad0fc4d0c438dafa5a578429ddd353c71197f8b54b1ec441395f2f7ee0 SHA512 a683943e252afdb1b9d626a07533ed11cf7a63af603c19640056c5d2b9c884ad9aff33ac54c0853ffca2f6cf94b0730eae6c05abf3e53e55e709d180c8152357 +DIST crunchy-0.2.2.crate 2995 BLAKE2B 74ddf8c5e0deb2ceab65c20a2743e1230739ac6aa3af60c9e867a7852270697a1278b7dee00df8949fc4268f9756a4a098df1211ab3b3e31a122652c3ba0a6fb SHA512 36dc0aebc41a3aac5f1b178a7e61b65bcd9bb5c8539b2024f79428200f7c62daa7098af55c6ab0765febd2f8969bd6c0ac8096f73cdc0958e5c4e4eb6a4f7025 +DIST flatbuffers-23.5.26.crate 23943 BLAKE2B 30b05e7463f2e1146834c74f69bec341d0894a9e3e07a7311f0029c093f08798bb25ae3ff96abbe66b05ba37ad3f8cafce1ff2eb656ff99ed34b22e87a309885 SHA512 b4d6caeec11c9c731ac1ee8b88b72dc1b2c2b0a6a6351732686b26fbd89c966db8ab389a37cb0556e097ca43224372ef0fbac5d4628bed9af9032499c65e20f1 +DIST flate2-1.0.27.crate 73460 BLAKE2B 5603848098ac02c9c83893df79ea9d9ad3df5b7e02ffa155ac74602bda7e28e14e6b7de2ff321b38d24fa3741ccea8a4c811abb47690cc295f90d4cf2bdd0bbf SHA512 e76e76444686433acabd16513e6e5860d4d6fa53a810f37266f36900f154acacac6dcd77b0373599a6d33a09175f5f02146d84726b982c59a78926950e19ff09 +DIST getrandom-0.2.10.crate 34955 BLAKE2B 8e7b8554ae360484ceca2a05f834c2664b08f41cbc6c955663e1f8f22fb5750481518bf1c7b49f49223a99a66914ef013347b9186acc97a20249f3222a13f9d4 SHA512 82af9e0417bff9272ed0478be4ac90426405ce210014b21899c6b95fde1b16893bf46295388ff5f13fa712a04c99c46b770fab83f41a1343af1590a86ca8da3b +DIST half-2.3.1.crate 50257 BLAKE2B 073192254d98ea786b450eb4e29d36c3a661ee2ac6e57b8f303a7da483ac60451de59a91fb4d4be3fab23ceb109674416162f8224d3e9bc05883e4f998182225 SHA512 b29acbca7b8f8fed6392346d03c710dad0f51cb2e358e7ea74a3aad4e10ffd22edb4154a56f877adc375da831a7597b51f7049335c0781a1b1110103e5eafc35 +DIST hashbrown-0.14.0.crate 116103 BLAKE2B 24bab03e8a8cb7623b92282c83bf8acaf0752c696ee1c010249e3ebb3646e7549d8d6d798b02c9d5b621afbebba7320f8a859d9a1af1523dbd46377b857dbb5f SHA512 f0fbdf81517f59a0b67f792a4097f1131d346b2b4cbda93590749cef7f9f1c9029e0e182f58c23b74d3028f7502c30b9593c1eb4da37f95388d74b14582b8959 +DIST heck-0.4.1.crate 11567 BLAKE2B 520aeea740cfa30b0cca12f73594ffa655f32959673b1c9caaca1ea0162e455546ae3033881394c0ba0516bcd5c9a997da02162e1585522d665813b9096eabd9 SHA512 8c80e959d2f10a2893f9a71994720f90747742bb5b61fc0a539eed3ea5679b140c48fd7f7690d7122cd6af5f7f20a19d412e3569fe741c6d31f6b2ce1e0b80e8 +DIST iana-time-zone-0.1.57.crate 19785 BLAKE2B 2304a63e4d3a477125ed07fccd5a84832f775c4a0fbd60a995e6f1850aaf3f5047c6f70975c9f6334f96def12770d470677e1f536e9817f8ab1df8a312622cfe SHA512 79bc0fe559dce022cd3c15ffc3b6f870c14a40de6d5a61b4a5a6ad28fe7efce82a16ac5102073a3510f3ba683843475f7fb8a4029bbafbc1cc25e48b98ce2fe8 +DIST iana-time-zone-haiku-0.1.2.crate 7185 BLAKE2B 37fa14b589ff092377b9271c414d4e584c5a531f13f70ac48df26df3cc03353db635b4630ba192fc65b800cce11823e91b91f03dfad85e4bed55aa18398156cb SHA512 448224ecafa935472ff6f0aab7cb71f9dabdbe71569c4b94fcc65baea925ef48841577687c9a31106a1826c2105e8dd73c748e9d27fd002648e5b0ce838af6b2 +DIST integer-encoding-3.0.4.crate 12446 BLAKE2B bcdb01101c3af348c299ccdf54ad006c7cee26570639cd390d42a98a40b84f3a5906a5de95a301e22633a62f57a9aaec038cbdc8f73a78d17c1ef5dbb127fcd5 SHA512 453686fa64aae578c5f8954ee1b34dcd895f6757a3c71dfa7eb944da85cab7c39498bb6b42aac93e1df473cb52de07316beedf59ade63a4dcba921c1dbce2ee3 +DIST jobserver-0.1.26.crate 22645 BLAKE2B 44bcc15330268ea29650e58605c7f21c35108eb64b790c005968955238e948d27b3d12e6bb06bfc0eb4a3fe5f9e5322bc0657200212bf87e08d9e043e008a5a8 SHA512 ad3ebb693018928daf399e918ce35ed0d4e643cfb5c78bde04697e41dc8adf2861023ea1cf2c5033a3026048ca0ebeb7f2f57a966ba8e420558e42dde8d494f7 +DIST js-sys-0.3.64.crate 80313 BLAKE2B 7cf5dcb2b9e0b63cb82771c9e98518a4cda70372c5aed07866a07d2aa51274622357e4b5a665499328f5a3c38f7c515303da50421bad4a496fbb658e2132325f SHA512 a4f389a4eb45c2122e7bcf365dccdce8fcf14b1b521b8b839746bba8783296e2f1b959d73bdd874743f49c61a24c4077dec52f63cc7d594cd42e9cd6ea9c2e64 +DIST lexical-core-0.8.5.crate 26680 BLAKE2B 71f3cc95f47fa636f68d6d25612a47d4a178e2ffe484aa66760e78fb71e55633c055892647decaac08120d1b8b3b79d80d1a23d46a74d13b5e52d6b912839ea0 SHA512 f98d2b5afd331c6f4f599d24599ed8791ee3628a2fa2b8172b698cfe9a180e1ccd2da4dca4dd33fc76ef3417114c580399106d01a8d6153b45b38bceacee1018 +DIST lexical-parse-float-0.8.5.crate 180161 BLAKE2B 881e4db32a21c26a1919fd1373aef1ea16a6fca3d799edb18ff0c9e4a79d481f8ade7a93f9ded2a660ad10cf815eb757f6eec7887945f8203c467e700af7a9a3 SHA512 ef012cbf18f2e306724dd700ac259aaa73b44f6c4531377deb9979c80d31ae66fc1a8b2671bd677e0ebfad8f77e9a5cf25707c67a1c5b1f554953c036cb39d46 +DIST lexical-parse-integer-0.8.6.crate 33647 BLAKE2B a0ebd7a51c271a163796b0f55bb85e16830bf06e26e3f10d9b13dc5b65af590c77f47fb64360a8738c5ad4be6e6932d58e83e1594a80c067859645c35b907c53 SHA512 e9a814d2928bf5bb2d9dce53e26c65356191c9e21c3aa0e674d58ed879aa52293272f3897f64372d996a3f8c471b0f59348ad48f15a21c2f35ed15f522ac2daa +DIST lexical-util-0.8.5.crate 85152 BLAKE2B 42a968c6f9d20cb4cb10906399d37d6581b425eadb31439fec4a71395819133249c4fb75b1d962100e77ba35b6f6b4cd428d5b5c161b405b22333ee390e671a6 SHA512 449c7f2a22c109cd179937c36e14d91c742e1a837a85fcf4fb58c21f05317511d1281b564d216a34760ae54a0df2d0ff5caf49da4aa9d43a8d87fcec0033cc39 +DIST lexical-write-float-0.8.5.crate 100281 BLAKE2B d5885d793ddcb8414fc9cd3085f0a0360b683df093b458f09fa4cf1dd670fbca7d9f86a19eca3082b32c4eb224cc9ab24a526350af0f894907391833888ca56f SHA512 35afe75db2fb4664e335349978fb8376a2b6cad48000e06652a3d3ce0b5fdbc422679821389856729724babc6cfe08ac8a1511c06bb743709787a4a47f956fd4 +DIST lexical-write-integer-0.8.5.crate 55427 BLAKE2B 54bb11be6c9377518384ad843d90d3bd344edadb889e1049ca8b58e34862e6d2a6730cd772c38859372d1068e110fd67db147c2d4c90bdd9bdb232ced7be4710 SHA512 a749846f8beb9b01ce61473f6ce123afb1b9f6efd91428cfff1fbbdd77422867e6eed4cd04c3ef25cd2d5be59864fa0e213ce296735e4021ac4632634b345838 +DIST libc-0.2.147.crate 686772 BLAKE2B ab2f0c65d071d46b8b88149add1c8429237ef6d9e0563d56ee1adbf23e6147dbb57fb68fbd02498f8ec75327693237a47e5e5259615ce8b0d5ed7a03bbf4fffb SHA512 bfb3c230b59d623b98726f92b7c3f897b47ba3d22fe9834c15f5b4c1b662289aba35a0ae3acfc704ad74696db8c691ee007b9cc6fa03ae65a18eb6bedc81931e +DIST libm-0.2.7.crate 115688 BLAKE2B e180347d10847c40a88e43d321e08561df053e6fea0cea2cac480c4162c2f31d8697b4572a384edae323d43781d3c6462b2d77220dd71b2fd0da3a2757487db1 SHA512 b7adbf657be812451fc50cd5e5f92b7a71d43b4e48761bd2738d65498c9abad851f8e86d3be06ae75cf39c7798c23cafe767bc5fd40f596774e858f69fcb46d9 +DIST log-0.4.20.crate 38307 BLAKE2B cb9c9a401b49bd68c18d5e42f2ed94446f1aeb184caa23cefacad4ce54a2a357143af54a5595c45d6f3c3d20b054c451d9e6ccdc09c19cca99ffffdaf8bbfc72 SHA512 8661b0c71d3b7fc0d679aa3d7f06910e6d3da1c53862aa06526000e1bcaa0b0b068415a1a9ab317c318f00d15346dba8a4f5d2a60d8850790bed9cfaaf757b3e +DIST lz4-1.24.0.crate 13361 BLAKE2B e0ebfab2aceb6817fea87d703b9c63d7248156d6ff4a051b4d41beceb0462551e9b4b7250a1bba8724fafbb90ab3618aed115d3f2f90cf184013d4eac76e93d4 SHA512 971e6265f12306ad228841ab5b72cfb80f001e57c2e3a815a8fe4a343ee2d93cfef6155ad4ff019873555b7e843ddffb1b70e22a057bb79b4688903c9407bcbc +DIST lz4-sys-1.9.4.crate 354842 BLAKE2B ced6f5f681003284d6720f3bf4af4089b991320fc1ba52a445d67ae118a573edbba9dac656a4f04dab50e3d4ea8c1b32339f3413a5e590a597c2407a963da646 SHA512 a0cd903494db1089965f5316694eb23e219002c147aad68794d57e7206aff641824e54f25f7c4cbe08bb06a63e6f5ee4c44447aa7f7057c8467872d69c6f0b06 +DIST miniz_oxide-0.7.1.crate 55194 BLAKE2B 56afbe0c0b3eca98105ae2d507493f365353cce29a6b04910ff26bc75899400fdbd067756cbda7b3d86f047fb8f3d737de00043a4a7348a813cc43e45824e33f SHA512 5eb6ffe34a866403273ff0267ff7838aeb50722ca57a03d5a1d842a5f19a3b4af570b133a3b9d64d78eafe49e4b9732b92dd63fd9c6b0ce59b3295daf10f6a3c +DIST num-0.4.1.crate 9522 BLAKE2B a7235566f657ea9dd3c15d4cf5ce85ac94f9f0e15ef5f4dd4f6bc7f8f09b9f654635a61785dfafef56dea980ee1f7441ea6fa366e51b9db707992a6b9d036bf9 SHA512 ea3b49c1b7a361266ee44213cd65765e58bfc51b9e805bdc71bed120a3b43f87ca60ba81b231a2c9a0ced617e10024d4e0961d8a3a52f26dbce1a22d550b7a84 +DIST num-bigint-0.4.4.crate 99369 BLAKE2B 09a44754e3a3d4f949b3714d96ddd7f3915164d611036675e3df421d6c0863e368eb0180978a4ec27fbfff529b4999d2593e411903516670c24c08fbed6a79de SHA512 0dcef3344a933509fdfe87d6adb0bb1bf67af3c692ccaeec5663a8f18ad0a251199ef9c7a24c25b95d1b255b413947e70f0a205669d549b13e54b6f4864ab3b5 +DIST num-complex-0.4.4.crate 29564 BLAKE2B 8ae65e8f2d87de96ec0a3d0e6d580584aff8cfbd0ebe56272dcf7cc5eea1b545fb9d597cbe4b1e25562b99a217a03ceef60e6cbda47c1e8cbd29b38d16cbe428 SHA512 632f9486df426d9254d2b6484c560b31e4ac0270de85878b9c4d14339a05ab318a90019f0724d2fac4d8496b03680650f899cedb1741c58eb7536cf3732db600 +DIST num-integer-0.1.45.crate 22529 BLAKE2B 4da3e801f71ba8f92c692497e200bfc8d32183c94eaad91260683b09f4697c03175fec7cff5a9ff3782d5db5d514d74f22f7a61a102c0f0d2e67a7a4b4f29222 SHA512 731bdc09c3af7f9d8b171041f2957aa60facef93b06886000d8ba60d410aabbbee358d700bf31b2588b2e077464f290f24a0b712df7bb7f12972675b6c9bd735 +DIST num-iter-0.1.43.crate 10655 BLAKE2B 41ee6d80f38f0767e134835ac84dacee8b50395b29c3e620b74cf4a843cfedfa71dc690e787b291a2b08750cd8386f1dad768e1b506ce088df33cf9e51b90a8e SHA512 97ac20f16d4518c8cbe944e5c80089fa6bb75d4632fb9f3c9d9891aaddb0e0f2209f6e854317f3d3b41bfb330c9d3ed830f3797f0120d4b1863b1d6fa3b9c07b +DIST num-rational-0.4.1.crate 27889 BLAKE2B c6db5b2165eb341268cc8b81df44caf25a18242d0ff1cc0959444ed9a51ba9985c1238d6d79433c3927267ceb181da6d491bf282560db6bafd7768b79ec65842 SHA512 a7547ca663543e9da9e18dd079762cde371b85d55874a54d6b343ba775a9373392c85cebad511c53b5af5db298bd5d57ccef6161c1c28587a6c9fa2c5962a0bd +DIST num-traits-0.2.16.crate 50130 BLAKE2B 1101d28cb4dce477657684a068792b94c7008a965e655edbabfeff51cbe6f008450dc6d7e4fc5dc4fe9c3ee8623ed77a7bde83ce2f68e75d618295fe6cebe0a8 SHA512 2ef65e2f6275b1000f611cc4d019b2f4846a8964b54d9b96462da10e3ac9edbf3d1de82e40094c76f7f5205740361b0eb0ced414bcddbaba5955144f728c6f94 +DIST once_cell-1.18.0.crate 32969 BLAKE2B a08d5beee50a7add28bd9e50b18709e7b34574f0f55f80909d5efb7ac5917e5f30bdcf3fb43ddd0a4f420a427390c7ffe1cc1c7191a3a1d939bc6e3139e6eef7 SHA512 9328968afdf3535b2d9e0113d75afa725259d76994ef2e1948ad7efa4ec8a65bac7cfdc31b749d5cd55ad4e28d2e28ac57b871e3067b89182453c7e2413a13b8 +DIST ordered-float-2.10.0.crate 15589 BLAKE2B 76561b2ab32b61ae69bef039f5f4636a05533cb8002b894ea18ce776ada1b5911c3067af2318126f359a305d7a9d3844053be62af1cbd2c3c9c1f45443a1cc9c SHA512 cb883ddd723d1bedfe13d16c9546dcb84d17d4fb1c6dc6d632a0c385d80b0b881694b3364a406e5d7f073c5a7e9e80810f343dd1d6f22df6188322b3e89cf77f +DIST parquet-46.0.0.crate 413516 BLAKE2B ccc95d99d5ac4f948404916920bd1a05fdc1bc340160dff894f28efe772b25d47aa2737f92fe82b48eec894990f972442a4260f04dbf2493e9de4f3767084956 SHA512 2bd2d7b69c7ea09528eb5dd6f216db4db9197ee99234151ab635221860d5d30e6383ccad71c9437bf2bc8a165021ece953bd221f1f8355954cda06038b0834e9 +DIST paste-1.0.14.crate 18157 BLAKE2B 35e8548611c51ee75f4d04926149e5e54870d7073d9b635d550a6fa0f85891f57f326bdbcff3dd8618cf40f8e08cf903ef87d9c034d5921d8b91e1db842cdd7c SHA512 3a793f0e5e773a7f7defc798a4c17ae9a40d715144632ea6cb0a8c785e14c4212046491df016bb9838281f8eaf327a79f01c1e2ac5f26785c028bc880faff9ee +DIST pkg-config-0.3.27.crate 18838 BLAKE2B 1295eb4f08751b3663cb2c7c2753f29bf2ccd80f4e5856909fe10b6f006c37fb9672c9518b9b416546469faa18821512673a66543c0bd1e848bddabc456d0a90 SHA512 41e9b8d4fce6b8244c2ac8566318a001b481bd42a182f1a832c81ce93c6a023e18af03aa3500b134c30195219d35080433bdba69b2594e9665081debfbb4533a +DIST pqdump-0.1.0.tar.gz 10707 BLAKE2B 331578f96328015147c9ba7d679559e85fac6b831ac5a6a72d578f7499f90516e09741e59d08f3bca646187a3891ec903d34fee94799a23da705ccab69da826c SHA512 d8f0171e868c03e994490c7fc43f9da3b73dc5c14b02eac08ea31f41a19bf4bfa818eda37c0d5c64e7df3cd6ae7f2f446e6146e7070e6ee8187d5e8822e00acb +DIST proc-macro-hack-0.5.20+deprecated.crate 15045 BLAKE2B fb7b9fa57ad64f2920e801482bfccc762bb7b2c8c1db7da32f393c7b47414fab37234c8a408a4ca9d7072a541df22b07775fc509f76f352fb6be9fe822f84dfd SHA512 278e786f8e0c93e346de900666b3d55d366324167a2e5e553565870c4444bfe661cf8c151a29cbd3176a4905ec49d69cffb81ae1e4a129f30404f930972c4b43 +DIST proc-macro2-1.0.66.crate 43575 BLAKE2B 9eb3e816b00fcf625c280ba14ad269f5893d0523473a24de07c21945f6f932fbd08efb3c339b35d903245510e3f065e1478439b024a325f2bb9f97bc7bcbb18d SHA512 85f5a762f9411142e5ac28144bd380f07f0633ed2e44d8a2545be9fb8f42abaca6b5d45631b4be83b8e8b9beca7438bc52f25615c3a410a3a1249474b1aca407 +DIST quote-1.0.33.crate 28090 BLAKE2B 77c4b166f1200e1ee2ab94a5014acd334c1fe4b7d72851d73768d491c56c6779a0882a304c1f30c88732a6168351f0f786b10516ae537cff993892a749175848 SHA512 c1e76c3c017e8554eebe309f8167fd56fce931981c06798aa85a0cc6d64a9cba6ab103f5a1324e69c6f9ca5dc47a8e31ff2e847850542748697afcd265b5939c +DIST rustc_version-0.4.0.crate 12175 BLAKE2B 6fda2ce03eab45d7193fa0d70175cc7ffb56b7be85fb1314092bdcfd3948ea145420569ace3a47218a4a2a6e44a818862cea6dd8cfb945475496f63b591c29da SHA512 f66da7c6efe431db06cd01180d84ba67fcd38f8cd6ef693762957c00ccc2211f23c08079d7f184776e08f28d2d6ca3bdb5f5016f7de245c6193d4722891ba1db +DIST rustversion-1.0.14.crate 17261 BLAKE2B db30d01914059a893bdb4c448ed0bf04852085c2d948bfbed8819a1d2317c34133cf609abdd806ad628b86974a9c1ab9d09f79743cb8e13257ef32cd444f49c6 SHA512 466d753c28c4899ab3da3e9f3366f7ecc435d484f51e0c07acfa5f3367af0de27ea3bc75efda22159b4990c976b1466a27e7c31c834c72a87d8234318357454b +DIST semver-1.0.18.crate 29703 BLAKE2B b1867f552ac87968d895c5e49123bcce0f8aa0ad384e421e5ac88bd04ae203ed6b731d5c77fb8488ec6601f1f02a8f2a207a9d21f1cc66d433032628f5d7beda SHA512 698dcd37b354cfd6ee452dce02d16051f23088ce53f0b4d099e1e4ad0f9350996f0b9b2e1c3ac7d5ed258accd92773266892e945fcae28055d4671c7ae5aac02 +DIST seq-macro-0.3.5.crate 13332 BLAKE2B 2e93de606214852f2d5818398565770d01425fa2cd8361397e877dfba2c890e472d46eebe2c8ea2483f99dd783c8e80383f700b81dab3cc019cbea977f4ec96d SHA512 5eea67d40e6c6217512140791dba33e0909bdef6ddbc09ab14ebf5ec862126be68413e0c4ea34dda416ef1a9b2e64e32d7c69ae14dff44a7965b04606b6ed596 +DIST snap-1.1.0.crate 33163 BLAKE2B f9441def95039050ff4cee05771524cc966959300d1206e472c26728213eabc64716da00273ce254e2504e83d7542a45f92d13d1cafd1028f9b7cd833e8b18c4 SHA512 3d374ece917ab052b260e2a6b5bd509c94b8545601b910c964368612055ba5cf7b748f23873f2ba5adcc47f0f4eb6063e52f6d4ba186653d43e5f5d03c0363b9 +DIST static_assertions-1.1.0.crate 18480 BLAKE2B 358dd5ac413d06f62da0388e2016c5fcb8ec68fd7dceb0dbbcb97665c032b7509b7e083c20701648b6a9174485f117c02682ae4bde7ef037e80a85cdf6a0c86e SHA512 46d0e35f77941dee6f60f574c130472248063dc38494c1c4f84f7c048244cc2a58a86fe17c0990e3f0f01406b75ed385a13d00058612b27cf0e867c8d31c92ee +DIST strsim-0.10.0.crate 11355 BLAKE2B bcb25ad0a7284e24e4f17ebe0ccb621bdc4118e499b50b094d98aa7e8fcc0b96716c9953c3516ce7ea78309d41d424892ded595259696a5bbffdcb07802b5c2f SHA512 78b318532addfcf5c1ccc1e14539e258aab9d3cd893cc45d82342549bde838c177d90f13c560671f8f32929af47d0b467db35e6876bd7697d8b3f9e055aeeac1 +DIST strum-0.24.1.crate 5636 BLAKE2B 81959b4ed8b78313bcd370eca0de10dd86b63c27eeacab66afb6e0c620bf1a13b66ee4a06ff90ce09b46dfd29d8ce32218414900a077ddcdbd8debfb05de243c SHA512 d842464b762790f4b785e494f72f7bae47b5a068cd06ddaad7a491d1abff53fa9cde280b06bbbb6b39a3a8f350a2384080ec4b3e4f16226cb076b1df153e6197 +DIST strum_macros-0.24.3.crate 20696 BLAKE2B fa86022cd1f701d8755fbf3e6356a38d46f4f168a1abd19d1d8fa63cbecf41746165791955c8cf1fba86cadf85ddb427ffd17bb360567187b55dfb9a899503c1 SHA512 8276343808afe71d68d7984d5a223a4fc630df0adb5a547cbcc6912fbffcf7e4ad38f115888a2dd3a8443d6fa7b9c7726318d4f5d1ab43f463dd97ec20df9134 +DIST syn-1.0.109.crate 237611 BLAKE2B e827445d00c79a8eeb91eacde472f1987addd6ce9e1df95d7abf6446a77ff4173a8006845f3ae71c1da47193cfb72e0ead9a6d6bad2573be12c17e90735d9ad9 SHA512 12816b9e8cf984024b2fbce9f0ae14cf94d4d2c06f08cc54fb793ce78770bb4cc1288eb7df0ba5e8e937756e1e8e295c53fe07a0c5dde1ea8ddba03b6203b37d +DIST syn-2.0.29.crate 241664 BLAKE2B 5b339433249d7ee17b032cc9ecb118169957d91f438619940aeba0003ab0015b01cc6afb00656b5492539a5396325ec16c37e33764b00d6f9b8dc6b5b5e6a9f0 SHA512 a6319ee743a7690c7858da8492ffb6a963d102beba07009e82b08082d33ac8e8ea2675bdfc3ac3684392b3bc3d7f2624983dc508dd8b8f1fb9a57ec8a5b82828 +DIST thrift-0.17.0.crate 45286 BLAKE2B 93fb20bd82fe6320c4348779fcb84d83feb050b7686fde4a7082a4658152f514621ddffe294d0c53718d85506b12659ac03e7cc808bfbc983f36ade5d44fd0c5 SHA512 760fc20570ec63f5b60350518a4acbfe5f85f93416c846b84ffdc757510792e9cf5623c290b98715dd35def7076a38a3239ae7d7099f8b52a9643749c222c934 +DIST tiny-keccak-2.0.2.crate 20129 BLAKE2B 105a2d2af36cc053cd95721ea563108f33b8a3feb2ae84c75a04a65ed5d548dfe35d8b2e48977a82f725c0ebcf914f21157c547f4a74bb4d98c2e894385139be SHA512 c0219f23361eb07e0a68575c461a36b7286d9bdebae89080d9e259178d402b0c7762ccf33e65a16951ea168392322c44a24eb55189cf143e22d09d6dfc4acec1 +DIST twox-hash-1.6.3.crate 21842 BLAKE2B 67c261b2b0a93293717a4e2e07dc11df2abde09da6fe713b9d04917ace73de1b59b8d4fd9449ab46cb7cf496fad1e440effdfa1fae6f5cae4ca78af8cd019c42 SHA512 f7ce63e6e5ca79ce9330caf40b32578a5d2088c5d8ed371604268760d6e212d447d9e3a95378378a283024155bccdaea47597902c488a94c5d5f79770baec8fc +DIST unicode-ident-1.0.11.crate 42067 BLAKE2B 3c7cac3d2bf1cbf1cf04716a482f130123e8e6940f7a90a17bc62fca44ac0069688165538f5329b95a72f735b594cfb85e3250738393ffd1b53cb0cd95077d89 SHA512 9682bbee339fb987c9d0bb6a54406d37b28b5c3587372d406402e4341900fec97e3234cd03b5c98b90b6378fd533dc452cac3de90d3ade19c4b09657e4abf6df +DIST unicode-width-0.1.10.crate 18968 BLAKE2B 6174e307fd3ee290d0a5d1d31233baaa5315cdb73f19b8580718e9f9eb04cfd3aeaeb474af1e50c4b9fecc6fc777937dedc527c9dc9ed14ccf42af099e591f31 SHA512 9836a8d489d18ea1ecfe1957ed6d5da7dce825e138cd1848aef093fa8d2eb83fcf01eabb1a2446df4f5ede4e67316e9e81b5d58b59d4e8c5d67870e8fa5dca3b +DIST utf8parse-0.2.1.crate 13435 BLAKE2B a1c111d7ffc60690f2aaa86f034c66ba1abe4e126f1774a4377d41eba3269369862f57515af387ea785d69a8adf46338b5e53761b5ee6f4f4380473f4d9cab0a SHA512 51fba8f1e7eb74b7020fd831e30a67fc8353ac2ee07335c8c3374a5570ac8117f165f6905d4b7f0360095b7b5ed3e739001d02a8cc3c89195baf2cd679136050 +DIST version_check-0.9.4.crate 14895 BLAKE2B fa1fa4008af165bfc1fdbe560488afd9d232cfafee94104fbcc4cbc52f234849bff9ddfa88109a1ac682f6d9c1d86b0459893d223f64e65adc08966aaf93dc89 SHA512 b172dc9a3759a4a683ffc39b9a40b03b9974b626a088217de87090466cef695226557c226cf3e469b2b25ee7297b7eb0d7719878cab42457f80146a81943c0c8 +DIST wasi-0.11.0+wasi-snapshot-preview1.crate 28131 BLAKE2B fe501889f25d65e2d032f885cc50c4f8bf7dd70fd5cbc438de349838370d8699e9627b0a4fc76030ea9fe6d508f41d0c9928a875fdbc47e73bfb17241cf7b155 SHA512 043500ab28cd9cb779475255da5d109ebab7fccca72b64873dc28d77bc5a157ba8d96b9e8f05223b5b36c7089bb7b4ba87657fc69bac16b78972f897294a865f +DIST wasm-bindgen-0.2.87.crate 175052 BLAKE2B bf8cf4aa1786ac5c2ba76e80500b5c54313adf9690ef370e60b894401bd1b81416da7bb46b90c014412c96f30f995bd1e52cf7f3a6be1111aea40866e8178396 SHA512 0c3099155ef079d2b91d2d5b135243d687bf865cdd9ae9d97d8cc2eb4c9bf7439b66b28d5b1d7e95048e53be63ed4909b6b3f2427951348de25ca7abb7a03705 +DIST wasm-bindgen-backend-0.2.87.crate 26821 BLAKE2B e230aa256a1f681ab3ffd2c83c3f6a810c305bb79a5e1d806b8b2b9f54ef0babc83809f6153b9ca511faa4b122f80bd1cc9eb97e7ae3cb4cba9e2dc1c6bd0b51 SHA512 317ee2bdf85067cb7f4b4ed6ff475ff9e5063143e9b7c8a28572211c09025935815227c4afa8c92823ac92102562d4d34531aa4891d8c922048d37e27377ee94 +DIST wasm-bindgen-macro-0.2.87.crate 13897 BLAKE2B 0926975b0328cdd5525820358795b7b68b4ab9dc460715ed84e5d276e76e936057140efb1ba875acf25f3d2862e680f9827bd05cc47560d54f7ec673f30244cb SHA512 af366d8d853b280014cdf5286f3b1f6d7fb0837ce6e359a81cb6f85161537c8e2cd06d7f893c957f5bf1548d34084d33a213670b471937782b56033a23cb15a6 +DIST wasm-bindgen-macro-support-0.2.87.crate 20006 BLAKE2B d32dfc7231e4fbc226586e66063538208f9e299fbf803c4e2d1e1e61b4a22f51cc7509bdd269a44f072f9843a083ee84d2326408fb3211009ce93542c3fdc6ce SHA512 9390aa2767fed1027be168612c424d4c7cd4423addd83b79afd8c67886f66303ca4846e6454302ecc78b47bc62e8ee46849a4c0d3edb98849ce8476901424e33 +DIST wasm-bindgen-shared-0.2.87.crate 7248 BLAKE2B 0393ce9452119fd5f92836a76b28d3a697f91fb09de39d1af0a2a83e81d48bd4a17f39b48f15ae97edca3e361d4f8fedae8de04173c4ba1711decc73f64000d5 SHA512 cb9ff537554f56fd07052ddc4adc904a57ee64e13298df1dfca58b361ce163c34640e7dd9ed301ec1375f335dfa424230e22638ea7569ceb34aeca4505f6c008 +DIST winapi-0.3.9.crate 1200382 BLAKE2B cb5799749ccd935ea2d7068d953cecf19f543d9db7dc16ad4584bb7005373ada34937a3ced7225544d8bc765da599911c7a3190efefb3a25b7c1bb7123b4f673 SHA512 ff8b7b78065f3d8999ec03c725a0460ebc059771bf071c7a3df3f0ecd733edf3b0a2450024d4e24e1aedddaecd9038ce1376c0d8bbf45132068cf45cf4a53a97 +DIST winapi-i686-pc-windows-gnu-0.4.0.crate 2918815 BLAKE2B 4d357e4d30f9552972170d65b9a5358b69c46a3e772fe05efc22f3d4ffc1caeeaad7aacdc7abd503a7ad0545f8bd7d22bf351dcb6df76f812fa4d45c34d65df0 SHA512 a672ccefd0730a8166fef1d4e39f9034d9ae426a3f5e28d1f4169fa5c5790767693f281d890e7804773b34acdb0ae1febac33cde8c50c0044a5a6152c7209ec2 +DIST winapi-x86_64-pc-windows-gnu-0.4.0.crate 2947998 BLAKE2B 2ad1ea8b5fa07d544e910ccba043ae925269b76b26c9da356305b34b86741dd8b9aff0b9ffe3d562db4fcd7d7c46a11ce9e3168b782b1d89ae6881742b7ede82 SHA512 4a654af6a5d649dc87e00497245096b35a2894ae66f155cb62389902c3b93ddcc5cf7d0d8b9dd97b291d2d80bc686af2298e80abef6ac69883f4a54e79712513 +DIST windows-0.48.0.crate 11864177 BLAKE2B 39c0e4f058f68a829ee08721818a0b04287af20dfe6e03a125b75566b4c8a58b56557d685600f1f9c215811154f9782f12368d42848445d54dcf9bfd6471349d SHA512 7c906f885fa0a730f1cb1ef4e62f5b602a49d44343febe1d38fcd4cbc28e0342766983796042585fe457aa229333558715b6270e378946faa8f398a7ecc2af8c +DIST windows-sys-0.48.0.crate 2628884 BLAKE2B 551e900de4f67187ef034b60df9fd0e0d8f82a3100ef28e1eabd543ac129d882dc86ffcc1714071aba09e4cb2ae2d2f07ace1a32b99fd989ce525cf05991edab SHA512 bdf534bcf3face31e9ebe11427a911a53f89f4ff5eaea8cccd094e139bfe14b2aec602b1cab1df774794d999477439d9adc6b627a8e33c20334fc348ba2c47ed +DIST windows-targets-0.48.5.crate 6904 BLAKE2B 7396bb210f37bd51da86f39fca3425c8f6610721d5c4e94f9fafa0a8a8046303b3fcc6979146bcfaa32f4406d242a0455f6cbb220f84c6ff84650e755acf5223 SHA512 e079eeef255a046be7f8e6a31c14f7b230254ebcf05eed2944827bb3d2a0dc30940d87593cf544d5e7ef35f6312b99430efcfb01421d91b02bb9c4bef7d98709 +DIST windows_aarch64_gnullvm-0.48.5.crate 418492 BLAKE2B 5c6f7d73ad05740f0bac304ed1ef9b2ea63b0d6ca8f875552ae299a0b73b1557e8fe996f1c2b69be9f2df350c9288690f49ee62239a2896991364331d6c55462 SHA512 20158d31454488f6053d3ad7b97d7fc6eae6cf37e4ba0e50c28bd29b368505eed64199ae31104d5f97b66846be54e5ed25c0ad31ea850819205c573a31ac0996 +DIST windows_aarch64_msvc-0.48.5.crate 798483 BLAKE2B 60c466d6536426425a34b5ca20da97c8127ebeb4fb9b1363911165bada484f8913fcd50e90410b5661e0c27dbfe8f4eeaa62fb17d1f3566bfc82b6255e11619b SHA512 223f016c6f1a44dbc5c8a8428b39438f75380ea06951b7c26ed0877b19d79410c6fde5e4c7f2c839b6e76159131f39a1230e0e3a208dfc425ba9117e3665c4ff +DIST windows_i686_gnu-0.48.5.crate 844891 BLAKE2B fdc37cd74a4982056bf22fdb7b84e1c55dc838f3cb19ff3648730a77e673ef4ecc0380b3e4277bb8df2fcfa25f57b69014713d9e3ed27c28e19b25b3ea2ab774 SHA512 931ba5c1e4eb8ae73248e00d9611298d1c4b4b0dae719fdeb9243930cd420a103a7bc2738e0a4887c42c8f25728d6c5d64ad141dc092bc3f1d0f35dbe37d303a +DIST windows_i686_msvc-0.48.5.crate 864300 BLAKE2B 3d3ea8be55e2d6ced0eeda18abe1dffb925a1a78f456d683e4450d9f2fd287ad2e8494d65b2b770c677a12b3a60d10f0435e16c61880e3867c3657fd44892442 SHA512 70e2fb4fdb006a4cbd43ab2c7e940b277a15fb1790dfa2d1fc1f1fd18bead4886f6dc046e44326603e4894d988578917b8932aba5d9a6a4cc8424911cad9dc7e +DIST windows_x86_64_gnu-0.48.5.crate 801619 BLAKE2B aa7e7e6a6ff9f9553ada3a0a39a9aa798e9d995a8eef36e0b6fdb2a0db93ddecee5548970575271fe43aec74797a420d0ee231d503b5bad1bd999059261e0e33 SHA512 1d6056fae430b3d042bdff3c6217c76be4b8b9f5dada9bad06beaac2db7d7ab9b0a82e44f498ec88e61afa73e99f56d84d445dc3847732b9ce5d947e08485f74 +DIST windows_x86_64_gnullvm-0.48.5.crate 418486 BLAKE2B 12a2199d434617c1df1a839e9f435620ad64b40c579f6d0c3677553ad7a48e5765d12c266b04946402e15c92cff2e4ac4979ce2130750ef426e2672119680284 SHA512 c016d5b5e73832b61ff67929d92fa8c16e154656294357266ad29ce1f44db4ca2d2935dba31a6b571187dc838b1d22f1e3b41fefffd1d719a338439adf1646aa +DIST windows_x86_64_msvc-0.48.5.crate 798412 BLAKE2B 8abc0721e2fb337fe17c91d278947d36122d9045b839ba0cf3e690202d242265b676f23cc301da5f9d98c56ca4ecb76f7d6f072ee71bf986a1deca87020b90e5 SHA512 fa1c5cd14ca2ff0082e2504cf59d317dc4dc6f7138d35c12f95d4476a9c13d8b7f5537d0ee251eee7c99411ad31b22263171b7fbd391daa5d3ea3488ceaa61a0 +DIST zstd-0.12.4.crate 30434 BLAKE2B 39dc5c1aaee0c6973ec27ca3447f7d3f0460ca7382c46660c1c72ad9af9c9dc85778b6e0addb6ed90ffd90848f5da7006fae7c0d41c8915965707b923ed7b1cd SHA512 69b94d18982d7adbf0d3a79dc013c98af97ec2b10e10ef4cd6c15a89049f343fd83db3a79c393a43e9d12d8c071a728b8666680cc5a23817a126340ba9500715 +DIST zstd-safe-6.0.6.crate 20828 BLAKE2B 426bf142868de682082d3b5fb4ac711a96b963856af763f3cc4544aa5bac32f14fc4c40f3b95cf2e91e0145cb0a1c67823c258ceaab48d368c8d56ddc6f8f440 SHA512 33f8aee9c584a2abdd3d965fa9ff15fad310fc3f9d73e04d5a3a871c3b7e96b7a833cf563ef81656c9226ec793f42bb9c08b1c5cc53c9ead3e29802d8fcfbc6a +DIST zstd-sys-2.0.8+zstd.1.5.5.crate 736270 BLAKE2B 9ee3bae57279efca7305f6ac9456c71eb5714b595cf75b0faac7232c91f9df127c75c02f68021291ea01d6ab42a51a550d84cec246cd47bb8f502bbd32ceee09 SHA512 acfbf6c464678438bcab289c8be2e67a2bdfb910143d77363bf1ad5227dffc4b60e224388b7e59186fd4d1e017b63fef49734e99e383cbda19b82b4ed382fcd8 diff --git a/sci-misc/pqdump/pqdump-0.1.0.ebuild b/sci-misc/pqdump/pqdump-0.1.0.ebuild new file mode 100644 index 000000000..377b17549 --- /dev/null +++ b/sci-misc/pqdump/pqdump-0.1.0.ebuild @@ -0,0 +1,146 @@ +# Copyright 2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +# Auto-Generated by cargo-ebuild 0.5.4 + +EAPI=8 + +CRATES=" + adler-1.0.2 + ahash-0.8.3 + alloc-no-stdlib-2.0.4 + alloc-stdlib-0.2.2 + android-tzdata-0.1.1 + android_system_properties-0.1.5 + anstream-0.5.0 + anstyle-1.0.2 + anstyle-parse-0.2.1 + anstyle-query-1.0.0 + anstyle-wincon-2.1.0 + arrow-array-46.0.0 + arrow-buffer-46.0.0 + arrow-cast-46.0.0 + arrow-data-46.0.0 + arrow-ipc-46.0.0 + arrow-schema-46.0.0 + arrow-select-46.0.0 + autocfg-1.1.0 + base64-0.21.3 + bitflags-1.3.2 + brotli-3.3.4 + brotli-decompressor-2.3.4 + bumpalo-3.13.0 + byteorder-1.4.3 + bytes-1.4.0 + cc-1.0.83 + cfg-if-1.0.0 + chrono-0.4.26 + clap-4.4.0 + clap_builder-4.4.0 + clap_derive-4.4.0 + clap_lex-0.5.1 + colorchoice-1.0.0 + comfy-table-7.0.1 + const-random-0.1.15 + const-random-macro-0.1.15 + core-foundation-sys-0.8.4 + crc32fast-1.3.2 + crunchy-0.2.2 + flatbuffers-23.5.26 + flate2-1.0.27 + getrandom-0.2.10 + half-2.3.1 + hashbrown-0.14.0 + heck-0.4.1 + iana-time-zone-0.1.57 + iana-time-zone-haiku-0.1.2 + integer-encoding-3.0.4 + jobserver-0.1.26 + js-sys-0.3.64 + lexical-core-0.8.5 + lexical-parse-float-0.8.5 + lexical-parse-integer-0.8.6 + lexical-util-0.8.5 + lexical-write-float-0.8.5 + lexical-write-integer-0.8.5 + libc-0.2.147 + libm-0.2.7 + log-0.4.20 + lz4-1.24.0 + lz4-sys-1.9.4 + miniz_oxide-0.7.1 + num-0.4.1 + num-bigint-0.4.4 + num-complex-0.4.4 + num-integer-0.1.45 + num-iter-0.1.43 + num-rational-0.4.1 + num-traits-0.2.16 + once_cell-1.18.0 + ordered-float-2.10.0 + parquet-46.0.0 + paste-1.0.14 + pkg-config-0.3.27 + proc-macro-hack-0.5.20+deprecated + proc-macro2-1.0.66 + quote-1.0.33 + rustc_version-0.4.0 + rustversion-1.0.14 + semver-1.0.18 + seq-macro-0.3.5 + snap-1.1.0 + static_assertions-1.1.0 + strsim-0.10.0 + strum-0.24.1 + strum_macros-0.24.3 + syn-1.0.109 + syn-2.0.29 + thrift-0.17.0 + tiny-keccak-2.0.2 + twox-hash-1.6.3 + unicode-ident-1.0.11 + unicode-width-0.1.10 + utf8parse-0.2.1 + version_check-0.9.4 + wasi-0.11.0+wasi-snapshot-preview1 + wasm-bindgen-0.2.87 + wasm-bindgen-backend-0.2.87 + wasm-bindgen-macro-0.2.87 + wasm-bindgen-macro-support-0.2.87 + wasm-bindgen-shared-0.2.87 + winapi-0.3.9 + winapi-i686-pc-windows-gnu-0.4.0 + winapi-x86_64-pc-windows-gnu-0.4.0 + windows-0.48.0 + windows-sys-0.48.0 + windows-targets-0.48.5 + windows_aarch64_gnullvm-0.48.5 + windows_aarch64_msvc-0.48.5 + windows_i686_gnu-0.48.5 + windows_i686_msvc-0.48.5 + windows_x86_64_gnu-0.48.5 + windows_x86_64_gnullvm-0.48.5 + windows_x86_64_msvc-0.48.5 + zstd-0.12.4 + zstd-safe-6.0.6 + zstd-sys-2.0.8+zstd.1.5.5 +" + +inherit cargo + +DESCRIPTION="simple program to dump Parquet files" +HOMEPAGE="https://github.com/Berrysoft/pqdump" +SRC_URI=" + https://github.com/Berrysoft/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz + $(cargo_crate_uris) +" + +LICENSE="BSD Apache-2.0 Apache-2.0-with-LLVM-exceptions BSD CC0-1.0 MIT Unicode-DFS-2016 Unlicense ZLIB" +SLOT="0" +KEYWORDS="~amd64" + +DEPEND="" +RDEPEND="${DEPEND}" +BDEPEND="" + +QA_FLAGS_IGNORED="usr/bin/${PN}" diff --git a/sci-physics/apfelxx/Manifest b/sci-physics/apfelxx/Manifest new file mode 100644 index 000000000..b461f2a76 --- /dev/null +++ b/sci-physics/apfelxx/Manifest @@ -0,0 +1 @@ +DIST apfelxx-4.8.0.tar.gz 21695802 BLAKE2B f28d28bafed79ec679fd44bbd3cba668b108668dceaffbc80091a022d1884121a9d2fb08e89ae439663765877aadb7c214b6196d2ea35ad8c25ba545ec3492ee SHA512 23fcde7262637cbe0ff0173a530d0e2d3f39a9daa8b8757e4769c41c4af72569b0e0b8ab59ad5a8dc08ec7718d40bd34abed66671d2116f4242d06b6c2e7c1cc diff --git a/sci-physics/apfelxx/apfelxx-4.8.0.ebuild b/sci-physics/apfelxx/apfelxx-4.8.0.ebuild new file mode 100644 index 000000000..d31224fa3 --- /dev/null +++ b/sci-physics/apfelxx/apfelxx-4.8.0.ebuild @@ -0,0 +1,39 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +CMAKE_MAKEFILE_GENERATOR="emake" +PYTHON_COMPAT=( python3_{10..12} ) + +inherit cmake python-single-r1 + +DESCRIPTION="Object oriented rewriting of the APFEL evolution code" +HOMEPAGE="https://github.com/vbertone/apfelxx" +SRC_URI="https://github.com/vbertone/apfelxx/archive/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="GPL-3+" +SLOT="0" +KEYWORDS="~amd64" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" +RDEPEND="${PYTHON_DEPS}" + +src_prepare() { + default + cmake_src_prepare + sed -i "/prefix./s/\/lib/\/$(get_libdir)/g" CMakeLists.txt || die + sed -i "s#DESTINATION lib#DESTINATION $(get_libdir)#g" CMakeLists.txt || die +} + +src_configure() { + local mycmakeargs=( + -DCMAKE_INSTALL_PREFIX="${EPREFIX}"/usr + ) + cmake_src_configure +} + +src_install() { + cmake_src_install + python_optimize +} diff --git a/sci-physics/apfelxx/metadata.xml b/sci-physics/apfelxx/metadata.xml new file mode 100644 index 000000000..27c6de8e1 --- /dev/null +++ b/sci-physics/apfelxx/metadata.xml @@ -0,0 +1,18 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>alexander@neuwirth-informatik.de</email> + <name>Alexander Puck Neuwirth</name> + </maintainer> + <maintainer type="project"> + <email>sci-physics@gentoo.org</email> + <name>Gentoo Physics Project</name> + </maintainer> + <longdescription lang="en"> + APFEL++ is a C++ rewriting of the Fortran 77 evolution code APFEL. However, APFEL++ is based on a completely new code design and guarantees a better performance along with a more optimal memory management. The new modular structure allows for better maintainability and easier extensibility. This makes APFEL++ suitable for a wide range of tasks: from the solution of the DGLAP evolution equations to the computation of deep-inelastic-scattering (DIS) and single-inclusive-annihilation cross sections. Also more complex computations, such as differential semi-inclusive DIS and Drell-Yan cross sections, are easily implementable in APFEL++. + </longdescription> + <upstream> + <remote-id type="github">vbertone/apfelxx</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-physics/cernlib/Manifest b/sci-physics/cernlib/Manifest new file mode 100644 index 000000000..d8be46729 --- /dev/null +++ b/sci-physics/cernlib/Manifest @@ -0,0 +1,2 @@ +DIST cernlib-2023.10.31.0-free.tar.gz 39191038 BLAKE2B 941592a65f0c8d7d0c6c3907c96d8209568579dac455ed28657a5635677d73e6580f48667a641a6ca9dd296bf82a40f6a75c5fc801fcefb7f8e9101b4dcd3202 SHA512 d015f89942bab695444d37847a8138c3a8736ceeb6f4826c659553bf1ae5eab2a77b2871645a125ea189e62520856955070fbb3ed2d208d35f82ee8b8559d089 +DIST cernlib-2023.10.31.0.tar.gz 39547453 BLAKE2B f37686e4a43b969a8cb604874b6181adf8529b9fc383ccd2e42fc369f92d4693ca8db682bc58638cb58e9941cf22551cfec26b33075e15fc6a0b3fab3dcf7d82 SHA512 9bc866d08e3bce2f571f9f4e21e34ca6c99467088d4dce4cbc9b6c62d8ee2b9018668fd66795996a5f6abb1082ac9559cf08bc7f5201421dbffcdd0db9459008 diff --git a/sci-physics/cernlib/cernlib-2023.10.31.0-r1.ebuild b/sci-physics/cernlib/cernlib-2023.10.31.0-r1.ebuild new file mode 100644 index 000000000..326fadde3 --- /dev/null +++ b/sci-physics/cernlib/cernlib-2023.10.31.0-r1.ebuild @@ -0,0 +1,73 @@ +EAPI=8 + +CMAKE_MAKEFILE_GENERATOR="emake" +inherit cmake fortran-2 + +MY_P="${P}" +DESCRIPTION="CERN program library for High Energy Physics" +HOMEPAGE="https://cernlib.web.cern.ch/cernlib/" +SRC_URI=" + free? ( https://cernlib.web.cern.ch/download/2023_source/tar/${P}-free.tar.gz ) + !free? ( https://cernlib.web.cern.ch/download/2023_source/tar/${P}.tar.gz ) +" + +LICENSE=" + free? ( BSD LGPL-2+ GPL-1+ ) + !free? ( all-rights-reserved ) +" +SLOT="0" +KEYWORDS="~amd64" +IUSE="+free" +RESTRICT="mirror" + +RDEPEND=" + x11-libs/motif:0 + x11-libs/libXaw + x11-libs/libXau + virtual/lapack + dev-lang/cfortran + x11-libs/xbae + net-libs/libnsl + virtual/libcrypt:= +" +DEPEND="${RDEPEND}" +BDEPEND=" + virtual/pkgconfig +" + +PATCHES=( + "${FILESDIR}"/${P}-cfortran.patch + "${FILESDIR}"/${P}-ctest.patch + "${FILESDIR}"/${P}-man.patch +) + +src_unpack() { + default + if use free; then + mv ${P}-free ${P} || die + fi +} + +src_prepare() { + cmake_src_prepare + # cfortran.patch + # Remove cfortran.h since it is already installed from dev-lang/cfortran + # thereby we avoid collisions if e.g. sci-physics/root[fortran] is installed. + rm cfortran/cfortran.h || die +} + +src_configure() { + # docs follow rpm like spliting into packages cernlib, cernlib-devel, etc. + # we move them into a folder that agrees with gentoo doc structure. + sed -i "s#/doc/#/doc/${PF}/#g" CMakeLists.txt || die + cmake_src_configure +} + +src_install() { + cmake_src_install + # man.patch + # The CMakeLists.txt already compresses the manual before install + # therefore we install it manually and avoid QA problems. + doman contrib/man/man1/*.1 + doman contrib/man/man8/*.8 +} diff --git a/sci-physics/cernlib/files/cernlib-2023.10.31.0-cfortran.patch b/sci-physics/cernlib/files/cernlib-2023.10.31.0-cfortran.patch new file mode 100644 index 000000000..b4426b3eb --- /dev/null +++ b/sci-physics/cernlib/files/cernlib-2023.10.31.0-cfortran.patch @@ -0,0 +1,21 @@ +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 0b56fc85..ead47c54 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -735,7 +735,6 @@ add_subdirectory(code_motif) + ######################################################################## + set(CERNLIB_MMAP 1) + install(FILES +-${CMAKE_CURRENT_SOURCE_DIR}/cfortran/cfortran.h + ${CMAKE_CURRENT_SOURCE_DIR}/cfortran/comis.h + ${CMAKE_CURRENT_SOURCE_DIR}/cfortran/cspack.h + ${CMAKE_CURRENT_SOURCE_DIR}/cfortran/geant315.h +@@ -757,7 +756,7 @@ ${CMAKE_CURRENT_SOURCE_DIR}/cfortran/paw.h + ${CMAKE_CURRENT_SOURCE_DIR}/cfortran/zebra.h + DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/ COMPONENT libs ) + +-set(head cfortran.h comis.h cspack.h geant315.h geant321.h gen.h graflib.h hbook.h hbook_94b.h higz.h hplot.h jetset74.h kernlib.h kuip.h lapack.h lepto62.h minuit.h packlib.h paw.h zebra.h ) ++set(head comis.h cspack.h geant315.h geant321.h gen.h graflib.h hbook.h hbook_94b.h higz.h hplot.h jetset74.h kernlib.h kuip.h lapack.h lepto62.h minuit.h packlib.h paw.h zebra.h ) + + install(CODE "execute_process(COMMAND ${CMAKE_COMMAND} -E make_directory ${CMAKE_INSTALL_INCLUDEDIR}/cfortran/)") + foreach ( m ${head} ) diff --git a/sci-physics/cernlib/files/cernlib-2023.10.31.0-ctest.patch b/sci-physics/cernlib/files/cernlib-2023.10.31.0-ctest.patch new file mode 100644 index 000000000..b329bb900 --- /dev/null +++ b/sci-physics/cernlib/files/cernlib-2023.10.31.0-ctest.patch @@ -0,0 +1,31 @@ +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 0b56fc85..78a28e11 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -162,9 +162,10 @@ macro(CLATestTarget ast) + list(FIND a "<" NEEDSHELL) + list(JOIN a " " MYCMD) + if (NEEDSHELL STREQUAL "-1") +- add_test(NAME test${exec} COMMAND ${CMAKE_CURRENT_BINARY_DIR}/${exec} {MYCMD} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) ++ add_test(NAME test${exec} COMMAND ${CMAKE_CURRENT_BINARY_DIR}/${exec} ${MYCMD} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) + if (CERNLIB_ENABLE_MEMORYTEST) +- add_test(NAME memory_test${exec} COMMAND ${VG} ${VGOPTIONS} ${CMAKE_CURRENT_BINARY_DIR}/${exec} {MYCMD} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) ++ add_test(NAME memory_test${exec} COMMAND ${VG} ${VGOPTIONS} ++ ${CMAKE_CURRENT_BINARY_DIR}/${exec} ${MYCMD} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) + endif() + else() + add_test(NAME test${exec} COMMAND sh -c "${CMAKE_CURRENT_BINARY_DIR}/${exec} ${MYCMD}" WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) +@@ -182,9 +183,11 @@ macro(CLBTestTarget ast) + list(JOIN a " " MYCMD) + if (NEEDSHELL STREQUAL "-1") + if (CERNLIB_ENABLE_MEMORYTEST) +- add_test(NAME memory_test${exec} COMMAND ${VG} ${VGOPTIONS} ${CMAKE_CURRENT_BINARY_DIR}/${exec}/${exec} {MYCMD} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/${exec}) ++ add_test(NAME memory_test${exec} COMMAND ${VG} ${VGOPTIONS} ++ ${CMAKE_CURRENT_BINARY_DIR}/${exec}/${exec} ${MYCMD} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/${exec}) + endif() +- add_test(NAME test${exec} COMMAND ${CMAKE_CURRENT_BINARY_DIR}/${exec}/${exec} {MYCMD} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/${exec}) ++ add_test(NAME test${exec} COMMAND ++ ${CMAKE_CURRENT_BINARY_DIR}/${exec}/${exec} ${MYCMD} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/${exec}) + else() + if (CERNLIB_ENABLE_MEMORYTEST) + add_test(NAME memory_test${exec} COMMAND sh -c "${VG} ${VGOPTIONS} ${CMAKE_CURRENT_BINARY_DIR}/${exec}/${exec} ${MYCMD}" WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/${exec}) diff --git a/sci-physics/cernlib/files/cernlib-2023.10.31.0-man.patch b/sci-physics/cernlib/files/cernlib-2023.10.31.0-man.patch new file mode 100644 index 000000000..636943899 --- /dev/null +++ b/sci-physics/cernlib/files/cernlib-2023.10.31.0-man.patch @@ -0,0 +1,22 @@ +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 0b56fc85..0db67942 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -410,7 +413,7 @@ else() + COMMENT "GZipping to ${CMAKE_CURRENT_BINARY_DIR}/${m}.gz." + ) + endif() +- install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${m}.gz DESTINATION ${CMAKE_INSTALL_DATADIR}/man/man1) ++#install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${m}.gz DESTINATION ${CMAKE_INSTALL_DATADIR}/man/man1) + endforeach ( m ${man1} ) + + foreach ( m ${man8} ) +@@ -425,7 +428,7 @@ else() + COMMENT "GZipping to ${CMAKE_CURRENT_BINARY_DIR}/${m}.gz." + ) + endif() +- install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${m}.gz DESTINATION ${CMAKE_INSTALL_DATADIR}/man/man8) ++#install(FILES ${CMAKE_CURRENT_BINARY_DIR}/${m}.gz DESTINATION ${CMAKE_INSTALL_DATADIR}/man/man8) + endforeach ( m ${man8} ) + + #install(PROGRAMS ${CMAKE_CURRENT_SOURCE_DIR}/patchy5/yexpand.script DESTINATION ${CMAKE_INSTALL_BINDIR}/ RENAME yexpand.script${COMPSUFFIXBIN} ) diff --git a/sci-physics/cernlib/metadata.xml b/sci-physics/cernlib/metadata.xml new file mode 100644 index 000000000..dcbfb9b47 --- /dev/null +++ b/sci-physics/cernlib/metadata.xml @@ -0,0 +1,24 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>alexander@neuwirth-informatik.de</email> + <name>Alexander Puck Neuwirth</name> + </maintainer> + <maintainer type="project"> + <email>sci-physics@gentoo.org</email> + <name>Gentoo Physics Project</name> + </maintainer> + <longdescription lang="en"> + The CERN Program Library is a large collection of general purpose + libraries and modules maintained and offered in both source and + object code form on the CERN central computers. Most of these + programs were developed at CERN and are therefore oriented towards + the needs of a physics research laboratory that is general + mathematics, data analysis, detectors simulation, data-handling + etc... applicable to a wide range of problems. + </longdescription> + <use> + <flag name="free"> Use free sources </flag> + </use> +</pkgmetadata> diff --git a/sci-physics/collier/Manifest b/sci-physics/collier/Manifest new file mode 100644 index 000000000..709444249 --- /dev/null +++ b/sci-physics/collier/Manifest @@ -0,0 +1 @@ +DIST collier-1.2.8.tar.gz 933258 BLAKE2B 9849ae140ed055a24010f020920f377a78665cb6f2c16ba060082c3573594a2f5772779b4a5596d306220b49ec2ffb7249705c0f05ea4eb22784518acb1038a0 SHA512 119b597da04dcd529efc35b5f96d2b2ad1f2f4403c3d0521a24b49fba973c5557378b68994ea6d30ca92057d32a30a6de299b2c707d56c231d197f33632297d9 diff --git a/sci-physics/collier/collier-1.2.8.ebuild b/sci-physics/collier/collier-1.2.8.ebuild new file mode 100644 index 000000000..b50f9a279 --- /dev/null +++ b/sci-physics/collier/collier-1.2.8.ebuild @@ -0,0 +1,36 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +CMAKE_MAKEFILE_GENERATOR="emake" + +inherit fortran-2 cmake + +MY_P=COLLIER-${PV} + +DESCRIPTION="A Complex One-Loop LIbrary with Extended Regularizations" +HOMEPAGE="https://collier.hepforge.org/index.html" +SRC_URI="https://collier.hepforge.org/downloads/?f=${P}.tar.gz -> ${P}.tar.gz" +S="${WORKDIR}/${MY_P}" + +LICENSE="GPL-3" +SLOT="0" +KEYWORDS="~amd64" + +IUSE="static-libs" +BDEPEND=" + virtual/fortran +" +PATCHES=( + "${FILESDIR}/${PN}-1.2.7-mod.patch" +) + +src_configure() { + local mycmakeargs=( + -Dstatic=$(usex static-libs ON OFF) + -DLIB_INSTALL_DIR="${EPREFIX}"/usr/$(get_libdir) + -DSYSCONFIG_INSTALL_DIR="${EPREFIX}"/usr/$(get_libdir)/cmake/collier + ) + cmake_src_configure +} diff --git a/sci-physics/collier/files/collier-1.2.7-mod.patch b/sci-physics/collier/files/collier-1.2.7-mod.patch new file mode 100644 index 000000000..030900b5c --- /dev/null +++ b/sci-physics/collier/files/collier-1.2.7-mod.patch @@ -0,0 +1,40 @@ +--- a/CMakeLists.txt 2023-05-08 17:21:39.559979698 +0200 ++++ b/CMakeLists.txt 2023-05-08 17:43:20.599147534 +0200 +@@ -282,7 +282,36 @@ + message("Collier install include prefix: ${INCLUDE_INSTALL_DIR}") + message("Collier install library prefix: ${LIB_INSTALL_DIR}") + +-set(COLLIER_HEADERS "${CMAKE_Fortran_MODULE_DIRECTORY}/collier.mod") ++set(COLLIER_HEADERS "${CMAKE_Fortran_MODULE_DIRECTORY}/collier.mod" ++ "${CMAKE_Fortran_MODULE_DIRECTORY}/cache.mod" ++ "${CMAKE_Fortran_MODULE_DIRECTORY}/buildtensors.mod" ++ "${CMAKE_Fortran_MODULE_DIRECTORY}/coli_aux2.mod" ++ "${CMAKE_Fortran_MODULE_DIRECTORY}/coli_stat.mod" ++ "${CMAKE_Fortran_MODULE_DIRECTORY}/collier_aux.mod" ++ "${CMAKE_Fortran_MODULE_DIRECTORY}/collier_coefs.mod" ++ "${CMAKE_Fortran_MODULE_DIRECTORY}/collier_global.mod" ++ "${CMAKE_Fortran_MODULE_DIRECTORY}/collier_init.mod" ++ "${CMAKE_Fortran_MODULE_DIRECTORY}/collier.mod" ++ "${CMAKE_Fortran_MODULE_DIRECTORY}/collier_tensors.mod" ++ "${CMAKE_Fortran_MODULE_DIRECTORY}/combinatorics.mod" ++ "${CMAKE_Fortran_MODULE_DIRECTORY}/dd_2pt.mod" ++ "${CMAKE_Fortran_MODULE_DIRECTORY}/dd_3pt.mod" ++ "${CMAKE_Fortran_MODULE_DIRECTORY}/dd_4pt.mod" ++ "${CMAKE_Fortran_MODULE_DIRECTORY}/dd_5pt.mod" ++ "${CMAKE_Fortran_MODULE_DIRECTORY}/dd_6pt.mod" ++ "${CMAKE_Fortran_MODULE_DIRECTORY}/dd_global.mod" ++ "${CMAKE_Fortran_MODULE_DIRECTORY}/dd_statistics.mod" ++ "${CMAKE_Fortran_MODULE_DIRECTORY}/globalc.mod" ++ "${CMAKE_Fortran_MODULE_DIRECTORY}/globald.mod" ++ "${CMAKE_Fortran_MODULE_DIRECTORY}/inittensors.mod" ++ "${CMAKE_Fortran_MODULE_DIRECTORY}/master.mod" ++ "${CMAKE_Fortran_MODULE_DIRECTORY}/reductionab.mod" ++ "${CMAKE_Fortran_MODULE_DIRECTORY}/reductionc.mod" ++ "${CMAKE_Fortran_MODULE_DIRECTORY}/reductiond.mod" ++ "${CMAKE_Fortran_MODULE_DIRECTORY}/reductionefg.mod" ++ "${CMAKE_Fortran_MODULE_DIRECTORY}/reductiontn.mod" ++ "${CMAKE_Fortran_MODULE_DIRECTORY}/tensorreduction.mod" ++) + set_target_properties(collier PROPERTIES PUBLIC_HEADER "${COLLIER_HEADERS}") + + include(PackageConfigInstall) diff --git a/sci-physics/collier/metadata.xml b/sci-physics/collier/metadata.xml new file mode 100644 index 000000000..f863d8237 --- /dev/null +++ b/sci-physics/collier/metadata.xml @@ -0,0 +1,22 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>alexander@neuwirth-informatik.de</email> + <name>Alexander Puck Neuwirth</name> + </maintainer> + <maintainer type="project"> + <email>sci-physics@gentoo.org</email> + <name>Gentoo Physics Project</name> + </maintainer> + <longdescription> + A package for evaluation of scalar and tensor one-loop integrals + based on the FF package by G.J. van Oldenborgh. + It features an easy Fortran, C++, and Mathematica interface + to the scalar one-loop functions of FF and in addition provides + the 2-, 3-, and 4-point tensor coefficient functions. + </longdescription> + <use> + <flag name="static">Build static library</flag> + </use> +</pkgmetadata> diff --git a/sci-physics/feynarts/Manifest b/sci-physics/feynarts/Manifest new file mode 100644 index 000000000..d66304b21 --- /dev/null +++ b/sci-physics/feynarts/Manifest @@ -0,0 +1 @@ +DIST FeynArts-3.11.tar.gz 3146405 BLAKE2B d22a19faecaa3a87ebf48b035736a04a6ae9b28e47300240edac541cb86438781092bf0a16d84808fb0256cf7547ba9d04024934007fa017cab08811d6b2b41b SHA512 2032172c86316b1703c0ff0c9cc511db0b97d6268bde30b6948ea98c5f2b39996071675d25aba4ed65af99f0c6535bce4e5eca8ca942be3591f922937c4aa79b diff --git a/sci-physics/feynarts/feynarts-3.11.ebuild b/sci-physics/feynarts/feynarts-3.11.ebuild new file mode 100644 index 000000000..ecf46b127 --- /dev/null +++ b/sci-physics/feynarts/feynarts-3.11.ebuild @@ -0,0 +1,29 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +MY_PN=FeynArts +MY_P=${MY_PN}-${PV} + +DESCRIPTION="FeynArts renders Feynman diagrams and generates their topologies." +HOMEPAGE="https://feynarts.de" +SRC_URI="https://feynarts.de/${MY_P}.tar.gz" +S="${WORKDIR}/${MY_P}" + +LICENSE="LGPL-3+" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + sci-mathematics/mathematica + " +DEPEND="${RDEPEND}" + +src_install() { + MMADIR=/usr/share/Mathematica/Applications + dosym "${MY_P}" "${MMADIR}/${MY_PN}" + dodir "${MMADIR}/${MY_P}" + insinto ${MMADIR} + doins -r "${S}" +} diff --git a/sci-physics/feynarts/metadata.xml b/sci-physics/feynarts/metadata.xml new file mode 100644 index 000000000..14606c162 --- /dev/null +++ b/sci-physics/feynarts/metadata.xml @@ -0,0 +1,19 @@ +<?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> + <maintainer type="project"> + <email>sci-physics@gentoo.org</email> + <name>Gentoo Physics Project</name> + </maintainer> + <maintainer type="person"> + <email>alexander@neuwirth-informatik.de</email> + <name>Alexander Puck Neuwirth</name> + </maintainer> + <longdescription lang="en"> + FeynArts is a Mathematica package for the generation and visualization of Feynman diagrams and amplitudes. + </longdescription> +</pkgmetadata> diff --git a/sci-physics/feyncalc/Manifest b/sci-physics/feyncalc/Manifest new file mode 100644 index 000000000..9514cfd33 --- /dev/null +++ b/sci-physics/feyncalc/Manifest @@ -0,0 +1,2 @@ +DIST FeynCalc-9.3.1.tar.gz 4296784 BLAKE2B bb9e2e17ee8c51ec9417f900982af494e44a19cad651065d769820756056d6accfa8955da1c03dcc054e32c8ca5a5b1974594e77f95cc0a8e7100919783d20ad SHA512 3e7f4e87920e26712008754498f2d7e3a5873f6adf3e7dbea1e98f7f0f9ff20e1e08941b959e18143d3f602aa3f0c1ac4c574f450bcd6d2e8ad68e775e95aeee +DIST FeynCalc-9999.tar.gz 4298804 BLAKE2B a4b404aed41d510f32ddf5a242d0c6129174ace1eeb92a19c2cf6f9620f82b37f3b01709d063619567590d38d4506431b5d9af6fbf3fe1184c07c683c1f2d3b4 SHA512 30ef3f0249b9dd639e0d83767d1aaea272c6ce3083d0a36a96ced11c68bd4d9c499efcd95abb209d56cd8ae3142b925c6b723c541821c7856e4ac787c2c52e34 diff --git a/sci-physics/feyncalc/feyncalc-9.3.1.ebuild b/sci-physics/feyncalc/feyncalc-9.3.1.ebuild new file mode 100644 index 000000000..2f54f878b --- /dev/null +++ b/sci-physics/feyncalc/feyncalc-9.3.1.ebuild @@ -0,0 +1,43 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +MY_PV=$(ver_rs 1-3 '_') +MY_PN=FeynCalc + +DESCRIPTION="FeynCalc is a Mathematica package for computing Feynman diagrams." +HOMEPAGE="https://feyncalc.github.io/" +SLOT="0" +SRC_URI="https://github.com/FeynCalc/feyncalc/archive/refs/tags/Release-${MY_PV}.tar.gz -> ${MY_PN}-${PV}.tar.gz" +S="${WORKDIR}/feyncalc-Release-${MY_PV}" + +LICENSE="GPL-3+" +KEYWORDS="~amd64" +IUSE="+FCtraditionalFormOutput" + +RDEPEND=" + sci-mathematics/mathematica + " +DEPEND="${RDEPEND}" + +src_configure() { + mv "${MY_PN}/DocOutput" "${MY_PN}/Documentation" || die + if use FCtraditionalFormOutput; then + echo '$FCTraditionalFormOutput=True;' > "${MY_PN}/FCConfig.m" || die + fi +} + +src_install() { + MMADIR=/usr/share/Mathematica/Applications + dodir "${MMADIR}/${MY_PN}" + insinto "${MMADIR}/" + doins -r "${S}/${MY_PN}" + # copy permissions + for f in $(find "${MY_PN}/*" ! -type l); do + fperms --reference="${S}/$f" "${MMADIR}/$f" + done + # documentation are notebook(.nb) files + dodoc -r ${MY_PN}/Documentation/English/* + docompress -x /usr/share/doc/${PF}/ +} diff --git a/sci-physics/feyncalc/feyncalc-9999.ebuild b/sci-physics/feyncalc/feyncalc-9999.ebuild new file mode 100644 index 000000000..1c26d976e --- /dev/null +++ b/sci-physics/feyncalc/feyncalc-9999.ebuild @@ -0,0 +1,47 @@ +# Copyright 2020 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +# Copyright 1999-2020 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +MY_PV=$(ver_rs 1-3 '_') +MY_PN=FeynCalc + +DESCRIPTION="FeynCalc is a Mathematica package for computing Feynman diagrams." +HOMEPAGE="https://feyncalc.github.io/" +SLOT="0" +SRC_URI="https://github.com/FeynCalc/feyncalc/archive/hotfix-stable.tar.gz -> ${MY_PN}-${PV}.tar.gz" +S="${WORKDIR}/feyncalc-hotfix-stable" + +LICENSE="GPL-3+" +IUSE="+FCtraditionalFormOutput" +REQUIRED_USE="" +PROPERTIES+=" live" + +RDEPEND=" + sci-mathematics/mathematica + " +DEPEND="${RDEPEND}" + +src_configure() { + mv "${MY_PN}/DocOutput" "${MY_PN}/Documentation" || die + if use FCtraditionalFormOutput; then + echo '$FCTraditionalFormOutput=True;' > "${MY_PN}/FCConfig.m" || die + fi +} + +src_install() { + MMADIR=/usr/share/Mathematica/Applications + dodir "${MMADIR}/${MY_PN}" + insinto "${MMADIR}/" + doins -r "${S}/${MY_PN}" + # copy permissions + for f in $(find "${MY_PN}/*" ! -type l); do + fperms --reference="${S}/$f" "${MMADIR}/$f" + done + # documentation are notebook(.nb) files + dodoc -r ${MY_PN}/Documentation/English/* + docompress -x /usr/share/doc/${PF}/ +} diff --git a/sci-physics/feyncalc/metadata.xml b/sci-physics/feyncalc/metadata.xml new file mode 100644 index 000000000..826061ef4 --- /dev/null +++ b/sci-physics/feyncalc/metadata.xml @@ -0,0 +1,25 @@ +<?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> + <maintainer type="project"> + <email>sci-physics@gentoo.org</email> + <name>Gentoo Physics Project</name> + </maintainer> + <maintainer type="person"> + <email>alexander@neuwirth-informatik.de</email> + <name>Alexander Puck Neuwirth</name> + </maintainer> + <longdescription lang="en"> + FeynCalc is a Mathematica package for symbolic evaluation of Feynman diagrams and algebraic calculations in quantum field theory and elementary particle physics. + </longdescription> + <use> + <flag name="FCtraditionalFormOutput">Use TraditionalForm typesetting.</flag> + </use> + <upstream> + <remote-id type="github">FeynCalc/feyncalc</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-physics/formcalc/Manifest b/sci-physics/formcalc/Manifest new file mode 100644 index 000000000..6ac4c74b1 --- /dev/null +++ b/sci-physics/formcalc/Manifest @@ -0,0 +1,2 @@ +DIST FormCalc-9.10.tar.gz 32070519 BLAKE2B e789d7eea0cc92f27033373fd6516e94ec66d1780ae7bb1254537fa508640436a4595dbf09594a2cad8b4178d1e950806089ae4584bff0f2848674325a734212 SHA512 30519fcd6a9e616f6bfa23825056afdc27111605ca66e35f6baebac5bcb7ff43e07c7d40ed90157c584be82392fc85a32b769e637a793817377a8ffc5601af6d +DIST FormCalc-9.9.tar.gz 32059045 BLAKE2B 69e3d063bf746d86d02f63d3a1fdce314582b190bafc66d063a6f25575476fcb6b60121b9133f850ffd5d173e437b160a2661072051083b3f4affc48fcb4bda7 SHA512 9661a07fac13348de13ec09dc8f043df02ef9a5391be64217d432e04d4d82ad3dea94f43951f839fbe8947338bc0ab721a9a9ebdc0900979e16ea89d857c87c7 diff --git a/sci-physics/formcalc/files/formcalc-9.9-compile.patch b/sci-physics/formcalc/files/formcalc-9.9-compile.patch new file mode 100644 index 000000000..48be7f06e --- /dev/null +++ b/sci-physics/formcalc/files/formcalc-9.9-compile.patch @@ -0,0 +1,50 @@ +--- a/compile 2022-07-20 14:51:59.605328833 +0200 ++++ b/compile 2022-07-20 15:37:09.122446647 +0200 +@@ -96,7 +96,7 @@ + + mcc="REALCC=\"$CC\" CC=\"$t/fcc\" \ + REALCXX=\"$CXX\" CXX=\"$t/f++\" \ +-PATH=\""'$$PATH'":$t\" $MCC -st $MCFLAGS $CFLAGS" ++PATH=\""'$$PATH'":$t\" $MCC -st -g $MCFLAGS $CFLAGS" + + # Mma 5.1's mcc needs -lpthread for static linking + mclibs="-lpthread" +@@ -104,37 +104,28 @@ + cc="$CC $CFLAGS" + + make -f - << _EOF_ || exit 1 +-all: $DEST/tform$exe \ ++all: \ + $DEST/ReadForm$exe $DEST/ToForm$exe \ + $DEST/ToFortran$exe $DEST/ToC$exe \ + $DEST/ReadData$exe $DEST/reorder$exe + +-$DEST/tform$exe: $SRC/bin/$BIN/tform$exe +- cp -p $SRC/bin/$BIN/* $DEST/ +- + $DEST/ReadForm$exe: $SRC/FormCalc/ReadForm.tm + $mcc -o $DEST/ReadForm$exe $SRC/FormCalc/ReadForm.tm $mclibs +- -strip $DEST/ReadForm$exe + + $DEST/ToForm$exe: $SRC/FormCalc/ToForm.c + $cc -o $DEST/ToForm$exe $SRC/FormCalc/ToForm.c +- -strip $DEST/ToForm$exe + + $DEST/ToFortran$exe: $SRC/FormCalc/ToFortran.c + $cc -o $DEST/ToFortran$exe $SRC/FormCalc/ToFortran.c +- -strip $DEST/ToFortran$exe + + $DEST/ToC$exe: $SRC/FormCalc/ToC.c + $cc -o $DEST/ToC$exe $SRC/FormCalc/ToC.c +- -strip $DEST/ToC$exe + + $DEST/ReadData$exe: $SRC/tools/ReadData.tm + $mcc -o $DEST/ReadData$exe $SRC/tools/ReadData.tm $mclibs +- -strip $DEST/ReadData$exe + + $DEST/reorder$exe: $SRC/tools/reorder.c + $cc -o $DEST/reorder$exe $SRC/tools/reorder.c +- -strip $DEST/reorder$exe + _EOF_ + + diff --git a/sci-physics/formcalc/formcalc-9.10-r1.ebuild b/sci-physics/formcalc/formcalc-9.10-r1.ebuild new file mode 100644 index 000000000..cefbd13bf --- /dev/null +++ b/sci-physics/formcalc/formcalc-9.10-r1.ebuild @@ -0,0 +1,47 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +MY_PN=FormCalc +MY_P=${MY_PN}-${PV} + +DESCRIPTION="FormCalc can be used for automatic Feynman diagram computation." +HOMEPAGE="https://feynarts.de/formcalc" +SRC_URI="https://feynarts.de/formcalc/${MY_P}.tar.gz" +S="${WORKDIR}/${MY_P}" + +LICENSE="LGPL-3+" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + sci-mathematics/mathematica + sci-mathematics/form[threads] + " +DEPEND="${RDEPEND}" +BDEPEND=" + sci-mathematics/mathematica + sci-mathematics/form + " +PATCHES=( "${FILESDIR}"/${PN}-9.9-compile.patch ) + +src_compile() { + # remove shipped binaries + rm bin/Linux-x86-64/* || die + rm bin/Linux-x86-64-kernel2.6/* || die + export DEST=Linux-x86-64 + ./compile ${LDFLAGS} || die +} + +src_install() { + MMADIR=/usr/share/Mathematica/Applications + # unversioned directory + dosym ${MY_P} ${MMADIR}/${MY_PN} + mv "${WORKDIR}/${MY_P}" "${ED}${MMADIR}" || die + # switch to system form + dosym `command -v form` ${MMADIR}/${MY_P}/Linux-x86-64/form + dosym `command -v tform` ${MMADIR}/${MY_P}/Linux-x86-64/tform + + dodoc manual/*.pdf +} diff --git a/sci-physics/formcalc/formcalc-9.9-r1.ebuild b/sci-physics/formcalc/formcalc-9.9-r1.ebuild new file mode 100644 index 000000000..6ccb521fb --- /dev/null +++ b/sci-physics/formcalc/formcalc-9.9-r1.ebuild @@ -0,0 +1,49 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +MY_PN=FormCalc +MY_P=${MY_PN}-${PV} + +DESCRIPTION="FormCalc can be used for automatic Feynman diagram computation." +HOMEPAGE="https://feynarts.de/formcalc" +SRC_URI="https://feynarts.de/formcalc/${MY_P}.tar.gz" +S="${WORKDIR}/${MY_P}" + +LICENSE="LGPL-3+" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + sci-mathematics/mathematica + sci-mathematics/form[threads] + " +DEPEND="${RDEPEND}" +BDEPEND=" + sci-mathematics/mathematica + sci-mathematics/form + " + +PATCHES=( "${FILESDIR}"/${P}-compile.patch ) + +src_compile() { + # remove shipped binaries + rm bin/Linux-x86-64/* || die + rm bin/Linux-x86-64-old/* || die + + export DEST=Linux-x86-64 + ./compile ${LDFLAGS} || die +} + +src_install() { + MMADIR=/usr/share/Mathematica/Applications + # unversioned directory + dosym ${MY_P} ${MMADIR}/${MY_PN} + mv "${WORKDIR}/${MY_P}" "${ED}${MMADIR}" || die + # switch to system form + dosym `command -v form` ${MMADIR}/${MY_P}/Linux-x86-64/form + dosym `command -v tform` ${MMADIR}/${MY_P}/Linux-x86-64/tform + + dodoc manual/*.pdf +} diff --git a/sci-physics/formcalc/metadata.xml b/sci-physics/formcalc/metadata.xml new file mode 100644 index 000000000..b103d8f63 --- /dev/null +++ b/sci-physics/formcalc/metadata.xml @@ -0,0 +1,19 @@ +<?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> + <maintainer type="project"> + <email>sci-physics@gentoo.org</email> + <name>Gentoo Physics Project</name> + </maintainer> + <maintainer type="person"> + <email>alexander@neuwirth-informatik.de</email> + <name>Alexander Puck Neuwirth</name> + </maintainer> + <longdescription lang="en"> + FormCalc is a Mathematica package for the calculation of tree-level and one-loop Feynman diagrams. It makes extensive use of the form tool. + </longdescription> +</pkgmetadata> diff --git a/sci-physics/hepunits/Manifest b/sci-physics/hepunits/Manifest new file mode 100644 index 000000000..9b6a3c900 --- /dev/null +++ b/sci-physics/hepunits/Manifest @@ -0,0 +1,2 @@ +DIST hepunits-2.3.2.tar.gz 13327 BLAKE2B 16986f4cf96eb927e5ae7268dc2975957846678bff0569fc5d5b9d36bb5dae251905283a07e5fcdd895b20982e1e2d32bce5048752d654ca085286e89b65837f SHA512 48d0a4939e19fc6f26b3bb5f8515d8e0d9d4cbed172c14ae30609c2039bdb77625dad8e1e628178481ee0f203d7d36cd2e0d3306f3b344fe14cd68827c4d9477 +DIST hepunits-2.3.3.tar.gz 13491 BLAKE2B ec212be4e53e7ea5aa195852ea6ad4f3aac8e3eb49676e6bef76d525be861ecd4480821b248d746950b45affccd31bf23d5232aee13058bb48ec8d76c4f70a14 SHA512 7a29dd6220c1fbe610f15ef66f02e499d7e2ade8c39827e3229ae74035d127ca7805b9e32c3859c5af4b001725d21514fd81f0408d7f0dc76e9ee34aa66191e8 diff --git a/sci-physics/hepunits/hepunits-2.3.2.ebuild b/sci-physics/hepunits/hepunits-2.3.2.ebuild new file mode 100644 index 000000000..34b3977a8 --- /dev/null +++ b/sci-physics/hepunits/hepunits-2.3.2.ebuild @@ -0,0 +1,23 @@ +EAPI=8 + +PYTHON_COMPAT=( python3_{9..11} ) +DISTUTILS_USE_PEP517=hatchling +inherit distutils-r1 + +DESCRIPTION="units and constants in the HEP system of units" +HOMEPAGE="https://github.com/scikit-hep/hepunits" + +LICENSE="BSD" +SLOT="0" +if [[ ${PV} == 9999 ]]; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/scikit-hep/hepunits" +else + inherit pypi + KEYWORDS="~amd64" +fi + +RDEPEND=" + >=dev-python/attrs-19.2[${PYTHON_USEDEP}] +" +DEPEND="${RDEPEND}" diff --git a/sci-physics/hepunits/hepunits-2.3.3.ebuild b/sci-physics/hepunits/hepunits-2.3.3.ebuild new file mode 100644 index 000000000..2fb8bb148 --- /dev/null +++ b/sci-physics/hepunits/hepunits-2.3.3.ebuild @@ -0,0 +1,25 @@ +EAPI=8 + +PYTHON_COMPAT=( python3_{10..12} ) +DISTUTILS_USE_PEP517=hatchling +inherit distutils-r1 + +DESCRIPTION="units and constants in the HEP system of units" +HOMEPAGE="https://github.com/scikit-hep/hepunits" + +LICENSE="BSD" +SLOT="0" +if [[ ${PV} == 9999 ]]; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/scikit-hep/hepunits" +else + inherit pypi + KEYWORDS="~amd64" +fi + +RDEPEND=" + >=dev-python/attrs-19.2[${PYTHON_USEDEP}] +" +DEPEND="${RDEPEND}" + +distutils_enable_tests pytest diff --git a/sci-physics/hepunits/hepunits-9999.ebuild b/sci-physics/hepunits/hepunits-9999.ebuild new file mode 100644 index 000000000..2fb8bb148 --- /dev/null +++ b/sci-physics/hepunits/hepunits-9999.ebuild @@ -0,0 +1,25 @@ +EAPI=8 + +PYTHON_COMPAT=( python3_{10..12} ) +DISTUTILS_USE_PEP517=hatchling +inherit distutils-r1 + +DESCRIPTION="units and constants in the HEP system of units" +HOMEPAGE="https://github.com/scikit-hep/hepunits" + +LICENSE="BSD" +SLOT="0" +if [[ ${PV} == 9999 ]]; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/scikit-hep/hepunits" +else + inherit pypi + KEYWORDS="~amd64" +fi + +RDEPEND=" + >=dev-python/attrs-19.2[${PYTHON_USEDEP}] +" +DEPEND="${RDEPEND}" + +distutils_enable_tests pytest diff --git a/sci-physics/hepunits/metadata.xml b/sci-physics/hepunits/metadata.xml new file mode 100644 index 000000000..41d598fa2 --- /dev/null +++ b/sci-physics/hepunits/metadata.xml @@ -0,0 +1,19 @@ +<?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> + <maintainer type="person"> + <email>alexander@neuwirth-informatik.de</email> + <name>Alexander Puck Neuwirth</name> + </maintainer> + <longdescription lang="en"> + hepunits collects the most commonly used units and constants in the HEP System of Units, as derived from the basic units originally defined by the CLHEP project + </longdescription> + <upstream> + <remote-id type="pypi">hepunits</remote-id> + <remote-id type="github">scikit-hep/hepunits</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-physics/hoppet/Manifest b/sci-physics/hoppet/Manifest new file mode 100644 index 000000000..cc73bfc3b --- /dev/null +++ b/sci-physics/hoppet/Manifest @@ -0,0 +1 @@ +DIST hoppet-1.2.0.tgz 575911 BLAKE2B 4d4dc1874b45b7237384ad3955808b5f4995c86b4d44165ef0c4d8b1da21880cdd1a3f1f1537f02ad7928baef5207e950be411465989ab876bcb806f355725cf SHA512 65ceb170cd417f229f8a974aa995138b8ee7ea5ef04538a5382b353181951e9d4489045234cd45c1ea8f88a5faf4755e3a0e246065711f137676bbf726a29f1f diff --git a/sci-physics/hoppet/hoppet-1.2.0.ebuild b/sci-physics/hoppet/hoppet-1.2.0.ebuild new file mode 100644 index 000000000..337881026 --- /dev/null +++ b/sci-physics/hoppet/hoppet-1.2.0.ebuild @@ -0,0 +1,35 @@ +# Copyright 2022-2024 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit fortran-2 + +DESCRIPTION="Higher Order Perturbative Parton Evolution Toolkit" +HOMEPAGE=" + https://hoppet.hepforge.org/ + https://github.com/gavinsalam/hoppet +" +SRC_URI="https://hoppet.hepforge.org/downloads/${P}.tgz" + +SLOT="0" +LICENSE="GPL-3+" +KEYWORDS="~amd64" + + +src_configure() { + default + # own custom configure + ./configure --prefix="${EPREFIX}"/usr FFLAGS="${FFLAGS} -fPIC" || die +} + +src_install() { + # Fix install to ED + sed -i "s#scripts/install-sh hoppet-config#\##g" Makefile || die + sed -i "s#/usr/lib/libhoppet#${ED}/usr/$(get_libdir)/libhoppet#g" src/Makefile || die + sed -i "s#/usr/include/hoppet#${ED}/usr/include/hoppet#g" src/Makefile || die + emake install + emake install-mod + dobin hoppet-config + find "${ED}" -name '*.la' -delete || die +} diff --git a/sci-physics/hoppet/metadata.xml b/sci-physics/hoppet/metadata.xml new file mode 100644 index 000000000..37900a238 --- /dev/null +++ b/sci-physics/hoppet/metadata.xml @@ -0,0 +1,19 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>alexander@neuwirth-informatik.de</email> + <name>Alexander Puck Neuwirth</name> + </maintainer> + <maintainer type="project"> + <email>sci-physics@gentoo.org</email> + <name>Gentoo Physics Project</name> + </maintainer> + + <longdescription lang="en"> + HOPPET is a Fortran 95 package for carrying out DGLAP evolution and other common manipulations of parton distribution functions (PDFs). + </longdescription> + <upstream> + <remote-id type="github">gavinsalam/hoppet</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-physics/lhapdf-sets/Manifest b/sci-physics/lhapdf-sets/Manifest new file mode 100644 index 000000000..6e1d34375 --- /dev/null +++ b/sci-physics/lhapdf-sets/Manifest @@ -0,0 +1,14 @@ +DIST CT10.tar.gz 10246366 BLAKE2B f0daf0a3ca6cd2f178f993944cdc29de5deb1f441d197e47c8b1c285a56abc0fdb1cd53ec5a8e7736e200397bea9ec9cf4d04420ce206e5c396b85b63f695d00 SHA512 90406bd102ab54b683fa3e6f3fc759febea2454a0b96c6a8d373cdec297f5d652097057a015c7d87241792ed9b5d9ac658a33155cdd7362f59110f8f06ecce73 +DIST CT14lo.tar.gz 474954 BLAKE2B 60e8d3695fa64a997f0431516086f037d8843a9310cb52910c28a8a8960838409bafb280cf776b25fde1b31225743b72a48a3d467b1f7a4ff5478d515607645b SHA512 bc6acfcf522262da227411555f10dd73456fb5d0ab9db334b99cf7953463e1fa3de8c78bbb95269e9a47629860d906d43948e6cf1719b00402645ec18249f959 +DIST CT14nlo.tar.gz 27067462 BLAKE2B b8d46593a62e80c320c76fb89f646ba0f31ab98811076120de1d21ef3b4849ff3d2e7b8d01d01dff5f1ee05a2266d94664e7f4a27347fa32c8ac4c68b0e72acb SHA512 1fcdfd24569966c1bc9c98f8ae2bf7d3a306700387b1351c92bc2b4f061db5d59d048c6cdd25095e1dc58344afa7f65a6526c611d747a5894398754483db77a2 +DIST CT14qed_proton.tar.gz 11064380 BLAKE2B b0b5834473a90d2adfedfa4dd467847349fc1b60907d387d1007387dcf557fac37871ea7430161edc0ecf6f8e8839077283dc8fcad610f03dd192efd70890c3f SHA512 a41f6f82e5505f66014e5523210c272254fb8018bbfac542eb1941e60c1c897ee687bfef1afbd981132cb772240fdd4d19b5dcd2b36b01f8e34ea959d9acd4f7 +DIST MRST2004qed.tar.gz 185079 BLAKE2B 62e0371de965698100755b14b0c282095b84b40800a58cd6776c458b03982f032f3b2464eb76174084dd22de9fd962e202a4896327b0a00579c3a632dac24ccc SHA512 404aacf0e241f572cc42ad4cf963deef1acd3d365fa68cfa3518878f921858046377ea39caf663fdced2cdde07af2f6ce695737f7fea229489df3d3f38283c95 +DIST MRST2007lomod.tar.gz 56685 BLAKE2B 8515b6f77302621f4b37f550840f07f0351e7ea98de16a37ceb4cb0f2ea64aa4b027462ffc442f34d1f4c349d67fac7b35353606d8920f17621c7187e508c689 SHA512 8e55627a01c85d90a62e4fb11b115c2faac2220479b6d558d3d6f1b801fc5c3e88abc377cd5437ccaeedd34b2ca42d6e833014566b796e5e1eebcf4d620e5dc0 +DIST NNPDF23_nlo_as_0118.tar.gz 21655966 BLAKE2B f92d0b90f27d1a096f327e5aa45cc4d36ad3789db6fcc477b21d6170495c8508edcc86000baf20e50366895a8a1fd1b7d30c136b77ea35c466b65016b66c3829 SHA512 5570273743d4efb9676e3b5f461d8944b841cbcb3f80949f63520f05c184bd551a2a3be3961d20d5de80e7e35e88f26e5eb5c20903d20ed44e2f33038d6c66af +DIST NNPDF23_nlo_as_0119_qed_mc.tar.gz 25223180 BLAKE2B 05dd8772d559e8f08e28dc16da6b256d875563b140e1954cedac9b5f541e9cd325c4dfd5adbb13af434e036cbafa9bfe19325f69ae00ed599cfac6791629d989 SHA512 fc6998d50a61bbe65eef827021c0f453164795c079daef6a4932f825f8db4ae318bbf0e8781b61f1d3ffa9a495b5c4813af3aa31c77694657a44356d93fa970f +DIST NNPDF23_nnlo_as_0119_qed_mc.tar.gz 28940412 BLAKE2B 57c7c98bb863258f87e236fea2d0233ac61350012aec6ba5cced75de0b4b945a5633d7fd487b0913b822df1c3ef804de2aacf34b1319d6973d959dc02ebbc9b2 SHA512 5088c30acbd1da4e412ba9f6a997ceaa34f426f41c7ebacaf4d2e8aa49b8b45052913e8d873b293d9f140c01e82c05735b66dd527a9aa124b86f73bf5e4d8c53 +DIST NNPDF31_nnlo_as_0118.tar.gz 43193739 BLAKE2B b826eaebb6483b844bc18cfca36be8ead1dc409641e445f8d31db58f31bde623b7e7753a94c0e2ee0dfe24b28909b9d06b17641a783c223d8ab7ce8e55902a5c SHA512 a62330979f4001933b52e2b1bd3142b4dacd27aeed1e49969108a842e00e7db59a7fe8d80b755c283f3bc706b36e3ec4597e124d95ad3a7f334fb956bebe7ae0 +DIST NNPDF31_nnlo_as_0118_luxqed.tar.gz 47462442 BLAKE2B 2b473d943ec49e28de63d002e4eadfd3002c63aa6ef9b4e792adf7acf8bb3a771f91298ac6575034407653d15aa4191da6090aaaa34d8a8091cb1a5d4562479a SHA512 5faafc9a2b23dc0a82c7f3ca26a6691cfa476f83741beab2b41a77e63fa5f10428bf43579670636689c0080421f4b08ec058aa63c047f04f6d892b1b848fd702 +DIST PDF4LHC15_nlo_asvar.tar.gz 578871 BLAKE2B a42a24d4af82f892e0dccfeeacedfcbb074be1ddc9649d55ff6c15e3923901173337ba4197248410d2a40e72ab627af9a0cea09e5ee98c37130aceb34402d9d4 SHA512 ef96970050b78f5a5bc54b43ee2d7ed0eb76796ea23ce864f1c8ff6de2d68f99023d5c4530f4e73197948c39886fcb832ed26dfa126ca0396e4fd08e353df8a0 +DIST cteq66.tar.gz 8647237 BLAKE2B 3ac47b6eee434f89ff329cfcb8268782af4ffa552ca4b412a59254e9b10410518f9fe9543b47f193d9cd31b06fc1101556df2be01c25ca17febcb9fb1855e5ca SHA512 25d0fa01dcdb59d71c7092367af8258471a2bc6dfd146766cc79f90ffb0feafa0f2011d0a37a7d75315c10ba7c7a6e3fa583d9c0a28119b072228ac800294e48 +DIST cteq6l1.tar.gz 317834 BLAKE2B eccad131853f9a760d0dfd43a3f8705f8edbac3ec7373de9ef9a8936f13ba06500ba5758cd04649dd1b85ac04fc778e9d96222877e74e9ff02263455b233fa41 SHA512 7177608e97077eaf45a292db4ea74eb9a28b4b500ab8be02098b4837a5583cd397828abc3bf43ead448926eaa75ae3968bd059ecde333d90ed6e4295cbe1873c diff --git a/sci-physics/lhapdf-sets/lhapdf-sets-0.ebuild b/sci-physics/lhapdf-sets/lhapdf-sets-0.ebuild new file mode 100644 index 000000000..784d94f97 --- /dev/null +++ b/sci-physics/lhapdf-sets/lhapdf-sets-0.ebuild @@ -0,0 +1,70 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 +LHA_VER="6.2.1" + +IUSE_LHAPDF_SETS=" + lhapdf_sets_nnpdf31_nnlo_as_0118_luxqed + lhapdf_sets_pdf4lhc15_nlo_asvar + lhapdf_sets_ct14qed_proton + lhapdf_sets_ct14lo + lhapdf_sets_ct14nlo + lhapdf_sets_ct10 + lhapdf_sets_mrst2007lomod + lhapdf_sets_nnpdf23_nlo_as_0119_qed_mc + lhapdf_sets_nnpdf23_nnlo_as_0119_qed_mc + lhapdf_sets_cteq66 + lhapdf_sets_cteq6l1 + lhapdf_sets_mrst2004qed + lhapdf_sets_nnpdf23_nlo_as_0118 + lhapdf_sets_nnpdf31_nnlo_as_0118 +" + +COMMON_URI="https://lhapdfsets.web.cern.ch/lhapdfsets/current" +HEPFORGE_URI="https://www.hepforge.org/downloads/lhapdf/pdfsets/v6.backup/${LHA_VER}" +# Alternatively to fetching them here already the user can install them by lhapdf install, +# BUT some codes need them during test and even compile (Herwig) stage. +# Also since it belongs to LHAPDF it is better to fetch them here. +SRC_URI=" + lhapdf_sets_nnpdf31_nnlo_as_0118_luxqed? ( ${COMMON_URI}/NNPDF31_nnlo_as_0118_luxqed.tar.gz ) + lhapdf_sets_pdf4lhc15_nlo_asvar? ( ${COMMON_URI}/PDF4LHC15_nlo_asvar.tar.gz ) + lhapdf_sets_ct14qed_proton? ( ${COMMON_URI}/CT14qed_proton.tar.gz ) + lhapdf_sets_ct14lo? ( ${COMMON_URI}/CT14lo.tar.gz ) + lhapdf_sets_ct14nlo? ( ${COMMON_URI}/CT14nlo.tar.gz ) + lhapdf_sets_ct10? ( ${COMMON_URI}/CT10.tar.gz ) + lhapdf_sets_mrst2007lomod? ( ${COMMON_URI}/MRST2007lomod.tar.gz ) + lhapdf_sets_nnpdf23_nlo_as_0119_qed_mc? ( ${COMMON_URI}/NNPDF23_nlo_as_0119_qed_mc.tar.gz ) + lhapdf_sets_nnpdf23_nnlo_as_0119_qed_mc? ( ${COMMON_URI}/NNPDF23_nnlo_as_0119_qed_mc.tar.gz ) + lhapdf_sets_cteq66? ( ${COMMON_URI}/cteq66.tar.gz ) + lhapdf_sets_cteq6l1? ( ${COMMON_URI}/cteq6l1.tar.gz ) + lhapdf_sets_mrst2004qed? ( ${HEPFORGE_URI}/MRST2004qed.tar.gz ) + lhapdf_sets_nnpdf23_nlo_as_0118? ( ${COMMON_URI}/NNPDF23_nlo_as_0118.tar.gz ) + lhapdf_sets_nnpdf31_nnlo_as_0118? ( ${COMMON_URI}/NNPDF31_nnlo_as_0118.tar.gz ) +" + +MY_PV=$(ver_cut 1-3) +MY_PF=LHAPDF-${MY_PV} + +DESCRIPTION="LHAPDF data grids" +HOMEPAGE="https://lhapdf.hepforge.org/" +KEYWORDS="~amd64 ~x86" +S="${WORKDIR}" + +LICENSE="public-domain" +SLOT="0" +IUSE="${IUSE_LHAPDF_SETS}" +SLOT="0" +RDEPEND="sci-physics/lhapdf" +DEPEND="${RDEPEND}" + +src_unpack() { + # unpack in destination only to avoid copy + return +} + +src_install() { + dodir /usr/share/LHAPDF/ + cd "${ED}/usr/share/LHAPDF/" || die + unpack ${A} +} diff --git a/sci-physics/lhapdf-sets/metadata.xml b/sci-physics/lhapdf-sets/metadata.xml new file mode 100644 index 000000000..73a7063eb --- /dev/null +++ b/sci-physics/lhapdf-sets/metadata.xml @@ -0,0 +1,12 @@ +<?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> + <maintainer type="person"> + <email>alexander@neuwirth-informatik.de</email> + <name>Alexander Puck Neuwirth</name> + </maintainer> +</pkgmetadata> diff --git a/sci-physics/mcfm/Manifest b/sci-physics/mcfm/Manifest new file mode 100644 index 000000000..9163b57a5 --- /dev/null +++ b/sci-physics/mcfm/Manifest @@ -0,0 +1 @@ +DIST MCFM-10.2.1.tar.gz 39365160 BLAKE2B 59b6fc55e4a21d4dea979d973cac0378763585088b7b5f032d671a30358e6bd8b6332fd3fa0eeca573177e46f642b3ba8b0c78c503bf37ac4ee0d6c0b962e4df SHA512 994f243b5460784eb5d62f81adf6c08d7ffd03df0d2fa8ac8e4522ab5127f54c3218cd4fe9984adff505c02804613c570d228f88c9343804e20d08f7187575c1 diff --git a/sci-physics/mcfm/files/mcfm-10.2.1-rest.patch b/sci-physics/mcfm/files/mcfm-10.2.1-rest.patch new file mode 100644 index 000000000..f43a1cb48 --- /dev/null +++ b/sci-physics/mcfm/files/mcfm-10.2.1-rest.patch @@ -0,0 +1,251 @@ +--- a/CMakeLists.txt 2022-09-19 02:30:49.215050000 +0200 ++++ b/CMakeLists.txt 2022-09-19 21:03:05.409746266 +0200 +@@ -41,48 +41,48 @@ + + include(ExternalProject) + +-ExternalProject_Add(qd +- DOWNLOAD_COMMAND mkdir -p ${CMAKE_BINARY_DIR}/lib && cp -r ${CMAKE_SOURCE_DIR}/lib/qd-2.3.22 ${CMAKE_BINARY_DIR}/lib/ +- PREFIX ${CMAKE_BINARY_DIR}/lib/qd-2.3.22 +- SOURCE_DIR ${CMAKE_BINARY_DIR}/lib/qd-2.3.22 +- BUILD_IN_SOURCE ON +- PATCH_COMMAND mkdir -p ${CMAKE_BINARY_DIR}/local +- CONFIGURE_COMMAND CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} FC=${CMAKE_Fortran_COMPILER} ./configure --with-pic --enable-fortran --enable-fma --prefix=${CMAKE_BINARY_DIR}/local --enable-shared --libdir=${CMAKE_BINARY_DIR}/local/lib +- BUILD_COMMAND ${MAKE} +- INSTALL_COMMAND ${CMAKE_MAKE_PROGRAM} install +-) +- +-ExternalProject_Add(qcdloop +- DOWNLOAD_COMMAND mkdir -p ${CMAKE_BINARY_DIR}/lib && cp -r ${CMAKE_SOURCE_DIR}/lib/qcdloop-2.0.5 ${CMAKE_BINARY_DIR}/lib +- PREFIX ${CMAKE_BINARY_DIR}/lib/qcdloop-2.0.5 +- SOURCE_DIR ${CMAKE_BINARY_DIR}/lib/qcdloop-2.0.5 +- BUILD_IN_SOURCE ON +- PATCH_COMMAND mkdir -p ${CMAKE_BINARY_DIR}/local +- CMAKE_ARGS -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} -DENABLE_FORTRAN_WRAPPER=ON -DCMAKE_INSTALL_PREFIX=${CMAKE_BINARY_DIR}/local -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER} -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} -DCMAKE_INSTALL_LIBDIR=lib +- BUILD_COMMAND ${MAKE} +- INSTALL_COMMAND ${CMAKE_MAKE_PROGRAM} install +-) +- +-ExternalProject_Add(liboneloop +- DOWNLOAD_COMMAND mkdir -p ${CMAKE_BINARY_DIR}/lib && cp -r ${CMAKE_SOURCE_DIR}/lib/oneloop ${CMAKE_BINARY_DIR}/lib/ +- PREFIX ${CMAKE_BINARY_DIR}/lib/oneloop +- SOURCE_DIR ${CMAKE_BINARY_DIR}/lib/oneloop +- BUILD_IN_SOURCE ON +- CMAKE_ARGS -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} -DCMAKE_Fortran_COMPILER=${CMAKE_Fortran_COMPILER} -DCMAKE_Fortran_FLAGS=-fPIC +- BUILD_COMMAND ${MAKE} +- INSTALL_COMMAND mkdir -p ${CMAKE_BINARY_DIR}/local/include && cp ${CMAKE_BINARY_DIR}/lib/oneloop/avh_olo.mod ${CMAKE_BINARY_DIR}/local/include +-) +- +-ExternalProject_Add(handyg +- DOWNLOAD_COMMAND mkdir -p ${CMAKE_BINARY_DIR}/lib && cp -r ${CMAKE_SOURCE_DIR}/lib/handyG ${CMAKE_BINARY_DIR}/lib/ +- PREFIX ${CMAKE_BINARY_DIR}/lib/handyG +- SOURCE_DIR ${CMAKE_BINARY_DIR}/lib/handyG +- BUILD_IN_SOURCE ON +- PATCH_COMMAND mkdir -p ${CMAKE_BINARY_DIR}/local +- CONFIGURE_COMMAND CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} FC=${CMAKE_Fortran_COMPILER} CFLAGS=-fPIC CXXFLAGS=-fPIC FFLAGS=-fPIC ./configure --prefix=${CMAKE_BINARY_DIR}/local --moduledir=${CMAKE_BINARY_DIR}/local/include +- BUILD_COMMAND ${MAKE} +- INSTALL_COMMAND ${CMAKE_MAKE_PROGRAM} install +-) ++#ExternalProject_Add(qd ++# DOWNLOAD_COMMAND mkdir -p ${CMAKE_BINARY_DIR}/lib && cp -r ${CMAKE_SOURCE_DIR}/lib/qd-2.3.22 ${CMAKE_BINARY_DIR}/lib/ ++# PREFIX ${CMAKE_BINARY_DIR}/lib/qd-2.3.22 ++# SOURCE_DIR ${CMAKE_BINARY_DIR}/lib/qd-2.3.22 ++# BUILD_IN_SOURCE ON ++# PATCH_COMMAND mkdir -p ${CMAKE_BINARY_DIR}/local ++# CONFIGURE_COMMAND CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} FC=${CMAKE_Fortran_COMPILER} ./configure --with-pic --enable-fortran --enable-fma --prefix=${CMAKE_BINARY_DIR}/local --enable-shared --libdir=${CMAKE_BINARY_DIR}/local/lib ++# BUILD_COMMAND ${MAKE} ++# INSTALL_COMMAND ${CMAKE_MAKE_PROGRAM} install ++#) ++# ++#ExternalProject_Add(qcdloop ++# DOWNLOAD_COMMAND mkdir -p ${CMAKE_BINARY_DIR}/lib && cp -r ${CMAKE_SOURCE_DIR}/lib/qcdloop-2.0.5 ${CMAKE_BINARY_DIR}/lib ++# PREFIX ${CMAKE_BINARY_DIR}/lib/qcdloop-2.0.5 ++# SOURCE_DIR ${CMAKE_BINARY_DIR}/lib/qcdloop-2.0.5 ++# BUILD_IN_SOURCE ON ++# PATCH_COMMAND mkdir -p ${CMAKE_BINARY_DIR}/local ++# CMAKE_ARGS -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} -DENABLE_FORTRAN_WRAPPER=ON -DCMAKE_INSTALL_PREFIX=${CMAKE_BINARY_DIR}/local -DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER} -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER} -DCMAKE_INSTALL_LIBDIR=lib ++# BUILD_COMMAND ${MAKE} ++# INSTALL_COMMAND ${CMAKE_MAKE_PROGRAM} install ++#) ++# ++#ExternalProject_Add(liboneloop ++# DOWNLOAD_COMMAND mkdir -p ${CMAKE_BINARY_DIR}/lib && cp -r ${CMAKE_SOURCE_DIR}/lib/oneloop ${CMAKE_BINARY_DIR}/lib/ ++# PREFIX ${CMAKE_BINARY_DIR}/lib/oneloop ++# SOURCE_DIR ${CMAKE_BINARY_DIR}/lib/oneloop ++# BUILD_IN_SOURCE ON ++# CMAKE_ARGS -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} -DCMAKE_Fortran_COMPILER=${CMAKE_Fortran_COMPILER} -DCMAKE_Fortran_FLAGS=-fPIC ++# BUILD_COMMAND ${MAKE} ++# INSTALL_COMMAND mkdir -p ${CMAKE_BINARY_DIR}/local/include && cp ${CMAKE_BINARY_DIR}/lib/oneloop/avh_olo.mod ${CMAKE_BINARY_DIR}/local/include ++#) ++# ++#ExternalProject_Add(handyg ++# DOWNLOAD_COMMAND mkdir -p ${CMAKE_BINARY_DIR}/lib && cp -r ${CMAKE_SOURCE_DIR}/lib/handyG ${CMAKE_BINARY_DIR}/lib/ ++# PREFIX ${CMAKE_BINARY_DIR}/lib/handyG ++# SOURCE_DIR ${CMAKE_BINARY_DIR}/lib/handyG ++# BUILD_IN_SOURCE ON ++# PATCH_COMMAND mkdir -p ${CMAKE_BINARY_DIR}/local ++# CONFIGURE_COMMAND CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} FC=${CMAKE_Fortran_COMPILER} CFLAGS=-fPIC CXXFLAGS=-fPIC FFLAGS=-fPIC ./configure --prefix=${CMAKE_BINARY_DIR}/local --moduledir=${CMAKE_BINARY_DIR}/local/include ++# BUILD_COMMAND ${MAKE} ++# INSTALL_COMMAND ${CMAKE_MAKE_PROGRAM} install ++#) + + ## Configuration options + +@@ -169,7 +169,7 @@ + add_subdirectory(lib/SpecialFunctions) + add_subdirectory(lib/AMOS) + +-add_dependencies(objlib qd qcdloop liboneloop handyg) ++#add_dependencies(objlib qd qcdloop liboneloop handyg) + + if(${with_vvamp}) + add_compile_definitions(WITH_VVAMP=1) +@@ -182,7 +182,7 @@ + PATCH_COMMAND mkdir -p ${CMAKE_BINARY_DIR}/local + CMAKE_ARGS -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE} -DCMAKE_Fortran_COMPILER=${CMAKE_Fortran_COMPILER} -DCMAKE_Fortran_FLAGS=-fPIC + BUILD_COMMAND ${MAKE} +- INSTALL_COMMAND mkdir -p ${CMAKE_BINARY_DIR}/local/include && cp ${CMAKE_BINARY_DIR}/VVamp/mod_vvamp.mod ${CMAKE_BINARY_DIR}/local/include ++ INSTALL_COMMAND mv ${CMAKE_BINARY_DIR}/VVamp/mod_vvamp.mod ${CMAKE_BINARY_DIR}/local/include + ) + add_library(vvamp STATIC IMPORTED) + set_property(TARGET vvamp PROPERTY IMPORTED_LOCATION "${CMAKE_BINARY_DIR}/VVamp/libvvamp.a") +@@ -192,7 +192,6 @@ + else() + set(linkvvamp "") + endif() +- + set_target_properties(objlib PROPERTIES + CXX_STANDARD 11 + Fortran_MODULE_DIRECTORY "${CMAKE_BINARY_DIR}/include" +@@ -222,48 +221,51 @@ + target_link_libraries(mcfm ${OpenMP_Fortran_LIBRARIES}) + endif() + +-add_library(oneloop STATIC IMPORTED) +-set_property(TARGET oneloop PROPERTY IMPORTED_LOCATION "${CMAKE_BINARY_DIR}/lib/oneloop/liboneloop.a") ++find_library(qcdloop qcdloop) + +-add_library(qcdloop_lib_static STATIC IMPORTED) +-set_property(TARGET qcdloop_lib_static PROPERTY IMPORTED_LOCATION "${CMAKE_BINARY_DIR}/local/lib/libqcdloop.a") +-set_property(TARGET qcdloop_lib_static PROPERTY IMPORTED_NO_SONAME TRUE) +-add_dependencies(qcdloop_lib_static qcdloop) +- +-add_library(qcdloop_lib_shared SHARED IMPORTED) +-set_property(TARGET qcdloop_lib_shared PROPERTY IMPORTED_LOCATION "${CMAKE_BINARY_DIR}/local/lib/libqcdloop.${CMAKE_SHARED_LIBRARY_SUFFIX}") +-set_property(TARGET qcdloop_lib_shared PROPERTY IMPORTED_NO_SONAME TRUE) +-add_dependencies(qcdloop_lib_shared qcdloop) +- +-add_library(qd_lib_static STATIC IMPORTED) +-set_property(TARGET qd_lib_static PROPERTY IMPORTED_LOCATION "${CMAKE_BINARY_DIR}/local/lib/libqd.a") +-set_property(TARGET qd_lib_static PROPERTY IMPORTED_NO_SONAME TRUE) +-add_dependencies(qd_lib_static qd) +- +-add_library(qd_lib_shared SHARED IMPORTED) +-set_property(TARGET qd_lib_shared PROPERTY IMPORTED_LOCATION "${CMAKE_BINARY_DIR}/local/lib/libqd.${CMAKE_SHARED_LIBRARY_SUFFIX}") +-set_property(TARGET qd_lib_shared PROPERTY IMPORTED_NO_SONAME TRUE) +-add_dependencies(qd_lib_shared qd) +- +-add_library(qdmod_lib_static STATIC IMPORTED) +-set_property(TARGET qdmod_lib_static PROPERTY IMPORTED_LOCATION "${CMAKE_BINARY_DIR}/local/lib/libqdmod.a") +-set_property(TARGET qdmod_lib_static PROPERTY IMPORTED_NO_SONAME TRUE) +-add_dependencies(qdmod_lib_static qd) +- +-add_library(qdmod_lib_shared SHARED IMPORTED) +-set_property(TARGET qdmod_lib_shared PROPERTY IMPORTED_LOCATION "${CMAKE_BINARY_DIR}/local/lib/libqdmod.${CMAKE_SHARED_LIBRARY_SUFFIX}") +-set_property(TARGET qdmod_lib_shared PROPERTY IMPORTED_NO_SONAME TRUE) +-add_dependencies(qdmod_lib_shared qd) +- +-add_library(handyg_lib_static STATIC IMPORTED) +-set_property(TARGET handyg_lib_static PROPERTY IMPORTED_LOCATION "${CMAKE_BINARY_DIR}/local/lib/libhandyg.a") +-set_property(TARGET handyg_lib_static PROPERTY IMPORTED_NO_SONAME TRUE) +-add_dependencies(handyg_lib_static handyg) +- +-add_dependencies(objlib qdmod_lib_static) +-add_dependencies(objlib qd_lib_static) +-add_dependencies(objlib qcdloop_lib_static) +-add_dependencies(objlib handyg_lib_static) ++#add_library(oneloop STATIC IMPORTED) ++#set_property(TARGET oneloop PROPERTY IMPORTED_LOCATION "${CMAKE_BINARY_DIR}/lib/oneloop/liboneloop.a") ++# ++#add_library(qcdloop_lib_static STATIC IMPORTED) ++#set_property(TARGET qcdloop_lib_static PROPERTY IMPORTED_LOCATION "${CMAKE_BINARY_DIR}/local/lib/libqcdloop.a") ++#set_property(TARGET qcdloop_lib_static PROPERTY IMPORTED_NO_SONAME TRUE) ++#add_dependencies(qcdloop_lib_static qcdloop) ++ ++#add_library(qcdloop_lib_shared SHARED IMPORTED) ++#set_property(TARGET qcdloop_lib_shared PROPERTY IMPORTED_LOCATION "${CMAKE_BINARY_DIR}/local/lib/libqcdloop.${CMAKE_SHARED_LIBRARY_SUFFIX}") ++#set_property(TARGET qcdloop_lib_shared PROPERTY IMPORTED_NO_SONAME TRUE) ++#add_dependencies(qcdloop_lib_shared qcdloop) ++# ++#add_library(qd_lib_static STATIC IMPORTED) ++#set_property(TARGET qd_lib_static PROPERTY IMPORTED_LOCATION "${CMAKE_BINARY_DIR}/local/lib/libqd.a") ++#set_property(TARGET qd_lib_static PROPERTY IMPORTED_NO_SONAME TRUE) ++#add_dependencies(qd_lib_static qd) ++# ++#add_library(qd_lib_shared SHARED IMPORTED) ++#set_property(TARGET qd_lib_shared PROPERTY IMPORTED_LOCATION "${CMAKE_BINARY_DIR}/local/lib/libqd.${CMAKE_SHARED_LIBRARY_SUFFIX}") ++#set_property(TARGET qd_lib_shared PROPERTY IMPORTED_NO_SONAME TRUE) ++#add_dependencies(qd_lib_shared qd) ++# ++#add_library(qdmod_lib_static STATIC IMPORTED) ++#set_property(TARGET qdmod_lib_static PROPERTY IMPORTED_LOCATION "${CMAKE_BINARY_DIR}/local/lib/libqdmod.a") ++#set_property(TARGET qdmod_lib_static PROPERTY IMPORTED_NO_SONAME TRUE) ++#add_dependencies(qdmod_lib_static qd) ++# ++#add_library(qdmod_lib_shared SHARED IMPORTED) ++#set_property(TARGET qdmod_lib_shared PROPERTY IMPORTED_LOCATION "${CMAKE_BINARY_DIR}/local/lib/libqdmod.${CMAKE_SHARED_LIBRARY_SUFFIX}") ++#set_property(TARGET qdmod_lib_shared PROPERTY IMPORTED_NO_SONAME TRUE) ++#add_dependencies(qdmod_lib_shared qd) ++# ++#add_library(handyg_lib_static STATIC IMPORTED) ++#set_property(TARGET handyg_lib_static PROPERTY IMPORTED_LOCATION "${CMAKE_BINARY_DIR}/local/lib/libhandyg.a") ++#set_property(TARGET handyg_lib_static PROPERTY IMPORTED_NO_SONAME TRUE) ++#add_dependencies(handyg_lib_static handyg) ++ ++#add_dependencies(objlib qdmod_lib_static) ++#add_dependencies(objlib qd_lib_static) ++#add_dependencies(objlib qcdloop_lib_static) ++#add_dependencies(objlib handyg_lib_static) ++target_link_libraries(objlib qdmod qd qcdloop handyg) + + if(use_internal_lhapdf) + ExternalProject_Add(lhapdf +@@ -285,13 +287,15 @@ + + add_dependencies(lhapdf_lib_static lhapdf) + target_link_libraries(mcfm lhapdf_lib_static) +- target_include_directories(objlib PRIVATE "${CMAKE_BINARY_DIR}/local/include" "${CMAKE_BINARY_DIR}/local/include/qd") ++ target_include_directories(objlib PRIVATE ++ "${CMAKE_BINARY_DIR}/include" "/usr/include" "/usr/include/qd") + add_dependencies(objlib lhapdf) + elseif(use_external_lhapdf) + find_library(lhapdf_lib NAMES LHAPDF REQUIRED) + target_link_libraries(mcfm ${lhapdf_lib}) + if (${lhapdf_include_path}) +- target_include_directories(objlib PRIVATE "${LHAPDF_INCLUDE_PATH}" "${CMAKE_BINARY_DIR}/local/include" "${CMAKE_BINARY_DIR}/local/include/qd") ++ target_include_directories(objlib PRIVATE "${LHAPDF_INCLUDE_PATH}" ++ "${CMAKE_BINARY_DIR}/include" "/usr/include" "/usr/include/qd") + endif() + endif() + +@@ -299,9 +303,9 @@ + + if(${with_library}) + if(use_internal_lhapdf) +- target_link_libraries(libmcfm qdmod_lib_static qd_lib_static qcdloop_lib_static oneloop handyg_lib_static ${linkvvamp} quadmath stdc++ lhapdf_lib_static) ++ target_link_libraries(libmcfm qdmod qd qcdloop avh_olo handyg ${linkvvamp} quadmath stdc++ lhapdf_lib_static) + else() +- target_link_libraries(libmcfm qdmod_lib_static qd_lib_static qcdloop_lib_static oneloop handyg_lib_static ${linkvvamp} quadmath stdc++ ${lhapdf_lib}) ++ target_link_libraries(libmcfm qdmod qd qcdloop avh_olo handyg ${linkvvamp} quadmath stdc++ ${lhapdf_lib}) + endif() + if (DEFINED OLDIR) + target_link_libraries(oltest libmcfm ${openloops_lib}) +@@ -320,7 +324,7 @@ + endif() + endif() + +-target_link_libraries(mcfm qdmod_lib_static qd_lib_static qcdloop_lib_static oneloop handyg_lib_static ${linkvvamp} quadmath stdc++) ++target_link_libraries(mcfm qdmod qd qcdloop avh_olo handyg ${linkvvamp} quadmath stdc++) + + set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE) + set(CMAKE_INSTALL_RPATH "${CMAKE_BINARY_DIR}/local/lib") diff --git a/sci-physics/mcfm/mcfm-10.2.1.ebuild b/sci-physics/mcfm/mcfm-10.2.1.ebuild new file mode 100644 index 000000000..9a928e4c9 --- /dev/null +++ b/sci-physics/mcfm/mcfm-10.2.1.ebuild @@ -0,0 +1,71 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +CMAKE_MAKEFILE_GENERATOR="emake" + +inherit cmake + +MY_PN=MCFM +MY_P=${MY_PN}-${PV} + +DESCRIPTION="Monte Carlo for FeMtobarn processes" +HOMEPAGE="https://mcfm.fnal.gov" +SRC_URI="https://mcfm.fnal.gov/downloads/${MY_P}.tar.gz" +S="${WORKDIR}/${MY_P}" + +LICENSE="GPL-3+" +SLOT="0" +KEYWORDS="~amd64" + +# Manual states multithreading bug in lhapdf-6.3.0 ?! +# MCFM has been tested against lhapdf-6.2.0 which ::gentoo already dropped +DEPEND=" + sci-physics/lhapdf + >=sci-libs/qd-2.3.22 + >=sci-physics/qcdloop-2.0.5 + >=sci-physics/oneloop-2020.07.31 + >=sci-libs/handyg-0.1.5 +" +RDEPEND="${DEPEND}" +BDEPEND=" + virtual/fortran +" + +PATCHES=( + "${FILESDIR}"/${P}-rest.patch +) +src_prepare() { + sed -i -e 's/\(name=".*\)"/\1_"/g' src/Mods/mod_qcdloop_c.f || die + cmake_src_prepare +} + +src_configure() { + local mycmakeargs=( + -Duse_external_lhapdf=ON + -Duse_internal_lhapdf=OFF + -Dlhapdf_include_path=ON + -Dwith_library=ON + -Dwith_vvamp=OFF + ) + cmake_src_configure + # Fix relative path in working dir to something absolute + sed -i "s/process\.DAT/${EPREFIX}\/usr\/share\/${MY_PN}\/process\.DAT/g" src/Procdep/chooser.f || die +} + +src_compile() { + # Single thread force needed since fortan mods depend on each other + # This problem only happend very rarely + export MAKEOPTS=-j1 + cmake_src_compile +} + +src_install() { + # this did not work + #cmake_src_install + dobin "${BUILD_DIR}"/mcfm + dolib.so "${BUILD_DIR}"/libmcfm.so + insinto "/usr/share/${MY_PN}/" + doins "Bin/process.DAT" +} diff --git a/sci-physics/mcfm/metadata.xml b/sci-physics/mcfm/metadata.xml new file mode 100644 index 000000000..a8720d7dd --- /dev/null +++ b/sci-physics/mcfm/metadata.xml @@ -0,0 +1,15 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>APN-Pucky@users.noreply.github.com</email> + <name>APN-Pucky</name> + </maintainer> + <maintainer type="project"> + <email>sci-physics@gentoo.org</email> + <name>Gentoo Physics Project</name> + </maintainer> + <longdescription lang="en"> + The program calculates cross-sections for various femtobarn-level processes at hadron-hadron colliders. A number of processes can be calculated at NLO order in QCD, while most other processes are included at NNLO order in QCD. The calculation of some processes can also account for next-to-leading order weak effects. + </longdescription> +</pkgmetadata> diff --git a/sci-physics/oneloop/Manifest b/sci-physics/oneloop/Manifest new file mode 100644 index 000000000..f698d0a23 --- /dev/null +++ b/sci-physics/oneloop/Manifest @@ -0,0 +1 @@ +DIST oneloop-2020.07.31.zip 166257 BLAKE2B 7869806c6e70388311b62ae1ad15b35292c81d5d87ff7f24ad53bb8e562631664545f36e3e32d6f31a39ca9489d7da64284ad10ed988cb7c4375626121d0a84f SHA512 eee46cfe60b1d887cb40033e63d7a04ca24b329692e443d28ecb9f070182d5c56ea5bbaefd2ae21b2776d907ea280ebf81cae0c332391e7e7e7d5e3be3084220 diff --git a/sci-physics/oneloop/files/oneloop-2020.07.31-config.patch b/sci-physics/oneloop/files/oneloop-2020.07.31-config.patch new file mode 100644 index 000000000..4af47e066 --- /dev/null +++ b/sci-physics/oneloop/files/oneloop-2020.07.31-config.patch @@ -0,0 +1,11 @@ +--- a/Config 2022-05-19 17:34:51.000000000 +0200 ++++ b/Config 2022-05-19 17:34:51.000000000 +0200 +@@ -3,7 +3,7 @@ + #FFLAGS = -Wall + + DPKIND = kind(1d0) +-QPKIND = kind(1q0) ++#QPKIND = kind(1q0) + #DPKIND = selected_real_kind(15) + #QPKIND = 16 + #DDTYPE = ddfun90 diff --git a/sci-physics/oneloop/metadata.xml b/sci-physics/oneloop/metadata.xml new file mode 100644 index 000000000..bdee6992b --- /dev/null +++ b/sci-physics/oneloop/metadata.xml @@ -0,0 +1,12 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>alexander@neuwirth-informatik.de</email> + <name>Alexander Puck Neuwirth</name> + </maintainer> + <maintainer type="project"> + <email>sci-physics@gentoo.org</email> + <name>Gentoo Physics Project</name> + </maintainer> +</pkgmetadata> diff --git a/sci-physics/oneloop/oneloop-2020.07.31.ebuild b/sci-physics/oneloop/oneloop-2020.07.31.ebuild new file mode 100644 index 000000000..8b98d1e1d --- /dev/null +++ b/sci-physics/oneloop/oneloop-2020.07.31.ebuild @@ -0,0 +1,49 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +# python only needed for create.py to get binaries +PYTHON_COMPAT=( python3_{10..11} ) +inherit toolchain-funcs python-any-r1 + +DESCRIPTION="Library of one-loop scalar functions" +HOMEPAGE="https://bitbucket.org/hameren/oneloop" +SRC_URI="https://bitbucket.org/hameren/oneloop/get/3762b8bad6ad.zip -> ${P}.zip" +S="${WORKDIR}/hameren-oneloop-3762b8bad6ad" + +LICENSE="GPL-3+" +SLOT="0" +KEYWORDS="~amd64" + +DEPEND="" +RDEPEND="${DEPEND}" +BDEPEND=" + ${PYTHON_DEPS} + app-arch/unzip + virtual/fortran +" + +PATCHES=( + "${FILESDIR}"/${P}-config.patch +) + +src_configure() { + tc-export FC + sed -i "/FC = /s/gfortran/${FC}/g" Config || die + sed -i "/FFLAGS = /s/ -O/${FFLAGS} -fPIC/g" Config || die +} + +src_compile() { + tc-export FC + emake -f make_cuttools + ${EPYTHON} ./create.py || die "Failed to compile" + #./create.py dynamic || die + ${FC} ${LDFLAGS} -Wl,-soname,libavh_olo.so -shared -o libavh_olo.so avh_olo.o || die "Failed to link" +} + +src_install() { + dolib.a libavh_olo.a + dolib.so libavh_olo.so + doheader avh_olo.mod +} diff --git a/sci-physics/particle/Manifest b/sci-physics/particle/Manifest new file mode 100644 index 000000000..a91580388 --- /dev/null +++ b/sci-physics/particle/Manifest @@ -0,0 +1,2 @@ +DIST particle-0.23.0.tar.gz 313512 BLAKE2B 33a0dc1cf612af8242b5080d0862f3b1e587254b46fa90f235cd6edba3919594c5077733600dfe88ad0959be889271c301324789abf0511a7fbe588942086877 SHA512 582c42beade0b28f28f3ee9f83f6d8cc75558f8a9aa5fbe3679c7aa68af40bd04f374741211d6f214bb828c24a017a89b541f780739a36d61d85a2fd5e00b530 +DIST particle-0.23.1.tar.gz 313729 BLAKE2B fc35163955e065b350dfa0825612a64214baeb1f5be41404af259136e6689e23419891513c059ccdfbe2cbf5891596fccd0b0b7f283031bb3352600b5be43441 SHA512 1b4f4516357fd9725d9d5b0a481467896e93e23a8956b2ce321b9cac1d200a8ee8dd9cc1b22d940b4708f29abe3417988677ac685b78287abe10afafa79fb381 diff --git a/sci-physics/particle/metadata.xml b/sci-physics/particle/metadata.xml new file mode 100644 index 000000000..1ec9e9afb --- /dev/null +++ b/sci-physics/particle/metadata.xml @@ -0,0 +1,19 @@ +<?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> + <maintainer type="person"> + <email>alexander@neuwirth-informatik.de</email> + <name>Alexander Puck Neuwirth</name> + </maintainer> + <longdescription lang="en"> + Particle provides a pythonic interface to the Particle Data Group (PDG) particle data tables and particle identification codes, with extended particle information and extra goodies. + </longdescription> + <upstream> + <remote-id type="pypi">particle</remote-id> + <remote-id type="github">scikit-hep/particle</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-physics/particle/particle-0.23.0.ebuild b/sci-physics/particle/particle-0.23.0.ebuild new file mode 100644 index 000000000..88da33c3e --- /dev/null +++ b/sci-physics/particle/particle-0.23.0.ebuild @@ -0,0 +1,44 @@ +EAPI=8 + +PYTHON_COMPAT=( python3_11 ) +DISTUTILS_USE_PEP517=hatchling +inherit distutils-r1 + +DESCRIPTION="PDG particle data and identification codes" +HOMEPAGE="https://github.com/scikit-hep/particle" + +LICENSE="BSD" +SLOT="0" + +if [[ ${PV} == 9999 ]]; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/scikit-hep/particle" +else + inherit pypi + KEYWORDS="~amd64" +fi + +RDEPEND=" + >=dev-python/attrs-19.2[${PYTHON_USEDEP}] + >=sci-physics/hepunits-2.0.0[${PYTHON_USEDEP}] + dev-python/deprecated[${PYTHON_USEDEP}] +" +DEPEND="${RDEPEND}" +BDEPEND=" + test? ( + >=dev-python/pytest-6.0.0[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + dev-python/tabulate[${PYTHON_USEDEP}] + ) +" +distutils_enable_tests pytest + +src_prepare() { + default + + sed -i -e 's:--benchmark-disable::' pyproject.toml || die +} + +python_test() { + epytest --ignore tests/particle/test_performance.py +} diff --git a/sci-physics/particle/particle-0.23.1.ebuild b/sci-physics/particle/particle-0.23.1.ebuild new file mode 100644 index 000000000..43f1e67ca --- /dev/null +++ b/sci-physics/particle/particle-0.23.1.ebuild @@ -0,0 +1,44 @@ +EAPI=8 + +PYTHON_COMPAT=( python3_{11..12} ) +DISTUTILS_USE_PEP517=hatchling +inherit distutils-r1 + +DESCRIPTION="PDG particle data and identification codes" +HOMEPAGE="https://github.com/scikit-hep/particle" + +LICENSE="BSD" +SLOT="0" + +if [[ ${PV} == 9999 ]]; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/scikit-hep/particle" +else + inherit pypi + KEYWORDS="~amd64" +fi + +RDEPEND=" + >=dev-python/attrs-19.2[${PYTHON_USEDEP}] + >=sci-physics/hepunits-2.0.0[${PYTHON_USEDEP}] + dev-python/deprecated[${PYTHON_USEDEP}] +" +DEPEND="${RDEPEND}" +BDEPEND=" + test? ( + >=dev-python/pytest-6.0.0[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + dev-python/tabulate[${PYTHON_USEDEP}] + ) +" +distutils_enable_tests pytest + +src_prepare() { + default + + sed -i -e 's:--benchmark-disable::' pyproject.toml || die +} + +python_test() { + epytest --ignore tests/particle/test_performance.py +} diff --git a/sci-physics/particle/particle-9999.ebuild b/sci-physics/particle/particle-9999.ebuild new file mode 100644 index 000000000..43f1e67ca --- /dev/null +++ b/sci-physics/particle/particle-9999.ebuild @@ -0,0 +1,44 @@ +EAPI=8 + +PYTHON_COMPAT=( python3_{11..12} ) +DISTUTILS_USE_PEP517=hatchling +inherit distutils-r1 + +DESCRIPTION="PDG particle data and identification codes" +HOMEPAGE="https://github.com/scikit-hep/particle" + +LICENSE="BSD" +SLOT="0" + +if [[ ${PV} == 9999 ]]; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/scikit-hep/particle" +else + inherit pypi + KEYWORDS="~amd64" +fi + +RDEPEND=" + >=dev-python/attrs-19.2[${PYTHON_USEDEP}] + >=sci-physics/hepunits-2.0.0[${PYTHON_USEDEP}] + dev-python/deprecated[${PYTHON_USEDEP}] +" +DEPEND="${RDEPEND}" +BDEPEND=" + test? ( + >=dev-python/pytest-6.0.0[${PYTHON_USEDEP}] + dev-python/pandas[${PYTHON_USEDEP}] + dev-python/tabulate[${PYTHON_USEDEP}] + ) +" +distutils_enable_tests pytest + +src_prepare() { + default + + sed -i -e 's:--benchmark-disable::' pyproject.toml || die +} + +python_test() { + epytest --ignore tests/particle/test_performance.py +} diff --git a/sci-physics/pyhepmc/Manifest b/sci-physics/pyhepmc/Manifest new file mode 100644 index 000000000..1351fa866 --- /dev/null +++ b/sci-physics/pyhepmc/Manifest @@ -0,0 +1 @@ +DIST pyhepmc-2.11.0.tar.gz 361596 BLAKE2B 18264f61bdef3c27f8aa4d48d25257c03f98cc89745533641119cf7ba6d5fe36c084d25ccaeed6769dc9226fd5f2c27060006030447a8ac8409ff6d752437d2c SHA512 31975d0bee5037c1cc36753ce6324342ed6a48b2d3f91f53d61f445f38f0fa3ecbeb0e29fcbc7f6778bafcc23c1f6a689b9516eae8da4cc620cd7c72b89e0b00 diff --git a/sci-physics/pyhepmc/metadata.xml b/sci-physics/pyhepmc/metadata.xml new file mode 100644 index 000000000..6f6a9a0bb --- /dev/null +++ b/sci-physics/pyhepmc/metadata.xml @@ -0,0 +1,19 @@ +<?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> + <maintainer type="person"> + <email>alexander@neuwirth-informatik.de</email> + <name>Alexander Puck Neuwirth</name> + </maintainer> + <longdescription lang="en"> + pyhepmc largely mirrors the C++ interface of the HepMC3 library, which is documented here. Parts of the documentation have been copied from HepMC3. Documentation is available as Python docstrings, so you can use Python's help() browser to learn about the API. Alternatively, you can consult the online reference generated from these docstrings which includes some examples. + </longdescription> + <upstream> + <remote-id type="pypi">pyhepmc</remote-id> + <remote-id type="github">scikit-hep/pyhepmc</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-physics/pyhepmc/pyhepmc-2.11.0.ebuild b/sci-physics/pyhepmc/pyhepmc-2.11.0.ebuild new file mode 100644 index 000000000..c28b094bb --- /dev/null +++ b/sci-physics/pyhepmc/pyhepmc-2.11.0.ebuild @@ -0,0 +1,20 @@ +EAPI=8 + +PYTHON_COMPAT=( python3_{10..12} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 pypi + +DESCRIPTION="A Pythonic wrapper for the HepMC3 C++ library." +HOMEPAGE="https://github.com/scikit-hep/pyhepmc" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + >=dev-python/numpy-1.0[${PYTHON_USEDEP}] +" +BDEPEND=" + ${RDEPEND} + dev-build/cmake +" diff --git a/sci-physics/pyhf/Manifest b/sci-physics/pyhf/Manifest new file mode 100644 index 000000000..756bfb423 --- /dev/null +++ b/sci-physics/pyhf/Manifest @@ -0,0 +1 @@ +DIST pyhf-0.7.3.tar.gz 113423 BLAKE2B 216ef186c539481e2819e3f3a198203f085aa99652ab335b1153309a780857c5ad53bc848bb1b12615cfa9b8ee97a67553cef5a0f899bbcf178bfea1b2ca11c5 SHA512 904491f9c161f0231d1e109cfa3a12b31a31b1aa7477752e1eafd1e6c4cec75551e53ce1f6d447bed8f295371dc20b032888a5175af0f2eb808e03c0a8993930 diff --git a/sci-physics/pyhf/metadata.xml b/sci-physics/pyhf/metadata.xml new file mode 100644 index 000000000..47738d1db --- /dev/null +++ b/sci-physics/pyhf/metadata.xml @@ -0,0 +1,18 @@ +<?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> + <maintainer type="person"> + <email>alexander@neuwirth-informatik.de</email> + <name>Alexander Puck Neuwirth</name> + </maintainer> + <longdescription lang="en"> + The HistFactory p.d.f. template [CERN-OPEN-2012-016] is per-se independent of its implementation in ROOT and sometimes, it’s useful to be able to run statistical analysis outside of ROOT, RooFit, RooStats framework. + </longdescription> + <upstream> + <remote-id type="pypi">particle</remote-id> + <remote-id type="github">scikit-hep/particle</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-physics/pyhf/pyhf-0.7.3.ebuild b/sci-physics/pyhf/pyhf-0.7.3.ebuild new file mode 100644 index 000000000..d97cd71f9 --- /dev/null +++ b/sci-physics/pyhf/pyhf-0.7.3.ebuild @@ -0,0 +1,35 @@ +# Copyright 2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_11 ) +DISTUTILS_USE_PEP517=hatchling + +inherit distutils-r1 pypi + +DESCRIPTION="pure-python fitting/limit-setting/interval estimation HistFactory-style" +HOMEPAGE=" + https://github.com/scikit-hep/pyhf + https://doi.org/10.5281/zenodo.1169739 + https://zenodo.org/record/8256635 + https://doi.org/10.21105/joss.02823 + https://inspirehep.net/literature/2598491 + https://arxiv.org/abs/2211.15838 + https://doi.org/10.22323/1.414.0245 +" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + >=dev-python/scipy-1.5.1[${PYTHON_USEDEP}] + >=dev-python/pyyaml-5.1[${PYTHON_USEDEP}] + >=dev-python/tqdm-4.56.0[${PYTHON_USEDEP}] + >=dev-python/jsonschema-4.15.0[${PYTHON_USEDEP}] + >=dev-python/jsonpatch-1.15[${PYTHON_USEDEP}] + >=dev-python/click-8.0.0[${PYTHON_USEDEP}] +" +DEPEND="${RDEPEND}" diff --git a/sci-physics/pylhe/Manifest b/sci-physics/pylhe/Manifest new file mode 100644 index 000000000..11dbc6d26 --- /dev/null +++ b/sci-physics/pylhe/Manifest @@ -0,0 +1,2 @@ +DIST pylhe-0.7.0.gh.tar.gz 140203 BLAKE2B 6c167b37bb6c978752de79586e4f655169b5134c6cd7637807e649323ebaca50d8a360b1ca32eeff2cc162efe5e13d7de92f72d5a9263a7b2c48a5b87b7b919c SHA512 1a338ab4e1c5dd1d8d80e4a03ad84eb59f19ebb151a4b1393b68ee6ecade920c88db6cb940d56bd1f238e833f59b266507ab678124ea49b4086fe05b7f9baa88 +DIST pylhe-0.8.0.gh.tar.gz 144541 BLAKE2B 5c6a6511acd1adefad6bf3769fdb5ac2a528a8cc939bb1209d7fd4dc31eef9060d129c330b34e3cfc7b640c9b82f68f043e4604f3a535865240ceda0a33dd691 SHA512 6fc3c525cbb5f2ebe8678d1e03940fde8bdc837f1da6a667c70069584de476ea73c72e817cc84637e018ca7cf21e8bb0f7b2721fe54ef78a9b0eee7900ec400e diff --git a/sci-physics/pylhe/files/pylhe-0.7.0-coverage.patch b/sci-physics/pylhe/files/pylhe-0.7.0-coverage.patch new file mode 100644 index 000000000..ea678ce8c --- /dev/null +++ b/sci-physics/pylhe/files/pylhe-0.7.0-coverage.patch @@ -0,0 +1,8 @@ +--- a/pytest.ini 2024-03-20 07:36:32.600030197 +0100 ++++ b/pytest.ini 2024-03-20 07:36:45.896874886 +0100 +@@ -1,4 +1,4 @@ + [pytest] + docstyle_convention = numpy + junit_family = xunit2 +-addopts = --ignore=setup.py --ignore=binder/ --ignore=docs/ --cov=pylhe --cov-report=term-missing --cov-config=.coveragerc --cov-report xml --doctest-modules --doctest-glob='*.rst' ++addopts = --ignore=setup.py --ignore=binder/ --ignore=docs/ --doctest-modules --doctest-glob='*.rst' diff --git a/sci-physics/pylhe/metadata.xml b/sci-physics/pylhe/metadata.xml new file mode 100644 index 000000000..86ede8deb --- /dev/null +++ b/sci-physics/pylhe/metadata.xml @@ -0,0 +1,19 @@ +<?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> + <maintainer type="person"> + <email>alexander@neuwirth-informatik.de</email> + <name>Alexander Puck Neuwirth</name> + </maintainer> + <longdescription lang="en"> + Small and thin Python interface to read Les Houches Event (LHE) files. + </longdescription> + <upstream> + <remote-id type="pypi">pylhe</remote-id> + <remote-id type="github">scikit-hep/pylhe</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-physics/pylhe/pylhe-0.7.0.ebuild b/sci-physics/pylhe/pylhe-0.7.0.ebuild new file mode 100644 index 000000000..45ef91695 --- /dev/null +++ b/sci-physics/pylhe/pylhe-0.7.0.ebuild @@ -0,0 +1,35 @@ +EAPI=8 + +PYTHON_COMPAT=( python3_{11..12} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 pypi + +DESCRIPTION="Lightweight Python interface to read Les Houches Event (LHE) files" +HOMEPAGE="https://github.com/scikit-hep/pylhe" +# pypi does not include tests +SRC_URI="https://github.com/scikit-hep/${PN}/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz" +# export is needed here! +export SETUPTOOLS_SCM_PRETEND_VERSION=${PV} + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + >=dev-python/graphviz-0.12.0[${PYTHON_USEDEP}] + >=sci-physics/particle-0.16[${PYTHON_USEDEP}] + >=dev-python/awkward-1.2.0[${PYTHON_USEDEP}] + >=dev-python/vector-0.8.1[${PYTHON_USEDEP}] +" +DEPEND="${RDEPEND}" +BDEPEND=" + dev-python/setuptools-scm[${PYTHON_USEDEP}] + test? ( + >=sci-physics/scikit-hep-testdata-0.4.36[${PYTHON_USEDEP}] + ) +" +PATCHES=( + "${FILESDIR}/${PN}"-0.7.0-coverage.patch +) + +distutils_enable_tests pytest diff --git a/sci-physics/pylhe/pylhe-0.8.0.ebuild b/sci-physics/pylhe/pylhe-0.8.0.ebuild new file mode 100644 index 000000000..45ef91695 --- /dev/null +++ b/sci-physics/pylhe/pylhe-0.8.0.ebuild @@ -0,0 +1,35 @@ +EAPI=8 + +PYTHON_COMPAT=( python3_{11..12} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 pypi + +DESCRIPTION="Lightweight Python interface to read Les Houches Event (LHE) files" +HOMEPAGE="https://github.com/scikit-hep/pylhe" +# pypi does not include tests +SRC_URI="https://github.com/scikit-hep/${PN}/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz" +# export is needed here! +export SETUPTOOLS_SCM_PRETEND_VERSION=${PV} + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + >=dev-python/graphviz-0.12.0[${PYTHON_USEDEP}] + >=sci-physics/particle-0.16[${PYTHON_USEDEP}] + >=dev-python/awkward-1.2.0[${PYTHON_USEDEP}] + >=dev-python/vector-0.8.1[${PYTHON_USEDEP}] +" +DEPEND="${RDEPEND}" +BDEPEND=" + dev-python/setuptools-scm[${PYTHON_USEDEP}] + test? ( + >=sci-physics/scikit-hep-testdata-0.4.36[${PYTHON_USEDEP}] + ) +" +PATCHES=( + "${FILESDIR}/${PN}"-0.7.0-coverage.patch +) + +distutils_enable_tests pytest diff --git a/sci-physics/qcdloop/Manifest b/sci-physics/qcdloop/Manifest new file mode 100644 index 000000000..84ca31226 --- /dev/null +++ b/sci-physics/qcdloop/Manifest @@ -0,0 +1,2 @@ +DIST qcdloop-2.0.5.tar.gz 199141 BLAKE2B b16c193bd267b838535a572dd3b1cf50ac9af03b65347877b550bcbdcc9cfdd42f08e198732c513cff8298632ea65be82f2986701de75cee80cec2f9c30e3368 SHA512 9bfa3bad7a8c808b2db5eda32a755da4dadf67eba10845eb798d447fd47062bd40aa877929b60d95ec6b4e3b4a2cbba6384a3d1b13f92cfdec06e76177532c0f +DIST qcdloop-2.0.9.tar.gz 214697 BLAKE2B 19d426cc61b8a8f08fc56522b5a2d48c7fea7027225e1317c2e2908b8a87367ff69077bfe5508ee50ee585d8d0f68ae4c1fdad312b4cbc73ca4f3fd735fa94c9 SHA512 c8031dbee1c83d2bd0fcca0b1d94f18e7d07b77c247ca7a15cfec9bc402391e89036a64507c48e743eeecb3a19fe25d4e766ff13ede9f042d4d723adc8adb238 diff --git a/sci-physics/qcdloop/files/qcdloop-2.0.5-cxx.patch b/sci-physics/qcdloop/files/qcdloop-2.0.5-cxx.patch new file mode 100644 index 000000000..56a665de2 --- /dev/null +++ b/sci-physics/qcdloop/files/qcdloop-2.0.5-cxx.patch @@ -0,0 +1,11 @@ +--- a/CMakeLists.txt 2022-09-19 11:13:08.777453946 +0200 ++++ b/CMakeLists.txt 2022-09-19 11:13:27.315507011 +0200 +@@ -20,7 +20,7 @@ + set(CMAKE_CXX_STANDARD_REQUIRED ON) + set(CMAKE_CXX_EXTENSIONS OFF) + set(VERSION "\"2.0.5\"") +-set(CMAKE_CXX_FLAGS "-Wall -Wextra -march=nocona -mtune=haswell -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -fext-numeric-literals") ++set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fext-numeric-literals") + set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -fsanitize=address -fPIC ${CMAKE_CXX_FLAGS}" CACHE STRING "debug compile flags" FORCE) + set(CMAKE_EXE_LINKER_FLAGS_DEBUG "-fsanitize=address" CACHE STRING "debug linker flags" FORCE) + set(prefix ${CMAKE_INSTALL_PREFIX}) diff --git a/sci-physics/qcdloop/files/qcdloop-2.0.9-cxx.patch b/sci-physics/qcdloop/files/qcdloop-2.0.9-cxx.patch new file mode 100644 index 000000000..b3babf764 --- /dev/null +++ b/sci-physics/qcdloop/files/qcdloop-2.0.9-cxx.patch @@ -0,0 +1,11 @@ +--- a/CMakeLists.txt 2022-09-19 11:13:08.777453946 +0200 ++++ b/CMakeLists.txt 2022-09-19 11:13:27.315507011 +0200 +@@ -20,7 +20,7 @@ + set(CMAKE_CXX_STANDARD_REQUIRED ON) + set(CMAKE_CXX_EXTENSIONS OFF) + set(VERSION "\"2.0.9\"") +-set(CMAKE_CXX_FLAGS "-Wall -Wextra -march=nocona -mtune=haswell -fvisibility-inlines-hidden -fmessage-length=0 -ftree-vectorize -fPIC -fstack-protector-strong -O2 -pipe -fext-numeric-literals") ++set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fext-numeric-literals") + set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -fsanitize=address -fPIC ${CMAKE_CXX_FLAGS}" CACHE STRING "debug compile flags" FORCE) + set(CMAKE_EXE_LINKER_FLAGS_DEBUG "-fsanitize=address" CACHE STRING "debug linker flags" FORCE) + set(prefix ${CMAKE_INSTALL_PREFIX}) diff --git a/sci-physics/qcdloop/metadata.xml b/sci-physics/qcdloop/metadata.xml new file mode 100644 index 000000000..84c79dc3b --- /dev/null +++ b/sci-physics/qcdloop/metadata.xml @@ -0,0 +1,18 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>alexander@neuwirth-informatik.de</email> + <name>Alexander Puck Neuwirth</name> + </maintainer> + <maintainer type="project"> + <email>sci-physics@gentoo.org</email> + <name>Gentoo Physics Project</name> + </maintainer> + <longdescription lang="en"> + QCDLoop is a library of one-loop scalar Feynman integrals, evaluated close to four dimensions. First documented in arXiv:0712.1851 and recently in arXiv:1605.03181. + </longdescription> + <upstream> + <remote-id type="github">scarrazza/qcdloop</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-physics/qcdloop/qcdloop-2.0.5.ebuild b/sci-physics/qcdloop/qcdloop-2.0.5.ebuild new file mode 100644 index 000000000..19a247ba2 --- /dev/null +++ b/sci-physics/qcdloop/qcdloop-2.0.5.ebuild @@ -0,0 +1,33 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +CMAKE_MAKEFILE_GENERATOR="emake" + +inherit cmake + +DESCRIPTION="An object-oriented one-loop scalar Feynman integrals framework" +HOMEPAGE="https://qcdloop.web.cern.ch/qcdloop/" +SRC_URI="https://github.com/scarrazza/${PN}/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="GPL-3+" +SLOT="0" +KEYWORDS="~amd64" + +DEPEND="" +RDEPEND="${DEPEND}" +BDEPEND=" + virtual/fortran +" + +PATCHES=( + "${FILESDIR}"/${P}-cxx.patch +) + +src_configure() { + local mycmakeargs=( + -DCMAKE_INSTALL_PREFIX="${ESYSROOT}/usr/$(get_libdir)" + ) + cmake_src_configure +} diff --git a/sci-physics/qcdloop/qcdloop-2.0.9.ebuild b/sci-physics/qcdloop/qcdloop-2.0.9.ebuild new file mode 100644 index 000000000..ccea20aa5 --- /dev/null +++ b/sci-physics/qcdloop/qcdloop-2.0.9.ebuild @@ -0,0 +1,50 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +CMAKE_MAKEFILE_GENERATOR="emake" + +inherit cmake + +DESCRIPTION="An object-oriented one-loop scalar Feynman integrals framework" +HOMEPAGE="https://qcdloop.web.cern.ch/qcdloop/" +SRC_URI="https://github.com/scarrazza/${PN}/archive/refs/tags/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="GPL-3+" +SLOT="0" +KEYWORDS="~amd64" + +DEPEND="" +RDEPEND="${DEPEND}" +BDEPEND=" + virtual/fortran +" + +PATCHES=( + "${FILESDIR}"/${P}-cxx.patch +) + +src_prepare() { + cmake_src_prepare + + # gentoo libdir love + sed -i \ + -e '/DESTINATION/s/lib/lib${LIB_SUFFIX}/g' \ + CMakeLists.txt || die + sed -i \ + -e '/libdir.*/s/lib/lib${LIB_SUFFIX}/g' \ + CMakeLists.txt || die + + #sed -i \ + # -e '/qcdloop/s/SHARED/STATIC/g' \ + # CMakeLists.txt || die +} + +src_configure() { + local mycmakeargs=( + -DCMAKE_INSTALL_PREFIX="${ESYSROOT}"/usr + -DENABLE_FORTRAN_WRAPPER=ON + ) + cmake_src_configure +} diff --git a/sci-physics/qgraf/Manifest b/sci-physics/qgraf/Manifest new file mode 100644 index 000000000..32519be3c --- /dev/null +++ b/sci-physics/qgraf/Manifest @@ -0,0 +1,3 @@ +DIST qgraf-3.4.2.tgz 358979 BLAKE2B 06c5cf82faab531d6d17387d62e80b2e395ad0ffd80a69dc49608588f4acdf23d226877db047d3906963b5f64d85329665fed0e10359ddbb649122fb328b78f8 SHA512 e86f94480eaf7cd0b4d79b60ec1420c21f0285133f2184d1c0a1d05ec0d9abc3e483d100d43c38fafc06bf8cecea413c0304adcb64d900522e877b1a24e7b61b +DIST qgraf-3.5.2.tgz 426930 BLAKE2B 0bd50cbefee9a91cdfe9a15a53fb018c1b15088b211a03dde63f08410bbac4acd7586ef4cece17debd5197d3d5b7a8c889aeec27d7f3f137df7ef95f1687a709 SHA512 1e1fbafc80c60a663537a5ca555f405ec1517beccf09e2f68fcd9c84963b4b20d3a66e77980c4c4ff68f82950dc41f4492dc0272fdf5e3c105861fcf4c0e8c80 +DIST qgraf-3.6.7.tgz 460592 BLAKE2B d4275d7e5b9138eab3a2848b1e75883a4d52b61bdddd2ecbefe674559a56d9315bb03bd86c5a607f01d708c634f35b180f4cfde99242e65a40bf3f81ce6fa9e3 SHA512 c721eb82975a6077da77a82f7875d0e0346e21932d0312109d1bab68391a0210fc3f7ff79327d515668dedee0c5fce4e01d7433177232c43a4e39d8204f01405 diff --git a/sci-physics/qgraf/metadata.xml b/sci-physics/qgraf/metadata.xml new file mode 100644 index 000000000..3fa7c9624 --- /dev/null +++ b/sci-physics/qgraf/metadata.xml @@ -0,0 +1,15 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <maintainer type="person"> + <email>alexander@neuwirth-informatik.de</email> + <name>Alexander Puck Neuwirth</name> + </maintainer> + <maintainer type="project" proxied="proxy"> + <email>sci-physics@gentoo.org</email> + <name>Gentoo Physics Project</name> + </maintainer> + <longdescription lang="en"> + Qgraf is a computer program that generates Feynman diagrams for various types of QFT models — it is a research tool created with the obvious aim of contributing to extend the range of feasible, perturbative QFT calculations. It generates neither 0-point nor non-connected diagrams, though. Diagrams are represented by symbolic expressions only; nevertheless, if some kind of graphical representation is required, have a look at the external links. + </longdescription> +</pkgmetadata> diff --git a/sci-physics/qgraf/qgraf-3.4.2.ebuild b/sci-physics/qgraf/qgraf-3.4.2.ebuild new file mode 100644 index 000000000..cdab94002 --- /dev/null +++ b/sci-physics/qgraf/qgraf-3.4.2.ebuild @@ -0,0 +1,32 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit toolchain-funcs fortran-2 + +DESCRIPTION="qgraf generates Feynman diagrams for various types of QFT models" +HOMEPAGE="http://cfif.ist.utl.pt/~paulo/qgraf.html" +SRC_URI="http://anonymous:anonymous@qgraf.tecnico.ulisboa.pt/v$(ver_cut 1-2)/qgraf-${PV}.tgz" +S="${WORKDIR}" + +LICENSE="all-rights-reserved" +RESTRICT="bindist mirror" +SLOT="0" +KEYWORDS="~amd64" +IUSE="doc examples" + +src_compile() { + $(tc-getFC) ${P}.f -o ${PN} ${FFLAGS} ${LDFLAGS} || die "Failed to compile" +} + +src_install() { + dobin ${PN} + + use doc && dodoc *.pdf + if use examples; then + docinto examples + dodoc phi3 qed qcd *.sty *.dat + docompress -x /usr/share/doc/${PF}/examples + fi +} diff --git a/sci-physics/qgraf/qgraf-3.5.2.ebuild b/sci-physics/qgraf/qgraf-3.5.2.ebuild new file mode 100644 index 000000000..4194295a4 --- /dev/null +++ b/sci-physics/qgraf/qgraf-3.5.2.ebuild @@ -0,0 +1,32 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit toolchain-funcs fortran-2 + +DESCRIPTION="qgraf generates Feynman diagrams for various types of QFT models" +HOMEPAGE="http://cfif.ist.utl.pt/~paulo/qgraf.html" +SRC_URI="http://anonymous:anonymous@qgraf.tecnico.ulisboa.pt/v$(ver_cut 1-2)/qgraf-${PV}.tgz" +S="${WORKDIR}" + +LICENSE="all-rights-reserved" +RESTRICT="bindist mirror" +SLOT="0" +KEYWORDS="~amd64" +IUSE="doc examples" + +src_compile() { + $(tc-getFC) ${P}.f08 -o ${PN} ${FFLAGS} ${LDFLAGS} || die "Failed to compile" +} + +src_install() { + dobin ${PN} + + use doc && dodoc *.pdf + if use examples; then + docinto examples + dodoc phi3 qed qcd *.sty *.dat + docompress -x /usr/share/doc/${PF}/examples + fi +} diff --git a/sci-physics/qgraf/qgraf-3.6.7.ebuild b/sci-physics/qgraf/qgraf-3.6.7.ebuild new file mode 100644 index 000000000..4194295a4 --- /dev/null +++ b/sci-physics/qgraf/qgraf-3.6.7.ebuild @@ -0,0 +1,32 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit toolchain-funcs fortran-2 + +DESCRIPTION="qgraf generates Feynman diagrams for various types of QFT models" +HOMEPAGE="http://cfif.ist.utl.pt/~paulo/qgraf.html" +SRC_URI="http://anonymous:anonymous@qgraf.tecnico.ulisboa.pt/v$(ver_cut 1-2)/qgraf-${PV}.tgz" +S="${WORKDIR}" + +LICENSE="all-rights-reserved" +RESTRICT="bindist mirror" +SLOT="0" +KEYWORDS="~amd64" +IUSE="doc examples" + +src_compile() { + $(tc-getFC) ${P}.f08 -o ${PN} ${FFLAGS} ${LDFLAGS} || die "Failed to compile" +} + +src_install() { + dobin ${PN} + + use doc && dodoc *.pdf + if use examples; then + docinto examples + dodoc phi3 qed qcd *.sty *.dat + docompress -x /usr/share/doc/${PF}/examples + fi +} diff --git a/sci-physics/quinoa/metadata.xml b/sci-physics/quinoa/metadata.xml deleted file mode 100644 index 2e043b786..000000000 --- a/sci-physics/quinoa/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>junghans@gentoo.org</email> - <name>Christoph Junghans</name> - </maintainer> - <maintainer type="project"> - <email>sci-physics@gentoo.org</email> - <name>Gentoo Physics Project</name> - </maintainer> -</pkgmetadata> diff --git a/sci-physics/quinoa/quinoa-9999.ebuild b/sci-physics/quinoa/quinoa-9999.ebuild deleted file mode 100644 index 18ba346a4..000000000 --- a/sci-physics/quinoa/quinoa-9999.ebuild +++ /dev/null @@ -1,45 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -DOCS_BUILDER="doxygen" -DOCS_DIR="doc" -DOCS_CONFIG_NAME="${PN}.doxy" - -inherit cmake docs git-r3 - -DESCRIPTION="Adaptive computational fluid dynamics" -HOMEPAGE="https://quinoacomputing.org/" -EGIT_REPO_URI="git://github.com/quinoacomputing/${PN}.git" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="" - -DEPEND=" - dev-cpp/highwayhash - dev-cpp/pstreams - dev-cpp/random123 - dev-libs/boost - dev-libs/boost-mpl-cartesian_product - >=dev-libs/pegtl-2 - dev-libs/pugixml - dev-libs/tut - dev-util/mad-numdiff - sci-libs/gmsh - sci-libs/h5part - sci-libs/hypre[mpi] - sci-libs/mkl - >=sci-libs/trilinos-12.10.1[netcdf] - >=sys-cluster/charm-6.7.1[mpi] - virtual/lapacke -" -RDEPEND="${DEPEND}" - -CMAKE_USE_DIR="${S}/src" - -src_compile() { - docs_compile - cmake_src_compile -} diff --git a/sci-physics/scikit-hep-testdata/Manifest b/sci-physics/scikit-hep-testdata/Manifest new file mode 100644 index 000000000..1051bc85d --- /dev/null +++ b/sci-physics/scikit-hep-testdata/Manifest @@ -0,0 +1 @@ +DIST scikit-hep-testdata-0.4.39.gh.tar.gz 340561478 BLAKE2B 9d0fc60c8bd9c11b5cd786389489b095a5498c7e08c744106d3bacd3f203f4b186f50a5e1ef6cbdcb23fc5d975807277cc25397ea8049e2acccbbc06c53f65d2 SHA512 fe31302178b8148b0486fe314a9d40c7a4318e53113878769484cc79dd55e5adb977357a175ffad887a205e1ea3e99a4f5be192581cca61554ba2187daad3bd2 diff --git a/sci-physics/scikit-hep-testdata/metadata.xml b/sci-physics/scikit-hep-testdata/metadata.xml new file mode 100644 index 000000000..ea2e37599 --- /dev/null +++ b/sci-physics/scikit-hep-testdata/metadata.xml @@ -0,0 +1,19 @@ +<?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> + <maintainer type="person"> + <email>alexander@neuwirth-informatik.de</email> + <name>Alexander Puck Neuwirth</name> + </maintainer> + <longdescription lang="en"> + A common package to provide example files (e.g. ROOT) for testing and developing packages against. The sample of files is representative of typical files found "in the wild". + </longdescription> + <upstream> + <remote-id type="pypi">scikit-hep-testdata</remote-id> + <remote-id type="github">scikit-hep/scikit-hep-testdata</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-physics/scikit-hep-testdata/scikit-hep-testdata-0.4.39.ebuild b/sci-physics/scikit-hep-testdata/scikit-hep-testdata-0.4.39.ebuild new file mode 100644 index 000000000..47d0f0bbd --- /dev/null +++ b/sci-physics/scikit-hep-testdata/scikit-hep-testdata-0.4.39.ebuild @@ -0,0 +1,30 @@ +EAPI=8 + +PYTHON_COMPAT=( python3_{10..12} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 pypi + +DESCRIPTION="A package to provide example files for testing and developing packages against." +HOMEPAGE="https://github.com/scikit-hep/scikit-hep-testdata" +# pypi does not include the data nor tests +SRC_URI="https://github.com/scikit-hep/${PN}/archive/refs/tags/v${PV}.tar.gz -> ${P}.gh.tar.gz" +S="${WORKDIR}/${P}" +# export is needed here! +export SETUPTOOLS_SCM_PRETEND_VERSION=${PV} +# otherwise we don't install the data +export SKHEP_DATA=1 + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + dev-python/pyyaml[${PYTHON_USEDEP}] + dev-python/requests[${PYTHON_USEDEP}] +" +DEPEND="${RDEPEND}" +BDEPEND=" + dev-python/setuptools-scm[${PYTHON_USEDEP}] +" + +distutils_enable_tests pytest diff --git a/sci-physics/spheno/Manifest b/sci-physics/spheno/Manifest new file mode 100644 index 000000000..5db72217b --- /dev/null +++ b/sci-physics/spheno/Manifest @@ -0,0 +1,2 @@ +DIST spheno-3.3.8.tar.gz 1415645 BLAKE2B 830cdbcd8f213f0de0cd0b72455d5919e390069f097bca5a0cabdbfb77ec21549c9455139ff960a0cdbd425368805c1f2d11384c240a8e82f66e33864f4fce7b SHA512 e6c923586eae198f62121e0410f9f1f87e7badfd58d90e3b5f600e8364ea054dfb8b58c1c39d74ec6067112fa6cad727797230bce6cfc6040e2bf4c6d01b0eae +DIST spheno-4.0.5.tar.gz 1587855 BLAKE2B d3cb92740be416934a928147d980e180be623dbbfeac7a1b0b16e7e4a36d2b3088e455b5348f6e65cfa2ac8d90286c0b65a81498527419ed4eaa42622651408b SHA512 387099c3d9c9c7baf4a5da6d46b819d53dc703f72cc3a73fac7c2e63b66623e328294ac131e128253002ab03a81e96c686702ac90a58479ae573f228d3a51379 diff --git a/sci-physics/spheno/files/spheno-3.3.8-gfortran.patch b/sci-physics/spheno/files/spheno-3.3.8-gfortran.patch new file mode 100644 index 000000000..8f6fa7e19 --- /dev/null +++ b/sci-physics/spheno/files/spheno-3.3.8-gfortran.patch @@ -0,0 +1,32 @@ +--- a/src/Makefile 2022-07-20 11:47:44.078639381 +0200 ++++ b/src/Makefile 2022-07-24 02:16:38.972041809 +0200 +@@ -9,10 +9,11 @@ + # options for various compilers + # + +-# Intels ifort, default in optimized mode +-F90 = ifort +-comp = -c -O -module ${Mdir} -I${InDir} +-LFlagsB = -O ++ ++# gentoo toolchain ++F90 = ${F90} ++comp = -c -O -J${Mdir} -I${InDir} ${FFLAGS} ${FCFLAGS} ${CFLAGS} ++LFlagsB = -O ${LDFLAGS} + + # Intels ifort, debug modus + ifeq (${F90},ifortg) +@@ -70,11 +71,11 @@ + # + .f90.a: + ${F90} ${comp} $< +- ar -ruc $@ $*.o ++ $(AR) -ruc $@ $*.o + rm -f $*.o + .F90.a: + ${F90} ${comp} ${PreDef} $< +- ar -ruc $@ $*.o ++ $(AR) -ruc $@ $*.o + rm -f $*.o + .f90.o: + ${F90} ${comp} $< diff --git a/sci-physics/spheno/files/spheno-4.0.5-gfortran.patch b/sci-physics/spheno/files/spheno-4.0.5-gfortran.patch new file mode 100644 index 000000000..1abf36367 --- /dev/null +++ b/sci-physics/spheno/files/spheno-4.0.5-gfortran.patch @@ -0,0 +1,29 @@ +--- a/src/Makefile 2023-05-04 12:33:44.804394098 +0200 ++++ b/src/Makefile 2023-05-04 12:34:37.023776033 +0200 +@@ -21,9 +21,9 @@ + #
+
+ # Intels ifort, default in optimized mode
+-F90 = ifort
+-comp = -c -O -module ${Mdir} -I${InDir}
+-LFlagsB = -O
++F90 = ${F90}
++comp = -c -O -J${Mdir} -I${InDir} ${FFLAGS} ${FCFLAGS} ${CFLAGS}
++LFlagsB = -O ${LDFLAGS}
+
+ # Intels ifort, debug modus
+ ifeq (${F90},ifortg)
+@@ -81,11 +81,11 @@ + #
+ .f90.a:
+ ${F90} ${comp} $<
+- ar ${linker} $@ $*.o
++ $(AR) ${linker} $@ $*.o
+ rm -f $*.o
+ .F90.a:
+ ${F90} ${comp} ${PreDef} $<
+- ar ${linker} $@ $*.o
++ $(AR) ${linker} $@ $*.o
+ rm -f $*.o
+ .f90.o:
+ ${F90} ${comp} $<
diff --git a/sci-physics/spheno/metadata.xml b/sci-physics/spheno/metadata.xml new file mode 100644 index 000000000..277841e1a --- /dev/null +++ b/sci-physics/spheno/metadata.xml @@ -0,0 +1,19 @@ +<?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> + <maintainer type="project"> + <email>sci-physics@gentoo.org</email> + <name>Gentoo Physics Project</name> + </maintainer> + <maintainer type="person"> + <email>alexander@neuwirth-informatik.de</email> + <name>Alexander Puck Neuwirth</name> + </maintainer> + <longdescription lang="en"> +The code calculates the SUSY spectrum using low energy data and a user supplied high scale model as input. The spectrum is used to calculate two- and three body decay modes of supersymmetric particle as well as of Higgs bosons. In addition the production cross sections for supersymmetric particle and Higgs bosons in e^+ e^- annihilation is calculated. Moreover, the branching of the decay $b \to s \gamma$, the SUSY contribution to anomalous magnetic moment of the muon as well as the SUSY contributions to the rho parameter due to sfermions are calculated. The code is written in F90 with an emphasis on easy generalisability. The structure is set such that complex phases as well as the extension to include the flavour structure can be done in a straight forward way. The 2-loop renormalization group equations as well as the one-loop finite corrections a la Bagger, Matchev, Pierce and Zhang are included. In addition the two-loop corrections to the neutral Higgs boson masses (a la Brignole, Degrassi, Slavich and Zwirner) and to the mu-parameter (a la Dedes and Slavich) are included. Starting with version 2.2.2 the SUSY Les Houches Accord is supported as well as the SPA conventions (for details see hep-ph/0511344). + </longdescription> +</pkgmetadata> diff --git a/sci-physics/spheno/spheno-3.3.8-r1.ebuild b/sci-physics/spheno/spheno-3.3.8-r1.ebuild new file mode 100644 index 000000000..7ed53c4c7 --- /dev/null +++ b/sci-physics/spheno/spheno-3.3.8-r1.ebuild @@ -0,0 +1,39 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit fortran-2 + +MY_PN=SPheno +MY_P=${MY_PN}-${PV} + +DESCRIPTION="SPheno stands for S(upersymmetric) Pheno(menology)" +HOMEPAGE="https://spheno.hepforge.org/" +SRC_URI="https://spheno.hepforge.org/downloads/?f=${MY_P}.tar.gz -> ${P}.tar.gz" +S="${WORKDIR}/${MY_P}" + +LICENSE="all-rights-reserved" +RESTRICT="bindist mirror" +SLOT="0" +KEYWORDS="~amd64" + +PATCHES=( "${FILESDIR}"/${P}-gfortran.patch ) + +src_compile() { + # single thread force needed since fortan mods depend on each other + emake -j1 F90="${FC}" +} + +src_install() { + dobin bin/${MY_PN} + # convenience symlink since the package is lowercase but the default produced binary is uppercase + dosym ${MY_PN} /usr/bin/${PN} + dolib.a lib/lib${MY_PN}.a + mv include ${PN} + doheader -r ${PN} + dodoc doc/* + docinto examples + dodoc input/* + docompress -x /usr/share/doc/${PF}/examples +} diff --git a/sci-physics/spheno/spheno-4.0.5.ebuild b/sci-physics/spheno/spheno-4.0.5.ebuild new file mode 100644 index 000000000..7ed53c4c7 --- /dev/null +++ b/sci-physics/spheno/spheno-4.0.5.ebuild @@ -0,0 +1,39 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit fortran-2 + +MY_PN=SPheno +MY_P=${MY_PN}-${PV} + +DESCRIPTION="SPheno stands for S(upersymmetric) Pheno(menology)" +HOMEPAGE="https://spheno.hepforge.org/" +SRC_URI="https://spheno.hepforge.org/downloads/?f=${MY_P}.tar.gz -> ${P}.tar.gz" +S="${WORKDIR}/${MY_P}" + +LICENSE="all-rights-reserved" +RESTRICT="bindist mirror" +SLOT="0" +KEYWORDS="~amd64" + +PATCHES=( "${FILESDIR}"/${P}-gfortran.patch ) + +src_compile() { + # single thread force needed since fortan mods depend on each other + emake -j1 F90="${FC}" +} + +src_install() { + dobin bin/${MY_PN} + # convenience symlink since the package is lowercase but the default produced binary is uppercase + dosym ${MY_PN} /usr/bin/${PN} + dolib.a lib/lib${MY_PN}.a + mv include ${PN} + doheader -r ${PN} + dodoc doc/* + docinto examples + dodoc input/* + docompress -x /usr/share/doc/${PF}/examples +} diff --git a/sci-physics/tauola/tauola-1.1.8.ebuild b/sci-physics/tauola/tauola-1.1.8.ebuild index 61ec51d9f..4d4742dd1 100644 --- a/sci-physics/tauola/tauola-1.1.8.ebuild +++ b/sci-physics/tauola/tauola-1.1.8.ebuild @@ -21,7 +21,7 @@ RDEPEND=" " DEPEND="${RDEPEND} doc? ( - app-doc/doxygen[dot] + app-text/doxygen[dot] app-text/ghostscript-gpl app-text/texlive ) diff --git a/sci-physics/uproot/Manifest b/sci-physics/uproot/Manifest new file mode 100644 index 000000000..bb52077be --- /dev/null +++ b/sci-physics/uproot/Manifest @@ -0,0 +1 @@ +DIST uproot-5.3.1.tar.gz 919910 BLAKE2B 6c138a56ecabb08905e1edde8c776c3dfae6cca3213bbc3546e7241979052178e1c9718c1fcf298573669bcc4c004806cd54ab16050405038f76f3ef356fb184 SHA512 2525f372caa3b25e3a11b170ce981ce253a7b9ca1fdb2c04b6bb1093b166d206a28e9bc22ffa19dead76870f521cee44a812cbf41a087b34fb9a3bc52c210733 diff --git a/sci-physics/uproot/metadata.xml b/sci-physics/uproot/metadata.xml new file mode 100644 index 000000000..1b293facb --- /dev/null +++ b/sci-physics/uproot/metadata.xml @@ -0,0 +1,21 @@ +<?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> + <maintainer type="person"> + <email>alexander@neuwirth-informatik.de</email> + <name>Alexander Puck Neuwirth</name> + </maintainer> + <longdescription lang="en"> + Uproot is a library for reading and writing ROOT files in pure Python and NumPy. + + Unlike the standard C++ ROOT implementation, Uproot is only an I/O library, primarily intended to stream data into machine learning libraries in Python. Unlike PyROOT and root_numpy, Uproot does not depend on C++ ROOT. Instead, it uses Numpy to cast blocks of data from the ROOT file as Numpy arrays. + </longdescription> + <upstream> + <remote-id type="pypi">uproot</remote-id> + <remote-id type="github">scikit-hep/uproot5</remote-id> + </upstream> +</pkgmetadata> diff --git a/sci-physics/uproot/uproot-5.3.1.ebuild b/sci-physics/uproot/uproot-5.3.1.ebuild new file mode 100644 index 000000000..cfc3880e9 --- /dev/null +++ b/sci-physics/uproot/uproot-5.3.1.ebuild @@ -0,0 +1,28 @@ +EAPI=8 + +PYTHON_COMPAT=( python3_{10..12} ) +DISTUTILS_USE_PEP517=hatchling +SETUPTOOLS_SCM_PRETEND_VERSION=${PV} +inherit distutils-r1 pypi + +DESCRIPTION="ROOT I/O in pure Python and Numpy." +HOMEPAGE="https://github.com/scikit-hep/uproot" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + >=dev-python/awkward-2.4.6[${PYTHON_USEDEP}] + >=dev-python/cramjam-2.5.0[${PYTHON_USEDEP}] + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/fsspec[${PYTHON_USEDEP}] + dev-python/packaging[${PYTHON_USEDEP}] +" +DEPEND="${RDEPEND}" +BDEPEND=" + dev-python/hatch-vcs[${PYTHON_USEDEP}] +" + +# way too many missing packages, isal, deflate, xxhash, http servers etc +# distutils_enable_tests pytest diff --git a/sci-visualization/clip/metadata.xml b/sci-visualization/clip/metadata.xml index e97c4322a..8f000a818 100644 --- a/sci-visualization/clip/metadata.xml +++ b/sci-visualization/clip/metadata.xml @@ -9,4 +9,7 @@ <email>sci@gentoo.org</email> <name>Gentoo Science Project</name> </maintainer> + <upstream> + <remote-id type="github">asmuth/clip</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-visualization/forge/forge-1.0.5.ebuild b/sci-visualization/forge/forge-1.0.5.ebuild index b222dac0c..dd708d35f 100644 --- a/sci-visualization/forge/forge-1.0.5.ebuild +++ b/sci-visualization/forge/forge-1.0.5.ebuild @@ -33,7 +33,7 @@ RDEPEND=" DEPEND="${RDEPEND}" BDEPEND=" doc? ( - app-doc/doxygen + app-text/doxygen dev-python/breathe dev-python/recommonmark dev-python/sphinx diff --git a/sci-visualization/forge/forge-1.0.7.ebuild b/sci-visualization/forge/forge-1.0.7.ebuild index b222dac0c..dd708d35f 100644 --- a/sci-visualization/forge/forge-1.0.7.ebuild +++ b/sci-visualization/forge/forge-1.0.7.ebuild @@ -33,7 +33,7 @@ RDEPEND=" DEPEND="${RDEPEND}" BDEPEND=" doc? ( - app-doc/doxygen + app-text/doxygen dev-python/breathe dev-python/recommonmark dev-python/sphinx diff --git a/sci-visualization/forge/forge-9999.ebuild b/sci-visualization/forge/forge-9999.ebuild index b222dac0c..dd708d35f 100644 --- a/sci-visualization/forge/forge-9999.ebuild +++ b/sci-visualization/forge/forge-9999.ebuild @@ -33,7 +33,7 @@ RDEPEND=" DEPEND="${RDEPEND}" BDEPEND=" doc? ( - app-doc/doxygen + app-text/doxygen dev-python/breathe dev-python/recommonmark dev-python/sphinx diff --git a/sci-visualization/fsleyes-props/Manifest b/sci-visualization/fsleyes-props/Manifest index 51fcf1b3c..6cafd64da 100644 --- a/sci-visualization/fsleyes-props/Manifest +++ b/sci-visualization/fsleyes-props/Manifest @@ -1 +1 @@ -DIST props-1.7.3.tar.gz 122655 BLAKE2B 158d1fe055ed977455888af6daa2f07d12cc98156ada67e3ffb78336423b18ecb321c8be0b3265e98a3352fd9f2dd6b1520b5bf6c3cae7ed9ca84053e4ad4f22 SHA512 9ae299ad67e9a0da8c09235e911679254df1331deb6f1ef1c3eff42a67877eff7766d91917c2c72103e2e0c247912b6e7f11c2f3abe5d91ccd0507854adda9a7 +DIST props-1.8.2.tar.gz 124579 BLAKE2B 5a4a399c18b3a8299fa62d378713988c42f25fba7baa90f52b81aad6786dafeda1dc3fb273f159e88d17b5319977ca007854253eba781b579fd771a84d812bba SHA512 66c6e6d47ecd17e7bde245a6b8c94b3710dbec01e16d1829a257c3315d2f013dcce878f972eb65d0642a0231445f1cc1b0b16987676f5c2ea19e62fe19a9432f diff --git a/sci-visualization/fsleyes-props/fsleyes-props-1.7.3.ebuild b/sci-visualization/fsleyes-props/fsleyes-props-1.7.3.ebuild deleted file mode 100644 index b3440c6ba..000000000 --- a/sci-visualization/fsleyes-props/fsleyes-props-1.7.3.ebuild +++ /dev/null @@ -1,41 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{8..9} ) - -inherit distutils-r1 virtualx - -MY_PN="props" - -DESCRIPTION="Object attribute management for the FSLeyes viewer" -HOMEPAGE="https://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/tree/master" -SRC_URI="https://git.fmrib.ox.ac.uk/fsl/fsleyes/${MY_PN}/-/archive/${PV}/${MY_PN}-${PV}.tar.gz" -S="${WORKDIR}/${MY_PN}-${PV}" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -RDEPEND=" - dev-python/numpy[${PYTHON_USEDEP}] - dev-python/matplotlib[${PYTHON_USEDEP}] - >=dev-python/wxpython-3.0.2.0[${PYTHON_USEDEP}] - >=sci-visualization/fsleyes-widgets-0.6[${PYTHON_USEDEP}] - >=dev-python/fslpy-1.4[${PYTHON_USEDEP}] -" - -distutils_enable_tests pytest -distutils_enable_sphinx doc dev-python/sphinx_rtd_theme - -python_prepare_all() { - # do not depend on pytest-cov - sed -i -e '/addopts/d' setup.cfg || die - - distutils-r1_python_prepare_all -} - -python_test() { - virtx epytest -} diff --git a/sci-visualization/fsleyes-props/fsleyes-props-1.8.2.ebuild b/sci-visualization/fsleyes-props/fsleyes-props-1.8.2.ebuild new file mode 100644 index 000000000..12364b0cc --- /dev/null +++ b/sci-visualization/fsleyes-props/fsleyes-props-1.8.2.ebuild @@ -0,0 +1,45 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_10 ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 virtualx + +MY_PN="props" + +DESCRIPTION="Object attribute management for the FSLeyes viewer" +HOMEPAGE="https://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/tree/master" +SRC_URI="https://git.fmrib.ox.ac.uk/fsl/fsleyes/${MY_PN}/-/archive/${PV}/${MY_PN}-${PV}.tar.gz" +S="${WORKDIR}/${MY_PN}-${PV}" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +RDEPEND=" + dev-python/numpy[${PYTHON_USEDEP}] + dev-python/matplotlib[${PYTHON_USEDEP}] + >=dev-python/wxpython-3.0.2.0[${PYTHON_USEDEP}] + >=sci-visualization/fsleyes-widgets-0.6[${PYTHON_USEDEP}] + >=dev-python/fslpy-1.4[${PYTHON_USEDEP}] +" + +distutils_enable_tests pytest +distutils_enable_sphinx doc dev-python/sphinx-rtd-theme + +python_prepare_all() { + # do not depend on pytest-cov + sed -i -e '/addopts/d' setup.cfg || die + + distutils-r1_python_prepare_all +} + +src_test() { + virtx distutils-r1_src_test +} + +python_test() { + epytest || die "Tests failed with ${EPYTHON}" +} diff --git a/sci-visualization/fsleyes-widgets/Manifest b/sci-visualization/fsleyes-widgets/Manifest index f81be256c..b88ec6d0e 100644 --- a/sci-visualization/fsleyes-widgets/Manifest +++ b/sci-visualization/fsleyes-widgets/Manifest @@ -1 +1 @@ -DIST fsleyes-widgets-0.12.2.tar.gz 1068565 BLAKE2B db322e7cadfef8d7ba5a63ed089a6979337837418afeb8e0cd10418a119f7e359a360b16dc2dc3756d1f353033d60b4387bff69b9dc864b515fab16daa939e6f SHA512 6c6da4bb2d61a1fe4cff8a7db887595de2df9b3e76984a0ab7492f859f8a47d14b4999e2a3e31c6f6e13f31b7557e55e6b04378dd970d227aa02920c250de088 +DIST fsleyes-widgets-0.12.3.tar.gz 1138692 BLAKE2B beb4125760b4aff463bc3f9ccb03ae3aa0c88a35af4d992a1f2cb728cb607e846e616a0c91bc3c725db613ef82d3d5acefd47195342aa7bfce2d9bfbcb90428c SHA512 93ebf267eee345ce57bc0096b294f399be9815848d5d2b3c8644a4d177ce37b77a37036bc7825541a7e3a8b364701ab5f6a24532a156b258787e0a0961657aed diff --git a/sci-visualization/fsleyes-widgets/fsleyes-widgets-0.12.2.ebuild b/sci-visualization/fsleyes-widgets/fsleyes-widgets-0.12.2.ebuild deleted file mode 100644 index 82a1e587c..000000000 --- a/sci-visualization/fsleyes-widgets/fsleyes-widgets-0.12.2.ebuild +++ /dev/null @@ -1,57 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{8..9} ) - -inherit distutils-r1 virtualx - -MY_P="widgets-${PV}" - -DESCRIPTION="GUI widgets and utilities for the FSLeyes viewer" -HOMEPAGE="https://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/tree/master" -SRC_URI="https://git.fmrib.ox.ac.uk/fsl/fsleyes/widgets/-/archive/${PV}/${MY_P}.tar.gz -> ${P}.tar.gz" -S="${WORKDIR}/${MY_P}" - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86" - -RDEPEND=" - =dev-python/numpy-1*[${PYTHON_USEDEP}] - >=dev-python/matplotlib-1.5[${PYTHON_USEDEP}] - >=dev-python/wxpython-3.0.2.0[${PYTHON_USEDEP}] -" - -distutils_enable_tests pytest -distutils_enable_sphinx doc dev-python/sphinx_rtd_theme - -python_prepare_all() { - # do not depend on pytest-cov - sed -i -e '/addopts/d' setup.cfg || die - - # assert 0 == 1 - sed -i -e 's:test_FloatSlider_mouse_non_gtk:_&:' \ - -e 's:test_FloatSlider_mouse_gtk:_&:' \ - -e 's:test_SliderSpinPanel_events:_&:' \ - tests/test_floatslider.py || die - - # assert None == 0 - sed -i -e 's:test_notebook_events:_&:' \ - tests/test_notebook.py || die - - # assert 25.0 < 5 - sed -i -e 's:test_RangePanel_events_slider:_&:' \ - -e 's:test_RangeSliderSpinPanel_onchange:_&:' \ - tests/test_rangeslider.py || die - - distutils-r1_python_prepare_all -} - -python_test() { - # If this could be set for the eclass, it might fix some of the tests: - # https://github.com/pauldmccarthy/fsleyes-widgets/issues/1#issuecomment-575387724 - #xvfbargs="-screen 0 1920x1200x24 +extension RANDR" - virtx epytest -} diff --git a/sci-visualization/fsleyes-widgets/fsleyes-widgets-0.12.3.ebuild b/sci-visualization/fsleyes-widgets/fsleyes-widgets-0.12.3.ebuild new file mode 100644 index 000000000..fdbb611c2 --- /dev/null +++ b/sci-visualization/fsleyes-widgets/fsleyes-widgets-0.12.3.ebuild @@ -0,0 +1,61 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_10 ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 virtualx + +MY_P="widgets-${PV}" + +DESCRIPTION="GUI widgets and utilities for the FSLeyes viewer" +HOMEPAGE="https://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/tree/master" +SRC_URI="https://git.fmrib.ox.ac.uk/fsl/fsleyes/widgets/-/archive/${PV}/${MY_P}.tar.gz -> ${P}.tar.gz" +S="${WORKDIR}/${MY_P}" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +RDEPEND=" + =dev-python/numpy-1*[${PYTHON_USEDEP}] + >=dev-python/matplotlib-1.5[${PYTHON_USEDEP}] + >=dev-python/wxpython-3.0.2.0[${PYTHON_USEDEP}] +" + +distutils_enable_tests pytest +distutils_enable_sphinx doc dev-python/sphinx-rtd-theme + +python_prepare_all() { + # do not depend on pytest-cov + sed -i -e '/addopts/d' setup.cfg || die + + # assert 0 == 1 + sed -i -e 's:test_FloatSlider_mouse_non_gtk:_&:' \ + -e 's:test_FloatSlider_mouse_gtk:_&:' \ + -e 's:test_SliderSpinPanel_events:_&:' \ + tests/test_floatslider.py || die + + # assert None == 0 + sed -i -e 's:test_notebook_events:_&:' \ + tests/test_notebook.py || die + + # assert 25.0 < 5 + sed -i -e 's:test_RangePanel_events_slider:_&:' \ + -e 's:test_RangeSliderSpinPanel_onchange:_&:' \ + tests/test_rangeslider.py || die + + distutils-r1_python_prepare_all +} + +src_test() { + virtx distutils-r1_src_test +} + +python_test() { + # If this could be set for the eclass, it might fix some of the tests: + # https://github.com/pauldmccarthy/fsleyes-widgets/issues/1#issuecomment-575387724 + #xvfbargs="-screen 0 1920x1200x24 +extension RANDR" + epytest +} diff --git a/sci-visualization/fsleyes/Manifest b/sci-visualization/fsleyes/Manifest index 776a7e0ee..a22884a06 100644 --- a/sci-visualization/fsleyes/Manifest +++ b/sci-visualization/fsleyes/Manifest @@ -1 +1 @@ -DIST fsleyes-1.3.3.tar.gz 91819897 BLAKE2B dde5d4f4831b1fe856c3f6a5eae438cab6570954ab3b11ba6d654fc1ffcbd44bca012c53f4b36bc7fa05a090144b249dea541f5b22147c105c35f01bf14517cf SHA512 a1ce870d88442be3f168e84c3cdc8d468b8a9751a20e2bee33755ef5712f82538e420e94b65ab0a9db3fa2bf91b8630a9868d550c7ee0dad9ff6a8a6c390a122 +DIST fsleyes-1.5.0.tar.gz 98895209 BLAKE2B 1f8b7545a894c281fb596b94d38330662fd5e6fa92e6bf88e480b214b925355e6f660e9312c7b82da41a1217edf1b7026d95832f31a08cbb0a3106e5bd3123e6 SHA512 cc74244ff56b66fca6ffeb10ae21dc69a0a771a1fb0fbaa6b95837cf8a25e674e7b0f81e96ce7583c22844e217f5b258ec0bd3639559de4e74e85847afdd70b7 diff --git a/sci-visualization/fsleyes/fsleyes-1.3.3.ebuild b/sci-visualization/fsleyes/fsleyes-1.3.3.ebuild deleted file mode 100644 index ac86c16fd..000000000 --- a/sci-visualization/fsleyes/fsleyes-1.3.3.ebuild +++ /dev/null @@ -1,65 +0,0 @@ -# Copyright 1999-2022 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{8..9} ) - -inherit xdg distutils-r1 desktop virtualx - -DESCRIPTION="The new FSL image viewer, released with FSL 5.0.10" -HOMEPAGE="https://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/tree/master" -SRC_URI=" - https://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/archive/${PV}/${P}.tar.gz - https://github.com/pauldmccarthy/fsleyes/archive/${PV}.tar.gz -> ${P}.tar.gz -" - -LICENSE="Apache-2.0" -SLOT="0" -KEYWORDS="~amd64" - -RDEPEND=" - >=dev-python/fslpy-3.6[${PYTHON_USEDEP}] - >=dev-python/jinja-2[${PYTHON_USEDEP}] - >=dev-python/matplotlib-1.5.1[${PYTHON_USEDEP}] - >=dev-python/numpy-1.14.0[${PYTHON_USEDEP}] - >=dev-python/pillow-3.2.0[${PYTHON_USEDEP}] - >=dev-python/pyopengl-3.1.0[${PYTHON_USEDEP}] - >=dev-python/pyopengl_accelerate-3.1.0[${PYTHON_USEDEP}] - =dev-python/pyparsing-2*[${PYTHON_USEDEP}] - >=dev-python/wxpython-4[${PYTHON_USEDEP}] - >=dev-python/scipy-0.18[${PYTHON_USEDEP}] - >=sci-libs/nibabel-2.3[${PYTHON_USEDEP}] - >=sci-visualization/fsleyes-widgets-0.12[${PYTHON_USEDEP}] - >=sci-visualization/fsleyes-props-1.7.2[${PYTHON_USEDEP}] - " - -PATCHES=( - "${FILESDIR}/${PN}-0.26.2-fsldir.patch" -) - -distutils_enable_tests pytest -distutils_enable_sphinx userdoc dev-python/sphinx_rtd_theme - -python_prepare_all() { - # do not depend on pytest-cov - sed -i -e '/addopts/d' setup.cfg || die - - distutils-r1_python_prepare_all -} - -python_install_all() { - distutils-r1_python_install_all - doicon -s 48 fsleyes/assets/linux/hicolor/48x48/apps/*.png - domenu fsleyes/assets/linux/*.desktop - insinto /usr/share/metainfo - doins fsleyes/assets/linux/*.appdata.xml - local size - for size in 16 32 128 256 512 ; do - newicon -s ${size} fsleyes/assets/icons/app_icon/${PN}.iconset/icon_${size}x${size}.png "${PN}.png" - done -} - -python_test() { - virtx epytest -} diff --git a/sci-visualization/fsleyes/fsleyes-1.5.0.ebuild b/sci-visualization/fsleyes/fsleyes-1.5.0.ebuild new file mode 100644 index 000000000..2b608c0d0 --- /dev/null +++ b/sci-visualization/fsleyes/fsleyes-1.5.0.ebuild @@ -0,0 +1,65 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_10 ) +DISTUTILS_USE_PEP517=setuptools +inherit xdg distutils-r1 desktop virtualx + +DESCRIPTION="The new FSL image viewer, released with FSL 5.0.10" +HOMEPAGE="https://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/tree/master" +SRC_URI=" + https://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes/-/archive/${PV}/${P}.tar.gz + https://github.com/pauldmccarthy/fsleyes/archive/${PV}.tar.gz -> ${P}.tar.gz +" + +LICENSE="Apache-2.0" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + >=dev-python/fslpy-3.9[${PYTHON_USEDEP}] + >=dev-python/jinja-2[${PYTHON_USEDEP}] + >=dev-python/matplotlib-1.5.1[${PYTHON_USEDEP}] + >=dev-python/numpy-1.14[${PYTHON_USEDEP}] + >=dev-python/pillow-3.2.0[${PYTHON_USEDEP}] + >=dev-python/pyopengl-3.1.0[${PYTHON_USEDEP}] + >=dev-python/pyopengl_accelerate-3.1.0[${PYTHON_USEDEP}] + >=dev-python/pyparsing-2[${PYTHON_USEDEP}] + >=dev-python/wxpython-4[${PYTHON_USEDEP}] + >=dev-python/scipy-0.18[${PYTHON_USEDEP}] + >=sci-libs/nibabel-2.3[${PYTHON_USEDEP}] + >=sci-visualization/fsleyes-widgets-0.12.3[${PYTHON_USEDEP}] + >=sci-visualization/fsleyes-props-1.8[${PYTHON_USEDEP}] + " + +PATCHES=( + "${FILESDIR}/${PN}-0.26.2-fsldir.patch" +) + +distutils_enable_tests pytest +distutils_enable_sphinx userdoc dev-python/sphinx-rtd-theme + +python_prepare_all() { + # do not depend on pytest-cov + sed -i -e '/addopts/d' setup.cfg || die + + distutils-r1_python_prepare_all +} + +python_install_all() { + distutils-r1_python_install_all + doicon -s 48 fsleyes/assets/linux/hicolor/48x48/apps/*.png + domenu fsleyes/assets/linux/*.desktop + insinto /usr/share/metainfo + doins fsleyes/assets/linux/*.appdata.xml + local size + for size in 16 32 128 256 512 ; do + newicon -s ${size} fsleyes/assets/icons/app_icon/${PN}.iconset/icon_${size}x${size}.png "${PN}.png" + done +} + +python_test() { + virtx epytest +} diff --git a/sci-visualization/fsleyes/metadata.xml b/sci-visualization/fsleyes/metadata.xml index 805623e43..d38edeff2 100644 --- a/sci-visualization/fsleyes/metadata.xml +++ b/sci-visualization/fsleyes/metadata.xml @@ -1,4 +1,4 @@ -<?xml version='1.0' encoding='UTF-8'?> +<?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> <pkgmetadata> <maintainer type="person"> @@ -15,4 +15,7 @@ to FSLView, and aims to improve and expand upon this functionality in many ways. </longdescription> + <upstream> + <remote-id type="github">pauldmccarthy/fsleyes</remote-id> + </upstream> </pkgmetadata> diff --git a/sci-visualization/mricrogl/Manifest b/sci-visualization/mricrogl/Manifest index 08377854e..8abe973fd 100644 --- a/sci-visualization/mricrogl/Manifest +++ b/sci-visualization/mricrogl/Manifest @@ -1,3 +1,2 @@ -DIST Metal-Demos-d07815f31093f28b47731f87f3f5ba5543f12d11.tar.gz 13455573 BLAKE2B ec5c7bc26676e0fcd85439657d63879a34ebdd25849c778525944e9555aedb39a0c083ebbf4abf2d67252db520c885edc22967309e610d8bac0ecc7a2f059759 SHA512 f5a5ef9022317c934464365cee1c9075ff8158cbc75a4cacbd7c8c25cc76b2f6ae6069d4745aa53d45ba82a399398506ff8a6aa2eb62784f9d658e21e2ab9a74 -DIST Python-for-Lazarus-.tar.gz 1097797 BLAKE2B 834dec6c03a4813796dbcdcba06a8b9004f03b1bc3a74124794a5a99599b03697b5926d094045becb7b466d91143a1d1c4eaf5e2ee70e2cdb01931097c503a51 SHA512 f1ec3fe1fdb130eef9c43961f5ec4d296467bce6cbffa18ca0017f47da723f27cf660af5970741362013bcffa72f1b50783f3c599bce45f32285172dd400f627 -DIST mricrogl-1.2.20200331.tar.gz 38545843 BLAKE2B 8b658fee21d4e8fcebfdccc6845fbd437dedd5e0e9b0d510e83de846959b5d44911143bb52285167149b9ba21d99deb40577398b4798e832da40876a7ba0aa32 SHA512 a5ce6667f3f2c6abc7a1ab4b46dca08783e5484a1c6d28ac05b7db51a7fba1dc5062a57d29012f50e5c9dd22ba0f1ce1f2047e28f81ba2b64ecbdfbffe6ebe49 +DIST mricrogl-1.2.20211007.tar.gz 59766871 BLAKE2B c9ea15b55cc58c2a350e369094098d107ba5464adb8f098c0d8941d7a471ea132d96eec9d7c684fdb87b726594421fd9bcead326dec685066c26b0786597a7af SHA512 faa3409f5ea711927c5f31c869136170cb3a6fc67b7f821e77a867aa2acda76e99f3a1aeeac60ae63df7eff34c163283df024add0dc6c02fa421b5f66f7f5dea +DIST mricrogl-1.2.20220720.tar.gz 59769179 BLAKE2B 2e7310c8e15db700988100acb5a4173a5411d9cbdbf56832c9acf9031dfe08dbc344b39657cc99e3b27275c0656c2e7ac1aaee39d2acc6731045f2332cf61622 SHA512 58eaf0f4ceacb0e39cb054a1761f3c0734a34c30dd9723bd9790bcc0f5665cd59bac4689ec28a07b2ac5f569b1cac10e005eb1017ad18384a318cee1e15fec2f diff --git a/sci-visualization/mricrogl/mricrogl-1.2.20200331.ebuild b/sci-visualization/mricrogl/mricrogl-1.2.20200331.ebuild deleted file mode 100644 index df2f1aa38..000000000 --- a/sci-visualization/mricrogl/mricrogl-1.2.20200331.ebuild +++ /dev/null @@ -1,49 +0,0 @@ -# Copyright 1999-2021 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -inherit desktop - -DEMOS_HASH="d07815f31093f28b47731f87f3f5ba5543f12d11" -PY4LAZ_HASH="8dc41685b547f0982755b90115d9a43a2d2b358c" - -DESCRIPTION="A simple medical imaging visualization tool" -HOMEPAGE="https://github.com/neurolabusc/MRIcroGL" -SRC_URI=" - https://github.com/rordenlab/MRIcroGL12/archive/v${PV}.tar.gz -> ${P}.tar.gz - https://github.com/neurolabusc/Metal-Demos/archive/${DEMOS_HASH}.tar.gz -> Metal-Demos-${DEMOS_HASH}.tar.gz - python? ( https://github.com/Alexey-T/Python-for-Lazarus/archive/${PY4LAZ_HASH}.tar.gz -> Python-for-Lazarus-${P4LAZ_HASH}.tar.gz ) - " - -LICENSE="BSD" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="dicom python" - -RDEPEND="dicom? ( sci-biology/dcm2niix )" -DEPEND="dev-lang/fpc - >=dev-lang/lazarus-1.6.2" - -S="${WORKDIR}/MRIcroGL12-${PV}" - -src_compile() { - sed -i -e "s:Metal-Demos/common:Metal-Demos-${DEMOS_HASH}/common:g" MRIcroGL_NoPython.lpi || die - if use python; then - lazbuild -build-ide= --add-package lazopenglcontext ./Python-for-Lazarus-${PY4LAZ}/python4lazarus/python4lazarus_package.lpk || die - else - lazbuild --verbose-pkgsearch lazopenglcontext - fi - lazbuild -B --lazarusdir="/usr/share/lazarus/" --pcp="system-lazarus-config" MRIcroGL_NoPython.lpi || die -} - -src_install() { - dobin MRIcroGL - - pushd Resources > /dev/null - insinto /usr/share/MRIcroGL - doins -r lut matcap Roboto.* script shader - doicon -s scalable mricrogl.svg - make_desktop_entry MRIcroGL MRIcroGL /usr/share/icons/hicolor/scalable/apps/mricrogl.svg - popd -} diff --git a/sci-visualization/mricrogl/mricrogl-1.2.20211007-r1.ebuild b/sci-visualization/mricrogl/mricrogl-1.2.20211007-r1.ebuild new file mode 100644 index 000000000..da8e446cf --- /dev/null +++ b/sci-visualization/mricrogl/mricrogl-1.2.20211007-r1.ebuild @@ -0,0 +1,66 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +MY_PN="MRIcroGL" +inherit desktop xdg-utils + +DESCRIPTION="A simple medical imaging visualization tool" +HOMEPAGE="https://github.com/neurolabusc/MRIcroGL" +SRC_URI="https://github.com/rordenlab/${MY_PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="dicom python" + +BDEPEND="dev-lang/lazarus" +DEPEND=" + dev-lang/fpc + x11-misc/appmenu-gtk-module[gtk2] + " +RDEPEND="dicom? ( sci-biology/dcm2niix )" + +S="${WORKDIR}/${MY_PN}-${PV}" + +src_compile() { + # Allegedly the Debian recipe contains some sort of Python support, wasn't able to test. + if use python; then + lazbuild -B \ + --lazarusdir="/usr/share/lazarus/" \ + --pcp="system-lazarus-config" \ + MRIcroGL_Debian.lpi || die + else + lazbuild -B \ + --lazarusdir="/usr/share/lazarus/" \ + --pcp="system-lazarus-config" \ + MRIcroGL_NoPython.lpi || die + fi +} + +src_install() { + dobin MRIcroGL + + pushd Resources > /dev/null + insinto /usr/share/MRIcroGL + doins -r lut matcap Roboto.* script shader + doicon -s scalable mricrogl.svg + make_desktop_entry MRIcroGL MRIcroGL /usr/share/icons/hicolor/scalable/apps/mricrogl.svg + popd +} + +pkg_postinst(){ + xdg_icon_cache_update + + ewarn "This package might exhibit nondeterministic lag at startup manifesting as a blank" + ewarn "window, which can either be closed (e.g. Alt+F4) manually leading to the actual" + ewarn "interface being launched, or will close itself after 10-20s and start the proper GUI" + ewarn "For more details on this look up: https://github.com/rordenlab/MRIcroGL/issues/49" +} + +pkg_postrm() { + xdg_icon_cache_update + xdg_mimeinfo_database_update + xdg_desktop_database_update +} diff --git a/sci-visualization/mricrogl/mricrogl-1.2.20220720-r1.ebuild b/sci-visualization/mricrogl/mricrogl-1.2.20220720-r1.ebuild new file mode 100644 index 000000000..da8e446cf --- /dev/null +++ b/sci-visualization/mricrogl/mricrogl-1.2.20220720-r1.ebuild @@ -0,0 +1,66 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +MY_PN="MRIcroGL" +inherit desktop xdg-utils + +DESCRIPTION="A simple medical imaging visualization tool" +HOMEPAGE="https://github.com/neurolabusc/MRIcroGL" +SRC_URI="https://github.com/rordenlab/${MY_PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="BSD" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="dicom python" + +BDEPEND="dev-lang/lazarus" +DEPEND=" + dev-lang/fpc + x11-misc/appmenu-gtk-module[gtk2] + " +RDEPEND="dicom? ( sci-biology/dcm2niix )" + +S="${WORKDIR}/${MY_PN}-${PV}" + +src_compile() { + # Allegedly the Debian recipe contains some sort of Python support, wasn't able to test. + if use python; then + lazbuild -B \ + --lazarusdir="/usr/share/lazarus/" \ + --pcp="system-lazarus-config" \ + MRIcroGL_Debian.lpi || die + else + lazbuild -B \ + --lazarusdir="/usr/share/lazarus/" \ + --pcp="system-lazarus-config" \ + MRIcroGL_NoPython.lpi || die + fi +} + +src_install() { + dobin MRIcroGL + + pushd Resources > /dev/null + insinto /usr/share/MRIcroGL + doins -r lut matcap Roboto.* script shader + doicon -s scalable mricrogl.svg + make_desktop_entry MRIcroGL MRIcroGL /usr/share/icons/hicolor/scalable/apps/mricrogl.svg + popd +} + +pkg_postinst(){ + xdg_icon_cache_update + + ewarn "This package might exhibit nondeterministic lag at startup manifesting as a blank" + ewarn "window, which can either be closed (e.g. Alt+F4) manually leading to the actual" + ewarn "interface being launched, or will close itself after 10-20s and start the proper GUI" + ewarn "For more details on this look up: https://github.com/rordenlab/MRIcroGL/issues/49" +} + +pkg_postrm() { + xdg_icon_cache_update + xdg_mimeinfo_database_update + xdg_desktop_database_update +} diff --git a/sys-cluster/easybuild-easyblocks/Manifest b/sys-cluster/easybuild-easyblocks/Manifest new file mode 100644 index 000000000..955f41791 --- /dev/null +++ b/sys-cluster/easybuild-easyblocks/Manifest @@ -0,0 +1,2 @@ +DIST easybuild-easyblocks-4.6.2.tar.gz 539757 BLAKE2B e33db4b390cdbe11237c5f5750426f15d264cf081e2846c7b9de9254f7a0fbdc1459795920fcc131ceb5681f0acc905a74f96cd841b73b523e030246b78393e8 SHA512 72cb4c057efdfeb4c45fbf1e036a6f231e7f01ad6e593d1c2352b27f002ed4f45cd625c4125b90b708b15f226fb9519a345217f7882c2155b399894986a4505c +DIST easybuild-easyblocks-4.9.0.tar.gz 574066 BLAKE2B 404ea11287d03edf497c85e9d58eba05d3257aed609eb3f65e3d1543e08e0be27a64fd7459ba30578a3bd2be2051020f711f6598af082d2cdec3fad65116a0ed SHA512 c75695c66f4683128be268471e996abde83fc9cc5f937699b81da5ea94bf02df84bc6b0a88c657a904730afbc4048e3a44cfbc5288a546c1962a51960393d5c7 diff --git a/sys-cluster/easybuild-easyblocks/easybuild-easyblocks-4.6.2.ebuild b/sys-cluster/easybuild-easyblocks/easybuild-easyblocks-4.6.2.ebuild new file mode 100644 index 000000000..6c5f7a6e6 --- /dev/null +++ b/sys-cluster/easybuild-easyblocks/easybuild-easyblocks-4.6.2.ebuild @@ -0,0 +1,29 @@ +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools +PYPI_NO_NORMALIZE=1 +inherit distutils-r1 pypi + +SUB_P=$(ver_cut 1) + +DESCRIPTION="Provides a collection of easyblocks for EasyBuild." +HOMEPAGE=" + https://easybuild.io/ + https://github.com/easybuilders/easybuild-easyblocks +" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + >=sys-cluster/easybuild-framework-${SUB_P}[${PYTHON_USEDEP}] +" +DEPEND="${RDEPEND}" + +src_prepare() { + # already there from easybuild_framework + rm easybuild/__init__.py || die + default +} diff --git a/sys-cluster/easybuild-easyblocks/easybuild-easyblocks-4.9.0.ebuild b/sys-cluster/easybuild-easyblocks/easybuild-easyblocks-4.9.0.ebuild new file mode 100644 index 000000000..d4cc85067 --- /dev/null +++ b/sys-cluster/easybuild-easyblocks/easybuild-easyblocks-4.9.0.ebuild @@ -0,0 +1,36 @@ +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools +PYPI_NO_NORMALIZE=1 + +inherit distutils-r1 + +SUB_P=$(ver_cut 1) + +DESCRIPTION="Provides a collection of easyblocks for EasyBuild." +HOMEPAGE=" + https://easybuild.io/ + https://github.com/easybuilders/easybuild-easyblocks +" + +LICENSE="GPL-2" +SLOT="0" +if [[ ${PV} == 9999 ]]; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/easybuilders/easybuild-easyblocks" +else + inherit pypi + KEYWORDS="~amd64" +fi + +RDEPEND=" + >=sys-cluster/easybuild-framework-${SUB_P}[${PYTHON_USEDEP}] +" +DEPEND="${RDEPEND}" + +src_prepare() { + # already there from easybuild_framework + rm easybuild/__init__.py || die + default +} diff --git a/sys-cluster/easybuild-easyblocks/easybuild-easyblocks-9999.ebuild b/sys-cluster/easybuild-easyblocks/easybuild-easyblocks-9999.ebuild new file mode 100644 index 000000000..b32a81c59 --- /dev/null +++ b/sys-cluster/easybuild-easyblocks/easybuild-easyblocks-9999.ebuild @@ -0,0 +1,37 @@ +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools +PYPI_NO_NORMALIZE=1 + +inherit distutils-r1 + +SUB_P=$(ver_cut 1) + +DESCRIPTION="Provides a collection of easyblocks for EasyBuild." +HOMEPAGE=" + https://easybuild.io/ + https://github.com/easybuilders/easybuild-easyblocks +" + +LICENSE="GPL-2" +SLOT="0" +if [[ ${PV} == 9999 ]]; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/easybuilders/easybuild-easyblocks" + SUB_P=9999 +else + inherit pypi + KEYWORDS="~amd64" +fi + +RDEPEND=" + >=sys-cluster/easybuild-framework-${SUB_P}[${PYTHON_USEDEP}] +" +DEPEND="${RDEPEND}" + +src_prepare() { + # already there from easybuild_framework + rm easybuild/__init__.py || die + default +} diff --git a/sys-cluster/easybuild-easyblocks/metadata.xml b/sys-cluster/easybuild-easyblocks/metadata.xml new file mode 100644 index 000000000..d7dba6355 --- /dev/null +++ b/sys-cluster/easybuild-easyblocks/metadata.xml @@ -0,0 +1,20 @@ +<?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> + <maintainer type="person"> + <email>alexander@neuwirth-informatik.de</email> + <name>Alexander Puck Neuwirth</name> + </maintainer> + <longdescription lang="en"> + The easybuild-easyblocks package provides a collection of easyblocks for EasyBuild. Easyblocks are Python modules that implement the install procedure for a (group of) software package(s). Together with the EasyBuild framework, they allow to easily build and install supported software packages. + </longdescription> + <upstream> + <remote-id type="pypi">easybuild-easyblocks</remote-id> + <remote-id type="github">easybuilders/easybuild-easyblocks</remote-id> + <bugs-to>https://github.com/easybuilders/easybuild-easyblocks/issues</bugs-to> + </upstream> +</pkgmetadata> diff --git a/sys-cluster/easybuild-easyconfigs/Manifest b/sys-cluster/easybuild-easyconfigs/Manifest new file mode 100644 index 000000000..b8328d6aa --- /dev/null +++ b/sys-cluster/easybuild-easyconfigs/Manifest @@ -0,0 +1,2 @@ +DIST easybuild-easyconfigs-4.6.2.tar.gz 7991765 BLAKE2B 02e7b629858177db19b7a63fcacd4898805ccfabd7bac343e05015d545d057bb04416b0b89245d3e3c206bc0f129920dda7d7ae1e421e9f7ce690ee6d01acd90 SHA512 4632dc0714b3e070b58a8192cb8054f0e21357701f59df054593ea754f5598c8e6446acd77c0e41f2fb920d31297ea5a5164fd81b26b926835868f24623cdce8 +DIST easybuild-easyconfigs-4.9.0.tar.gz 9636057 BLAKE2B 5b7710c99eb0d728d4df6582db40b7dc72d86cfca32548c79344a2b918e53e56360c97225ab2cf577bf2ba170bf67de211758afb83e696ec157165316b01cf02 SHA512 a39dc1eddc569163b21abdca9633a4c35519f609a03012ef7ec3f58c40a58961450b626c3701c325a2e485e5a00d161d737239c19ea657546b52b2c16de307f5 diff --git a/sys-cluster/easybuild-easyconfigs/easybuild-easyconfigs-4.6.2.ebuild b/sys-cluster/easybuild-easyconfigs/easybuild-easyconfigs-4.6.2.ebuild new file mode 100644 index 000000000..08434dc1c --- /dev/null +++ b/sys-cluster/easybuild-easyconfigs/easybuild-easyconfigs-4.6.2.ebuild @@ -0,0 +1,25 @@ +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools +PYPI_NO_NORMALIZE=1 +inherit distutils-r1 pypi + +SUB_P=$(ver_cut 1) +SUB_PP=$(ver_cut 2) + +DESCRIPTION="Provides a collection of well-tested easyconfig files for EasyBuild." +HOMEPAGE=" + https://easybuild.io/ + https://github.com/easybuilders/easybuild-easyconfigs +" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + >=sys-cluster/easybuild-framework-${SUB_P}[${PYTHON_USEDEP}] + >=sys-cluster/easybuild-easyblocks-${SUB_P}.${SUB_PP}[${PYTHON_USEDEP}] +" +DEPEND="${RDEPEND}" diff --git a/sys-cluster/easybuild-easyconfigs/easybuild-easyconfigs-4.9.0.ebuild b/sys-cluster/easybuild-easyconfigs/easybuild-easyconfigs-4.9.0.ebuild new file mode 100644 index 000000000..5d5750a61 --- /dev/null +++ b/sys-cluster/easybuild-easyconfigs/easybuild-easyconfigs-4.9.0.ebuild @@ -0,0 +1,34 @@ +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools +PYPI_NO_NORMALIZE=1 + +inherit distutils-r1 + +SUB_P=$(ver_cut 1) +SUB_PP=${SUB_P}.$(ver_cut 2) + +DESCRIPTION="Provides a collection of well-tested easyconfig files for EasyBuild." +HOMEPAGE=" + https://easybuild.io/ + https://github.com/easybuilders/easybuild-easyconfigs +" + +LICENSE="GPL-2" +SLOT="0" +if [[ ${PV} == 9999 ]]; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/easybuilders/easybuild-easyconfigs" + SUB_P=9999 + SUB_PP=9999 +else + inherit pypi + KEYWORDS="~amd64" +fi + +RDEPEND=" + >=sys-cluster/easybuild-framework-${SUB_P}[${PYTHON_USEDEP}] + >=sys-cluster/easybuild-easyblocks-${SUB_PP}[${PYTHON_USEDEP}] +" +DEPEND="${RDEPEND}" diff --git a/sys-cluster/easybuild-easyconfigs/easybuild-easyconfigs-9999.ebuild b/sys-cluster/easybuild-easyconfigs/easybuild-easyconfigs-9999.ebuild new file mode 100644 index 000000000..5d5750a61 --- /dev/null +++ b/sys-cluster/easybuild-easyconfigs/easybuild-easyconfigs-9999.ebuild @@ -0,0 +1,34 @@ +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools +PYPI_NO_NORMALIZE=1 + +inherit distutils-r1 + +SUB_P=$(ver_cut 1) +SUB_PP=${SUB_P}.$(ver_cut 2) + +DESCRIPTION="Provides a collection of well-tested easyconfig files for EasyBuild." +HOMEPAGE=" + https://easybuild.io/ + https://github.com/easybuilders/easybuild-easyconfigs +" + +LICENSE="GPL-2" +SLOT="0" +if [[ ${PV} == 9999 ]]; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/easybuilders/easybuild-easyconfigs" + SUB_P=9999 + SUB_PP=9999 +else + inherit pypi + KEYWORDS="~amd64" +fi + +RDEPEND=" + >=sys-cluster/easybuild-framework-${SUB_P}[${PYTHON_USEDEP}] + >=sys-cluster/easybuild-easyblocks-${SUB_PP}[${PYTHON_USEDEP}] +" +DEPEND="${RDEPEND}" diff --git a/sys-cluster/easybuild-easyconfigs/metadata.xml b/sys-cluster/easybuild-easyconfigs/metadata.xml new file mode 100644 index 000000000..4f1fac641 --- /dev/null +++ b/sys-cluster/easybuild-easyconfigs/metadata.xml @@ -0,0 +1,20 @@ +<?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> + <maintainer type="person"> + <email>alexander@neuwirth-informatik.de</email> + <name>Alexander Puck Neuwirth</name> + </maintainer> + <longdescription lang="en"> + The easybuild-easyconfigs package provides a collection of well-tested example easyconfig files for EasyBuild. Easyconfig files are used to specify which software to build, which version of the software (and its dependencies), which build parameters to use (e.g., which compiler toolchain to use), etc. + </longdescription> + <upstream> + <remote-id type="pypi">easybuild-easyconfigs</remote-id> + <remote-id type="github">easybuilders/easybuild-easyconfigs</remote-id> + <bugs-to>https://github.com/easybuilders/easybuild-easyconfigs/issues</bugs-to> + </upstream> +</pkgmetadata> diff --git a/sys-cluster/easybuild-framework/Manifest b/sys-cluster/easybuild-framework/Manifest new file mode 100644 index 000000000..6845b4e9c --- /dev/null +++ b/sys-cluster/easybuild-framework/Manifest @@ -0,0 +1,2 @@ +DIST easybuild-framework-4.6.2.tar.gz 2019284 BLAKE2B a32ae1fc43d490b32fc6c44790493204de935d16257846ec46830fc4d18a7343b860317c0ba33a16d89f12f657c33f7bb7359a70bf26a17c4e0dd16b8c78e2cd SHA512 ac8a06301c6c95edded262cb55b02ea8ada9ea14dfb7b7354a3bb29fcd9ad9a8d0011edbf2175085b8cec721f08a2b5f5e74aaa191d381a787eb5438c6c7f8cc +DIST easybuild-framework-4.9.0.tar.gz 2064113 BLAKE2B 637498e7d52f0e9a6e9bd25c843052d9fc3c730f93b40c37381263b8861b0dd1b8ebf1d13af514d841d43284eb81b7555fcdaacbc1ac2c1bd655748c01540677 SHA512 b7b52d8987f13d9f859df0874adb7b855f8b4961215d9e9cb4a63a15911affe1591d718076277419be0c31e76845cf5cbe4fe553676ac71b8ff33a82d3c17a0e diff --git a/sys-cluster/easybuild-framework/easybuild-framework-4.6.2.ebuild b/sys-cluster/easybuild-framework/easybuild-framework-4.6.2.ebuild new file mode 100644 index 000000000..0f7421835 --- /dev/null +++ b/sys-cluster/easybuild-framework/easybuild-framework-4.6.2.ebuild @@ -0,0 +1,33 @@ +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools +PYPI_NO_NORMALIZE=1 +inherit distutils-r1 pypi + +DESCRIPTION="The easybuild-framework package is the core of EasyBuild." +HOMEPAGE=" + https://easybuild.io/ + https://github.com/easybuilders/easybuild-framework +" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" +dev-python/flake8[${PYTHON_USEDEP}] +dev-python/keyring[${PYTHON_USEDEP}] +dev-python/GitPython[${PYTHON_USEDEP}] +dev-python/pyyaml[${PYTHON_USEDEP}] +dev-python/autopep8[${PYTHON_USEDEP}] +dev-python/requests[${PYTHON_USEDEP}] +dev-python/cryptography[${PYTHON_USEDEP}] +dev-python/rich[${PYTHON_USEDEP}] +dev-python/archspec[${PYTHON_USEDEP}] +" +DEPEND="${RDEPEND}" + +PATCHES=( + "${FILESDIR}"/${P}-test.patch +) diff --git a/sys-cluster/easybuild-framework/easybuild-framework-4.9.0.ebuild b/sys-cluster/easybuild-framework/easybuild-framework-4.9.0.ebuild new file mode 100644 index 000000000..c88f89f6f --- /dev/null +++ b/sys-cluster/easybuild-framework/easybuild-framework-4.9.0.ebuild @@ -0,0 +1,40 @@ +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools +PYPI_NO_NORMALIZE=1 + +inherit distutils-r1 + +DESCRIPTION="The easybuild-framework package is the core of EasyBuild." +HOMEPAGE=" + https://easybuild.io/ + https://github.com/easybuilders/easybuild-framework +" + +LICENSE="GPL-2" +SLOT="0" +if [[ ${PV} == 9999 ]]; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/easybuilders/easybuild-framework" +else + inherit pypi + KEYWORDS="~amd64" +fi + +RDEPEND=" + dev-python/flake8[${PYTHON_USEDEP}] + dev-python/keyring[${PYTHON_USEDEP}] + dev-python/GitPython[${PYTHON_USEDEP}] + dev-python/pyyaml[${PYTHON_USEDEP}] + dev-python/autopep8[${PYTHON_USEDEP}] + dev-python/requests[${PYTHON_USEDEP}] + dev-python/archspec[${PYTHON_USEDEP}] + dev-python/cryptography[${PYTHON_USEDEP}] + dev-python/rich[${PYTHON_USEDEP}] +" +DEPEND="${RDEPEND}" + +PATCHES=( + "${FILESDIR}"/${PN}-4.6.2-test.patch +) diff --git a/sys-cluster/easybuild-framework/easybuild-framework-9999.ebuild b/sys-cluster/easybuild-framework/easybuild-framework-9999.ebuild new file mode 100644 index 000000000..c88f89f6f --- /dev/null +++ b/sys-cluster/easybuild-framework/easybuild-framework-9999.ebuild @@ -0,0 +1,40 @@ +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools +PYPI_NO_NORMALIZE=1 + +inherit distutils-r1 + +DESCRIPTION="The easybuild-framework package is the core of EasyBuild." +HOMEPAGE=" + https://easybuild.io/ + https://github.com/easybuilders/easybuild-framework +" + +LICENSE="GPL-2" +SLOT="0" +if [[ ${PV} == 9999 ]]; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/easybuilders/easybuild-framework" +else + inherit pypi + KEYWORDS="~amd64" +fi + +RDEPEND=" + dev-python/flake8[${PYTHON_USEDEP}] + dev-python/keyring[${PYTHON_USEDEP}] + dev-python/GitPython[${PYTHON_USEDEP}] + dev-python/pyyaml[${PYTHON_USEDEP}] + dev-python/autopep8[${PYTHON_USEDEP}] + dev-python/requests[${PYTHON_USEDEP}] + dev-python/archspec[${PYTHON_USEDEP}] + dev-python/cryptography[${PYTHON_USEDEP}] + dev-python/rich[${PYTHON_USEDEP}] +" +DEPEND="${RDEPEND}" + +PATCHES=( + "${FILESDIR}"/${PN}-4.6.2-test.patch +) diff --git a/sys-cluster/easybuild-framework/files/easybuild-framework-4.6.2-test.patch b/sys-cluster/easybuild-framework/files/easybuild-framework-4.6.2-test.patch new file mode 100644 index 000000000..db1a65b5a --- /dev/null +++ b/sys-cluster/easybuild-framework/files/easybuild-framework-4.6.2-test.patch @@ -0,0 +1,11 @@ +--- a/setup.py 2022-10-22 17:31:01.312465269 +0200 ++++ b/setup.py 2022-10-22 17:30:50.826310864 +0200 +@@ -72,7 +72,7 @@ + "easybuild.toolchains.fft", "easybuild.toolchains.linalg", "easybuild.tools", "easybuild.tools.containers", + "easybuild.tools.deprecated", "easybuild.tools.job", "easybuild.tools.toolchain", + "easybuild.tools.module_naming_scheme", "easybuild.tools.package", "easybuild.tools.package.package_naming_scheme", +- "easybuild.tools.py2vs3", "easybuild.tools.repository", "test.framework", "test", ++ "easybuild.tools.py2vs3", "easybuild.tools.repository", + ] + + setup( diff --git a/sys-cluster/easybuild-framework/metadata.xml b/sys-cluster/easybuild-framework/metadata.xml new file mode 100644 index 000000000..5d61e5c64 --- /dev/null +++ b/sys-cluster/easybuild-framework/metadata.xml @@ -0,0 +1,20 @@ +<?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> + <maintainer type="person"> + <email>alexander@neuwirth-informatik.de</email> + <name>Alexander Puck Neuwirth</name> + </maintainer> + <longdescription lang="en"> + The easybuild-framework package is the core of EasyBuild. It supports the implementation and use of so-called easyblocks which implement the software install procedure for a particular (group of) software package(s). + </longdescription> + <upstream> + <remote-id type="pypi">easybuild-framework</remote-id> + <remote-id type="github">easybuilders/easybuild-framework</remote-id> + <bugs-to>https://github.com/easybuilders/easybuild-framework/issues</bugs-to> + </upstream> +</pkgmetadata> diff --git a/sys-cluster/easybuild/Manifest b/sys-cluster/easybuild/Manifest new file mode 100644 index 000000000..b17222baf --- /dev/null +++ b/sys-cluster/easybuild/Manifest @@ -0,0 +1,2 @@ +DIST easybuild-4.6.2.tar.gz 10680 BLAKE2B ed9dcaf1e138dd0d56fbff51151b5e0a6c0842495a950fe6a37a16435ab679bd0f60d34a703f6791b1486001fa3508e23d8a82ae6cc39f90137f03b5a93f5a0e SHA512 34097122968d31cf7fa8503f1566ff43c4fd34849c02050eb2f7304028479afd224128a0b83c195150b9ff6680b903a6b20fee715c9511bde292e2c4ac88397b +DIST easybuild-4.9.0.tar.gz 10622 BLAKE2B bf7c69db95d49e2d992541baa145346e173fc35eab6002afd59a62d7c2007fea41672d81a3f1cf0e170f630dcf4bbea957b254fbffd5237738180d2df0976964 SHA512 3a1a4433e58d90f90dd8ba2700f7dcc07a07333d7f103ea23f82145af76a41af436d9e606fbe95fc5cfcf4be07399a3b3d5cc10c57c0bd77ea8018ba4e852c8d diff --git a/sys-cluster/easybuild/easybuild-4.6.2.ebuild b/sys-cluster/easybuild/easybuild-4.6.2.ebuild new file mode 100644 index 000000000..fe08d45ad --- /dev/null +++ b/sys-cluster/easybuild/easybuild-4.6.2.ebuild @@ -0,0 +1,31 @@ +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools +inherit distutils-r1 pypi + +DESCRIPTION="EasyBuild is a software build and installation framework." +HOMEPAGE=" + https://easybuild.io/ + https://github.com/easybuilders/easybuild +" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64" + +RDEPEND=" + dev-libs/openssl + dev-tcltk/tclx + || ( >=sys-cluster/lmod-6.5.1 >=sys-cluster/modules-4.6.0-r1 ) + ~sys-cluster/easybuild-framework-${PV}[${PYTHON_USEDEP}] + ~sys-cluster/easybuild-easyblocks-${PV}[${PYTHON_USEDEP}] + ~sys-cluster/easybuild-easyconfigs-${PV}[${PYTHON_USEDEP}] +" +DEPEND="${RDEPEND}" + +pkg_postinst() { + elog "Remember to set the module install path" + elog "ml use \$installpath/modules/all" + elog "where --installpath is passed to eb" +} diff --git a/sys-cluster/easybuild/easybuild-4.9.0.ebuild b/sys-cluster/easybuild/easybuild-4.9.0.ebuild new file mode 100644 index 000000000..9a38672aa --- /dev/null +++ b/sys-cluster/easybuild/easybuild-4.9.0.ebuild @@ -0,0 +1,40 @@ +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools + +inherit distutils-r1 optfeature + +DESCRIPTION="EasyBuild is a software build and installation framework." +HOMEPAGE=" + https://easybuild.io/ + https://github.com/easybuilders/easybuild +" + +LICENSE="GPL-2" +SLOT="0" +if [[ ${PV} == 9999 ]]; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/easybuilders/easybuild" +else + inherit pypi + KEYWORDS="~amd64" +fi + +RDEPEND=" + dev-libs/openssl + dev-tcltk/tclx + || ( >=sys-cluster/lmod-6.5.1 >=sys-cluster/modules-4.6.0-r1 ) + ~sys-cluster/easybuild-framework-${PV}[${PYTHON_USEDEP}] + ~sys-cluster/easybuild-easyblocks-${PV}[${PYTHON_USEDEP}] + ~sys-cluster/easybuild-easyconfigs-${PV}[${PYTHON_USEDEP}] +" +DEPEND="${RDEPEND}" + +pkg_postinst() { + elog "Remember to set the module install path" + elog "ml use \$installpath/modules/all" + elog "where --installpath is passed to eb" + + optfeature "GitHub PR integration" dev-python/keyring dev-python/GitPython +} diff --git a/sys-cluster/easybuild/easybuild-9999.ebuild b/sys-cluster/easybuild/easybuild-9999.ebuild new file mode 100644 index 000000000..9a38672aa --- /dev/null +++ b/sys-cluster/easybuild/easybuild-9999.ebuild @@ -0,0 +1,40 @@ +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) +DISTUTILS_USE_PEP517=setuptools + +inherit distutils-r1 optfeature + +DESCRIPTION="EasyBuild is a software build and installation framework." +HOMEPAGE=" + https://easybuild.io/ + https://github.com/easybuilders/easybuild +" + +LICENSE="GPL-2" +SLOT="0" +if [[ ${PV} == 9999 ]]; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/easybuilders/easybuild" +else + inherit pypi + KEYWORDS="~amd64" +fi + +RDEPEND=" + dev-libs/openssl + dev-tcltk/tclx + || ( >=sys-cluster/lmod-6.5.1 >=sys-cluster/modules-4.6.0-r1 ) + ~sys-cluster/easybuild-framework-${PV}[${PYTHON_USEDEP}] + ~sys-cluster/easybuild-easyblocks-${PV}[${PYTHON_USEDEP}] + ~sys-cluster/easybuild-easyconfigs-${PV}[${PYTHON_USEDEP}] +" +DEPEND="${RDEPEND}" + +pkg_postinst() { + elog "Remember to set the module install path" + elog "ml use \$installpath/modules/all" + elog "where --installpath is passed to eb" + + optfeature "GitHub PR integration" dev-python/keyring dev-python/GitPython +} diff --git a/sys-cluster/easybuild/metadata.xml b/sys-cluster/easybuild/metadata.xml new file mode 100644 index 000000000..d7af184b5 --- /dev/null +++ b/sys-cluster/easybuild/metadata.xml @@ -0,0 +1,20 @@ +<?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> + <maintainer type="person"> + <email>alexander@neuwirth-informatik.de</email> + <name>Alexander Puck Neuwirth</name> + </maintainer> + <longdescription lang="en"> + EasyBuild is a software build and installation framework that allows you to manage (scientific) software on High Performance Computing (HPC) systems in an efficient way. + </longdescription> + <upstream> + <remote-id type="pypi">easybuild</remote-id> + <remote-id type="github">easybuilders/easybuild</remote-id> + <bugs-to>https://github.com/easybuilders/easybuild/issues</bugs-to> + </upstream> +</pkgmetadata> diff --git a/sys-cluster/modules/metadata.xml b/sys-cluster/modules/metadata.xml index a67a56343..4842f7c2c 100644 --- a/sys-cluster/modules/metadata.xml +++ b/sys-cluster/modules/metadata.xml @@ -18,6 +18,8 @@ </longdescription> <upstream> <remote-id type="sourceforge">modules</remote-id> + <remote-id type="github">cea-hpc/modules</remote-id> + <bugs-to>https://github.com/cea-hpc/modules/issues</bugs-to> </upstream> <use> <flag name="compat">Build Modules version 3 compat support</flag> diff --git a/sys-cluster/modules/modules-4.6.0-r1.ebuild b/sys-cluster/modules/modules-4.6.0-r1.ebuild new file mode 100644 index 000000000..3aade0b38 --- /dev/null +++ b/sys-cluster/modules/modules-4.6.0-r1.ebuild @@ -0,0 +1,82 @@ +# Copyright 2020 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..11} ) + +inherit autotools python-single-r1 + +DESCRIPTION="Dynamic modification of a user's environment via modulefiles" +HOMEPAGE="http://modules.sourceforge.net/" +SRC_URI="https://github.com/cea-hpc/modules/releases/download/v${PV}/${P}.tar.bz2" + +LICENSE="GPL-2" +SLOT="0" +KEYWORDS="~amd64 ~x86" +IUSE="compat test" +REQUIRED_USE="${PYTHON_REQUIRED_USE}" +RESTRICT="!test? ( test )" + +DEPEND=" + ${PYTHON_DEPS} + dev-lang/tcl:0= + dev-tcltk/tclx + compat? ( x11-libs/libX11 ) +" +# lmod is strong blocked since both want to install a module binary +RDEPEND=" + ${DEPEND} + !sys-cluster/lmod +" +BDEPEND=" + test? ( dev-util/dejagnu ) +" + +src_prepare() { + default + + cd "${S}/lib" || die + eautoreconf + + if use compat; then + cd "${S}/compat" || die + eautoreconf + fi +} + +src_configure() { + local myconf=( + --disable-versioning + --with-initconf-in=etcdir + --enable-multilib-support + --disable-set-shell-startup + --prefix="${EPREFIX}/usr/share/Modules" + --mandir="${EPREFIX}/usr/share/man" + --docdir="${EPREFIX}/usr/share/doc/${P}" + --libdir="${EPREFIX}/usr/share/Modules/$(get_libdir)" + --datarootdir="${EPREFIX}/usr/share" + --modulefilesdir="${EPREFIX}/etc/modulefiles" + --with-tcl="${EPREFIX}/usr/$(get_libdir)" + --with-python="${PYTHON}" + --with-quarantine-vars="LD_LIBRARY_PATH LD_PRELOAD" + $(use_enable compat compat-version) + ) + econf "${myconf[@]}" "${EXTRA_ECONF[@]}" || die "configure failed" +} + +src_test() { + # Remove known-broken tests + # These test fine, but fail for random differences in the gentoo environment + rm "${S}"/testsuite/modules.70-maint/210-clear.exp || die "rm failed" + rm "${S}"/testsuite/modules.00-init/110-quar.exp || die "rm failed" + + RUNTESTARGS=-v emake test +} + +src_install() { + default + dosym ../../usr/share/Modules/init/profile.sh /etc/profile.d/modules.sh + dosym ../../usr/share/Modules/init/profile.csh /etc/profile.d/modules.csh + dodir /etc/modulefiles +} diff --git a/sys-cluster/modules/modules-4.6.0.ebuild b/sys-cluster/modules/modules-4.6.0.ebuild deleted file mode 100644 index fc1d72946..000000000 --- a/sys-cluster/modules/modules-4.6.0.ebuild +++ /dev/null @@ -1,78 +0,0 @@ -# Copyright 2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python3_{7..9} ) - -inherit autotools python-single-r1 - -DESCRIPTION="Dynamic modification of a user's environment via modulefiles" -HOMEPAGE="http://modules.sourceforge.net/" -SRC_URI="https://github.com/cea-hpc/modules/releases/download/v${PV}/${P}.tar.bz2" - -LICENSE="GPL-2" -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="compat test" -REQUIRED_USE="${PYTHON_REQUIRED_USE}" -RESTRICT="!test? ( test )" - -DEPEND=" - ${PYTHON_DEPS} - dev-lang/tcl:0= - dev-tcltk/tclx - compat? ( x11-libs/libX11 ) -" -RDEPEND="${DEPEND}" -BDEPEND=" - test? ( dev-util/dejagnu ) -" - -src_prepare() { - default - - cd "${S}/lib" || die - eautoreconf - - if use compat; then - cd "${S}/compat" || die - eautoreconf - fi -} - -src_configure() { - local myconf=( - --disable-versioning - --with-initconf-in=etcdir - --enable-multilib-support - --disable-set-shell-startup - --prefix="${EPREFIX}/usr/share/Modules" - --mandir="${EPREFIX}/usr/share/man" - --docdir="${EPREFIX}/usr/share/doc/${P}" - --libdir="${EPREFIX}/usr/share/Modules/$(get_libdir)" - --datarootdir="${EPREFIX}/usr/share" - --modulefilesdir="${EPREFIX}/etc/modulefiles" - --with-tcl="${EPREFIX}/usr/$(get_libdir)" - --with-python="${PYTHON}" - --with-quarantine-vars="LD_LIBRARY_PATH LD_PRELOAD" - $(use_enable compat compat-version) - ) - econf "${myconf[@]}" "${EXTRA_ECONF[@]}" || die "configure failed" -} - -src_test() { - # Remove known-broken tests - # These test fine, but fail for random differences in the gentoo environment - rm "${S}"/testsuite/modules.70-maint/210-clear.exp || die "rm failed" - rm "${S}"/testsuite/modules.00-init/110-quar.exp || die "rm failed" - - RUNTESTARGS=-v emake test -} - -src_install() { - default - dosym ../../usr/share/Modules/init/profile.sh /etc/profile.d/modules.sh - dosym ../../usr/share/Modules/init/profile.csh /etc/profile.d/modules.csh - dodir /etc/modulefiles -} diff --git a/sys-devel/DPC++/DPC++-2021.12.ebuild b/sys-devel/DPC++/DPC++-2021.12.ebuild new file mode 100644 index 000000000..348b6f8d6 --- /dev/null +++ b/sys-devel/DPC++/DPC++-2021.12.ebuild @@ -0,0 +1,177 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..12} ) +inherit cmake python-any-r1 +DOCS_BUILDER="doxygen" +DOCS_DIR="build/docs" +DOCS_CONFIG_NAME="doxygen.cfg" +DOCS_DEPEND=" + media-gfx/graphviz + virtual/latex-base + $(python_gen_any_dep ' + dev-python/sphinx[${PYTHON_USEDEP}] + dev-python/recommonmark[${PYTHON_USEDEP}] + dev-python/myst-parser[${PYTHON_USEDEP}] + ') +" +inherit docs + +# We cannot unbundle this because it has to be compiled with the clang/llvm +# that we are building here. Otherwise we run into problems running the compiler. +CPU_EMUL_PV="2022-08-22" +VC_INTR_PV="0.8.1" # Newer versions cause compile failure + +DESCRIPTION="oneAPI Data Parallel C++ compiler" +HOMEPAGE="https://github.com/intel/llvm" +SRC_URI=" + https://github.com/intel/llvm/archive/refs/tags/${PV//./-}.tar.gz -> ${P}.tar.gz + https://github.com/intel/vc-intrinsics/archive/refs/tags/v${VC_INTR_PV}.tar.gz -> ${P}-vc-intrinsics-${VC_INTR_PV}.tar.gz + esimd_emulator? ( https://github.com/intel/cm-cpu-emulation/archive/refs/tags/v${CPU_EMUL_PV}.tar.gz -> ${P}-cm-cpu-emulation-${CPU_EMUL_PV}.tar.gz ) +" +S="${WORKDIR}/llvm-${PV//./-}" +CMAKE_USE_DIR="${S}/llvm" +BUILD_DIR="${S}/build" + +LICENSE="Apache-2.0 MIT" +SLOT="0/5" # Based on libsycl.so +KEYWORDS="~amd64" + +ALL_LLVM_TARGETS=( AArch64 AMDGPU ARM AVR BPF Hexagon Lanai Mips MSP430 + NVPTX PowerPC RISCV Sparc SystemZ WebAssembly X86 XCore ) +ALL_LLVM_TARGETS=( "${ALL_LLVM_TARGETS[@]/#/llvm_targets_}" ) +LLVM_TARGET_USEDEPS=${ALL_LLVM_TARGETS[@]/%/(-)?} + +IUSE="cuda hip test esimd_emulator ${ALL_LLVM_TARGETS[*]}" +REQUIRED_USE=" + ?? ( cuda hip ) + cuda? ( llvm_targets_NVPTX ) + hip? ( llvm_targets_AMDGPU ) +" +RESTRICT="!test? ( test )" + +BDEPEND="virtual/pkgconfig" + +DEPEND=" + dev-libs/boost:= + dev-libs/level-zero:= + dev-libs/opencl-icd-loader + dev-util/opencl-headers + dev-util/spirv-headers + dev-util/spirv-tools + media-libs/libva + dev-build/libtool + esimd_emulator? ( dev-libs/libffi:= ) + cuda? ( dev-util/nvidia-cuda-toolkit:= ) + hip? ( dev-util/hip:= ) +" +RDEPEND="${DEPEND}" + +PATCHES=( + "${FILESDIR}/${P}-system-libs.patch" +) + +src_configure() { + # Extracted from buildbot/configure.py + local mycmakeargs=( + -DLLVM_ENABLE_ASSERTIONS=ON + -DLLVM_TARGETS_TO_BUILD="${LLVM_TARGETS// /;}" + -DLLVM_EXTERNAL_PROJECTS="sycl;llvm-spirv;opencl;libdevice;xpti;xptifw" + -DLLVM_EXTERNAL_SYCL_SOURCE_DIR="${S}/sycl" + -DLLVM_EXTERNAL_LLVM_SPIRV_SOURCE_DIR="${S}/llvm-spirv" + -DLLVM_EXTERNAL_XPTI_SOURCE_DIR="${S}/xpti" + -DXPTI_SOURCE_DIR="${S}/xpti" + -DLLVM_EXTERNAL_XPTIFW_SOURCE_DIR="${S}/xptifw" + -DLLVM_EXTERNAL_LIBDEVICE_SOURCE_DIR="${S}/libdevice" + -DLLVM_ENABLE_PROJECTS="clang;sycl;llvm-spirv;opencl;libdevice;xpti;xptifw" + -DLLVM_BUILD_TOOLS=ON + -DSYCL_ENABLE_WERROR=OFF + -DSYCL_INCLUDE_TESTS="$(usex test)" + -DCLANG_INCLUDE_TESTS="$(usex test)" + -DLLVM_INCLUDE_TESTS="$(usex test)" + -DLLVM_SPIRV_INCLUDE_TESTS="$(usex test)" + -DLLVM_ENABLE_DOXYGEN="$(usex doc)" + -DLLVM_ENABLE_SPHINX="$(usex doc)" + -DLLVM_BUILD_DOCS="$(usex doc)" + -DSYCL_ENABLE_XPTI_TRACING=ON + -DLLVM_ENABLE_LLD=OFF + -DXPTI_ENABLE_WERROR=OFF + -DSYCL_BUILD_PI_ESIMD_EMULATOR="$(usex esimd_emulator)" + -DSYCL_BUILD_PI_CUDA="$(usex cuda)" + -DSYCL_BUILD_PI_HIP="$(usex hip)" + -DLLVM_EXTERNAL_SPIRV_HEADERS_SOURCE_DIR="${ESYSROOT}/usr" + -DLEVEL_ZERO_LIBRARY="${ESYSROOT}/usr/lib64/libze_loader.so" + -DLEVEL_ZERO_INCLUDE_DIR="${ESYSROOT}/usr/include" + -DLLVMGenXIntrinsics_SOURCE_DIR="${WORKDIR}/vc-intrinsics-${VC_INTR_PV}" + -DSYCL_CLANG_EXTRA_FLAGS="${CXXFLAGS}" + # The sycl part of the build system insists on installing during compiling + # Install it to some temporary directory + -DCMAKE_INSTALL_PREFIX="${BUILD_DIR}/install" + -DCMAKE_INSTALL_MANDIR="${BUILD_DIR}/install/share/man" + -DCMAKE_INSTALL_INFODIR="${BUILD_DIR}/install/share/info" + -DCMAKE_INSTALL_DOCDIR="${BUILD_DIR}/install/share/doc/${PF}" + ) + + if use hip; then + mycmakeargs+=( + -DSYCL_BUILD_PI_HIP_PLATFORM=AMD + -DLIBCLC_GENERATE_REMANGLED_VARIANTS=ON + -DLIBCLC_TARGETS_TO_BUILD=";amdgcn--;amdgcn--amdhsa" + ) + fi + + if use cuda; then + mycmakeargs+=( + -DLIBCLC_GENERATE_REMANGLED_VARIANTS=ON + -DLIBCLC_TARGETS_TO_BUILD=";nvptx64--;nvptx64--nvidiacl" + ) + fi + + if use esimd_emulator; then + mycmakeargs+=( + -DLibFFI_INCLUDE_DIR="${ESYSROOT}/usr/lib64/libffi/include" + -DUSE_LOCAL_CM_EMU_SOURCE="${WORKDIR}/cm-cpu-emulation-${CPU_EMUL_PV}" + ) + fi + + if use doc; then + mycmakeargs+=( -DSPHINX_WARNINGS_AS_ERRORS=OFF ) + fi + + cmake_src_configure +} + +src_compile() { + # Build sycl (this also installs some stuff already) + cmake_build deploy-sycl-toolchain + + use doc && cmake_build doxygen-sycl + + # Install all other files into the same temporary directory + cmake_build install +} + +src_test() { + cmake_build check +} + +src_install() { + einstalldocs + + local LLVM_INTEL_DIR="/usr/lib/llvm/intel" + dodir "${LLVM_INTEL_DIR}" + + # Copy our temporary directory to the image directory + mv "${BUILD_DIR}/install"/* "${ED}/${LLVM_INTEL_DIR}" || die + + # Copied from llvm ebuild, put env file last so we don't overwrite main llvm/clang + newenvd - "60llvm-intel" <<-_EOF_ + PATH="${EPREFIX}${LLVM_INTEL_DIR}/bin" + # we need to duplicate it in ROOTPATH for Portage to respect... + ROOTPATH="${EPREFIX}${LLVM_INTEL_DIR}/bin" + MANPATH="${EPREFIX}${LLVM_INTEL_DIR}/share/man" + LDPATH="${EPREFIX}${LLVM_INTEL_DIR}/lib:${EPREFIX}${LLVM_INTEL_DIR}/lib64" + _EOF_ +} diff --git a/sys-devel/DPC++/DPC++-2022.09.ebuild b/sys-devel/DPC++/DPC++-2022.09.ebuild new file mode 100644 index 000000000..ee2077566 --- /dev/null +++ b/sys-devel/DPC++/DPC++-2022.09.ebuild @@ -0,0 +1,176 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..12} ) +inherit cmake python-any-r1 +DOCS_BUILDER="doxygen" +DOCS_DIR="build/docs" +DOCS_CONFIG_NAME="doxygen.cfg" +DOCS_DEPEND=" + media-gfx/graphviz + virtual/latex-base + $(python_gen_any_dep ' + dev-python/sphinx[${PYTHON_USEDEP}] + dev-python/recommonmark[${PYTHON_USEDEP}] + dev-python/myst-parser[${PYTHON_USEDEP}] + ') +" +inherit docs + +# We cannot unbundle this because it has to be compiled with the clang/llvm +# that we are building here. Otherwise we run into problems running the compiler. +CPU_EMUL_PV="2022-08-22" +VC_INTR_PV="0.8.1" # Newer versions cause compile failure + +DESCRIPTION="oneAPI Data Parallel C++ compiler" +HOMEPAGE="https://github.com/intel/llvm" +SRC_URI=" + https://github.com/intel/llvm/archive/refs/tags/${PV//./-}.tar.gz -> ${P}.tar.gz + https://github.com/intel/vc-intrinsics/archive/refs/tags/v${VC_INTR_PV}.tar.gz -> ${P}-vc-intrinsics-${VC_INTR_PV}.tar.gz + esimd_emulator? ( https://github.com/intel/cm-cpu-emulation/archive/refs/tags/v${CPU_EMUL_PV}.tar.gz -> ${P}-cm-cpu-emulation-${CPU_EMUL_PV}.tar.gz ) +" +S="${WORKDIR}/llvm-${PV//./-}" +CMAKE_USE_DIR="${S}/llvm" +BUILD_DIR="${S}/build" + +LICENSE="Apache-2.0 MIT" +SLOT="0/6" # Based on libsycl.so +KEYWORDS="~amd64" + +ALL_LLVM_TARGETS=( AArch64 AMDGPU ARM AVR BPF Hexagon Lanai Mips MSP430 + NVPTX PowerPC RISCV Sparc SystemZ WebAssembly X86 XCore ) +ALL_LLVM_TARGETS=( "${ALL_LLVM_TARGETS[@]/#/llvm_targets_}" ) +LLVM_TARGET_USEDEPS=${ALL_LLVM_TARGETS[@]/%/(-)?} + +IUSE="cuda hip test esimd_emulator ${ALL_LLVM_TARGETS[*]}" +REQUIRED_USE=" + ?? ( cuda hip ) + cuda? ( llvm_targets_NVPTX ) + hip? ( llvm_targets_AMDGPU ) +" +RESTRICT="!test? ( test )" + +BDEPEND="virtual/pkgconfig" + +DEPEND=" + dev-libs/boost:= + dev-libs/level-zero:= + dev-libs/opencl-icd-loader + dev-util/opencl-headers + dev-util/spirv-headers + dev-util/spirv-tools + media-libs/libva + dev-build/libtool + esimd_emulator? ( dev-libs/libffi:= ) + cuda? ( dev-util/nvidia-cuda-toolkit:= ) + hip? ( dev-util/hip:= ) +" +RDEPEND="${DEPEND}" + +PATCHES=( + "${FILESDIR}/${P}-system-libs.patch" +) + +src_configure() { + # Extracted from buildbot/configure.py + local mycmakeargs=( + -DLLVM_ENABLE_ASSERTIONS=ON + -DLLVM_TARGETS_TO_BUILD="${LLVM_TARGETS// /;}" + -DLLVM_EXTERNAL_PROJECTS="sycl;llvm-spirv;opencl;libdevice;xpti;xptifw" + -DLLVM_EXTERNAL_SYCL_SOURCE_DIR="${S}/sycl" + -DLLVM_EXTERNAL_LLVM_SPIRV_SOURCE_DIR="${S}/llvm-spirv" + -DLLVM_EXTERNAL_XPTI_SOURCE_DIR="${S}/xpti" + -DXPTI_SOURCE_DIR="${S}/xpti" + -DLLVM_EXTERNAL_XPTIFW_SOURCE_DIR="${S}/xptifw" + -DLLVM_EXTERNAL_LIBDEVICE_SOURCE_DIR="${S}/libdevice" + -DLLVM_ENABLE_PROJECTS="clang;sycl;llvm-spirv;opencl;libdevice;xpti;xptifw" + -DLLVM_BUILD_TOOLS=ON + -DSYCL_ENABLE_WERROR=OFF + -DSYCL_INCLUDE_TESTS="$(usex test)" + -DCLANG_INCLUDE_TESTS="$(usex test)" + -DLLVM_INCLUDE_TESTS="$(usex test)" + -DLLVM_SPIRV_INCLUDE_TESTS="$(usex test)" + -DLLVM_ENABLE_DOXYGEN="$(usex doc)" + -DLLVM_ENABLE_SPHINX="$(usex doc)" + -DLLVM_BUILD_DOCS="$(usex doc)" + -DSYCL_ENABLE_XPTI_TRACING=ON + -DLLVM_ENABLE_LLD=OFF + -DXPTI_ENABLE_WERROR=OFF + -DSYCL_ENABLE_PLUGINS="level_zero;opencl;$(usev esimd_emulator);$(usev hip);$(usev cuda)" + -DLLVM_EXTERNAL_SPIRV_HEADERS_SOURCE_DIR="${ESYSROOT}/usr" + -DBOOST_MP11_SOURCE_DIR="${ESYSROOT}/usr " + -DLEVEL_ZERO_LIBRARY="${ESYSROOT}/usr/lib64/libze_loader.so" + -DLEVEL_ZERO_INCLUDE_DIR="${ESYSROOT}/usr/include" + -DLLVMGenXIntrinsics_SOURCE_DIR="${WORKDIR}/vc-intrinsics-${VC_INTR_PV}" + -DSYCL_CLANG_EXTRA_FLAGS="${CXXFLAGS}" + # The sycl part of the build system insists on installing during compiling + # Install it to some temporary directory + -DCMAKE_INSTALL_PREFIX="${BUILD_DIR}/install" + -DCMAKE_INSTALL_MANDIR="${BUILD_DIR}/install/share/man" + -DCMAKE_INSTALL_INFODIR="${BUILD_DIR}/install/share/info" + -DCMAKE_INSTALL_DOCDIR="${BUILD_DIR}/install/share/doc/${PF}" + ) + + if use hip; then + mycmakeargs+=( + -DSYCL_BUILD_PI_HIP_PLATFORM=AMD + -DLIBCLC_GENERATE_REMANGLED_VARIANTS=ON + -DLIBCLC_TARGETS_TO_BUILD=";amdgcn--;amdgcn--amdhsa" + ) + fi + + if use cuda; then + mycmakeargs+=( + -DLIBCLC_GENERATE_REMANGLED_VARIANTS=ON + -DLIBCLC_TARGETS_TO_BUILD=";nvptx64--;nvptx64--nvidiacl" + ) + fi + + if use esimd_emulator; then + mycmakeargs+=( + -DLibFFI_INCLUDE_DIR="${ESYSROOT}/usr/lib64/libffi/include" + -DUSE_LOCAL_CM_EMU_SOURCE="${WORKDIR}/cm-cpu-emulation-${CPU_EMUL_PV}" + ) + fi + + if use doc; then + mycmakeargs+=( -DSPHINX_WARNINGS_AS_ERRORS=OFF ) + fi + + cmake_src_configure +} + +src_compile() { + # Build sycl (this also installs some stuff already) + cmake_build deploy-sycl-toolchain + + use doc && cmake_build doxygen-sycl + + # Install all other files into the same temporary directory + cmake_build install +} + +src_test() { + cmake_build check +} + +src_install() { + einstalldocs + + local LLVM_INTEL_DIR="/usr/lib/llvm/intel" + dodir "${LLVM_INTEL_DIR}" + + # Copy our temporary directory to the image directory + mv "${BUILD_DIR}/install"/* "${ED}/${LLVM_INTEL_DIR}" || die + + # Copied from llvm ebuild, put env file last so we don't overwrite main llvm/clang + newenvd - "60llvm-intel" <<-_EOF_ + PATH="${EPREFIX}${LLVM_INTEL_DIR}/bin" + # we need to duplicate it in ROOTPATH for Portage to respect... + ROOTPATH="${EPREFIX}${LLVM_INTEL_DIR}/bin" + MANPATH="${EPREFIX}${LLVM_INTEL_DIR}/share/man" + LDPATH="${EPREFIX}${LLVM_INTEL_DIR}/lib:${EPREFIX}${LLVM_INTEL_DIR}/lib64" + _EOF_ +} diff --git a/sys-devel/DPC++/DPC++-2022.12.ebuild b/sys-devel/DPC++/DPC++-2022.12.ebuild new file mode 100644 index 000000000..be9a59fec --- /dev/null +++ b/sys-devel/DPC++/DPC++-2022.12.ebuild @@ -0,0 +1,184 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{10..12} ) +inherit cmake python-any-r1 +DOCS_BUILDER="doxygen" +DOCS_DIR="build/docs" +DOCS_CONFIG_NAME="doxygen.cfg" +DOCS_DEPEND=" + media-gfx/graphviz + virtual/latex-base + $(python_gen_any_dep ' + dev-python/sphinx[${PYTHON_USEDEP}] + dev-python/recommonmark[${PYTHON_USEDEP}] + dev-python/myst-parser[${PYTHON_USEDEP}] + ') +" +inherit docs + +# We cannot unbundle this because it has to be compiled with the clang/llvm +# that we are building here. Otherwise we run into problems running the compiler. +CPU_EMUL_PV="2022-08-22" +VC_INTR_PV="0.10.0" # Newer versions cause compile failure +UR_COMMIT="fd711c920acc4434cb52ff18b078c082d9d7f44d" + +DESCRIPTION="oneAPI Data Parallel C++ compiler" +HOMEPAGE="https://github.com/intel/llvm" +SRC_URI=" + https://github.com/intel/llvm/archive/refs/tags/${PV//./-}.tar.gz -> ${P}.tar.gz + https://github.com/intel/vc-intrinsics/archive/refs/tags/v${VC_INTR_PV}.tar.gz -> ${P}-vc-intrinsics-${VC_INTR_PV}.tar.gz + https://github.com/oneapi-src/unified-runtime/archive/${UR_COMMIT}.tar.gz -> ${P}-unified-runtime-${UR_COMMIT}.tar.gz + esimd_emulator? ( https://github.com/intel/cm-cpu-emulation/archive/refs/tags/v${CPU_EMUL_PV}.tar.gz -> ${P}-cm-cpu-emulation-${CPU_EMUL_PV}.tar.gz ) +" +S="${WORKDIR}/llvm-${PV//./-}" +CMAKE_USE_DIR="${S}/llvm" +BUILD_DIR="${S}/build" + +LICENSE="Apache-2.0 MIT" +SLOT="0/6" # Based on libsycl.so +KEYWORDS="~amd64" + +ALL_LLVM_TARGETS=( AArch64 AMDGPU ARM AVR BPF Hexagon Lanai Mips MSP430 + NVPTX PowerPC RISCV Sparc SystemZ WebAssembly X86 XCore ) +ALL_LLVM_TARGETS=( "${ALL_LLVM_TARGETS[@]/#/llvm_targets_}" ) +LLVM_TARGET_USEDEPS=${ALL_LLVM_TARGETS[@]/%/(-)?} + +IUSE="cuda hip test esimd_emulator ${ALL_LLVM_TARGETS[*]}" +REQUIRED_USE=" + ?? ( cuda hip ) + cuda? ( llvm_targets_NVPTX ) + hip? ( llvm_targets_AMDGPU ) +" +RESTRICT="!test? ( test )" + +BDEPEND="virtual/pkgconfig" + +DEPEND=" + dev-libs/boost:= + dev-libs/level-zero:= + dev-libs/opencl-icd-loader + dev-util/opencl-headers + dev-util/spirv-headers + dev-util/spirv-tools + media-libs/libva + dev-build/libtool + esimd_emulator? ( dev-libs/libffi:= ) + cuda? ( dev-util/nvidia-cuda-toolkit:= ) + hip? ( dev-util/hip:= ) +" +RDEPEND="${DEPEND}" + +PATCHES=( + "${FILESDIR}/${P}-system-libs.patch" + "${FILESDIR}/${P}-gcc13.patch" +) + +src_configure() { + # Extracted from buildbot/configure.py + local mycmakeargs=( + -DLLVM_ENABLE_ASSERTIONS=ON + -DLLVM_TARGETS_TO_BUILD="${LLVM_TARGETS// /;}" + -DLLVM_EXTERNAL_PROJECTS="sycl;llvm-spirv;opencl;libdevice;xpti;xptifw" + -DLLVM_EXTERNAL_SYCL_SOURCE_DIR="${S}/sycl" + -DLLVM_EXTERNAL_LLVM_SPIRV_SOURCE_DIR="${S}/llvm-spirv" + -DLLVM_EXTERNAL_XPTI_SOURCE_DIR="${S}/xpti" + -DXPTI_SOURCE_DIR="${S}/xpti" + -DLLVM_EXTERNAL_XPTIFW_SOURCE_DIR="${S}/xptifw" + -DLLVM_EXTERNAL_LIBDEVICE_SOURCE_DIR="${S}/libdevice" + -DLLVM_ENABLE_PROJECTS="clang;sycl;llvm-spirv;opencl;libdevice;xpti;xptifw" + -DLLVM_BUILD_TOOLS=ON + -DSYCL_ENABLE_WERROR=OFF + -DSYCL_INCLUDE_TESTS="$(usex test)" + -DCLANG_INCLUDE_TESTS="$(usex test)" + -DLLVM_INCLUDE_TESTS="$(usex test)" + -DLLVM_SPIRV_INCLUDE_TESTS="$(usex test)" + -DLLVM_ENABLE_DOXYGEN="$(usex doc)" + -DLLVM_ENABLE_SPHINX="$(usex doc)" + -DLLVM_BUILD_DOCS="$(usex doc)" + -DSYCL_ENABLE_XPTI_TRACING=ON + -DLLVM_ENABLE_LLD=OFF + -DXPTI_ENABLE_WERROR=OFF + -DSYCL_ENABLE_PLUGINS="level_zero;opencl;$(usev esimd_emulator);$(usev hip);$(usev cuda)" + -DLLVM_EXTERNAL_SPIRV_HEADERS_SOURCE_DIR="${ESYSROOT}/usr" + -DBOOST_MP11_SOURCE_DIR="${ESYSROOT}/usr " + -DLEVEL_ZERO_LIBRARY="${ESYSROOT}/usr/lib64/libze_loader.so" + -DLEVEL_ZERO_INCLUDE_DIR="${ESYSROOT}/usr/include" + -DLLVMGenXIntrinsics_SOURCE_DIR="${WORKDIR}/vc-intrinsics-${VC_INTR_PV}" + -DSYCL_CLANG_EXTRA_FLAGS="${CXXFLAGS}" + -DUNIFIED_RUNTIME_SOURCE_DIR="${WORKDIR}/unified-runtime-${UR_COMMIT}" + # The sycl part of the build system insists on installing during compiling + # Install it to some temporary directory + -DCMAKE_INSTALL_PREFIX="${BUILD_DIR}/install" + -DCMAKE_INSTALL_MANDIR="${BUILD_DIR}/install/share/man" + -DCMAKE_INSTALL_INFODIR="${BUILD_DIR}/install/share/info" + -DCMAKE_INSTALL_DOCDIR="${BUILD_DIR}/install/share/doc/${PF}" + ) + + if use hip; then + mycmakeargs+=( + -DSYCL_BUILD_PI_HIP_PLATFORM=AMD + -DLIBCLC_GENERATE_REMANGLED_VARIANTS=ON + -DLIBCLC_TARGETS_TO_BUILD=";amdgcn--;amdgcn--amdhsa" + ) + fi + + if use cuda; then + mycmakeargs+=( + -DLIBCLC_GENERATE_REMANGLED_VARIANTS=ON + -DLIBCLC_TARGETS_TO_BUILD=";nvptx64--;nvptx64--nvidiacl" + ) + fi + + if use esimd_emulator; then + mycmakeargs+=( + -DLibFFI_INCLUDE_DIR="${ESYSROOT}/usr/lib64/libffi/include" + -DUSE_LOCAL_CM_EMU_SOURCE="${WORKDIR}/cm-cpu-emulation-${CPU_EMUL_PV}" + ) + fi + + if use doc; then + mycmakeargs+=( -DSPHINX_WARNINGS_AS_ERRORS=OFF ) + fi + + cmake_src_configure +} + +src_compile() { + # Build sycl (this also installs some stuff already) + cmake_build deploy-sycl-toolchain + + use doc && cmake_build doxygen-sycl + + # Install all other files into the same temporary directory + cmake_build install +} + +src_test() { + cmake_build check +} + +src_install() { + einstalldocs + + local LLVM_INTEL_DIR="/usr/lib/llvm/intel" + dodir "${LLVM_INTEL_DIR}" + + # Copy our temporary directory to the image directory + mv "${BUILD_DIR}/install"/* "${ED}/${LLVM_INTEL_DIR}" || die + + # Convienence symlinks + dosym "${LLVM_INTEL_DIR}/bin/clang" "/usr/bin/icx" + dosym "${LLVM_INTEL_DIR}/bin/clang++" "/usr/bin/icpx" + + # Copied from llvm ebuild, put env file last so we don't overwrite main llvm/clang + newenvd - "60llvm-intel" <<-_EOF_ + PATH="${EPREFIX}${LLVM_INTEL_DIR}/bin" + # we need to duplicate it in ROOTPATH for Portage to respect... + ROOTPATH="${EPREFIX}${LLVM_INTEL_DIR}/bin" + MANPATH="${EPREFIX}${LLVM_INTEL_DIR}/share/man" + LDPATH="${EPREFIX}${LLVM_INTEL_DIR}/lib:${EPREFIX}${LLVM_INTEL_DIR}/lib64" + _EOF_ +} diff --git a/sys-devel/DPC++/Manifest b/sys-devel/DPC++/Manifest new file mode 100644 index 000000000..324ee6cfc --- /dev/null +++ b/sys-devel/DPC++/Manifest @@ -0,0 +1,10 @@ +DIST DPC++-2021.12-cm-cpu-emulation-2022-08-22.tar.gz 328563 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86dfbf9163e77675227eb1db2242edf0de6e3f6be45ddfc1077d4cfb83e997f4839f2abb4e15688f4e657c263a0102d7fda627d6c57f1bcc2582560f3fdb5664 SHA512 fabd973739c17c3c702d8ea1345df165a272053fe7c6564fb81f00a3a316e1ed69d4fdbd73f408841600cf9705e31fc688c6d88e7b095e8f97b1090b3ecd8ccc +DIST DPC++-2022.09-vc-intrinsics-0.8.1.tar.gz 138462 BLAKE2B 0f86f5fbeb7931a564eb598d527fd67e96489d0f2e7dba7166ffa468470022eff05e150877c3dd380ad003beb8651a0ac9ffe9c3dceeae6552c46b5f3e00aa64 SHA512 9763f1b624121694d6880ca3ffdf2e344ce3ed1a39c1c1e7dc06195b79acccce5e3d86032bba5c0de440376821c383f8ff59fdd57b0ae93fede17595b0fe0b42 +DIST DPC++-2022.09.tar.gz 171848301 BLAKE2B 48f57fee53370135b25a4e5f27926375fe9e4b707909f5841afa4c0d27a53932404f066db6384b8e8c327f1328cd00339e1c055935eb38fca2a8ce34f3556727 SHA512 f17ac91d4ec03c067595abd8355a54484c2cd8b79bb8b1ed8c90fabd8d83b73cce0271a8b3aa26e2c92e8083a2b3cf145c7e78b68e568c3cb036c80b8a4f9e12 +DIST DPC++-2022.12-cm-cpu-emulation-2022-08-22.tar.gz 328563 BLAKE2B 86dfbf9163e77675227eb1db2242edf0de6e3f6be45ddfc1077d4cfb83e997f4839f2abb4e15688f4e657c263a0102d7fda627d6c57f1bcc2582560f3fdb5664 SHA512 fabd973739c17c3c702d8ea1345df165a272053fe7c6564fb81f00a3a316e1ed69d4fdbd73f408841600cf9705e31fc688c6d88e7b095e8f97b1090b3ecd8ccc +DIST DPC++-2022.12-unified-runtime-fd711c920acc4434cb52ff18b078c082d9d7f44d.tar.gz 249206 BLAKE2B 52da2e773e3d617ca1fd491a71c0c9ce0d943f550278339aa9fa14c8997aff26a5cd642a414f4fb2aece198a7d912b7c9092a9d89c7f62f417f43406f73bf4a6 SHA512 356351abe965b5129d0c0ec2c459e950461192762c501b5089d12a1135fd970ff2572ac99255bb743798f890f485621fc21173124d67a9b142d36ac07c09d936 +DIST DPC++-2022.12-vc-intrinsics-0.10.0.tar.gz 138920 BLAKE2B a73ccbbc56bff3cf0656eb505b5201db1889dec0c2b608c1a999bb0302a9bc9c275480a2d3aa31e04faed5c827a55aa6d36e4603f4716b5998ed4f2df4ec8850 SHA512 5c9e5eae2da9f4975f9d11249a27751c387dd2a425b40d9ff67890857557cfc503e93f0315329658443d060c48b72fd4eee776d5592f0b9e5cb485d659d55658 +DIST DPC++-2022.12.tar.gz 176940515 BLAKE2B ef4ca7096ae18c2ae19c8e781dd120621f59741533d76f3f3739d8d043a11edfff036a45aed187735c5e7fe34d707f2dd85c336b4995ac64acd0f91f1558c4ca SHA512 132c016af101f5fb1f86a77ad7714883adf30803700bcf5349bc5f16618606e6697f920992bb6bd61ddaa8f6c9259eabbc1a163a05249f7731400c7b584fb222 diff --git a/sys-devel/DPC++/files/DPC++-2021.12-system-libs.patch b/sys-devel/DPC++/files/DPC++-2021.12-system-libs.patch new file mode 100644 index 000000000..a9d7f468f --- /dev/null +++ b/sys-devel/DPC++/files/DPC++-2021.12-system-libs.patch @@ -0,0 +1,274 @@ +diff --git a/opencl/CMakeLists.txt b/opencl/CMakeLists.txt +index ad6fc3327..f68e18b51 100644 +--- a/opencl/CMakeLists.txt ++++ b/opencl/CMakeLists.txt +@@ -23,29 +23,8 @@ set(OCL_LOADER_REPO + set(OCL_HEADERS_TAG 23710f1b99186065c1768fc3098ba681adc0f253) + set(OCL_LOADER_TAG 5f8249691ec8c25775789498951f8e9eb62c201d) + +-# OpenCL Headers +-if(NOT OpenCL_HEADERS) +- message(STATUS "Will fetch OpenCL headers from ${OCL_HEADERS_REPO}") +- +- FetchContent_Declare(ocl-headers +- GIT_REPOSITORY ${OCL_HEADERS_REPO} +- GIT_TAG ${OCL_HEADERS_TAG} +- ) +-else() +- message(STATUS "OpenCL headers are added manually ${OpenCL_HEADERS}") +- +- FetchContent_Declare(ocl-headers +- URL ${OpenCL_HEADERS} +- ) +-endif() +- +-FetchContent_MakeAvailable(ocl-headers) +-FetchContent_GetProperties(ocl-headers) + set(OpenCL_INCLUDE_DIR +- ${ocl-headers_SOURCE_DIR} CACHE PATH "Path to OpenCL Headers") +- +-target_compile_definitions(Headers INTERFACE -DCL_TARGET_OPENCL_VERSION=220) +-add_library(OpenCL-Headers ALIAS Headers) ++ /usr/include CACHE PATH "Path to OpenCL Headers") + + # OpenCL Library (ICD Loader) + +@@ -57,25 +36,4 @@ set(OPENCL_ICD_LOADER_HEADERS_DIR + # library. + set(BUILD_SHARED_LIBS ON) + +-if(NOT OpenCL_LIBRARY_SRC) +- message(STATUS "Will fetch OpenCL ICD Loader from ${OCL_LOADER_REPO}") +- +- FetchContent_Declare(ocl-icd +- GIT_REPOSITORY ${OCL_LOADER_REPO} +- GIT_TAG ${OCL_LOADER_TAG} +- ) +-else() +- # TODO: add possibility to use prebuilt OpenCL library rather than building +- # together with llvm. +- message(STATUS +- "OpenCL ICD Loader sources added manually ${OpenCL_LIBRARY_SRC}") +- +- FetchContent_Declare(ocl-icd +- URL ${OpenCL_LIBRARY_SRC} +- ) +-endif() +- +-FetchContent_MakeAvailable(ocl-icd) +-add_library(OpenCL-ICD ALIAS OpenCL) +- + add_subdirectory(opencl-aot) +diff --git a/opencl/opencl-aot/CMakeLists.txt b/opencl/opencl-aot/CMakeLists.txt +index ff905fd88..5232fe7a6 100644 +--- a/opencl/opencl-aot/CMakeLists.txt ++++ b/opencl/opencl-aot/CMakeLists.txt +@@ -19,5 +19,4 @@ endif() + + target_link_libraries(${OPENCL_AOT_PROJECT_NAME} + PRIVATE +- OpenCL-Headers +- OpenCL-ICD) ++ OpenCL) +diff --git a/sycl/CMakeLists.txt b/sycl/CMakeLists.txt +index 0894e7413..5645799a8 100644 +--- a/sycl/CMakeLists.txt ++++ b/sycl/CMakeLists.txt +@@ -103,7 +103,7 @@ file(COPY ${OpenCL_INCLUDE_DIR}/CL + # Include OpenCL Headers into final bundle. + install(DIRECTORY ${OpenCL_INCLUDE_DIR}/CL + DESTINATION ${SYCL_INCLUDE_DIR}/sycl +- COMPONENT OpenCL-Headers) ++ COMPONENT OpenCL) + + option(SYCL_BUILD_PI_CUDA + "Enables the CUDA backend for the Plugin Interface" OFF) +@@ -295,7 +295,7 @@ set( SYCL_TOOLCHAIN_DEPLOY_COMPONENTS + sycl-post-link + sycl-ls + clang-resource-headers +- OpenCL-Headers ++ OpenCL + opencl-aot + sycl-headers + sycl-headers-extras +@@ -306,8 +306,8 @@ set( SYCL_TOOLCHAIN_DEPLOY_COMPONENTS + ${XPTIFW_LIBS} + ) + +-if(OpenCL_INSTALL_KHRONOS_ICD_LOADER AND TARGET OpenCL-ICD) +- list(APPEND SYCL_TOOLCHAIN_DEPLOY_COMPONENTS OpenCL-ICD) ++if(OpenCL_INSTALL_KHRONOS_ICD_LOADER AND TARGET OpenCL) ++ list(APPEND SYCL_TOOLCHAIN_DEPLOY_COMPONENTS OpenCL) + endif() + + if(SYCL_BUILD_PI_CUDA) +diff --git a/sycl/cmake/modules/AddSYCLUnitTest.cmake b/sycl/cmake/modules/AddSYCLUnitTest.cmake +index 030ff6139..235522b58 100644 +--- a/sycl/cmake/modules/AddSYCLUnitTest.cmake ++++ b/sycl/cmake/modules/AddSYCLUnitTest.cmake +@@ -31,7 +31,7 @@ macro(add_sycl_unittest test_dirname link_variant) + target_link_libraries(${test_dirname} + PRIVATE + LLVMTestingSupport +- OpenCL-Headers ++ OpenCL + ${SYCL_LINK_LIBS} + ) + target_include_directories(${test_dirname} +diff --git a/sycl/plugins/cuda/CMakeLists.txt b/sycl/plugins/cuda/CMakeLists.txt +index ff6dd8bc6..260b10268 100644 +--- a/sycl/plugins/cuda/CMakeLists.txt ++++ b/sycl/plugins/cuda/CMakeLists.txt +@@ -41,7 +41,7 @@ target_include_directories(pi_cuda + + target_link_libraries(pi_cuda + PRIVATE +- OpenCL-Headers ++ OpenCL + cudadrv + ) + +diff --git a/sycl/plugins/esimd_emulator/CMakeLists.txt b/sycl/plugins/esimd_emulator/CMakeLists.txt +index 4ce9e1ff5..5b6cbf1bf 100755 +--- a/sycl/plugins/esimd_emulator/CMakeLists.txt ++++ b/sycl/plugins/esimd_emulator/CMakeLists.txt +@@ -40,6 +40,7 @@ if (DEFINED CM_LOCAL_SOURCE_DIR) + INSTALL_DIR ${CMAKE_CURRENT_BINARY_DIR}/cm-emu_install + CMAKE_ARGS -DLIBVA_INSTALL_PATH=/usr + -D__SYCL_EXPLICIT_SIMD_PLUGIN__=true ++ -DLibFFI_INCLUDE_DIR=${LibFFI_INCLUDE_DIR} + -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> + BUILD_BYPRODUCTS ${LIBCM} ${LIBIGFXCMRT_EMU} + ) +@@ -123,7 +124,7 @@ else() + ) + endif() + +-add_dependencies(pi_esimd_emulator OpenCL-Headers) ++add_dependencies(pi_esimd_emulator OpenCL) + add_dependencies(pi_esimd_emulator cm-emu) + add_dependencies(sycl-toolchain pi_esimd_emulator) + +diff --git a/sycl/plugins/hip/CMakeLists.txt b/sycl/plugins/hip/CMakeLists.txt +index 7b3d9c395..e696ceeb0 100644 +--- a/sycl/plugins/hip/CMakeLists.txt ++++ b/sycl/plugins/hip/CMakeLists.txt +@@ -17,7 +17,7 @@ add_library(pi_hip SHARED + ) + add_dependencies(sycl-toolchain pi_hip) + set_target_properties(pi_hip PROPERTIES LINKER_LANGUAGE CXX) +-target_link_libraries(pi_hip PUBLIC OpenCL-Headers) ++target_link_libraries(pi_hip PUBLIC OpenCL) + + # Setup include directories + target_include_directories(pi_hip +diff --git a/sycl/plugins/level_zero/CMakeLists.txt b/sycl/plugins/level_zero/CMakeLists.txt +index f4e6a48bc..f674c6a57 100755 +--- a/sycl/plugins/level_zero/CMakeLists.txt ++++ b/sycl/plugins/level_zero/CMakeLists.txt +@@ -48,7 +48,7 @@ if (NOT DEFINED LEVEL_ZERO_LIBRARY OR NOT DEFINED LEVEL_ZERO_INCLUDE_DIR) + LOG_BUILD 1 + LOG_INSTALL 1 + STEP_TARGETS configure,build,install +- DEPENDS OpenCL-Headers ++ DEPENDS OpenCL + BUILD_BYPRODUCTS ${LEVEL_ZERO_LOADER} + ) + ExternalProject_Add_Step(level-zero-loader llvminstall +@@ -82,7 +82,7 @@ else() + COMMAND + ${CMAKE_COMMAND} -E copy ${LEVEL_ZERO_LIBRARY_SRC} ${LLVM_LIBRARY_OUTPUT_INTDIR} + COMMAND +- ${CMAKE_COMMAND} -E copy_directory ${LEVEL_ZERO_INCLUDE_DIR} ${LLVM_BINARY_DIR}/include/sycl ++ ${CMAKE_COMMAND} -E copy_directory ${LEVEL_ZERO_INCLUDE_DIR}/level_zero ${LLVM_BINARY_DIR}/include/sycl/level_zero + DEPENDS + ${LEVEL_ZERO_LIBRARY} + ${LEVEL_ZERO_INCLUDE_DIR} +@@ -140,7 +140,7 @@ add_dependencies(sycl-toolchain pi_level_zero) + target_link_libraries(pi_level_zero + PRIVATE + "${LEVEL_ZERO_LOADER}" +- OpenCL-Headers ++ OpenCL + ) + + if (UNIX) +diff --git a/sycl/plugins/opencl/CMakeLists.txt b/sycl/plugins/opencl/CMakeLists.txt +index d3d5c3a4c..d08809c99 100644 +--- a/sycl/plugins/opencl/CMakeLists.txt ++++ b/sycl/plugins/opencl/CMakeLists.txt +@@ -25,8 +25,7 @@ target_include_directories(pi_opencl PRIVATE "${sycl_inc_dir}") + #link pi_opencl with OpenCL headers and ICD Loader. + target_link_libraries(pi_opencl + PRIVATE +- OpenCL-Headers +- OpenCL-ICD ++ OpenCL + ) + if (MSVC) + # by defining __SYCL_BUILD_SYCL_DLL, we can use __declspec(dllexport) +diff --git a/sycl/source/CMakeLists.txt b/sycl/source/CMakeLists.txt +index 46f33bdb4..6e65cd6a8 100644 +--- a/sycl/source/CMakeLists.txt ++++ b/sycl/source/CMakeLists.txt +@@ -76,14 +76,14 @@ function(add_sycl_rt_library LIB_NAME) + ) + #TODO: Remove dependency on icd loader and opencl headers. + target_link_libraries(${LIB_OBJ_NAME} +- PRIVATE OpenCL-Headers ++ PRIVATE OpenCL + ) + + find_package(Threads REQUIRED) + + target_link_libraries(${LIB_NAME} + PRIVATE +- OpenCL-ICD ++ OpenCL + ${CMAKE_DL_LIBS} + ${CMAKE_THREAD_LIBS_INIT} + PUBLIC +diff --git a/sycl/tools/CMakeLists.txt b/sycl/tools/CMakeLists.txt +index a4f567482..7af557fd2 100644 +--- a/sycl/tools/CMakeLists.txt ++++ b/sycl/tools/CMakeLists.txt +@@ -20,9 +20,8 @@ endif() + + target_link_libraries(get_device_count_by_type + PRIVATE +- OpenCL-Headers ++ OpenCL + LevelZeroLoader::Headers +- OpenCL-ICD + ${LEVEL_ZERO_LIBRARY} + # The CUDA and HIP for NVIDA plugins need cudadrv + $<$<OR:$<BOOL:${SYCL_BUILD_PI_CUDA}>,$<AND:$<BOOL:${SYCL_BUILD_PI_HIP}>,$<STREQUAL:${SYCL_BUILD_PI_HIP_PLATFORM},NVIDIA>>>:cudadrv> +diff --git a/sycl/tools/pi-trace/CMakeLists.txt b/sycl/tools/pi-trace/CMakeLists.txt +index e305fd22d..5aea609ff 100644 +--- a/sycl/tools/pi-trace/CMakeLists.txt ++++ b/sycl/tools/pi-trace/CMakeLists.txt +@@ -1,8 +1,8 @@ + add_library(pi_trace SHARED pi_trace.cpp) + target_compile_definitions(pi_trace PRIVATE XPTI_CALLBACK_API_EXPORTS) + target_link_libraries(pi_trace PRIVATE xptifw) +-if (TARGET OpenCL-Headers) +- target_link_libraries(pi_trace PRIVATE OpenCL-Headers) ++if (TARGET OpenCL) ++ target_link_libraries(pi_trace PRIVATE OpenCL) + endif() + + target_include_directories(pi_trace PRIVATE +diff --git a/sycl/tools/sycl-ls/CMakeLists.txt b/sycl/tools/sycl-ls/CMakeLists.txt +index f5909cf49..f9c52e3a3 100644 +--- a/sycl/tools/sycl-ls/CMakeLists.txt ++++ b/sycl/tools/sycl-ls/CMakeLists.txt +@@ -11,7 +11,7 @@ endif() + target_link_libraries(sycl-ls + PRIVATE + ${sycl_lib} +- OpenCL-Headers ++ OpenCL + ) + install(TARGETS sycl-ls + RUNTIME DESTINATION "bin" COMPONENT sycl-ls) diff --git a/sys-devel/DPC++/files/DPC++-2022.09-system-libs.patch b/sys-devel/DPC++/files/DPC++-2022.09-system-libs.patch new file mode 100644 index 000000000..7d2cdc823 --- /dev/null +++ b/sys-devel/DPC++/files/DPC++-2022.09-system-libs.patch @@ -0,0 +1,217 @@ +diff --git a/opencl/CMakeLists.txt b/opencl/CMakeLists.txt +index 954317fe2..ba3bf19d3 100644 +--- a/opencl/CMakeLists.txt ++++ b/opencl/CMakeLists.txt +@@ -23,29 +23,8 @@ set(OCL_LOADER_REPO + set(OCL_HEADERS_TAG dcd5bede6859d26833cd85f0d6bbcee7382dc9b3) + set(OCL_LOADER_TAG 792682ad3d877ab38573b997808bab3b43902b70) + +-# OpenCL Headers +-if(NOT OpenCL_HEADERS) +- message(STATUS "Will fetch OpenCL headers from ${OCL_HEADERS_REPO}") +- +- FetchContent_Declare(ocl-headers +- GIT_REPOSITORY ${OCL_HEADERS_REPO} +- GIT_TAG ${OCL_HEADERS_TAG} +- ) +-else() +- message(STATUS "OpenCL headers are added manually ${OpenCL_HEADERS}") +- +- FetchContent_Declare(ocl-headers +- URL ${OpenCL_HEADERS} +- ) +-endif() +- +-FetchContent_MakeAvailable(ocl-headers) +-FetchContent_GetProperties(ocl-headers) + set(OpenCL_INCLUDE_DIR +- ${ocl-headers_SOURCE_DIR} CACHE PATH "Path to OpenCL Headers") +- +-target_compile_definitions(Headers INTERFACE -DCL_TARGET_OPENCL_VERSION=220) +-add_library(OpenCL-Headers ALIAS Headers) ++ /usr/include CACHE PATH "Path to OpenCL Headers") + + # OpenCL Library (ICD Loader) + +@@ -57,25 +36,4 @@ set(OPENCL_ICD_LOADER_HEADERS_DIR + # library. + set(BUILD_SHARED_LIBS ON) + +-if(NOT OpenCL_LIBRARY_SRC) +- message(STATUS "Will fetch OpenCL ICD Loader from ${OCL_LOADER_REPO}") +- +- FetchContent_Declare(ocl-icd +- GIT_REPOSITORY ${OCL_LOADER_REPO} +- GIT_TAG ${OCL_LOADER_TAG} +- ) +-else() +- # TODO: add possibility to use prebuilt OpenCL library rather than building +- # together with llvm. +- message(STATUS +- "OpenCL ICD Loader sources added manually ${OpenCL_LIBRARY_SRC}") +- +- FetchContent_Declare(ocl-icd +- URL ${OpenCL_LIBRARY_SRC} +- ) +-endif() +- +-FetchContent_MakeAvailable(ocl-icd) +-add_library(OpenCL-ICD ALIAS OpenCL) +- + add_subdirectory(opencl-aot) +diff --git a/opencl/opencl-aot/CMakeLists.txt b/opencl/opencl-aot/CMakeLists.txt +index ff905fd88..b673f79a4 100644 +--- a/opencl/opencl-aot/CMakeLists.txt ++++ b/opencl/opencl-aot/CMakeLists.txt +@@ -19,5 +19,5 @@ endif() + + target_link_libraries(${OPENCL_AOT_PROJECT_NAME} + PRIVATE +- OpenCL-Headers +- OpenCL-ICD) ++ OpenCL ++) +diff --git a/sycl/cmake/modules/AddSYCL.cmake b/sycl/cmake/modules/AddSYCL.cmake +index aa0cfcadd..9cfa5aadd 100644 +--- a/sycl/cmake/modules/AddSYCL.cmake ++++ b/sycl/cmake/modules/AddSYCL.cmake +@@ -47,7 +47,7 @@ function(add_sycl_plugin PLUGIN_NAME) + ${sycl_inc_dir} + LIBRARIES + ${ARG_LIBRARIES} +- OpenCL-Headers ++ OpenCL + ) + + install(TARGETS pi_${PLUGIN_NAME} +diff --git a/sycl/cmake/modules/AddSYCLUnitTest.cmake b/sycl/cmake/modules/AddSYCLUnitTest.cmake +index 9f5e6dc30..fe0e18b2f 100644 +--- a/sycl/cmake/modules/AddSYCLUnitTest.cmake ++++ b/sycl/cmake/modules/AddSYCLUnitTest.cmake +@@ -53,7 +53,7 @@ macro(add_sycl_unittest test_dirname link_variant) + target_link_libraries(${test_dirname} + PRIVATE + LLVMTestingSupport +- OpenCL-Headers ++ OpenCL + ${SYCL_LINK_LIBS} + ) + target_include_directories(${test_dirname} +diff --git a/sycl/plugins/esimd_emulator/CMakeLists.txt b/sycl/plugins/esimd_emulator/CMakeLists.txt +index 0b32c3925..e8b8616bc 100755 +--- a/sycl/plugins/esimd_emulator/CMakeLists.txt ++++ b/sycl/plugins/esimd_emulator/CMakeLists.txt +@@ -58,6 +58,7 @@ if ((DEFINED USE_DEFAULT_CM_EMU_SOURCE) OR (DEFINED USE_LOCAL_CM_EMU_SOURCE)) + INSTALL_DIR ${CMAKE_CURRENT_BINARY_DIR}/cm-emu_install + CMAKE_ARGS -DLIBVA_INSTALL_PATH=/usr + -D__SYCL_EXPLICIT_SIMD_PLUGIN__=true ++ -DLibFFI_INCLUDE_DIR=${LibFFI_INCLUDE_DIR} + -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> + BUILD_BYPRODUCTS ${LIBCM} ${LIBIGFXCMRT_EMU} + ) +diff --git a/sycl/plugins/level_zero/CMakeLists.txt b/sycl/plugins/level_zero/CMakeLists.txt +index 9391ff1e5..aa823e8fa 100755 +--- a/sycl/plugins/level_zero/CMakeLists.txt ++++ b/sycl/plugins/level_zero/CMakeLists.txt +@@ -82,7 +82,7 @@ else() + COMMAND + ${CMAKE_COMMAND} -E copy ${LEVEL_ZERO_LIBRARY_SRC} ${LLVM_LIBRARY_OUTPUT_INTDIR} + COMMAND +- ${CMAKE_COMMAND} -E copy_directory ${LEVEL_ZERO_INCLUDE_DIR} ${LLVM_BINARY_DIR}/include/sycl ++ ${CMAKE_COMMAND} -E copy_directory ${LEVEL_ZERO_INCLUDE_DIR}/level_zero ${LLVM_BINARY_DIR}/include/sycl/level_zero + DEPENDS + ${LEVEL_ZERO_LIBRARY} + ${LEVEL_ZERO_INCLUDE_DIR} +diff --git a/sycl/plugins/opencl/CMakeLists.txt b/sycl/plugins/opencl/CMakeLists.txt +index 9943827e4..29fae166e 100644 +--- a/sycl/plugins/opencl/CMakeLists.txt ++++ b/sycl/plugins/opencl/CMakeLists.txt +@@ -15,7 +15,7 @@ add_sycl_plugin(opencl + "${sycl_inc_dir}/sycl/detail/pi.h" + "pi_opencl.cpp" + LIBRARIES +- OpenCL-ICD ++ OpenCL + ) + + set_target_properties(pi_opencl PROPERTIES LINKER_LANGUAGE CXX) +diff --git a/sycl/source/CMakeLists.txt b/sycl/source/CMakeLists.txt +index 23b161480..4a5c48625 100644 +--- a/sycl/source/CMakeLists.txt ++++ b/sycl/source/CMakeLists.txt +@@ -82,7 +82,7 @@ function(add_sycl_rt_library LIB_NAME LIB_OBJ_NAME) + ) + #TODO: Remove dependency on opencl headers. + target_link_libraries(${LIB_OBJ_NAME} +- PRIVATE OpenCL-Headers ++ PRIVATE OpenCL + ) + + find_package(Threads REQUIRED) +diff --git a/sycl/tools/CMakeLists.txt b/sycl/tools/CMakeLists.txt +index eb62c48e1..6a7ff9aef 100644 +--- a/sycl/tools/CMakeLists.txt ++++ b/sycl/tools/CMakeLists.txt +@@ -38,9 +38,8 @@ endif() + + target_link_libraries(get_device_count_by_type + PRIVATE +- OpenCL-Headers ++ OpenCL + LevelZeroLoader::Headers +- OpenCL-ICD + ${LEVEL_ZERO_LIBRARY} + # The CUDA and HIP for NVIDA plugins need cudadrv + $<$<OR:$<BOOL:${SYCL_BUILD_PI_CUDA}>,$<AND:$<BOOL:${SYCL_BUILD_PI_HIP}>,$<STREQUAL:${SYCL_BUILD_PI_HIP_PLATFORM},NVIDIA>>>:cudadrv> +diff --git a/sycl/tools/sycl-ls/CMakeLists.txt b/sycl/tools/sycl-ls/CMakeLists.txt +index f5909cf49..f9c52e3a3 100644 +--- a/sycl/tools/sycl-ls/CMakeLists.txt ++++ b/sycl/tools/sycl-ls/CMakeLists.txt +@@ -11,7 +11,7 @@ endif() + target_link_libraries(sycl-ls + PRIVATE + ${sycl_lib} +- OpenCL-Headers ++ OpenCL + ) + install(TARGETS sycl-ls + RUNTIME DESTINATION "bin" COMPONENT sycl-ls) +diff --git a/sycl/tools/sycl-prof/CMakeLists.txt b/sycl/tools/sycl-prof/CMakeLists.txt +index 09586c1b8..ff708db67 100644 +--- a/sycl/tools/sycl-prof/CMakeLists.txt ++++ b/sycl/tools/sycl-prof/CMakeLists.txt +@@ -16,7 +16,7 @@ add_library(sycl_profiler_collector SHARED collector.cpp) + target_compile_definitions(sycl_profiler_collector PRIVATE XPTI_CALLBACK_API_EXPORTS) + target_link_libraries(sycl_profiler_collector PRIVATE xptifw) + if (TARGET OpenCL-Headers) +- target_link_libraries(sycl_profiler_collector PRIVATE OpenCL-Headers) ++ target_link_libraries(sycl_profiler_collector PRIVATE OpenCL) + endif() + target_include_directories(sycl_profiler_collector PRIVATE + "${sycl_inc_dir}" +diff --git a/sycl/tools/sycl-sanitize/CMakeLists.txt b/sycl/tools/sycl-sanitize/CMakeLists.txt +index 16e7a1a49..e27b2cb21 100644 +--- a/sycl/tools/sycl-sanitize/CMakeLists.txt ++++ b/sycl/tools/sycl-sanitize/CMakeLists.txt +@@ -14,7 +14,7 @@ add_library(sycl_sanitizer_collector SHARED collector.cpp) + target_compile_definitions(sycl_sanitizer_collector PRIVATE XPTI_CALLBACK_API_EXPORTS) + target_link_libraries(sycl_sanitizer_collector PRIVATE xptifw) + if (TARGET OpenCL-Headers) +- target_link_libraries(sycl_sanitizer_collector PRIVATE OpenCL-Headers) ++ target_link_libraries(sycl_sanitizer_collector PRIVATE OpenCL) + endif() + + target_include_directories(sycl_sanitizer_collector PRIVATE +diff --git a/sycl/tools/sycl-trace/CMakeLists.txt b/sycl/tools/sycl-trace/CMakeLists.txt +index 385a348f6..721e29125 100644 +--- a/sycl/tools/sycl-trace/CMakeLists.txt ++++ b/sycl/tools/sycl-trace/CMakeLists.txt +@@ -46,7 +46,7 @@ add_custom_target(ze-pretty-printers + target_compile_definitions(sycl_pi_trace_collector PRIVATE XPTI_CALLBACK_API_EXPORTS) + target_link_libraries(sycl_pi_trace_collector PRIVATE xptifw) + if (TARGET OpenCL-Headers) +- target_link_libraries(sycl_pi_trace_collector PRIVATE OpenCL-Headers) ++ target_link_libraries(sycl_pi_trace_collector PRIVATE OpenCL) + endif() + + target_include_directories(sycl_pi_trace_collector PRIVATE diff --git a/sys-devel/DPC++/files/DPC++-2022.12-gcc13.patch b/sys-devel/DPC++/files/DPC++-2022.12-gcc13.patch new file mode 100644 index 000000000..047170cd3 --- /dev/null +++ b/sys-devel/DPC++/files/DPC++-2022.12-gcc13.patch @@ -0,0 +1,12 @@ +diff --git a/sycl/include/sycl/sycl_span.hpp b/sycl/include/sycl/sycl_span.hpp +index 33b942fbc..395694573 100644 +--- a/sycl/include/sycl/sycl_span.hpp ++++ b/sycl/include/sycl/sycl_span.hpp +@@ -128,6 +128,7 @@ template<class Container> + #include <cassert> // for assert + #include <cstddef> // for byte + #include <iterator> // for iterators ++#include <cstdint> + #include <type_traits> // for remove_cv, etc + + #define _SYCL_SPAN_TEMPLATE_VIS diff --git a/sys-devel/DPC++/files/DPC++-2022.12-system-libs.patch b/sys-devel/DPC++/files/DPC++-2022.12-system-libs.patch new file mode 100644 index 000000000..c5d9d138b --- /dev/null +++ b/sys-devel/DPC++/files/DPC++-2022.12-system-libs.patch @@ -0,0 +1,273 @@ +diff --git a/opencl/CMakeLists.txt b/opencl/CMakeLists.txt +index 954317fe2..ba3bf19d3 100644 +--- a/opencl/CMakeLists.txt ++++ b/opencl/CMakeLists.txt +@@ -23,29 +23,8 @@ set(OCL_LOADER_REPO + set(OCL_HEADERS_TAG dcd5bede6859d26833cd85f0d6bbcee7382dc9b3) + set(OCL_LOADER_TAG 792682ad3d877ab38573b997808bab3b43902b70) + +-# OpenCL Headers +-if(NOT OpenCL_HEADERS) +- message(STATUS "Will fetch OpenCL headers from ${OCL_HEADERS_REPO}") +- +- FetchContent_Declare(ocl-headers +- GIT_REPOSITORY ${OCL_HEADERS_REPO} +- GIT_TAG ${OCL_HEADERS_TAG} +- ) +-else() +- message(STATUS "OpenCL headers are added manually ${OpenCL_HEADERS}") +- +- FetchContent_Declare(ocl-headers +- URL ${OpenCL_HEADERS} +- ) +-endif() +- +-FetchContent_MakeAvailable(ocl-headers) +-FetchContent_GetProperties(ocl-headers) + set(OpenCL_INCLUDE_DIR +- ${ocl-headers_SOURCE_DIR} CACHE PATH "Path to OpenCL Headers") +- +-target_compile_definitions(Headers INTERFACE -DCL_TARGET_OPENCL_VERSION=220) +-add_library(OpenCL-Headers ALIAS Headers) ++ /usr/include CACHE PATH "Path to OpenCL Headers") + + # OpenCL Library (ICD Loader) + +@@ -57,25 +36,4 @@ set(OPENCL_ICD_LOADER_HEADERS_DIR + # library. + set(BUILD_SHARED_LIBS ON) + +-if(NOT OpenCL_LIBRARY_SRC) +- message(STATUS "Will fetch OpenCL ICD Loader from ${OCL_LOADER_REPO}") +- +- FetchContent_Declare(ocl-icd +- GIT_REPOSITORY ${OCL_LOADER_REPO} +- GIT_TAG ${OCL_LOADER_TAG} +- ) +-else() +- # TODO: add possibility to use prebuilt OpenCL library rather than building +- # together with llvm. +- message(STATUS +- "OpenCL ICD Loader sources added manually ${OpenCL_LIBRARY_SRC}") +- +- FetchContent_Declare(ocl-icd +- URL ${OpenCL_LIBRARY_SRC} +- ) +-endif() +- +-FetchContent_MakeAvailable(ocl-icd) +-add_library(OpenCL-ICD ALIAS OpenCL) +- + add_subdirectory(opencl-aot) +diff --git a/opencl/opencl-aot/CMakeLists.txt b/opencl/opencl-aot/CMakeLists.txt +index ff905fd88..b673f79a4 100644 +--- a/opencl/opencl-aot/CMakeLists.txt ++++ b/opencl/opencl-aot/CMakeLists.txt +@@ -19,5 +19,5 @@ endif() + + target_link_libraries(${OPENCL_AOT_PROJECT_NAME} + PRIVATE +- OpenCL-Headers +- OpenCL-ICD) ++ OpenCL ++) +diff --git a/sycl/CMakeLists.txt b/sycl/CMakeLists.txt +index 86c5b420d..1d834de4f 100644 +--- a/sycl/CMakeLists.txt ++++ b/sycl/CMakeLists.txt +@@ -142,7 +142,7 @@ file(COPY ${OpenCL_INCLUDE_DIR}/CL + # Include OpenCL Headers into final bundle. + install(DIRECTORY ${OpenCL_INCLUDE_DIR}/CL + DESTINATION ${SYCL_INCLUDE_DIR}/sycl +- COMPONENT OpenCL-Headers) ++ COMPONENT OpenCL) + + # Option to enable online kernel fusion via a JIT compiler + option(SYCL_ENABLE_KERNEL_FUSION "Enable kernel fusion via JIT compiler" OFF) +@@ -371,7 +371,7 @@ set( SYCL_TOOLCHAIN_DEPLOY_COMPONENTS + sycl-post-link + sycl-ls + clang-resource-headers +- OpenCL-Headers ++ OpenCL + opencl-aot + sycl-headers + sycl-headers-extras +@@ -391,9 +391,7 @@ if (TARGET sycl-trace) + list(APPEND SYCL_TOOLCHAIN_DEPLOY_COMPONENTS sycl-trace) + endif() + +-if(OpenCL_INSTALL_KHRONOS_ICD_LOADER AND TARGET OpenCL-ICD) +- list(APPEND SYCL_TOOLCHAIN_DEPLOY_COMPONENTS OpenCL-ICD) +-endif() ++list(APPEND SYCL_TOOLCHAIN_DEPLOY_COMPONENTS OpenCL) + + # Build and install lld as part of the sycl-toolchain if available + if("lld" IN_LIST LLVM_ENABLE_PROJECTS) +diff --git a/sycl/cmake/modules/AddSYCL.cmake b/sycl/cmake/modules/AddSYCL.cmake +index dbf539e9a..5933b9770 100644 +--- a/sycl/cmake/modules/AddSYCL.cmake ++++ b/sycl/cmake/modules/AddSYCL.cmake +@@ -47,7 +47,7 @@ function(add_sycl_plugin PLUGIN_NAME) + ${sycl_inc_dir} + LIBRARIES + ${ARG_LIBRARIES} +- OpenCL-Headers ++ OpenCL + ) + + install(TARGETS pi_${PLUGIN_NAME} +diff --git a/sycl/cmake/modules/AddSYCLUnitTest.cmake b/sycl/cmake/modules/AddSYCLUnitTest.cmake +index 9f5e6dc30..fe0e18b2f 100644 +--- a/sycl/cmake/modules/AddSYCLUnitTest.cmake ++++ b/sycl/cmake/modules/AddSYCLUnitTest.cmake +@@ -53,7 +53,7 @@ macro(add_sycl_unittest test_dirname link_variant) + target_link_libraries(${test_dirname} + PRIVATE + LLVMTestingSupport +- OpenCL-Headers ++ OpenCL + ${SYCL_LINK_LIBS} + ) + target_include_directories(${test_dirname} +diff --git a/sycl/plugins/esimd_emulator/CMakeLists.txt b/sycl/plugins/esimd_emulator/CMakeLists.txt +index 0b32c3925..e8b8616bc 100755 +--- a/sycl/plugins/esimd_emulator/CMakeLists.txt ++++ b/sycl/plugins/esimd_emulator/CMakeLists.txt +@@ -58,6 +58,7 @@ if ((DEFINED USE_DEFAULT_CM_EMU_SOURCE) OR (DEFINED USE_LOCAL_CM_EMU_SOURCE)) + INSTALL_DIR ${CMAKE_CURRENT_BINARY_DIR}/cm-emu_install + CMAKE_ARGS -DLIBVA_INSTALL_PATH=/usr + -D__SYCL_EXPLICIT_SIMD_PLUGIN__=true ++ -DLibFFI_INCLUDE_DIR=${LibFFI_INCLUDE_DIR} + -DCMAKE_INSTALL_PREFIX=<INSTALL_DIR> + BUILD_BYPRODUCTS ${LIBCM} ${LIBIGFXCMRT_EMU} + ) +diff --git a/sycl/plugins/level_zero/CMakeLists.txt b/sycl/plugins/level_zero/CMakeLists.txt +index 7b0ce7eae..b9ee52376 100755 +--- a/sycl/plugins/level_zero/CMakeLists.txt ++++ b/sycl/plugins/level_zero/CMakeLists.txt +@@ -44,7 +44,7 @@ if (NOT DEFINED LEVEL_ZERO_LIBRARY OR NOT DEFINED LEVEL_ZERO_INCLUDE_DIR) + LOG_BUILD 1 + LOG_INSTALL 1 + STEP_TARGETS configure,build,install +- DEPENDS OpenCL-Headers ++ DEPENDS OpenCL + BUILD_BYPRODUCTS ${LEVEL_ZERO_LOADER} + ) + ExternalProject_Add_Step(level-zero-loader llvminstall +@@ -78,7 +78,7 @@ else() + COMMAND + ${CMAKE_COMMAND} -E copy ${LEVEL_ZERO_LIBRARY_SRC} ${LLVM_LIBRARY_OUTPUT_INTDIR} + COMMAND +- ${CMAKE_COMMAND} -E copy_directory ${LEVEL_ZERO_INCLUDE_DIR} ${LLVM_BINARY_DIR}/include/sycl ++ ${CMAKE_COMMAND} -E copy_directory ${LEVEL_ZERO_INCLUDE_DIR}/level_zero ${LLVM_BINARY_DIR}/include/sycl/level_zero + DEPENDS + ${LEVEL_ZERO_LIBRARY} + ${LEVEL_ZERO_INCLUDE_DIR} +diff --git a/sycl/plugins/opencl/CMakeLists.txt b/sycl/plugins/opencl/CMakeLists.txt +index 9943827e4..29fae166e 100644 +--- a/sycl/plugins/opencl/CMakeLists.txt ++++ b/sycl/plugins/opencl/CMakeLists.txt +@@ -15,7 +15,7 @@ add_sycl_plugin(opencl + "${sycl_inc_dir}/sycl/detail/pi.h" + "pi_opencl.cpp" + LIBRARIES +- OpenCL-ICD ++ OpenCL + ) + + set_target_properties(pi_opencl PROPERTIES LINKER_LANGUAGE CXX) +diff --git a/sycl/plugins/unified_runtime/CMakeLists.txt b/sycl/plugins/unified_runtime/CMakeLists.txt +index f442db4a4..9ca733695 100755 +--- a/sycl/plugins/unified_runtime/CMakeLists.txt ++++ b/sycl/plugins/unified_runtime/CMakeLists.txt +@@ -3,18 +3,6 @@ + + include(FetchContent) + +-set(UNIFIED_RUNTIME_REPO "https://github.com/oneapi-src/unified-runtime.git") +-set(UNIFIED_RUNTIME_TAG fd711c920acc4434cb52ff18b078c082d9d7f44d) +- +-message(STATUS "Will fetch Unified Runtime from ${UNIFIED_RUNTIME_REPO}") +-FetchContent_Declare(unified-runtime +- GIT_REPOSITORY ${UNIFIED_RUNTIME_REPO} +- GIT_TAG ${UNIFIED_RUNTIME_TAG} +-) +- +-FetchContent_MakeAvailable(unified-runtime) +-FetchContent_GetProperties(unified-runtime) +- + set(UNIFIED_RUNTIME_SOURCE_DIR + ${unified-runtime_SOURCE_DIR} CACHE PATH "Path to Unified Runtime Headers") + set(UNIFIED_RUNTIME_INCLUDE_DIR "${UNIFIED_RUNTIME_SOURCE_DIR}/include") +diff --git a/sycl/source/CMakeLists.txt b/sycl/source/CMakeLists.txt +index c61b10da7..02a7fab32 100644 +--- a/sycl/source/CMakeLists.txt ++++ b/sycl/source/CMakeLists.txt +@@ -84,7 +84,7 @@ function(add_sycl_rt_library LIB_NAME LIB_OBJ_NAME) + ) + #TODO: Remove dependency on opencl headers. + target_link_libraries(${LIB_OBJ_NAME} +- PRIVATE OpenCL-Headers ++ PRIVATE OpenCL + ) + + find_package(Threads REQUIRED) +diff --git a/sycl/tools/sycl-ls/CMakeLists.txt b/sycl/tools/sycl-ls/CMakeLists.txt +index f5909cf49..f9c52e3a3 100644 +--- a/sycl/tools/sycl-ls/CMakeLists.txt ++++ b/sycl/tools/sycl-ls/CMakeLists.txt +@@ -11,7 +11,7 @@ endif() + target_link_libraries(sycl-ls + PRIVATE + ${sycl_lib} +- OpenCL-Headers ++ OpenCL + ) + install(TARGETS sycl-ls + RUNTIME DESTINATION "bin" COMPONENT sycl-ls) +diff --git a/sycl/tools/sycl-prof/CMakeLists.txt b/sycl/tools/sycl-prof/CMakeLists.txt +index 09586c1b8..bc8f37379 100644 +--- a/sycl/tools/sycl-prof/CMakeLists.txt ++++ b/sycl/tools/sycl-prof/CMakeLists.txt +@@ -15,9 +15,7 @@ target_compile_options(sycl-prof PRIVATE -fno-exceptions -fno-rtti) + add_library(sycl_profiler_collector SHARED collector.cpp) + target_compile_definitions(sycl_profiler_collector PRIVATE XPTI_CALLBACK_API_EXPORTS) + target_link_libraries(sycl_profiler_collector PRIVATE xptifw) +-if (TARGET OpenCL-Headers) +- target_link_libraries(sycl_profiler_collector PRIVATE OpenCL-Headers) +-endif() ++target_link_libraries(sycl_profiler_collector PRIVATE OpenCL) + target_include_directories(sycl_profiler_collector PRIVATE + "${sycl_inc_dir}" + "${sycl_src_dir}" +diff --git a/sycl/tools/sycl-sanitize/CMakeLists.txt b/sycl/tools/sycl-sanitize/CMakeLists.txt +index 16e7a1a49..4ef93e8e2 100644 +--- a/sycl/tools/sycl-sanitize/CMakeLists.txt ++++ b/sycl/tools/sycl-sanitize/CMakeLists.txt +@@ -13,9 +13,7 @@ target_compile_options(sycl-sanitize PRIVATE -fno-exceptions -fno-rtti) + add_library(sycl_sanitizer_collector SHARED collector.cpp) + target_compile_definitions(sycl_sanitizer_collector PRIVATE XPTI_CALLBACK_API_EXPORTS) + target_link_libraries(sycl_sanitizer_collector PRIVATE xptifw) +-if (TARGET OpenCL-Headers) +- target_link_libraries(sycl_sanitizer_collector PRIVATE OpenCL-Headers) +-endif() ++target_link_libraries(sycl_sanitizer_collector PRIVATE OpenCL) + + target_include_directories(sycl_sanitizer_collector PRIVATE + "${CMAKE_CURRENT_SOURCE_DIR}/../xpti_helpers/" +diff --git a/sycl/tools/sycl-trace/CMakeLists.txt b/sycl/tools/sycl-trace/CMakeLists.txt +index 6f36b83a2..24f0d115b 100644 +--- a/sycl/tools/sycl-trace/CMakeLists.txt ++++ b/sycl/tools/sycl-trace/CMakeLists.txt +@@ -62,9 +62,7 @@ endif() + + target_compile_definitions(sycl_pi_trace_collector PRIVATE XPTI_CALLBACK_API_EXPORTS) + target_link_libraries(sycl_pi_trace_collector PRIVATE xptifw) +-if (TARGET OpenCL-Headers) +- target_link_libraries(sycl_pi_trace_collector PRIVATE OpenCL-Headers) +-endif() ++target_link_libraries(sycl_pi_trace_collector PRIVATE OpenCL) + + target_include_directories(sycl_pi_trace_collector PRIVATE + "${CMAKE_CURRENT_SOURCE_DIR}/../xpti_helpers/" diff --git a/sys-devel/DPC++/metadata.xml b/sys-devel/DPC++/metadata.xml new file mode 100644 index 000000000..771c45a25 --- /dev/null +++ b/sys-devel/DPC++/metadata.xml @@ -0,0 +1,16 @@ +<?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> + <upstream> + <remote-id type="github">intel/llvm</remote-id> + </upstream> + <use> + <flag name="cuda">use the cuda backend</flag> + <flag name="esimd_emulator">enable ESIMD CPU emulation</flag> + <flag name="hip">use the HIP backend</flag> + </use> +</pkgmetadata> diff --git a/sys-devel/ittapi/Manifest b/sys-devel/ittapi/Manifest new file mode 100644 index 000000000..f8d38ff32 --- /dev/null +++ b/sys-devel/ittapi/Manifest @@ -0,0 +1,2 @@ +DIST ittapi-3.23.0.tar.gz 132481 BLAKE2B c1caf9755e3f0dfa0de2d3e1bca29f3596b68669d8b119822ab23617fdfc33df8d049ed9e8fd66b0865abd311a72b8362e9f26ff45875880cedd1d545f475500 SHA512 2e4aae2e3867588d38734f4425e416fb1ee6fd7df64c72823b481256cf9b7c18a50b6dba22727e16ada9ba0ac10ad0a96fc0d7c6d68edd2b64a899ea047651b5 +DIST ittapi-3.24.0.tar.gz 209498 BLAKE2B f7d13bf8a9633f01719c54cd6e29c2106572dc2bb883d9166af420b6c856cc126a398933cdda73f556b020128292dddb68f67eb97dc1bc597253cea7ade3ca6a SHA512 8d0b8213c0d18514eca581ebb868d7458094bb53760815c68e0648c785d4be0634b09c44bc6565483014425ae422ff390d19e365c19110cc8b5e1a4cced7a51b diff --git a/sys-devel/ittapi/ittapi-3.23.0.ebuild b/sys-devel/ittapi/ittapi-3.23.0.ebuild new file mode 100644 index 000000000..38ae1b432 --- /dev/null +++ b/sys-devel/ittapi/ittapi-3.23.0.ebuild @@ -0,0 +1,26 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit cmake + +DESCRIPTION="Intel Instrumentation and Tracing Technology and Just-In-Time API " +HOMEPAGE="https://github.com/intel/ittapi" +SRC_URI="https://github.com/intel/ittapi/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="|| ( GPL-2 BSD )" +SLOT="0" +KEYWORDS="~amd64" + +src_prepare() { + # Make it a shared library + sed -i -e 's/STATIC/SHARED/g' CMakeLists.txt || die + cmake_src_prepare +} + +src_install() { + dolib.so "${BUILD_DIR}/bin/"*.so + doheader -r "${S}/include/"* + einstalldocs +} diff --git a/sys-devel/ittapi/ittapi-3.24.0.ebuild b/sys-devel/ittapi/ittapi-3.24.0.ebuild new file mode 100644 index 000000000..38ae1b432 --- /dev/null +++ b/sys-devel/ittapi/ittapi-3.24.0.ebuild @@ -0,0 +1,26 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +inherit cmake + +DESCRIPTION="Intel Instrumentation and Tracing Technology and Just-In-Time API " +HOMEPAGE="https://github.com/intel/ittapi" +SRC_URI="https://github.com/intel/ittapi/archive/refs/tags/v${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="|| ( GPL-2 BSD )" +SLOT="0" +KEYWORDS="~amd64" + +src_prepare() { + # Make it a shared library + sed -i -e 's/STATIC/SHARED/g' CMakeLists.txt || die + cmake_src_prepare +} + +src_install() { + dolib.so "${BUILD_DIR}/bin/"*.so + doheader -r "${S}/include/"* + einstalldocs +} diff --git a/sys-devel/ittapi/metadata.xml b/sys-devel/ittapi/metadata.xml new file mode 100644 index 000000000..f71d530b0 --- /dev/null +++ b/sys-devel/ittapi/metadata.xml @@ -0,0 +1,11 @@ +<?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> + <upstream> + <remote-id type="github">intel/ittapi</remote-id> + </upstream> +</pkgmetadata> diff --git a/sys-devel/oneDPL/Manifest b/sys-devel/oneDPL/Manifest new file mode 100644 index 000000000..c3002057c --- /dev/null +++ b/sys-devel/oneDPL/Manifest @@ -0,0 +1,3 @@ +DIST oneDPL-2021.7.1-release.tar.gz 3704195 BLAKE2B 32b47a8ed27a59487b030af8a1cb5f521fb9c03c25bebeb682d601a92594fd2e7c0437b209fead1e3a2b7ad0ad9b6afe736fcef97266619f19cac32d965fb5fa SHA512 264b5e866985e23c28e411d89a5e2e4bb306ac70976c4b3d40991d53dc70a211ab67821f7ea94ff57f093205b1e9f0bb41308e394b4dc0d439b771a6316c1709 +DIST oneDPL-2022.0.0-release.tar.gz 3729700 BLAKE2B f1da5c7a69583b08646ba5dd55fc9a178c2174804518b1ef6af094f2bde9b9df61ff45856a79a98cff91baee43e58e54d701e924e2f7f0d059f0ded2bd09fbc6 SHA512 c254cabd98328303e47b6054ffd0893aaa5862abda48febcbaca82190d901c6e49c9c64cdd91b08417e1618eae05cbaf392dfdbec5f6f03535a89d74d368689b +DIST oneDPL-2022.2.0-rc1.tar.gz 3764454 BLAKE2B 32f2bdc43df7209dc0b14c5bbe8ef8352af04aed8848be10378a4c0cf2877e4e76b05dc5e68dcf392256ca7e0f16a086f1f1cec8e4c7cf2a021705406ad0ec94 SHA512 006ade274211b767874e7375cad5a3763266104484092d9b4177f47699f36d920cdecb3fbb45b6e5fd45cce721ae8aec5b4ae90139ef9f5497d2661fa5d1fec0 diff --git a/sys-devel/oneDPL/metadata.xml b/sys-devel/oneDPL/metadata.xml new file mode 100644 index 000000000..474176a00 --- /dev/null +++ b/sys-devel/oneDPL/metadata.xml @@ -0,0 +1,14 @@ +<?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> + <upstream> + <remote-id type="github">oneapi-src/oneDPL</remote-id> + </upstream> + <use> + <flag name="esimd_emulator">enable ESIMD CPU emulation</flag> + </use> +</pkgmetadata> diff --git a/sys-devel/oneDPL/oneDPL-2021.7.1.ebuild b/sys-devel/oneDPL/oneDPL-2021.7.1.ebuild new file mode 100644 index 000000000..7db9cb0b6 --- /dev/null +++ b/sys-devel/oneDPL/oneDPL-2021.7.1.ebuild @@ -0,0 +1,58 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +# Missing deps for documentation +# PYTHON_COMPAT=( python3_{10..11} ) +# DOCS_BUILDER="sphinx" +# DOCS_DIR="documentation/library_guide" +# DOCS_AUTODOC=0 +inherit cmake #python-any-r1 docs + +DESCRIPTION="oneAPI Data Parallel C++ Library" +HOMEPAGE="https://github.com/oneapi-src/oneDPL" +SRC_URI="https://github.com/oneapi-src/oneDPL/archive/refs/tags/${P}-release.tar.gz" +S="${WORKDIR}/${PN}-${P}-release" + +LICENSE="Apache-2.0-with-LLVM-exceptions" +SLOT="0" +KEYWORDS="~amd64" + +#TODO: Figure out how to use the test +RESTRICT="test" + +BDEPEND="virtual/pkgconfig" + +DEPEND=" + sys-devel/DPC++:0/5 + dev-libs/level-zero + dev-cpp/tbb +" +RDEPEND="${DEPEND}" + +src_prepare() { + # Not using the DPC++ compiler doesn't really make sense here + export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++" + export CC="${ESYSROOT}/usr/lib/llvm/intel/bin/clang" + cmake_src_prepare +} + +src_configure() { + local mycmakeargs=( + -DONEDPL_DEVICE_BACKEND="level_zero" + -DONEDPL_BACKEND="dpcpp" + ) + + cmake_src_configure +} + +src_compile() { + cmake_src_compile + # docs_compile +} + +src_install() { + einstalldocs + doheader -r "${S}/include/oneapi" +} diff --git a/sys-devel/oneDPL/oneDPL-2022.0.0-r1.ebuild b/sys-devel/oneDPL/oneDPL-2022.0.0-r1.ebuild new file mode 100644 index 000000000..895c53c37 --- /dev/null +++ b/sys-devel/oneDPL/oneDPL-2022.0.0-r1.ebuild @@ -0,0 +1,65 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +# Missing deps for documentation +# PYTHON_COMPAT=( python3_{10..11} ) +# DOCS_BUILDER="sphinx" +# DOCS_DIR="documentation/library_guide" +# DOCS_AUTODOC=0 +inherit cmake #python-any-r1 docs + +DESCRIPTION="oneAPI Data Parallel C++ Library" +HOMEPAGE="https://github.com/oneapi-src/oneDPL" +SRC_URI="https://github.com/oneapi-src/oneDPL/archive/refs/tags/${P}-release.tar.gz" +S="${WORKDIR}/${PN}-${P}-release" + +LICENSE="Apache-2.0-with-LLVM-exceptions" +SLOT="0" +KEYWORDS="~amd64" + +IUSE="esimd_emulator" +#TODO: Figure out how to use the test +RESTRICT="test" + +BDEPEND="virtual/pkgconfig" + +DEPEND=" + sys-devel/DPC++:0/6[esimd_emulator?] + dev-libs/level-zero + dev-cpp/tbb +" +RDEPEND="${DEPEND}" + +src_prepare() { + # Not using the DPC++ compiler doesn't really make sense here + export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++" + export CC="${ESYSROOT}/usr/lib/llvm/intel/bin/clang" + cmake_src_prepare +} + +src_configure() { + local mycmakeargs=( + -DONEDPL_DEVICE_BACKEND="level_zero" + -DONEDPL_BACKEND="dpcpp" + -DONEDPL_ENABLE_SIMD="$(usex esimd_emulator)" + ) + + cmake_src_configure +} + +src_compile() { + cmake_src_compile + cmake -P cmake/scripts/generate_config.cmake || die + # docs_compile +} + +src_install() { + einstalldocs + doheader -r "${S}/include/oneapi" + insinto "/usr/$(get_libdir)/cmake/oneDPL/" + doins output/*.cmake + insinto "/usr/$(get_libdir)/pkgconfig/" + doins output/pkgconfig-lin/*.pc +} diff --git a/sys-devel/oneDPL/oneDPL-2022.2.0.ebuild b/sys-devel/oneDPL/oneDPL-2022.2.0.ebuild new file mode 100644 index 000000000..7b1010ab1 --- /dev/null +++ b/sys-devel/oneDPL/oneDPL-2022.2.0.ebuild @@ -0,0 +1,66 @@ +# Copyright 2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +# Missing deps for documentation +# PYTHON_COMPAT=( python3_{10..11} ) +# DOCS_BUILDER="sphinx" +# DOCS_DIR="documentation/library_guide" +# DOCS_AUTODOC=0 +inherit cmake #python-any-r1 docs + +DESCRIPTION="oneAPI Data Parallel C++ Library" +HOMEPAGE="https://github.com/oneapi-src/oneDPL" +SRC_URI="https://github.com/oneapi-src/oneDPL/archive/refs/tags/${P}-rc1.tar.gz" +S="${WORKDIR}/${PN}-${P}-rc1" + +LICENSE="Apache-2.0-with-LLVM-exceptions" +SLOT="0" +KEYWORDS="~amd64" + +IUSE="esimd_emulator" +#TODO: Figure out how to use the test +RESTRICT="test" + +BDEPEND="virtual/pkgconfig" + +DEPEND=" + sys-devel/DPC++:0/6[esimd_emulator?] + dev-libs/level-zero + dev-cpp/tbb +" +RDEPEND="${DEPEND}" + +src_prepare() { + # Not using the DPC++ compiler doesn't really make sense here + export CXX="${ESYSROOT}/usr/lib/llvm/intel/bin/clang++" + export CC="${ESYSROOT}/usr/lib/llvm/intel/bin/clang" + cmake_src_prepare +} + +src_configure() { + local mycmakeargs=( + -DONEDPL_DEVICE_TYPE="GPU" + -DONEDPL_DEVICE_BACKEND="level_zero" + -DONEDPL_BACKEND="dpcpp" + -DONEDPL_ENABLE_SIMD="$(usex esimd_emulator)" + ) + + cmake_src_configure +} + +src_compile() { + cmake_src_compile + cmake -P cmake/scripts/generate_config.cmake || die + # docs_compile +} + +src_install() { + einstalldocs + doheader -r "${S}/include/oneapi" + insinto "/usr/$(get_libdir)/cmake/oneDPL/" + doins output/*.cmake + insinto "/usr/$(get_libdir)/pkgconfig/" + doins output/pkgconfig-lin/*.pc +} diff --git a/x11-misc/xdg-java/Manifest b/x11-misc/xdg-java/Manifest new file mode 100644 index 000000000..1cad78fa2 --- /dev/null +++ b/x11-misc/xdg-java/Manifest @@ -0,0 +1 @@ +DIST xdg-java-0.1.1-sources.tar.gz 19734 BLAKE2B 402eedd9d0c6e8fd2ddb138fcbd16b06d653af6e219f5ca91df73dce9cbbed3764e39e886a67b4290fd079c71a2b86b2be2a31cee368d12f2e022deeb8887612 SHA512 01f63339bc21a502693c803f38762e66fc0ad570acf0ba6fde17519d820e9f6b94183f30b265ab68467a7c37a9df65612aed3774b6b6f955113c2bac9f1f7077 diff --git a/x11-misc/xdg-java/metadata.xml b/x11-misc/xdg-java/metadata.xml new file mode 100644 index 000000000..45a5f9d39 --- /dev/null +++ b/x11-misc/xdg-java/metadata.xml @@ -0,0 +1,14 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd"> +<pkgmetadata> + <longdescription> + This is a Java API that provides an easy to use implementations of various Free Desktop specifications. Use the correct application specific configuration, data and cache directories. Safely read and write desktop entries without worrying about parsing and escaping. + </longdescription> + <maintainer type="project"> + <email>sci@gentoo.org</email> + <name>Gentoo Science Project</name> + </maintainer> + <upstream> + <remote-id type="github">kothar/xdg-java</remote-id> + </upstream> +</pkgmetadata> diff --git a/x11-misc/xdg-java/xdg-java-0.1.1.ebuild b/x11-misc/xdg-java/xdg-java-0.1.1.ebuild new file mode 100644 index 000000000..8723b0774 --- /dev/null +++ b/x11-misc/xdg-java/xdg-java-0.1.1.ebuild @@ -0,0 +1,45 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +JAVA_PKG_IUSE="doc source test" +JAVA_TESTING_FRAMEWORKS="junit-4" + +inherit java-pkg-2 java-pkg-simple + +DESCRIPTION="Java bindings for various FreeDesktop.org standards" +HOMEPAGE="https://github.com/kothar/xdg-java" + +if [[ ${PV} == 9999 ]]; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/kothar/xdg-java.git" + S="${WORKDIR}/${P}" + MAVEN_ID="net.kothar:xdg-java:9999" +else + SRC_URI=" + https://github.com/kothar/${PN}/archive/refs/tags/${PV}.tar.gz -> ${P}-sources.tar.gz + " + S="${WORKDIR}/${P}" + MAVEN_ID="net.kothar:xdg-java:0.1.1" + KEYWORDS="~amd64" +fi + +LICENSE="LGPL-2.1" +SLOT="0" + +DEPEND=">=virtual/jdk-1.8:*" + +BDEPEND=" + >=virtual/jdk-1.8:* + test? ( + >=dev-java/junit-4.13.2:4 + ) +" + +RDEPEND=">=virtual/jre-1.8:*" + +JAVA_SRC_DIR="src/main/java" + +JAVA_TEST_GENTOO_CLASSPATH="junit-4" +JAVA_TEST_SRC_DIR="src/test/java" diff --git a/x11-misc/xdg-java/xdg-java-9999.ebuild b/x11-misc/xdg-java/xdg-java-9999.ebuild new file mode 100644 index 000000000..8723b0774 --- /dev/null +++ b/x11-misc/xdg-java/xdg-java-9999.ebuild @@ -0,0 +1,45 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +JAVA_PKG_IUSE="doc source test" +JAVA_TESTING_FRAMEWORKS="junit-4" + +inherit java-pkg-2 java-pkg-simple + +DESCRIPTION="Java bindings for various FreeDesktop.org standards" +HOMEPAGE="https://github.com/kothar/xdg-java" + +if [[ ${PV} == 9999 ]]; then + inherit git-r3 + EGIT_REPO_URI="https://github.com/kothar/xdg-java.git" + S="${WORKDIR}/${P}" + MAVEN_ID="net.kothar:xdg-java:9999" +else + SRC_URI=" + https://github.com/kothar/${PN}/archive/refs/tags/${PV}.tar.gz -> ${P}-sources.tar.gz + " + S="${WORKDIR}/${P}" + MAVEN_ID="net.kothar:xdg-java:0.1.1" + KEYWORDS="~amd64" +fi + +LICENSE="LGPL-2.1" +SLOT="0" + +DEPEND=">=virtual/jdk-1.8:*" + +BDEPEND=" + >=virtual/jdk-1.8:* + test? ( + >=dev-java/junit-4.13.2:4 + ) +" + +RDEPEND=">=virtual/jre-1.8:*" + +JAVA_SRC_DIR="src/main/java" + +JAVA_TEST_GENTOO_CLASSPATH="junit-4" +JAVA_TEST_SRC_DIR="src/test/java" |
