commit: 4e76e5b45022d702af9a61fd2d65787b222b6d40 Author: Arthur Zamarin <arthurzam <AT> gentoo <DOT> org> AuthorDate: Sat Apr 27 14:59:46 2024 +0000 Commit: Arthur Zamarin <arthurzam <AT> gentoo <DOT> org> CommitDate: Sat Apr 27 14:59:46 2024 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=4e76e5b4
sci-biology/HTSeq: treeclean Closes: https://bugs.gentoo.org/910015 Bug: https://bugs.gentoo.org/923242 Signed-off-by: Arthur Zamarin <arthurzam <AT> gentoo.org> profiles/package.mask | 6 ---- sci-biology/HTSeq/HTSeq-2.0.2.ebuild | 66 ------------------------------------ sci-biology/HTSeq/HTSeq-9999.ebuild | 66 ------------------------------------ sci-biology/HTSeq/Manifest | 1 - sci-biology/HTSeq/metadata.xml | 12 ------- 5 files changed, 151 deletions(-) diff --git a/profiles/package.mask b/profiles/package.mask index 4316edbc5c4f..15c680723ac1 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -357,12 +357,6 @@ sys-firmware/bluez-firmware # Removal on 2024-04-25. Bug #924683. dev-python/sumtypes -# Michał Górny <[email protected]> (2024-03-26) -# Uses deprecated distutils-r1 API. The current version is outdated, -# from mid-2022. No reverse dependencies. -# Removal on 2024-04-25. Bug #910015. -sci-biology/HTSeq - # Michał Górny <[email protected]> (2024-03-26) # Uses deprecated distutils-r1 API. Depends on dev-qt/qtwebengine:5. # Includes the libraries with no other reverse dependencies. diff --git a/sci-biology/HTSeq/HTSeq-2.0.2.ebuild b/sci-biology/HTSeq/HTSeq-2.0.2.ebuild deleted file mode 100644 index b4b7974e60d0..000000000000 --- a/sci-biology/HTSeq/HTSeq-2.0.2.ebuild +++ /dev/null @@ -1,66 +0,0 @@ -# Copyright 1999-2023 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -DISTUTILS_IN_SOURCE_BUILD=1 -PYTHON_COMPAT=( python3_{9..11} ) - -inherit distutils-r1 flag-o-matic - -DESCRIPTION="Python support for SAM/BAM/Bowtie/FASTA/Q/GFF/GTF files" -HOMEPAGE="https://htseq.readthedocs.io/"; - -if [[ ${PV} == *9999 ]]; then - inherit git-r3 - EGIT_REPO_URI="https://github.com/htseq/htseq.git"; -else - SRC_URI="https://github.com/htseq/htseq/archive/release_${PV}.tar.gz -> ${P}.gh.tar.gz" - - S="${WORKDIR}"/htseq-release_${PV} - KEYWORDS="~amd64" -fi - -LICENSE="GPL-3+" -SLOT="0" - -RDEPEND=" - dev-python/numpy[${PYTHON_USEDEP}] - sci-biology/pysam[${PYTHON_USEDEP}]" -DEPEND="${RDEPEND} - test? ( - dev-python/matplotlib[${PYTHON_USEDEP}] - dev-python/pandas[${PYTHON_USEDEP}] - dev-python/scipy[${PYTHON_USEDEP}] - )" -BDEPEND=" - >=dev-lang/swig-3.0.8 - dev-python/cython[${PYTHON_USEDEP}]" - -distutils_enable_tests pytest - -src_configure() { - # mask broken asserts in src/step_vector.h:72 - append-cppflags -DNDEBUG - - distutils-r1_src_configure -} - -python_test() { - distutils_install_for_testing - - # Due to the build directories creating a competing - # hierarchy, we move to the test/ dir to avoid implicitly - # injecting the root HTSeq/ dir into the PYTHONPATH, - # which leads the python module lookup astray: - # ${PWD} - # ├── build - # │ ├── lib - # │ │ └── HTSeq - # │ [...] - # ├── HTSeq - # └── test - cd test/ || die - ln -s ../example_data || die - epytest -} diff --git a/sci-biology/HTSeq/HTSeq-9999.ebuild b/sci-biology/HTSeq/HTSeq-9999.ebuild deleted file mode 100644 index b4b7974e60d0..000000000000 --- a/sci-biology/HTSeq/HTSeq-9999.ebuild +++ /dev/null @@ -1,66 +0,0 @@ -# Copyright 1999-2023 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -DISTUTILS_IN_SOURCE_BUILD=1 -PYTHON_COMPAT=( python3_{9..11} ) - -inherit distutils-r1 flag-o-matic - -DESCRIPTION="Python support for SAM/BAM/Bowtie/FASTA/Q/GFF/GTF files" -HOMEPAGE="https://htseq.readthedocs.io/"; - -if [[ ${PV} == *9999 ]]; then - inherit git-r3 - EGIT_REPO_URI="https://github.com/htseq/htseq.git"; -else - SRC_URI="https://github.com/htseq/htseq/archive/release_${PV}.tar.gz -> ${P}.gh.tar.gz" - - S="${WORKDIR}"/htseq-release_${PV} - KEYWORDS="~amd64" -fi - -LICENSE="GPL-3+" -SLOT="0" - -RDEPEND=" - dev-python/numpy[${PYTHON_USEDEP}] - sci-biology/pysam[${PYTHON_USEDEP}]" -DEPEND="${RDEPEND} - test? ( - dev-python/matplotlib[${PYTHON_USEDEP}] - dev-python/pandas[${PYTHON_USEDEP}] - dev-python/scipy[${PYTHON_USEDEP}] - )" -BDEPEND=" - >=dev-lang/swig-3.0.8 - dev-python/cython[${PYTHON_USEDEP}]" - -distutils_enable_tests pytest - -src_configure() { - # mask broken asserts in src/step_vector.h:72 - append-cppflags -DNDEBUG - - distutils-r1_src_configure -} - -python_test() { - distutils_install_for_testing - - # Due to the build directories creating a competing - # hierarchy, we move to the test/ dir to avoid implicitly - # injecting the root HTSeq/ dir into the PYTHONPATH, - # which leads the python module lookup astray: - # ${PWD} - # ├── build - # │ ├── lib - # │ │ └── HTSeq - # │ [...] - # ├── HTSeq - # └── test - cd test/ || die - ln -s ../example_data || die - epytest -} diff --git a/sci-biology/HTSeq/Manifest b/sci-biology/HTSeq/Manifest deleted file mode 100644 index 89b37aa1c25b..000000000000 --- a/sci-biology/HTSeq/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST HTSeq-2.0.2.gh.tar.gz 48468261 BLAKE2B c68ec67906f3cf78954e94214b82fd51bc19e0c505f994a3df4bfc682d804fa26f4883e9a8fa1e8ddf1e4f8ba8690d605705ebdd2d1695470984c2f04b6a19ce SHA512 96c0b4de6c9cfa9e405f02e366ecfed63bb0dba0ab76fe872f6f48b52a4956b08fa75efa4b1e4c6e4560e34b4e2921bf1ec9671831226ad415ed421a88ec3f6d diff --git a/sci-biology/HTSeq/metadata.xml b/sci-biology/HTSeq/metadata.xml deleted file mode 100644 index 6ada1a530737..000000000000 --- a/sci-biology/HTSeq/metadata.xml +++ /dev/null @@ -1,12 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<!DOCTYPE pkgmetadata SYSTEM "https://www.gentoo.org/dtd/metadata.dtd";> -<pkgmetadata> - <maintainer type="project"> - <email>[email protected]</email> - <name>Gentoo Biology Project</name> - </maintainer> - <upstream> - <remote-id type="pypi">HTSeq</remote-id> - <remote-id type="github">htseq/htseq</remote-id> - </upstream> -</pkgmetadata>
