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author | V3n3RiX <venerix@koprulu.sector> | 2022-07-09 15:43:36 +0100 |
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committer | V3n3RiX <venerix@koprulu.sector> | 2022-07-09 15:43:36 +0100 |
commit | 2719f73b6813d11d13a9650cdd2ab8ec6e69385d (patch) | |
tree | 8c816148bcbd22757d892089c989ae614eae4f5a /sci-biology/HTSeq/HTSeq-2.0.2.ebuild | |
parent | 0f558761aa2dee1017b4751e4017205e015a9560 (diff) |
gentoo resync : 09.07.2022
Diffstat (limited to 'sci-biology/HTSeq/HTSeq-2.0.2.ebuild')
-rw-r--r-- | sci-biology/HTSeq/HTSeq-2.0.2.ebuild | 68 |
1 files changed, 68 insertions, 0 deletions
diff --git a/sci-biology/HTSeq/HTSeq-2.0.2.ebuild b/sci-biology/HTSeq/HTSeq-2.0.2.ebuild new file mode 100644 index 000000000000..678968788ff7 --- /dev/null +++ b/sci-biology/HTSeq/HTSeq-2.0.2.ebuild @@ -0,0 +1,68 @@ +# Copyright 1999-2022 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +DISTUTILS_IN_SOURCE_BUILD=1 +PYTHON_COMPAT=( python3_{8..10} ) + +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_${PV} + KEYWORDS="~amd64" +fi + +LICENSE="GPL-3+" +SLOT="0" +IUSE="test" +RESTRICT="!test? ( test )" + +RDEPEND=" + dev-python/numpy[${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 +} |