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| author |   David Seifert <soap@gentoo.org> | 2023-02-19 16:22:52 +0100 |
|---|---|---|
| committer | David Seifert <soap@gentoo.org> | 2023-02-19 16:22:52 +0100 |
| commit | cd493f9e3374c2cf9f36ebd06d8dac3f2732faf1 (patch) | |
| tree | 470f08722f27c4893b3bf8f2f88a61bee29597de /sci-biology | |
| parent | app-portage/gs-elpa: add 0.2.2 (diff) | |
| download | gentoo-cd493f9e3374c2cf9f36ebd06d8dac3f2732faf1.tar.gz gentoo-cd493f9e3374c2cf9f36ebd06d8dac3f2732faf1.tar.bz2 gentoo-cd493f9e3374c2cf9f36ebd06d8dac3f2732faf1.zip | |
sci-biology/pysam: add 0.20.0
Signed-off-by: David Seifert <soap@gentoo.org>
Diffstat (limited to 'sci-biology')
| -rw-r--r-- | sci-biology/pysam/Manifest | 1 | ||||
| -rw-r--r-- | sci-biology/pysam/pysam-0.20.0.ebuild | 69 |
2 files changed, 70 insertions, 0 deletions
diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest index f1a1fe7298b7..fc762c874c2d 100644 --- a/sci-biology/pysam/Manifest +++ b/sci-biology/pysam/Manifest @@ -1 +1,2 @@ DIST pysam-0.19.1.gh.tar.gz 3649711 BLAKE2B dac3ab5a86ef95048e966fc007a0aa1c96ca8498f7c2672c2ed024f34b508bac42048e58b8ae0b538cea137a51e1874bb5c2c4976c7f3dc657a4c2cf5f9a27fb SHA512 719f3a15e7dd277a90cce7f938b674ff86ef6b8f2d3440c3a0bf2ea22c4fbc2b3c9e0cf297d958c99e09dcd6e9905f32e8c632158aa8d5af8210e79705e1c479 +DIST pysam-0.20.0.gh.tar.gz 3748498 BLAKE2B 1c1b99e5ec34641c196dd574e634cc87d49baa594243eca20ad1f99d2c01b8aadead70a729f389c93cf6f5e95f20d9c7e3d050a47821d1b0dcaaff39d88e6825 SHA512 3f8402057e1d5c807886d1d38180dbdbfa8557700fa97bd59cb42df4d7cc461dcbe54808a169ba5f9696651e801fd0431480cd033b601cd4e9c11bf8bbf14e49 diff --git a/sci-biology/pysam/pysam-0.20.0.ebuild b/sci-biology/pysam/pysam-0.20.0.ebuild new file mode 100644 index 000000000000..6372f1602f70 --- /dev/null +++ b/sci-biology/pysam/pysam-0.20.0.ebuild @@ -0,0 +1,69 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{9..11} ) + +inherit distutils-r1 + +DESCRIPTION="Python interface for the SAM/BAM sequence alignment and mapping format" +HOMEPAGE=" + https://github.com/pysam-developers/pysam + https://pypi.org/project/pysam/" +SRC_URI="https://github.com/pysam-developers/pysam/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +RDEPEND="=sci-libs/htslib-1.16*:=" +DEPEND="${RDEPEND} + dev-python/cython[${PYTHON_USEDEP}] + dev-python/setuptools[${PYTHON_USEDEP}]" +BDEPEND=" + test? ( + =sci-biology/bcftools-1.16* + =sci-biology/samtools-1.16* + )" + +distutils_enable_tests pytest + +DISTUTILS_IN_SOURCE_BUILD=1 + +EPYTEST_DESELECT=( + # only work with bundled htslib + 'tests/tabix_test.py::TestRemoteFileHTTP' + 'tests/tabix_test.py::TestRemoteFileHTTPWithHeader' + # broken test + # https://github.com/pysam-developers/pysam/issues/1151#issuecomment-1365662253 + 'tests/AlignmentFilePileup_test.py::TestPileupObjects::testIteratorOutOfScope' +) + +python_prepare_all() { + # unbundle htslib + export HTSLIB_MODE="external" + export HTSLIB_INCLUDE_DIR="${ESYSROOT}"/usr/include + export HTSLIB_LIBRARY_DIR="${ESYSROOT}"/usr/$(get_libdir) + rm -r htslib || die + + # prevent setup.py from adding RPATHs (except $ORIGIN) + sed -e '/runtime_library_dirs=htslib_library_dirs/d' \ + -i setup.py || die + + if use test; then + einfo "Building test data" + emake -C tests/pysam_data + emake -C tests/cbcf_data + fi + + distutils-r1_python_prepare_all +} + +python_compile() { + # breaks with parallel build + # need to avoid dropping .so plugins into + # build-lib, which breaks tests + esetup.py build_ext --inplace -j1 + distutils-r1_python_compile -j1 +} |