commit: 216304d0c8594445dc9eff50c4b955ff6acf61c9 Author: Quincy Fleming <quincyf467 <AT> protonmail <DOT> com> AuthorDate: Sun Mar 16 02:41:41 2025 +0000 Commit: Nowa Ammerlaan <nowa <AT> gentoo <DOT> org> CommitDate: Fri Mar 21 14:59:01 2025 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=216304d0
sci-biology/pysam: add 0.23.0 Bug: https://bugs.gentoo.org/910017 Signed-off-by: Quincy Fleming <quincyf467 <AT> protonmail.com> Signed-off-by: Nowa Ammerlaan <nowa <AT> gentoo.org> sci-biology/pysam/Manifest | 1 + sci-biology/pysam/pysam-0.23.0.ebuild | 68 +++++++++++++++++++++++++++++++++++ 2 files changed, 69 insertions(+) diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest index 2859d25293fc..74b074fbd507 100644 --- a/sci-biology/pysam/Manifest +++ b/sci-biology/pysam/Manifest @@ -1 +1,2 @@ DIST pysam-0.22.1.gh.tar.gz 3885851 BLAKE2B 6f83c445c7e63e28823f443b0f106726303b0609f4040e9dca930c820d48c2adfe13d33ecffb514ce75c3b03968af050652689a0be39aaabca1af546e9188480 SHA512 fb8dc7c4a6ae908d8d409789f2706cce589d4b6a1057bcc4043f8a26a5b390f79d30d1a1cbe69cbf370caabf261ed8367685393240765080e94f1782ed7f0350 +DIST pysam-0.23.0.gh.tar.gz 4076476 BLAKE2B 74f5fd99aff357c59aa4cd13214fbb87577d213461feff2afd59679c6b442ccee1fe23a7b7d6ddc723f57f4e00516fb7b67207e8f8619b707d1f909c62663006 SHA512 7c7b3806dbf316f7d9283dbabcd86e55d5dd18a01a127af5f26279e2266fb9b6e44546de0d22c82de963eca19c9e9b3ed1cc00c465acc2ddd810824902c87add diff --git a/sci-biology/pysam/pysam-0.23.0.ebuild b/sci-biology/pysam/pysam-0.23.0.ebuild new file mode 100644 index 000000000000..cac7c9b72ffc --- /dev/null +++ b/sci-biology/pysam/pysam-0.23.0.ebuild @@ -0,0 +1,68 @@ +# Copyright 1999-2025 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 +DISTUTILS_EXT=1 +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..13} ) + +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 -> ${P}.gh.tar.gz" + +LICENSE="MIT" +SLOT="0" +KEYWORDS="~amd64 ~x86" + +RDEPEND="=sci-libs/htslib-1.21*:=" +DEPEND="${RDEPEND}" +BDEPEND=" + dev-python/cython[${PYTHON_USEDEP}] + test? ( + =sci-biology/bcftools-1.21* + =sci-biology/samtools-1.21* + )" + +distutils_enable_tests pytest + +EPYTEST_DESELECT=( + # only work with bundled htslib + 'tests/tabix_test.py::TestRemoteFileHTTP' + 'tests/tabix_test.py::TestRemoteFileHTTPWithHeader' + + 'tests/AlignedSegment_test.py::TestBaseModifications' +) + +python_prepare_all() { + + # unbundle htslib + export HTSLIB_MODE="external" + export HTSLIB_INCLUDE_DIR="${ESYSROOT}"/usr/include + export HTSLIB_LIBRARY_DIR="${ESYSROOT}"/usr/$(get_libdir) + rm -r htslib || die + + if use test; then + einfo "Building test data" + emake -C tests/pysam_data + emake -C tests/cbcf_data + fi + + # breaks with parallel build + # need to avoid dropping .so plugins into + # build-lib, which breaks tests + DISTUTILS_ARGS=( + build_ext + --inplace + -j1 + ) + distutils-r1_python_prepare_all +} + +python_test() { + rm -rf pysam || die + epytest +}
