commit: 485c37afa2cfd44b7a88cdf73d251fa74a0e8e6d Author: Quincy Fleming <quincyf467 <AT> protonmail <DOT> com> AuthorDate: Sun Mar 16 02:44:35 2025 +0000 Commit: Nowa Ammerlaan <nowa <AT> gentoo <DOT> org> CommitDate: Fri Mar 21 14:59:02 2025 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=485c37af
sci-biology/pysam: sync live build Closes: https://bugs.gentoo.org/910017 Signed-off-by: Quincy Fleming <quincyf467 <AT> protonmail.com> Closes: https://github.com/gentoo/gentoo/pull/41086 Signed-off-by: Nowa Ammerlaan <nowa <AT> gentoo.org> sci-biology/pysam/pysam-9999.ebuild | 43 +++++++++++++++++++------------------ 1 file changed, 22 insertions(+), 21 deletions(-) diff --git a/sci-biology/pysam/pysam-9999.ebuild b/sci-biology/pysam/pysam-9999.ebuild index a162ddf2158b..d4bf32a59aab 100644 --- a/sci-biology/pysam/pysam-9999.ebuild +++ b/sci-biology/pysam/pysam-9999.ebuild @@ -1,9 +1,10 @@ -# Copyright 1999-2023 Gentoo Authors +# Copyright 1999-2025 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=8 - -PYTHON_COMPAT=( python3_{9..11} ) +DISTUTILS_EXT=1 +DISTUTILS_USE_PEP517=setuptools +PYTHON_COMPAT=( python3_{10..13} ) inherit distutils-r1 @@ -23,24 +24,23 @@ HOMEPAGE=" LICENSE="MIT" SLOT="0" -RDEPEND=">=sci-libs/htslib-1.17" -DEPEND="${RDEPEND} - dev-python/cython[${PYTHON_USEDEP}] - dev-python/setuptools[${PYTHON_USEDEP}]" +RDEPEND=">=sci-libs/htslib-1.21" +DEPEND="${RDEPEND}" BDEPEND=" + dev-python/cython[${PYTHON_USEDEP}] test? ( - >=sci-biology/bcftools-1.17 - >=sci-biology/samtools-1.17 + >=sci-biology/bcftools-1.21 + >=sci-biology/samtools-1.21 )" distutils_enable_tests pytest -DISTUTILS_IN_SOURCE_BUILD=1 - EPYTEST_DESELECT=( # only work with bundled htslib 'tests/tabix_test.py::TestRemoteFileHTTP' 'tests/tabix_test.py::TestRemoteFileHTTPWithHeader' + + 'tests/AlignedSegment_test.py::TestBaseModifications' ) python_prepare_all() { @@ -50,23 +50,24 @@ python_prepare_all() { export HTSLIB_LIBRARY_DIR="${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 + DISTUTILS_ARGS=( + build_ext + --inplace + -j1 + ) + distutils-r1_python_prepare_all +} + +python_test() { + rm -rf pysam || die + epytest }
