# 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 if [[ ${PV} == *9999 ]]; then inherit git-r3 EGIT_REPO_URI="https://github.com/pysam-developers/pysam.git" else SRC_URI="https://github.com/pysam-developers/pysam/archive/v${PV}.tar.gz -> ${P}.gh.tar.gz" KEYWORDS="~amd64 ~x86" fi DESCRIPTION="Python interface for the SAM/BAM sequence alignment and mapping format" HOMEPAGE=" https://github.com/pysam-developers/pysam https://pypi.org/project/pysam/" LICENSE="MIT" SLOT="0" RDEPEND=">=sci-libs/htslib-1.21" DEPEND="${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 }