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# 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 -> ${P}.gh.tar.gz"
LICENSE="MIT"
SLOT="0"
KEYWORDS="~amd64 ~x86"
RDEPEND="=sci-libs/htslib-1.15.1*:="
DEPEND="${RDEPEND}
dev-python/cython[${PYTHON_USEDEP}]
dev-python/setuptools[${PYTHON_USEDEP}]"
BDEPEND="
test? (
=sci-biology/bcftools-1.15.1*
=sci-biology/samtools-1.15.1*
)"
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'
)
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
}
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