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# Copyright 1999-2020 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=7
PYTHON_COMPAT=( python3_{7..9} )
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 -> ${P}.tar.gz"
LICENSE="MIT"
SLOT="0"
KEYWORDS="~amd64 ~x86"
RDEPEND="=sci-libs/htslib-1.10*:="
DEPEND="${RDEPEND}
dev-python/cython[${PYTHON_USEDEP}]
dev-python/setuptools[${PYTHON_USEDEP}]"
BDEPEND="
test? (
=sci-biology/bcftools-1.10*
=sci-biology/samtools-1.10*
)"
distutils_enable_tests pytest
DISTUTILS_IN_SOURCE_BUILD=1
python_prepare_all() {
# unbundle htslib
export HTSLIB_MODE="external"
export HTSLIB_INCLUDE_DIR="${EPREFIX}"/usr/include
export HTSLIB_LIBRARY_DIR="${EPREFIX}"/usr/$(get_libdir)
rm -r htslib || die
# prevent setup.py from adding RPATHs (except $ORIGIN)
sed -e '/runtime_library_dirs=htslib_library_dirs/d' \
-i setup.py || die
eapply "${FILESDIR}"/${PN}-0.16.0.1-fix-tests.patch
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
local MAKEOPTS=-j1
distutils-r1_python_compile
}
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