# Copyright 1999-2020 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=7 PYTHON_COMPAT=( python3_{6..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 }