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# Copyright 1999-2023 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
EAPI=8
DISTUTILS_IN_SOURCE_BUILD=1
PYTHON_COMPAT=( python3_{9..11} )
inherit distutils-r1 flag-o-matic
DESCRIPTION="Python support for SAM/BAM/Bowtie/FASTA/Q/GFF/GTF files"
HOMEPAGE="https://htseq.readthedocs.io/"
if [[ ${PV} == *9999 ]]; then
inherit git-r3
EGIT_REPO_URI="https://github.com/htseq/htseq.git"
else
SRC_URI="https://github.com/htseq/htseq/archive/release_${PV}.tar.gz -> ${P}.gh.tar.gz"
S="${WORKDIR}"/htseq-release_${PV}
KEYWORDS="~amd64"
fi
LICENSE="GPL-3+"
SLOT="0"
RDEPEND="
dev-python/numpy[${PYTHON_USEDEP}]
sci-biology/pysam[${PYTHON_USEDEP}]"
DEPEND="${RDEPEND}
test? (
dev-python/matplotlib[${PYTHON_USEDEP}]
dev-python/pandas[${PYTHON_USEDEP}]
dev-python/scipy[${PYTHON_USEDEP}]
)"
BDEPEND="
>=dev-lang/swig-3.0.8
dev-python/cython[${PYTHON_USEDEP}]"
distutils_enable_tests pytest
src_configure() {
# mask broken asserts in src/step_vector.h:72
append-cppflags -DNDEBUG
distutils-r1_src_configure
}
python_test() {
distutils_install_for_testing
# Due to the build directories creating a competing
# hierarchy, we move to the test/ dir to avoid implicitly
# injecting the root HTSeq/ dir into the PYTHONPATH,
# which leads the python module lookup astray:
# ${PWD}
# ├── build
# │ ├── lib
# │ │ └── HTSeq
# │ [...]
# ├── HTSeq
# └── test
cd test/ || die
ln -s ../example_data || die
epytest
}
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