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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..10} )
inherit distutils-r1 optfeature
DESCRIPTION="Python modules for computational molecular biology"
HOMEPAGE="https://www.biopython.org/ https://pypi.org/project/biopython/"
SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
LICENSE="HPND"
SLOT="0"
KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
RDEPEND="
dev-python/matplotlib[${PYTHON_USEDEP}]
dev-python/networkx[${PYTHON_USEDEP}]
dev-python/numpy[${PYTHON_USEDEP}]
dev-python/rdflib[${PYTHON_USEDEP}]
dev-python/pygraphviz[${PYTHON_USEDEP}]
>=dev-python/reportlab-3.5.13-r1[${PYTHON_USEDEP}]
dev-python/pydot[${PYTHON_USEDEP}]"
DEPEND="${RDEPEND}"
BDEPEND="sys-devel/flex"
DOCS=( {CONTRIB,DEPRECATED,NEWS,README}.rst Doc/. )
python_test() {
distutils_install_for_testing
cp -r {Doc,Tests} "${TEST_DIR}"/lib/ || die
# need to create symlinks for doctests
mkdir -p "${TEST_DIR}"/lib/Bio/Align || die
ln -r -s "${S}"/Bio/Align/substitution_matrices \
"${TEST_DIR}"/lib/Bio/Align/substitution_matrices || die
cd "${TEST_DIR}"/lib/Tests || die
rm test_BioSQL_{psycopg2.py,MySQLdb.py,mysql_connector.py} || die
"${EPYTHON}" run_tests.py --offline --verbose || die
}
python_install_all() {
# remove files causing ecompressdir to fail
rm Doc/examples/ls_orchid.gbk.{gz,bz2} || die
distutils-r1_python_install_all
dodir /usr/share/${PN}
cp -r --preserve=mode Scripts Tests "${ED}"/usr/share/${PN} || die
}
pkg_postinst() {
optfeature_header "For database support you need to install:"
optfeature "MySQL database support" dev-python/mysqlclient
optfeature "PostgreSQL database support" dev-python/psycopg:2
optfeature_header "Some applications need extra packages:"
optfeature "EMBOSS (The European Molecular Biology Open Software Suite)" sci-biology/emboss
}
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