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# Copyright 1999-2021 Gentoo Authors
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# Distributed under the terms of the GNU General Public License v2
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EAPI=7
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PYTHON_COMPAT=( python3_{7..9} )
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inherit distutils-r1 optfeature
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DESCRIPTION="Python modules for computational molecular biology"
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HOMEPAGE="https://www.biopython.org/ https://pypi.org/project/biopython/"
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SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
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LICENSE="HPND"
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SLOT="0"
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KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
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RDEPEND="
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dev-python/matplotlib[${PYTHON_USEDEP}]
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dev-python/networkx[${PYTHON_USEDEP}]
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dev-python/numpy[${PYTHON_USEDEP}]
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dev-python/rdflib[${PYTHON_USEDEP}]
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dev-python/pygraphviz[${PYTHON_USEDEP}]
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>=dev-python/reportlab-3.5.13-r1[${PYTHON_USEDEP}]
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dev-python/pydot[${PYTHON_USEDEP}]"
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DEPEND="${RDEPEND}"
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BDEPEND="sys-devel/flex"
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DOCS=( {CONTRIB,DEPRECATED,NEWS,README}.rst Doc/. )
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python_test() {
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distutils_install_for_testing
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cp -r {Doc,Tests} "${TEST_DIR}"/lib/ || die
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# need to create symlinks for doctests
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mkdir -p "${TEST_DIR}"/lib/Bio/Align/substitution_matrices || die
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ln -r -s "${S}"/Bio/Align/substitution_matrices/data \
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"${TEST_DIR}"/lib/Bio/Align/substitution_matrices/data || die
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cd "${TEST_DIR}"/lib/Tests || die
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rm test_BioSQL_{psycopg2.py,MySQLdb.py,mysql_connector.py} || die
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"${EPYTHON}" run_tests.py --offline --verbose || die
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}
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python_install_all() {
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# remove files causing ecompressdir to fail
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rm Doc/examples/ls_orchid.gbk.{gz,bz2} || die
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distutils-r1_python_install_all
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dodir /usr/share/${PN}
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cp -r --preserve=mode Scripts Tests "${ED}"/usr/share/${PN} || die
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}
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pkg_postinst() {
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optfeature_header "For database support you need to install:"
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optfeature "MySQL database support" dev-python/mysql-python
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optfeature "PostgreSQL database support" dev-python/psycopg
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optfeature_header "Some applications need extra packages:"
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optfeature "EMBOSS (The European Molecular Biology Open Software Suite)" sci-biology/emboss
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}
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