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60 lines
1.6 KiB
60 lines
1.6 KiB
# Copyright 1999-2024 Gentoo Authors
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# Distributed under the terms of the GNU General Public License v2
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EAPI=8
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PYTHON_COMPAT=( python3_{9..11} )
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DISTUTILS_USE_PEP517="setuptools"
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DISTUTILS_EXT=1
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inherit distutils-r1 optfeature pypi
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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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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="app-alternatives/lex"
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DOCS=( {CONTRIB,DEPRECATED,NEWS,README}.rst Doc/. )
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PATCHES=(
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"${FILESDIR}/${P}-reportlab4.patch"
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"${FILESDIR}/${P}-python3.12.patch"
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)
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python_test() {
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cd Tests || 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/mysqlclient
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optfeature "PostgreSQL database support" dev-python/psycopg:2
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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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