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author | V3n3RiX <venerix@koprulu.sector> | 2021-12-22 14:08:05 +0000 |
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committer | V3n3RiX <venerix@koprulu.sector> | 2021-12-22 14:08:05 +0000 |
commit | 93a93e9a3b53c1a73142a305ea1f8136846942ee (patch) | |
tree | b9791a06ab3284e27b568412c59316c66240c682 /sci-biology/biopython/biopython-1.79.ebuild | |
parent | 2771f79232c273bc2a57d23bf335dd81ccf6af28 (diff) |
gentoo resync : 22.12.2021
Diffstat (limited to 'sci-biology/biopython/biopython-1.79.ebuild')
-rw-r--r-- | sci-biology/biopython/biopython-1.79.ebuild | 62 |
1 files changed, 62 insertions, 0 deletions
diff --git a/sci-biology/biopython/biopython-1.79.ebuild b/sci-biology/biopython/biopython-1.79.ebuild new file mode 100644 index 000000000000..cef9a670130a --- /dev/null +++ b/sci-biology/biopython/biopython-1.79.ebuild @@ -0,0 +1,62 @@ +# Copyright 1999-2021 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{8..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 + + optfeature_header "Some applications need extra packages:" + optfeature "EMBOSS (The European Molecular Biology Open Software Suite)" sci-biology/emboss +} |