diff options
author | V3n3RiX <venerix@koprulu.sector> | 2023-02-24 09:47:15 +0000 |
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committer | V3n3RiX <venerix@koprulu.sector> | 2023-02-24 09:47:15 +0000 |
commit | 4003c614d3c4b320c45ab1f4b817459d4709443b (patch) | |
tree | fcc0c42e92c56abe0ea39b717b2c3b019c335e41 /sci-biology/biopython/biopython-1.81.ebuild | |
parent | 58177544118b9a8393d7501ee5e0e35cd32f2ad4 (diff) |
gentoo auto-resync : 24:02:2023 - 09:47:15
Diffstat (limited to 'sci-biology/biopython/biopython-1.81.ebuild')
-rw-r--r-- | sci-biology/biopython/biopython-1.81.ebuild | 61 |
1 files changed, 61 insertions, 0 deletions
diff --git a/sci-biology/biopython/biopython-1.81.ebuild b/sci-biology/biopython/biopython-1.81.ebuild new file mode 100644 index 000000000000..8b90d610c6ae --- /dev/null +++ b/sci-biology/biopython/biopython-1.81.ebuild @@ -0,0 +1,61 @@ +# Copyright 1999-2023 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=8 + +PYTHON_COMPAT=( python3_{9..11} ) + +inherit distutils-r1 optfeature pypi + +DESCRIPTION="Python modules for computational molecular biology" +HOMEPAGE="https://www.biopython.org/ https://pypi.org/project/biopython/" + +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 +} |