commit: de858ae7cf457b2ef508edce83f809403346ac0f Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Mon Dec 20 13:32:52 2021 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Mon Dec 20 13:32:52 2021 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=de858ae7
sci-biology/biopython: add 1.79 Bug: https://bugs.gentoo.org/757867 Bug: https://bugs.gentoo.org/780345 Signed-off-by: David Seifert <soap <AT> gentoo.org> sci-biology/biopython/Manifest | 1 + sci-biology/biopython/biopython-1.79.ebuild | 62 +++++++++++++++++++++++++++++ 2 files changed, 63 insertions(+) diff --git a/sci-biology/biopython/Manifest b/sci-biology/biopython/Manifest index 420f6d1f83d8..9bc0eede97dc 100644 --- a/sci-biology/biopython/Manifest +++ b/sci-biology/biopython/Manifest @@ -1 +1,2 @@ DIST biopython-1.77.tar.gz 16837021 BLAKE2B b5586f0ea3e476b11801dcc98039d5eea7b191e11d390192c0cf348018ded005fe2ad5dc9ba71c83aebc9cdde20c97244905dcc3aeb5436a97588da9f8c79c3e SHA512 6f4b03d46c591e1f49dd1e76bcc4ac5c9aaa2bf748c9dd37ffc5de5a613fbeed38f89b418c01601dd99c65b13b2e294bc8d81ffafc42a9ff1b309c84f840d0d5 +DIST biopython-1.79.tar.gz 16738730 BLAKE2B 8c97fc23e458f7bc98b0ed0226bd6fb42f6c6f3ce03d562b13fac66c5061451595cd5bd01cad07bbe1fc6b20f4de21b0f03766b5a20e602545da888047a57185 SHA512 81e2718f4015bb038637b4d1181e6bea48018fec1e769c5f0ab75442a769336899191f1222e82e1b9569c1fac470500d7582420e5cbe9bce0056b41751adeaaa 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 +}
