commit: 31a70e941154558bcf8afe94c3dd16c90d4f4e40 Author: David Seifert <soap <AT> gentoo <DOT> org> AuthorDate: Sun May 27 14:31:03 2018 +0000 Commit: David Seifert <soap <AT> gentoo <DOT> org> CommitDate: Sun May 27 14:31:36 2018 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=31a70e94
sci-biology/biopython: Bump to 1.71 Closes: https://bugs.gentoo.org/653006 Package-Manager: Portage-2.3.40, Repoman-2.3.9 sci-biology/biopython/Manifest | 1 + sci-biology/biopython/biopython-1.71.ebuild | 57 +++++++++++++++++++++++++++++ 2 files changed, 58 insertions(+) diff --git a/sci-biology/biopython/Manifest b/sci-biology/biopython/Manifest index 55331efbbcb..70af7c92d44 100644 --- a/sci-biology/biopython/Manifest +++ b/sci-biology/biopython/Manifest @@ -1 +1,2 @@ DIST biopython-1.68.tar.gz 14445813 BLAKE2B 566931c4e522e95278f7f6a9dc07ecc091dc54b69cdea8bb07603339af4f1fd38e3df87482e97729acb776dd2df19a4e61d49ee7608ec5cb0f24966e28c2e3dd SHA512 0ca994475654bb68ff326c8e86cbd4547cd87b42e1633dda039ad668e1298884b22e169f6b25ab514e929861334a93b7db6d057a3486cea9997ca2de95c61a69 +DIST biopython-1.71.tar.gz 16031832 BLAKE2B 2062065b77fc35ea8a3f09ec967482c233a6e0bbfc7d09187ff5e892848b45fa7bd6d7b6027b38c3d4c9a9c601785521fa7edb91fa960b46c8e49aed91b1f5dc SHA512 003955e92295e98526c88abb573db9bdc37877fc41395551b541e7106ffa603327a36c6f4d999838c0be38b378901235c9dbd7cb7fc25c14a5d7001939fe23bd diff --git a/sci-biology/biopython/biopython-1.71.ebuild b/sci-biology/biopython/biopython-1.71.ebuild new file mode 100644 index 00000000000..f770b57a2a6 --- /dev/null +++ b/sci-biology/biopython/biopython-1.71.ebuild @@ -0,0 +1,57 @@ +# Copyright 1999-2018 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +PYTHON_COMPAT=( python2_7 python3_{4,5,6} ) + +inherit distutils-r1 eutils + +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}/${P}.tar.gz" + +LICENSE="HPND" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND=" + dev-python/matplotlib[${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[${PYTHON_USEDEP}] + dev-python/pydot[${PYTHON_USEDEP}]" +DEPEND="${RDEPEND} + sys-devel/flex" + +DOCS=( CONTRIB DEPRECATED NEWS README Doc/. ) + +python_test() { + distutils_install_for_testing + cp -r "${S}"/{Doc,Tests} "${TEST_DIR}"/lib/ || die + cd "${TEST_DIR}"/lib/Tests || die + rm test_BioSQL_{psycopg2.py,MySQLdb.py,mysql_connector.py} || die + "${EPYTHON}" run_tests.py --offline --verbose || die +} + +python_install_all() { + # remove files causing ecompressdir to fail + rm Doc/examples/ls_orchid.gbk.bz2 || die + + distutils-r1_python_install_all + + dodir /usr/share/${PN} + cp -r --preserve=mode Scripts Tests "${ED}"/usr/share/${PN} || die +} + +pkg_postinst() { + elog "For database support you need to install:" + optfeature "MySQL" dev-python/mysql-python + optfeature "PostGreSQL" dev-python/psycopg + + elog "Some applications need extra packages:" + optfeature "EMBOSS (The European Molecular Biology Open Software Suite)" sci-biology/emboss +}
