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Fri, 21 Aug 2020 23:21:09 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 6261C32B for ; Fri, 21 Aug 2020 23:21:08 +0000 (UTC) From: "David Seifert" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "David Seifert" Message-ID: <1598052044.6cbf10bd4d0104c5a03acc7bd54c1068e6b02de3.soap@gentoo> Subject: [gentoo-commits] repo/gentoo:master commit in: sci-biology/biopython/ X-VCS-Repository: repo/gentoo X-VCS-Files: sci-biology/biopython/Manifest sci-biology/biopython/biopython-1.77.ebuild X-VCS-Directories: sci-biology/biopython/ X-VCS-Committer: soap X-VCS-Committer-Name: David Seifert X-VCS-Revision: 6cbf10bd4d0104c5a03acc7bd54c1068e6b02de3 X-VCS-Branch: master Date: Fri, 21 Aug 2020 23:21:08 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Auto-Response-Suppress: DR, RN, NRN, OOF, AutoReply X-Archives-Salt: b233c1a6-d611-478f-9e81-81bd88ad1b48 X-Archives-Hash: c31151921c9b912cf6d419ec27b99f2b commit: 6cbf10bd4d0104c5a03acc7bd54c1068e6b02de3 Author: David Seifert gentoo org> AuthorDate: Fri Aug 21 23:20:44 2020 +0000 Commit: David Seifert gentoo org> CommitDate: Fri Aug 21 23:20:44 2020 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=6cbf10bd sci-biology/biopython: Version bump to 1.77 Package-Manager: Portage-3.0.4, Repoman-3.0.1 Signed-off-by: David Seifert gentoo.org> sci-biology/biopython/Manifest | 1 + sci-biology/biopython/biopython-1.77.ebuild | 62 +++++++++++++++++++++++++++++ 2 files changed, 63 insertions(+) diff --git a/sci-biology/biopython/Manifest b/sci-biology/biopython/Manifest index ee3ffae9c3f..cff73fbcbc3 100644 --- a/sci-biology/biopython/Manifest +++ b/sci-biology/biopython/Manifest @@ -1 +1,2 @@ DIST biopython-1.73.tar.gz 15715102 BLAKE2B b2c40f9ed02681f19607c88f91b469784985acefc6e81770a54e5c13c715915344bc7fd72e4a88ae50879a2463965ac6d0d04c6d263908887028d1e065620b95 SHA512 d067330ef8e25ca6881b56f4e5e89e16a816c89760473e2f32a6236ab202f805294650aa944f0b098987425bcb65727317da7a26deb4d4937f02b00123ea9a8f +DIST biopython-1.77.tar.gz 16837021 BLAKE2B b5586f0ea3e476b11801dcc98039d5eea7b191e11d390192c0cf348018ded005fe2ad5dc9ba71c83aebc9cdde20c97244905dcc3aeb5436a97588da9f8c79c3e SHA512 6f4b03d46c591e1f49dd1e76bcc4ac5c9aaa2bf748c9dd37ffc5de5a613fbeed38f89b418c01601dd99c65b13b2e294bc8d81ffafc42a9ff1b309c84f840d0d5 diff --git a/sci-biology/biopython/biopython-1.77.ebuild b/sci-biology/biopython/biopython-1.77.ebuild new file mode 100644 index 00000000000..486e9fe694d --- /dev/null +++ b/sci-biology/biopython/biopython-1.77.ebuild @@ -0,0 +1,62 @@ +# Copyright 1999-2020 Gentoo Authors +# Distributed under the terms of the GNU General Public License v2 + +EAPI=7 + +PYTHON_COMPAT=( python3_{6..9} ) + +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}/${P}.tar.gz" + +LICENSE="HPND" +SLOT="0" +KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" + +RDEPEND=" + dev-python/matplotlib[${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 "${TEST_DIR}"/lib/Bio/Align/substitution_matrices || die + ln -r -s "${S}"/Bio/Align/substitution_matrices/data \ + "${TEST_DIR}"/lib/Bio/Align/substitution_matrices/data || die + + cd "${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() { + 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 +}