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Sun, 16 Apr 2023 12:36:15 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id CAF31A39 for ; Sun, 16 Apr 2023 12:36:13 +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: <1681648520.a41f49e0eec39e31152d2829b0131417cb86850c.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-1.79.ebuild X-VCS-Directories: sci-biology/biopython/ X-VCS-Committer: soap X-VCS-Committer-Name: David Seifert X-VCS-Revision: a41f49e0eec39e31152d2829b0131417cb86850c X-VCS-Branch: master Date: Sun, 16 Apr 2023 12:36:13 +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: 9daec228-6345-4825-8eb1-78c8a7fa5d1a X-Archives-Hash: 8bc8889c09bc6ddfbd80ebcab462db30 commit: a41f49e0eec39e31152d2829b0131417cb86850c Author: David Seifert gentoo org> AuthorDate: Sun Apr 16 12:35:20 2023 +0000 Commit: David Seifert gentoo org> CommitDate: Sun Apr 16 12:35:20 2023 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=a41f49e0 sci-biology/biopython: drop 1.79 Signed-off-by: David Seifert gentoo.org> sci-biology/biopython/Manifest | 1 - sci-biology/biopython/biopython-1.79.ebuild | 62 ----------------------------- 2 files changed, 63 deletions(-) diff --git a/sci-biology/biopython/Manifest b/sci-biology/biopython/Manifest index c693a5a8a963..0c16022dea2c 100644 --- a/sci-biology/biopython/Manifest +++ b/sci-biology/biopython/Manifest @@ -1,2 +1 @@ -DIST biopython-1.79.tar.gz 16738730 BLAKE2B 8c97fc23e458f7bc98b0ed0226bd6fb42f6c6f3ce03d562b13fac66c5061451595cd5bd01cad07bbe1fc6b20f4de21b0f03766b5a20e602545da888047a57185 SHA512 81e2718f4015bb038637b4d1181e6bea48018fec1e769c5f0ab75442a769336899191f1222e82e1b9569c1fac470500d7582420e5cbe9bce0056b41751adeaaa DIST biopython-1.81.tar.gz 19324875 BLAKE2B be3a85f5b60638987d6186af498411b494f8d27389f24cd1b9e658bc6b1a29c799ec8b20a9ac0b955c6d4c239706f4dbb5b75f6d56908f63d731b1d56c9fd587 SHA512 1595fad6631bfb6cf4e1a92ed72e6093e2a0c24f3c0bd4182267ec9742fb03dff16099eedde139598aa6b5b8380bbac9e48246cb9ab8b44109333d60adfd00ed diff --git a/sci-biology/biopython/biopython-1.79.ebuild b/sci-biology/biopython/biopython-1.79.ebuild deleted file mode 100644 index c6a93b3af58d..000000000000 --- a/sci-biology/biopython/biopython-1.79.ebuild +++ /dev/null @@ -1,62 +0,0 @@ -# Copyright 1999-2023 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=8 - -PYTHON_COMPAT=( python3_{9..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:2 - - optfeature_header "Some applications need extra packages:" - optfeature "EMBOSS (The European Molecular Biology Open Software Suite)" sci-biology/emboss -}