From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by finch.gentoo.org (Postfix) with ESMTPS id 29CAE138334 for ; Sun, 29 Dec 2019 08:53:39 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 8E435E0C2F; Sun, 29 Dec 2019 08:53:32 +0000 (UTC) Received: from smtp.gentoo.org (mail.gentoo.org [IPv6:2001:470:ea4a:1:5054:ff:fec7:86e4]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 687AEE0C2F for ; Sun, 29 Dec 2019 08:53:32 +0000 (UTC) Received: from oystercatcher.gentoo.org (oystercatcher.gentoo.org [148.251.78.52]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id C365934DCC2 for ; Sun, 29 Dec 2019 08:53:30 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 116D1AC for ; Sun, 29 Dec 2019 08:53:26 +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: <1577609589.73c3e34900c4f49a05e4445033a21900b04e626e.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-1.68.ebuild sci-biology/biopython/biopython-1.71.ebuild X-VCS-Directories: sci-biology/biopython/ X-VCS-Committer: soap X-VCS-Committer-Name: David Seifert X-VCS-Revision: 73c3e34900c4f49a05e4445033a21900b04e626e X-VCS-Branch: master Date: Sun, 29 Dec 2019 08:53:26 +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: aeffba72-4afc-417b-b039-1452b03060b0 X-Archives-Hash: 59105fa007bd69da0ee977c7352925fa commit: 73c3e34900c4f49a05e4445033a21900b04e626e Author: David Seifert gentoo org> AuthorDate: Sun Dec 29 08:53:09 2019 +0000 Commit: David Seifert gentoo org> CommitDate: Sun Dec 29 08:53:09 2019 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=73c3e349 sci-biology/biopython: Remove old Package-Manager: Portage-2.3.83, Repoman-2.3.20 Signed-off-by: David Seifert gentoo.org> sci-biology/biopython/Manifest | 2 - sci-biology/biopython/biopython-1.68.ebuild | 55 ---------------------------- sci-biology/biopython/biopython-1.71.ebuild | 57 ----------------------------- 3 files changed, 114 deletions(-) diff --git a/sci-biology/biopython/Manifest b/sci-biology/biopython/Manifest index 02d90810dc5..ee3ffae9c3f 100644 --- a/sci-biology/biopython/Manifest +++ b/sci-biology/biopython/Manifest @@ -1,3 +1 @@ -DIST biopython-1.68.tar.gz 14445813 BLAKE2B 566931c4e522e95278f7f6a9dc07ecc091dc54b69cdea8bb07603339af4f1fd38e3df87482e97729acb776dd2df19a4e61d49ee7608ec5cb0f24966e28c2e3dd SHA512 0ca994475654bb68ff326c8e86cbd4547cd87b42e1633dda039ad668e1298884b22e169f6b25ab514e929861334a93b7db6d057a3486cea9997ca2de95c61a69 -DIST biopython-1.71.tar.gz 16031832 BLAKE2B 2062065b77fc35ea8a3f09ec967482c233a6e0bbfc7d09187ff5e892848b45fa7bd6d7b6027b38c3d4c9a9c601785521fa7edb91fa960b46c8e49aed91b1f5dc SHA512 003955e92295e98526c88abb573db9bdc37877fc41395551b541e7106ffa603327a36c6f4d999838c0be38b378901235c9dbd7cb7fc25c14a5d7001939fe23bd DIST biopython-1.73.tar.gz 15715102 BLAKE2B b2c40f9ed02681f19607c88f91b469784985acefc6e81770a54e5c13c715915344bc7fd72e4a88ae50879a2463965ac6d0d04c6d263908887028d1e065620b95 SHA512 d067330ef8e25ca6881b56f4e5e89e16a816c89760473e2f32a6236ab202f805294650aa944f0b098987425bcb65727317da7a26deb4d4937f02b00123ea9a8f diff --git a/sci-biology/biopython/biopython-1.68.ebuild b/sci-biology/biopython/biopython-1.68.ebuild deleted file mode 100644 index f76da59c1b8..00000000000 --- a/sci-biology/biopython/biopython-1.68.ebuild +++ /dev/null @@ -1,55 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -PYTHON_COMPAT=( python2_7 python3_5 pypy ) - -inherit distutils-r1 eutils - -DESCRIPTION="Python modules for computational molecular biology" -HOMEPAGE="http://www.biopython.org/ https://pypi.org/project/biopython/" -SRC_URI="http://www.biopython.org/DIST/${P}.tar.gz" - -LICENSE="HPND" -SLOT="0" -KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux" -IUSE="" - -RDEPEND=" - dev-python/matplotlib[$(python_gen_usedep 'python*')] - dev-python/networkx[$(python_gen_usedep 'python*')] - dev-python/numpy[$(python_gen_usedep 'python*')] - dev-python/rdflib[$(python_gen_usedep 'python*')] - dev-python/pygraphviz[$(python_gen_usedep 'python2*')] - dev-python/reportlab[$(python_gen_usedep 'python*')] - dev-python/pydot[$(python_gen_usedep 'python2*')] - " -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 - ${PYTHON} run_tests.py --offline --verbose || die -} - -python_install_all() { - distutils-r1_python_install_all - - dodir /usr/share/${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 - elog "Some applications need extra packages:" - optfeature "EMBOSS (The European Molecular Biology Open Software Suite)" sci-biology/emboss -} diff --git a/sci-biology/biopython/biopython-1.71.ebuild b/sci-biology/biopython/biopython-1.71.ebuild deleted file mode 100644 index 8b9a0cd7112..00000000000 --- a/sci-biology/biopython/biopython-1.71.ebuild +++ /dev/null @@ -1,57 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -PYTHON_COMPAT=( python2_7 python3_{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 -}