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 6AE60138330 for ; Sat, 3 Sep 2016 11:25:05 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 71AB9E0B45; Sat, 3 Sep 2016 11:25:03 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 03C74E0B45 for ; Sat, 3 Sep 2016 11:25:02 +0000 (UTC) Received: from oystercatcher.gentoo.org (oystercatcher.gentoo.org [148.251.78.52]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id B6C6F340775 for ; Sat, 3 Sep 2016 11:25:01 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id A46931B9B for ; Sat, 3 Sep 2016 11:24:59 +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: <1472901892.7440b9fd9976ffc4cbca598082c9e52f541040c8.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 X-VCS-Directories: sci-biology/biopython/ X-VCS-Committer: soap X-VCS-Committer-Name: David Seifert X-VCS-Revision: 7440b9fd9976ffc4cbca598082c9e52f541040c8 X-VCS-Branch: master Date: Sat, 3 Sep 2016 11:24:59 +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-Archives-Salt: a4027a57-7479-4f31-9ebd-c5e4cdaedc6d X-Archives-Hash: 61ac163e13f7418199e31f44e2bda4e7 commit: 7440b9fd9976ffc4cbca598082c9e52f541040c8 Author: David Seifert gentoo org> AuthorDate: Sat Sep 3 11:24:35 2016 +0000 Commit: David Seifert gentoo org> CommitDate: Sat Sep 3 11:24:52 2016 +0000 URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=7440b9fd sci-biology/biopython: Version bump Package-Manager: portage-2.3.0 sci-biology/biopython/Manifest | 1 + sci-biology/biopython/biopython-1.68.ebuild | 56 +++++++++++++++++++++++++++++ 2 files changed, 57 insertions(+) diff --git a/sci-biology/biopython/Manifest b/sci-biology/biopython/Manifest index a54d05e..9e5a8d9 100644 --- a/sci-biology/biopython/Manifest +++ b/sci-biology/biopython/Manifest @@ -1,2 +1,3 @@ DIST biopython-1.65.tar.gz 12641342 SHA256 463cc81db84e9bfcdfb15629511c81ed556a6c0287e670dbfe80f03c65d2a88e SHA512 2a9c6a89d0279374c243938d13bfdd6f2b124a08afbfb0c262e1e4827c48a141fb9941f4cdb960f76b523f0ac152095a8c6ea566d9b469ce9daf8a7e7993f7af WHIRLPOOL 40757938c0eb7e30c9609ef5aa2d397fa21ad92cd20c9b6300cde1b381a0e6c21e4ebb7f4d25bf02651789437d7d86341154b907ccc0007759c17939f2e29da2 DIST biopython-1.66.tar.gz 13724754 SHA256 5178ea3b343b1d8710f39205386093e5369ed653aa020e1b0c4b7622a59346c1 SHA512 6bb01f1058728f957527447df82ffbb9027e74564e81c8308b3404d033a0f12fef50da05b343bd4c4eae98508931eedc9c4bc23b2efdf36bbb49f1557fa52d71 WHIRLPOOL 0cfe3f4829ec72afa466b17cf6745cc334105713ebeeb06019e2df94acc1289aeb07a7bba70a50afeae00de90c48d2455a1af8cf26f916ceb4c0ab92a4a05fbd +DIST biopython-1.68.tar.gz 14445813 SHA256 d1dc09d1ddc8e90833f507cf09f80fa9ee1537d319058d1c44fe9c09be3d0c1f SHA512 0ca994475654bb68ff326c8e86cbd4547cd87b42e1633dda039ad668e1298884b22e169f6b25ab514e929861334a93b7db6d057a3486cea9997ca2de95c61a69 WHIRLPOOL 9348354d0063efe0f9051f46e3be60540c5df21a43c094d74e64d37279736921d890cd639c904336eb21b2996e9948b8a050017b77569d2333ac80aa5b8bf156 diff --git a/sci-biology/biopython/biopython-1.68.ebuild b/sci-biology/biopython/biopython-1.68.ebuild new file mode 100644 index 00000000..265181c --- /dev/null +++ b/sci-biology/biopython/biopython-1.68.ebuild @@ -0,0 +1,56 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI=6 + +PYTHON_COMPAT=( python2_7 python3_{3,4,5} pypy ) + +inherit distutils-r1 eutils + +DESCRIPTION="Python modules for computational molecular biology" +HOMEPAGE="http://www.biopython.org/ https://pypi.python.org/pypi/biopython/" +SRC_URI="http://www.biopython.org/DIST/${P}.tar.gz" + +LICENSE="HPND" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" +IUSE="" + +RDEPEND=" + dev-python/matplotlib[$(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[$(python_gen_usedep 'python*')] + media-gfx/pydot[$(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 +}