From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) by finch.gentoo.org (Postfix) with ESMTP id C4A731381FA for ; Tue, 3 Jun 2014 00:26:42 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id B802AE0949; Tue, 3 Jun 2014 00:26:41 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) (using TLSv1.2 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 3D732E0949 for ; Tue, 3 Jun 2014 00:26:40 +0000 (UTC) Received: from spoonbill.gentoo.org (spoonbill.gentoo.org [81.93.255.5]) (using TLSv1.2 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id C02B633FCF2 for ; Tue, 3 Jun 2014 00:26:39 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by spoonbill.gentoo.org (Postfix) with ESMTP id 89689181A9 for ; Tue, 3 Jun 2014 00:26:37 +0000 (UTC) From: "Martin Mokrejs" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Martin Mokrejs" Message-ID: <1401755039.10c67b74e2889910c6b679fbdaccbb3326adc635.mmokrejs@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/biopython/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/biopython/ChangeLog sci-biology/biopython/biopython-1.63-r2.ebuild sci-biology/biopython/biopython-1.64.ebuild sci-biology/biopython/metadata.xml X-VCS-Directories: sci-biology/biopython/ X-VCS-Committer: mmokrejs X-VCS-Committer-Name: Martin Mokrejs X-VCS-Revision: 10c67b74e2889910c6b679fbdaccbb3326adc635 X-VCS-Branch: master Date: Tue, 3 Jun 2014 00:26:37 +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: c1ed4527-e01f-4d92-8c39-ad0f6a843bc1 X-Archives-Hash: cde9055154fa90483f60005d319d468e commit: 10c67b74e2889910c6b679fbdaccbb3326adc635 Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Tue Jun 3 00:23:59 2014 +0000 Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Tue Jun 3 00:23:59 2014 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=10c67b74 sci-biology/biopython-1.64: version bump with some notable bugfixes Package-Manager: portage-2.2.7 --- sci-biology/biopython/ChangeLog | 10 +++++ sci-biology/biopython/biopython-1.63-r2.ebuild | 54 ++++++++++++++++++++++++++ sci-biology/biopython/biopython-1.64.ebuild | 54 ++++++++++++++++++++++++++ sci-biology/biopython/metadata.xml | 5 +++ 4 files changed, 123 insertions(+) diff --git a/sci-biology/biopython/ChangeLog b/sci-biology/biopython/ChangeLog new file mode 100644 index 0000000..c60a939 --- /dev/null +++ b/sci-biology/biopython/ChangeLog @@ -0,0 +1,10 @@ +# ChangeLog for sci-biology/biopython +# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2 +# $Header: $ + +*biopython-1.63-r2 (03 Jun 2014) +*biopython-1.64 (03 Jun 2014) + + 03 Jun 2014; Martin Mokrejs + +biopython-1.63-r2.ebuild, +biopython-1.64.ebuild, +metadata.xml: + sci-biology/biopython-1.64: version bump with some notable bugfixes diff --git a/sci-biology/biopython/biopython-1.63-r2.ebuild b/sci-biology/biopython/biopython-1.63-r2.ebuild new file mode 100644 index 0000000..435c757 --- /dev/null +++ b/sci-biology/biopython/biopython-1.63-r2.ebuild @@ -0,0 +1,54 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/biopython/biopython-1.62.ebuild,v 1.1 2013/09/17 16:07:56 jlec Exp $ + +EAPI=5 + +PYTHON_COMPAT=( python{2_6,2_7} ) + +inherit distutils-r1 eutils + +DESCRIPTION="Python modules for computational molecular biology" +HOMEPAGE="http://www.biopython.org/ http://pypi.python.org/pypi/biopython/" +SRC_URI="http://www.biopython.org/DIST/${P}.tar.gz" + +LICENSE="HPND" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" +IUSE="mysql postgres" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND="${PYTHON_DEPS} + dev-python/matplotlib[${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[${PYTHON_USEDEP}] + media-gfx/pydot[${PYTHON_USEDEP}] + mysql? ( dev-python/mysql-python[${PYTHON_USEDEP}] ) + postgres? ( dev-python/psycopg[${PYTHON_USEDEP}] )" +DEPEND="${RDEPEND} + sys-devel/flex" + +DOCS=( CONTRIB DEPRECATED NEWS README Doc/. ) + +src_prepare() { + epatch "${FILESDIR}/SffIO_error_in_check_eof.patch" + epatch "${FILESDIR}/SffIO_broken_padding.patch" + epatch "${FILESDIR}/SffIO-crossed-trimpoints.patch" + distutils-r1_src_prepare +} + +python_test() { + cd Tests || die + ${PYTHON} run_tests.py || die +} + +python_install_all() { + distutils-r1_python_install_all + + dodir /usr/share/${PN} + cp -r --preserve=mode Scripts Tests "${ED}"/usr/share/${PN} || die +} diff --git a/sci-biology/biopython/biopython-1.64.ebuild b/sci-biology/biopython/biopython-1.64.ebuild new file mode 100644 index 0000000..366fa7a --- /dev/null +++ b/sci-biology/biopython/biopython-1.64.ebuild @@ -0,0 +1,54 @@ +# Copyright 1999-2014 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/biopython/biopython-1.62.ebuild,v 1.1 2013/09/17 16:07:56 jlec Exp $ + +EAPI=5 + +PYTHON_COMPAT=( python{2_6,2_7} ) + +inherit distutils-r1 eutils + +DESCRIPTION="Python modules for computational molecular biology" +HOMEPAGE="http://www.biopython.org/ http://pypi.python.org/pypi/biopython/" +SRC_URI="http://www.biopython.org/DIST/${P}.tar.gz" + +LICENSE="HPND" +SLOT="0" +KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" +IUSE="mysql postgres" + +REQUIRED_USE="${PYTHON_REQUIRED_USE}" + +RDEPEND="${PYTHON_DEPS} + dev-python/matplotlib[${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[${PYTHON_USEDEP}] + media-gfx/pydot[${PYTHON_USEDEP}] + mysql? ( dev-python/mysql-python[${PYTHON_USEDEP}] ) + postgres? ( dev-python/psycopg[${PYTHON_USEDEP}] )" +DEPEND="${RDEPEND} + sys-devel/flex" + +DOCS=( CONTRIB DEPRECATED NEWS README Doc/. ) + +#src_prepare() { +# epatch "${FILESDIR}/SffIO_error_in_check_eof.patch" +# epatch "${FILESDIR}/SffIO_broken_padding.patch" +# epatch "${FILESDIR}/SffIO-crossed-trimpoints.patch" +# distutils-r1_src_prepare +#} + +python_test() { + cd Tests || die + ${PYTHON} run_tests.py || die +} + +python_install_all() { + distutils-r1_python_install_all + + dodir /usr/share/${PN} + cp -r --preserve=mode Scripts Tests "${ED}"/usr/share/${PN} || die +} diff --git a/sci-biology/biopython/metadata.xml b/sci-biology/biopython/metadata.xml new file mode 100644 index 0000000..f17a827 --- /dev/null +++ b/sci-biology/biopython/metadata.xml @@ -0,0 +1,5 @@ + + + + sci-biology +