commit: 10c67b74e2889910c6b679fbdaccbb3326adc635 Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz> AuthorDate: Tue Jun 3 00:23:59 2014 +0000 Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> 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 <[email protected]> + +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 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd";> +<pkgmetadata> + <herd>sci-biology</herd> +</pkgmetadata>
