[gentoo-commits] proj/sci:master commit in: sci-biology/biopython/

[Martin Mokrejs]

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 <mmokrejs@×××××××××××××××.cz>
+  +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>