[gentoo-commits] dev/dev-zero:master commit in: profiles/, sci-biology/biopython/

[gentoo-commits] dev/dev-zero:master commit in: profiles/, sci-biology/biopython/

[Tiziano Müller]

commit:     a040b84602dd0e14247d2467d148c4227ccc534a
Author:     Tiziano Müller <dev-zero <AT> gentoo <DOT> org>
AuthorDate: Sat Mar 26 14:58:27 2016 +0000
Commit:     Tiziano Müller <dev-zero <AT> gentoo <DOT> org>
CommitDate: Sat Mar 26 14:58:27 2016 +0000
URL:        https://gitweb.gentoo.org/dev/dev-zero.git/commit/?id=a040b846

sci-biology/biopython: add revbump for EAPI=6 and python-3.5 compat

 profiles/categories                            |  1 +
 sci-biology/biopython/Manifest                 |  2 +
 sci-biology/biopython/biopython-1.66-r1.ebuild | 56 ++++++++++++++++++++++++++
 sci-biology/biopython/metadata.xml             |  8 ++++
 4 files changed, 67 insertions(+)

diff --git a/profiles/categories b/profiles/categories
index 38fa978..a276bb0 100644
--- a/profiles/categories
+++ b/profiles/categories
@@ -86,3 +86,4 @@ sys-process
 app-i18n
 sci-chemistry
 sci-electronics
+sci-biology

diff --git a/sci-biology/biopython/Manifest b/sci-biology/biopython/Manifest
new file mode 100644
index 0000000..a54d05e
--- /dev/null
+++ b/sci-biology/biopython/Manifest
@@ -0,0 +1,2 @@
+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

diff --git a/sci-biology/biopython/biopython-1.66-r1.ebuild b/sci-biology/biopython/biopython-1.66-r1.ebuild
new file mode 100644
index 0000000..e32eccf
--- /dev/null
+++ b/sci-biology/biopython/biopython-1.66-r1.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 ./test_BioSQL_MySQLdb.py ./test_BioSQL_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
+	echo
+	elog "Some applications need extra packages:"
+	optfeature "EMBOSS (The European Molecular Biology Open Software Suite)" sci-biology/emboss
+}

diff --git a/sci-biology/biopython/metadata.xml b/sci-biology/biopython/metadata.xml
new file mode 100644
index 0000000..959160f
--- /dev/null
+++ b/sci-biology/biopython/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci-biology@gentoo.org</email>
+    <name>Gentoo Biology Project</name>
+  </maintainer>
+</pkgmetadata>