sci-biology/biopython: Bump to 1.71

Closes: https://bugs.gentoo.org/653006
Package-Manager: Portage-2.3.40, Repoman-2.3.9

diff --git a/sci-biology/biopython/Manifest b/sci-biology/biopython/Manifest
index 55331efbbcb8390ea55edadf0471b2bbe636ea92..70af7c92d44d2548fee2428fa0850886ec06ca2e 100644 (file)
--- a/sci-biology/biopython/Manifest
+++ b/sci-biology/biopython/Manifest
@@ -1 +1,2 @@
 DIST biopython-1.68.tar.gz 14445813 BLAKE2B 566931c4e522e95278f7f6a9dc07ecc091dc54b69cdea8bb07603339af4f1fd38e3df87482e97729acb776dd2df19a4e61d49ee7608ec5cb0f24966e28c2e3dd SHA512 0ca994475654bb68ff326c8e86cbd4547cd87b42e1633dda039ad668e1298884b22e169f6b25ab514e929861334a93b7db6d057a3486cea9997ca2de95c61a69
+DIST biopython-1.71.tar.gz 16031832 BLAKE2B 2062065b77fc35ea8a3f09ec967482c233a6e0bbfc7d09187ff5e892848b45fa7bd6d7b6027b38c3d4c9a9c601785521fa7edb91fa960b46c8e49aed91b1f5dc SHA512 003955e92295e98526c88abb573db9bdc37877fc41395551b541e7106ffa603327a36c6f4d999838c0be38b378901235c9dbd7cb7fc25c14a5d7001939fe23bd

diff --git a/sci-biology/biopython/biopython-1.71.ebuild b/sci-biology/biopython/biopython-1.71.ebuild
new file mode 100644 (file)
index 0000000..f770b57
--- /dev/null
+++ b/sci-biology/biopython/biopython-1.71.ebuild
@@ -0,0 +1,57 @@
+# Copyright 1999-2018 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python2_7 python3_{4,5,6} )
+
+inherit distutils-r1 eutils
+
+DESCRIPTION="Python modules for computational molecular biology"
+HOMEPAGE="https://www.biopython.org/ https://pypi.org/project/biopython/"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="HPND"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+RDEPEND="
+       dev-python/matplotlib[${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[${PYTHON_USEDEP}]
+       dev-python/pydot[${PYTHON_USEDEP}]"
+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
+       "${EPYTHON}" run_tests.py --offline --verbose || die
+}
+
+python_install_all() {
+       # remove files causing ecompressdir to fail
+       rm Doc/examples/ls_orchid.gbk.bz2 || die
+
+       distutils-r1_python_install_all
+
+       dodir /usr/share/${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 "Some applications need extra packages:"
+       optfeature "EMBOSS (The European Molecular Biology Open Software Suite)" sci-biology/emboss
+}