commit: 6cbf10bd4d0104c5a03acc7bd54c1068e6b02de3
Author: David Seifert <soap <AT> gentoo <DOT> org>
AuthorDate: Fri Aug 21 23:20:44 2020 +0000
Commit: David Seifert <soap <AT> gentoo <DOT> org>
CommitDate: Fri Aug 21 23:20:44 2020 +0000
URL: https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=6cbf10bd
sci-biology/biopython: Version bump to 1.77
Package-Manager: Portage-3.0.4, Repoman-3.0.1
Signed-off-by: David Seifert <soap <AT> gentoo.org>
sci-biology/biopython/Manifest | 1 +
sci-biology/biopython/biopython-1.77.ebuild | 62 +++++++++++++++++++++++++++++
2 files changed, 63 insertions(+)
diff --git a/sci-biology/biopython/Manifest b/sci-biology/biopython/Manifest
index ee3ffae9c3f..cff73fbcbc3 100644
--- a/sci-biology/biopython/Manifest
+++ b/sci-biology/biopython/Manifest
@@ -1 +1,2 @@
DIST biopython-1.73.tar.gz 15715102 BLAKE2B
b2c40f9ed02681f19607c88f91b469784985acefc6e81770a54e5c13c715915344bc7fd72e4a88ae50879a2463965ac6d0d04c6d263908887028d1e065620b95
SHA512
d067330ef8e25ca6881b56f4e5e89e16a816c89760473e2f32a6236ab202f805294650aa944f0b098987425bcb65727317da7a26deb4d4937f02b00123ea9a8f
+DIST biopython-1.77.tar.gz 16837021 BLAKE2B
b5586f0ea3e476b11801dcc98039d5eea7b191e11d390192c0cf348018ded005fe2ad5dc9ba71c83aebc9cdde20c97244905dcc3aeb5436a97588da9f8c79c3e
SHA512
6f4b03d46c591e1f49dd1e76bcc4ac5c9aaa2bf748c9dd37ffc5de5a613fbeed38f89b418c01601dd99c65b13b2e294bc8d81ffafc42a9ff1b309c84f840d0d5
diff --git a/sci-biology/biopython/biopython-1.77.ebuild
b/sci-biology/biopython/biopython-1.77.ebuild
new file mode 100644
index 00000000000..486e9fe694d
--- /dev/null
+++ b/sci-biology/biopython/biopython-1.77.ebuild
@@ -0,0 +1,62 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python3_{6..9} )
+
+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}/${P}.tar.gz"
+
+LICENSE="HPND"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+
+RDEPEND="
+ dev-python/matplotlib[${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-3.5.13-r1[${PYTHON_USEDEP}]
+ dev-python/pydot[${PYTHON_USEDEP}]"
+DEPEND="${RDEPEND}"
+BDEPEND="sys-devel/flex"
+
+DOCS=( {CONTRIB,DEPRECATED,NEWS,README}.rst Doc/. )
+
+python_test() {
+ distutils_install_for_testing
+ cp -r {Doc,Tests} "${TEST_DIR}"/lib/ || die
+
+ # need to create symlinks for doctests
+ mkdir -p "${TEST_DIR}"/lib/Bio/Align/substitution_matrices || die
+ ln -r -s "${S}"/Bio/Align/substitution_matrices/data \
+ "${TEST_DIR}"/lib/Bio/Align/substitution_matrices/data || die
+
+ cd "${TEST_DIR}"/lib/Tests || die
+ rm test_BioSQL_{psycopg2.py,MySQLdb.py,mysql_connector.py} || die
+ "${EPYTHON}" run_tests.py --offline --verbose || die
+}
+
+python_install_all() {
+ # remove files causing ecompressdir to fail
+ rm Doc/examples/ls_orchid.gbk.{gz,bz2} || die
+
+ distutils-r1_python_install_all
+
+ dodir /usr/share/${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
+}
