gentoo resync : 28.04.2019

4 files changed, 66 insertions, 6 deletions

diff --git a/sci-biology/biopython/Manifest b/sci-biology/biopython/Manifest
index 8d1a080b69ee..acc4141192b8 100644
--- a/sci-biology/biopython/Manifest
+++ b/sci-biology/biopython/Manifest
@@ -1,5 +1,7 @@
 DIST biopython-1.68.tar.gz 14445813 BLAKE2B 566931c4e522e95278f7f6a9dc07ecc091dc54b69cdea8bb07603339af4f1fd38e3df87482e97729acb776dd2df19a4e61d49ee7608ec5cb0f24966e28c2e3dd SHA512 0ca994475654bb68ff326c8e86cbd4547cd87b42e1633dda039ad668e1298884b22e169f6b25ab514e929861334a93b7db6d057a3486cea9997ca2de95c61a69
 DIST biopython-1.71.tar.gz 16031832 BLAKE2B 2062065b77fc35ea8a3f09ec967482c233a6e0bbfc7d09187ff5e892848b45fa7bd6d7b6027b38c3d4c9a9c601785521fa7edb91fa960b46c8e49aed91b1f5dc SHA512 003955e92295e98526c88abb573db9bdc37877fc41395551b541e7106ffa603327a36c6f4d999838c0be38b378901235c9dbd7cb7fc25c14a5d7001939fe23bd
-EBUILD biopython-1.68.ebuild 1641 BLAKE2B a66e9c4a4c4987809faa18742b345fad45c6c6e536c1a87dfc552345637f1b7df28426a314df4b2f7e523002229395e978b75548b907f0a7aac6d80ee893d1b3 SHA512 e30c9f8b542ef0508a6fea508461521cbdc140a0c1e1f08eddfaef6dd73c10496f1d2fdc26261c26a5c860ffba845c1e6bb6f82d8722d0c7a1a89253c3a7a7f1
-EBUILD biopython-1.71.ebuild 1621 BLAKE2B c880eb5d4bde244ee427a576400d5a3fb2703f85fe07a68949a4ff1b0fa7ac1def332cd67b12731bd3629e62ffef318ce55f0768300c20d05eda72fef82a594c SHA512 1c9147003fc3a47e515e94b89bb718e80358db9956382937b9e675240d08608ef57090013a824c7cf504b517697c182385a6073c7cb1e8037a439fde75ca3935
+DIST biopython-1.73.tar.gz 15715102 BLAKE2B b2c40f9ed02681f19607c88f91b469784985acefc6e81770a54e5c13c715915344bc7fd72e4a88ae50879a2463965ac6d0d04c6d263908887028d1e065620b95 SHA512 d067330ef8e25ca6881b56f4e5e89e16a816c89760473e2f32a6236ab202f805294650aa944f0b098987425bcb65727317da7a26deb4d4937f02b00123ea9a8f
+EBUILD biopython-1.68.ebuild 1634 BLAKE2B 43d435496fc239c847b19a4e66bf52f920454ee6fd810b94d0d32bde6381059abb9561f90d06e5d1ca83a80721958c6051f79d0c92e5b76dc8d930ed54254f78 SHA512 70b8d2a8f84f70edc6a6225a8958328d8657dbb8b01c0716b7b1c15320914e827129c30da32b670f6ba9ab4d24a8f6cf01ea728b5d14e1607e9cef5c35f7b47f
+EBUILD biopython-1.71.ebuild 1616 BLAKE2B e1e4b60cfe88dd00ef28135f137657147112249bc60738d145c5036bab3d1436878834f9ac03c829aa39c40696d0350d9ea98040be43e7f393752f9baf63ac21 SHA512 ae8fa77eefe2bb67c430bd6351a60e2a5d1e0193be4c8e6330f81edbac90b4730d5ec59b1bd25baf04452a9d8ea4f9b7550b703ecf20b1af9c9473b6465b2e5a
+EBUILD biopython-1.73.ebuild 1684 BLAKE2B c98e92b2e989b2a398912b1335049750565933b202cc1e1d77d83f1aa13071bb5dd1ce63ac37113a2bf03cc1394dcb7011fb2346728d3463c353460101b847a5 SHA512 b71c3acc6b6f97564b31b3bfc4a8fe47ad1c95fcd07f265964f3cf381ef3d2c2917d2bc2ef8446ef3290eaf447a1c77ff38fc7d1459694c8884dc45cd8350e9a
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/biopython/biopython-1.68.ebuild b/sci-biology/biopython/biopython-1.68.ebuild
index 9c8442e39090..f76da59c1b84 100644
--- a/sci-biology/biopython/biopython-1.68.ebuild
+++ b/sci-biology/biopython/biopython-1.68.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
 
-PYTHON_COMPAT=( python2_7 python3_{4,5} pypy )
+PYTHON_COMPAT=( python2_7 python3_5 pypy )
 
 inherit distutils-r1 eutils
 
diff --git a/sci-biology/biopython/biopython-1.71.ebuild b/sci-biology/biopython/biopython-1.71.ebuild
index 73a714248aea..8b9a0cd7112e 100644
--- a/sci-biology/biopython/biopython-1.71.ebuild
+++ b/sci-biology/biopython/biopython-1.71.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
 
-PYTHON_COMPAT=( python2_7 python3_{4,5,6} )
+PYTHON_COMPAT=( python2_7 python3_{5,6} )
 
 inherit distutils-r1 eutils
 
diff --git a/sci-biology/biopython/biopython-1.73.ebuild b/sci-biology/biopython/biopython-1.73.ebuild
new file mode 100644
index 000000000000..f0d335a5933a
--- /dev/null
+++ b/sci-biology/biopython/biopython-1.73.ebuild
@@ -0,0 +1,58 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python2_7 python3_{5,6,7} )
+
+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-3.5.13-r1[${PYTHON_USEDEP}]
+	dev-python/pydot[${PYTHON_USEDEP}]"
+DEPEND="${RDEPEND}
+	dev-python/setuptools[${PYTHON_USEDEP}]
+	sys-devel/flex"
+
+DOCS=( {CONTRIB,DEPRECATED,NEWS,README}.rst 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.{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
+}