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

2023-04-16 Thread David Seifert 
commit: a41f49e0eec39e31152d2829b0131417cb86850c
Author: David Seifert  gentoo  org>
AuthorDate: Sun Apr 16 12:35:20 2023 +
Commit: David Seifert  gentoo  org>
CommitDate: Sun Apr 16 12:35:20 2023 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=a41f49e0

sci-biology/biopython: drop 1.79

Signed-off-by: David Seifert  gentoo.org>

 sci-biology/biopython/Manifest  |  1 -
 sci-biology/biopython/biopython-1.79.ebuild | 62 -
 2 files changed, 63 deletions(-)

diff --git a/sci-biology/biopython/Manifest b/sci-biology/biopython/Manifest
index c693a5a8a963..0c16022dea2c 100644
--- a/sci-biology/biopython/Manifest
+++ b/sci-biology/biopython/Manifest
@@ -1,2 +1 @@
-DIST biopython-1.79.tar.gz 16738730 BLAKE2B 
8c97fc23e458f7bc98b0ed0226bd6fb42f6c6f3ce03d562b13fac66c5061451595cd5bd01cad07bbe1fc6b20f4de21b0f03766b5a20e602545da888047a57185
 SHA512 
81e2718f4015bb038637b4d1181e6bea48018fec1e769c5f0ab75442a769336899191f1222e82e1b9569c1fac470500d7582420e5cbe9bce0056b41751adeaaa
 DIST biopython-1.81.tar.gz 19324875 BLAKE2B 
be3a85f5b60638987d6186af498411b494f8d27389f24cd1b9e658bc6b1a29c799ec8b20a9ac0b955c6d4c239706f4dbb5b75f6d56908f63d731b1d56c9fd587
 SHA512 
1595fad6631bfb6cf4e1a92ed72e6093e2a0c24f3c0bd4182267ec9742fb03dff16099eedde139598aa6b5b8380bbac9e48246cb9ab8b44109333d60adfd00ed

diff --git a/sci-biology/biopython/biopython-1.79.ebuild 
b/sci-biology/biopython/biopython-1.79.ebuild
deleted file mode 100644
index c6a93b3af58d..
--- a/sci-biology/biopython/biopython-1.79.ebuild
+++ /dev/null
@@ -1,62 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{9..10} )
-
-inherit distutils-r1 optfeature
-
-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 "${TEST_DIR}"/lib/Bio/Align || die
-   ln -r -s "${S}"/Bio/Align/substitution_matrices \
-   "${TEST_DIR}"/lib/Bio/Align/substitution_matrices || die
-
-   cd "${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() {
-   optfeature_header "For database support you need to install:"
-   optfeature "MySQL database support" dev-python/mysqlclient
-   optfeature "PostgreSQL database support" dev-python/psycopg:2
-
-   optfeature_header "Some applications need extra packages:"
-   optfeature "EMBOSS (The European Molecular Biology Open Software 
Suite)" sci-biology/emboss
-}

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

2023-02-23 Thread Andrew Ammerlaan 
commit: d0d613f06aae55ab73f71229d00724034ca3c765
Author: Andrew Ammerlaan  gentoo  org>
AuthorDate: Fri Feb 24 07:10:27 2023 +
Commit: Andrew Ammerlaan  gentoo  org>
CommitDate: Fri Feb 24 07:10:27 2023 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=d0d613f0

sci-biology/biopython: add 1.81

Signed-off-by: Andrew Ammerlaan  gentoo.org>

 sci-biology/biopython/Manifest  |  1 +
 sci-biology/biopython/biopython-1.81.ebuild | 61 +
 2 files changed, 62 insertions(+)

diff --git a/sci-biology/biopython/Manifest b/sci-biology/biopython/Manifest
index 014c48aa8401..c693a5a8a963 100644
--- a/sci-biology/biopython/Manifest
+++ b/sci-biology/biopython/Manifest
@@ -1 +1,2 @@
 DIST biopython-1.79.tar.gz 16738730 BLAKE2B 
8c97fc23e458f7bc98b0ed0226bd6fb42f6c6f3ce03d562b13fac66c5061451595cd5bd01cad07bbe1fc6b20f4de21b0f03766b5a20e602545da888047a57185
 SHA512 
81e2718f4015bb038637b4d1181e6bea48018fec1e769c5f0ab75442a769336899191f1222e82e1b9569c1fac470500d7582420e5cbe9bce0056b41751adeaaa
+DIST biopython-1.81.tar.gz 19324875 BLAKE2B 
be3a85f5b60638987d6186af498411b494f8d27389f24cd1b9e658bc6b1a29c799ec8b20a9ac0b955c6d4c239706f4dbb5b75f6d56908f63d731b1d56c9fd587
 SHA512 
1595fad6631bfb6cf4e1a92ed72e6093e2a0c24f3c0bd4182267ec9742fb03dff16099eedde139598aa6b5b8380bbac9e48246cb9ab8b44109333d60adfd00ed

diff --git a/sci-biology/biopython/biopython-1.81.ebuild 
b/sci-biology/biopython/biopython-1.81.ebuild
new file mode 100644
index ..8b90d610c6ae
--- /dev/null
+++ b/sci-biology/biopython/biopython-1.81.ebuild
@@ -0,0 +1,61 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{9..11} )
+
+inherit distutils-r1 optfeature pypi
+
+DESCRIPTION="Python modules for computational molecular biology"
+HOMEPAGE="https://www.biopython.org/ https://pypi.org/project/biopython/;
+
+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 || die
+   ln -r -s "${S}"/Bio/Align/substitution_matrices \
+   "${TEST_DIR}"/lib/Bio/Align/substitution_matrices || 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() {
+   optfeature_header "For database support you need to install:"
+   optfeature "MySQL database support" dev-python/mysqlclient
+   optfeature "PostgreSQL database support" dev-python/psycopg:2
+
+   optfeature_header "Some applications need extra packages:"
+   optfeature "EMBOSS (The European Molecular Biology Open Software 
Suite)" sci-biology/emboss
+}

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

2022-06-04 Thread Michał Górny 
commit: 09c5ece62c0bca2fbcb4f39162b25862f4c10d83
Author: Michał Górny  gentoo  org>
AuthorDate: Sat Jun  4 07:08:05 2022 +
Commit: Michał Górny  gentoo  org>
CommitDate: Sat Jun  4 07:41:58 2022 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=09c5ece6

sci-biology/biopython: Use slot for dev-python/psycopg

Signed-off-by: Michał Górny  gentoo.org>

 sci-biology/biopython/biopython-1.79.ebuild | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-biology/biopython/biopython-1.79.ebuild 
b/sci-biology/biopython/biopython-1.79.ebuild
index cef9a670130a..a2939330806e 100644
--- a/sci-biology/biopython/biopython-1.79.ebuild
+++ b/sci-biology/biopython/biopython-1.79.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2021 Gentoo Authors
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=8
@@ -55,7 +55,7 @@ python_install_all() {
 pkg_postinst() {
optfeature_header "For database support you need to install:"
optfeature "MySQL database support" dev-python/mysqlclient
-   optfeature "PostgreSQL database support" dev-python/psycopg
+   optfeature "PostgreSQL database support" dev-python/psycopg:2
 
optfeature_header "Some applications need extra packages:"
optfeature "EMBOSS (The European Molecular Biology Open Software 
Suite)" sci-biology/emboss

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

2021-12-30 Thread David Seifert 
commit: 3ca7e670a753666e8f51fc8f34f038bf18e07a69
Author: David Seifert  gentoo  org>
AuthorDate: Thu Dec 30 18:12:11 2021 +
Commit: David Seifert  gentoo  org>
CommitDate: Thu Dec 30 18:12:11 2021 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=3ca7e670

sci-biology/biopython: drop 1.77

Closes: https://bugs.gentoo.org/757867
Closes: https://bugs.gentoo.org/780345
Signed-off-by: David Seifert  gentoo.org>

 sci-biology/biopython/Manifest  |  1 -
 sci-biology/biopython/biopython-1.77.ebuild | 61 -
 2 files changed, 62 deletions(-)

diff --git a/sci-biology/biopython/Manifest b/sci-biology/biopython/Manifest
index 9bc0eede97dc..014c48aa8401 100644
--- a/sci-biology/biopython/Manifest
+++ b/sci-biology/biopython/Manifest
@@ -1,2 +1 @@
-DIST biopython-1.77.tar.gz 16837021 BLAKE2B 
b5586f0ea3e476b11801dcc98039d5eea7b191e11d390192c0cf348018ded005fe2ad5dc9ba71c83aebc9cdde20c97244905dcc3aeb5436a97588da9f8c79c3e
 SHA512 
6f4b03d46c591e1f49dd1e76bcc4ac5c9aaa2bf748c9dd37ffc5de5a613fbeed38f89b418c01601dd99c65b13b2e294bc8d81ffafc42a9ff1b309c84f840d0d5
 DIST biopython-1.79.tar.gz 16738730 BLAKE2B 
8c97fc23e458f7bc98b0ed0226bd6fb42f6c6f3ce03d562b13fac66c5061451595cd5bd01cad07bbe1fc6b20f4de21b0f03766b5a20e602545da888047a57185
 SHA512 
81e2718f4015bb038637b4d1181e6bea48018fec1e769c5f0ab75442a769336899191f1222e82e1b9569c1fac470500d7582420e5cbe9bce0056b41751adeaaa

diff --git a/sci-biology/biopython/biopython-1.77.ebuild 
b/sci-biology/biopython/biopython-1.77.ebuild
deleted file mode 100644
index 1dcbc2101c45..
--- a/sci-biology/biopython/biopython-1.77.ebuild
+++ /dev/null
@@ -1,61 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7..9} )
-
-inherit distutils-r1 optfeature
-
-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() {
-   optfeature_header "For database support you need to install:"
-   optfeature "MySQL database support" dev-python/mysql-python
-   optfeature "PostgreSQL database support" dev-python/psycopg
-   optfeature_header "Some applications need extra packages:"
-   optfeature "EMBOSS (The European Molecular Biology Open Software 
Suite)" sci-biology/emboss
-}

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

2021-12-20 Thread David Seifert 
commit: de858ae7cf457b2ef508edce83f809403346ac0f
Author: David Seifert  gentoo  org>
AuthorDate: Mon Dec 20 13:32:52 2021 +
Commit: David Seifert  gentoo  org>
CommitDate: Mon Dec 20 13:32:52 2021 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=de858ae7

sci-biology/biopython: add 1.79

Bug: https://bugs.gentoo.org/757867
Bug: https://bugs.gentoo.org/780345
Signed-off-by: David Seifert  gentoo.org>

 sci-biology/biopython/Manifest  |  1 +
 sci-biology/biopython/biopython-1.79.ebuild | 62 +
 2 files changed, 63 insertions(+)

diff --git a/sci-biology/biopython/Manifest b/sci-biology/biopython/Manifest
index 420f6d1f83d8..9bc0eede97dc 100644
--- a/sci-biology/biopython/Manifest
+++ b/sci-biology/biopython/Manifest
@@ -1 +1,2 @@
 DIST biopython-1.77.tar.gz 16837021 BLAKE2B 
b5586f0ea3e476b11801dcc98039d5eea7b191e11d390192c0cf348018ded005fe2ad5dc9ba71c83aebc9cdde20c97244905dcc3aeb5436a97588da9f8c79c3e
 SHA512 
6f4b03d46c591e1f49dd1e76bcc4ac5c9aaa2bf748c9dd37ffc5de5a613fbeed38f89b418c01601dd99c65b13b2e294bc8d81ffafc42a9ff1b309c84f840d0d5
+DIST biopython-1.79.tar.gz 16738730 BLAKE2B 
8c97fc23e458f7bc98b0ed0226bd6fb42f6c6f3ce03d562b13fac66c5061451595cd5bd01cad07bbe1fc6b20f4de21b0f03766b5a20e602545da888047a57185
 SHA512 
81e2718f4015bb038637b4d1181e6bea48018fec1e769c5f0ab75442a769336899191f1222e82e1b9569c1fac470500d7582420e5cbe9bce0056b41751adeaaa

diff --git a/sci-biology/biopython/biopython-1.79.ebuild 
b/sci-biology/biopython/biopython-1.79.ebuild
new file mode 100644
index ..cef9a670130a
--- /dev/null
+++ b/sci-biology/biopython/biopython-1.79.ebuild
@@ -0,0 +1,62 @@
+# Copyright 1999-2021 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{8..10} )
+
+inherit distutils-r1 optfeature
+
+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 "${TEST_DIR}"/lib/Bio/Align || die
+   ln -r -s "${S}"/Bio/Align/substitution_matrices \
+   "${TEST_DIR}"/lib/Bio/Align/substitution_matrices || die
+
+   cd "${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() {
+   optfeature_header "For database support you need to install:"
+   optfeature "MySQL database support" dev-python/mysqlclient
+   optfeature "PostgreSQL database support" dev-python/psycopg
+
+   optfeature_header "Some applications need extra packages:"
+   optfeature "EMBOSS (The European Molecular Biology Open Software 
Suite)" sci-biology/emboss
+}

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

2021-04-04 Thread Andreas Sturmlechner 
commit: 4cfced047715b0602b68bb064f16e2882165c77f
Author: Andreas Sturmlechner  gentoo  org>
AuthorDate: Sat Apr  3 11:05:35 2021 +
Commit: Andreas Sturmlechner  gentoo  org>
CommitDate: Sun Apr  4 18:55:06 2021 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=4cfced04

sci-biology/biopython: Use optfeature_header() instead of custom elog

Signed-off-by: Andreas Sturmlechner  gentoo.org>

 sci-biology/biopython/biopython-1.77.ebuild | 11 +--
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/sci-biology/biopython/biopython-1.77.ebuild 
b/sci-biology/biopython/biopython-1.77.ebuild
index 387404a1aed..1dcbc2101c4 100644
--- a/sci-biology/biopython/biopython-1.77.ebuild
+++ b/sci-biology/biopython/biopython-1.77.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
@@ -53,10 +53,9 @@ python_install_all() {
 }
 
 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_header "For database support you need to install:"
+   optfeature "MySQL database support" dev-python/mysql-python
+   optfeature "PostgreSQL database support" dev-python/psycopg
+   optfeature_header "Some applications need extra packages:"
optfeature "EMBOSS (The European Molecular Biology Open Software 
Suite)" sci-biology/emboss
 }

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

2020-09-07 Thread David Seifert 
commit: 395db0fe0b9edde5afb9ffd612e3f1b31cfc49fc
Author: David Seifert  gentoo  org>
AuthorDate: Mon Sep  7 08:53:45 2020 +
Commit: David Seifert  gentoo  org>
CommitDate: Mon Sep  7 08:53:45 2020 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=395db0fe

sci-biology/biopython: Inherit optfeature.eclass

Package-Manager: Portage-3.0.5, Repoman-3.0.1
Signed-off-by: David Seifert  gentoo.org>

 sci-biology/biopython/biopython-1.77.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/biopython/biopython-1.77.ebuild 
b/sci-biology/biopython/biopython-1.77.ebuild
index 486e9fe694d..a25abc9312c 100644
--- a/sci-biology/biopython/biopython-1.77.ebuild
+++ b/sci-biology/biopython/biopython-1.77.ebuild
@@ -5,7 +5,7 @@ EAPI=7
 
 PYTHON_COMPAT=( python3_{6..9} )
 
-inherit distutils-r1 eutils
+inherit distutils-r1 optfeature
 
 DESCRIPTION="Python modules for computational molecular biology"
 HOMEPAGE="https://www.biopython.org/ https://pypi.org/project/biopython/;

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

2020-08-22 Thread David Seifert 
commit: 422ca7a3d7fbb0f7e0a63a4f19934281226dcc49
Author: David Seifert  gentoo  org>
AuthorDate: Sat Aug 22 12:06:34 2020 +
Commit: David Seifert  gentoo  org>
CommitDate: Sat Aug 22 12:06:34 2020 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=422ca7a3

sci-biology/biopython: Remove old 1.73

Package-Manager: Portage-3.0.4, Repoman-3.0.1
Signed-off-by: David Seifert  gentoo.org>

 sci-biology/biopython/Manifest  |  1 -
 sci-biology/biopython/biopython-1.73.ebuild | 57 -
 2 files changed, 58 deletions(-)

diff --git a/sci-biology/biopython/Manifest b/sci-biology/biopython/Manifest
index cff73fbcbc3..420f6d1f83d 100644
--- a/sci-biology/biopython/Manifest
+++ b/sci-biology/biopython/Manifest
@@ -1,2 +1 @@
-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-1.73.ebuild 
b/sci-biology/biopython/biopython-1.73.ebuild
deleted file mode 100644
index 94acdfc2a2c..000
--- a/sci-biology/biopython/biopython-1.73.ebuild
+++ /dev/null
@@ -1,57 +0,0 @@
-# Copyright 1999-2020 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{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
-}

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

2020-08-21 Thread David Seifert 
commit: 6cbf10bd4d0104c5a03acc7bd54c1068e6b02de3
Author: David Seifert  gentoo  org>
AuthorDate: Fri Aug 21 23:20:44 2020 +
Commit: David Seifert  gentoo  org>
CommitDate: Fri Aug 21 23:20:44 2020 +
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  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 000..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
+}

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

2019-12-29 Thread Andreas Sturmlechner 
commit: d2f6030aec456c8d6dd692b1d1bd90269e607544
Author: Andreas Sturmlechner  gentoo  org>
AuthorDate: Sat Dec 28 16:48:55 2019 +
Commit: Andreas Sturmlechner  gentoo  org>
CommitDate: Sun Dec 29 13:22:56 2019 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=d2f6030a

sci-biology/biopython: Drop python2_7

Package-Manager: Portage-2.3.84, Repoman-2.3.20
Signed-off-by: Andreas Sturmlechner  gentoo.org>

 sci-biology/biopython/biopython-1.73.ebuild | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/sci-biology/biopython/biopython-1.73.ebuild 
b/sci-biology/biopython/biopython-1.73.ebuild
index f0d335a5933..340130b54c7 100644
--- a/sci-biology/biopython/biopython-1.73.ebuild
+++ b/sci-biology/biopython/biopython-1.73.ebuild
@@ -3,8 +3,7 @@
 
 EAPI=7
 
-PYTHON_COMPAT=( python2_7 python3_{5,6,7} )
-
+PYTHON_COMPAT=( python3_{5,6,7} )
 inherit distutils-r1 eutils
 
 DESCRIPTION="Python modules for computational molecular biology"

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

2019-12-29 Thread David Seifert 
commit: 73c3e34900c4f49a05e4445033a21900b04e626e
Author: David Seifert  gentoo  org>
AuthorDate: Sun Dec 29 08:53:09 2019 +
Commit: David Seifert  gentoo  org>
CommitDate: Sun Dec 29 08:53:09 2019 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=73c3e349

sci-biology/biopython: Remove old

Package-Manager: Portage-2.3.83, Repoman-2.3.20
Signed-off-by: David Seifert  gentoo.org>

 sci-biology/biopython/Manifest  |  2 -
 sci-biology/biopython/biopython-1.68.ebuild | 55 
 sci-biology/biopython/biopython-1.71.ebuild | 57 -
 3 files changed, 114 deletions(-)

diff --git a/sci-biology/biopython/Manifest b/sci-biology/biopython/Manifest
index 02d90810dc5..ee3ffae9c3f 100644
--- a/sci-biology/biopython/Manifest
+++ b/sci-biology/biopython/Manifest
@@ -1,3 +1 @@
-DIST biopython-1.68.tar.gz 14445813 BLAKE2B 
566931c4e522e95278f7f6a9dc07ecc091dc54b69cdea8bb07603339af4f1fd38e3df87482e97729acb776dd2df19a4e61d49ee7608ec5cb0f24966e28c2e3dd
 SHA512 
0ca994475654bb68ff326c8e86cbd4547cd87b42e1633dda039ad668e1298884b22e169f6b25ab514e929861334a93b7db6d057a3486cea9997ca2de95c61a69
-DIST biopython-1.71.tar.gz 16031832 BLAKE2B 
2062065b77fc35ea8a3f09ec967482c233a6e0bbfc7d09187ff5e892848b45fa7bd6d7b6027b38c3d4c9a9c601785521fa7edb91fa960b46c8e49aed91b1f5dc
 SHA512 
003955e92295e98526c88abb573db9bdc37877fc41395551b541e7106ffa603327a36c6f4d999838c0be38b378901235c9dbd7cb7fc25c14a5d7001939fe23bd
 DIST biopython-1.73.tar.gz 15715102 BLAKE2B 
b2c40f9ed02681f19607c88f91b469784985acefc6e81770a54e5c13c715915344bc7fd72e4a88ae50879a2463965ac6d0d04c6d263908887028d1e065620b95
 SHA512 
d067330ef8e25ca6881b56f4e5e89e16a816c89760473e2f32a6236ab202f805294650aa944f0b098987425bcb65727317da7a26deb4d4937f02b00123ea9a8f

diff --git a/sci-biology/biopython/biopython-1.68.ebuild 
b/sci-biology/biopython/biopython-1.68.ebuild
deleted file mode 100644
index f76da59c1b8..000
--- a/sci-biology/biopython/biopython-1.68.ebuild
+++ /dev/null
@@ -1,55 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 python3_5 pypy )
-
-inherit distutils-r1 eutils
-
-DESCRIPTION="Python modules for computational molecular biology"
-HOMEPAGE="http://www.biopython.org/ https://pypi.org/project/biopython/;
-SRC_URI="http://www.biopython.org/DIST/${P}.tar.gz;
-
-LICENSE="HPND"
-SLOT="0"
-KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
-IUSE=""
-
-RDEPEND="
-   dev-python/matplotlib[$(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[$(python_gen_usedep 'python*')]
-   dev-python/pydot[$(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,MySQLdb.py,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
-   elog
-   elog "Some applications need extra packages:"
-   optfeature "EMBOSS (The European Molecular Biology Open Software 
Suite)" sci-biology/emboss
-}

diff --git a/sci-biology/biopython/biopython-1.71.ebuild 
b/sci-biology/biopython/biopython-1.71.ebuild
deleted file mode 100644
index 8b9a0cd7112..000
--- a/sci-biology/biopython/biopython-1.71.ebuild
+++ /dev/null
@@ -1,57 +0,0 @@
-# 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} )
-
-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

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

2019-04-21 Thread David Seifert 
commit: 2838d71e279cd5d3975c88bc52d2ee43bf820f50
Author: David Seifert  gentoo  org>
AuthorDate: Sun Apr 21 12:19:03 2019 +
Commit: David Seifert  gentoo  org>
CommitDate: Sun Apr 21 12:19:03 2019 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=2838d71e

sci-biology/biopython: Bump to version 1.73

Package-Manager: Portage-2.3.62, Repoman-2.3.12
Signed-off-by: David Seifert  gentoo.org>

 sci-biology/biopython/Manifest  |  1 +
 sci-biology/biopython/biopython-1.73.ebuild | 58 +
 2 files changed, 59 insertions(+)

diff --git a/sci-biology/biopython/Manifest b/sci-biology/biopython/Manifest
index 70af7c92d44..02d90810dc5 100644
--- a/sci-biology/biopython/Manifest
+++ b/sci-biology/biopython/Manifest
@@ -1,2 +1,3 @@
 DIST biopython-1.68.tar.gz 14445813 BLAKE2B 
566931c4e522e95278f7f6a9dc07ecc091dc54b69cdea8bb07603339af4f1fd38e3df87482e97729acb776dd2df19a4e61d49ee7608ec5cb0f24966e28c2e3dd
 SHA512 
0ca994475654bb68ff326c8e86cbd4547cd87b42e1633dda039ad668e1298884b22e169f6b25ab514e929861334a93b7db6d057a3486cea9997ca2de95c61a69
 DIST biopython-1.71.tar.gz 16031832 BLAKE2B 
2062065b77fc35ea8a3f09ec967482c233a6e0bbfc7d09187ff5e892848b45fa7bd6d7b6027b38c3d4c9a9c601785521fa7edb91fa960b46c8e49aed91b1f5dc
 SHA512 
003955e92295e98526c88abb573db9bdc37877fc41395551b541e7106ffa603327a36c6f4d999838c0be38b378901235c9dbd7cb7fc25c14a5d7001939fe23bd
+DIST biopython-1.73.tar.gz 15715102 BLAKE2B 
b2c40f9ed02681f19607c88f91b469784985acefc6e81770a54e5c13c715915344bc7fd72e4a88ae50879a2463965ac6d0d04c6d263908887028d1e065620b95
 SHA512 
d067330ef8e25ca6881b56f4e5e89e16a816c89760473e2f32a6236ab202f805294650aa944f0b098987425bcb65727317da7a26deb4d4937f02b00123ea9a8f

diff --git a/sci-biology/biopython/biopython-1.73.ebuild 
b/sci-biology/biopython/biopython-1.73.ebuild
new file mode 100644
index 000..f0d335a5933
--- /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
+}

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

2018-07-01 Thread Pacho Ramos 
commit: 1a6fc78f6c7bb3bfce5c0f56ccd72a62ff116e02
Author: Pacho Ramos  gentoo  org>
AuthorDate: Sun Jul  1 15:16:32 2018 +
Commit: Pacho Ramos  gentoo  org>
CommitDate: Sun Jul  1 15:19:30 2018 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=1a6fc78f

sci-biology/biopython: amd64 stable, bug #659292

Package-Manager: Portage-2.3.41, Repoman-2.3.9

 sci-biology/biopython/biopython-1.71.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/biopython/biopython-1.71.ebuild 
b/sci-biology/biopython/biopython-1.71.ebuild
index f770b57a2a6..222bf460e3e 100644
--- a/sci-biology/biopython/biopython-1.71.ebuild
+++ b/sci-biology/biopython/biopython-1.71.ebuild
@@ -13,7 +13,7 @@ SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
 
 LICENSE="HPND"
 SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+KEYWORDS="amd64 ~x86 ~amd64-linux ~x86-linux"
 IUSE=""
 
 RDEPEND="

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

2018-05-27 Thread David Seifert 
commit: 31a70e941154558bcf8afe94c3dd16c90d4f4e40
Author: David Seifert  gentoo  org>
AuthorDate: Sun May 27 14:31:03 2018 +
Commit: David Seifert  gentoo  org>
CommitDate: Sun May 27 14:31:36 2018 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=31a70e94

sci-biology/biopython: Bump to 1.71

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

 sci-biology/biopython/Manifest  |  1 +
 sci-biology/biopython/biopython-1.71.ebuild | 57 +
 2 files changed, 58 insertions(+)

diff --git a/sci-biology/biopython/Manifest b/sci-biology/biopython/Manifest
index 55331efbbcb..70af7c92d44 100644
--- 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
index 000..f770b57a2a6
--- /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
+}

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

2017-02-02 Thread David Seifert 
commit: 96a447fb3d267e8df35abca48f8bdf3cb3ba0627
Author: David Seifert  gentoo  org>
AuthorDate: Thu Feb  2 18:18:30 2017 +
Commit: David Seifert  gentoo  org>
CommitDate: Thu Feb  2 18:43:17 2017 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=96a447fb

sci-biology/biopython: Remove ppc from KEYWORDS

Package-Manager: Portage-2.3.3, Repoman-2.3.1
Closes: https://github.com/gentoo/gentoo/pull/3766

 sci-biology/biopython/biopython-1.68.ebuild | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/biopython/biopython-1.68.ebuild 
b/sci-biology/biopython/biopython-1.68.ebuild
index 5bf6fa6..8a75334 100644
--- a/sci-biology/biopython/biopython-1.68.ebuild
+++ b/sci-biology/biopython/biopython-1.68.ebuild
@@ -14,7 +14,7 @@ SRC_URI="http://www.biopython.org/DIST/${P}.tar.gz;
 
 LICENSE="HPND"
 SLOT="0"
-KEYWORDS="amd64 ppc x86 ~amd64-linux ~x86-linux"
+KEYWORDS="amd64 x86 ~amd64-linux ~x86-linux"
 IUSE=""
 
 RDEPEND="

[gentoo-commits] repo/gentoo:master commit in: sci-biology/biopython/files/, sci-biology/biopython/

2017-01-02 Thread Justin Lecher 
commit: 8ffc5a1942e322e42d57a77eb5d89a9a15501ae9
Author: Justin Lecher  gentoo  org>
AuthorDate: Mon Jan  2 21:51:34 2017 +
Commit: Justin Lecher  gentoo  org>
CommitDate: Mon Jan  2 22:09:05 2017 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=8ffc5a19

sci-biology/biopython: Drop old

Package-Manager: Portage-2.3.3, Repoman-2.3.1
Signed-off-by: Justin Lecher  gentoo.org>

 sci-biology/biopython/Manifest |  2 -
 sci-biology/biopython/biopython-1.65.ebuild| 56 --
 sci-biology/biopython/biopython-1.66.ebuild| 56 --
 .../files/biopython-1.65-test-fix-backport.patch   | 40 
 4 files changed, 154 deletions(-)

diff --git a/sci-biology/biopython/Manifest b/sci-biology/biopython/Manifest
index 9e5a8d9..415ede8 100644
--- a/sci-biology/biopython/Manifest
+++ b/sci-biology/biopython/Manifest
@@ -1,3 +1 @@
-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
 DIST biopython-1.68.tar.gz 14445813 SHA256 
d1dc09d1ddc8e90833f507cf09f80fa9ee1537d319058d1c44fe9c09be3d0c1f SHA512 
0ca994475654bb68ff326c8e86cbd4547cd87b42e1633dda039ad668e1298884b22e169f6b25ab514e929861334a93b7db6d057a3486cea9997ca2de95c61a69
 WHIRLPOOL 
9348354d0063efe0f9051f46e3be60540c5df21a43c094d74e64d37279736921d890cd639c904336eb21b2996e9948b8a050017b77569d2333ac80aa5b8bf156

diff --git a/sci-biology/biopython/biopython-1.65.ebuild 
b/sci-biology/biopython/biopython-1.65.ebuild
deleted file mode 100644
index 64bb66c..
--- a/sci-biology/biopython/biopython-1.65.ebuild
+++ /dev/null
@@ -1,56 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 python3_4 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="${RDEPEND}
-   sys-devel/flex"
-
-DOCS=( CONTRIB DEPRECATED NEWS README Doc/. )
-
-PATCHES=( "${FILESDIR}"/${P}-test-fix-backport.patch )
-
-python_test() {
-   [[ ${EPYTHON} == pypy ]] && return
-   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
-}
-
-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/biopython-1.66.ebuild 
b/sci-biology/biopython/biopython-1.66.ebuild
deleted file mode 100644
index 1e6a2a4..
--- a/sci-biology/biopython/biopython-1.66.ebuild
+++ /dev/null
@@ -1,56 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=5
-
-PYTHON_COMPAT=( python2_7 python3_{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*')]

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

2016-09-03 Thread David Seifert 
commit: 7440b9fd9976ffc4cbca598082c9e52f541040c8
Author: David Seifert  gentoo  org>
AuthorDate: Sat Sep  3 11:24:35 2016 +
Commit: David Seifert  gentoo  org>
CommitDate: Sat Sep  3 11:24:52 2016 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=7440b9fd

sci-biology/biopython: Version bump

Package-Manager: portage-2.3.0

 sci-biology/biopython/Manifest  |  1 +
 sci-biology/biopython/biopython-1.68.ebuild | 56 +
 2 files changed, 57 insertions(+)

diff --git a/sci-biology/biopython/Manifest b/sci-biology/biopython/Manifest
index a54d05e..9e5a8d9 100644
--- a/sci-biology/biopython/Manifest
+++ b/sci-biology/biopython/Manifest
@@ -1,2 +1,3 @@
 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
+DIST biopython-1.68.tar.gz 14445813 SHA256 
d1dc09d1ddc8e90833f507cf09f80fa9ee1537d319058d1c44fe9c09be3d0c1f SHA512 
0ca994475654bb68ff326c8e86cbd4547cd87b42e1633dda039ad668e1298884b22e169f6b25ab514e929861334a93b7db6d057a3486cea9997ca2de95c61a69
 WHIRLPOOL 
9348354d0063efe0f9051f46e3be60540c5df21a43c094d74e64d37279736921d890cd639c904336eb21b2996e9948b8a050017b77569d2333ac80aa5b8bf156

diff --git a/sci-biology/biopython/biopython-1.68.ebuild 
b/sci-biology/biopython/biopython-1.68.ebuild
new file mode 100644
index ..265181c
--- /dev/null
+++ b/sci-biology/biopython/biopython-1.68.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,MySQLdb.py,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
+   elog
+   elog "Some applications need extra packages:"
+   optfeature "EMBOSS (The European Molecular Biology Open Software 
Suite)" sci-biology/emboss
+}

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

2016-03-27 Thread David Seifert 
commit: 3263d4e22681ee9a7061e72ae43e031edf23141b
Author: David Seifert  gentoo  org>
AuthorDate: Sun Mar 27 17:43:36 2016 +
Commit: David Seifert  gentoo  org>
CommitDate: Sun Mar 27 17:44:07 2016 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=3263d4e2

sci-biology/biopython: Add python3_5 support

Package-Manager: portage-2.2.28

 sci-biology/biopython/biopython-1.66.ebuild | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-biology/biopython/biopython-1.66.ebuild 
b/sci-biology/biopython/biopython-1.66.ebuild
index d5c5fb6..f791b83 100644
--- a/sci-biology/biopython/biopython-1.66.ebuild
+++ b/sci-biology/biopython/biopython-1.66.ebuild
@@ -1,10 +1,10 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
 EAPI=5
 
-PYTHON_COMPAT=( python2_7 python3_{3,4} pypy )
+PYTHON_COMPAT=( python2_7 python3_{3,4,5} pypy )
 
 inherit distutils-r1 eutils

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

2015-10-26 Thread Justin Lecher 
commit: f40ae6aa62652f4c594808356512cc822aebd8aa
Author: Justin Lecher  gentoo  org>
AuthorDate: Mon Oct 26 10:29:44 2015 +
Commit: Justin Lecher  gentoo  org>
CommitDate: Mon Oct 26 10:30:01 2015 +
URL:https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=f40ae6aa

sci-biology/biopython: Version Bump

Package-Manager: portage-2.2.23
Signed-off-by: Justin Lecher  gentoo.org>

 sci-biology/biopython/Manifest  |  1 +
 sci-biology/biopython/biopython-1.66.ebuild | 56 +
 2 files changed, 57 insertions(+)

diff --git a/sci-biology/biopython/Manifest b/sci-biology/biopython/Manifest
index e835e24..a54d05e 100644
--- a/sci-biology/biopython/Manifest
+++ b/sci-biology/biopython/Manifest
@@ -1 +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.ebuild 
b/sci-biology/biopython/biopython-1.66.ebuild
new file mode 100644
index 000..d5c5fb6
--- /dev/null
+++ b/sci-biology/biopython/biopython-1.66.ebuild
@@ -0,0 +1,56 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 python3_{3,4} 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
+}