[gentoo-commits] proj/sci:master commit in: sci-biology/gffutils/

2023-05-02 Thread Andrew Ammerlaan 
commit: 2063f30830d744d566cddc2c454ec70e5600dae7
Author: Andrew Ammerlaan  gentoo  org>
AuthorDate: Tue May  2 12:25:02 2023 +
Commit: Andrew Ammerlaan  gentoo  org>
CommitDate: Tue May  2 12:25:02 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=2063f308

sci-biology/gffutils: drop 0.10.1

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

 sci-biology/gffutils/gffutils-0.10.1.ebuild | 42 -
 1 file changed, 42 deletions(-)

diff --git a/sci-biology/gffutils/gffutils-0.10.1.ebuild 
b/sci-biology/gffutils/gffutils-0.10.1.ebuild
deleted file mode 100644
index 96bceed2f..0
--- a/sci-biology/gffutils/gffutils-0.10.1.ebuild
+++ /dev/null
@@ -1,42 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{10..11} )
-
-inherit distutils-r1
-
-DESCRIPTION="GFF and GTF file manipulation and interconversion"
-HOMEPAGE="https://gffutils.readthedocs.io/en/latest/;
-SRC_URI="https://github.com/daler/gffutils/archive/v${PV}.tar.gz -> 
${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="test"
-# Nose tests no longer supported
-RESTRICT="test"
-
-RDEPEND="
-   dev-python/simplejson[${PYTHON_USEDEP}]
-   dev-python/argh[${PYTHON_USEDEP}]
-   dev-python/argcomplete[${PYTHON_USEDEP}]
-   sci-biology/biopython[${PYTHON_USEDEP}]
-   sci-biology/pybedtools[${PYTHON_USEDEP}]
-   sci-biology/pyfaidx[${PYTHON_USEDEP}]
-"
-DEPEND="${RDEPEND}"
-
-python_prepare_all() {
-   if use test; then
-   sed -i -e "s:/tmp/gffutils-test:${T}:g" gffutils/test/test.py 
|| die
-   fi
-   distutils-r1_python_prepare_all
-}
-
-distutils_enable_tests nose
-python_test() {
-   distutils_install_for_testing
-   nosetests -v -x --with-doctest -a '!slow' || die
-}

[gentoo-commits] proj/sci:master commit in: sci-biology/gffutils/

2023-05-02 Thread Andrew Ammerlaan 
commit: ebd8a0ddb0f27499a56e6b6fc63115950453e158
Author: Andrew Ammerlaan  gentoo  org>
AuthorDate: Tue May  2 12:25:29 2023 +
Commit: Andrew Ammerlaan  gentoo  org>
CommitDate: Tue May  2 12:25:29 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=ebd8a0dd

sci-biology/gffutils: add missing RESTRICT="!test? ( test )"

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

 sci-biology/gffutils/gffutils-0.11.1.ebuild | 1 +
 1 file changed, 1 insertion(+)

diff --git a/sci-biology/gffutils/gffutils-0.11.1.ebuild 
b/sci-biology/gffutils/gffutils-0.11.1.ebuild
index 7d39ee5de..8ee8fd4b5 100644
--- a/sci-biology/gffutils/gffutils-0.11.1.ebuild
+++ b/sci-biology/gffutils/gffutils-0.11.1.ebuild
@@ -17,6 +17,7 @@ KEYWORDS="~amd64 ~x86"
 IUSE="test"
 # Nose tests no longer supported, migration on next release
 #RESTRICT="test"
+RESTRICT="!test? ( test )"
 
 RDEPEND="
dev-python/simplejson[${PYTHON_USEDEP}]

[gentoo-commits] proj/sci:master commit in: sci-biology/gffutils/

2023-05-02 Thread Andrew Ammerlaan 
commit: 6ce2af61c38f3532fc372f64ffa2a63939bab309
Author: Andrew Ammerlaan  gentoo  org>
AuthorDate: Tue May  2 12:24:42 2023 +
Commit: Andrew Ammerlaan  gentoo  org>
CommitDate: Tue May  2 12:24:42 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=6ce2af61

sci-biology/gffutils: disable py3.9

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

 sci-biology/gffutils/gffutils-0.10.1.ebuild | 2 +-
 sci-biology/gffutils/gffutils-0.11.1.ebuild | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/sci-biology/gffutils/gffutils-0.10.1.ebuild 
b/sci-biology/gffutils/gffutils-0.10.1.ebuild
index 06182853e..96bceed2f 100644
--- a/sci-biology/gffutils/gffutils-0.10.1.ebuild
+++ b/sci-biology/gffutils/gffutils-0.10.1.ebuild
@@ -3,7 +3,7 @@
 
 EAPI=8
 
-PYTHON_COMPAT=( python3_{9..11} )
+PYTHON_COMPAT=( python3_{10..11} )
 
 inherit distutils-r1
 

diff --git a/sci-biology/gffutils/gffutils-0.11.1.ebuild 
b/sci-biology/gffutils/gffutils-0.11.1.ebuild
index 0c92f3468..7d39ee5de 100644
--- a/sci-biology/gffutils/gffutils-0.11.1.ebuild
+++ b/sci-biology/gffutils/gffutils-0.11.1.ebuild
@@ -3,7 +3,7 @@
 
 EAPI=8
 
-PYTHON_COMPAT=( python3_{9..11} )
+PYTHON_COMPAT=( python3_{10..11} )
 
 inherit distutils-r1

[gentoo-commits] proj/sci:master commit in: sci-biology/gffutils/

2023-03-24 Thread Horea Christian 
commit: 5aebdd92b5637fad779aeaa19ca9045338ba126e
Author: Horea Christian  chymera  eu>
AuthorDate: Sat Mar 25 05:16:40 2023 +
Commit: Horea Christian  gmail  com>
CommitDate: Sat Mar 25 05:16:40 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=5aebdd92

sci-biology/gffutils: drop 0.8.7.1

Signed-off-by: Horea Christian  chymera.eu>

 sci-biology/gffutils/gffutils-0.8.7.1.ebuild | 23 ---
 1 file changed, 23 deletions(-)

diff --git a/sci-biology/gffutils/gffutils-0.8.7.1.ebuild 
b/sci-biology/gffutils/gffutils-0.8.7.1.ebuild
deleted file mode 100644
index 29506bb9c..0
--- a/sci-biology/gffutils/gffutils-0.8.7.1.ebuild
+++ /dev/null
@@ -1,23 +0,0 @@
-# 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
-
-DESCRIPTION="GFF and GTF file manipulation and interconversion"
-HOMEPAGE="https://gffutils.readthedocs.io/en/latest/;
-SRC_URI="https://github.com/daler/gffutils/archive/v${PV}.tar.gz -> 
${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-RDEPEND="
-   sci-biology/pyfaidx[${PYTHON_USEDEP}]
-   dev-python/simplejson[${PYTHON_USEDEP}]
-   dev-python/argh[${PYTHON_USEDEP}]
-   dev-python/argcomplete[${PYTHON_USEDEP}]"
-DEPEND="${RDEPEND}"

[gentoo-commits] proj/sci:master commit in: sci-biology/gffutils/

2023-03-24 Thread Horea Christian 
commit: 2db7a214c3b7d8da2111658975f134527c6b84c4
Author: Horea Christian  chymera  eu>
AuthorDate: Sat Mar 25 05:16:31 2023 +
Commit: Horea Christian  gmail  com>
CommitDate: Sat Mar 25 05:16:31 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=2db7a214

sci-biology/gffutils: add 0.11.1

Signed-off-by: Horea Christian  chymera.eu>

 sci-biology/gffutils/gffutils-0.11.1.ebuild | 41 +
 1 file changed, 41 insertions(+)

diff --git a/sci-biology/gffutils/gffutils-0.11.1.ebuild 
b/sci-biology/gffutils/gffutils-0.11.1.ebuild
new file mode 100644
index 0..0c92f3468
--- /dev/null
+++ b/sci-biology/gffutils/gffutils-0.11.1.ebuild
@@ -0,0 +1,41 @@
+# 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
+
+DESCRIPTION="GFF and GTF file manipulation and interconversion"
+HOMEPAGE="https://gffutils.readthedocs.io/en/latest/;
+SRC_URI="https://github.com/daler/gffutils/archive/v${PV}.tar.gz -> 
${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+# Nose tests no longer supported, migration on next release
+#RESTRICT="test"
+
+RDEPEND="
+   dev-python/simplejson[${PYTHON_USEDEP}]
+   dev-python/argh[${PYTHON_USEDEP}]
+   dev-python/argcomplete[${PYTHON_USEDEP}]
+   sci-biology/biopython[${PYTHON_USEDEP}]
+   sci-biology/pybedtools[${PYTHON_USEDEP}]
+   sci-biology/pyfaidx[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+
+python_prepare_all() {
+   if use test; then
+   sed -i -e "s:/tmp/gffutils-test:${T}:g" gffutils/test/test.py 
|| die
+   fi
+   distutils-r1_python_prepare_all
+}
+
+python_test() {
+   distutils_install_for_testing
+   nosetests -v -x --with-doctest -a '!slow' || die
+}

[gentoo-commits] proj/sci:master commit in: sci-biology/gffutils/

2023-03-24 Thread Horea Christian 
commit: 58c91a2f36087e3dcc9495d1846218a9c3e27561
Author: Horea Christian  chymera  eu>
AuthorDate: Sat Mar 25 05:10:13 2023 +
Commit: Horea Christian  gmail  com>
CommitDate: Sat Mar 25 05:10:13 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=58c91a2f

sci-biology/gffutils: update EAPI 7 -> 8

Signed-off-by: Horea Christian  chymera.eu>

 sci-biology/gffutils/gffutils-0.10.1.ebuild  | 7 +--
 sci-biology/gffutils/gffutils-0.8.7.1.ebuild | 4 ++--
 2 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/sci-biology/gffutils/gffutils-0.10.1.ebuild 
b/sci-biology/gffutils/gffutils-0.10.1.ebuild
index 5d024a687..06182853e 100644
--- a/sci-biology/gffutils/gffutils-0.10.1.ebuild
+++ b/sci-biology/gffutils/gffutils-0.10.1.ebuild
@@ -1,9 +1,9 @@
 # Copyright 1999-2023 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=7
+EAPI=8
 
-PYTHON_COMPAT=( python3_{7..9} )
+PYTHON_COMPAT=( python3_{9..11} )
 
 inherit distutils-r1
 
@@ -14,6 +14,9 @@ 
SRC_URI="https://github.com/daler/gffutils/archive/v${PV}.tar.gz -> ${P}.tar.gz"
 LICENSE="MIT"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
+IUSE="test"
+# Nose tests no longer supported
+RESTRICT="test"
 
 RDEPEND="
dev-python/simplejson[${PYTHON_USEDEP}]

diff --git a/sci-biology/gffutils/gffutils-0.8.7.1.ebuild 
b/sci-biology/gffutils/gffutils-0.8.7.1.ebuild
index ea347faa2..29506bb9c 100644
--- a/sci-biology/gffutils/gffutils-0.8.7.1.ebuild
+++ b/sci-biology/gffutils/gffutils-0.8.7.1.ebuild
@@ -1,9 +1,9 @@
 # Copyright 1999-2023 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=7
+EAPI=8
 
-PYTHON_COMPAT=( python3_{7..9} )
+PYTHON_COMPAT=( python3_{9..11} )
 
 inherit distutils-r1

[gentoo-commits] proj/sci:master commit in: sci-biology/gffutils/

2023-03-24 Thread Horea Christian 
commit: 7987da509f38db2760af8b6f53306d37165ce6c4
Author: Horea Christian  chymera  eu>
AuthorDate: Sat Mar 25 03:10:53 2023 +
Commit: Horea Christian  gmail  com>
CommitDate: Sat Mar 25 03:10:53 2023 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=7987da50

sci-biology/gffutils: update HOMEPAGE

Signed-off-by: Horea Christian  chymera.eu>

 sci-biology/gffutils/gffutils-0.10.1.ebuild  | 4 ++--
 sci-biology/gffutils/gffutils-0.8.7.1.ebuild | 4 ++--
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/sci-biology/gffutils/gffutils-0.10.1.ebuild 
b/sci-biology/gffutils/gffutils-0.10.1.ebuild
index c7a437264..5d024a687 100644
--- a/sci-biology/gffutils/gffutils-0.10.1.ebuild
+++ b/sci-biology/gffutils/gffutils-0.10.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2023 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
@@ -8,7 +8,7 @@ PYTHON_COMPAT=( python3_{7..9} )
 inherit distutils-r1
 
 DESCRIPTION="GFF and GTF file manipulation and interconversion"
-HOMEPAGE="https://pythonhosted.org/gffutils/;
+HOMEPAGE="https://gffutils.readthedocs.io/en/latest/;
 SRC_URI="https://github.com/daler/gffutils/archive/v${PV}.tar.gz -> 
${P}.tar.gz"
 
 LICENSE="MIT"

diff --git a/sci-biology/gffutils/gffutils-0.8.7.1.ebuild 
b/sci-biology/gffutils/gffutils-0.8.7.1.ebuild
index c6b304fb1..ea347faa2 100644
--- a/sci-biology/gffutils/gffutils-0.8.7.1.ebuild
+++ b/sci-biology/gffutils/gffutils-0.8.7.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2023 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
@@ -8,7 +8,7 @@ PYTHON_COMPAT=( python3_{7..9} )
 inherit distutils-r1
 
 DESCRIPTION="GFF and GTF file manipulation and interconversion"
-HOMEPAGE="https://pythonhosted.org/gffutils/;
+HOMEPAGE="https://gffutils.readthedocs.io/en/latest/;
 SRC_URI="https://github.com/daler/gffutils/archive/v${PV}.tar.gz -> 
${P}.tar.gz"
 
 LICENSE="MIT"

[gentoo-commits] proj/sci:master commit in: sci-biology/gffutils/

2020-12-30 Thread Aisha Tammy 
commit: 8e819929a999cf108b584da4d77b8d834b00fefb
Author: Andrew Ammerlaan  riseup  net>
AuthorDate: Wed Dec 30 18:20:12 2020 +
Commit: Aisha Tammy  aisha  cc>
CommitDate: Wed Dec 30 18:26:23 2020 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=8e819929

sci-biology/gffutils: drop py3.6

Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan  riseup.net>
Closes: https://github.com/gentoo/sci/pull/1008
Signed-off-by: Aisha Tammy  aisha.cc>

 sci-biology/gffutils/gffutils-0.10.1.ebuild  | 5 ++---
 sci-biology/gffutils/gffutils-0.8.7.1.ebuild | 5 ++---
 2 files changed, 4 insertions(+), 6 deletions(-)

diff --git a/sci-biology/gffutils/gffutils-0.10.1.ebuild 
b/sci-biology/gffutils/gffutils-0.10.1.ebuild
index f33541347..c7a437264 100644
--- a/sci-biology/gffutils/gffutils-0.10.1.ebuild
+++ b/sci-biology/gffutils/gffutils-0.10.1.ebuild
@@ -3,7 +3,7 @@
 
 EAPI=7
 
-PYTHON_COMPAT=( python3_{6..9} )
+PYTHON_COMPAT=( python3_{7..9} )
 
 inherit distutils-r1
 
@@ -13,8 +13,7 @@ 
SRC_URI="https://github.com/daler/gffutils/archive/v${PV}.tar.gz -> ${P}.tar.gz"
 
 LICENSE="MIT"
 SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
+KEYWORDS="~amd64 ~x86"
 
 RDEPEND="
dev-python/simplejson[${PYTHON_USEDEP}]

diff --git a/sci-biology/gffutils/gffutils-0.8.7.1.ebuild 
b/sci-biology/gffutils/gffutils-0.8.7.1.ebuild
index 333716f7a..c6b304fb1 100644
--- a/sci-biology/gffutils/gffutils-0.8.7.1.ebuild
+++ b/sci-biology/gffutils/gffutils-0.8.7.1.ebuild
@@ -3,7 +3,7 @@
 
 EAPI=7
 
-PYTHON_COMPAT=( python3_{6..9} )
+PYTHON_COMPAT=( python3_{7..9} )
 
 inherit distutils-r1
 
@@ -13,8 +13,7 @@ 
SRC_URI="https://github.com/daler/gffutils/archive/v${PV}.tar.gz -> ${P}.tar.gz"
 
 LICENSE="MIT"
 SLOT="0"
-KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
-IUSE=""
+KEYWORDS="~amd64 ~x86"
 
 RDEPEND="
sci-biology/pyfaidx[${PYTHON_USEDEP}]

[gentoo-commits] proj/sci:master commit in: sci-biology/gffutils/

2020-09-27 Thread Horea Christian 
commit: 6fdee212269c999a4ec6ceb020115f6b9959d20f
Author: Horea Christian  chymera  eu>
AuthorDate: Sun Sep 27 07:33:55 2020 +
Commit: Horea Christian  gmail  com>
CommitDate: Sun Sep 27 07:33:55 2020 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=6fdee212

sci-biology/gffutils: version bump 0.10.1, test and PYTHON_COMPAT fix

Package-Manager: Portage-3.0.8, Repoman-3.0.1
Signed-off-by: Horea Christian  chymera.eu>

 ...utils-0.8.7.1.ebuild => gffutils-0.10.1.ebuild} | 26 +-
 sci-biology/gffutils/gffutils-0.8.7.1.ebuild   |  6 ++---
 2 files changed, 24 insertions(+), 8 deletions(-)

diff --git a/sci-biology/gffutils/gffutils-0.8.7.1.ebuild 
b/sci-biology/gffutils/gffutils-0.10.1.ebuild
similarity index 51%
copy from sci-biology/gffutils/gffutils-0.8.7.1.ebuild
copy to sci-biology/gffutils/gffutils-0.10.1.ebuild
index 787a5668a..f33541347 100644
--- a/sci-biology/gffutils/gffutils-0.8.7.1.ebuild
+++ b/sci-biology/gffutils/gffutils-0.10.1.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-PYTHON_COMPAT=( python2_7 )
+PYTHON_COMPAT=( python3_{6..9} )
 
 inherit distutils-r1
 
@@ -17,8 +17,24 @@ KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 IUSE=""
 
 RDEPEND="
-   sci-biology/pyfaidx[${PYTHON_USEDEP}]
dev-python/simplejson[${PYTHON_USEDEP}]
dev-python/argh[${PYTHON_USEDEP}]
-   dev-python/argcomplete[${PYTHON_USEDEP}]"
+   dev-python/argcomplete[${PYTHON_USEDEP}]
+   sci-biology/biopython[${PYTHON_USEDEP}]
+   sci-biology/pybedtools[${PYTHON_USEDEP}]
+   sci-biology/pyfaidx[${PYTHON_USEDEP}]
+"
 DEPEND="${RDEPEND}"
+
+python_prepare_all() {
+   if use test; then
+   sed -i -e "s:/tmp/gffutils-test:${T}:g" gffutils/test/test.py 
|| die
+   fi
+   distutils-r1_python_prepare_all
+}
+
+distutils_enable_tests nose
+python_test() {
+   distutils_install_for_testing
+   nosetests -v -x --with-doctest -a '!slow' || die
+}

diff --git a/sci-biology/gffutils/gffutils-0.8.7.1.ebuild 
b/sci-biology/gffutils/gffutils-0.8.7.1.ebuild
index 787a5668a..333716f7a 100644
--- a/sci-biology/gffutils/gffutils-0.8.7.1.ebuild
+++ b/sci-biology/gffutils/gffutils-0.8.7.1.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2020 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-PYTHON_COMPAT=( python2_7 )
+PYTHON_COMPAT=( python3_{6..9} )
 
 inherit distutils-r1

[gentoo-commits] proj/sci:master commit in: sci-biology/gffutils/

2017-11-16 Thread Martin Mokrejs 
commit: 24eca4914c2cb8f6a81cc5cb886ac227d44236e3
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Thu Nov 16 09:06:22 2017 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Thu Nov 16 09:06:22 2017 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=24eca491

sci-biology/gffutils: add missing DEPEND on dev-python/argcomplete

Package-Manager: Portage-2.3.13, Repoman-2.3.3

 sci-biology/gffutils/gffutils-0.8.7.1.ebuild | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/sci-biology/gffutils/gffutils-0.8.7.1.ebuild 
b/sci-biology/gffutils/gffutils-0.8.7.1.ebuild
index 2f8d19625..787a5668a 100644
--- a/sci-biology/gffutils/gffutils-0.8.7.1.ebuild
+++ b/sci-biology/gffutils/gffutils-0.8.7.1.ebuild
@@ -19,5 +19,6 @@ IUSE=""
 RDEPEND="
sci-biology/pyfaidx[${PYTHON_USEDEP}]
dev-python/simplejson[${PYTHON_USEDEP}]
-   dev-python/argh[${PYTHON_USEDEP}]"
+   dev-python/argh[${PYTHON_USEDEP}]
+   dev-python/argcomplete[${PYTHON_USEDEP}]"
 DEPEND="${RDEPEND}"

[gentoo-commits] proj/sci:master commit in: sci-biology/gffutils/

2017-11-16 Thread Martin Mokrejs 
commit: 2f30c658a273d1e82c103173a208a89e4bf23086
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Thu Nov 16 09:04:07 2017 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Thu Nov 16 09:04:07 2017 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=2f30c658

sci-biology/gffutils: add missing DEPEND on dev-python/argh

Package-Manager: Portage-2.3.13, Repoman-2.3.3

 sci-biology/gffutils/gffutils-0.8.7.1.ebuild | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/sci-biology/gffutils/gffutils-0.8.7.1.ebuild 
b/sci-biology/gffutils/gffutils-0.8.7.1.ebuild
index 3a9d8de84..2f8d19625 100644
--- a/sci-biology/gffutils/gffutils-0.8.7.1.ebuild
+++ b/sci-biology/gffutils/gffutils-0.8.7.1.ebuild
@@ -18,5 +18,6 @@ IUSE=""
 
 RDEPEND="
sci-biology/pyfaidx[${PYTHON_USEDEP}]
-   dev-python/simplejson[${PYTHON_USEDEP}]"
+   dev-python/simplejson[${PYTHON_USEDEP}]
+   dev-python/argh[${PYTHON_USEDEP}]"
 DEPEND="${RDEPEND}"

[gentoo-commits] proj/sci:master commit in: sci-biology/gffutils/

2017-11-16 Thread Martin Mokrejs 
commit: 2254303b958dbae3a97c00e233fcf5ce6677d070
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Thu Nov 16 08:24:09 2017 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Thu Nov 16 08:24:09 2017 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=2254303b

sci-biology/gffutils: add missing DEPEND on dev-python/simplejson

Package-Manager: Portage-2.3.13, Repoman-2.3.3

 sci-biology/gffutils/gffutils-0.8.7.1.ebuild | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/sci-biology/gffutils/gffutils-0.8.7.1.ebuild 
b/sci-biology/gffutils/gffutils-0.8.7.1.ebuild
index a20b8e8b7..3a9d8de84 100644
--- a/sci-biology/gffutils/gffutils-0.8.7.1.ebuild
+++ b/sci-biology/gffutils/gffutils-0.8.7.1.ebuild
@@ -16,5 +16,7 @@ SLOT="0"
 KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
 IUSE=""
 
-RDEPEND="sci-biology/pyfaidx[${PYTHON_USEDEP}]"
+RDEPEND="
+   sci-biology/pyfaidx[${PYTHON_USEDEP}]
+   dev-python/simplejson[${PYTHON_USEDEP}]"
 DEPEND="${RDEPEND}"

[gentoo-commits] proj/sci:master commit in: sci-biology/gffutils/

2015-06-06 Thread Justin Lecher 
commit: 01b55b7d8ba8dfb626ad37bd1db3c7f5d2b678d3
Author: Justin Lecher jlec AT gentoo DOT org
AuthorDate: Sat Jun  6 10:11:09 2015 +
Commit: Justin Lecher jlec AT gentoo DOT org
CommitDate: Sat Jun  6 10:11:09 2015 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=01b55b7d

sci-biology/gffutils: Add github to remote-id in metadata.xml

Package-Manager: portage-2.2.20

 sci-biology/gffutils/ChangeLog| 3 +++
 sci-biology/gffutils/metadata.xml | 3 +++
 2 files changed, 6 insertions(+)

diff --git a/sci-biology/gffutils/ChangeLog b/sci-biology/gffutils/ChangeLog
index 486a807..c617293 100644
--- a/sci-biology/gffutils/ChangeLog
+++ b/sci-biology/gffutils/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  06 Jun 2015; Justin Lecher j...@gentoo.org metadata.xml:
+  sci-biology/gffutils: Add github to remote-id in metadata.xml
+
   13 Apr 2015; Justin Lecher j...@gentoo.org gffutils-0.8.3.ebuild:
   sci-biology/gffutils: Streamline ebuild
 

diff --git a/sci-biology/gffutils/metadata.xml 
b/sci-biology/gffutils/metadata.xml
index b7551a6..32143ba 100644
--- a/sci-biology/gffutils/metadata.xml
+++ b/sci-biology/gffutils/metadata.xml
@@ -6,4 +6,7 @@
 emailmschu@gmail.com/email
 nameMichael Schubert/name
   /maintainer
+  upstream
+remote-id type=githubdaler/gffutils/remote-id
+  /upstream
 /pkgmetadata

[gentoo-commits] proj/sci:master commit in: sci-biology/gffutils/

2015-04-13 Thread Justin Lecher 
commit: d30355d1fca263599755a7e077de5d57978dfcb5
Author: layman layman AT localhost
AuthorDate: Sun Apr 12 16:03:39 2015 +
Commit: Justin Lecher jlec AT gentoo DOT org
CommitDate: Sun Apr 12 16:03:39 2015 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=d30355d1

sci-biology/gffutils: add gffutils

Package-Manager: portage-2.2.14-prefix

 sci-biology/gffutils/ChangeLog |  9 +
 sci-biology/gffutils/gffutils-0.8.3.ebuild | 20 
 sci-biology/gffutils/metadata.xml  |  9 +
 3 files changed, 38 insertions(+)

diff --git a/sci-biology/gffutils/ChangeLog b/sci-biology/gffutils/ChangeLog
new file mode 100644
index 000..fe1e811
--- /dev/null
+++ b/sci-biology/gffutils/ChangeLog
@@ -0,0 +1,9 @@
+# ChangeLog for sci-biology/gffutils
+# Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*gffutils-0.8.3 (12 Apr 2015)
+
+  12 Apr 2015; Michael Schubert mschu@gmail.com +gffutils-0.8.3.ebuild,
+  +metadata.xml:
+  sci-biology/gffutils: add gffutils

diff --git a/sci-biology/gffutils/gffutils-0.8.3.ebuild 
b/sci-biology/gffutils/gffutils-0.8.3.ebuild
new file mode 100644
index 000..25c23d4
--- /dev/null
+++ b/sci-biology/gffutils/gffutils-0.8.3.ebuild
@@ -0,0 +1,20 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 )
+
+inherit distutils-r1
+
+DESCRIPTION=GFF and GTF file manipulation and interconversion
+HOMEPAGE=https://pythonhosted.org/gffutils/;
+SRC_URI=https://github.com/daler/gffutils/archive/v${PV}.tar.gz;
+
+LICENSE=MIT
+SLOT=0
+IUSE=
+
+DEPEND=sci-biology/pyfaidx[${PYTHON_USEDEP}]
+RDEPEND=${DEPEND}

diff --git a/sci-biology/gffutils/metadata.xml 
b/sci-biology/gffutils/metadata.xml
new file mode 100644
index 000..b7551a6
--- /dev/null
+++ b/sci-biology/gffutils/metadata.xml
@@ -0,0 +1,9 @@
+?xml version=1.0 encoding=UTF-8?
+!DOCTYPE pkgmetadata SYSTEM http://www.gentoo.org/dtd/metadata.dtd;
+pkgmetadata
+  herdsci-biology/herd
+  maintainer
+emailmschu@gmail.com/email
+nameMichael Schubert/name
+  /maintainer
+/pkgmetadata

[gentoo-commits] proj/sci:master commit in: sci-biology/gffutils/

2015-04-13 Thread Justin Lecher 
commit: 5ce25231a00388d2eb6c1f717fa1ec00e6cea813
Author: Justin Lecher jlec AT gentoo DOT org
AuthorDate: Mon Apr 13 06:15:38 2015 +
Commit: Justin Lecher jlec AT gentoo DOT org
CommitDate: Mon Apr 13 06:17:03 2015 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=5ce25231

sci-biology/gffutils: Streamline ebuild

Package-Manager: portage-2.2.18
Signed-off-by: Justin Lecher jlec AT gentoo.org

 sci-biology/gffutils/ChangeLog | 3 +++
 sci-biology/gffutils/gffutils-0.8.3.ebuild | 7 ---
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/sci-biology/gffutils/ChangeLog b/sci-biology/gffutils/ChangeLog
index fe1e811..486a807 100644
--- a/sci-biology/gffutils/ChangeLog
+++ b/sci-biology/gffutils/ChangeLog
@@ -2,6 +2,9 @@
 # Copyright 1999-2015 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  13 Apr 2015; Justin Lecher j...@gentoo.org gffutils-0.8.3.ebuild:
+  sci-biology/gffutils: Streamline ebuild
+
 *gffutils-0.8.3 (12 Apr 2015)
 
   12 Apr 2015; Michael Schubert mschu@gmail.com +gffutils-0.8.3.ebuild,

diff --git a/sci-biology/gffutils/gffutils-0.8.3.ebuild 
b/sci-biology/gffutils/gffutils-0.8.3.ebuild
index 25c23d4..82fa6b4 100644
--- a/sci-biology/gffutils/gffutils-0.8.3.ebuild
+++ b/sci-biology/gffutils/gffutils-0.8.3.ebuild
@@ -10,11 +10,12 @@ inherit distutils-r1
 
 DESCRIPTION=GFF and GTF file manipulation and interconversion
 HOMEPAGE=https://pythonhosted.org/gffutils/;
-SRC_URI=https://github.com/daler/gffutils/archive/v${PV}.tar.gz;
+SRC_URI=https://github.com/daler/gffutils/archive/v${PV}.tar.gz - 
${P}.tar.gz
 
 LICENSE=MIT
 SLOT=0
+KEYWORDS=~amd64 ~x86 ~amd64-linux ~x86-linux
 IUSE=
 
-DEPEND=sci-biology/pyfaidx[${PYTHON_USEDEP}]
-RDEPEND=${DEPEND}
+RDEPEND=sci-biology/pyfaidx[${PYTHON_USEDEP}]
+DEPEND=${RDEPEND}