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* [gentoo-commits] proj/sci:master commit in: sci-biology/gffutils/
@ 2015-04-13  6:25 Justin Lecher
  0 siblings, 0 replies; 17+ messages in thread
From: Justin Lecher @ 2015-04-13  6:25 UTC (permalink / raw
  To: gentoo-commits

commit:     d30355d1fca263599755a7e077de5d57978dfcb5
Author:     layman <layman <AT> localhost>
AuthorDate: Sun Apr 12 16:03:39 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Apr 12 16:03:39 2015 +0000
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 0000000..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.dev@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 0000000..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 0000000..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>
+  <herd>sci-biology</herd>
+  <maintainer>
+    <email>mschu.dev@gmail.com</email>
+    <name>Michael Schubert</name>
+  </maintainer>
+</pkgmetadata>


^ permalink raw reply related	[flat|nested] 17+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/gffutils/
@ 2015-04-13  6:25 Justin Lecher
  0 siblings, 0 replies; 17+ messages in thread
From: Justin Lecher @ 2015-04-13  6:25 UTC (permalink / raw
  To: gentoo-commits

commit:     5ce25231a00388d2eb6c1f717fa1ec00e6cea813
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Mon Apr 13 06:15:38 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Mon Apr 13 06:17:03 2015 +0000
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 <jlec@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.dev@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}"


^ permalink raw reply related	[flat|nested] 17+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/gffutils/
@ 2015-06-06 10:23 Justin Lecher
  0 siblings, 0 replies; 17+ messages in thread
From: Justin Lecher @ 2015-06-06 10:23 UTC (permalink / raw
  To: gentoo-commits

commit:     01b55b7d8ba8dfb626ad37bd1db3c7f5d2b678d3
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Jun  6 10:11:09 2015 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Jun  6 10:11:09 2015 +0000
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 <jlec@gentoo.org> metadata.xml:
+  sci-biology/gffutils: Add github to remote-id in metadata.xml
+
   13 Apr 2015; Justin Lecher <jlec@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 @@
     <email>mschu.dev@gmail.com</email>
     <name>Michael Schubert</name>
   </maintainer>
+  <upstream>
+    <remote-id type="github">daler/gffutils</remote-id>
+  </upstream>
 </pkgmetadata>


^ permalink raw reply related	[flat|nested] 17+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/gffutils/
@ 2017-04-20 17:05 Martin Mokrejs
  0 siblings, 0 replies; 17+ messages in thread
From: Martin Mokrejs @ 2017-04-20 17:05 UTC (permalink / raw
  To: gentoo-commits

commit:     03891018f1ec83244249614d4c269c22a346bfc3
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Apr 20 16:55:09 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Apr 20 16:55:09 2017 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=03891018

sci-biology/gffutils: version bump

Package-Manager: Portage-2.3.5, Repoman-2.3.2

 sci-biology/gffutils/{gffutils-0.8.3.ebuild => gffutils-0.8.7.1.ebuild} | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/sci-biology/gffutils/gffutils-0.8.3.ebuild b/sci-biology/gffutils/gffutils-0.8.7.1.ebuild
similarity index 92%
rename from sci-biology/gffutils/gffutils-0.8.3.ebuild
rename to sci-biology/gffutils/gffutils-0.8.7.1.ebuild
index 63b614fdd..a20b8e8b7 100644
--- a/sci-biology/gffutils/gffutils-0.8.3.ebuild
+++ b/sci-biology/gffutils/gffutils-0.8.7.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2015 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=5


^ permalink raw reply related	[flat|nested] 17+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/gffutils/
@ 2017-11-16  8:24 Martin Mokrejs
  0 siblings, 0 replies; 17+ messages in thread
From: Martin Mokrejs @ 2017-11-16  8:24 UTC (permalink / raw
  To: gentoo-commits

commit:     2254303b958dbae3a97c00e233fcf5ce6677d070
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Nov 16 08:24:09 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Nov 16 08:24:09 2017 +0000
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}"


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* [gentoo-commits] proj/sci:master commit in: sci-biology/gffutils/
@ 2017-11-16  9:04 Martin Mokrejs
  0 siblings, 0 replies; 17+ messages in thread
From: Martin Mokrejs @ 2017-11-16  9:04 UTC (permalink / raw
  To: gentoo-commits

commit:     2f30c658a273d1e82c103173a208a89e4bf23086
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Nov 16 09:04:07 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Nov 16 09:04:07 2017 +0000
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}"


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* [gentoo-commits] proj/sci:master commit in: sci-biology/gffutils/
@ 2017-11-16  9:06 Martin Mokrejs
  0 siblings, 0 replies; 17+ messages in thread
From: Martin Mokrejs @ 2017-11-16  9:06 UTC (permalink / raw
  To: gentoo-commits

commit:     24eca4914c2cb8f6a81cc5cb886ac227d44236e3
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Nov 16 09:06:22 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Nov 16 09:06:22 2017 +0000
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}"


^ permalink raw reply related	[flat|nested] 17+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/gffutils/
@ 2020-09-27  7:34 Horea Christian
  0 siblings, 0 replies; 17+ messages in thread
From: Horea Christian @ 2020-09-27  7:34 UTC (permalink / raw
  To: gentoo-commits

commit:     6fdee212269c999a4ec6ceb020115f6b9959d20f
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Sun Sep 27 07:33:55 2020 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Sun Sep 27 07:33:55 2020 +0000
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 <chr <AT> 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
 


^ permalink raw reply related	[flat|nested] 17+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/gffutils/
@ 2020-12-30 18:26 Aisha Tammy
  0 siblings, 0 replies; 17+ messages in thread
From: Aisha Tammy @ 2020-12-30 18:26 UTC (permalink / raw
  To: gentoo-commits

commit:     8e819929a999cf108b584da4d77b8d834b00fefb
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Wed Dec 30 18:20:12 2020 +0000
Commit:     Aisha Tammy <gentoo <AT> aisha <DOT> cc>
CommitDate: Wed Dec 30 18:26:23 2020 +0000
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 <andrewammerlaan <AT> riseup.net>
Closes: https://github.com/gentoo/sci/pull/1008
Signed-off-by: Aisha Tammy <gentoo <AT> 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}]


^ permalink raw reply related	[flat|nested] 17+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/gffutils/
@ 2023-03-25  3:14 Horea Christian
  0 siblings, 0 replies; 17+ messages in thread
From: Horea Christian @ 2023-03-25  3:14 UTC (permalink / raw
  To: gentoo-commits

commit:     7987da509f38db2760af8b6f53306d37165ce6c4
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Sat Mar 25 03:10:53 2023 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Sat Mar 25 03:10:53 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=7987da50

sci-biology/gffutils: update HOMEPAGE

Signed-off-by: Horea Christian <chr <AT> 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"


^ permalink raw reply related	[flat|nested] 17+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/gffutils/
@ 2023-03-25  5:10 Horea Christian
  0 siblings, 0 replies; 17+ messages in thread
From: Horea Christian @ 2023-03-25  5:10 UTC (permalink / raw
  To: gentoo-commits

commit:     58c91a2f36087e3dcc9495d1846218a9c3e27561
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Sat Mar 25 05:10:13 2023 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Sat Mar 25 05:10:13 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=58c91a2f

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

Signed-off-by: Horea Christian <chr <AT> 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
 


^ permalink raw reply related	[flat|nested] 17+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/gffutils/
@ 2023-03-25  5:16 Horea Christian
  0 siblings, 0 replies; 17+ messages in thread
From: Horea Christian @ 2023-03-25  5:16 UTC (permalink / raw
  To: gentoo-commits

commit:     2db7a214c3b7d8da2111658975f134527c6b84c4
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Sat Mar 25 05:16:31 2023 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Sat Mar 25 05:16:31 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=2db7a214

sci-biology/gffutils: add 0.11.1

Signed-off-by: Horea Christian <chr <AT> 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 000000000..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
+}


^ permalink raw reply related	[flat|nested] 17+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/gffutils/
@ 2023-03-25  5:16 Horea Christian
  0 siblings, 0 replies; 17+ messages in thread
From: Horea Christian @ 2023-03-25  5:16 UTC (permalink / raw
  To: gentoo-commits

commit:     5aebdd92b5637fad779aeaa19ca9045338ba126e
Author:     Horea Christian <chr <AT> chymera <DOT> eu>
AuthorDate: Sat Mar 25 05:16:40 2023 +0000
Commit:     Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Sat Mar 25 05:16:40 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=5aebdd92

sci-biology/gffutils: drop 0.8.7.1

Signed-off-by: Horea Christian <chr <AT> 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..000000000
--- 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}"


^ permalink raw reply related	[flat|nested] 17+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/gffutils/
@ 2023-05-02 12:25 Andrew Ammerlaan
  0 siblings, 0 replies; 17+ messages in thread
From: Andrew Ammerlaan @ 2023-05-02 12:25 UTC (permalink / raw
  To: gentoo-commits

commit:     6ce2af61c38f3532fc372f64ffa2a63939bab309
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue May  2 12:24:42 2023 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue May  2 12:24:42 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=6ce2af61

sci-biology/gffutils: disable py3.9

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> 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
 


^ permalink raw reply related	[flat|nested] 17+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/gffutils/
@ 2023-05-02 12:25 Andrew Ammerlaan
  0 siblings, 0 replies; 17+ messages in thread
From: Andrew Ammerlaan @ 2023-05-02 12:25 UTC (permalink / raw
  To: gentoo-commits

commit:     2063f30830d744d566cddc2c454ec70e5600dae7
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue May  2 12:25:02 2023 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue May  2 12:25:02 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=2063f308

sci-biology/gffutils: drop 0.10.1

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> 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..000000000
--- 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
-}


^ permalink raw reply related	[flat|nested] 17+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/gffutils/
@ 2023-05-02 12:25 Andrew Ammerlaan
  0 siblings, 0 replies; 17+ messages in thread
From: Andrew Ammerlaan @ 2023-05-02 12:25 UTC (permalink / raw
  To: gentoo-commits

commit:     ebd8a0ddb0f27499a56e6b6fc63115950453e158
Author:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue May  2 12:25:29 2023 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue May  2 12:25:29 2023 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=ebd8a0dd

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

Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> 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}]


^ permalink raw reply related	[flat|nested] 17+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/gffutils/
@ 2024-07-19 12:43 Andrew Ammerlaan
  0 siblings, 0 replies; 17+ messages in thread
From: Andrew Ammerlaan @ 2024-07-19 12:43 UTC (permalink / raw
  To: gentoo-commits

commit:     acafe6e0405a9bcd41829884a04736f8d94e4d8c
Author:     Michael Schubert <mschu.dev <AT> gmail <DOT> com>
AuthorDate: Fri Jul 12 11:44:16 2024 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Fri Jul 19 12:35:07 2024 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=acafe6e0

sci-bioloy/gffutils: version bump 0.13; fix tests

Signed-off-by: Michael Schubert <mschu.dev <AT> gmail.com>
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>

 sci-biology/gffutils/gffutils-0.11.1.ebuild | 42 -----------------------------
 sci-biology/gffutils/gffutils-0.13.ebuild   | 32 ++++++++++++++++++++++
 sci-biology/gffutils/metadata.xml           |  4 ---
 3 files changed, 32 insertions(+), 46 deletions(-)

diff --git a/sci-biology/gffutils/gffutils-0.11.1.ebuild b/sci-biology/gffutils/gffutils-0.11.1.ebuild
deleted file mode 100644
index 8ee8fd4b5..000000000
--- a/sci-biology/gffutils/gffutils-0.11.1.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 -> ${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE="test"
-# Nose tests no longer supported, migration on next release
-#RESTRICT="test"
-RESTRICT="!test? ( test )"
-
-RDEPEND="
-	dev-python/simplejson[${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
-}

diff --git a/sci-biology/gffutils/gffutils-0.13.ebuild b/sci-biology/gffutils/gffutils-0.13.ebuild
new file mode 100644
index 000000000..fbd90b6d9
--- /dev/null
+++ b/sci-biology/gffutils/gffutils-0.13.ebuild
@@ -0,0 +1,32 @@
+# Copyright 1999-2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=setuptools
+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 -> ${P}.gh.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+RDEPEND="
+	dev-python/simplejson[${PYTHON_USEDEP}]
+	dev-python/argh[${PYTHON_USEDEP}]
+	dev-python/argcomplete[${PYTHON_USEDEP}]
+	dev-python/pyfaidx[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+
+# https://github.com/daler/gffutils/issues/233 + cli not installed yet
+EPYTEST_DESELECT=(
+	gffutils/test/test_biopython_integration.py::test_roundtrip
+	gffutils/test/test_cli.py::test_issue_224
+)
+
+distutils_enable_tests pytest

diff --git a/sci-biology/gffutils/metadata.xml b/sci-biology/gffutils/metadata.xml
index c9fe23ced..dc2c60220 100644
--- a/sci-biology/gffutils/metadata.xml
+++ b/sci-biology/gffutils/metadata.xml
@@ -5,10 +5,6 @@
 		<email>mschu.dev@gmail.com</email>
 		<name>Michael Schubert</name>
 	</maintainer>
-	<maintainer type="project">
-		<email>sci-biology@gentoo.org</email>
-		<name>Gentoo Biology Project</name>
-	</maintainer>
 	<upstream>
 		<remote-id type="github">daler/gffutils</remote-id>
 	</upstream>


^ permalink raw reply related	[flat|nested] 17+ messages in thread
end of thread, other threads:[~2024-07-19 12:43 UTC | newest]

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2023-03-25  3:14 Horea Christian
2020-12-30 18:26 Aisha Tammy
2020-09-27  7:34 Horea Christian
2017-11-16  9:06 Martin Mokrejs
2017-11-16  9:04 Martin Mokrejs
2017-11-16  8:24 Martin Mokrejs
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