* [gentoo-commits] proj/sci:master commit in: sci-biology/pysamstats/
@ 2016-04-11 13:07 Martin Mokrejs
0 siblings, 0 replies; 4+ messages in thread
From: Martin Mokrejs @ 2016-04-11 13:07 UTC (permalink / raw
To: gentoo-commits
commit: 0561406b09f038d22217d0d455a569d4eb8192e2
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Mon Apr 11 13:04:48 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Mon Apr 11 13:04:48 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=0561406b
sci-biology/pysamstats: new package
Package-Manager: portage-2.2.28
sci-biology/pysamstats/metadata.xml | 12 ++++++++++++
sci-biology/pysamstats/pysamstats-0.24.2.ebuild | 23 +++++++++++++++++++++++
2 files changed, 35 insertions(+)
diff --git a/sci-biology/pysamstats/metadata.xml b/sci-biology/pysamstats/metadata.xml
new file mode 100644
index 0000000..f68a1b6
--- /dev/null
+++ b/sci-biology/pysamstats/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>mmokrejs@fold.natur.cuni.cz</email>
+ <name>Martin Mokrejs</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci-biology@gentoo.org</email>
+ <name>Gentoo Biology Project</name>
+ </maintainer>
+</pkgmetadata>
diff --git a/sci-biology/pysamstats/pysamstats-0.24.2.ebuild b/sci-biology/pysamstats/pysamstats-0.24.2.ebuild
new file mode 100644
index 0000000..39c5fe4
--- /dev/null
+++ b/sci-biology/pysamstats/pysamstats-0.24.2.ebuild
@@ -0,0 +1,23 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+PYTHON_COMPAT=( python2_7 python3_4 )
+
+inherit distutils-r1
+
+DESCRIPTION="Calculate statistics against genome positions from a SAM, BAM or CRAM file"
+HOMEPAGE="https://github.com/alimanfoo/pysamstats
+ https://pypi.python.org/pypi/pysamstats"
+SRC_URI="mirror://pypi/p/${PN}/${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+IUSE=""
+
+DEPEND="dev-python/cython
+ >=sci-biology/pysam-0.8.4"
+RDEPEND="${DEPEND}"
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/pysamstats/
@ 2018-03-22 23:03 Martin Mokrejs
0 siblings, 0 replies; 4+ messages in thread
From: Martin Mokrejs @ 2018-03-22 23:03 UTC (permalink / raw
To: gentoo-commits
commit: a6fb6ab33ce03df29683bf5d64a4cde95e665318
Author: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Thu Mar 22 23:02:55 2018 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Thu Mar 22 23:02:55 2018 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=a6fb6ab3
sci-biology/pysamstats: drop KEYWORD
needs working pysam, see bug #645060
Package-Manager: Portage-2.3.24, Repoman-2.3.6
sci-biology/pysamstats/pysamstats-0.24.2.ebuild | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/sci-biology/pysamstats/pysamstats-0.24.2.ebuild b/sci-biology/pysamstats/pysamstats-0.24.2.ebuild
index a388be4e5..d6e1350a4 100644
--- a/sci-biology/pysamstats/pysamstats-0.24.2.ebuild
+++ b/sci-biology/pysamstats/pysamstats-0.24.2.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2018 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
EAPI=6
@@ -7,14 +7,14 @@ PYTHON_COMPAT=( python2_7 python3_4 )
inherit distutils-r1
-DESCRIPTION="Calculate statistics against genome positions from a SAM, BAM or CRAM file"
+DESCRIPTION="Calculate stats against genome positions from SAM/BAM/CRAM file"
HOMEPAGE="https://github.com/alimanfoo/pysamstats
https://pypi.python.org/pypi/pysamstats"
SRC_URI="mirror://pypi/p/${PN}/${P}.tar.gz"
LICENSE="MIT"
SLOT="0"
-KEYWORDS="~amd64"
+KEYWORDS="" # needs working pysam, see bug #645060
IUSE=""
DEPEND="dev-python/cython
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/pysamstats/
@ 2021-01-05 6:08 Horea Christian
0 siblings, 0 replies; 4+ messages in thread
From: Horea Christian @ 2021-01-05 6:08 UTC (permalink / raw
To: gentoo-commits
commit: feaaa59c1d2f9181bcd111cabbc841f89b9b3d41
Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Mon Jan 4 12:59:18 2021 +0000
Commit: Horea Christian <horea.christ <AT> gmail <DOT> com>
CommitDate: Tue Jan 5 06:07:59 2021 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=feaaa59c
sci-biology/pysamstats: bump py targets, add keywords
Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>
Signed-off-by: Horea Christian <chr <AT> chymera.eu>
sci-biology/pysamstats/pysamstats-1.1.2.ebuild | 31 +++++++++++++++-----------
1 file changed, 18 insertions(+), 13 deletions(-)
diff --git a/sci-biology/pysamstats/pysamstats-1.1.2.ebuild b/sci-biology/pysamstats/pysamstats-1.1.2.ebuild
index 06bb7c69b..445ec2162 100644
--- a/sci-biology/pysamstats/pysamstats-1.1.2.ebuild
+++ b/sci-biology/pysamstats/pysamstats-1.1.2.ebuild
@@ -1,25 +1,30 @@
-# Copyright 1999-2020 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
# Distributed under the terms of the GNU General Public License v2
-EAPI=6
+EAPI=7
-PYTHON_COMPAT=( python2_7 python3_4 )
+PYTHON_COMPAT=( python3_{7,8,9} )
inherit distutils-r1
DESCRIPTION="Calculate stats against genome positions from SAM/BAM/CRAM file"
HOMEPAGE="https://github.com/alimanfoo/pysamstats
https://pypi.python.org/pypi/pysamstats"
-SRC_URI="mirror://pypi/p/${PN}/${P}.tar.gz"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
LICENSE="MIT"
SLOT="0"
-KEYWORDS="" # needs working pysam, see bug #645060
-IUSE=""
-
-DEPEND="
- dev-python/cython
- dev-python/numpy
- dev-python/pytables
- >=sci-biology/pysam-0.15.1"
-RDEPEND="${DEPEND}"
+KEYWORDS="~amd64 ~x86"
+
+# TODO: fix this
+# ModuleNotFoundError: No module named 'pysamstats.opt'
+# happens even with the --install option
+RESTRICT="test"
+
+BDEPEND="dev-python/cython[${PYTHON_USEDEP}]"
+RDEPEND="
+ dev-python/numpy[${PYTHON_USEDEP}]
+ sci-biology/pysam[${PYTHON_USEDEP}]
+"
+
+distutils_enable_tests pytest
^ permalink raw reply related [flat|nested] 4+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/pysamstats/
@ 2023-05-02 12:15 Andrew Ammerlaan
0 siblings, 0 replies; 4+ messages in thread
From: Andrew Ammerlaan @ 2023-05-02 12:15 UTC (permalink / raw
To: gentoo-commits
commit: 2a18d4692818d5745073530283176f88b955b27f
Author: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
AuthorDate: Tue May 2 12:10:47 2023 +0000
Commit: Andrew Ammerlaan <andrewammerlaan <AT> gentoo <DOT> org>
CommitDate: Tue May 2 12:15:17 2023 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=2a18d469
sci-biology/pysamstats: treeclean
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> gentoo.org>
sci-biology/pysamstats/metadata.xml | 16 --------------
sci-biology/pysamstats/pysamstats-1.1.2.ebuild | 30 --------------------------
2 files changed, 46 deletions(-)
diff --git a/sci-biology/pysamstats/metadata.xml b/sci-biology/pysamstats/metadata.xml
deleted file mode 100644
index cc923c1df..000000000
--- a/sci-biology/pysamstats/metadata.xml
+++ /dev/null
@@ -1,16 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <maintainer type="person">
- <email>mmokrejs@fold.natur.cuni.cz</email>
- <name>Martin Mokrejs</name>
- </maintainer>
- <maintainer type="project">
- <email>sci-biology@gentoo.org</email>
- <name>Gentoo Biology Project</name>
- </maintainer>
- <upstream>
- <remote-id type="github">alimanfoo/pysamstats</remote-id>
- <remote-id type="pypi">pysamstats</remote-id>
- </upstream>
-</pkgmetadata>
diff --git a/sci-biology/pysamstats/pysamstats-1.1.2.ebuild b/sci-biology/pysamstats/pysamstats-1.1.2.ebuild
deleted file mode 100644
index 445ec2162..000000000
--- a/sci-biology/pysamstats/pysamstats-1.1.2.ebuild
+++ /dev/null
@@ -1,30 +0,0 @@
-# Copyright 1999-2021 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=7
-
-PYTHON_COMPAT=( python3_{7,8,9} )
-
-inherit distutils-r1
-
-DESCRIPTION="Calculate stats against genome positions from SAM/BAM/CRAM file"
-HOMEPAGE="https://github.com/alimanfoo/pysamstats
- https://pypi.python.org/pypi/pysamstats"
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-
-# TODO: fix this
-# ModuleNotFoundError: No module named 'pysamstats.opt'
-# happens even with the --install option
-RESTRICT="test"
-
-BDEPEND="dev-python/cython[${PYTHON_USEDEP}]"
-RDEPEND="
- dev-python/numpy[${PYTHON_USEDEP}]
- sci-biology/pysam[${PYTHON_USEDEP}]
-"
-
-distutils_enable_tests pytest
^ permalink raw reply related [flat|nested] 4+ messages in thread
end of thread, other threads:[~2023-05-02 12:15 UTC | newest]
Thread overview: 4+ messages (download: mbox.gz follow: Atom feed
-- links below jump to the message on this page --
2018-03-22 23:03 [gentoo-commits] proj/sci:master commit in: sci-biology/pysamstats/ Martin Mokrejs
-- strict thread matches above, loose matches on Subject: below --
2023-05-02 12:15 Andrew Ammerlaan
2021-01-05 6:08 Horea Christian
2016-04-11 13:07 Martin Mokrejs
This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox