[gentoo-commits] proj/sci:master commit in: sci-biology/cutadapt/, sci-biology/cutadapt/files/

2021-05-20 Thread Aisha Tammy 
commit: baf55ad9bd948fa0762f6251d7388f3226c9920d
Author: Aisha Tammy  aisha  cc>
AuthorDate: Fri May 21 02:01:45 2021 +
Commit: Aisha Tammy  aisha  cc>
CommitDate: Fri May 21 02:02:03 2021 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=baf55ad9

sci-biology/cutadapt: version bump to 3.3

Package-Manager: Portage-3.0.18, Repoman-3.0.3
Signed-off-by: Aisha Tammy  aisha.cc>

 sci-biology/cutadapt/cutadapt-3.3.ebuild   | 42 ++
 .../cutadapt/files/cutadapt-3.3-skiptest.patch | 13 +++
 2 files changed, 55 insertions(+)

diff --git a/sci-biology/cutadapt/cutadapt-3.3.ebuild 
b/sci-biology/cutadapt/cutadapt-3.3.ebuild
new file mode 100644
index 0..e1990f222
--- /dev/null
+++ b/sci-biology/cutadapt/cutadapt-3.3.ebuild
@@ -0,0 +1,42 @@
+# 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
+
+DESCRIPTION="Remove adapter sequences from high-throughput sequencing data"
+HOMEPAGE="https://github.com/marcelm/cutadapt";
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="
+   dev-python/dnaio[${PYTHON_USEDEP}]
+   dev-python/xopen[${PYTHON_USEDEP}]
+"
+RDEPEND="
+   ${PYTHON_DEPS}
+   ${DEPEND}
+"
+BDEPEND="
+   test? (
+   dev-python/cython
+   dev-python/pytest-mock
+   dev-python/pytest-timeout
+   )
+"
+
+PATCHES=( "${FILESDIR}"/${PN}-3.3-skiptest.patch )
+
+distutils_enable_tests pytest
+
+# needs call to installed cutadapt executable
+python_test() {
+   distutils_install_for_testing
+   pytest -vv || die "pytest failed with ${EPYTHON}"
+}

diff --git a/sci-biology/cutadapt/files/cutadapt-3.3-skiptest.patch 
b/sci-biology/cutadapt/files/cutadapt-3.3-skiptest.patch
new file mode 100644
index 0..c2dc2a741
--- /dev/null
+++ b/sci-biology/cutadapt/files/cutadapt-3.3-skiptest.patch
@@ -0,0 +1,13 @@
+diff --git a/tests/test_command.py b/tests/test_command.py
+index a81b04a..cf40233 100644
+--- a/tests/test_command.py
 b/tests/test_command.py
+@@ -76,7 +76,7 @@ def test_force_fasta_output(tmpdir, cores):
+ assert_files_equal(cutpath("small.fasta"), out_path)
+ 
+ 
+-@pytest.mark.skipif(sys.platform == "win32", reason="Maybe this can be made 
to work")
++@pytest.mark.skipif(reason="Maybe this can be made to work")
+ def test_non_utf8_locale():
+ subprocess.check_call(
+ [sys.executable, "-m", "cutadapt", "-o", os.devnull, 
datapath("small.fastq")],

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

2020-09-22 Thread Aisha Tammy 
commit: 3b6605165f97987a79ac9103821765e835af4d17
Author: Aisha Tammy  aisha  cc>
AuthorDate: Tue Sep 22 00:17:04 2020 +
Commit: Aisha Tammy  aisha  cc>
CommitDate: Tue Sep 22 14:11:41 2020 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=3b660516

sci-biology/cutadapt: update to latest

Package-Manager: Portage-3.0.7, Repoman-3.0.1
Signed-off-by: Aisha Tammy  aisha.cc>

 sci-biology/cutadapt/cutadapt-2.10.ebuild | 42 +++
 sci-biology/cutadapt/metadata.xml |  4 +++
 2 files changed, 46 insertions(+)

diff --git a/sci-biology/cutadapt/cutadapt-2.10.ebuild 
b/sci-biology/cutadapt/cutadapt-2.10.ebuild
new file mode 100644
index 0..e21219dd8
--- /dev/null
+++ b/sci-biology/cutadapt/cutadapt-2.10.ebuild
@@ -0,0 +1,42 @@
+# 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
+
+DESCRIPTION="Remove adapter sequences from high-throughput sequencing data"
+HOMEPAGE="https://github.com/marcelm/cutadapt";
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+
+DEPEND="
+   dev-python/dnaio[${PYTHON_USEDEP}]
+   dev-python/xopen[${PYTHON_USEDEP}]
+"
+RDEPEND="
+   ${PYTHON_DEPS}
+   ${DEPEND}
+"
+BDEPEND="
+   test? (
+   dev-python/cython
+   dev-python/pytest-mock
+   dev-python/pytest-timeout
+   dev-python/sphinx
+   dev-python/sphinx-issues
+   )
+"
+
+distutils_enable_tests pytest
+
+# needs call to installed cutadapt executable
+python_test() {
+   distutils_install_for_testing
+   pytest -vv || die "pytest failed with ${EPYTHON}"
+}

diff --git a/sci-biology/cutadapt/metadata.xml 
b/sci-biology/cutadapt/metadata.xml
index 6099a3fab..6a2aeb852 100644
--- a/sci-biology/cutadapt/metadata.xml
+++ b/sci-biology/cutadapt/metadata.xml
@@ -5,6 +5,10 @@
mmokr...@fold.natur.cuni.cz
Martin Mokrejs

+   
+   gen...@aisha.cc
+   Aisha Tammy
+   

sci-biol...@gentoo.org
Gentoo Biology Project

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

2020-09-22 Thread Aisha Tammy 
commit: 01005268a3dff26c967c8dcd780a573b4e75f9ae
Author: Aisha Tammy  aisha  cc>
AuthorDate: Tue Sep 22 00:18:27 2020 +
Commit: Aisha Tammy  aisha  cc>
CommitDate: Tue Sep 22 14:11:41 2020 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=01005268

sci-biology/cutadapt: drop live version

Package-Manager: Portage-3.0.7, Repoman-3.0.1
Signed-off-by: Aisha Tammy  aisha.cc>

 sci-biology/cutadapt/cutadapt-.ebuild | 19 ---
 1 file changed, 19 deletions(-)

diff --git a/sci-biology/cutadapt/cutadapt-.ebuild 
b/sci-biology/cutadapt/cutadapt-.ebuild
deleted file mode 100644
index 4cbcb5a45..0
--- a/sci-biology/cutadapt/cutadapt-.ebuild
+++ /dev/null
@@ -1,19 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1 git-r3
-
-DESCRIPTION="Remove adapter sequences from high-throughput sequencing data"
-HOMEPAGE="https://github.com/marcelm/cutadapt";
-EGIT_REPO_URI="https://github.com/marcelm/cutadapt";
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS=""
-IUSE=""
-
-DEPEND=">=dev-python/xopen-0.1.1[${PYTHON_USEDEP}]"

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

2020-09-22 Thread Aisha Tammy 
commit: f6e23f9d9c7a74f395fa8b98bc399c8296bd40ff
Author: Aisha Tammy  aisha  cc>
AuthorDate: Tue Sep 22 00:19:03 2020 +
Commit: Aisha Tammy  aisha  cc>
CommitDate: Tue Sep 22 14:11:41 2020 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=f6e23f9d

sci-biology/cutadapt: drop old version

Package-Manager: Portage-3.0.7, Repoman-3.0.1
Signed-off-by: Aisha Tammy  aisha.cc>

 sci-biology/cutadapt/cutadapt-1.9.1.ebuild | 19 ---
 1 file changed, 19 deletions(-)

diff --git a/sci-biology/cutadapt/cutadapt-1.9.1.ebuild 
b/sci-biology/cutadapt/cutadapt-1.9.1.ebuild
deleted file mode 100644
index 7570d57b0..0
--- a/sci-biology/cutadapt/cutadapt-1.9.1.ebuild
+++ /dev/null
@@ -1,19 +0,0 @@
-# Copyright 1999-2017 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="Remove adapter sequences from high-throughput sequencing data"
-HOMEPAGE="https://github.com/marcelm/cutadapt";
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-DEPEND=">=dev-python/xopen-0.1.1[${PYTHON_USEDEP}]"

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

2017-05-21 Thread Martin Mokrejs 
commit: e6074ac17b14d6d2baf11ae676d1d65132f2521b
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Sun May 21 20:06:20 2017 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Sun May 21 20:06:20 2017 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=e6074ac1

sci-biology/cutadapt: add recent new dependency

Package-Manager: Portage-2.3.5, Repoman-2.3.2

 sci-biology/cutadapt/cutadapt-1.9.1.ebuild | 4 +++-
 sci-biology/cutadapt/cutadapt-.ebuild  | 4 +++-
 2 files changed, 6 insertions(+), 2 deletions(-)

diff --git a/sci-biology/cutadapt/cutadapt-1.9.1.ebuild 
b/sci-biology/cutadapt/cutadapt-1.9.1.ebuild
index bd412150b..7570d57b0 100644
--- a/sci-biology/cutadapt/cutadapt-1.9.1.ebuild
+++ b/sci-biology/cutadapt/cutadapt-1.9.1.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
@@ -15,3 +15,5 @@ LICENSE="MIT"
 SLOT="0"
 KEYWORDS="~amd64 ~x86"
 IUSE=""
+
+DEPEND=">=dev-python/xopen-0.1.1[${PYTHON_USEDEP}]"

diff --git a/sci-biology/cutadapt/cutadapt-.ebuild 
b/sci-biology/cutadapt/cutadapt-.ebuild
index 13fc54d09..4cbcb5a45 100644
--- a/sci-biology/cutadapt/cutadapt-.ebuild
+++ b/sci-biology/cutadapt/cutadapt-.ebuild
@@ -1,4 +1,4 @@
-# Copyright 1999-2016 Gentoo Foundation
+# Copyright 1999-2017 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
@@ -15,3 +15,5 @@ LICENSE="MIT"
 SLOT="0"
 KEYWORDS=""
 IUSE=""
+
+DEPEND=">=dev-python/xopen-0.1.1[${PYTHON_USEDEP}]"

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

2016-03-15 Thread Martin Mokrejs 
commit: 6be3a6751679b0fbff675ab05b677d19664963a5
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Tue Mar 15 20:38:21 2016 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Tue Mar 15 20:38:21 2016 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=6be3a675

sci-biology/cutadapt: version bump and remove old ones; update HOMEPAGE

Package-Manager: portage-2.2.26

 sci-biology/cutadapt/cutadapt-1.4.1.ebuild | 18 --
 sci-biology/cutadapt/cutadapt-1.5.ebuild   | 18 --
 .../{cutadapt-1.2.1.ebuild => cutadapt-1.9.1.ebuild}   |  2 +-
 sci-biology/cutadapt/cutadapt-.ebuild  |  2 +-
 4 files changed, 2 insertions(+), 38 deletions(-)

diff --git a/sci-biology/cutadapt/cutadapt-1.4.1.ebuild 
b/sci-biology/cutadapt/cutadapt-1.4.1.ebuild
deleted file mode 100644
index 46b6071..000
--- a/sci-biology/cutadapt/cutadapt-1.4.1.ebuild
+++ /dev/null
@@ -1,18 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="Remove adapter sequences from high-throughput sequencing data"
-HOMEPAGE="https://code.google.com/p/cutadapt/";
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""

diff --git a/sci-biology/cutadapt/cutadapt-1.5.ebuild 
b/sci-biology/cutadapt/cutadapt-1.5.ebuild
deleted file mode 100644
index 46b6071..000
--- a/sci-biology/cutadapt/cutadapt-1.5.ebuild
+++ /dev/null
@@ -1,18 +0,0 @@
-# Copyright 1999-2016 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Id$
-
-EAPI=6
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit distutils-r1
-
-DESCRIPTION="Remove adapter sequences from high-throughput sequencing data"
-HOMEPAGE="https://code.google.com/p/cutadapt/";
-SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
-
-LICENSE="MIT"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""

diff --git a/sci-biology/cutadapt/cutadapt-1.2.1.ebuild 
b/sci-biology/cutadapt/cutadapt-1.9.1.ebuild
similarity index 88%
rename from sci-biology/cutadapt/cutadapt-1.2.1.ebuild
rename to sci-biology/cutadapt/cutadapt-1.9.1.ebuild
index 46b6071..ee91f3c 100644
--- a/sci-biology/cutadapt/cutadapt-1.2.1.ebuild
+++ b/sci-biology/cutadapt/cutadapt-1.9.1.ebuild
@@ -9,7 +9,7 @@ PYTHON_COMPAT=( python2_7 )
 inherit distutils-r1
 
 DESCRIPTION="Remove adapter sequences from high-throughput sequencing data"
-HOMEPAGE="https://code.google.com/p/cutadapt/";
+HOMEPAGE="https://github.com/marcelm/cutadapt";
 SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
 
 LICENSE="MIT"

diff --git a/sci-biology/cutadapt/cutadapt-.ebuild 
b/sci-biology/cutadapt/cutadapt-.ebuild
index 46c2382..213ea85 100644
--- a/sci-biology/cutadapt/cutadapt-.ebuild
+++ b/sci-biology/cutadapt/cutadapt-.ebuild
@@ -9,7 +9,7 @@ PYTHON_COMPAT=( python2_7 )
 inherit distutils-r1 git-r3
 
 DESCRIPTION="Remove adapter sequences from high-throughput sequencing data"
-HOMEPAGE="https://code.google.com/p/cutadapt/";
+HOMEPAGE="https://github.com/marcelm/cutadapt";
 EGIT_REPO_URI="https://github.com/marcelm/cutadapt";
 
 LICENSE="MIT"

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

2016-02-14 Thread Justin Lecher 
commit: 160fcc1ada2d510b4b5ebb171d08b3e367d707bf
Author: Justin Lecher  gentoo  org>
AuthorDate: Sun Feb 14 17:28:16 2016 +
Commit: Justin Lecher  gentoo  org>
CommitDate: Sun Feb 14 17:28:16 2016 +
URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=160fcc1a

sci-biology/cutadapt: Bump to EAPI=6

* Use git-r3.eclass * drop multiversion code

Package-Manager: portage-2.2.27
Signed-off-by: Justin Lecher  gentoo.org>

 sci-biology/cutadapt/cutadapt-1.2.1.ebuild | 15 ---
 sci-biology/cutadapt/cutadapt-1.4.1.ebuild | 15 ---
 sci-biology/cutadapt/cutadapt-1.5.ebuild   | 15 ---
 sci-biology/cutadapt/cutadapt-.ebuild  | 17 +
 4 files changed, 17 insertions(+), 45 deletions(-)

diff --git a/sci-biology/cutadapt/cutadapt-1.2.1.ebuild 
b/sci-biology/cutadapt/cutadapt-1.2.1.ebuild
index 0ad277b..46b6071 100644
--- a/sci-biology/cutadapt/cutadapt-1.2.1.ebuild
+++ b/sci-biology/cutadapt/cutadapt-1.2.1.ebuild
@@ -1,25 +1,18 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=5
+EAPI=6
 
 PYTHON_COMPAT=( python2_7 )
 
 inherit distutils-r1
 
-[ "$PV" == "" ] && inherit git-2
-
 DESCRIPTION="Remove adapter sequences from high-throughput sequencing data"
 HOMEPAGE="https://code.google.com/p/cutadapt/";
-if [ "$PV" == "" ]; then
-   EGIT_REPO_URI="https://github.com/marcelm/cutadapt";
-   KEYWORDS=""
-else
-   SRC_URI="mirror://pypi/c/${PN}/${P}.tar.gz"
-   KEYWORDS="~amd64 ~x86"
-fi
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
 
 LICENSE="MIT"
 SLOT="0"
+KEYWORDS="~amd64 ~x86"
 IUSE=""

diff --git a/sci-biology/cutadapt/cutadapt-1.4.1.ebuild 
b/sci-biology/cutadapt/cutadapt-1.4.1.ebuild
index 0ad277b..46b6071 100644
--- a/sci-biology/cutadapt/cutadapt-1.4.1.ebuild
+++ b/sci-biology/cutadapt/cutadapt-1.4.1.ebuild
@@ -1,25 +1,18 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=5
+EAPI=6
 
 PYTHON_COMPAT=( python2_7 )
 
 inherit distutils-r1
 
-[ "$PV" == "" ] && inherit git-2
-
 DESCRIPTION="Remove adapter sequences from high-throughput sequencing data"
 HOMEPAGE="https://code.google.com/p/cutadapt/";
-if [ "$PV" == "" ]; then
-   EGIT_REPO_URI="https://github.com/marcelm/cutadapt";
-   KEYWORDS=""
-else
-   SRC_URI="mirror://pypi/c/${PN}/${P}.tar.gz"
-   KEYWORDS="~amd64 ~x86"
-fi
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
 
 LICENSE="MIT"
 SLOT="0"
+KEYWORDS="~amd64 ~x86"
 IUSE=""

diff --git a/sci-biology/cutadapt/cutadapt-1.5.ebuild 
b/sci-biology/cutadapt/cutadapt-1.5.ebuild
index 0ad277b..46b6071 100644
--- a/sci-biology/cutadapt/cutadapt-1.5.ebuild
+++ b/sci-biology/cutadapt/cutadapt-1.5.ebuild
@@ -1,25 +1,18 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=5
+EAPI=6
 
 PYTHON_COMPAT=( python2_7 )
 
 inherit distutils-r1
 
-[ "$PV" == "" ] && inherit git-2
-
 DESCRIPTION="Remove adapter sequences from high-throughput sequencing data"
 HOMEPAGE="https://code.google.com/p/cutadapt/";
-if [ "$PV" == "" ]; then
-   EGIT_REPO_URI="https://github.com/marcelm/cutadapt";
-   KEYWORDS=""
-else
-   SRC_URI="mirror://pypi/c/${PN}/${P}.tar.gz"
-   KEYWORDS="~amd64 ~x86"
-fi
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
 
 LICENSE="MIT"
 SLOT="0"
+KEYWORDS="~amd64 ~x86"
 IUSE=""

diff --git a/sci-biology/cutadapt/cutadapt-.ebuild 
b/sci-biology/cutadapt/cutadapt-.ebuild
index 2d94832..46c2382 100644
--- a/sci-biology/cutadapt/cutadapt-.ebuild
+++ b/sci-biology/cutadapt/cutadapt-.ebuild
@@ -1,25 +1,18 @@
-# Copyright 1999-2014 Gentoo Foundation
+# Copyright 1999-2016 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
 # $Id$
 
-EAPI=5
+EAPI=6
 
 PYTHON_COMPAT=( python2_7 )
 
-inherit distutils-r1
-
-[ "$PV" == "" ] && inherit git-2
+inherit distutils-r1 git-r3
 
 DESCRIPTION="Remove adapter sequences from high-throughput sequencing data"
 HOMEPAGE="https://code.google.com/p/cutadapt/";
-if [ "$PV" == "" ]; then
-   EGIT_REPO_URI="https://github.com/marcelm/cutadapt";
-   KEYWORDS=""
-else
-   
SRC_URI="https://pypi.python.org/packages/source/c/cutadapt/"${PN}"-"${PV}".tar.gz";
-   KEYWORDS="~amd64 ~x86"
-fi
+EGIT_REPO_URI="https://github.com/marcelm/cutadapt";
 
 LICENSE="MIT"
 SLOT="0"
+KEYWORDS=""
 IUSE=""

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

2014-09-11 Thread Jauhien Piatlicki 
commit: bfe36351e943ded8d08f95ea4c8df7a62be72f86
Author: Jauhien Piatlicki  gentoo  org>
AuthorDate: Thu Sep 11 15:38:36 2014 +
Commit: Jauhien Piatlicki  gentoo  org>
CommitDate: Thu Sep 11 15:38:36 2014 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=bfe36351

sci-biology/cutadapt: version bump

---
 sci-biology/cutadapt/ChangeLog   |  5 +
 sci-biology/cutadapt/cutadapt-1.5.ebuild | 25 +
 2 files changed, 30 insertions(+)

diff --git a/sci-biology/cutadapt/ChangeLog b/sci-biology/cutadapt/ChangeLog
index 3ed05cf..29f4e2e 100644
--- a/sci-biology/cutadapt/ChangeLog
+++ b/sci-biology/cutadapt/ChangeLog
@@ -2,6 +2,11 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*cutadapt-1.5 (11 Sep 2014)
+
+  11 Sep 2014; Jauhien Piatlicki  +cutadapt-1.5.ebuild:
+  version bump
+
   11 Sep 2014; Jauhien Piatlicki  cutadapt-1.2.1.ebuild,
   cutadapt-1.4.1.ebuild:
   fix SRC_URI

diff --git a/sci-biology/cutadapt/cutadapt-1.5.ebuild 
b/sci-biology/cutadapt/cutadapt-1.5.ebuild
new file mode 100644
index 000..49d7ae6
--- /dev/null
+++ b/sci-biology/cutadapt/cutadapt-1.5.ebuild
@@ -0,0 +1,25 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=5
+
+PYTHON_COMPAT=( python{2_6,2_7} )
+
+inherit distutils-r1
+
+[ "$PV" == "" ] && inherit git-2
+
+DESCRIPTION="Remove adapter sequences from high-throughput sequencing data"
+HOMEPAGE="https://code.google.com/p/cutadapt/";
+if [ "$PV" == "" ]; then
+   EGIT_REPO_URI="https://github.com/marcelm/cutadapt";
+   KEYWORDS=""
+else
+   SRC_URI="mirror://pypi/c/${PN}/${P}.tar.gz"
+   KEYWORDS="~amd64 ~x86"
+fi
+
+LICENSE="MIT"
+SLOT="0"
+IUSE=""

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

2014-09-11 Thread Jauhien Piatlicki 
commit: 4b04b146b2efedc84b0f1b1b2739b663d32a1fcf
Author: Jauhien Piatlicki  gentoo  org>
AuthorDate: Thu Sep 11 15:34:49 2014 +
Commit: Jauhien Piatlicki  gentoo  org>
CommitDate: Thu Sep 11 15:34:49 2014 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=4b04b146

sci-biology/cutadapt: fix SRC_URI

---
 sci-biology/cutadapt/ChangeLog | 6 +-
 sci-biology/cutadapt/cutadapt-1.2.1.ebuild | 2 +-
 sci-biology/cutadapt/cutadapt-1.4.1.ebuild | 2 +-
 3 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/sci-biology/cutadapt/ChangeLog b/sci-biology/cutadapt/ChangeLog
index 8b0823d..3ed05cf 100644
--- a/sci-biology/cutadapt/ChangeLog
+++ b/sci-biology/cutadapt/ChangeLog
@@ -1,7 +1,11 @@
 # ChangeLog for sci-biology/cutadapt
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  11 Sep 2014; Jauhien Piatlicki  cutadapt-1.2.1.ebuild,
+  cutadapt-1.4.1.ebuild:
+  fix SRC_URI
+
   16 Jun 2013; Justin Lecher  -cutadapt-1.0.ebuild,
   +cutadapt-1.2.1.ebuild, metadata.xml:
   Version Bump; Bump to EAPI5 and distutils-r1.eclass

diff --git a/sci-biology/cutadapt/cutadapt-1.2.1.ebuild 
b/sci-biology/cutadapt/cutadapt-1.2.1.ebuild
index 985fa12..49d7ae6 100644
--- a/sci-biology/cutadapt/cutadapt-1.2.1.ebuild
+++ b/sci-biology/cutadapt/cutadapt-1.2.1.ebuild
@@ -16,7 +16,7 @@ if [ "$PV" == "" ]; then
EGIT_REPO_URI="https://github.com/marcelm/cutadapt";
KEYWORDS=""
 else
-   
SRC_URI="https://pypi.python.org/packages/source/c/cutadapt/"${PN}"-"${PV}".tar.gz";
+   SRC_URI="mirror://pypi/c/${PN}/${P}.tar.gz"
KEYWORDS="~amd64 ~x86"
 fi
 

diff --git a/sci-biology/cutadapt/cutadapt-1.4.1.ebuild 
b/sci-biology/cutadapt/cutadapt-1.4.1.ebuild
index 985fa12..49d7ae6 100644
--- a/sci-biology/cutadapt/cutadapt-1.4.1.ebuild
+++ b/sci-biology/cutadapt/cutadapt-1.4.1.ebuild
@@ -16,7 +16,7 @@ if [ "$PV" == "" ]; then
EGIT_REPO_URI="https://github.com/marcelm/cutadapt";
KEYWORDS=""
 else
-   
SRC_URI="https://pypi.python.org/packages/source/c/cutadapt/"${PN}"-"${PV}".tar.gz";
+   SRC_URI="mirror://pypi/c/${PN}/${P}.tar.gz"
KEYWORDS="~amd64 ~x86"
 fi

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

2014-03-25 Thread Martin Mokrejs 
commit: db87525a418029e3903315e6c4e74c28e385999a
Author: Martin Mokrejš  fold  natur  cuni  cz>
AuthorDate: Tue Mar 25 10:46:02 2014 +
Commit: Martin Mokrejs  fold  natur  cuni  cz>
CommitDate: Tue Mar 25 10:46:02 2014 +
URL:
http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=db87525a

sci-biology/cutadapt: switch to use newer source code location, add support for 
github snapshots, version bump

---
 sci-biology/cutadapt/cutadapt-1.2.1.ebuild| 11 +--
 .../cutadapt/{cutadapt-1.2.1.ebuild => cutadapt-1.4.1.ebuild} | 11 +--
 .../cutadapt/{cutadapt-1.2.1.ebuild => cutadapt-.ebuild}  | 11 +--
 3 files changed, 27 insertions(+), 6 deletions(-)

diff --git a/sci-biology/cutadapt/cutadapt-1.2.1.ebuild 
b/sci-biology/cutadapt/cutadapt-1.2.1.ebuild
index 232fd4a..985fa12 100644
--- a/sci-biology/cutadapt/cutadapt-1.2.1.ebuild
+++ b/sci-biology/cutadapt/cutadapt-1.2.1.ebuild
@@ -8,11 +8,18 @@ PYTHON_COMPAT=( python{2_6,2_7} )
 
 inherit distutils-r1
 
+[ "$PV" == "" ] && inherit git-2
+
 DESCRIPTION="Remove adapter sequences from high-throughput sequencing data"
 HOMEPAGE="https://code.google.com/p/cutadapt/";
-SRC_URI="https://cutadapt.googlecode.com/files/"${PN}"-"${PV}".tar.gz";
+if [ "$PV" == "" ]; then
+   EGIT_REPO_URI="https://github.com/marcelm/cutadapt";
+   KEYWORDS=""
+else
+   
SRC_URI="https://pypi.python.org/packages/source/c/cutadapt/"${PN}"-"${PV}".tar.gz";
+   KEYWORDS="~amd64 ~x86"
+fi
 
 LICENSE="MIT"
 SLOT="0"
-KEYWORDS="~amd64 ~x86"
 IUSE=""

diff --git a/sci-biology/cutadapt/cutadapt-1.2.1.ebuild 
b/sci-biology/cutadapt/cutadapt-1.4.1.ebuild
similarity index 57%
copy from sci-biology/cutadapt/cutadapt-1.2.1.ebuild
copy to sci-biology/cutadapt/cutadapt-1.4.1.ebuild
index 232fd4a..985fa12 100644
--- a/sci-biology/cutadapt/cutadapt-1.2.1.ebuild
+++ b/sci-biology/cutadapt/cutadapt-1.4.1.ebuild
@@ -8,11 +8,18 @@ PYTHON_COMPAT=( python{2_6,2_7} )
 
 inherit distutils-r1
 
+[ "$PV" == "" ] && inherit git-2
+
 DESCRIPTION="Remove adapter sequences from high-throughput sequencing data"
 HOMEPAGE="https://code.google.com/p/cutadapt/";
-SRC_URI="https://cutadapt.googlecode.com/files/"${PN}"-"${PV}".tar.gz";
+if [ "$PV" == "" ]; then
+   EGIT_REPO_URI="https://github.com/marcelm/cutadapt";
+   KEYWORDS=""
+else
+   
SRC_URI="https://pypi.python.org/packages/source/c/cutadapt/"${PN}"-"${PV}".tar.gz";
+   KEYWORDS="~amd64 ~x86"
+fi
 
 LICENSE="MIT"
 SLOT="0"
-KEYWORDS="~amd64 ~x86"
 IUSE=""

diff --git a/sci-biology/cutadapt/cutadapt-1.2.1.ebuild 
b/sci-biology/cutadapt/cutadapt-.ebuild
similarity index 57%
copy from sci-biology/cutadapt/cutadapt-1.2.1.ebuild
copy to sci-biology/cutadapt/cutadapt-.ebuild
index 232fd4a..985fa12 100644
--- a/sci-biology/cutadapt/cutadapt-1.2.1.ebuild
+++ b/sci-biology/cutadapt/cutadapt-.ebuild
@@ -8,11 +8,18 @@ PYTHON_COMPAT=( python{2_6,2_7} )
 
 inherit distutils-r1
 
+[ "$PV" == "" ] && inherit git-2
+
 DESCRIPTION="Remove adapter sequences from high-throughput sequencing data"
 HOMEPAGE="https://code.google.com/p/cutadapt/";
-SRC_URI="https://cutadapt.googlecode.com/files/"${PN}"-"${PV}".tar.gz";
+if [ "$PV" == "" ]; then
+   EGIT_REPO_URI="https://github.com/marcelm/cutadapt";
+   KEYWORDS=""
+else
+   
SRC_URI="https://pypi.python.org/packages/source/c/cutadapt/"${PN}"-"${PV}".tar.gz";
+   KEYWORDS="~amd64 ~x86"
+fi
 
 LICENSE="MIT"
 SLOT="0"
-KEYWORDS="~amd64 ~x86"
 IUSE=""