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

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* [gentoo-commits] proj/sci:master commit in: sci-biology/cutadapt/
@ 2012-03-03  1:15 Martin Mokrejs
  0 siblings, 0 replies; 11+ messages in thread
From: Martin Mokrejs @ 2012-03-03  1:15 UTC (permalink / raw
  To: gentoo-commits

commit:     eb39645b99fda8b346992ac6eaa4a3e90d8b0317
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Mar  3 01:15:23 2012 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Mar  3 01:15:23 2012 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=eb39645b

sci-biology/cutadapt: new package

(Portage version: 2.1.10.49/git/Linux x86_64, unsigned Manifest commit)

---
 sci-biology/cutadapt/ChangeLog           |   10 ++++++++++
 sci-biology/cutadapt/cutadapt-1.0.ebuild |   21 +++++++++++++++++++++
 sci-biology/cutadapt/metadata.xml        |    9 +++++++++
 3 files changed, 40 insertions(+), 0 deletions(-)

diff --git a/sci-biology/cutadapt/ChangeLog b/sci-biology/cutadapt/ChangeLog
new file mode 100644
index 0000000..7a23b4e
--- /dev/null
+++ b/sci-biology/cutadapt/ChangeLog
@@ -0,0 +1,10 @@
+# ChangeLog for sci-biology/cutadapt
+# Copyright 1999-2012 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*cutadapt-1.0 (02 Mar 2012)
+
+  02 Mar 2012; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  +cutadapt-1.0.ebuild, +metadata.xml:
+  initial ebuild
+

diff --git a/sci-biology/cutadapt/cutadapt-1.0.ebuild b/sci-biology/cutadapt/cutadapt-1.0.ebuild
new file mode 100644
index 0000000..add090c
--- /dev/null
+++ b/sci-biology/cutadapt/cutadapt-1.0.ebuild
@@ -0,0 +1,21 @@
+# Copyright 1999-2012 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=2
+PYTHON_DEPEND="2:2.6"
+SUPPORT_PYTHON_ABIS="1"
+
+inherit distutils
+
+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"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}"

diff --git a/sci-biology/cutadapt/metadata.xml b/sci-biology/cutadapt/metadata.xml
new file mode 100644
index 0000000..07b5255
--- /dev/null
+++ b/sci-biology/cutadapt/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>mmokrejs@fold.natur.cuni.cz</email>
+		<name>Martin Mokrejs</name>
+	</maintainer>
+</pkgmetadata>



^ permalink raw reply related	[flat|nested] 11+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/cutadapt/
@ 2014-03-25 10:48 Martin Mokrejs
  0 siblings, 0 replies; 11+ messages in thread
From: Martin Mokrejs @ 2014-03-25 10:48 UTC (permalink / raw
  To: gentoo-commits

commit:     db87525a418029e3903315e6c4e74c28e385999a
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Mar 25 10:46:02 2014 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Mar 25 10:46:02 2014 +0000
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-9999.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
 
+[ "$PV" == "9999" ] && inherit git-2
+
 DESCRIPTION="Remove adapter sequences from high-throughput sequencing data"
 HOMEPAGE="https://code.google.com/p/cutadapt/"
-SRC_URI="https://cutadapt.googlecode.com/files/"${PN}"-"${PV}".tar.gz"
+if [ "$PV" == "9999" ]; 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
 
+[ "$PV" == "9999" ] && inherit git-2
+
 DESCRIPTION="Remove adapter sequences from high-throughput sequencing data"
 HOMEPAGE="https://code.google.com/p/cutadapt/"
-SRC_URI="https://cutadapt.googlecode.com/files/"${PN}"-"${PV}".tar.gz"
+if [ "$PV" == "9999" ]; 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-9999.ebuild
similarity index 57%
copy from sci-biology/cutadapt/cutadapt-1.2.1.ebuild
copy to sci-biology/cutadapt/cutadapt-9999.ebuild
index 232fd4a..985fa12 100644
--- a/sci-biology/cutadapt/cutadapt-1.2.1.ebuild
+++ b/sci-biology/cutadapt/cutadapt-9999.ebuild
@@ -8,11 +8,18 @@ PYTHON_COMPAT=( python{2_6,2_7} )
 
 inherit distutils-r1
 
+[ "$PV" == "9999" ] && inherit git-2
+
 DESCRIPTION="Remove adapter sequences from high-throughput sequencing data"
 HOMEPAGE="https://code.google.com/p/cutadapt/"
-SRC_URI="https://cutadapt.googlecode.com/files/"${PN}"-"${PV}".tar.gz"
+if [ "$PV" == "9999" ]; 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=""


^ permalink raw reply related	[flat|nested] 11+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/cutadapt/
@ 2014-09-11 15:38 Jauhien Piatlicki
  0 siblings, 0 replies; 11+ messages in thread
From: Jauhien Piatlicki @ 2014-09-11 15:38 UTC (permalink / raw
  To: gentoo-commits

commit:     4b04b146b2efedc84b0f1b1b2739b663d32a1fcf
Author:     Jauhien Piatlicki <jauhien <AT> gentoo <DOT> org>
AuthorDate: Thu Sep 11 15:34:49 2014 +0000
Commit:     Jauhien Piatlicki <jauhien <AT> gentoo <DOT> org>
CommitDate: Thu Sep 11 15:34:49 2014 +0000
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 <jauhien@gentoo.org> cutadapt-1.2.1.ebuild,
+  cutadapt-1.4.1.ebuild:
+  fix SRC_URI
+
   16 Jun 2013; Justin Lecher <jlec@gentoo.org> -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 [ "$PV" == "9999" ]; then
 	EGIT_REPO_URI="https://github.com/marcelm/cutadapt"
 	KEYWORDS=""
 else
-	SRC_URI="https://pypi.python.org/packages/source/c/cutadapt/"${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 [ "$PV" == "9999" ]; then
 	EGIT_REPO_URI="https://github.com/marcelm/cutadapt"
 	KEYWORDS=""
 else
-	SRC_URI="https://pypi.python.org/packages/source/c/cutadapt/"${PN}"-"${PV}".tar.gz"
+	SRC_URI="mirror://pypi/c/${PN}/${P}.tar.gz"
 	KEYWORDS="~amd64 ~x86"
 fi
 


^ permalink raw reply related	[flat|nested] 11+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/cutadapt/
@ 2014-09-11 15:38 Jauhien Piatlicki
  0 siblings, 0 replies; 11+ messages in thread
From: Jauhien Piatlicki @ 2014-09-11 15:38 UTC (permalink / raw
  To: gentoo-commits

commit:     bfe36351e943ded8d08f95ea4c8df7a62be72f86
Author:     Jauhien Piatlicki <jauhien <AT> gentoo <DOT> org>
AuthorDate: Thu Sep 11 15:38:36 2014 +0000
Commit:     Jauhien Piatlicki <jauhien <AT> gentoo <DOT> org>
CommitDate: Thu Sep 11 15:38:36 2014 +0000
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 <jauhien@gentoo.org> +cutadapt-1.5.ebuild:
+  version bump
+
   11 Sep 2014; Jauhien Piatlicki <jauhien@gentoo.org> 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 0000000..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
+
+[ "$PV" == "9999" ] && inherit git-2
+
+DESCRIPTION="Remove adapter sequences from high-throughput sequencing data"
+HOMEPAGE="https://code.google.com/p/cutadapt/"
+if [ "$PV" == "9999" ]; 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=""


^ permalink raw reply related	[flat|nested] 11+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/cutadapt/
@ 2016-02-14 17:32 Justin Lecher
  0 siblings, 0 replies; 11+ messages in thread
From: Justin Lecher @ 2016-02-14 17:32 UTC (permalink / raw
  To: gentoo-commits

commit:     160fcc1ada2d510b4b5ebb171d08b3e367d707bf
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Feb 14 17:28:16 2016 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Feb 14 17:28:16 2016 +0000
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 <jlec <AT> 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-9999.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
 
-[ "$PV" == "9999" ] && inherit git-2
-
 DESCRIPTION="Remove adapter sequences from high-throughput sequencing data"
 HOMEPAGE="https://code.google.com/p/cutadapt/"
-if [ "$PV" == "9999" ]; 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
 
-[ "$PV" == "9999" ] && inherit git-2
-
 DESCRIPTION="Remove adapter sequences from high-throughput sequencing data"
 HOMEPAGE="https://code.google.com/p/cutadapt/"
-if [ "$PV" == "9999" ]; 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
 
-[ "$PV" == "9999" ] && inherit git-2
-
 DESCRIPTION="Remove adapter sequences from high-throughput sequencing data"
 HOMEPAGE="https://code.google.com/p/cutadapt/"
-if [ "$PV" == "9999" ]; 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-9999.ebuild b/sci-biology/cutadapt/cutadapt-9999.ebuild
index 2d94832..46c2382 100644
--- a/sci-biology/cutadapt/cutadapt-9999.ebuild
+++ b/sci-biology/cutadapt/cutadapt-9999.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" == "9999" ] && 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 [ "$PV" == "9999" ]; then
-	EGIT_REPO_URI="https://github.com/marcelm/cutadapt"
-	KEYWORDS=""
-else
-	SRC_URI="https://pypi.python.org/packages/source/c/cutadapt/"${PN}"-"${PV}".tar.gz"
-	KEYWORDS="~amd64 ~x86"
-fi
+EGIT_REPO_URI="https://github.com/marcelm/cutadapt"
 
 LICENSE="MIT"
 SLOT="0"
+KEYWORDS=""
 IUSE=""


^ permalink raw reply related	[flat|nested] 11+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/cutadapt/
@ 2016-03-15 20:42 Martin Mokrejs
  0 siblings, 0 replies; 11+ messages in thread
From: Martin Mokrejs @ 2016-03-15 20:42 UTC (permalink / raw
  To: gentoo-commits

commit:     6be3a6751679b0fbff675ab05b677d19664963a5
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Mar 15 20:38:21 2016 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Mar 15 20:38:21 2016 +0000
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-9999.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..0000000
--- 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..0000000
--- 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-9999.ebuild b/sci-biology/cutadapt/cutadapt-9999.ebuild
index 46c2382..213ea85 100644
--- a/sci-biology/cutadapt/cutadapt-9999.ebuild
+++ b/sci-biology/cutadapt/cutadapt-9999.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"


^ permalink raw reply related	[flat|nested] 11+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/cutadapt/
@ 2017-05-21 20:06 Martin Mokrejs
  0 siblings, 0 replies; 11+ messages in thread
From: Martin Mokrejs @ 2017-05-21 20:06 UTC (permalink / raw
  To: gentoo-commits

commit:     e6074ac17b14d6d2baf11ae676d1d65132f2521b
Author:     Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun May 21 20:06:20 2017 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun May 21 20:06:20 2017 +0000
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-9999.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-9999.ebuild b/sci-biology/cutadapt/cutadapt-9999.ebuild
index 13fc54d09..4cbcb5a45 100644
--- a/sci-biology/cutadapt/cutadapt-9999.ebuild
+++ b/sci-biology/cutadapt/cutadapt-9999.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}]"


^ permalink raw reply related	[flat|nested] 11+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/cutadapt/
@ 2020-09-22 14:15 Aisha Tammy
  0 siblings, 0 replies; 11+ messages in thread
From: Aisha Tammy @ 2020-09-22 14:15 UTC (permalink / raw
  To: gentoo-commits

commit:     01005268a3dff26c967c8dcd780a573b4e75f9ae
Author:     Aisha Tammy <gentoo <AT> aisha <DOT> cc>
AuthorDate: Tue Sep 22 00:18:27 2020 +0000
Commit:     Aisha Tammy <gentoo <AT> aisha <DOT> cc>
CommitDate: Tue Sep 22 14:11:41 2020 +0000
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 <gentoo <AT> aisha.cc>

 sci-biology/cutadapt/cutadapt-9999.ebuild | 19 -------------------
 1 file changed, 19 deletions(-)

diff --git a/sci-biology/cutadapt/cutadapt-9999.ebuild b/sci-biology/cutadapt/cutadapt-9999.ebuild
deleted file mode 100644
index 4cbcb5a45..000000000
--- a/sci-biology/cutadapt/cutadapt-9999.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}]"


^ permalink raw reply related	[flat|nested] 11+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/cutadapt/
@ 2020-09-22 14:15 Aisha Tammy
  0 siblings, 0 replies; 11+ messages in thread
From: Aisha Tammy @ 2020-09-22 14:15 UTC (permalink / raw
  To: gentoo-commits

commit:     3b6605165f97987a79ac9103821765e835af4d17
Author:     Aisha Tammy <gentoo <AT> aisha <DOT> cc>
AuthorDate: Tue Sep 22 00:17:04 2020 +0000
Commit:     Aisha Tammy <gentoo <AT> aisha <DOT> cc>
CommitDate: Tue Sep 22 14:11:41 2020 +0000
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 <gentoo <AT> 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 000000000..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 @@
 		<email>mmokrejs@fold.natur.cuni.cz</email>
 		<name>Martin Mokrejs</name>
 	</maintainer>
+	<maintainer type="person">
+		<email>gentoo@aisha.cc</email>
+		<name>Aisha Tammy</name>
+	</maintainer>
 	<maintainer type="project">
 		<email>sci-biology@gentoo.org</email>
 		<name>Gentoo Biology Project</name>


^ permalink raw reply related	[flat|nested] 11+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/cutadapt/
@ 2020-09-22 14:15 Aisha Tammy
  0 siblings, 0 replies; 11+ messages in thread
From: Aisha Tammy @ 2020-09-22 14:15 UTC (permalink / raw
  To: gentoo-commits

commit:     f6e23f9d9c7a74f395fa8b98bc399c8296bd40ff
Author:     Aisha Tammy <gentoo <AT> aisha <DOT> cc>
AuthorDate: Tue Sep 22 00:19:03 2020 +0000
Commit:     Aisha Tammy <gentoo <AT> aisha <DOT> cc>
CommitDate: Tue Sep 22 14:11:41 2020 +0000
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 <gentoo <AT> 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..000000000
--- 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}]"


^ permalink raw reply related	[flat|nested] 11+ messages in thread

* [gentoo-commits] proj/sci:master commit in: sci-biology/cutadapt/
@ 2024-09-29 13:33 Alexey Shvetsov
  0 siblings, 0 replies; 11+ messages in thread
From: Alexey Shvetsov @ 2024-09-29 13:33 UTC (permalink / raw
  To: gentoo-commits

commit:     fd08b2a5d7d48adea7a3f1d07d3783c15ce0f24b
Author:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
AuthorDate: Sun Sep 29 13:31:30 2024 +0000
Commit:     Alexey Shvetsov <alexxy <AT> gentoo <DOT> org>
CommitDate: Sun Sep 29 13:33:31 2024 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=fd08b2a5

sci-biology/cutadapt: new package, add 4.9

Signed-off-by: Alexey Shvetsov <alexxy <AT> gentoo.org>

 sci-biology/cutadapt/cutadapt-4.9.ebuild | 28 ++++++++++++++++++++++++++++
 sci-biology/cutadapt/metadata.xml        | 12 ++++++++++++
 2 files changed, 40 insertions(+)

diff --git a/sci-biology/cutadapt/cutadapt-4.9.ebuild b/sci-biology/cutadapt/cutadapt-4.9.ebuild
new file mode 100644
index 000000000..cd1a8fe7c
--- /dev/null
+++ b/sci-biology/cutadapt/cutadapt-4.9.ebuild
@@ -0,0 +1,28 @@
+# Copyright 1999-2020 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..13} )
+DISTUTILS_USE_PEP517=setuptools
+
+inherit distutils-r1 pypi
+
+DESCRIPTION="Adapter trimming and other preprocessing of high-throughput sequencing reads"
+HOMEPAGE="https://github.com/marcelm/cutadapt/"
+SRC_URI="$(pypi_sdist_url "${PN^}" "${PV}")"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64"
+
+IUSE="test"
+DEPEND="
+	>=dev-python/xopen-1.6.0[${PYTHON_USEDEP}]
+	>=dev-python/dnaio-1.2.0[${PYTHON_USEDEP}]
+"
+RDEPEND="
+	${DEPEND}
+	test? ( dev-python/pytest )
+"
+distutils_enable_tests pytest

diff --git a/sci-biology/cutadapt/metadata.xml b/sci-biology/cutadapt/metadata.xml
new file mode 100644
index 000000000..028038de8
--- /dev/null
+++ b/sci-biology/cutadapt/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="project">
+		<email>sci@gentoo.org</email>
+		<name>Gentoo Science</name>
+	</maintainer>
+	<upstream>
+		<remote-id type="pypi">cutadapt</remote-id>
+		<remote-id type="github">marcelm/cutadapt</remote-id>
+	</upstream>
+</pkgmetadata>


^ permalink raw reply related	[flat|nested] 11+ messages in thread

end of thread, other threads:[~2024-09-29 13:33 UTC | newest]

Thread overview: 11+ messages (download: mbox.gz follow: Atom feed
-- links below jump to the message on this page --
2014-03-25 10:48 [gentoo-commits] proj/sci:master commit in: sci-biology/cutadapt/ Martin Mokrejs
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2024-09-29 13:33 Alexey Shvetsov
2020-09-22 14:15 Aisha Tammy
2020-09-22 14:15 Aisha Tammy
2020-09-22 14:15 Aisha Tammy
2017-05-21 20:06 Martin Mokrejs
2016-03-15 20:42 Martin Mokrejs
2016-02-14 17:32 Justin Lecher
2014-09-11 15:38 Jauhien Piatlicki
2014-09-11 15:38 Jauhien Piatlicki
2012-03-03  1:15 Martin Mokrejs

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