From: "Justin Lecher" <jlec@gentoo.org>
To: gentoo-commits@lists.gentoo.org
Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/biopython/, sci-biology/biopython/files/
Date: Sun, 29 Dec 2013 00:31:21 +0000 (UTC) [thread overview]
Message-ID: <1388276946.4c137a437dca9f76da755afa10c90f2f67e7059b.jlec@gentoo> (raw)
commit: 4c137a437dca9f76da755afa10c90f2f67e7059b
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Dec 29 00:29:06 2013 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sun Dec 29 00:29:06 2013 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=4c137a43
import into tree
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
---
sci-biology/biopython/ChangeLog | 346 ---------------------
sci-biology/biopython/biopython-1.62-r1.ebuild | 51 ---
.../biopython/files/biopython-1.62-SffIO.patch | 36 ---
sci-biology/biopython/metadata.xml | 5 -
4 files changed, 438 deletions(-)
diff --git a/sci-biology/biopython/ChangeLog b/sci-biology/biopython/ChangeLog
deleted file mode 100644
index baf3b3a..0000000
--- a/sci-biology/biopython/ChangeLog
+++ /dev/null
@@ -1,346 +0,0 @@
-# ChangeLog for sci-biology/biopython
-# Copyright 1999-2013 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/biopython/ChangeLog,v 1.72 2013/09/17 16:07:56 jlec Exp $
-
-*biopython-1.62-r1 (25 Sep 2013)
-
- 25 Sep 2013; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
- +biopython-1.62-r1.ebuild, +files/biopython-1.51-flex.patch,
- +files/biopython-1.62-SffIO.patch, +files/SeqRecord.py.patch,
- +files/adjust-trimpoints.patch, +metadata.xml:
- Upstream accidentally dropped some of my patch chunks while preparing 1.62
- release. Bringing them back myself at least through sci overlay.
-
-*biopython-1.62 (17 Sep 2013)
-
- 17 Sep 2013; Justin Lecher <jlec@gentoo.org> +biopython-1.62.ebuild:
- Version Bump
-
- 02 Jul 2013; Justin Lecher <jlec@gentoo.org> biopython-1.61.ebuild:
- Fix deps for python
-
- 06 Jun 2013; Justin Lecher <jlec@gentoo.org> biopython-1.61.ebuild:
- Keyword ~-linux
-
-*biopython-1.61 (26 Apr 2013)
-
- 26 Apr 2013; Justin Lecher <jlec@gentoo.org> +biopython-1.61.ebuild,
- metadata.xml:
- Version Bump
-
- 14 Dec 2012; Ulrich Müller <ulm@gentoo.org> biopython-1.57.ebuild,
- biopython-1.58.ebuild, biopython-1.59.ebuild:
- Update LICENSE, HPND according to LICENSE file.
-
-*biopython-1.59 (27 Feb 2012)
-
- 27 Feb 2012; Andrey Kislyuk <weaver@gentoo.org> +biopython-1.59.ebuild:
- Version bump
-
- 26 Dec 2011; Andrey Kislyuk <weaver@gentoo.org> +biopython-1.58.ebuild:
- Version bump
-
-*biopython-1.58 (26 Dec 2011)
-
- 26 Dec 2011; Andrey Kislyuk <weaver@gentoo.org> +biopython-1.58.ebuild:
- Version bump
-
- 23 Jun 2011; Markos Chandras <hwoarang@gentoo.org> -biopython-1.56.ebuild:
- Remove old ebuilds. Requested by Arfrever
-
- 28 May 2011; Brent Baude <ranger@gentoo.org> biopython-1.57.ebuild:
- Marking biopython-1.57 ppc for bug 365877
-
- 24 May 2011; Markus Meier <maekke@gentoo.org> biopython-1.57.ebuild:
- x86 stable, bug #365877
-
- 06 May 2011; Justin Lecher <jlec@gentoo.org> biopython-1.56.ebuild,
- biopython-1.57.ebuild:
- Cleaned DESCRIPTION
-
- 05 May 2011; Markos Chandras <hwoarang@gentoo.org> biopython-1.57.ebuild:
- Stable on amd64 wrt bug #365877
-
-*biopython-1.57 (03 Apr 2011)
-
- 03 Apr 2011; Arfrever Frehtes Taifersar Arahesis <arfrever@gentoo.org>
- +biopython-1.57.ebuild:
- Version bump.
-
- 30 Jan 2011; Arfrever Frehtes Taifersar Arahesis <arfrever@gentoo.org>
- -biopython-1.55.ebuild:
- Delete.
-
- 30 Jan 2011; Raúl Porcel <armin76@gentoo.org> biopython-1.55.ebuild,
- biopython-1.56.ebuild:
- Drop alpha/sparc keywords
-
- 15 Jan 2011; Pawel Hajdan jr <phajdan.jr@gentoo.org>
- biopython-1.56.ebuild:
- x86 stable wrt bug #351498
-
- 14 Jan 2011; Brent Baude <ranger@gentoo.org> biopython-1.56.ebuild:
- stable ppc, bug 351498
-
- 13 Jan 2011; Markos Chandras <hwoarang@gentoo.org> biopython-1.56.ebuild:
- Stable on amd64 wrt bug #351498
-
- 06 Jan 2011; Brent Baude <ranger@gentoo.org> biopython-1.55.ebuild:
- Marking biopython-1.55 ppc for bug 341519
-
-*biopython-1.56 (13 Dec 2010)
-
- 13 Dec 2010; Arfrever Frehtes Taifersar Arahesis <arfrever@gentoo.org>
- -biopython-1.53.ebuild, -biopython-1.54.ebuild, +biopython-1.56.ebuild:
- Version bump.
-
- 31 Oct 2010; Raúl Porcel <armin76@gentoo.org> biopython-1.55.ebuild:
- alpha/sparc stable wrt #341519
-
- 21 Oct 2010; Thomas Kahle <tomka@gentoo.org> biopython-1.55.ebuild:
- x86 stable per bug 341519
-
- 19 Oct 2010; Markos Chandras <hwoarang@gentoo.org> biopython-1.55.ebuild:
- Stable on amd64 wrt bug #341519
-
- 15 Oct 2010; Brent Baude <ranger@gentoo.org> biopython-1.54.ebuild:
- stable ppc, bug 327151
-
- 10 Oct 2010; Raúl Porcel <armin76@gentoo.org> biopython-1.54.ebuild:
- sparc stable wrt #327151
-
-*biopython-1.55 (17 Sep 2010)
-
- 17 Sep 2010; Arfrever Frehtes Taifersar Arahesis <arfrever@gentoo.org>
- +biopython-1.55.ebuild:
- Version bump.
-
- 12 Sep 2010; Tobias Klausmann <klausman@gentoo.org> biopython-1.54.ebuild:
- Stable on alpha, bug #327151
-
- 12 Jul 2010; Christian Faulhammer <fauli@gentoo.org>
- biopython-1.54.ebuild:
- stable x86, bug 327151
-
- 06 Jul 2010; Markos Chandras <hwoarang@gentoo.org> biopython-1.54.ebuild:
- Stable on amd64 wrt bug #327151
-
-*biopython-1.54 (05 Jun 2010)
-
- 05 Jun 2010; Arfrever Frehtes Taifersar Arahesis <arfrever@gentoo.org>
- -biopython-1.49.ebuild, -files/biopython-1.49-flex.patch,
- -biopython-1.51.ebuild, -biopython-1.52.ebuild, +biopython-1.54.ebuild:
- Version bump.
-
- 13 Feb 2010; Raúl Porcel <armin76@gentoo.org> biopython-1.53.ebuild:
- alpha/sparc stable wrt #301964
-
- 07 Feb 2010; Markus Meier <maekke@gentoo.org> biopython-1.53.ebuild:
- amd64/x86 stable, bug #301964
-
- 24 Jan 2010; Brent Baude <ranger@gentoo.org> biopython-1.53.ebuild:
- stable ppc, bug 301964
-
-*biopython-1.53 (21 Dec 2009)
-
- 21 Dec 2009; Arfrever Frehtes Taifersar Arahesis <arfrever@gentoo.org>
- +biopython-1.53.ebuild:
- Version bump. Set SUPPORT_PYTHON_ABIS.
-
- 31 Oct 2009; Markus Meier <maekke@gentoo.org> biopython-1.52.ebuild:
- amd64/x86 stable, bug #290931
-
-*biopython-1.52 (23 Sep 2009)
-
- 23 Sep 2009; Andrey Kislyuk <weaver@gentoo.org> +biopython-1.52.ebuild:
- Version bump
-
-*biopython-1.51 (09 Sep 2009)
-
- 09 Sep 2009; Andrey Kislyuk <weaver@gentoo.org>
- +files/biopython-1.51-flex.patch, +biopython-1.51.ebuild:
- Version bump
-
- 26 Aug 2009; Christian Faulhammer <fauli@gentoo.org> metadata.xml:
- remove now unused flag description
-
- 26 Aug 2009; Christian Faulhammer <fauli@gentoo.org>
- -biopython-1.42.ebuild, -files/biopython-1.43-buildkdtree.patch,
- -biopython-1.44.ebuild, -files/biopython-1.44-sequtils-complement.patch,
- -biopython-1.47.ebuild, -files/biopython-1.47-kdtree.patch:
- clean up
-
- 26 Aug 2009; Tobias Klausmann <klausman@gentoo.org> biopython-1.49.ebuild:
- Stable on alpha, bug #277822
-
- 02 Aug 2009; nixnut <nixnut@gentoo.org> biopython-1.49.ebuild:
- ppc stable #277822
-
- 20 Jul 2009; Jeremy Olexa <darkside@gentoo.org> biopython-1.49.ebuild:
- amd64 stable, bug 277822
-
- 17 Jul 2009; Ferris McCormick <fmccor@gentoo.org> biopython-1.49.ebuild:
- Sparc stable --- bug #277822 --- ran tests successfully.
-
- 14 Jul 2009; Christian Faulhammer <fauli@gentoo.org>
- biopython-1.49.ebuild:
- stable x86, bug 277822
-
- 24 Mar 2009; Olivier Fisette <ribosome@gentoo.org> metadata.xml:
- Giving up maintainership of this package.
-
-*biopython-1.49 (16 Jan 2009)
-
- 16 Jan 2009; Olivier Fisette <ribosome@gentoo.org>
- +files/biopython-1.49-flex.patch, +biopython-1.49.ebuild:
- Version bump. Thanks to Juan Aguado <juantxorena@gmail.com> for his work.
- Fixes bug #248799.
-
- 06 Aug 2008; Ulrich Mueller <ulm@gentoo.org> metadata.xml:
- Add USE flag description to metadata wrt GLEP 56.
-
- 14 Jul 2008; nixnut <nixnut@gentoo.org> biopython-1.44.ebuild:
- Stable on ppc wrt bug 221159
-
- 07 Jul 2008; Raúl Porcel <armin76@gentoo.org> biopython-1.44.ebuild:
- alpha/sparc/x86 stable wrt #221159
-
-*biopython-1.47 (06 Jul 2008)
-
- 06 Jul 2008; Olivier Fisette <ribosome@gentoo.org>
- +files/biopython-1.47-kdtree.patch, +biopython-1.47.ebuild:
- New version. Better documentation installation. Added scripts and test
- suite. KDTree now enabled by default (requires switching to EAPI 1).
-
- 06 Jul 2008; Olivier Fisette <ribosome@gentoo.org> biopython-1.44.ebuild:
- Stable on amd64.
-
- 30 Jan 2008; Olivier Fisette <ribosome@gentoo.org> biopython-1.42.ebuild,
- biopython-1.44.ebuild:
- Q.A.: Quoted variables.
-
- 30 Jan 2008; Olivier Fisette <ribosome@gentoo.org> -biopython-1.43.ebuild:
- Removed buggy version (see bug #202602).
-
-*biopython-1.44 (30 Jan 2008)
-
- 30 Jan 2008; Olivier Fisette <ribosome@gentoo.org>
- +files/biopython-1.44-sequtils-complement.patch, +biopython-1.44.ebuild:
- Fixed six_frame_translations function. Thanks to JTRiley
- <justin.t.riley@gmail.com> for his patch. (Fixes bug #202606.)
-
-*biopython-1.43 (17 May 2007)
-
- 17 May 2007; Olivier Fisette <ribosome@gentoo.org>
- +files/biopython-1.43-buildkdtree.patch, -biopython-1.40b.ebuild,
- +biopython-1.43.ebuild:
- New upstream version. Ebuild clean-up. Pruned old version.
-
- 16 May 2007; Raúl Porcel <armin76@gentoo.org> biopython-1.42.ebuild:
- alpha stable wrt #153774
-
- 05 Nov 2006; Christian Faulhammer <opfer@gentoo.org>
- biopython-1.42.ebuild:
- stabled x86, bug #153774
-
- 03 Nov 2006; <blubb@gentoo.org> biopython-1.42.ebuild:
- stable on amd64
-
- 03 Nov 2006; Olivier Fisette <ribosome@gentoo.org> -biopython-1.41.ebuild:
- Pruned old version.
-
- 02 Nov 2006; nixnut <nixnut@gentoo.org> biopython-1.42.ebuild:
- Stable on ppc wrt bug 153774
-
- 02 Nov 2006; Jason Wever <weeve@gentoo.org> biopython-1.42.ebuild:
- Stable on SPARC wrt bug #153774.
-
- 14 Sep 2006; Olivier Fisette <ribosome@gentoo.org> metadata.xml:
- Taking over maintainership.
-
-*biopython-1.42 (12 Sep 2006)
-
- 12 Sep 2006; Olivier Fisette <ribosome@gentoo.org> +biopython-1.42.ebuild:
- New upstream version.
-
- 19 Jan 2006; George Shapovalov <george@gentoo.org> +biopython-1.41.ebuild:
- new version, cleaned up install
-
- 30 Aug 2005; Olivier Fisette <ribosome@gentoo.org> -biopython-1.24.ebuild,
- -biopython-1.30.ebuild:
- Removed obsolete versions.
-
- 12 Jun 2005; Bryan Østergaard <kloeri@gentoo.org> biopython-1.40b.ebuild:
- Stable on alpha.
-
- 21 May 2005; Jason Wever <weeve@gentoo.org> biopython-1.40b.ebuild:
- Stable on SPARC.
-
- 13 May 2005; Olivier Fisette <ribosome@gentoo.org> -biopython-1.10.ebuild,
- -biopython-1.21.ebuild, -biopython-1.23.ebuild, biopython-1.40b.ebuild:
- Removed obsolete versions. Added 1.40b to x86.
-
-*biopython-1.40b (19 Feb 2005)
-
- 19 Feb 2005; Olivier Fisette <ribosome@gentoo.org>
- +biopython-1.40b.ebuild:
- New version. Should fix bug #82498.
-
- 29 Dec 2004; Ciaran McCreesh <ciaranm@gentoo.org> :
- Change encoding to UTF-8 for GLEP 31 compliance
-
-*biopython-1.23 (23 Dec 2004)
-
- 23 Dec 2004; Olivier Fisette <ribosome@gentoo.org> +metadata.xml,
- +biopython-1.10.ebuild, +biopython-1.21.ebuild, +biopython-1.23.ebuild,
- +biopython-1.24.ebuild, +biopython-1.30.ebuild:
- Moved from app-sci/biopython to sci-biology/biopython.
-
- 13 Dec 2004; Jason Wever <weeve@gentoo.org> biopython-1.24.ebuild:
- Stable on sparc.
-
-*biopython-1.30 (07 Oct 2004)
-
- 07 Oct 2004; George Shapovalvo <george@gentoo.org> biopython-1.30.ebuild :
- new version (#51833)
- amd64 has problems with KDTree, will try to look into this more later
-
- 05 May 2004; Bryan Østergaard <kloeri@gentoo.org> biopython-1.24.ebuild:
- Stable on alpha.
-
- 03 Apr 2004; Peter Bienstman <pbienst@gentoo.org> biopython-1.24.ebuild:
- Marked stable on x86
-
-*biopython-1.24 (29 Feb 2004)
-
- 29 Feb 2004; Peter Bienstman <pbienst@gentoo.org> biopython-1.24.ebuild :
- version bump
-
-*biopython-1.23 (30 Dec 2003)
-
- 29 Feb 2004; Peter Bienstman <pbienst@gentoo.org> biopython-1.23.ebuild :
- marked stable on x86
-
- 30 Dec 2003; George Shapovalvo <george@gentoo.org> biopython-1.23.ebuild :
- new version, reworked to use distutils. Thanks to
- Peter Bienstman <Peter.Bienstman@rug.ac.be> for an update (#35727)
-
- 02 Sep 2003; Alastair Tse <liquidx@gentoo.org> biopython-1.10.ebuild,
- biopython-1.21.ebuild:
- moved dev-python/Numeric to dev-python/numeric
-
-*biopython-1.21 (08 Aug 2003)
-
- 08 Aug 2003; George Shapovalov <george@gentoo.org> biopython-1.21.ebuild :
- new version, added few docs (#25428)
- thanks to Daniel Jaeggi <daniel@jaeggi.co.uk> for notification
-
- 04 Jul 2003; Alastair Tse <liquidx@gentoo.org> biopython-1.10.ebuild:
- renamed reportlab dep
-
-*biopython-1.10 (18 Feb 2003)
-
- 18 Feb 2003; George Shapovalov <george@gentoo.org> ChangeLog, biopython-1.10.ebuild, files/digest-biopython-1.10 :
- initial release (#11617)
- Biopython - python module for Computational Moelcular Biology
- ebuild submitted by Daniel Jaeggi <daniel@jaeggi.co.uk>
diff --git a/sci-biology/biopython/biopython-1.62-r1.ebuild b/sci-biology/biopython/biopython-1.62-r1.ebuild
deleted file mode 100644
index d3e61a2..0000000
--- a/sci-biology/biopython/biopython-1.62-r1.ebuild
+++ /dev/null
@@ -1,51 +0,0 @@
-# Copyright 1999-2013 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/biopython/biopython-1.62.ebuild,v 1.1 2013/09/17 16:07:56 jlec Exp $
-
-EAPI=5
-
-PYTHON_COMPAT=( python{2_6,2_7} )
-
-inherit distutils-r1 eutils
-
-DESCRIPTION="Python modules for computational molecular biology"
-HOMEPAGE="http://www.biopython.org/ http://pypi.python.org/pypi/biopython/"
-SRC_URI="http://www.biopython.org/DIST/${P}.tar.gz"
-
-LICENSE="HPND"
-SLOT="0"
-KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
-IUSE="mysql postgres"
-
-REQUIRED_USE="${PYTHON_REQUIRED_USE}"
-
-RDEPEND="${PYTHON_DEPS}
- dev-python/matplotlib[${PYTHON_USEDEP}]
- dev-python/networkx[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/pygraphviz[${PYTHON_USEDEP}]
- dev-python/reportlab[${PYTHON_USEDEP}]
- media-gfx/pydot[${PYTHON_USEDEP}]
- mysql? ( dev-python/mysql-python[${PYTHON_USEDEP}] )
- postgres? ( dev-python/psycopg[${PYTHON_USEDEP}] )"
-DEPEND="${RDEPEND}
- sys-devel/flex"
-
-DOCS=( CONTRIB DEPRECATED NEWS README Doc/. )
-
-src_prepare() {
- distutils-r1_src_prepare
- epatch "${FILESDIR}/${PN}-1.62-SffIO.patch"
-}
-
-python_test() {
- cd Tests || die
- ${PYTHON} run_tests.py || die
-}
-
-python_install_all() {
- distutils-r1_python_install_all
-
- dodir /usr/share/${PN}
- cp -r --preserve=mode Scripts Tests "${ED}"/usr/share/${PN} || die
-}
diff --git a/sci-biology/biopython/files/biopython-1.62-SffIO.patch b/sci-biology/biopython/files/biopython-1.62-SffIO.patch
deleted file mode 100644
index 7f2208e..0000000
--- a/sci-biology/biopython/files/biopython-1.62-SffIO.patch
+++ /dev/null
@@ -1,36 +0,0 @@
---- Bio/SeqIO/SffIO.py.ori 2013-09-25 13:28:51.000000000 +0200
-+++ Bio/SeqIO/SffIO.py 2013-09-25 13:37:44.000000000 +0200
-@@ -383,7 +383,14 @@
- if padding:
- padding = 8 - padding
- if handle.read(padding).count(_null) != padding:
-- raise ValueError("Post quality %i byte padding region contained data"
-+ import warnings
-+ from Bio import BiopythonParserWarning
-+ warnings.warn("Your SFF file is valid but post quality %i byte "
-+ "padding region contains UNUSED data. Was the "
-+ "SFF file created by SRA sff-dump >2.1.7 and <2.1.10? "
-+ "It did not clear some internal buffer while writing "
-+ "out new data so that previous values remained in the"
-+ "output unless overwritten by new real values."
- % padding)
- #print read, name, record_offset
- yield name, record_offset
---- Bio/SeqIO/SffIO.py.ori 2013-09-25 14:07:14.000000000 +0200
-+++ Bio/SeqIO/SffIO.py 2013-09-25 14:08:59.000000000 +0200
-@@ -596,7 +596,14 @@
- if padding:
- padding = 8 - padding
- if handle.read(padding).count(_null) != padding:
-- raise ValueError("Post quality %i byte padding region contained data"
-+ import warnings
-+ from Bio import BiopythonParserWarning
-+ warnings.warn("Your SFF file is valid but post quality %i byte "
-+ "padding region contains UNUSED data. Was the "
-+ "SFF file created by SRA sff-dump >2.1.7 and <2.1.10? "
-+ "It did not clear some internal buffer while writing "
-+ "out new data so that previous values remained in the"
-+ "output unless overwritten by new real values."
- % padding)
- #Follow Roche and apply most aggressive of qual and adapter clipping.
- #Note Roche seems to ignore adapter clip fields when writing SFF,
diff --git a/sci-biology/biopython/metadata.xml b/sci-biology/biopython/metadata.xml
deleted file mode 100644
index f17a827..0000000
--- a/sci-biology/biopython/metadata.xml
+++ /dev/null
@@ -1,5 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <herd>sci-biology</herd>
-</pkgmetadata>
next reply other threads:[~2013-12-29 0:31 UTC|newest]
Thread overview: 10+ messages / expand[flat|nested] mbox.gz Atom feed top
2013-12-29 0:31 Justin Lecher [this message]
-- strict thread matches above, loose matches on Subject: below --
2016-07-23 7:25 [gentoo-commits] proj/sci:master commit in: sci-biology/biopython/, sci-biology/biopython/files/ Martin Mokrejs
2014-05-07 10:29 Justin Lecher
2014-04-18 18:23 Martin Mokrejs
2014-04-18 18:14 Martin Mokrejs
2014-03-23 16:09 Martin Mokrejs
2014-03-23 16:00 Martin Mokrejs
2013-09-25 12:29 Martin Mokrejs
2012-03-21 11:20 Justin Lecher
2011-12-07 15:14 Martin Mokrejs
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