From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) by finch.gentoo.org (Postfix) with ESMTP id 1853F138247 for ; Sun, 29 Dec 2013 00:31:28 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id E6EBCE0AE2; Sun, 29 Dec 2013 00:31:25 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) (using TLSv1 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id 27394E0AE2 for ; Sun, 29 Dec 2013 00:31:25 +0000 (UTC) Received: from hornbill.gentoo.org (hornbill.gentoo.org [94.100.119.163]) (using TLSv1 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 1B4DB33F141 for ; Sun, 29 Dec 2013 00:31:24 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by hornbill.gentoo.org (Postfix) with ESMTP id 66541110444 for ; Sun, 29 Dec 2013 00:31:21 +0000 (UTC) From: "Justin Lecher" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Justin Lecher" Message-ID: <1388276946.4c137a437dca9f76da755afa10c90f2f67e7059b.jlec@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/biopython/, sci-biology/biopython/files/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/biopython/ChangeLog sci-biology/biopython/biopython-1.62-r1.ebuild sci-biology/biopython/files/biopython-1.62-SffIO.patch sci-biology/biopython/metadata.xml X-VCS-Directories: sci-biology/biopython/ sci-biology/biopython/files/ X-VCS-Committer: jlec X-VCS-Committer-Name: Justin Lecher X-VCS-Revision: 4c137a437dca9f76da755afa10c90f2f67e7059b X-VCS-Branch: master Date: Sun, 29 Dec 2013 00:31:21 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Archives-Salt: 1a28f74e-1cb9-4e4b-8ae0-7db877a7198d X-Archives-Hash: 9c97734d783083f84b87be2e34f68fc4 commit: 4c137a437dca9f76da755afa10c90f2f67e7059b Author: Justin Lecher gentoo org> AuthorDate: Sun Dec 29 00:29:06 2013 +0000 Commit: Justin Lecher gentoo 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 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 - +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 +biopython-1.62.ebuild: - Version Bump - - 02 Jul 2013; Justin Lecher biopython-1.61.ebuild: - Fix deps for python - - 06 Jun 2013; Justin Lecher biopython-1.61.ebuild: - Keyword ~-linux - -*biopython-1.61 (26 Apr 2013) - - 26 Apr 2013; Justin Lecher +biopython-1.61.ebuild, - metadata.xml: - Version Bump - - 14 Dec 2012; Ulrich Müller 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 +biopython-1.59.ebuild: - Version bump - - 26 Dec 2011; Andrey Kislyuk +biopython-1.58.ebuild: - Version bump - -*biopython-1.58 (26 Dec 2011) - - 26 Dec 2011; Andrey Kislyuk +biopython-1.58.ebuild: - Version bump - - 23 Jun 2011; Markos Chandras -biopython-1.56.ebuild: - Remove old ebuilds. Requested by Arfrever - - 28 May 2011; Brent Baude biopython-1.57.ebuild: - Marking biopython-1.57 ppc for bug 365877 - - 24 May 2011; Markus Meier biopython-1.57.ebuild: - x86 stable, bug #365877 - - 06 May 2011; Justin Lecher biopython-1.56.ebuild, - biopython-1.57.ebuild: - Cleaned DESCRIPTION - - 05 May 2011; Markos Chandras biopython-1.57.ebuild: - Stable on amd64 wrt bug #365877 - -*biopython-1.57 (03 Apr 2011) - - 03 Apr 2011; Arfrever Frehtes Taifersar Arahesis - +biopython-1.57.ebuild: - Version bump. - - 30 Jan 2011; Arfrever Frehtes Taifersar Arahesis - -biopython-1.55.ebuild: - Delete. - - 30 Jan 2011; Raúl Porcel biopython-1.55.ebuild, - biopython-1.56.ebuild: - Drop alpha/sparc keywords - - 15 Jan 2011; Pawel Hajdan jr - biopython-1.56.ebuild: - x86 stable wrt bug #351498 - - 14 Jan 2011; Brent Baude biopython-1.56.ebuild: - stable ppc, bug 351498 - - 13 Jan 2011; Markos Chandras biopython-1.56.ebuild: - Stable on amd64 wrt bug #351498 - - 06 Jan 2011; Brent Baude 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 - -biopython-1.53.ebuild, -biopython-1.54.ebuild, +biopython-1.56.ebuild: - Version bump. - - 31 Oct 2010; Raúl Porcel biopython-1.55.ebuild: - alpha/sparc stable wrt #341519 - - 21 Oct 2010; Thomas Kahle biopython-1.55.ebuild: - x86 stable per bug 341519 - - 19 Oct 2010; Markos Chandras biopython-1.55.ebuild: - Stable on amd64 wrt bug #341519 - - 15 Oct 2010; Brent Baude biopython-1.54.ebuild: - stable ppc, bug 327151 - - 10 Oct 2010; Raúl Porcel biopython-1.54.ebuild: - sparc stable wrt #327151 - -*biopython-1.55 (17 Sep 2010) - - 17 Sep 2010; Arfrever Frehtes Taifersar Arahesis - +biopython-1.55.ebuild: - Version bump. - - 12 Sep 2010; Tobias Klausmann biopython-1.54.ebuild: - Stable on alpha, bug #327151 - - 12 Jul 2010; Christian Faulhammer - biopython-1.54.ebuild: - stable x86, bug 327151 - - 06 Jul 2010; Markos Chandras biopython-1.54.ebuild: - Stable on amd64 wrt bug #327151 - -*biopython-1.54 (05 Jun 2010) - - 05 Jun 2010; Arfrever Frehtes Taifersar Arahesis - -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 biopython-1.53.ebuild: - alpha/sparc stable wrt #301964 - - 07 Feb 2010; Markus Meier biopython-1.53.ebuild: - amd64/x86 stable, bug #301964 - - 24 Jan 2010; Brent Baude biopython-1.53.ebuild: - stable ppc, bug 301964 - -*biopython-1.53 (21 Dec 2009) - - 21 Dec 2009; Arfrever Frehtes Taifersar Arahesis - +biopython-1.53.ebuild: - Version bump. Set SUPPORT_PYTHON_ABIS. - - 31 Oct 2009; Markus Meier biopython-1.52.ebuild: - amd64/x86 stable, bug #290931 - -*biopython-1.52 (23 Sep 2009) - - 23 Sep 2009; Andrey Kislyuk +biopython-1.52.ebuild: - Version bump - -*biopython-1.51 (09 Sep 2009) - - 09 Sep 2009; Andrey Kislyuk - +files/biopython-1.51-flex.patch, +biopython-1.51.ebuild: - Version bump - - 26 Aug 2009; Christian Faulhammer metadata.xml: - remove now unused flag description - - 26 Aug 2009; Christian Faulhammer - -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 biopython-1.49.ebuild: - Stable on alpha, bug #277822 - - 02 Aug 2009; nixnut biopython-1.49.ebuild: - ppc stable #277822 - - 20 Jul 2009; Jeremy Olexa biopython-1.49.ebuild: - amd64 stable, bug 277822 - - 17 Jul 2009; Ferris McCormick biopython-1.49.ebuild: - Sparc stable --- bug #277822 --- ran tests successfully. - - 14 Jul 2009; Christian Faulhammer - biopython-1.49.ebuild: - stable x86, bug 277822 - - 24 Mar 2009; Olivier Fisette metadata.xml: - Giving up maintainership of this package. - -*biopython-1.49 (16 Jan 2009) - - 16 Jan 2009; Olivier Fisette - +files/biopython-1.49-flex.patch, +biopython-1.49.ebuild: - Version bump. Thanks to Juan Aguado for his work. - Fixes bug #248799. - - 06 Aug 2008; Ulrich Mueller metadata.xml: - Add USE flag description to metadata wrt GLEP 56. - - 14 Jul 2008; nixnut biopython-1.44.ebuild: - Stable on ppc wrt bug 221159 - - 07 Jul 2008; Raúl Porcel biopython-1.44.ebuild: - alpha/sparc/x86 stable wrt #221159 - -*biopython-1.47 (06 Jul 2008) - - 06 Jul 2008; Olivier Fisette - +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 biopython-1.44.ebuild: - Stable on amd64. - - 30 Jan 2008; Olivier Fisette biopython-1.42.ebuild, - biopython-1.44.ebuild: - Q.A.: Quoted variables. - - 30 Jan 2008; Olivier Fisette -biopython-1.43.ebuild: - Removed buggy version (see bug #202602). - -*biopython-1.44 (30 Jan 2008) - - 30 Jan 2008; Olivier Fisette - +files/biopython-1.44-sequtils-complement.patch, +biopython-1.44.ebuild: - Fixed six_frame_translations function. Thanks to JTRiley - for his patch. (Fixes bug #202606.) - -*biopython-1.43 (17 May 2007) - - 17 May 2007; Olivier Fisette - +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 biopython-1.42.ebuild: - alpha stable wrt #153774 - - 05 Nov 2006; Christian Faulhammer - biopython-1.42.ebuild: - stabled x86, bug #153774 - - 03 Nov 2006; biopython-1.42.ebuild: - stable on amd64 - - 03 Nov 2006; Olivier Fisette -biopython-1.41.ebuild: - Pruned old version. - - 02 Nov 2006; nixnut biopython-1.42.ebuild: - Stable on ppc wrt bug 153774 - - 02 Nov 2006; Jason Wever biopython-1.42.ebuild: - Stable on SPARC wrt bug #153774. - - 14 Sep 2006; Olivier Fisette metadata.xml: - Taking over maintainership. - -*biopython-1.42 (12 Sep 2006) - - 12 Sep 2006; Olivier Fisette +biopython-1.42.ebuild: - New upstream version. - - 19 Jan 2006; George Shapovalov +biopython-1.41.ebuild: - new version, cleaned up install - - 30 Aug 2005; Olivier Fisette -biopython-1.24.ebuild, - -biopython-1.30.ebuild: - Removed obsolete versions. - - 12 Jun 2005; Bryan Østergaard biopython-1.40b.ebuild: - Stable on alpha. - - 21 May 2005; Jason Wever biopython-1.40b.ebuild: - Stable on SPARC. - - 13 May 2005; Olivier Fisette -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 - +biopython-1.40b.ebuild: - New version. Should fix bug #82498. - - 29 Dec 2004; Ciaran McCreesh : - Change encoding to UTF-8 for GLEP 31 compliance - -*biopython-1.23 (23 Dec 2004) - - 23 Dec 2004; Olivier Fisette +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 biopython-1.24.ebuild: - Stable on sparc. - -*biopython-1.30 (07 Oct 2004) - - 07 Oct 2004; George Shapovalvo 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 biopython-1.24.ebuild: - Stable on alpha. - - 03 Apr 2004; Peter Bienstman biopython-1.24.ebuild: - Marked stable on x86 - -*biopython-1.24 (29 Feb 2004) - - 29 Feb 2004; Peter Bienstman biopython-1.24.ebuild : - version bump - -*biopython-1.23 (30 Dec 2003) - - 29 Feb 2004; Peter Bienstman biopython-1.23.ebuild : - marked stable on x86 - - 30 Dec 2003; George Shapovalvo biopython-1.23.ebuild : - new version, reworked to use distutils. Thanks to - Peter Bienstman for an update (#35727) - - 02 Sep 2003; Alastair Tse 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 biopython-1.21.ebuild : - new version, added few docs (#25428) - thanks to Daniel Jaeggi for notification - - 04 Jul 2003; Alastair Tse biopython-1.10.ebuild: - renamed reportlab dep - -*biopython-1.10 (18 Feb 2003) - - 18 Feb 2003; George Shapovalov 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 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 @@ - - - - sci-biology -