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 7D3401381F3 for ; Wed, 25 Sep 2013 12:30:02 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 2CED2E0BEF; Wed, 25 Sep 2013 12:30:00 +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 A248CE0729 for ; Wed, 25 Sep 2013 12:29:59 +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 423E833EDE4 for ; Wed, 25 Sep 2013 12:29:58 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by hornbill.gentoo.org (Postfix) with ESMTP id 8AFD4E5309 for ; Wed, 25 Sep 2013 12:29:55 +0000 (UTC) From: "Martin Mokrejs" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Martin Mokrejs" Message-ID: <1380112161.6801f6ae30dccc74032f18035561acff1e4123b4.mmokrejs@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: mmokrejs X-VCS-Committer-Name: Martin Mokrejs X-VCS-Revision: 6801f6ae30dccc74032f18035561acff1e4123b4 X-VCS-Branch: master Date: Wed, 25 Sep 2013 12:29:55 +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: e7649811-d38f-4578-b2a8-f8892a66cd58 X-Archives-Hash: 994b577bb2eec9d2d0d440da9ae357d7 commit: 6801f6ae30dccc74032f18035561acff1e4123b4 Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Wed Sep 25 12:29:21 2013 +0000 Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Wed Sep 25 12:29:21 2013 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=6801f6ae Upstream accidentally dropped some of my patch chunks while preparing 1.62 release. Bringing them back myself at least through sci overlay. --- 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 insertions(+) diff --git a/sci-biology/biopython/ChangeLog b/sci-biology/biopython/ChangeLog new file mode 100644 index 0000000..baf3b3a --- /dev/null +++ b/sci-biology/biopython/ChangeLog @@ -0,0 +1,346 @@ +# 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 new file mode 100644 index 0000000..d3e61a2 --- /dev/null +++ b/sci-biology/biopython/biopython-1.62-r1.ebuild @@ -0,0 +1,51 @@ +# 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 new file mode 100644 index 0000000..7f2208e --- /dev/null +++ b/sci-biology/biopython/files/biopython-1.62-SffIO.patch @@ -0,0 +1,36 @@ +--- 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 new file mode 100644 index 0000000..f17a827 --- /dev/null +++ b/sci-biology/biopython/metadata.xml @@ -0,0 +1,5 @@ + + + + sci-biology +