From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from pigeon.gentoo.org ([208.92.234.80] helo=lists.gentoo.org) by finch.gentoo.org with esmtp (Exim 4.60) (envelope-from ) id 1RYJCW-000512-CI for garchives@archives.gentoo.org; Wed, 07 Dec 2011 15:14:28 +0000 Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 22BDB21C0AA; Wed, 7 Dec 2011 15:14:20 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) by pigeon.gentoo.org (Postfix) with ESMTP id BAD4321C0AA for ; Wed, 7 Dec 2011 15:14:19 +0000 (UTC) Received: from pelican.gentoo.org (unknown [66.219.59.40]) (using TLSv1 with cipher AECDH-AES256-SHA (256/256 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id DC81D1B4010 for ; Wed, 7 Dec 2011 15:14:18 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by pelican.gentoo.org (Postfix) with ESMTP id 5E97B80042 for ; Wed, 7 Dec 2011 15:14:18 +0000 (UTC) From: "Martin Mokrejs" To: gentoo-commits@lists.gentoo.org Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Martin Mokrejs" Message-ID: <2b2fcccc5d7105abbcc6e9e7a9088826f1f1ee9b.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-1.58.ebuild sci-biology/biopython/files/biopython-1.51-flex.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: 2b2fcccc5d7105abbcc6e9e7a9088826f1f1ee9b Date: Wed, 7 Dec 2011 15:14:18 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: quoted-printable X-Archives-Salt: 0312ac4a-241f-456b-bddb-47973b8c4125 X-Archives-Hash: 296aa326dd85aa5c93a03782842bae9f commit: 2b2fcccc5d7105abbcc6e9e7a9088826f1f1ee9b Author: Martin Mokrejs fold natur cuni cz> AuthorDate: Wed Dec 7 15:13:46 2011 +0000 Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Wed Dec 7 15:13:46 2011 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=3Dproj/sci.git;a=3Dc= ommit;h=3D2b2fcccc sci-biology/biopython: 1.58 version bump (Portage version: 2.1.10.38/git/Linux i686, unsigned Manifest commit) --- sci-biology/biopython/ChangeLog | 309 ++++++++++++++= ++++++ sci-biology/biopython/biopython-1.58.ebuild | 55 ++++ .../biopython/files/biopython-1.51-flex.patch | 21 ++ sci-biology/biopython/metadata.xml | 5 + 4 files changed, 390 insertions(+), 0 deletions(-) diff --git a/sci-biology/biopython/ChangeLog b/sci-biology/biopython/Chan= geLog new file mode 100644 index 0000000..b7c1c09 --- /dev/null +++ b/sci-biology/biopython/ChangeLog @@ -0,0 +1,309 @@ +# ChangeLog for sci-biology/biopython +# Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/biopython/ChangeLog,v 1.6= 5 2011/06/23 14:55:47 hwoarang Exp $ + +*biopython-1.58 (07 Dec 2011) + + 07 Dec 2011; Martin Mokrejs + +files/biopython-1.51-flex.patch, +biopython-1.58.ebuild, +metadata.xm= l: + Version bump. + + 23 Jun 2011; Markos Chandras -biopython-1.56.ebu= ild: + 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.ebui= ld: + 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; Ra=C3=BAl Porcel biopython-1.55.ebui= ld, + 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.ebui= ld: + 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; Ra=C3=BAl Porcel biopython-1.55.ebui= ld: + 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.ebui= ld: + Stable on amd64 wrt bug #341519 + + 15 Oct 2010; Brent Baude biopython-1.54.ebuild: + stable ppc, bug 327151 + + 10 Oct 2010; Ra=C3=BAl Porcel biopython-1.54.ebui= ld: + 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.ebu= ild: + 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.ebui= ld: + 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; Ra=C3=BAl Porcel biopython-1.53.ebui= ld: + 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.patc= h, + -biopython-1.47.ebuild, -files/biopython-1.47-kdtree.patch: + clean up + + 26 Aug 2009; Tobias Klausmann biopython-1.49.ebu= ild: + 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.ebuil= d: + 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 wo= rk. + 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; Ra=C3=BAl Porcel biopython-1.44.ebui= ld: + 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.ebui= ld: + Stable on amd64. + + 30 Jan 2008; Olivier Fisette biopython-1.42.ebui= ld, + biopython-1.44.ebuild: + Q.A.: Quoted variables. + + 30 Jan 2008; Olivier Fisette -biopython-1.43.ebu= ild: + 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.ebuil= d: + 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; Ra=C3=BAl Porcel biopython-1.42.ebui= ld: + 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.ebu= ild: + 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.ebu= ild: + New upstream version. + + 19 Jan 2006; George Shapovalov +biopython-1.41.ebu= ild: + new version, cleaned up install + + 30 Aug 2005; Olivier Fisette -biopython-1.24.ebu= ild, + -biopython-1.30.ebuild: + Removed obsolete versions. + + 12 Jun 2005; Bryan =C3=98stergaard 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.ebu= ild, + -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.ebui= ld : + new version (#51833) + amd64 has problems with KDTree, will try to look into this more later + + 05 May 2004; Bryan =C3=98stergaard biopython-1.24.= ebuild: + Stable on alpha. + + 03 Apr 2004; Peter Bienstman biopython-1.24.ebuil= d: + Marked stable on x86 + +*biopython-1.24 (29 Feb 2004) + + 29 Feb 2004; Peter Bienstman biopython-1.24.ebuil= d : + version bump + +*biopython-1.23 (30 Dec 2003) + + 29 Feb 2004; Peter Bienstman biopython-1.23.ebuil= d : + marked stable on x86 + + 30 Dec 2003; George Shapovalvo biopython-1.23.ebui= ld : + new version, reworked to use distutils. Thanks to=20 + 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.ebui= ld : + 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, biopytho= n-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-1.58.ebuild b/sci-biology/bi= opython/biopython-1.58.ebuild new file mode 100644 index 0000000..8a9b445 --- /dev/null +++ b/sci-biology/biopython/biopython-1.58.ebuild @@ -0,0 +1,55 @@ +# Copyright 1999-2011 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/biopython/biopython-1.57.= ebuild,v 1.5 2011/05/28 13:52:36 ranger Exp $ + +EAPI=3D3 +PYTHON_DEPEND=3D"2" +SUPPORT_PYTHON_ABIS=3D"1" +RESTRICT_PYTHON_ABIS=3D"3.* *-jython" + +inherit distutils eutils + +DESCRIPTION=3D"Python modules for computational molecular biology" +HOMEPAGE=3D"http://www.biopython.org/ http://pypi.python.org/pypi/biopyt= hon/" +SRC_URI=3D"http://www.biopython.org/DIST/${P}.tar.gz" + +LICENSE=3D"as-is" +SLOT=3D"0" +KEYWORDS=3D"~amd64 ~ppc ~x86" +IUSE=3D"mysql postgres" + +RDEPEND=3D" + dev-python/numpy + dev-python/reportlab + mysql? ( dev-python/mysql-python ) + postgres? ( dev-python/psycopg )" +DEPEND=3D"${RDEPEND} + sys-devel/flex" + +PYTHON_CFLAGS=3D("2.* + -fno-strict-aliasing") + +DISTUTILS_USE_SEPARATE_SOURCE_DIRECTORIES=3D"1" +DOCS=3D"CONTRIB DEPRECATED NEWS README" +PYTHON_MODNAME=3D"Bio BioSQL" + +src_prepare() { + distutils_src_prepare + epatch "${FILESDIR}/${PN}-1.51-flex.patch" +} + +src_test() { + testing() { + cd Tests + PYTHONPATH=3D"$(ls -d ../build/lib.*)" "$(PYTHON)" run_tests.py + } + python_execute_function --nonfatal -s testing +} + +src_install() { + distutils_src_install + + insinto /usr/share/doc/${PF} + doins -r Doc/* || die "Installation of documentation failed" + insinto /usr/share/${PN} + cp -r --preserve=3Dmode Scripts Tests "${ED}usr/share/${PN}" || die "In= stallation of shared files failed" +} diff --git a/sci-biology/biopython/files/biopython-1.51-flex.patch b/sci-= biology/biopython/files/biopython-1.51-flex.patch new file mode 100644 index 0000000..afd5094 --- /dev/null +++ b/sci-biology/biopython/files/biopython-1.51-flex.patch @@ -0,0 +1,21 @@ +--- setup.py.old 2008-11-25 18:03:16.000000000 +0100 ++++ setup.py 2008-11-25 18:04:14.000000000 +0100 +@@ -341,12 +341,12 @@ + include_dirs=3D["Bio"] + ), + #Commented out due to the build dependency on flex, see Bug 2619 +-# Extension('Bio.PDB.mmCIF.MMCIFlex', +-# ['Bio/PDB/mmCIF/lex.yy.c', +-# 'Bio/PDB/mmCIF/MMCIFlexmodule.c'], +-# include_dirs=3D["Bio"], +-# libraries=3D["fl"] +-# ), ++ Extension('Bio.PDB.mmCIF.MMCIFlex', ++ ['Bio/PDB/mmCIF/lex.yy.c', ++ 'Bio/PDB/mmCIF/MMCIFlexmodule.c'], ++ include_dirs=3D["Bio"], ++ libraries=3D["fl"] ++ ), + Extension('Bio.Nexus.cnexus', + ['Bio/Nexus/cnexus.c'] + ), diff --git a/sci-biology/biopython/metadata.xml b/sci-biology/biopython/m= etadata.xml new file mode 100644 index 0000000..34294c6 --- /dev/null +++ b/sci-biology/biopython/metadata.xml @@ -0,0 +1,5 @@ + + + +sci-biology +