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 1SAJbd-0002qL-2S for garchives@archives.gentoo.org; Wed, 21 Mar 2012 11:21:29 +0000 Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 535D4E09F7; Wed, 21 Mar 2012 11:20:27 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) by pigeon.gentoo.org (Postfix) with ESMTP id 02C6DE09F7 for ; Wed, 21 Mar 2012 11:20:26 +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 737C01B4053 for ; Wed, 21 Mar 2012 11:20:26 +0000 (UTC) Received: from localhost.localdomain (localhost [127.0.0.1]) by hornbill.gentoo.org (Postfix) with ESMTP id 331CEE5431 for ; Wed, 21 Mar 2012 11:20:25 +0000 (UTC) From: "Justin Lecher" To: gentoo-commits@lists.gentoo.org Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Justin Lecher" Message-ID: <1332328800.96fa03b29208beadce34b013c5851a4c8f6e27e1.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-1.58.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: jlec X-VCS-Committer-Name: Justin Lecher X-VCS-Revision: 96fa03b29208beadce34b013c5851a4c8f6e27e1 X-VCS-Branch: master Date: Wed, 21 Mar 2012 11:20:25 +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: 3c218a98-7086-4cb0-94d0-89ff18ea8f23 X-Archives-Hash: 20cd1bce0a41ce36872d9fd79e7ddb5d commit: 96fa03b29208beadce34b013c5851a4c8f6e27e1 Author: Justin Lecher gentoo org> AuthorDate: Wed Mar 21 11:20:00 2012 +0000 Commit: Justin Lecher gentoo org> CommitDate: Wed Mar 21 11:20:00 2012 +0000 URL: http://git.overlays.gentoo.org/gitweb/?p=3Dproj/sci.git;a=3Dc= ommit;h=3D96fa03b2 This version and newer is in the tree --- 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, 0 insertions(+), 390 deletions(-) diff --git a/sci-biology/biopython/ChangeLog b/sci-biology/biopython/Chan= geLog deleted file mode 100644 index b7c1c09..0000000 --- a/sci-biology/biopython/ChangeLog +++ /dev/null @@ -1,309 +0,0 @@ -# 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 deleted file mode 100644 index 8a9b445..0000000 --- a/sci-biology/biopython/biopython-1.58.ebuild +++ /dev/null @@ -1,55 +0,0 @@ -# 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 deleted file mode 100644 index afd5094..0000000 --- a/sci-biology/biopython/files/biopython-1.51-flex.patch +++ /dev/null @@ -1,21 +0,0 @@ ---- 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 deleted file mode 100644 index 34294c6..0000000 --- a/sci-biology/biopython/metadata.xml +++ /dev/null @@ -1,5 +0,0 @@ - - - -sci-biology -