[gentoo-commits] proj/sci:master commit in: sci-biology/biopython/, sci-biology/biopython/files/

["Martin Mokrejs" <mmokrejs@fold.natur.cuni.cz>]

commit:     2b2fcccc5d7105abbcc6e9e7a9088826f1f1ee9b
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Dec  7 15:13:46 2011 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Wed Dec  7 15:13:46 2011 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=2b2fcccc

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/ChangeLog
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 1.65 2011/06/23 14:55:47 hwoarang Exp $
+
+*biopython-1.58 (07 Dec 2011)
+
+  07 Dec 2011; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+  +files/biopython-1.51-flex.patch, +biopython-1.58.ebuild, +metadata.xml:
+  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-1.58.ebuild b/sci-biology/biopython/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=3
+PYTHON_DEPEND="2"
+SUPPORT_PYTHON_ABIS="1"
+RESTRICT_PYTHON_ABIS="3.* *-jython"
+
+inherit distutils 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/${P}.tar.gz"
+
+LICENSE="as-is"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86"
+IUSE="mysql postgres"
+
+RDEPEND="
+	dev-python/numpy
+	dev-python/reportlab
+	mysql? ( dev-python/mysql-python )
+	postgres? ( dev-python/psycopg )"
+DEPEND="${RDEPEND}
+	sys-devel/flex"
+
+PYTHON_CFLAGS=("2.* + -fno-strict-aliasing")
+
+DISTUTILS_USE_SEPARATE_SOURCE_DIRECTORIES="1"
+DOCS="CONTRIB DEPRECATED NEWS README"
+PYTHON_MODNAME="Bio BioSQL"
+
+src_prepare() {
+	distutils_src_prepare
+	epatch "${FILESDIR}/${PN}-1.51-flex.patch"
+}
+
+src_test() {
+	testing() {
+		cd Tests
+		PYTHONPATH="$(ls -d ../build/lib.*)" "$(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=mode Scripts Tests "${ED}usr/share/${PN}" || die "Installation 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=["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=["Bio"],
+-#              libraries=["fl"]
+-#              ),
++    Extension('Bio.PDB.mmCIF.MMCIFlex',
++              ['Bio/PDB/mmCIF/lex.yy.c',
++               'Bio/PDB/mmCIF/MMCIFlexmodule.c'],
++              include_dirs=["Bio"],
++              libraries=["fl"]
++              ),
+     Extension('Bio.Nexus.cnexus',
+               ['Bio/Nexus/cnexus.c']
+               ),

diff --git a/sci-biology/biopython/metadata.xml b/sci-biology/biopython/metadata.xml
new file mode 100644
index 0000000..34294c6
--- /dev/null
+++ b/sci-biology/biopython/metadata.xml
@@ -0,0 +1,5 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci-biology</herd>
+</pkgmetadata>