* [gentoo-commits] proj/sci:master commit in: sci-biology/biopython/, sci-biology/biopython/files/
@ 2011-12-07 15:14 Martin Mokrejs
0 siblings, 0 replies; 10+ messages in thread
From: Martin Mokrejs @ 2011-12-07 15:14 UTC (permalink / raw
To: gentoo-commits
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>
^ permalink raw reply related [flat|nested] 10+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/biopython/, sci-biology/biopython/files/
@ 2012-03-21 11:20 Justin Lecher
0 siblings, 0 replies; 10+ messages in thread
From: Justin Lecher @ 2012-03-21 11:20 UTC (permalink / raw
To: gentoo-commits
commit: 96fa03b29208beadce34b013c5851a4c8f6e27e1
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed Mar 21 11:20:00 2012 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed Mar 21 11:20:00 2012 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=96fa03b2
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/ChangeLog
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 1.65 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
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=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
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=["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
deleted file mode 100644
index 34294c6..0000000
--- a/sci-biology/biopython/metadata.xml
+++ /dev/null
@@ -1,5 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-<herd>sci-biology</herd>
-</pkgmetadata>
^ permalink raw reply related [flat|nested] 10+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/biopython/, sci-biology/biopython/files/
@ 2013-09-25 12:29 Martin Mokrejs
0 siblings, 0 replies; 10+ messages in thread
From: Martin Mokrejs @ 2013-09-25 12:29 UTC (permalink / raw
To: gentoo-commits
commit: 6801f6ae30dccc74032f18035561acff1e4123b4
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Wed Sep 25 12:29:21 2013 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> 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 <mmokrejs@fold.natur.cuni.cz>
+ +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 <jlec@gentoo.org> +biopython-1.62.ebuild:
+ Version Bump
+
+ 02 Jul 2013; Justin Lecher <jlec@gentoo.org> biopython-1.61.ebuild:
+ Fix deps for python
+
+ 06 Jun 2013; Justin Lecher <jlec@gentoo.org> biopython-1.61.ebuild:
+ Keyword ~-linux
+
+*biopython-1.61 (26 Apr 2013)
+
+ 26 Apr 2013; Justin Lecher <jlec@gentoo.org> +biopython-1.61.ebuild,
+ metadata.xml:
+ Version Bump
+
+ 14 Dec 2012; Ulrich Müller <ulm@gentoo.org> 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 <weaver@gentoo.org> +biopython-1.59.ebuild:
+ Version bump
+
+ 26 Dec 2011; Andrey Kislyuk <weaver@gentoo.org> +biopython-1.58.ebuild:
+ Version bump
+
+*biopython-1.58 (26 Dec 2011)
+
+ 26 Dec 2011; Andrey Kislyuk <weaver@gentoo.org> +biopython-1.58.ebuild:
+ 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-1.62-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 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
^ permalink raw reply related [flat|nested] 10+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/biopython/, sci-biology/biopython/files/
@ 2013-12-29 0:31 Justin Lecher
0 siblings, 0 replies; 10+ messages in thread
From: Justin Lecher @ 2013-12-29 0:31 UTC (permalink / raw
To: gentoo-commits
commit: 4c137a437dca9f76da755afa10c90f2f67e7059b
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sun Dec 29 00:29:06 2013 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> 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 <jlec <AT> 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 <mmokrejs@fold.natur.cuni.cz>
- +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 <jlec@gentoo.org> +biopython-1.62.ebuild:
- Version Bump
-
- 02 Jul 2013; Justin Lecher <jlec@gentoo.org> biopython-1.61.ebuild:
- Fix deps for python
-
- 06 Jun 2013; Justin Lecher <jlec@gentoo.org> biopython-1.61.ebuild:
- Keyword ~-linux
-
-*biopython-1.61 (26 Apr 2013)
-
- 26 Apr 2013; Justin Lecher <jlec@gentoo.org> +biopython-1.61.ebuild,
- metadata.xml:
- Version Bump
-
- 14 Dec 2012; Ulrich Müller <ulm@gentoo.org> 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 <weaver@gentoo.org> +biopython-1.59.ebuild:
- Version bump
-
- 26 Dec 2011; Andrey Kislyuk <weaver@gentoo.org> +biopython-1.58.ebuild:
- Version bump
-
-*biopython-1.58 (26 Dec 2011)
-
- 26 Dec 2011; Andrey Kislyuk <weaver@gentoo.org> +biopython-1.58.ebuild:
- 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-1.62-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 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <herd>sci-biology</herd>
-</pkgmetadata>
^ permalink raw reply related [flat|nested] 10+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/biopython/, sci-biology/biopython/files/
@ 2014-03-23 16:00 Martin Mokrejs
0 siblings, 0 replies; 10+ messages in thread
From: Martin Mokrejs @ 2014-03-23 16:00 UTC (permalink / raw
To: gentoo-commits
commit: b6bc96d05888bcfb2a2ebac3a477663d1915c57c
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Mar 23 15:52:18 2014 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Mar 23 15:52:18 2014 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=b6bc96d0
sci-biology/biopython-1.63-r1: version bump and an upstream patch to improve error message
Package-Manager: portage-2.2.7
---
sci-biology/biopython/ChangeLog | 17 +++
sci-biology/biopython/biopython-1.62-r3.ebuild | 51 +++++++
sci-biology/biopython/biopython-1.62-r4.ebuild | 51 +++++++
sci-biology/biopython/biopython-1.63-r1.ebuild | 51 +++++++
sci-biology/biopython/biopython-1.63.ebuild | 50 +++++++
sci-biology/biopython/files/SeqRecord.py.patch | 148 +++++++++++++++++++++
.../biopython/files/SffIO_error_in_check_eof.patch | 14 ++
.../biopython/files/adjust-trimpoints.patch | 76 +++++++++++
.../biopython/files/biopython-1.51-flex.patch | 21 +++
.../biopython/files/biopython-1.62-SffIO.patch | 36 +++++
sci-biology/biopython/metadata.xml | 5 +
11 files changed, 520 insertions(+)
diff --git a/sci-biology/biopython/ChangeLog b/sci-biology/biopython/ChangeLog
new file mode 100644
index 0000000..6dfe5e2
--- /dev/null
+++ b/sci-biology/biopython/ChangeLog
@@ -0,0 +1,17 @@
+# ChangeLog for sci-biology/biopython
+# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*biopython-1.62-r3 (23 Mar 2014)
+*biopython-1.62-r4 (23 Mar 2014)
+*biopython-1.63-r1 (23 Mar 2014)
+*biopython-1.63 (23 Mar 2014)
+
+ 23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ +biopython-1.62-r3.ebuild, +biopython-1.62-r4.ebuild,
+ +biopython-1.63-r1.ebuild, +biopython-1.63.ebuild, +files/SeqRecord.py.patch,
+ +files/SffIO_error_in_check_eof.patch, +files/adjust-trimpoints.patch,
+ +files/biopython-1.51-flex.patch, +files/biopython-1.62-SffIO.patch,
+ +metadata.xml:
+ sci-biology/biopython-1.63-r1: version bump and an upstream patch to improve
+ error message
diff --git a/sci-biology/biopython/biopython-1.62-r3.ebuild b/sci-biology/biopython/biopython-1.62-r3.ebuild
new file mode 100644
index 0000000..1eed5a9
--- /dev/null
+++ b/sci-biology/biopython/biopython-1.62-r3.ebuild
@@ -0,0 +1,51 @@
+# Copyright 1999-2014 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/biopython-1.62-r4.ebuild b/sci-biology/biopython/biopython-1.62-r4.ebuild
new file mode 100644
index 0000000..1eed5a9
--- /dev/null
+++ b/sci-biology/biopython/biopython-1.62-r4.ebuild
@@ -0,0 +1,51 @@
+# Copyright 1999-2014 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/biopython-1.63-r1.ebuild b/sci-biology/biopython/biopython-1.63-r1.ebuild
new file mode 100644
index 0000000..aac2bdf
--- /dev/null
+++ b/sci-biology/biopython/biopython-1.63-r1.ebuild
@@ -0,0 +1,51 @@
+# Copyright 1999-2014 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() {
+ epatch "${FILESDIR}"/SffIO_error_in_check_eof.patch
+ distutils-r1_src_prepare
+}
+
+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/biopython-1.63.ebuild b/sci-biology/biopython/biopython-1.63.ebuild
new file mode 100644
index 0000000..5180b33
--- /dev/null
+++ b/sci-biology/biopython/biopython-1.63.ebuild
@@ -0,0 +1,50 @@
+# Copyright 1999-2014 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
+}
+
+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/SeqRecord.py.patch b/sci-biology/biopython/files/SeqRecord.py.patch
new file mode 100644
index 0000000..ac3785f
--- /dev/null
+++ b/sci-biology/biopython/files/SeqRecord.py.patch
@@ -0,0 +1,148 @@
+diff --git a/Bio/SeqIO/SffIO.py b/Bio/SeqIO/SffIO.py
+index 1971dba..43b38fd 100644
+--- a/Bio/SeqIO/SffIO.py
++++ b/Bio/SeqIO/SffIO.py
+@@ -539,8 +539,15 @@ _valid_UAN_read_name = re.compile(r'^[a-zA-Z0-9]{14}$')
+
+
+ def _sff_read_seq_record(handle, number_of_flows_per_read, flow_chars,
+- key_sequence, alphabet, trim=False):
+- """Parse the next read in the file, return data as a SeqRecord (PRIVATE)."""
++ key_sequence, alphabet, trim=False, interpret_qual_trims=True, interpret_adapter_trims=False):
++ """Parse the next read in the file, return data as a SeqRecord (PRIVATE).
++ Allow user to specify which type of clipping values should be applied
++ while reading the SFF stream. To be backwards compatible, we interpret
++ only the quality-based trim points by default. That results in lower-cased
++ sequences in the low-qual region, regardless what adapter-based clip points
++ say. This should be the desired behavior. More discussion at
++ https://redmine.open-bio.org/issues/3437
++ """
+ #Now on to the reads...
+ #the read header format (fixed part):
+ #read_header_length H
+@@ -589,20 +596,41 @@ def _sff_read_seq_record(handle, number_of_flows_per_read, flow_chars,
+ warnings.warn("Post quality %i byte padding region contained data, SFF data is not broken"
+ % padding)
+ #Follow Roche and apply most aggressive of qual and adapter clipping.
+- #Note Roche seems to ignore adapter clip fields when writing SFF,
+- #and uses just the quality clipping values for any clipping.
+- clip_left = max(clip_qual_left, clip_adapter_left)
+- #Right clipping of zero means no clipping
+- if clip_qual_right:
+- if clip_adapter_right:
+- clip_right = min(clip_qual_right, clip_adapter_right)
++ #Note Roche does not use adapter clip fields when writing SFF files
++ #but instead combines the adapter clipping information with quality-based
++ #values and writes the most aggressive combination into clip fields (as
++ #allowed by SFF specs).
++
++ if interpret_qual_trims:
++ if interpret_adapter_trims:
++ clip_left = max(clip_qual_left, clip_adapter_left)
++ #Right clipping of zero means no clipping
++ if clip_qual_right:
++ if clip_adapter_right:
++ clip_right = min(clip_qual_right, clip_adapter_right)
++ else:
++ #Typical case with Roche SFF files
++ clip_right = clip_qual_right
++ elif clip_adapter_right:
++ clip_right = clip_adapter_right
++ else:
++ clip_right = seq_len
+ else:
+- #Typical case with Roche SFF files
+- clip_right = clip_qual_right
+- elif clip_adapter_right:
+- clip_right = clip_adapter_right
++ clip_left = clip_qual_left
++ if clip_qual_right:
++ clip_right = clip_qual_right
++ else:
++ clip_right = seq_len
++ elif interpret_adapter_trims:
++ clip_left = clip_adapter_left
++ if clip_adapter_right:
++ clip_right = clip_adapter_right
++ else:
++ clip_right = seq_len
+ else:
+- clip_right = seq_len
++ clip_left = 0
++ clip_right = seq_len
++
+ #Now build a SeqRecord
+ if trim:
+ seq = seq[clip_left:clip_right].upper()
+diff --git a/Bio/SeqRecord.py b/Bio/SeqRecord.py
+index c90e13b..66bdea0 100644
+--- a/Bio/SeqRecord.py
++++ b/Bio/SeqRecord.py
+@@ -14,6 +14,8 @@ __docformat__ = "epytext en" # Simple markup to show doctests nicely
+ # also BioSQL.BioSeq.DBSeq which is the "Database Seq" class)
+
+
++from Bio.Seq import Seq
++
+ class _RestrictedDict(dict):
+ """Dict which only allows sequences of given length as values (PRIVATE).
+
+@@ -76,7 +78,7 @@ class _RestrictedDict(dict):
+ if not hasattr(value, "__len__") or not hasattr(value, "__getitem__") \
+ or (hasattr(self, "_length") and len(value) != self._length):
+ raise TypeError("We only allow python sequences (lists, tuples or "
+- "strings) of length %i." % self._length)
++ "strings) of length %i whereas you passed an object of length %s." % (self._length, str(len(value))))
+ dict.__setitem__(self, key, value)
+
+ def update(self, new_dict):
+@@ -290,10 +292,11 @@ class SeqRecord(object):
+ """)
+
+ def _set_seq(self, value):
+- #TODO - Add a deprecation warning that the seq should be write only?
+- if self._per_letter_annotations:
+- #TODO - Make this a warning? Silently empty the dictionary?
+- raise ValueError("You must empty the letter annotations first!")
++ # we should be much more user friendly and accept even a plain sequence string
++ # and make the Seq or MutableSeq object ourselves
++ if not isinstance(value, Seq):
++ raise ValueError("You must pass a Seq object containing the new sequence instead of just plain string.")
++ else:
+ self._seq = value
+ try:
+ self._per_letter_annotations = _RestrictedDict(length=len(self.seq))
+@@ -696,7 +699,7 @@ class SeqRecord(object):
+ SeqIO.write(self, handle, format_spec)
+ return handle.getvalue()
+
+- def __len__(self):
++ def __len__(self, trim=False, interpret_qual_trims=True, interpret_adapter_trims=False):
+ """Returns the length of the sequence.
+
+ For example, using Bio.SeqIO to read in a FASTA nucleotide file:
+@@ -707,6 +710,10 @@ class SeqRecord(object):
+ 309
+ >>> len(record.seq)
+ 309
++
++ It should be possible to get length of a raw object, of trimmed
++ object by quality or adapter criteria or both, whenever user wants
++ to, not only when data is parsed from input.
+ """
+ return len(self.seq)
+
+@@ -725,6 +732,13 @@ class SeqRecord(object):
+ """
+ return True
+
++ def apply_trimpoints(self, trim=False, interpret_qual_trims=False, interpret_adapter_trims=False):
++ """We should apply either of the quality-based or adapter-based annotated
++ trim points and return a new, sliced object.
++ """
++ pass
++
++
+ def __add__(self, other):
+ """Add another sequence or string to this sequence.
+
diff --git a/sci-biology/biopython/files/SffIO_error_in_check_eof.patch b/sci-biology/biopython/files/SffIO_error_in_check_eof.patch
new file mode 100644
index 0000000..9059604
--- /dev/null
+++ b/sci-biology/biopython/files/SffIO_error_in_check_eof.patch
@@ -0,0 +1,14 @@
+diff --git a/Bio/SeqIO/SffIO.py b/Bio/SeqIO/SffIO.py
+index 2bb0dac..735d55b 100644
+--- a/Bio/SeqIO/SffIO.py
++++ b/Bio/SeqIO/SffIO.py
+@@ -941,7 +941,8 @@ def _check_eof(handle, index_offset, index_length):
+ BiopythonParserWarning)
+
+ offset = handle.tell()
+- assert offset % 8 == 0
++ assert offset % 8 == 0, \
++ "Wanted offset %i %% 8 = %i to be zero" % (offset, offset % 8)
+ # Should now be at the end of the file...
+ extra = handle.read(4)
+ if extra == _sff:
diff --git a/sci-biology/biopython/files/adjust-trimpoints.patch b/sci-biology/biopython/files/adjust-trimpoints.patch
new file mode 100644
index 0000000..dd6d548
--- /dev/null
+++ b/sci-biology/biopython/files/adjust-trimpoints.patch
@@ -0,0 +1,76 @@
+diff --git a/Bio/SeqIO/SffIO.py b/Bio/SeqIO/SffIO.py
+index 1971dba..43b38fd 100644
+--- a/Bio/SeqIO/SffIO.py
++++ b/Bio/SeqIO/SffIO.py
+@@ -539,8 +539,15 @@ _valid_UAN_read_name = re.compile(r'^[a-zA-Z0-9]{14}$')
+
+
+ def _sff_read_seq_record(handle, number_of_flows_per_read, flow_chars,
+- key_sequence, alphabet, trim=False):
+- """Parse the next read in the file, return data as a SeqRecord (PRIVATE)."""
++ key_sequence, alphabet, trim=False, interpret_qual_trims=True, interpret_adapter_trims=False):
++ """Parse the next read in the file, return data as a SeqRecord (PRIVATE).
++ Allow user to specify which type of clipping values should be applied
++ while reading the SFF stream. To be backwards compatible, we interpret
++ only the quality-based trim points by default. That results in lower-cased
++ sequences in the low-qual region, regardless what adapter-based clip points
++ say. This should be the desired behavior. More discussion at
++ https://redmine.open-bio.org/issues/3437
++ """
+ #Now on to the reads...
+ #the read header format (fixed part):
+ #read_header_length H
+@@ -589,20 +596,41 @@ def _sff_read_seq_record(handle, number_of_flows_per_read, flow_chars,
+ warnings.warn("Post quality %i byte padding region contained data, SFF data is not broken"
+ % padding)
+ #Follow Roche and apply most aggressive of qual and adapter clipping.
+- #Note Roche seems to ignore adapter clip fields when writing SFF,
+- #and uses just the quality clipping values for any clipping.
+- clip_left = max(clip_qual_left, clip_adapter_left)
+- #Right clipping of zero means no clipping
+- if clip_qual_right:
+- if clip_adapter_right:
+- clip_right = min(clip_qual_right, clip_adapter_right)
++ #Note Roche does not use adapter clip fields when writing SFF files
++ #but instead combines the adapter clipping information with quality-based
++ #values and writes the most aggressive combination into clip fields (as
++ #allowed by SFF specs).
++
++ if interpret_qual_trims:
++ if interpret_adapter_trims:
++ clip_left = max(clip_qual_left, clip_adapter_left)
++ #Right clipping of zero means no clipping
++ if clip_qual_right:
++ if clip_adapter_right:
++ clip_right = min(clip_qual_right, clip_adapter_right)
++ else:
++ #Typical case with Roche SFF files
++ clip_right = clip_qual_right
++ elif clip_adapter_right:
++ clip_right = clip_adapter_right
++ else:
++ clip_right = seq_len
+ else:
+- #Typical case with Roche SFF files
+- clip_right = clip_qual_right
+- elif clip_adapter_right:
+- clip_right = clip_adapter_right
++ clip_left = clip_qual_left
++ if clip_qual_right:
++ clip_right = clip_qual_right
++ else:
++ clip_right = seq_len
++ elif interpret_adapter_trims:
++ clip_left = clip_adapter_left
++ if clip_adapter_right:
++ clip_right = clip_adapter_right
++ else:
++ clip_right = seq_len
+ else:
+- clip_right = seq_len
++ clip_left = 0
++ clip_right = seq_len
++
+ #Now build a SeqRecord
+ if trim:
+ seq = seq[clip_left:clip_right].upper()
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/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 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <herd>sci-biology</herd>
+</pkgmetadata>
^ permalink raw reply related [flat|nested] 10+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/biopython/, sci-biology/biopython/files/
@ 2014-03-23 16:09 Martin Mokrejs
0 siblings, 0 replies; 10+ messages in thread
From: Martin Mokrejs @ 2014-03-23 16:09 UTC (permalink / raw
To: gentoo-commits
commit: 031391850b6768a55ed2c98a93eeb255954b51d2
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sun Mar 23 16:07:50 2014 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sun Mar 23 16:07:50 2014 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=03139185
sci-biology/biopython-1.63-r1: added missing deps on dev-python/rdflib to sync with official sci-biology/biopython-1.63; dropping sci-biology/biopython-1.63 from overlay
Package-Manager: portage-2.2.7
---
sci-biology/biopython/ChangeLog | 8 ++
sci-biology/biopython/biopython-1.62-r3.ebuild | 51 -------
sci-biology/biopython/biopython-1.62-r4.ebuild | 51 -------
sci-biology/biopython/biopython-1.63-r1.ebuild | 1 +
sci-biology/biopython/biopython-1.63.ebuild | 50 -------
sci-biology/biopython/files/SeqRecord.py.patch | 148 ---------------------
.../biopython/files/adjust-trimpoints.patch | 76 -----------
7 files changed, 9 insertions(+), 376 deletions(-)
diff --git a/sci-biology/biopython/ChangeLog b/sci-biology/biopython/ChangeLog
index 6dfe5e2..037227d 100644
--- a/sci-biology/biopython/ChangeLog
+++ b/sci-biology/biopython/ChangeLog
@@ -2,6 +2,14 @@
# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ -biopython-1.62-r3.ebuild, -biopython-1.62-r4.ebuild, -biopython-1.63.ebuild,
+ -files/SeqRecord.py.patch, -files/adjust-trimpoints.patch,
+ biopython-1.63-r1.ebuild:
+ sci-biology/biopython-1.63-r1: added missing deps on dev-python/rdflib to sync
+ with official sci-biology/biopython-1.63; dropping sci-biology/biopython-1.63
+ from overlay
+
*biopython-1.62-r3 (23 Mar 2014)
*biopython-1.62-r4 (23 Mar 2014)
*biopython-1.63-r1 (23 Mar 2014)
diff --git a/sci-biology/biopython/biopython-1.62-r3.ebuild b/sci-biology/biopython/biopython-1.62-r3.ebuild
deleted file mode 100644
index 1eed5a9..0000000
--- a/sci-biology/biopython/biopython-1.62-r3.ebuild
+++ /dev/null
@@ -1,51 +0,0 @@
-# Copyright 1999-2014 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/biopython-1.62-r4.ebuild b/sci-biology/biopython/biopython-1.62-r4.ebuild
deleted file mode 100644
index 1eed5a9..0000000
--- a/sci-biology/biopython/biopython-1.62-r4.ebuild
+++ /dev/null
@@ -1,51 +0,0 @@
-# Copyright 1999-2014 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/biopython-1.63-r1.ebuild b/sci-biology/biopython/biopython-1.63-r1.ebuild
index aac2bdf..e99f846 100644
--- a/sci-biology/biopython/biopython-1.63-r1.ebuild
+++ b/sci-biology/biopython/biopython-1.63-r1.ebuild
@@ -23,6 +23,7 @@ RDEPEND="${PYTHON_DEPS}
dev-python/matplotlib[${PYTHON_USEDEP}]
dev-python/networkx[${PYTHON_USEDEP}]
dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/rdflib[${PYTHON_USEDEP}]
dev-python/pygraphviz[${PYTHON_USEDEP}]
dev-python/reportlab[${PYTHON_USEDEP}]
media-gfx/pydot[${PYTHON_USEDEP}]
diff --git a/sci-biology/biopython/biopython-1.63.ebuild b/sci-biology/biopython/biopython-1.63.ebuild
deleted file mode 100644
index 5180b33..0000000
--- a/sci-biology/biopython/biopython-1.63.ebuild
+++ /dev/null
@@ -1,50 +0,0 @@
-# Copyright 1999-2014 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
-}
-
-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/SeqRecord.py.patch b/sci-biology/biopython/files/SeqRecord.py.patch
deleted file mode 100644
index ac3785f..0000000
--- a/sci-biology/biopython/files/SeqRecord.py.patch
+++ /dev/null
@@ -1,148 +0,0 @@
-diff --git a/Bio/SeqIO/SffIO.py b/Bio/SeqIO/SffIO.py
-index 1971dba..43b38fd 100644
---- a/Bio/SeqIO/SffIO.py
-+++ b/Bio/SeqIO/SffIO.py
-@@ -539,8 +539,15 @@ _valid_UAN_read_name = re.compile(r'^[a-zA-Z0-9]{14}$')
-
-
- def _sff_read_seq_record(handle, number_of_flows_per_read, flow_chars,
-- key_sequence, alphabet, trim=False):
-- """Parse the next read in the file, return data as a SeqRecord (PRIVATE)."""
-+ key_sequence, alphabet, trim=False, interpret_qual_trims=True, interpret_adapter_trims=False):
-+ """Parse the next read in the file, return data as a SeqRecord (PRIVATE).
-+ Allow user to specify which type of clipping values should be applied
-+ while reading the SFF stream. To be backwards compatible, we interpret
-+ only the quality-based trim points by default. That results in lower-cased
-+ sequences in the low-qual region, regardless what adapter-based clip points
-+ say. This should be the desired behavior. More discussion at
-+ https://redmine.open-bio.org/issues/3437
-+ """
- #Now on to the reads...
- #the read header format (fixed part):
- #read_header_length H
-@@ -589,20 +596,41 @@ def _sff_read_seq_record(handle, number_of_flows_per_read, flow_chars,
- warnings.warn("Post quality %i byte padding region contained data, SFF data is not broken"
- % padding)
- #Follow Roche and apply most aggressive of qual and adapter clipping.
-- #Note Roche seems to ignore adapter clip fields when writing SFF,
-- #and uses just the quality clipping values for any clipping.
-- clip_left = max(clip_qual_left, clip_adapter_left)
-- #Right clipping of zero means no clipping
-- if clip_qual_right:
-- if clip_adapter_right:
-- clip_right = min(clip_qual_right, clip_adapter_right)
-+ #Note Roche does not use adapter clip fields when writing SFF files
-+ #but instead combines the adapter clipping information with quality-based
-+ #values and writes the most aggressive combination into clip fields (as
-+ #allowed by SFF specs).
-+
-+ if interpret_qual_trims:
-+ if interpret_adapter_trims:
-+ clip_left = max(clip_qual_left, clip_adapter_left)
-+ #Right clipping of zero means no clipping
-+ if clip_qual_right:
-+ if clip_adapter_right:
-+ clip_right = min(clip_qual_right, clip_adapter_right)
-+ else:
-+ #Typical case with Roche SFF files
-+ clip_right = clip_qual_right
-+ elif clip_adapter_right:
-+ clip_right = clip_adapter_right
-+ else:
-+ clip_right = seq_len
- else:
-- #Typical case with Roche SFF files
-- clip_right = clip_qual_right
-- elif clip_adapter_right:
-- clip_right = clip_adapter_right
-+ clip_left = clip_qual_left
-+ if clip_qual_right:
-+ clip_right = clip_qual_right
-+ else:
-+ clip_right = seq_len
-+ elif interpret_adapter_trims:
-+ clip_left = clip_adapter_left
-+ if clip_adapter_right:
-+ clip_right = clip_adapter_right
-+ else:
-+ clip_right = seq_len
- else:
-- clip_right = seq_len
-+ clip_left = 0
-+ clip_right = seq_len
-+
- #Now build a SeqRecord
- if trim:
- seq = seq[clip_left:clip_right].upper()
-diff --git a/Bio/SeqRecord.py b/Bio/SeqRecord.py
-index c90e13b..66bdea0 100644
---- a/Bio/SeqRecord.py
-+++ b/Bio/SeqRecord.py
-@@ -14,6 +14,8 @@ __docformat__ = "epytext en" # Simple markup to show doctests nicely
- # also BioSQL.BioSeq.DBSeq which is the "Database Seq" class)
-
-
-+from Bio.Seq import Seq
-+
- class _RestrictedDict(dict):
- """Dict which only allows sequences of given length as values (PRIVATE).
-
-@@ -76,7 +78,7 @@ class _RestrictedDict(dict):
- if not hasattr(value, "__len__") or not hasattr(value, "__getitem__") \
- or (hasattr(self, "_length") and len(value) != self._length):
- raise TypeError("We only allow python sequences (lists, tuples or "
-- "strings) of length %i." % self._length)
-+ "strings) of length %i whereas you passed an object of length %s." % (self._length, str(len(value))))
- dict.__setitem__(self, key, value)
-
- def update(self, new_dict):
-@@ -290,10 +292,11 @@ class SeqRecord(object):
- """)
-
- def _set_seq(self, value):
-- #TODO - Add a deprecation warning that the seq should be write only?
-- if self._per_letter_annotations:
-- #TODO - Make this a warning? Silently empty the dictionary?
-- raise ValueError("You must empty the letter annotations first!")
-+ # we should be much more user friendly and accept even a plain sequence string
-+ # and make the Seq or MutableSeq object ourselves
-+ if not isinstance(value, Seq):
-+ raise ValueError("You must pass a Seq object containing the new sequence instead of just plain string.")
-+ else:
- self._seq = value
- try:
- self._per_letter_annotations = _RestrictedDict(length=len(self.seq))
-@@ -696,7 +699,7 @@ class SeqRecord(object):
- SeqIO.write(self, handle, format_spec)
- return handle.getvalue()
-
-- def __len__(self):
-+ def __len__(self, trim=False, interpret_qual_trims=True, interpret_adapter_trims=False):
- """Returns the length of the sequence.
-
- For example, using Bio.SeqIO to read in a FASTA nucleotide file:
-@@ -707,6 +710,10 @@ class SeqRecord(object):
- 309
- >>> len(record.seq)
- 309
-+
-+ It should be possible to get length of a raw object, of trimmed
-+ object by quality or adapter criteria or both, whenever user wants
-+ to, not only when data is parsed from input.
- """
- return len(self.seq)
-
-@@ -725,6 +732,13 @@ class SeqRecord(object):
- """
- return True
-
-+ def apply_trimpoints(self, trim=False, interpret_qual_trims=False, interpret_adapter_trims=False):
-+ """We should apply either of the quality-based or adapter-based annotated
-+ trim points and return a new, sliced object.
-+ """
-+ pass
-+
-+
- def __add__(self, other):
- """Add another sequence or string to this sequence.
-
diff --git a/sci-biology/biopython/files/adjust-trimpoints.patch b/sci-biology/biopython/files/adjust-trimpoints.patch
deleted file mode 100644
index dd6d548..0000000
--- a/sci-biology/biopython/files/adjust-trimpoints.patch
+++ /dev/null
@@ -1,76 +0,0 @@
-diff --git a/Bio/SeqIO/SffIO.py b/Bio/SeqIO/SffIO.py
-index 1971dba..43b38fd 100644
---- a/Bio/SeqIO/SffIO.py
-+++ b/Bio/SeqIO/SffIO.py
-@@ -539,8 +539,15 @@ _valid_UAN_read_name = re.compile(r'^[a-zA-Z0-9]{14}$')
-
-
- def _sff_read_seq_record(handle, number_of_flows_per_read, flow_chars,
-- key_sequence, alphabet, trim=False):
-- """Parse the next read in the file, return data as a SeqRecord (PRIVATE)."""
-+ key_sequence, alphabet, trim=False, interpret_qual_trims=True, interpret_adapter_trims=False):
-+ """Parse the next read in the file, return data as a SeqRecord (PRIVATE).
-+ Allow user to specify which type of clipping values should be applied
-+ while reading the SFF stream. To be backwards compatible, we interpret
-+ only the quality-based trim points by default. That results in lower-cased
-+ sequences in the low-qual region, regardless what adapter-based clip points
-+ say. This should be the desired behavior. More discussion at
-+ https://redmine.open-bio.org/issues/3437
-+ """
- #Now on to the reads...
- #the read header format (fixed part):
- #read_header_length H
-@@ -589,20 +596,41 @@ def _sff_read_seq_record(handle, number_of_flows_per_read, flow_chars,
- warnings.warn("Post quality %i byte padding region contained data, SFF data is not broken"
- % padding)
- #Follow Roche and apply most aggressive of qual and adapter clipping.
-- #Note Roche seems to ignore adapter clip fields when writing SFF,
-- #and uses just the quality clipping values for any clipping.
-- clip_left = max(clip_qual_left, clip_adapter_left)
-- #Right clipping of zero means no clipping
-- if clip_qual_right:
-- if clip_adapter_right:
-- clip_right = min(clip_qual_right, clip_adapter_right)
-+ #Note Roche does not use adapter clip fields when writing SFF files
-+ #but instead combines the adapter clipping information with quality-based
-+ #values and writes the most aggressive combination into clip fields (as
-+ #allowed by SFF specs).
-+
-+ if interpret_qual_trims:
-+ if interpret_adapter_trims:
-+ clip_left = max(clip_qual_left, clip_adapter_left)
-+ #Right clipping of zero means no clipping
-+ if clip_qual_right:
-+ if clip_adapter_right:
-+ clip_right = min(clip_qual_right, clip_adapter_right)
-+ else:
-+ #Typical case with Roche SFF files
-+ clip_right = clip_qual_right
-+ elif clip_adapter_right:
-+ clip_right = clip_adapter_right
-+ else:
-+ clip_right = seq_len
- else:
-- #Typical case with Roche SFF files
-- clip_right = clip_qual_right
-- elif clip_adapter_right:
-- clip_right = clip_adapter_right
-+ clip_left = clip_qual_left
-+ if clip_qual_right:
-+ clip_right = clip_qual_right
-+ else:
-+ clip_right = seq_len
-+ elif interpret_adapter_trims:
-+ clip_left = clip_adapter_left
-+ if clip_adapter_right:
-+ clip_right = clip_adapter_right
-+ else:
-+ clip_right = seq_len
- else:
-- clip_right = seq_len
-+ clip_left = 0
-+ clip_right = seq_len
-+
- #Now build a SeqRecord
- if trim:
- seq = seq[clip_left:clip_right].upper()
^ permalink raw reply related [flat|nested] 10+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/biopython/, sci-biology/biopython/files/
@ 2014-04-18 18:14 Martin Mokrejs
0 siblings, 0 replies; 10+ messages in thread
From: Martin Mokrejs @ 2014-04-18 18:14 UTC (permalink / raw
To: gentoo-commits
commit: 20c8e6ec36a2cdd5af944030720b059fb8d10891
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Apr 18 18:11:59 2014 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Apr 18 18:11:59 2014 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=20c8e6ec
sci-biology/biopython: upstream patch to downgrade an assert to a warning
Package-Manager: portage-2.2.7
---
sci-biology/biopython/ChangeLog | 11 ++
...hon-1.63-r1.ebuild => biopython-1.62-r3.ebuild} | 5 +-
...hon-1.63-r1.ebuild => biopython-1.62-r4.ebuild} | 5 +-
sci-biology/biopython/biopython-1.63-r1.ebuild | 3 +-
sci-biology/biopython/files/SeqRecord.py.patch | 148 +++++++++++++++++++++
.../biopython/files/SffIO_broken_padding.patch | 27 ++++
.../biopython/files/adjust-trimpoints.patch | 76 +++++++++++
7 files changed, 270 insertions(+), 5 deletions(-)
diff --git a/sci-biology/biopython/ChangeLog b/sci-biology/biopython/ChangeLog
index 037227d..c326c4a 100644
--- a/sci-biology/biopython/ChangeLog
+++ b/sci-biology/biopython/ChangeLog
@@ -2,6 +2,17 @@
# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+*biopython-1.62-r3 (18 Apr 2014)
+*biopython-1.62-r4 (18 Apr 2014)
+
+ 18 Apr 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ +biopython-1.62-r3.ebuild, +biopython-1.62-r4.ebuild,
+ +files/SeqRecord.py.patch, +files/SffIO_broken_padding.patch,
+ +files/adjust-trimpoints.patch, biopython-1.63-r1.ebuild,
+ files/SffIO_error_in_check_eof.patch, files/biopython-1.51-flex.patch,
+ files/biopython-1.62-SffIO.patch:
+ sci-biology/biopython: upstream patch to downgrade an assert to a warning
+
23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
-biopython-1.62-r3.ebuild, -biopython-1.62-r4.ebuild, -biopython-1.63.ebuild,
-files/SeqRecord.py.patch, -files/adjust-trimpoints.patch,
diff --git a/sci-biology/biopython/biopython-1.63-r1.ebuild b/sci-biology/biopython/biopython-1.62-r3.ebuild
similarity index 90%
copy from sci-biology/biopython/biopython-1.63-r1.ebuild
copy to sci-biology/biopython/biopython-1.62-r3.ebuild
index e99f846..09e6ed7 100644
--- a/sci-biology/biopython/biopython-1.63-r1.ebuild
+++ b/sci-biology/biopython/biopython-1.62-r3.ebuild
@@ -23,7 +23,6 @@ RDEPEND="${PYTHON_DEPS}
dev-python/matplotlib[${PYTHON_USEDEP}]
dev-python/networkx[${PYTHON_USEDEP}]
dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/rdflib[${PYTHON_USEDEP}]
dev-python/pygraphviz[${PYTHON_USEDEP}]
dev-python/reportlab[${PYTHON_USEDEP}]
media-gfx/pydot[${PYTHON_USEDEP}]
@@ -35,8 +34,10 @@ DEPEND="${RDEPEND}
DOCS=( CONTRIB DEPRECATED NEWS README Doc/. )
src_prepare() {
- epatch "${FILESDIR}"/SffIO_error_in_check_eof.patch
distutils-r1_src_prepare
+ epatch "${FILESDIR}/${PN}-1.62-SffIO.patch"
+ epatch "${FILESDIR}/SffIO_error_in_check_eof.patch"
+ epatch "${FILESDIR}/SffIO_broken_padding.patch"
}
python_test() {
diff --git a/sci-biology/biopython/biopython-1.63-r1.ebuild b/sci-biology/biopython/biopython-1.62-r4.ebuild
similarity index 90%
copy from sci-biology/biopython/biopython-1.63-r1.ebuild
copy to sci-biology/biopython/biopython-1.62-r4.ebuild
index e99f846..09e6ed7 100644
--- a/sci-biology/biopython/biopython-1.63-r1.ebuild
+++ b/sci-biology/biopython/biopython-1.62-r4.ebuild
@@ -23,7 +23,6 @@ RDEPEND="${PYTHON_DEPS}
dev-python/matplotlib[${PYTHON_USEDEP}]
dev-python/networkx[${PYTHON_USEDEP}]
dev-python/numpy[${PYTHON_USEDEP}]
- dev-python/rdflib[${PYTHON_USEDEP}]
dev-python/pygraphviz[${PYTHON_USEDEP}]
dev-python/reportlab[${PYTHON_USEDEP}]
media-gfx/pydot[${PYTHON_USEDEP}]
@@ -35,8 +34,10 @@ DEPEND="${RDEPEND}
DOCS=( CONTRIB DEPRECATED NEWS README Doc/. )
src_prepare() {
- epatch "${FILESDIR}"/SffIO_error_in_check_eof.patch
distutils-r1_src_prepare
+ epatch "${FILESDIR}/${PN}-1.62-SffIO.patch"
+ epatch "${FILESDIR}/SffIO_error_in_check_eof.patch"
+ epatch "${FILESDIR}/SffIO_broken_padding.patch"
}
python_test() {
diff --git a/sci-biology/biopython/biopython-1.63-r1.ebuild b/sci-biology/biopython/biopython-1.63-r1.ebuild
index e99f846..b600748 100644
--- a/sci-biology/biopython/biopython-1.63-r1.ebuild
+++ b/sci-biology/biopython/biopython-1.63-r1.ebuild
@@ -35,7 +35,8 @@ DEPEND="${RDEPEND}
DOCS=( CONTRIB DEPRECATED NEWS README Doc/. )
src_prepare() {
- epatch "${FILESDIR}"/SffIO_error_in_check_eof.patch
+ epatch "${FILESDIR}/SffIO_error_in_check_eof.patch"
+ epatch "${FILESDIR}/SffIO_broken_padding.patch"
distutils-r1_src_prepare
}
diff --git a/sci-biology/biopython/files/SeqRecord.py.patch b/sci-biology/biopython/files/SeqRecord.py.patch
new file mode 100644
index 0000000..ac3785f
--- /dev/null
+++ b/sci-biology/biopython/files/SeqRecord.py.patch
@@ -0,0 +1,148 @@
+diff --git a/Bio/SeqIO/SffIO.py b/Bio/SeqIO/SffIO.py
+index 1971dba..43b38fd 100644
+--- a/Bio/SeqIO/SffIO.py
++++ b/Bio/SeqIO/SffIO.py
+@@ -539,8 +539,15 @@ _valid_UAN_read_name = re.compile(r'^[a-zA-Z0-9]{14}$')
+
+
+ def _sff_read_seq_record(handle, number_of_flows_per_read, flow_chars,
+- key_sequence, alphabet, trim=False):
+- """Parse the next read in the file, return data as a SeqRecord (PRIVATE)."""
++ key_sequence, alphabet, trim=False, interpret_qual_trims=True, interpret_adapter_trims=False):
++ """Parse the next read in the file, return data as a SeqRecord (PRIVATE).
++ Allow user to specify which type of clipping values should be applied
++ while reading the SFF stream. To be backwards compatible, we interpret
++ only the quality-based trim points by default. That results in lower-cased
++ sequences in the low-qual region, regardless what adapter-based clip points
++ say. This should be the desired behavior. More discussion at
++ https://redmine.open-bio.org/issues/3437
++ """
+ #Now on to the reads...
+ #the read header format (fixed part):
+ #read_header_length H
+@@ -589,20 +596,41 @@ def _sff_read_seq_record(handle, number_of_flows_per_read, flow_chars,
+ warnings.warn("Post quality %i byte padding region contained data, SFF data is not broken"
+ % padding)
+ #Follow Roche and apply most aggressive of qual and adapter clipping.
+- #Note Roche seems to ignore adapter clip fields when writing SFF,
+- #and uses just the quality clipping values for any clipping.
+- clip_left = max(clip_qual_left, clip_adapter_left)
+- #Right clipping of zero means no clipping
+- if clip_qual_right:
+- if clip_adapter_right:
+- clip_right = min(clip_qual_right, clip_adapter_right)
++ #Note Roche does not use adapter clip fields when writing SFF files
++ #but instead combines the adapter clipping information with quality-based
++ #values and writes the most aggressive combination into clip fields (as
++ #allowed by SFF specs).
++
++ if interpret_qual_trims:
++ if interpret_adapter_trims:
++ clip_left = max(clip_qual_left, clip_adapter_left)
++ #Right clipping of zero means no clipping
++ if clip_qual_right:
++ if clip_adapter_right:
++ clip_right = min(clip_qual_right, clip_adapter_right)
++ else:
++ #Typical case with Roche SFF files
++ clip_right = clip_qual_right
++ elif clip_adapter_right:
++ clip_right = clip_adapter_right
++ else:
++ clip_right = seq_len
+ else:
+- #Typical case with Roche SFF files
+- clip_right = clip_qual_right
+- elif clip_adapter_right:
+- clip_right = clip_adapter_right
++ clip_left = clip_qual_left
++ if clip_qual_right:
++ clip_right = clip_qual_right
++ else:
++ clip_right = seq_len
++ elif interpret_adapter_trims:
++ clip_left = clip_adapter_left
++ if clip_adapter_right:
++ clip_right = clip_adapter_right
++ else:
++ clip_right = seq_len
+ else:
+- clip_right = seq_len
++ clip_left = 0
++ clip_right = seq_len
++
+ #Now build a SeqRecord
+ if trim:
+ seq = seq[clip_left:clip_right].upper()
+diff --git a/Bio/SeqRecord.py b/Bio/SeqRecord.py
+index c90e13b..66bdea0 100644
+--- a/Bio/SeqRecord.py
++++ b/Bio/SeqRecord.py
+@@ -14,6 +14,8 @@ __docformat__ = "epytext en" # Simple markup to show doctests nicely
+ # also BioSQL.BioSeq.DBSeq which is the "Database Seq" class)
+
+
++from Bio.Seq import Seq
++
+ class _RestrictedDict(dict):
+ """Dict which only allows sequences of given length as values (PRIVATE).
+
+@@ -76,7 +78,7 @@ class _RestrictedDict(dict):
+ if not hasattr(value, "__len__") or not hasattr(value, "__getitem__") \
+ or (hasattr(self, "_length") and len(value) != self._length):
+ raise TypeError("We only allow python sequences (lists, tuples or "
+- "strings) of length %i." % self._length)
++ "strings) of length %i whereas you passed an object of length %s." % (self._length, str(len(value))))
+ dict.__setitem__(self, key, value)
+
+ def update(self, new_dict):
+@@ -290,10 +292,11 @@ class SeqRecord(object):
+ """)
+
+ def _set_seq(self, value):
+- #TODO - Add a deprecation warning that the seq should be write only?
+- if self._per_letter_annotations:
+- #TODO - Make this a warning? Silently empty the dictionary?
+- raise ValueError("You must empty the letter annotations first!")
++ # we should be much more user friendly and accept even a plain sequence string
++ # and make the Seq or MutableSeq object ourselves
++ if not isinstance(value, Seq):
++ raise ValueError("You must pass a Seq object containing the new sequence instead of just plain string.")
++ else:
+ self._seq = value
+ try:
+ self._per_letter_annotations = _RestrictedDict(length=len(self.seq))
+@@ -696,7 +699,7 @@ class SeqRecord(object):
+ SeqIO.write(self, handle, format_spec)
+ return handle.getvalue()
+
+- def __len__(self):
++ def __len__(self, trim=False, interpret_qual_trims=True, interpret_adapter_trims=False):
+ """Returns the length of the sequence.
+
+ For example, using Bio.SeqIO to read in a FASTA nucleotide file:
+@@ -707,6 +710,10 @@ class SeqRecord(object):
+ 309
+ >>> len(record.seq)
+ 309
++
++ It should be possible to get length of a raw object, of trimmed
++ object by quality or adapter criteria or both, whenever user wants
++ to, not only when data is parsed from input.
+ """
+ return len(self.seq)
+
+@@ -725,6 +732,13 @@ class SeqRecord(object):
+ """
+ return True
+
++ def apply_trimpoints(self, trim=False, interpret_qual_trims=False, interpret_adapter_trims=False):
++ """We should apply either of the quality-based or adapter-based annotated
++ trim points and return a new, sliced object.
++ """
++ pass
++
++
+ def __add__(self, other):
+ """Add another sequence or string to this sequence.
+
diff --git a/sci-biology/biopython/files/SffIO_broken_padding.patch b/sci-biology/biopython/files/SffIO_broken_padding.patch
new file mode 100644
index 0000000..a009c58
--- /dev/null
+++ b/sci-biology/biopython/files/SffIO_broken_padding.patch
@@ -0,0 +1,27 @@
+diff --git a/Bio/SeqIO/SffIO.py b/Bio/SeqIO/SffIO.py
+index 735d55b..b89cf41 100644
+--- a/Bio/SeqIO/SffIO.py
++++ b/Bio/SeqIO/SffIO.py
+@@ -933,12 +933,20 @@ def _check_eof(handle, index_offset, index_length):
+ "null padding region ended '.sff' which could "
+ "be the start of a concatenated SFF file? "
+ "See offset %i" % (padding, offset))
++ if padding and not extra:
++ #TODO - Is this error harmless enough to just ignore?
++ import warnings
++ from Bio import BiopythonParserWarning
++ warnings.warn("Your SFF file is technically invalid as it is missing "
++ "a terminal %i byte null padding region." % padding,
++ BiopythonParserWarning)
++ return
+ if extra.count(_null) != padding:
+ import warnings
+ from Bio import BiopythonParserWarning
+ warnings.warn("Your SFF file is invalid, post index %i byte "
+- "null padding region contained data." % padding,
+- BiopythonParserWarning)
++ "null padding region contained data: %r"
++ % (padding, extra), BiopythonParserWarning)
+
+ offset = handle.tell()
+ assert offset % 8 == 0, \
diff --git a/sci-biology/biopython/files/adjust-trimpoints.patch b/sci-biology/biopython/files/adjust-trimpoints.patch
new file mode 100644
index 0000000..dd6d548
--- /dev/null
+++ b/sci-biology/biopython/files/adjust-trimpoints.patch
@@ -0,0 +1,76 @@
+diff --git a/Bio/SeqIO/SffIO.py b/Bio/SeqIO/SffIO.py
+index 1971dba..43b38fd 100644
+--- a/Bio/SeqIO/SffIO.py
++++ b/Bio/SeqIO/SffIO.py
+@@ -539,8 +539,15 @@ _valid_UAN_read_name = re.compile(r'^[a-zA-Z0-9]{14}$')
+
+
+ def _sff_read_seq_record(handle, number_of_flows_per_read, flow_chars,
+- key_sequence, alphabet, trim=False):
+- """Parse the next read in the file, return data as a SeqRecord (PRIVATE)."""
++ key_sequence, alphabet, trim=False, interpret_qual_trims=True, interpret_adapter_trims=False):
++ """Parse the next read in the file, return data as a SeqRecord (PRIVATE).
++ Allow user to specify which type of clipping values should be applied
++ while reading the SFF stream. To be backwards compatible, we interpret
++ only the quality-based trim points by default. That results in lower-cased
++ sequences in the low-qual region, regardless what adapter-based clip points
++ say. This should be the desired behavior. More discussion at
++ https://redmine.open-bio.org/issues/3437
++ """
+ #Now on to the reads...
+ #the read header format (fixed part):
+ #read_header_length H
+@@ -589,20 +596,41 @@ def _sff_read_seq_record(handle, number_of_flows_per_read, flow_chars,
+ warnings.warn("Post quality %i byte padding region contained data, SFF data is not broken"
+ % padding)
+ #Follow Roche and apply most aggressive of qual and adapter clipping.
+- #Note Roche seems to ignore adapter clip fields when writing SFF,
+- #and uses just the quality clipping values for any clipping.
+- clip_left = max(clip_qual_left, clip_adapter_left)
+- #Right clipping of zero means no clipping
+- if clip_qual_right:
+- if clip_adapter_right:
+- clip_right = min(clip_qual_right, clip_adapter_right)
++ #Note Roche does not use adapter clip fields when writing SFF files
++ #but instead combines the adapter clipping information with quality-based
++ #values and writes the most aggressive combination into clip fields (as
++ #allowed by SFF specs).
++
++ if interpret_qual_trims:
++ if interpret_adapter_trims:
++ clip_left = max(clip_qual_left, clip_adapter_left)
++ #Right clipping of zero means no clipping
++ if clip_qual_right:
++ if clip_adapter_right:
++ clip_right = min(clip_qual_right, clip_adapter_right)
++ else:
++ #Typical case with Roche SFF files
++ clip_right = clip_qual_right
++ elif clip_adapter_right:
++ clip_right = clip_adapter_right
++ else:
++ clip_right = seq_len
+ else:
+- #Typical case with Roche SFF files
+- clip_right = clip_qual_right
+- elif clip_adapter_right:
+- clip_right = clip_adapter_right
++ clip_left = clip_qual_left
++ if clip_qual_right:
++ clip_right = clip_qual_right
++ else:
++ clip_right = seq_len
++ elif interpret_adapter_trims:
++ clip_left = clip_adapter_left
++ if clip_adapter_right:
++ clip_right = clip_adapter_right
++ else:
++ clip_right = seq_len
+ else:
+- clip_right = seq_len
++ clip_left = 0
++ clip_right = seq_len
++
+ #Now build a SeqRecord
+ if trim:
+ seq = seq[clip_left:clip_right].upper()
^ permalink raw reply related [flat|nested] 10+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/biopython/, sci-biology/biopython/files/
@ 2014-04-18 18:23 Martin Mokrejs
0 siblings, 0 replies; 10+ messages in thread
From: Martin Mokrejs @ 2014-04-18 18:23 UTC (permalink / raw
To: gentoo-commits
commit: 74035c984818c6829c1f82cbcc1f419ff45f93d0
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Fri Apr 18 18:21:20 2014 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Fri Apr 18 18:21:20 2014 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=74035c98
sci-biology/biopython: ops, taking back my own testing patches
Package-Manager: portage-2.2.7
---
sci-biology/biopython/ChangeLog | 4 +
sci-biology/biopython/files/SeqRecord.py.patch | 148 ---------------------
.../biopython/files/adjust-trimpoints.patch | 76 -----------
3 files changed, 4 insertions(+), 224 deletions(-)
diff --git a/sci-biology/biopython/ChangeLog b/sci-biology/biopython/ChangeLog
index c326c4a..796f6a9 100644
--- a/sci-biology/biopython/ChangeLog
+++ b/sci-biology/biopython/ChangeLog
@@ -2,6 +2,10 @@
# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
# $Header: $
+ 18 Apr 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
+ -files/SeqRecord.py.patch, -files/adjust-trimpoints.patch:
+ sci-biology/biopython: ops, taking back my own testing patches
+
*biopython-1.62-r3 (18 Apr 2014)
*biopython-1.62-r4 (18 Apr 2014)
diff --git a/sci-biology/biopython/files/SeqRecord.py.patch b/sci-biology/biopython/files/SeqRecord.py.patch
deleted file mode 100644
index ac3785f..0000000
--- a/sci-biology/biopython/files/SeqRecord.py.patch
+++ /dev/null
@@ -1,148 +0,0 @@
-diff --git a/Bio/SeqIO/SffIO.py b/Bio/SeqIO/SffIO.py
-index 1971dba..43b38fd 100644
---- a/Bio/SeqIO/SffIO.py
-+++ b/Bio/SeqIO/SffIO.py
-@@ -539,8 +539,15 @@ _valid_UAN_read_name = re.compile(r'^[a-zA-Z0-9]{14}$')
-
-
- def _sff_read_seq_record(handle, number_of_flows_per_read, flow_chars,
-- key_sequence, alphabet, trim=False):
-- """Parse the next read in the file, return data as a SeqRecord (PRIVATE)."""
-+ key_sequence, alphabet, trim=False, interpret_qual_trims=True, interpret_adapter_trims=False):
-+ """Parse the next read in the file, return data as a SeqRecord (PRIVATE).
-+ Allow user to specify which type of clipping values should be applied
-+ while reading the SFF stream. To be backwards compatible, we interpret
-+ only the quality-based trim points by default. That results in lower-cased
-+ sequences in the low-qual region, regardless what adapter-based clip points
-+ say. This should be the desired behavior. More discussion at
-+ https://redmine.open-bio.org/issues/3437
-+ """
- #Now on to the reads...
- #the read header format (fixed part):
- #read_header_length H
-@@ -589,20 +596,41 @@ def _sff_read_seq_record(handle, number_of_flows_per_read, flow_chars,
- warnings.warn("Post quality %i byte padding region contained data, SFF data is not broken"
- % padding)
- #Follow Roche and apply most aggressive of qual and adapter clipping.
-- #Note Roche seems to ignore adapter clip fields when writing SFF,
-- #and uses just the quality clipping values for any clipping.
-- clip_left = max(clip_qual_left, clip_adapter_left)
-- #Right clipping of zero means no clipping
-- if clip_qual_right:
-- if clip_adapter_right:
-- clip_right = min(clip_qual_right, clip_adapter_right)
-+ #Note Roche does not use adapter clip fields when writing SFF files
-+ #but instead combines the adapter clipping information with quality-based
-+ #values and writes the most aggressive combination into clip fields (as
-+ #allowed by SFF specs).
-+
-+ if interpret_qual_trims:
-+ if interpret_adapter_trims:
-+ clip_left = max(clip_qual_left, clip_adapter_left)
-+ #Right clipping of zero means no clipping
-+ if clip_qual_right:
-+ if clip_adapter_right:
-+ clip_right = min(clip_qual_right, clip_adapter_right)
-+ else:
-+ #Typical case with Roche SFF files
-+ clip_right = clip_qual_right
-+ elif clip_adapter_right:
-+ clip_right = clip_adapter_right
-+ else:
-+ clip_right = seq_len
- else:
-- #Typical case with Roche SFF files
-- clip_right = clip_qual_right
-- elif clip_adapter_right:
-- clip_right = clip_adapter_right
-+ clip_left = clip_qual_left
-+ if clip_qual_right:
-+ clip_right = clip_qual_right
-+ else:
-+ clip_right = seq_len
-+ elif interpret_adapter_trims:
-+ clip_left = clip_adapter_left
-+ if clip_adapter_right:
-+ clip_right = clip_adapter_right
-+ else:
-+ clip_right = seq_len
- else:
-- clip_right = seq_len
-+ clip_left = 0
-+ clip_right = seq_len
-+
- #Now build a SeqRecord
- if trim:
- seq = seq[clip_left:clip_right].upper()
-diff --git a/Bio/SeqRecord.py b/Bio/SeqRecord.py
-index c90e13b..66bdea0 100644
---- a/Bio/SeqRecord.py
-+++ b/Bio/SeqRecord.py
-@@ -14,6 +14,8 @@ __docformat__ = "epytext en" # Simple markup to show doctests nicely
- # also BioSQL.BioSeq.DBSeq which is the "Database Seq" class)
-
-
-+from Bio.Seq import Seq
-+
- class _RestrictedDict(dict):
- """Dict which only allows sequences of given length as values (PRIVATE).
-
-@@ -76,7 +78,7 @@ class _RestrictedDict(dict):
- if not hasattr(value, "__len__") or not hasattr(value, "__getitem__") \
- or (hasattr(self, "_length") and len(value) != self._length):
- raise TypeError("We only allow python sequences (lists, tuples or "
-- "strings) of length %i." % self._length)
-+ "strings) of length %i whereas you passed an object of length %s." % (self._length, str(len(value))))
- dict.__setitem__(self, key, value)
-
- def update(self, new_dict):
-@@ -290,10 +292,11 @@ class SeqRecord(object):
- """)
-
- def _set_seq(self, value):
-- #TODO - Add a deprecation warning that the seq should be write only?
-- if self._per_letter_annotations:
-- #TODO - Make this a warning? Silently empty the dictionary?
-- raise ValueError("You must empty the letter annotations first!")
-+ # we should be much more user friendly and accept even a plain sequence string
-+ # and make the Seq or MutableSeq object ourselves
-+ if not isinstance(value, Seq):
-+ raise ValueError("You must pass a Seq object containing the new sequence instead of just plain string.")
-+ else:
- self._seq = value
- try:
- self._per_letter_annotations = _RestrictedDict(length=len(self.seq))
-@@ -696,7 +699,7 @@ class SeqRecord(object):
- SeqIO.write(self, handle, format_spec)
- return handle.getvalue()
-
-- def __len__(self):
-+ def __len__(self, trim=False, interpret_qual_trims=True, interpret_adapter_trims=False):
- """Returns the length of the sequence.
-
- For example, using Bio.SeqIO to read in a FASTA nucleotide file:
-@@ -707,6 +710,10 @@ class SeqRecord(object):
- 309
- >>> len(record.seq)
- 309
-+
-+ It should be possible to get length of a raw object, of trimmed
-+ object by quality or adapter criteria or both, whenever user wants
-+ to, not only when data is parsed from input.
- """
- return len(self.seq)
-
-@@ -725,6 +732,13 @@ class SeqRecord(object):
- """
- return True
-
-+ def apply_trimpoints(self, trim=False, interpret_qual_trims=False, interpret_adapter_trims=False):
-+ """We should apply either of the quality-based or adapter-based annotated
-+ trim points and return a new, sliced object.
-+ """
-+ pass
-+
-+
- def __add__(self, other):
- """Add another sequence or string to this sequence.
-
diff --git a/sci-biology/biopython/files/adjust-trimpoints.patch b/sci-biology/biopython/files/adjust-trimpoints.patch
deleted file mode 100644
index dd6d548..0000000
--- a/sci-biology/biopython/files/adjust-trimpoints.patch
+++ /dev/null
@@ -1,76 +0,0 @@
-diff --git a/Bio/SeqIO/SffIO.py b/Bio/SeqIO/SffIO.py
-index 1971dba..43b38fd 100644
---- a/Bio/SeqIO/SffIO.py
-+++ b/Bio/SeqIO/SffIO.py
-@@ -539,8 +539,15 @@ _valid_UAN_read_name = re.compile(r'^[a-zA-Z0-9]{14}$')
-
-
- def _sff_read_seq_record(handle, number_of_flows_per_read, flow_chars,
-- key_sequence, alphabet, trim=False):
-- """Parse the next read in the file, return data as a SeqRecord (PRIVATE)."""
-+ key_sequence, alphabet, trim=False, interpret_qual_trims=True, interpret_adapter_trims=False):
-+ """Parse the next read in the file, return data as a SeqRecord (PRIVATE).
-+ Allow user to specify which type of clipping values should be applied
-+ while reading the SFF stream. To be backwards compatible, we interpret
-+ only the quality-based trim points by default. That results in lower-cased
-+ sequences in the low-qual region, regardless what adapter-based clip points
-+ say. This should be the desired behavior. More discussion at
-+ https://redmine.open-bio.org/issues/3437
-+ """
- #Now on to the reads...
- #the read header format (fixed part):
- #read_header_length H
-@@ -589,20 +596,41 @@ def _sff_read_seq_record(handle, number_of_flows_per_read, flow_chars,
- warnings.warn("Post quality %i byte padding region contained data, SFF data is not broken"
- % padding)
- #Follow Roche and apply most aggressive of qual and adapter clipping.
-- #Note Roche seems to ignore adapter clip fields when writing SFF,
-- #and uses just the quality clipping values for any clipping.
-- clip_left = max(clip_qual_left, clip_adapter_left)
-- #Right clipping of zero means no clipping
-- if clip_qual_right:
-- if clip_adapter_right:
-- clip_right = min(clip_qual_right, clip_adapter_right)
-+ #Note Roche does not use adapter clip fields when writing SFF files
-+ #but instead combines the adapter clipping information with quality-based
-+ #values and writes the most aggressive combination into clip fields (as
-+ #allowed by SFF specs).
-+
-+ if interpret_qual_trims:
-+ if interpret_adapter_trims:
-+ clip_left = max(clip_qual_left, clip_adapter_left)
-+ #Right clipping of zero means no clipping
-+ if clip_qual_right:
-+ if clip_adapter_right:
-+ clip_right = min(clip_qual_right, clip_adapter_right)
-+ else:
-+ #Typical case with Roche SFF files
-+ clip_right = clip_qual_right
-+ elif clip_adapter_right:
-+ clip_right = clip_adapter_right
-+ else:
-+ clip_right = seq_len
- else:
-- #Typical case with Roche SFF files
-- clip_right = clip_qual_right
-- elif clip_adapter_right:
-- clip_right = clip_adapter_right
-+ clip_left = clip_qual_left
-+ if clip_qual_right:
-+ clip_right = clip_qual_right
-+ else:
-+ clip_right = seq_len
-+ elif interpret_adapter_trims:
-+ clip_left = clip_adapter_left
-+ if clip_adapter_right:
-+ clip_right = clip_adapter_right
-+ else:
-+ clip_right = seq_len
- else:
-- clip_right = seq_len
-+ clip_left = 0
-+ clip_right = seq_len
-+
- #Now build a SeqRecord
- if trim:
- seq = seq[clip_left:clip_right].upper()
^ permalink raw reply related [flat|nested] 10+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/biopython/, sci-biology/biopython/files/
@ 2014-05-07 10:29 Justin Lecher
0 siblings, 0 replies; 10+ messages in thread
From: Justin Lecher @ 2014-05-07 10:29 UTC (permalink / raw
To: gentoo-commits
commit: 8f906e56d735e0cb1b85041448dbfadcf6d5e8c8
Author: Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Wed May 7 10:29:21 2014 +0000
Commit: Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Wed May 7 10:29:21 2014 +0000
URL: http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=8f906e56
Imported to tree
Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>
---
sci-biology/biopython/ChangeLog | 40 ----------------
sci-biology/biopython/biopython-1.62-r3.ebuild | 53 ----------------------
sci-biology/biopython/biopython-1.62-r4.ebuild | 53 ----------------------
sci-biology/biopython/biopython-1.63-r1.ebuild | 53 ----------------------
.../biopython/files/SffIO_broken_padding.patch | 27 -----------
.../biopython/files/SffIO_error_in_check_eof.patch | 14 ------
.../biopython/files/biopython-1.51-flex.patch | 21 ---------
.../biopython/files/biopython-1.62-SffIO.patch | 36 ---------------
sci-biology/biopython/metadata.xml | 5 --
9 files changed, 302 deletions(-)
diff --git a/sci-biology/biopython/ChangeLog b/sci-biology/biopython/ChangeLog
deleted file mode 100644
index 796f6a9..0000000
--- a/sci-biology/biopython/ChangeLog
+++ /dev/null
@@ -1,40 +0,0 @@
-# ChangeLog for sci-biology/biopython
-# Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
-# $Header: $
-
- 18 Apr 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
- -files/SeqRecord.py.patch, -files/adjust-trimpoints.patch:
- sci-biology/biopython: ops, taking back my own testing patches
-
-*biopython-1.62-r3 (18 Apr 2014)
-*biopython-1.62-r4 (18 Apr 2014)
-
- 18 Apr 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
- +biopython-1.62-r3.ebuild, +biopython-1.62-r4.ebuild,
- +files/SeqRecord.py.patch, +files/SffIO_broken_padding.patch,
- +files/adjust-trimpoints.patch, biopython-1.63-r1.ebuild,
- files/SffIO_error_in_check_eof.patch, files/biopython-1.51-flex.patch,
- files/biopython-1.62-SffIO.patch:
- sci-biology/biopython: upstream patch to downgrade an assert to a warning
-
- 23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
- -biopython-1.62-r3.ebuild, -biopython-1.62-r4.ebuild, -biopython-1.63.ebuild,
- -files/SeqRecord.py.patch, -files/adjust-trimpoints.patch,
- biopython-1.63-r1.ebuild:
- sci-biology/biopython-1.63-r1: added missing deps on dev-python/rdflib to sync
- with official sci-biology/biopython-1.63; dropping sci-biology/biopython-1.63
- from overlay
-
-*biopython-1.62-r3 (23 Mar 2014)
-*biopython-1.62-r4 (23 Mar 2014)
-*biopython-1.63-r1 (23 Mar 2014)
-*biopython-1.63 (23 Mar 2014)
-
- 23 Mar 2014; Martin Mokrejs <mmokrejs@fold.natur.cuni.cz>
- +biopython-1.62-r3.ebuild, +biopython-1.62-r4.ebuild,
- +biopython-1.63-r1.ebuild, +biopython-1.63.ebuild, +files/SeqRecord.py.patch,
- +files/SffIO_error_in_check_eof.patch, +files/adjust-trimpoints.patch,
- +files/biopython-1.51-flex.patch, +files/biopython-1.62-SffIO.patch,
- +metadata.xml:
- sci-biology/biopython-1.63-r1: version bump and an upstream patch to improve
- error message
diff --git a/sci-biology/biopython/biopython-1.62-r3.ebuild b/sci-biology/biopython/biopython-1.62-r3.ebuild
deleted file mode 100644
index 09e6ed7..0000000
--- a/sci-biology/biopython/biopython-1.62-r3.ebuild
+++ /dev/null
@@ -1,53 +0,0 @@
-# Copyright 1999-2014 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"
- epatch "${FILESDIR}/SffIO_error_in_check_eof.patch"
- epatch "${FILESDIR}/SffIO_broken_padding.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/biopython-1.62-r4.ebuild b/sci-biology/biopython/biopython-1.62-r4.ebuild
deleted file mode 100644
index 09e6ed7..0000000
--- a/sci-biology/biopython/biopython-1.62-r4.ebuild
+++ /dev/null
@@ -1,53 +0,0 @@
-# Copyright 1999-2014 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"
- epatch "${FILESDIR}/SffIO_error_in_check_eof.patch"
- epatch "${FILESDIR}/SffIO_broken_padding.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/biopython-1.63-r1.ebuild b/sci-biology/biopython/biopython-1.63-r1.ebuild
deleted file mode 100644
index b600748..0000000
--- a/sci-biology/biopython/biopython-1.63-r1.ebuild
+++ /dev/null
@@ -1,53 +0,0 @@
-# Copyright 1999-2014 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/rdflib[${PYTHON_USEDEP}]
- dev-python/pygraphviz[${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="${RDEPEND}
- sys-devel/flex"
-
-DOCS=( CONTRIB DEPRECATED NEWS README Doc/. )
-
-src_prepare() {
- epatch "${FILESDIR}/SffIO_error_in_check_eof.patch"
- epatch "${FILESDIR}/SffIO_broken_padding.patch"
- distutils-r1_src_prepare
-}
-
-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/SffIO_broken_padding.patch b/sci-biology/biopython/files/SffIO_broken_padding.patch
deleted file mode 100644
index a009c58..0000000
--- a/sci-biology/biopython/files/SffIO_broken_padding.patch
+++ /dev/null
@@ -1,27 +0,0 @@
-diff --git a/Bio/SeqIO/SffIO.py b/Bio/SeqIO/SffIO.py
-index 735d55b..b89cf41 100644
---- a/Bio/SeqIO/SffIO.py
-+++ b/Bio/SeqIO/SffIO.py
-@@ -933,12 +933,20 @@ def _check_eof(handle, index_offset, index_length):
- "null padding region ended '.sff' which could "
- "be the start of a concatenated SFF file? "
- "See offset %i" % (padding, offset))
-+ if padding and not extra:
-+ #TODO - Is this error harmless enough to just ignore?
-+ import warnings
-+ from Bio import BiopythonParserWarning
-+ warnings.warn("Your SFF file is technically invalid as it is missing "
-+ "a terminal %i byte null padding region." % padding,
-+ BiopythonParserWarning)
-+ return
- if extra.count(_null) != padding:
- import warnings
- from Bio import BiopythonParserWarning
- warnings.warn("Your SFF file is invalid, post index %i byte "
-- "null padding region contained data." % padding,
-- BiopythonParserWarning)
-+ "null padding region contained data: %r"
-+ % (padding, extra), BiopythonParserWarning)
-
- offset = handle.tell()
- assert offset % 8 == 0, \
diff --git a/sci-biology/biopython/files/SffIO_error_in_check_eof.patch b/sci-biology/biopython/files/SffIO_error_in_check_eof.patch
deleted file mode 100644
index 9059604..0000000
--- a/sci-biology/biopython/files/SffIO_error_in_check_eof.patch
+++ /dev/null
@@ -1,14 +0,0 @@
-diff --git a/Bio/SeqIO/SffIO.py b/Bio/SeqIO/SffIO.py
-index 2bb0dac..735d55b 100644
---- a/Bio/SeqIO/SffIO.py
-+++ b/Bio/SeqIO/SffIO.py
-@@ -941,7 +941,8 @@ def _check_eof(handle, index_offset, index_length):
- BiopythonParserWarning)
-
- offset = handle.tell()
-- assert offset % 8 == 0
-+ assert offset % 8 == 0, \
-+ "Wanted offset %i %% 8 = %i to be zero" % (offset, offset % 8)
- # Should now be at the end of the file...
- extra = handle.read(4)
- if extra == _sff:
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=["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/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 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
- <herd>sci-biology</herd>
-</pkgmetadata>
^ permalink raw reply related [flat|nested] 10+ messages in thread
* [gentoo-commits] proj/sci:master commit in: sci-biology/biopython/, sci-biology/biopython/files/
@ 2016-07-23 7:25 Martin Mokrejs
0 siblings, 0 replies; 10+ messages in thread
From: Martin Mokrejs @ 2016-07-23 7:25 UTC (permalink / raw
To: gentoo-commits
commit: f301a33fa321175c12de267ecfbf4d1b727be3f0
Author: Martin Mokrejš <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Sat Jul 23 07:25:08 2016 +0000
Commit: Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Sat Jul 23 07:25:08 2016 +0000
URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=f301a33f
sci-biology/biopython: version bump with one minor upstream patch
Package-Manager: portage-2.2.28
sci-biology/biopython/biopython-1.67-r1.ebuild | 60 +++++++++++++++
.../biopython/files/biopython-1.67-pull-884.patch | 87 ++++++++++++++++++++++
sci-biology/biopython/metadata.xml | 8 ++
3 files changed, 155 insertions(+)
diff --git a/sci-biology/biopython/biopython-1.67-r1.ebuild b/sci-biology/biopython/biopython-1.67-r1.ebuild
new file mode 100644
index 0000000..197e265
--- /dev/null
+++ b/sci-biology/biopython/biopython-1.67-r1.ebuild
@@ -0,0 +1,60 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=5
+
+PYTHON_COMPAT=( python2_7 python3_{3,4,5} pypy )
+
+inherit distutils-r1 eutils
+
+DESCRIPTION="Python modules for computational molecular biology"
+HOMEPAGE="http://www.biopython.org/ https://pypi.python.org/pypi/biopython/"
+SRC_URI="http://www.biopython.org/DIST/${P}.tar.gz"
+
+LICENSE="HPND"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+RDEPEND="
+ dev-python/matplotlib[$(python_gen_usedep 'python*')]
+ dev-python/networkx[$(python_gen_usedep 'python*')]
+ dev-python/numpy[$(python_gen_usedep 'python*')]
+ dev-python/rdflib[$(python_gen_usedep 'python*')]
+ dev-python/pygraphviz[$(python_gen_usedep 'python2*')]
+ dev-python/reportlab[$(python_gen_usedep 'python*')]
+ media-gfx/pydot[$(python_gen_usedep 'python2*')]
+ "
+DEPEND="${RDEPEND}
+ sys-devel/flex"
+
+DOCS=( CONTRIB DEPRECATED NEWS README Doc/. )
+
+src_prepare(){
+ epatch "${FILESDIR}"/biopython-1.67-pull-884.patch
+}
+
+python_test() {
+ distutils_install_for_testing
+ cp -r "${S}"/{Doc,Tests} "${TEST_DIR}"/lib/ || die
+ cd "${TEST_DIR}"/lib/Tests || die
+ rm ./test_BioSQL_psycopg2.py ./test_BioSQL_MySQLdb.py ./test_BioSQL_mysql_connector.py || die
+ ${PYTHON} run_tests.py --offline --verbose || die
+}
+
+python_install_all() {
+ distutils-r1_python_install_all
+
+ dodir /usr/share/${PN}
+ cp -r --preserve=mode Scripts Tests "${ED}"/usr/share/${PN} || die
+}
+
+pkg_postinst() {
+ elog "For database support you need to install:"
+ optfeature "MySQL" dev-python/mysql-python
+ optfeature "PostGreSQL" dev-python/psycopg
+ echo
+ elog "Some applications need extra packages:"
+ optfeature "EMBOSS (The European Molecular Biology Open Software Suite)" sci-biology/emboss
+}
diff --git a/sci-biology/biopython/files/biopython-1.67-pull-884.patch b/sci-biology/biopython/files/biopython-1.67-pull-884.patch
new file mode 100644
index 0000000..f2a2537
--- /dev/null
+++ b/sci-biology/biopython/files/biopython-1.67-pull-884.patch
@@ -0,0 +1,87 @@
+--- Bio/SeqRecord.py.old 2016-06-08 15:27:00.000000000 +0200
++++ Bio/SeqRecord.py 2016-07-22 17:48:19.620712535 +0200
+@@ -292,19 +292,28 @@
+ >>> sub_record.letter_annotations = {}
+ >>> sub_record.letter_annotations
+ {}
++
++ Note that if replacing the record's sequence with a sequence of a
++ different length you must first clear the letter_annotations dict.
+ """)
+
+ def _set_seq(self, value):
+ # TODO - Add a deprecation warning that the seq should be write only?
+ if self._per_letter_annotations:
+- # TODO - Make this a warning? Silently empty the dictionary?
+- raise ValueError("You must empty the letter annotations first!")
+- self._seq = value
+- try:
+- self._per_letter_annotations = _RestrictedDict(length=len(self.seq))
+- except AttributeError:
+- # e.g. seq is None
+- self._per_letter_annotations = _RestrictedDict(length=0)
++ if len(self) != len(value):
++ # TODO - Make this a warning? Silently empty the dictionary?
++ raise ValueError("You must empty the letter annotations first!")
++ else:
++ # Leave the existing per letter annotations unchanged:
++ self._seq = value
++ else:
++ self._seq = value
++ # Reset the (empty) letter annotations dict with new length:
++ try:
++ self._per_letter_annotations = _RestrictedDict(length=len(self.seq))
++ except AttributeError:
++ # e.g. seq is None
++ self._per_letter_annotations = _RestrictedDict(length=0)
+
+ seq = property(fget=lambda self: self._seq,
+ fset=_set_seq,
+@@ -427,10 +436,17 @@
+ if self.seq is None:
+ raise ValueError("If the sequence is None, we cannot slice it.")
+ parent_length = len(self)
+- answer = self.__class__(self.seq[index],
+- id=self.id,
+- name=self.name,
+- description=self.description)
++ from BioSQL.BioSeq import DBSeqRecord
++ if isinstance(self, DBSeqRecord):
++ answer = SeqRecord(self.seq[index],
++ id=self.id,
++ name=self.name,
++ description=self.description)
++ else:
++ answer = self.__class__(self.seq[index],
++ id=self.id,
++ name=self.name,
++ description=self.description)
+ # TODO - The description may no longer apply.
+ # It would be safer to change it to something
+ # generic like "edited" or the default value.
+--- Tests/test_SeqRecord.py.old 2016-06-08 15:27:00.000000000 +0200
++++ Tests/test_SeqRecord.py 2016-07-22 17:48:45.401428898 +0200
+@@ -72,6 +72,23 @@
+ except (TypeError, ValueError) as e:
+ pass
+
++ def test_replacing_seq(self):
++ """Replacing .seq if .letter_annotation present."""
++ rec = SeqRecord(Seq("ACGT", generic_dna),
++ id="Test", name="Test", description="Test",
++ letter_annotations={"example": [1, 2, 3, 4]})
++ try:
++ rec.seq = Seq("ACGTACGT", generic_dna)
++ self.fail("Changing .seq length with letter_annotations present should fail!")
++ except ValueError as e:
++ self.assertEqual(str(e), "You must empty the letter annotations first!")
++ # Check we can replace IF the length is the same
++ self.assertEqual(str(rec.seq), "ACGT")
++ self.assertEqual(rec.letter_annotations, {"example": [1, 2, 3, 4]})
++ rec.seq = Seq("NNNN" , generic_dna)
++ self.assertEqual(str(rec.seq), "NNNN")
++ self.assertEqual(rec.letter_annotations, {"example": [1, 2, 3, 4]})
++
+ def test_valid_id(self):
+ with self.assertRaises(TypeError):
+ SeqRecord(Seq("ACGT", generic_dna), id=dict())
diff --git a/sci-biology/biopython/metadata.xml b/sci-biology/biopython/metadata.xml
new file mode 100644
index 0000000..959160f
--- /dev/null
+++ b/sci-biology/biopython/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci-biology@gentoo.org</email>
+ <name>Gentoo Biology Project</name>
+ </maintainer>
+</pkgmetadata>
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