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

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

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>