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

[Justin Lecher]

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@×××××××××××××××.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@g.o> +biopython-1.62.ebuild:
-  Version Bump
-
-  02 Jul 2013; Justin Lecher <jlec@g.o> biopython-1.61.ebuild:
-  Fix deps for python
-
-  06 Jun 2013; Justin Lecher <jlec@g.o> biopython-1.61.ebuild:
-  Keyword ~-linux
-
-*biopython-1.61 (26 Apr 2013)
-
-  26 Apr 2013; Justin Lecher <jlec@g.o> +biopython-1.61.ebuild,
-  metadata.xml:
-  Version Bump
-
-  14 Dec 2012; Ulrich Müller <ulm@g.o> 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@g.o> +biopython-1.59.ebuild:
-  Version bump
-
-  26 Dec 2011; Andrey Kislyuk <weaver@g.o> +biopython-1.58.ebuild:
-  Version bump
-
-*biopython-1.58 (26 Dec 2011)
-
-  26 Dec 2011; Andrey Kislyuk <weaver@g.o> +biopython-1.58.ebuild:
-  Version bump
-
-  23 Jun 2011; Markos Chandras <hwoarang@g.o> -biopython-1.56.ebuild:
-  Remove old ebuilds. Requested by Arfrever
-
-  28 May 2011; Brent Baude <ranger@g.o> biopython-1.57.ebuild:
-  Marking biopython-1.57 ppc for bug 365877
-
-  24 May 2011; Markus Meier <maekke@g.o> biopython-1.57.ebuild:
-  x86 stable, bug #365877
-
-  06 May 2011; Justin Lecher <jlec@g.o> biopython-1.56.ebuild,
-  biopython-1.57.ebuild:
-  Cleaned DESCRIPTION
-
-  05 May 2011; Markos Chandras <hwoarang@g.o> biopython-1.57.ebuild:
-  Stable on amd64 wrt bug #365877
-
-*biopython-1.57 (03 Apr 2011)
-
-  03 Apr 2011; Arfrever Frehtes Taifersar Arahesis <arfrever@g.o>
-  +biopython-1.57.ebuild:
-  Version bump.
-
-  30 Jan 2011; Arfrever Frehtes Taifersar Arahesis <arfrever@g.o>
-  -biopython-1.55.ebuild:
-  Delete.
-
-  30 Jan 2011; Raúl Porcel <armin76@g.o> biopython-1.55.ebuild,
-  biopython-1.56.ebuild:
-  Drop alpha/sparc keywords
-
-  15 Jan 2011; Pawel Hajdan jr <phajdan.jr@g.o>
-  biopython-1.56.ebuild:
-  x86 stable wrt bug #351498
-
-  14 Jan 2011; Brent Baude <ranger@g.o> biopython-1.56.ebuild:
-  stable ppc, bug 351498
-
-  13 Jan 2011; Markos Chandras <hwoarang@g.o> biopython-1.56.ebuild:
-  Stable on amd64 wrt bug #351498
-
-  06 Jan 2011; Brent Baude <ranger@g.o> 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@g.o>
-  -biopython-1.53.ebuild, -biopython-1.54.ebuild, +biopython-1.56.ebuild:
-  Version bump.
-
-  31 Oct 2010; Raúl Porcel <armin76@g.o> biopython-1.55.ebuild:
-  alpha/sparc stable wrt #341519
-
-  21 Oct 2010; Thomas Kahle <tomka@g.o> biopython-1.55.ebuild:
-  x86 stable per bug 341519
-
-  19 Oct 2010; Markos Chandras <hwoarang@g.o> biopython-1.55.ebuild:
-  Stable on amd64 wrt bug #341519
-
-  15 Oct 2010; Brent Baude <ranger@g.o> biopython-1.54.ebuild:
-  stable ppc, bug 327151
-
-  10 Oct 2010; Raúl Porcel <armin76@g.o> biopython-1.54.ebuild:
-  sparc stable wrt #327151
-
-*biopython-1.55 (17 Sep 2010)
-
-  17 Sep 2010; Arfrever Frehtes Taifersar Arahesis <arfrever@g.o>
-  +biopython-1.55.ebuild:
-  Version bump.
-
-  12 Sep 2010; Tobias Klausmann <klausman@g.o> biopython-1.54.ebuild:
-  Stable on alpha, bug #327151
-
-  12 Jul 2010; Christian Faulhammer <fauli@g.o>
-  biopython-1.54.ebuild:
-  stable x86, bug 327151
-
-  06 Jul 2010; Markos Chandras <hwoarang@g.o> biopython-1.54.ebuild:
-  Stable on amd64 wrt bug #327151
-
-*biopython-1.54 (05 Jun 2010)
-
-  05 Jun 2010; Arfrever Frehtes Taifersar Arahesis <arfrever@g.o>
-  -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@g.o> biopython-1.53.ebuild:
-  alpha/sparc stable wrt #301964
-
-  07 Feb 2010; Markus Meier <maekke@g.o> biopython-1.53.ebuild:
-  amd64/x86 stable, bug #301964
-
-  24 Jan 2010; Brent Baude <ranger@g.o> biopython-1.53.ebuild:
-  stable ppc, bug 301964
-
-*biopython-1.53 (21 Dec 2009)
-
-  21 Dec 2009; Arfrever Frehtes Taifersar Arahesis <arfrever@g.o>
-  +biopython-1.53.ebuild:
-  Version bump. Set SUPPORT_PYTHON_ABIS.
-
-  31 Oct 2009; Markus Meier <maekke@g.o> biopython-1.52.ebuild:
-  amd64/x86 stable, bug #290931
-
-*biopython-1.52 (23 Sep 2009)
-
-  23 Sep 2009; Andrey Kislyuk <weaver@g.o> +biopython-1.52.ebuild:
-  Version bump
-
-*biopython-1.51 (09 Sep 2009)
-
-  09 Sep 2009; Andrey Kislyuk <weaver@g.o>
-  +files/biopython-1.51-flex.patch, +biopython-1.51.ebuild:
-  Version bump
-
-  26 Aug 2009; Christian Faulhammer <fauli@g.o> metadata.xml:
-  remove now unused flag description
-
-  26 Aug 2009; Christian Faulhammer <fauli@g.o>
-  -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@g.o> biopython-1.49.ebuild:
-  Stable on alpha, bug #277822
-
-  02 Aug 2009; nixnut <nixnut@g.o> biopython-1.49.ebuild:
-  ppc stable #277822
-
-  20 Jul 2009; Jeremy Olexa <darkside@g.o> biopython-1.49.ebuild:
-  amd64 stable, bug 277822
-
-  17 Jul 2009; Ferris McCormick <fmccor@g.o> biopython-1.49.ebuild:
-  Sparc stable --- bug #277822 --- ran tests successfully.
-
-  14 Jul 2009; Christian Faulhammer <fauli@g.o>
-  biopython-1.49.ebuild:
-  stable x86, bug 277822
-
-  24 Mar 2009; Olivier Fisette <ribosome@g.o> metadata.xml:
-  Giving up maintainership of this package.
-
-*biopython-1.49 (16 Jan 2009)
-
-  16 Jan 2009; Olivier Fisette <ribosome@g.o>
-  +files/biopython-1.49-flex.patch, +biopython-1.49.ebuild:
-  Version bump. Thanks to Juan Aguado <juantxorena@×××××.com> for his work.
-  Fixes bug #248799.
-
-  06 Aug 2008; Ulrich Mueller <ulm@g.o> metadata.xml:
-  Add USE flag description to metadata wrt GLEP 56.
-
-  14 Jul 2008; nixnut <nixnut@g.o> biopython-1.44.ebuild:
-  Stable on ppc wrt bug 221159
-
-  07 Jul 2008; Raúl Porcel <armin76@g.o> biopython-1.44.ebuild:
-  alpha/sparc/x86 stable wrt #221159
-
-*biopython-1.47 (06 Jul 2008)
-
-  06 Jul 2008; Olivier Fisette <ribosome@g.o>
-  +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@g.o> biopython-1.44.ebuild:
-  Stable on amd64.
-
-  30 Jan 2008; Olivier Fisette <ribosome@g.o> biopython-1.42.ebuild,
-  biopython-1.44.ebuild:
-  Q.A.: Quoted variables.
-
-  30 Jan 2008; Olivier Fisette <ribosome@g.o> -biopython-1.43.ebuild:
-  Removed buggy version (see bug #202602).
-
-*biopython-1.44 (30 Jan 2008)
-
-  30 Jan 2008; Olivier Fisette <ribosome@g.o>
-  +files/biopython-1.44-sequtils-complement.patch, +biopython-1.44.ebuild:
-  Fixed six_frame_translations function. Thanks to JTRiley
-  <justin.t.riley@×××××.com> for his patch. (Fixes bug #202606.)
-
-*biopython-1.43 (17 May 2007)
-
-  17 May 2007; Olivier Fisette <ribosome@g.o>
-  +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@g.o> biopython-1.42.ebuild:
-  alpha stable wrt #153774
-
-  05 Nov 2006; Christian Faulhammer <opfer@g.o>
-  biopython-1.42.ebuild:
-  stabled x86, bug #153774
-
-  03 Nov 2006; <blubb@g.o> biopython-1.42.ebuild:
-  stable on amd64
-
-  03 Nov 2006; Olivier Fisette <ribosome@g.o> -biopython-1.41.ebuild:
-  Pruned old version.
-
-  02 Nov 2006; nixnut <nixnut@g.o> biopython-1.42.ebuild:
-  Stable on ppc wrt bug 153774
-
-  02 Nov 2006; Jason Wever <weeve@g.o> biopython-1.42.ebuild:
-  Stable on SPARC wrt bug #153774.
-
-  14 Sep 2006; Olivier Fisette <ribosome@g.o> metadata.xml:
-  Taking over maintainership.
-
-*biopython-1.42 (12 Sep 2006)
-
-  12 Sep 2006; Olivier Fisette <ribosome@g.o> +biopython-1.42.ebuild:
-  New upstream version.
-
-  19 Jan 2006; George Shapovalov <george@g.o> +biopython-1.41.ebuild:
-  new version, cleaned up install
-
-  30 Aug 2005; Olivier Fisette <ribosome@g.o> -biopython-1.24.ebuild,
-  -biopython-1.30.ebuild:
-  Removed obsolete versions.
-
-  12 Jun 2005; Bryan Østergaard <kloeri@g.o> biopython-1.40b.ebuild:
-  Stable on alpha.
-
-  21 May 2005; Jason Wever <weeve@g.o> biopython-1.40b.ebuild:
-  Stable on SPARC.
-
-  13 May 2005; Olivier Fisette <ribosome@g.o> -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@g.o>
-  +biopython-1.40b.ebuild:
-  New version. Should fix bug #82498.
-
-  29 Dec 2004; Ciaran McCreesh <ciaranm@g.o> :
-  Change encoding to UTF-8 for GLEP 31 compliance
-
-*biopython-1.23 (23 Dec 2004)
-
-  23 Dec 2004; Olivier Fisette <ribosome@g.o> +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@g.o> biopython-1.24.ebuild:
-  Stable on sparc.
-
-*biopython-1.30 (07 Oct 2004)
-
-  07 Oct 2004; George Shapovalvo <george@g.o> 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@g.o> biopython-1.24.ebuild:
-  Stable on alpha.
-
-  03 Apr 2004; Peter Bienstman <pbienst@g.o> biopython-1.24.ebuild:
-  Marked stable on x86
-
-*biopython-1.24 (29 Feb 2004)
-
-  29 Feb 2004; Peter Bienstman <pbienst@g.o> biopython-1.24.ebuild :
-  version bump
-
-*biopython-1.23 (30 Dec 2003)
-
-  29 Feb 2004; Peter Bienstman <pbienst@g.o> biopython-1.23.ebuild :
-  marked stable on x86
-
-  30 Dec 2003; George Shapovalvo <george@g.o> biopython-1.23.ebuild :
-  new version, reworked to use distutils. Thanks to 
-  Peter Bienstman <Peter.Bienstman@××××××.be> for an update (#35727)
-
-  02 Sep 2003; Alastair Tse <liquidx@g.o> 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@g.o> biopython-1.21.ebuild :
-  new version, added few docs (#25428)
-  thanks to Daniel Jaeggi <daniel@×××××××××.uk> for notification
-
-  04 Jul 2003; Alastair Tse <liquidx@g.o> biopython-1.10.ebuild:
-  renamed reportlab dep
-
-*biopython-1.10 (18 Feb 2003)
-
-  18 Feb 2003; George Shapovalov <george@g.o> 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@×××××××××.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>