This version and newer is in the tree

5 files changed, 0 insertions, 391 deletions

diff --git a/sci-biology/biopython/ChangeLog b/sci-biology/biopython/ChangeLog
deleted file mode 100644
index b7c1c09f8..000000000
--- 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/Manifest b/sci-biology/biopython/Manifest
deleted file mode 100644
index 4bc432514..000000000
--- a/sci-biology/biopython/Manifest
+++ /dev/null
@@ -1 +0,0 @@
-DIST biopython-1.58.tar.gz 8035063 RMD160 3e05426017e98cdc45cacfb08b1b5d7c3d4b10ff SHA1 3db0819d0046cfcd1c9aaf39aa7db40b9aa2645e SHA256 f9183facf01d3b0b489401f43a0cae8249c3dd1f7452d939f137980f5e683e73
diff --git a/sci-biology/biopython/biopython-1.58.ebuild b/sci-biology/biopython/biopython-1.58.ebuild
deleted file mode 100644
index 8a9b445be..000000000
--- 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 afd509444..000000000
--- 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 34294c65c..000000000
--- 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>