clean up

(Portage version: 2.1.6.13/cvs/Linux i686)

7 files changed, 7 insertions, 234 deletions

diff --git a/sci-biology/biopython/ChangeLog b/sci-biology/biopython/ChangeLog
index ba8c6b653d6d..a5392f8a8dc3 100644
--- a/sci-biology/biopython/ChangeLog
+++ b/sci-biology/biopython/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-biology/biopython
 # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/biopython/ChangeLog,v 1.33 2009/08/26 12:38:25 klausman Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/biopython/ChangeLog,v 1.34 2009/08/26 14:40:46 fauli Exp $
+
+  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
diff --git a/sci-biology/biopython/biopython-1.42.ebuild b/sci-biology/biopython/biopython-1.42.ebuild
deleted file mode 100644
index 6a6effd10809..000000000000
--- a/sci-biology/biopython/biopython-1.42.ebuild
+++ /dev/null
@@ -1,33 +0,0 @@
-# Copyright 1999-2008 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/biopython/biopython-1.42.ebuild,v 1.7 2008/01/30 03:30:15 ribosome Exp $
-
-inherit distutils
-
-IUSE=""
-
-DESCRIPTION="Biopython - Python modules for computational molecular biology"
-SRC_URI="http://www.biopython.org/DIST/${P}.tar.gz"
-HOMEPAGE="http://www.biopython.org"
-
-DEPEND=">=dev-lang/python-2.2
-		>=dev-python/egenix-mx-base-2.0.3
-		>=dev-python/numeric-19.0
-		>=dev-python/reportlab-1.11"
-
-SLOT="0"
-LICENSE="as-is"
-KEYWORDS="alpha amd64 ppc sparc x86"
-
-src_compile() {
-	distutils_src_compile
-}
-
-src_install() {
-	DOCS="Doc/*.txt Doc/*.tex Doc/install/*.txt"
-	distutils_src_install
-
-	dohtml Doc/install/*.html
-	dohtml Doc/*.html
-	cp -r Doc/examples/ Doc/*.pdf "${D}"/usr/share/doc/${PF}/
-}
diff --git a/sci-biology/biopython/biopython-1.44.ebuild b/sci-biology/biopython/biopython-1.44.ebuild
deleted file mode 100644
index 040c0a36fb83..000000000000
--- a/sci-biology/biopython/biopython-1.44.ebuild
+++ /dev/null
@@ -1,44 +0,0 @@
-# Copyright 1999-2008 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/biopython/biopython-1.44.ebuild,v 1.5 2008/07/14 16:57:21 nixnut Exp $
-
-inherit distutils eutils
-
-DESCRIPTION="Biopython - Python modules for computational molecular biology"
-LICENSE="as-is"
-HOMEPAGE="http://www.biopython.org"
-SRC_URI="http://www.biopython.org/DIST/${P}.tar.gz"
-
-SLOT="0"
-IUSE="kdtree"
-KEYWORDS="alpha amd64 ppc sparc x86"
-
-DEPEND=">=dev-lang/python-2.2
-		>=dev-python/egenix-mx-base-2.0.3
-		>=dev-python/numeric-19.0
-		>=dev-python/reportlab-1.11"
-
-src_unpack() {
-	unpack ${A}
-	cd "${S}"
-	epatch "${FILESDIR}/${PN}-1.43-buildkdtree.patch"
-	epatch "${FILESDIR}/${P}-sequtils-complement.patch"
-	if use kdtree; then
-		sed -i -e 's/USE_KDTREE = False/USE_KDTREE = True/' \
-				setup.py || die "Could not apply patch for KDTree support."
-	fi
-}
-
-src_compile() {
-	distutils_src_compile
-}
-
-src_install() {
-	DOCS="Doc/*.txt Doc/*.tex Doc/install/*.txt"
-	distutils_src_install
-
-	dohtml Doc/install/*.html || die "Failed to install HTML install docs."
-	dohtml Doc/*.html || die "Failed to install HTML docs."
-	cp -r Doc/examples/ Doc/*.pdf "${D}"/usr/share/doc/${PF}/ || \
-			die "Failed to install documentation."
-}
diff --git a/sci-biology/biopython/biopython-1.47.ebuild b/sci-biology/biopython/biopython-1.47.ebuild
deleted file mode 100644
index 99812e58e75a..000000000000
--- a/sci-biology/biopython/biopython-1.47.ebuild
+++ /dev/null
@@ -1,53 +0,0 @@
-# Copyright 1999-2008 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/biopython/biopython-1.47.ebuild,v 1.1 2008/07/06 15:21:41 ribosome Exp $
-
-EAPI=1
-
-inherit distutils eutils
-
-DESCRIPTION="Biopython - Python modules for computational molecular biology"
-LICENSE="as-is"
-HOMEPAGE="http://www.biopython.org"
-SRC_URI="http://www.biopython.org/DIST/${P}.tar.gz"
-
-SLOT="0"
-IUSE="+kdtree"
-KEYWORDS="~alpha ~amd64 ~ppc ~sparc ~x86"
-
-DEPEND=">=dev-lang/python-2.2
-		>=dev-python/egenix-mx-base-2.0.3
-		>=dev-python/numeric-19.0
-		>=dev-python/reportlab-1.11"
-
-src_unpack() {
-	unpack ${A}
-	cd "${S}"
-	epatch "${FILESDIR}/${PN}-1.47-kdtree.patch"
-	if use kdtree; then
-		sed -i -e 's/USE_KDTREE = False/USE_KDTREE = True/' \
-				setup.py || die "Could not apply patch for KDTree support."
-	fi
-}
-
-src_compile() {
-	distutils_src_compile
-}
-
-src_install() {
-	DOCS="CONTRIB DEPRECATED NEWS README"
-	distutils_src_install
-
-	dodir "/usr/share/doc/${PF}"
-	cp -r Doc/* "${D}/usr/share/doc/${PF}/" || \
-			die "Failed to install documentation."
-	dodir "/usr/share/${PN}"
-	cp -r --preserve=mode Scripts Tests "${D}/usr/share/${PN}/" || \
-			die "Failed to install shared files."
-}
-
-src_test() {
-	cd "${S}/Tests"
-	PYTHONPATH="${PYTHONPATH}:${S}" \
-			python run_tests.py --no-gui || die "Tests failed."
-}
diff --git a/sci-biology/biopython/files/biopython-1.43-buildkdtree.patch b/sci-biology/biopython/files/biopython-1.43-buildkdtree.patch
deleted file mode 100644
index cefb16d7d95d..000000000000
--- a/sci-biology/biopython/files/biopython-1.43-buildkdtree.patch
+++ /dev/null
@@ -1,28 +0,0 @@
---- setup.py.old	2007-03-17 15:21:04.000000000 -0400
-+++ setup.py	2007-05-17 14:02:42.000000000 -0400
-@@ -64,6 +64,7 @@
-         _CHECKED = check_dependencies()
-     return _CHECKED
- 
-+USE_KDTREE = False
- def check_dependencies():
-     """Return whether the installation should continue."""
-     # There should be some way for the user to tell specify not to
-@@ -112,15 +113,8 @@
-         
-     
-     # Compile KDTree ? Not compiled by default
--    print "\n*** Bio.KDTree *** NOT built by default "
--    kdtree_msg = """
--The Bio.PDB.NeighborSearch module depends on the Bio.KDTree module,
--which in turn, depends on C++ code that does not compile cleanly on
--all platforms. Hence, Bio.KDTree is not built by default.
--
--Would you like to build Bio.KDTree ?"""
--
--    if get_yes_or_no (kdtree_msg, 0):
-+    global USE_KDTREE
-+    if USE_KDTREE:
-         NUMPY_PACKAGES.append("Bio.KDTree")
-         NUMPY_EXTENSIONS.append(
-             CplusplusExtension('Bio.KDTree._CKDTree', 
diff --git a/sci-biology/biopython/files/biopython-1.44-sequtils-complement.patch b/sci-biology/biopython/files/biopython-1.44-sequtils-complement.patch
deleted file mode 100644
index 16fc44d77cd0..000000000000
--- a/sci-biology/biopython/files/biopython-1.44-sequtils-complement.patch
+++ /dev/null
@@ -1,32 +0,0 @@
---- biopython-1.44/Bio/SeqUtils/__init__.py.old	2007-09-14 09:38:35.000000000 -0400
-+++ biopython-1.44/Bio/SeqUtils/__init__.py	2007-12-17 11:07:27.000000000 -0500
-@@ -7,8 +7,7 @@
- # license.  Please see the LICENSE file that should have been included
- # as part of this package.
- 
--import os, sys, getopt, re, time
--from string import maketrans
-+import re, time
- from Bio import SeqIO
- from Bio import Translate
- from Bio.Seq import Seq
-@@ -277,8 +276,9 @@
-    nice looking 6 frame translation with GC content - code from xbbtools
-    similar to DNA Striders six-frame translation
-    """
--   comp = complement(seq)
--   anti = reverse(comp)
-+   from Bio.Seq import reverse_complement
-+   anti = reverse_complement(seq)
-+   comp = anti[::-1]
-    length = len(seq)
-    frames = {}
-    for i in range(0,3):
-@@ -399,6 +399,7 @@
- # {{{ 
- 
- if __name__ == '__main__':
-+   import sys, getopt
-    # crude command line options to use most functions directly on a FASTA file
-    options = {'apply_on_multi_fasta':0,
-               'quick':0,
diff --git a/sci-biology/biopython/files/biopython-1.47-kdtree.patch b/sci-biology/biopython/files/biopython-1.47-kdtree.patch
deleted file mode 100644
index 5d9563f2dc0c..000000000000
--- a/sci-biology/biopython/files/biopython-1.47-kdtree.patch
+++ /dev/null
@@ -1,43 +0,0 @@
---- setup.py.old	2007-03-17 15:21:04.000000000 -0400
-+++ setup.py	2007-05-17 14:02:42.000000000 -0400
-@@ -64,6 +64,7 @@
-         _CHECKED = check_dependencies()
-     return _CHECKED
- 
-+USE_KDTREE = False
- def check_dependencies():
-     """Return whether the installation should continue."""
-     # There should be some way for the user to tell specify not to
-@@ -112,15 +113,8 @@
-         
-     
-     # Compile KDTree ? Not compiled by default
--    print "\n*** Bio.KDTree *** NOT built by default "
--    kdtree_msg = """
--The Bio.PDB.NeighborSearch module depends on the Bio.KDTree module,
--which in turn, depends on C++ code that does not compile cleanly on
--all platforms. Hence, Bio.KDTree is not built by default.
--
--Would you like to build Bio.KDTree ?"""
--
--    if get_yes_or_no (kdtree_msg, 0):
-+    global USE_KDTREE
-+    if USE_KDTREE:
-         NUMPY_PACKAGES.append("Bio.KDTree")
-         NUMPY_EXTENSIONS.append(
-             CplusplusExtension('Bio.KDTree._CKDTree', 
---- Tests/test_KDTree.py.old	2008-07-05 16:32:25.000000000 -0400
-+++ Tests/test_KDTree.py	2008-07-05 16:41:33.000000000 -0400
-@@ -1,4 +1,11 @@
--from Bio.KDTree.KDTree import _neighbor_test, _test
-+from Bio import MissingExternalDependencyError
-+
-+try:
-+	from Bio.KDTree.KDTree import _neighbor_test, _test
-+except ImportError:
-+	message = 'Could not import KDTree module ' \
-+			'(not important if you do not plan to use BIO.KDTree).'
-+	raise MissingExternalDependencyError(message)
- 
- nr_points=5000
- dim=3