clean up

Package-Manager: portage-2.1.6.13/cvs/Linux i686

8 files changed, 18 insertions, 244 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/Manifest b/sci-biology/biopython/Manifest
index 8b1a6633bee1..47c3849f7db5 100644
--- a/sci-biology/biopython/Manifest
+++ b/sci-biology/biopython/Manifest
@@ -1,14 +1,15 @@
-AUX biopython-1.43-buildkdtree.patch 981 RMD160 3930f852a6ed3b783390d00e7c3ffdeccd2ee270 SHA1 45aaa6c57c4e42f8c21b00ca3d9837a32955da18 SHA256 6cbce6137e90670a53f83c4ac6c9c83523aa4b7730ed691a8be6fd884a4ddb9e
-AUX biopython-1.44-sequtils-complement.patch 1033 RMD160 d7f8822ad8946e364bb4491a502055e7bf482478 SHA1 f08b0659db5053f13a7f871f037d5beb133745c8 SHA256 9e2f0e85e8be14971667037ac49edec94d73241c88a7cf9caeba6234955ed780
-AUX biopython-1.47-kdtree.patch 1489 RMD160 4babd067661cee10806337bff3fa4f9203bd61a8 SHA1 5eeb0ec76d023578e09d0bca4c75c5aa334b751c SHA256 6c844e18c50d120d34e6a1b5c587ac4fee17465db941fe47ea2bcf974a1cc297
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
 AUX biopython-1.49-flex.patch 782 RMD160 a69deb13b97f80ec6aed7ec7975e0de4846fe2fa SHA1 dad1c962a632efeccbbec61b79feb71abccbe030 SHA256 ad957b435fc70b218a7a65eb492b0eae5f82b7c6371d2f1451c9dd714fa056dc
-DIST biopython-1.42.tar.gz 3933507 RMD160 9f3027fb1b3326885376eaf7a5a714a26e0bc333 SHA1 107321d782b0a00bc3c302cd8c7e4b82c013d6d7 SHA256 ba4d00fdf7de67196ecba317dee09a14850b40596bd83d73e458c5f19fc9fc58
-DIST biopython-1.44.tar.gz 3840036 RMD160 ecbbe2f46f0e5d124d910632dc9a7fd051202c0b SHA1 ca2a35c9e92a219256fe4fc2a232df5328f9f5d9 SHA256 e47c4a7c612e11cb6c1c0515274ce231646b31bbf1c9e3ac58998928c0ad3c72
-DIST biopython-1.47.tar.gz 4114907 RMD160 6b17c7d9d405734a7768a4fdc8f06bb0e60a2987 SHA1 0e73762b23d02f2e1e4ee51c0497ac86f40057e2 SHA256 a83544c3ed155acfa3f38929b44a890e77806799399193e48b8787efa89b6213
 DIST biopython-1.49.tar.gz 4148803 RMD160 3d6893cd788c39512a314345bb2ea441c715c17d SHA1 f2ea7f3b8985facdf8f4d4c86ee300e4a8f1a5fb SHA256 0d8876bef579dde2f53063b486bdbde62fc272bf33d1463753f27c5d31651236
-EBUILD biopython-1.42.ebuild 846 RMD160 a0fcfacfda3111e43e6197881e0771849b652e50 SHA1 9782363628761d4971e6fb1c2b0d585fc5468d38 SHA256 dfdefa0933e1a373132143962cc8688e4e5c75f45491b9afe895eb61672c9263
-EBUILD biopython-1.44.ebuild 1278 RMD160 323530a8d272c9b7cc9f18cd21deba01974640cd SHA1 e8469153b7e3e81a192f4b1f1bf755142cbb18d5 SHA256 530d9fc1595bc8feac2c7dfdb4ff05ac55cb9a1751d3e1b237ccde8d418d3ce8
-EBUILD biopython-1.47.ebuild 1367 RMD160 3902055e493865ec25cb67bf273f903789f6fa63 SHA1 96e87a40dffee3005bf02ca369cdfd16548b067e SHA256 b896b898a32c8cd83cfcaf02fd2b874644e1c6555130cd3052d3cb5d281febd5
 EBUILD biopython-1.49.ebuild 1331 RMD160 0605df9299d7330e18479fee64ecdaabeec20838 SHA1 2d4470d85e66d23ab6ab28751d22b5bbcfcd4181 SHA256 26dc2867b099275abb45e4663a2e742a7414066596c306a0137da864abb89c21
-MISC ChangeLog 6274 RMD160 8eb35e212a25a63ec1022b0d1a718752c532f3c5 SHA1 37279ac5d4a0c518f379449c8fb4c468ad9ad886 SHA256 79edc34aca5061254591e2e614495e91548bf80ec955785be2bec3261c357cd1
+MISC ChangeLog 6542 RMD160 2ce96d3c1ec96d2cb76d183c61d03105060a4429 SHA1 1ce1a8b96d032b0e8e584d1a38e688a8a7dddd69 SHA256 6c0eba5ed20afabb75693b1dc19be88b35352d66ec6df373b62d0205dbe443ca
 MISC metadata.xml 275 RMD160 593ddb95d6fec13860f6b22c23a79356d707ae9a SHA1 95b53999259ec92e9d5d0572aba347944aa63d21 SHA256 575cd7696af32aa6f1cb77880036def20b66898d4c91501b6b87852fca982c71
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.11 (GNU/Linux)
+
+iEYEARECAAYFAkqVSYAACgkQNQqtfCuFneNctwCfftS4FNjSChzmIitvUG9pg95V
+CnIAnAswMon5t17SQER7UG7DW4u2Vxli
+=9pFb
+-----END PGP SIGNATURE-----
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