biopython: add a 1.54 beta ebuild.

8 files changed, 92 insertions, 142 deletions

diff --git a/sci-biology/biopython/ChangeLog b/sci-biology/biopython/ChangeLog
index e2231c5..c752551 100644
--- a/sci-biology/biopython/ChangeLog
+++ b/sci-biology/biopython/ChangeLog
@@ -1,6 +1,60 @@
 # ChangeLog for sci-biology/biopython
-# Copyright 2002-2009 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/biopython/ChangeLog,v 1.28 2009/03/24 20:51:55 ribosome Exp $
+# Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/biopython/ChangeLog,v 1.42 2010/02/13 19:10:21 armin76 Exp $
+
+  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.
diff --git a/sci-biology/biopython/Manifest b/sci-biology/biopython/Manifest
index 2b44004..1201651 100644
--- a/sci-biology/biopython/Manifest
+++ b/sci-biology/biopython/Manifest
@@ -1,8 +1,5 @@
-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
-AUX biopython-1.49-flex.patch 782 RMD160 a69deb13b97f80ec6aed7ec7975e0de4846fe2fa SHA1 dad1c962a632efeccbbec61b79feb71abccbe030 SHA256 ad957b435fc70b218a7a65eb492b0eae5f82b7c6371d2f1451c9dd714fa056dc
-DIST biopython-1.51b.tar.gz 5295918 RMD160 2683164b8fa3f20bf5a05a28eb36a6c5b9e6391f SHA1 0fbe3c2dbe8f47945a1fc29a61326a0922853e1b SHA256 679c40dd97358a5d432a21c340934fd43e3679268db6e753188b0190e5fc43cb
-EBUILD biopython-1.51_beta.ebuild 1339 RMD160 d2bd4fddaf22e9c78ef292bf69384b555f2ff895 SHA1 926ee6e7f19cc3f1be8e0fc206989947081e51a5 SHA256 10669f2c9ec427de8d455bca5ac2f320a1da9b38cbb0e3e1969203f29a7e6522
-MISC ChangeLog 5736 RMD160 b0b762d995e6edbdb16f9eadd1f921802f049d68 SHA1 ac1751e87624703a02376880d003dbd338412385 SHA256 2033b86e513a60e9daa1e04ba500fd44d0535e3244e3cff2fefd49ae6b98b5a6
-MISC metadata.xml 275 RMD160 593ddb95d6fec13860f6b22c23a79356d707ae9a SHA1 95b53999259ec92e9d5d0572aba347944aa63d21 SHA256 575cd7696af32aa6f1cb77880036def20b66898d4c91501b6b87852fca982c71
+AUX biopython-1.51-flex.patch 782 RMD160 a69deb13b97f80ec6aed7ec7975e0de4846fe2fa SHA1 dad1c962a632efeccbbec61b79feb71abccbe030 SHA256 ad957b435fc70b218a7a65eb492b0eae5f82b7c6371d2f1451c9dd714fa056dc
+DIST biopython-1.54b.tar.gz 6710918 RMD160 084fea4ddba140f0754b842513aaa79bf9ab19eb SHA1 dcd2dd3046835d20d30143e9affb15a3e13ab278 SHA256 a41d488e0e739762d6d678812a70f1ae6395340f44807ee799822506eedccc67
+EBUILD biopython-1.54_beta.ebuild 1527 RMD160 61796ab5319538511692a43d8f57e6bef06488a9 SHA1 ed4c4431ccc65fc50dbfda72e69c41b2183d1fc6 SHA256 d0a859b6dffb9b9d22346907832b1c47264b50fbfd562408a715c1c11a560a06
+MISC ChangeLog 7511 RMD160 a1e05afa13152baa388abf8ad30787e1d242548a SHA1 b54c3ce6701a362805269563bc2c964083e7f652 SHA256 52259066ee1f7c2940b7e899773eb2430819b34f412abc20bf83eb922e401b3a
+MISC metadata.xml 164 RMD160 2f441200f2672ab5f1efae7cbdb08b284603903c SHA1 61a50baedfd041e663d6c2a41a28b57e22dbb6de SHA256 f0897b09e661dc603041dab249d73253034659189becf1a34cca37a7d51ef72f
diff --git a/sci-biology/biopython/biopython-1.51_beta.ebuild b/sci-biology/biopython/biopython-1.54_beta.ebuild
index f1dc311..f0c36a5 100644
--- a/sci-biology/biopython/biopython-1.51_beta.ebuild
+++ b/sci-biology/biopython/biopython-1.54_beta.ebuild
@@ -1,54 +1,60 @@
-# Copyright 1999-2009 Gentoo Foundation
+# Copyright 1999-2010 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/biopython/biopython-1.49.ebuild,v 1.1 2009/01/16 17:04:14 ribosome Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/biopython/biopython-1.53.ebuild,v 1.5 2010/02/13 19:10:21 armin76 Exp $
 
-NEED_PYTHON=2.3
-inherit distutils eutils
+EAPI="2"
+SUPPORT_PYTHON_ABIS="1"
 
-MY_PV=${PV/_beta/b}
-MY_P=${PN}-${MY_PV}
+inherit base distutils eutils
+
+MY_P=${P/_beta/b}
 DESCRIPTION="Biopython - Python modules for computational molecular biology"
-LICENSE="as-is"
-HOMEPAGE="http://www.biopython.org"
+HOMEPAGE="http://www.biopython.org http://pypi.python.org/pypi/biopython"
 SRC_URI="http://www.biopython.org/DIST/${MY_P}.tar.gz"
 
+LICENSE="as-is"
 SLOT="0"
+KEYWORDS="alpha amd64 ppc sparc x86"
 IUSE="mysql postgres"
-KEYWORDS="~alpha ~amd64 ~ppc ~sparc ~x86"
 
-DEPEND="dev-python/numpy
+RDEPEND="dev-python/numpy
 	>=dev-python/reportlab-2.0
-	sys-devel/flex"
-
-RDEPEND="${DEPEND}
 	mysql? ( dev-python/mysql-python )
 	postgres? ( dev-python/psycopg )"
+DEPEND="${RDEPEND}
+	sys-devel/flex"
+RESTRICT_PYTHON_ABIS="3.*"
 S=${WORKDIR}/${MY_P}
 
-src_unpack() {
-	unpack ${A}
-	cd "${S}"
-	epatch "${FILESDIR}/biopython-1.49-flex.patch"
-}
+PATCHES=(
+	"${FILESDIR}/${PN}-1.51-flex.patch"
+)
+
+DISTUTILS_USE_SEPARATE_SOURCE_DIRECTORIES="1"
+DOCS="CONTRIB DEPRECATED NEWS README"
+PYTHON_MODNAME="Bio BioSQL"
 
 src_compile() {
 	distutils_src_compile
 }
 
+src_test() {
+	testing() {
+		cd Tests
+		PYTHONPATH="$(ls -d ../build/lib.*)" "$(PYTHON)" run_tests.py
+	}
+	python_execute_function -s testing
+}
+
 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}"
+	rm -f Tests/*.pyc || \
+			die "Failed to remove precompiled test files."
 	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 cefb16d..0000000
--- 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 16fc44d..0000000
--- 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 5d9563f..0000000
--- 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
diff --git a/sci-biology/biopython/files/biopython-1.49-flex.patch b/sci-biology/biopython/files/biopython-1.51-flex.patch
index afd5094..afd5094 100644
--- a/sci-biology/biopython/files/biopython-1.49-flex.patch
+++ b/sci-biology/biopython/files/biopython-1.51-flex.patch
diff --git a/sci-biology/biopython/metadata.xml b/sci-biology/biopython/metadata.xml
index c2a4a7c..34294c6 100644
--- a/sci-biology/biopython/metadata.xml
+++ b/sci-biology/biopython/metadata.xml
@@ -2,8 +2,4 @@
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
 <herd>sci-biology</herd>
-<use>
-  <flag name='kdtree'>Do not build KDTree module and its dependencies
-    (NeighborSearch)</flag>
-</use>
 </pkgmetadata>