diff options
author | 2010-05-01 15:29:11 -0500 | |
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committer | 2010-05-01 15:29:11 -0500 | |
commit | 30e2e3b96c8944f4df67646a223f135f336ec5f1 (patch) | |
tree | 280f50f952b0d9b5af015495dace9a711b1a42c1 /sci-biology | |
parent | namd, charm: moved to the main tree. (diff) | |
download | dberkholz-30e2e3b96c8944f4df67646a223f135f336ec5f1.tar.gz dberkholz-30e2e3b96c8944f4df67646a223f135f336ec5f1.tar.bz2 dberkholz-30e2e3b96c8944f4df67646a223f135f336ec5f1.zip |
biopython: add a 1.54 beta ebuild.
Diffstat (limited to 'sci-biology')
-rw-r--r-- | sci-biology/biopython/ChangeLog | 58 | ||||
-rw-r--r-- | sci-biology/biopython/Manifest | 13 | ||||
-rw-r--r-- | sci-biology/biopython/biopython-1.54_beta.ebuild (renamed from sci-biology/biopython/biopython-1.51_beta.ebuild) | 56 | ||||
-rw-r--r-- | sci-biology/biopython/files/biopython-1.43-buildkdtree.patch | 28 | ||||
-rw-r--r-- | sci-biology/biopython/files/biopython-1.44-sequtils-complement.patch | 32 | ||||
-rw-r--r-- | sci-biology/biopython/files/biopython-1.47-kdtree.patch | 43 | ||||
-rw-r--r-- | sci-biology/biopython/files/biopython-1.51-flex.patch (renamed from sci-biology/biopython/files/biopython-1.49-flex.patch) | 0 | ||||
-rw-r--r-- | sci-biology/biopython/metadata.xml | 4 |
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> |