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| author |   Andrey Kislyuk <weaver@gentoo.org> | 2009-09-09 21:45:48 +0000 |
|---|---|---|
| committer | Andrey Kislyuk <weaver@gentoo.org> | 2009-09-09 21:45:48 +0000 |
| commit | 617139b26bd8e5bf65ac6c528fa606e2f9d0e74b (patch) | |
| tree | 73e0a13e717b266e4b70541a7daa2185639fa8d2 /sci-biology/biopython | |
| parent | Bump to 8.4.0. Fixes #276125 (diff) | |
| download | gentoo-2-617139b26bd8e5bf65ac6c528fa606e2f9d0e74b.tar.gz gentoo-2-617139b26bd8e5bf65ac6c528fa606e2f9d0e74b.tar.bz2 gentoo-2-617139b26bd8e5bf65ac6c528fa606e2f9d0e74b.zip | |
Version bump
(Portage version: 2.2_rc30/cvs/Linux x86_64)
Diffstat (limited to 'sci-biology/biopython')
| -rw-r--r-- | sci-biology/biopython/ChangeLog | 8 | ||||
| -rw-r--r-- | sci-biology/biopython/biopython-1.51.ebuild | 53 | ||||
| -rw-r--r-- | sci-biology/biopython/files/biopython-1.51-flex.patch | 21 |
3 files changed, 81 insertions, 1 deletions
diff --git a/sci-biology/biopython/ChangeLog b/sci-biology/biopython/ChangeLog index 98efdff1863e..7e79a08d9b25 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 1.35 2009/08/26 14:45:14 fauli Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-biology/biopython/ChangeLog,v 1.36 2009/09/09 21:45:48 weaver Exp $ + +*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 diff --git a/sci-biology/biopython/biopython-1.51.ebuild b/sci-biology/biopython/biopython-1.51.ebuild new file mode 100644 index 000000000000..3614eed87af8 --- /dev/null +++ b/sci-biology/biopython/biopython-1.51.ebuild @@ -0,0 +1,53 @@ +# Copyright 1999-2009 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Header: /var/cvsroot/gentoo-x86/sci-biology/biopython/biopython-1.51.ebuild,v 1.1 2009/09/09 21:45:48 weaver Exp $ + +EAPI="2" + +NEED_PYTHON=2.4 +inherit distutils eutils base + +DESCRIPTION="Biopython - Python modules for computational molecular biology" +LICENSE="as-is" +HOMEPAGE="http://www.biopython.org" +SRC_URI="http://www.biopython.org/DIST/${P}.tar.gz" + +SLOT="0" +IUSE="mysql postgres" +KEYWORDS="~alpha ~amd64 ~ppc ~sparc ~x86" + +DEPEND="dev-python/numpy + >=dev-python/reportlab-2.0 + sys-devel/flex" + +RDEPEND="${DEPEND} + mysql? ( dev-python/mysql-python ) + postgres? ( dev-python/psycopg )" + +PATCHES=( + "${FILESDIR}"/${P}-flex.patch +) + +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}" + 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-1.51-flex.patch b/sci-biology/biopython/files/biopython-1.51-flex.patch new file mode 100644 index 000000000000..afd509444c68 --- /dev/null +++ b/sci-biology/biopython/files/biopython-1.51-flex.patch @@ -0,0 +1,21 @@ +--- 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'] + ), |