[gentoo-science] biopython-1.51

[Björn Thorwirth]

Hi All!

Here is an ebuild for new biopython 1.51. taken and adapted from bug
#278130
-- 
Bjoern Thorwirth, Zentrum für Medizinische Biotechnologie,
Universität Duisburg-Essen, Universitätsstr. 2, 45117 Essen, Germany
phone +49 201 183-4026, bjoern.thorwi...@uni-due.de



# 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-1.49.ebuild,v 1.2 
2009/07/14 15:31:35 fauli Exp $

NEED_PYTHON=2.4
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="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 )"

src_unpack() {
        unpack ${A}
        cd "${S}"
        epatch "${FILESDIR}/${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  || die "Tests failed."
}

--- 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']
               ),