New upstream version (fixes bug #248799).

(Portage version: 2.2_rc21/cvs/Linux 2.6.27-gentoo-r7 x86_64)

3 files changed, 83 insertions, 2 deletions

diff --git a/sci-biology/biopython/ChangeLog b/sci-biology/biopython/ChangeLog
index 127fa2230028..4180a4714b76 100644
--- a/sci-biology/biopython/ChangeLog
+++ b/sci-biology/biopython/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-biology/biopython
-# Copyright 2002-2008 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-biology/biopython/ChangeLog,v 1.26 2008/08/06 14:53:49 ulm Exp $
+# Copyright 2002-2009 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/biopython/ChangeLog,v 1.27 2009/01/16 17:04:14 ribosome Exp $
+
+*biopython-1.49 (16 Jan 2009)
+
+  16 Jan 2009; Olivier Fisette <ribosome@gentoo.org>
+  +files/biopython-1.49-flex.patch, +biopython-1.49.ebuild:
+  Version bump. Thanks to Juan Aguado <juantxorena@gmail.com> for his work.
+  Fixes bug #248799.
 
   06 Aug 2008; Ulrich Mueller <ulm@gentoo.org> metadata.xml:
   Add USE flag description to metadata wrt GLEP 56.
diff --git a/sci-biology/biopython/biopython-1.49.ebuild b/sci-biology/biopython/biopython-1.49.ebuild
new file mode 100644
index 000000000000..a85481d50c21
--- /dev/null
+++ b/sci-biology/biopython/biopython-1.49.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-1.49.ebuild,v 1.1 2009/01/16 17:04:14 ribosome Exp $
+
+NEED_PYTHON=2.3
+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 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-1.49-flex.patch b/sci-biology/biopython/files/biopython-1.49-flex.patch
new file mode 100644
index 000000000000..afd509444c68
--- /dev/null
+++ b/sci-biology/biopython/files/biopython-1.49-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']
+               ),