Version bump

Package-Manager: portage-2.2_rc30/cvs/Linux x86_64

4 files changed, 85 insertions, 12 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/Manifest b/sci-biology/biopython/Manifest
index 718bf5e3c2c7..f22e775549f0 100644
--- a/sci-biology/biopython/Manifest
+++ b/sci-biology/biopython/Manifest
@@ -1,15 +1,8 @@
------BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
-
 AUX biopython-1.49-flex.patch 782 RMD160 a69deb13b97f80ec6aed7ec7975e0de4846fe2fa SHA1 dad1c962a632efeccbbec61b79feb71abccbe030 SHA256 ad957b435fc70b218a7a65eb492b0eae5f82b7c6371d2f1451c9dd714fa056dc
+AUX biopython-1.51-flex.patch 782 RMD160 a69deb13b97f80ec6aed7ec7975e0de4846fe2fa SHA1 dad1c962a632efeccbbec61b79feb71abccbe030 SHA256 ad957b435fc70b218a7a65eb492b0eae5f82b7c6371d2f1451c9dd714fa056dc
 DIST biopython-1.49.tar.gz 4148803 RMD160 3d6893cd788c39512a314345bb2ea441c715c17d SHA1 f2ea7f3b8985facdf8f4d4c86ee300e4a8f1a5fb SHA256 0d8876bef579dde2f53063b486bdbde62fc272bf33d1463753f27c5d31651236
+DIST biopython-1.51.tar.gz 5557548 RMD160 9136c75a8451af5f7576a63f11655353c38639c8 SHA1 1d48208fc0fd5549958fea3eac40d12f032a6473 SHA256 0ebf44e6376d7b44fb2857e751d388f30402d6a81798821e40a7f7b92a4b036b
 EBUILD biopython-1.49.ebuild 1331 RMD160 0605df9299d7330e18479fee64ecdaabeec20838 SHA1 2d4470d85e66d23ab6ab28751d22b5bbcfcd4181 SHA256 26dc2867b099275abb45e4663a2e742a7414066596c306a0137da864abb89c21
-MISC ChangeLog 6649 RMD160 577c8f6655a96a399c6d0392a176f42a01bfada9 SHA1 e70d9bc3e57a6159488a3ca07151d8f57244f06b SHA256 2bcffefa20de9410fcc169f436daca47075947d3b2aecfb0a0c933a94c65095d
+EBUILD biopython-1.51.ebuild 1316 RMD160 a06b5470c80c6fac7a4b342b22c5bb972a9291aa SHA1 ae1383952199597614e2c2aa3ca71f3f16eccc85 SHA256 d1a1d59118d53ca9a378a8662e02aa773ef234f3c27e914f423e7d768d464b4f
+MISC ChangeLog 6807 RMD160 eae2ea7b14570280aab984fe9b5090f1cd2a1fc7 SHA1 4ad50e2c6c5fadcca13f5a6e27f12a2fa5a1d120 SHA256 1ac090c56885c7e315a903b3c36fe1c1b8425a347cd1fa8a16eda6072ea19ec1
 MISC metadata.xml 164 RMD160 2f441200f2672ab5f1efae7cbdb08b284603903c SHA1 61a50baedfd041e663d6c2a41a28b57e22dbb6de SHA256 f0897b09e661dc603041dab249d73253034659189becf1a34cca37a7d51ef72f
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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']
+               ),