New upstream version (fixes bug #248799).

Package-Manager: portage-2.2_rc21/cvs/Linux 2.6.27-gentoo-r7 x86_64

4 files changed, 87 insertions, 13 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/Manifest b/sci-biology/biopython/Manifest
index d4734f811ac0..4c16fdc43541 100644
--- a/sci-biology/biopython/Manifest
+++ b/sci-biology/biopython/Manifest
@@ -1,21 +1,14 @@
------BEGIN PGP SIGNED MESSAGE-----
-Hash: SHA1
-
 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-1.42.tar.gz 3933507 RMD160 9f3027fb1b3326885376eaf7a5a714a26e0bc333 SHA1 107321d782b0a00bc3c302cd8c7e4b82c013d6d7 SHA256 ba4d00fdf7de67196ecba317dee09a14850b40596bd83d73e458c5f19fc9fc58
 DIST biopython-1.44.tar.gz 3840036 RMD160 ecbbe2f46f0e5d124d910632dc9a7fd051202c0b SHA1 ca2a35c9e92a219256fe4fc2a232df5328f9f5d9 SHA256 e47c4a7c612e11cb6c1c0515274ce231646b31bbf1c9e3ac58998928c0ad3c72
 DIST biopython-1.47.tar.gz 4114907 RMD160 6b17c7d9d405734a7768a4fdc8f06bb0e60a2987 SHA1 0e73762b23d02f2e1e4ee51c0497ac86f40057e2 SHA256 a83544c3ed155acfa3f38929b44a890e77806799399193e48b8787efa89b6213
+DIST biopython-1.49.tar.gz 4148803 RMD160 3d6893cd788c39512a314345bb2ea441c715c17d SHA1 f2ea7f3b8985facdf8f4d4c86ee300e4a8f1a5fb SHA256 0d8876bef579dde2f53063b486bdbde62fc272bf33d1463753f27c5d31651236
 EBUILD biopython-1.42.ebuild 846 RMD160 a0fcfacfda3111e43e6197881e0771849b652e50 SHA1 9782363628761d4971e6fb1c2b0d585fc5468d38 SHA256 dfdefa0933e1a373132143962cc8688e4e5c75f45491b9afe895eb61672c9263
 EBUILD biopython-1.44.ebuild 1278 RMD160 323530a8d272c9b7cc9f18cd21deba01974640cd SHA1 e8469153b7e3e81a192f4b1f1bf755142cbb18d5 SHA256 530d9fc1595bc8feac2c7dfdb4ff05ac55cb9a1751d3e1b237ccde8d418d3ce8
 EBUILD biopython-1.47.ebuild 1367 RMD160 3902055e493865ec25cb67bf273f903789f6fa63 SHA1 96e87a40dffee3005bf02ca369cdfd16548b067e SHA256 b896b898a32c8cd83cfcaf02fd2b874644e1c6555130cd3052d3cb5d281febd5
-MISC ChangeLog 5377 RMD160 73bc577e390ac8708314f8d93ca21c2dfcae87e4 SHA1 893a34f591ed04af0152fe4270b2e711d45c9f9b SHA256 611c008ff6a78d292b9da694c7872154ddf5f2cedde41f6e36951c24944f05d5
+EBUILD biopython-1.49.ebuild 1336 RMD160 89ba764da31fda6763a317b869b09ee6361678b5 SHA1 c202327cc1d927b732f16663b1de82dcec61c6c7 SHA256 43d6cbc8a44ffde354ace14d11189e4fd17211f157108ae2ebe3e75fe293374f
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 MISC metadata.xml 370 RMD160 df6ae9fb652328f8373c937d7a903d11ceb3ced1 SHA1 70245dfcf6402bd4a1c78d120b7abc6abf3549a0 SHA256 5cc8f03cda86220a0a1e50664c63a06dab6e0e0d7097b3d630729b7f802e6284
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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']
+               ),