New version. Better documentation installation. Added scripts and test suite. KDTree now enabled by default (requires switching to EAPI 1).

Package-Manager: portage-2.1.4.4

4 files changed, 108 insertions, 2 deletions

diff --git a/sci-biology/biopython/ChangeLog b/sci-biology/biopython/ChangeLog
index a3b1ef535df2..d8b5baa7cc28 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 1.22 2008/07/06 15:16:27 ribosome Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/biopython/ChangeLog,v 1.23 2008/07/06 15:21:41 ribosome Exp $
+
+*biopython-1.47 (06 Jul 2008)
+
+  06 Jul 2008; Olivier Fisette <ribosome@gentoo.org>
+  +files/biopython-1.47-kdtree.patch, +biopython-1.47.ebuild:
+  New version. Better documentation installation. Added scripts and test
+  suite. KDTree now enabled by default (requires switching to EAPI 1).
 
   06 Jul 2008; Olivier Fisette <ribosome@gentoo.org> biopython-1.44.ebuild:
   Stable on amd64.
diff --git a/sci-biology/biopython/Manifest b/sci-biology/biopython/Manifest
index 52a7164f5766..d2d34dd9b067 100644
--- a/sci-biology/biopython/Manifest
+++ b/sci-biology/biopython/Manifest
@@ -1,8 +1,11 @@
 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
 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
 EBUILD biopython-1.42.ebuild 846 RMD160 a0fcfacfda3111e43e6197881e0771849b652e50 SHA1 9782363628761d4971e6fb1c2b0d585fc5468d38 SHA256 dfdefa0933e1a373132143962cc8688e4e5c75f45491b9afe895eb61672c9263
 EBUILD biopython-1.44.ebuild 1284 RMD160 a8ba899090b49cf0bd5816cb98bd3df3a26b01fb SHA1 03d6cecff0a1c0ded5e07425fc8f80aef3e2241c SHA256 d5885ed8247c927d5581b7b54a502bb0a14241afddfb228dad9b3937ce003f27
-MISC ChangeLog 4770 RMD160 56bbbd990941702567158f8b4c5b40bcac608ee0 SHA1 9bea483e82a9b71413eeec19e79414151491f84e SHA256 155847c825b6c85370a06ead8f2eaf27fc3de2f75e603fa7547b397782263230
+EBUILD biopython-1.47.ebuild 1367 RMD160 3902055e493865ec25cb67bf273f903789f6fa63 SHA1 96e87a40dffee3005bf02ca369cdfd16548b067e SHA256 b896b898a32c8cd83cfcaf02fd2b874644e1c6555130cd3052d3cb5d281febd5
+MISC ChangeLog 5061 RMD160 2ea2dd0e6d1c7a8104ca030646a9b3a2a1d33ec0 SHA1 437a602856d5a86d5c975b88c1d94384a38c998c SHA256 a55e32ebbb7e7f826326ec56e35c71e41347126e6cd554601ac90a21623510c0
 MISC metadata.xml 262 RMD160 4eabcbcb990d4d5e3b34db8c27bcd2c0cfcf7501 SHA1 3c024ca60a2b93ed0e0311f6b05ef5ef117bee31 SHA256 89af818a993faf14a4a87e2f254943420156c2a317c385480a9533ba682b650f
diff --git a/sci-biology/biopython/biopython-1.47.ebuild b/sci-biology/biopython/biopython-1.47.ebuild
new file mode 100644
index 000000000000..99812e58e75a
--- /dev/null
+++ b/sci-biology/biopython/biopython-1.47.ebuild
@@ -0,0 +1,53 @@
+# Copyright 1999-2008 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-biology/biopython/biopython-1.47.ebuild,v 1.1 2008/07/06 15:21:41 ribosome Exp $
+
+EAPI=1
+
+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="+kdtree"
+KEYWORDS="~alpha ~amd64 ~ppc ~sparc ~x86"
+
+DEPEND=">=dev-lang/python-2.2
+		>=dev-python/egenix-mx-base-2.0.3
+		>=dev-python/numeric-19.0
+		>=dev-python/reportlab-1.11"
+
+src_unpack() {
+	unpack ${A}
+	cd "${S}"
+	epatch "${FILESDIR}/${PN}-1.47-kdtree.patch"
+	if use kdtree; then
+		sed -i -e 's/USE_KDTREE = False/USE_KDTREE = True/' \
+				setup.py || die "Could not apply patch for KDTree support."
+	fi
+}
+
+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}"
+	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-1.47-kdtree.patch b/sci-biology/biopython/files/biopython-1.47-kdtree.patch
new file mode 100644
index 000000000000..5d9563f2dc0c
--- /dev/null
+++ b/sci-biology/biopython/files/biopython-1.47-kdtree.patch
@@ -0,0 +1,43 @@
+--- setup.py.old	2007-03-17 15:21:04.000000000 -0400
++++ setup.py	2007-05-17 14:02:42.000000000 -0400
+@@ -64,6 +64,7 @@
+         _CHECKED = check_dependencies()
+     return _CHECKED
+ 
++USE_KDTREE = False
+ def check_dependencies():
+     """Return whether the installation should continue."""
+     # There should be some way for the user to tell specify not to
+@@ -112,15 +113,8 @@
+         
+     
+     # Compile KDTree ? Not compiled by default
+-    print "\n*** Bio.KDTree *** NOT built by default "
+-    kdtree_msg = """
+-The Bio.PDB.NeighborSearch module depends on the Bio.KDTree module,
+-which in turn, depends on C++ code that does not compile cleanly on
+-all platforms. Hence, Bio.KDTree is not built by default.
+-
+-Would you like to build Bio.KDTree ?"""
+-
+-    if get_yes_or_no (kdtree_msg, 0):
++    global USE_KDTREE
++    if USE_KDTREE:
+         NUMPY_PACKAGES.append("Bio.KDTree")
+         NUMPY_EXTENSIONS.append(
+             CplusplusExtension('Bio.KDTree._CKDTree', 
+--- Tests/test_KDTree.py.old	2008-07-05 16:32:25.000000000 -0400
++++ Tests/test_KDTree.py	2008-07-05 16:41:33.000000000 -0400
+@@ -1,4 +1,11 @@
+-from Bio.KDTree.KDTree import _neighbor_test, _test
++from Bio import MissingExternalDependencyError
++
++try:
++	from Bio.KDTree.KDTree import _neighbor_test, _test
++except ImportError:
++	message = 'Could not import KDTree module ' \
++			'(not important if you do not plan to use BIO.KDTree).'
++	raise MissingExternalDependencyError(message)
+ 
+ nr_points=5000
+ dim=3