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

(Portage version: 2.1.4.4)

3 files changed, 104 insertions, 1 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/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