Version bump

(Portage version: 2.2_rc67/cvs/Linux x86_64)

3 files changed, 134 insertions, 1 deletions

diff --git a/sci-chemistry/xia2/ChangeLog b/sci-chemistry/xia2/ChangeLog
index b4b08366275a..c91e4ca9661b 100644
--- a/sci-chemistry/xia2/ChangeLog
+++ b/sci-chemistry/xia2/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-chemistry/xia2
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/xia2/ChangeLog,v 1.3 2010/04/22 19:29:41 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/xia2/ChangeLog,v 1.4 2010/07/27 18:57:43 jlec Exp $
+
+*xia2-0.3.1.7 (27 Jul 2010)
+
+  27 Jul 2010; Justin Lecher <jlec@gentoo.org>
+  +files/0.3.1.7-fix-syntax.patch, +xia2-0.3.1.7.ebuild:
+  Version bump
 
   22 Apr 2010; Justin Lecher <jlec@gentoo.org> xia2-0.3.1.6.ebuild:
   Keyworded for ~*-linux
diff --git a/sci-chemistry/xia2/files/0.3.1.7-fix-syntax.patch b/sci-chemistry/xia2/files/0.3.1.7-fix-syntax.patch
new file mode 100644
index 000000000000..ec8ada48aad1
--- /dev/null
+++ b/sci-chemistry/xia2/files/0.3.1.7-fix-syntax.patch
@@ -0,0 +1,61 @@
+diff --git a/xia2-0.3.1.7/Applications/xia2find.py b/xia2-0.3.1.7/Applications/xia2find.py
+index 1a3b0e2..e0b8a1e 100755
+--- a/xia2-0.3.1.7/Applications/xia2find.py
++++ b/xia2-0.3.1.7/Applications/xia2find.py
+@@ -38,7 +38,7 @@ from Schema.Sweep import SweepFactory
+ from Experts.FindImages import image2template_directory
+ 
+ known_image_extensions = ['img', 'mccd', 'mar2300', 'mar1200', 'mar3450',
+-                          'osc', 'cbf', 'mar2000']]
++                          'osc', 'cbf', 'mar2000']
+ known_sweeps = { }
+ 
+ def is_image_name(file):
+diff --git a/xia2-0.3.1.7/Experts/DRStrategyExpert.py b/xia2-0.3.1.7/Experts/DRStrategyExpert.py
+index 28b1dc3..dba3ef7 100644
+--- a/xia2-0.3.1.7/Experts/DRStrategyExpert.py
++++ b/xia2-0.3.1.7/Experts/DRStrategyExpert.py
+@@ -48,24 +48,24 @@ strategy_dict = {
+     'default':{
+     'score':1,
+     'pipeline':{
+-    'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'}
++    'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'},
+     'depends-on':['labelit.screen', 'xds', 'xscale', 'scala', 'combat',
+                   'pointless-1.1.0.4']},
+     'default':{
+     'score':2,
+     'pipeline':{
+-    'indexer':'labelit', 'integrater':'mosflm', 'scaler':'mosflm'}
++    'indexer':'labelit', 'integrater':'mosflm', 'scaler':'mosflm'},
+     'depends-on':['labelit.screen', 'mosflm', 'scala', 'reindex',
+                   'pointless-1.1.0.4']},
+     'mosaic':{
+     'score':1,
+     'pipeline':{
+-    'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'}
++    'indexer':'labelit', 'integrater':'xds', 'scaler':'xds-hybrid'},
+     'depends-on':['labelit.screen', 'xds', 'xscale', 'scala', 'combat',
+                   'pointless-1.1.0.4']},
+     'mosaic':{
+     'score':2,
+     'pipeline':{
+-    'indexer':'xds', 'integrater':'xds', 'scaler':'xds'}
++    'indexer':'xds', 'integrater':'xds', 'scaler':'xds'},
+     'depends-on':['xds', 'xscale']}
+     }
+diff --git a/xia2core-0.3.1.7/Python/Examples/CCP4/Cad.py b/xia2core-0.3.1.7/Python/Examples/CCP4/Cad.py
+index 88f9218..5fb6f2a 100644
+--- a/xia2core-0.3.1.7/Python/Examples/CCP4/Cad.py
++++ b/xia2core-0.3.1.7/Python/Examples/CCP4/Cad.py
+@@ -49,8 +49,8 @@ def Cad(DriverType = None):
+             self.add_command_line(hklin)
+ 
+             self.set_task('Rewriting reflections %s => %s' % 
+-                      `   (os.path.split(hklin)[-1],
+-                       `   os.path.split(self.getHklout())[-1]))
++                         (os.path.split(hklin)[-1],
++                          os.path.split(self.getHklout())[-1]))
+ 
+             self.start()
+ 
diff --git a/sci-chemistry/xia2/xia2-0.3.1.7.ebuild b/sci-chemistry/xia2/xia2-0.3.1.7.ebuild
new file mode 100644
index 000000000000..6b3152269410
--- /dev/null
+++ b/sci-chemistry/xia2/xia2-0.3.1.7.ebuild
@@ -0,0 +1,66 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/xia2/xia2-0.3.1.7.ebuild,v 1.1 2010/07/27 18:57:43 jlec Exp $
+
+EAPI="3"
+
+PYTHON_DEPEND="2"
+
+inherit eutils python
+
+DESCRIPTION="An automated data reduction system for crystallography"
+HOMEPAGE="http://www.xia2.org/xia/"
+SRC_URI="http://www.ccp4.ac.uk/${PN}/${P}.tar.bz2"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+RDEPEND="
+	>=sci-chemistry/ccp4-apps-6.1.2
+	sci-chemistry/mosflm
+	sci-chemistry/pointless
+	>=sci-libs/ccp4-libs-6.1.2
+	sci-libs/cctbx"
+DEPEND="${RDEPEND}"
+
+pkg_setup() {
+	python_set_active_version 2
+}
+
+src_prepare() {
+	find . -name '*.bat' -delete || die
+
+	epatch "${FILESDIR}"/${PV}-fix-syntax.patch
+	python_convert_shebangs -r $(python_get_version) .
+}
+
+src_install() {
+	rm -rf ${P}/binaries ${PN}core-${PV}/Test || die
+
+	insinto /usr/share/ccp4/XIAROOT/
+	doins -r * || die
+
+	# Set programs executable
+# fperms cannot handle wildcards
+	chmod 755 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/* || die
+	chmod 644 "${ED}"/usr/share/ccp4/XIAROOT/${P}/Applications/*.py || die
+
+	cat >> "${T}"/23XIA <<- EOF
+	XIA2_HOME="${EPREFIX}"/usr/share/ccp4/XIAROOT
+	XIA2CORE_ROOT="${EPREFIX}"/usr/share/ccp4/XIAROOT/xia2core-${PV}
+	XIA2_ROOT="${EPREFIX}"/usr/share/ccp4/XIAROOT/xia2-${PV}
+	PATH="${EPREFIX}"/usr/share/ccp4/XIAROOT/xia2-${PV}/Applications
+	EOF
+
+	doenvd "${T}"/23XIA
+}
+
+pkg_postinst() {
+	python_mod_optimize /usr/share/ccp4/XIAROOT
+}
+
+pkg_postrm() {
+	python_mod_cleanup /usr/share/ccp4/XIAROOT
+}