sci-chemistry/xia version bump to 0.2.7.2 and

fixing fperms --> chmod

4 files changed, 104 insertions, 1 deletions

diff --git a/sci-chemistry/xia2/ChangeLog b/sci-chemistry/xia2/ChangeLog
index b1269ea3e..53e18a0e9 100644
--- a/sci-chemistry/xia2/ChangeLog
+++ b/sci-chemistry/xia2/ChangeLog
@@ -2,6 +2,12 @@
 # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*xia2-0.2.7.2 (06 Mar 2009)
+
+  06 Mar 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
+  +files/0.2.7.2-fix-syntax.patch, +xia2-0.2.7.2.ebuild:
+  version bump to 0.2.7.2 and fix fperms --> chmod
+
   27 Feb 2009; Justin Lecher (jlec) <jlec@j-schmitz.net> ChangeLog:
   version bump to 0.2.7.0 
   Intial addition to sci overlay (Thanks Donnie for writing the ebuild)
diff --git a/sci-chemistry/xia2/Manifest b/sci-chemistry/xia2/Manifest
index cf3d8ca18..5972044b8 100644
--- a/sci-chemistry/xia2/Manifest
+++ b/sci-chemistry/xia2/Manifest
@@ -1,5 +1,8 @@
 AUX 0.2.7.0-fix-syntax.patch 2339 RMD160 b5d533b0ad9435be11cc224319ddc0fc5e41c647 SHA1 0d92641b05ad895b7f45fcedb987937269b4703c SHA256 68bf360f4e5cba17c4c0b343a9a11c47ad798caa38a954bbd2db1421103f8611
+AUX 0.2.7.2-fix-syntax.patch 1872 RMD160 e6954d0987f5de1bb371a889f0253f627bd14223 SHA1 569c9dfd87511b40b0958d3c013157a7d898c68f SHA256 eebfe74e1c934a03d458de87185412bac6f8195db599464eaf8643d3fdd6342d
 DIST xia2-0.2.7.0.tar.bz2 29859914 RMD160 778d5cdcac1e0702b8406e50488bcebfc439952e SHA1 c248a9615a34de634521a2066fa2c8fa256c28ef SHA256 c7a6f8733287df45dbfab2cb372fb0c61ebd750e4b3241a6ca611850b7155b18
+DIST xia2-0.2.7.2.tar.bz2 49601591 RMD160 a8c177bc23f6e07bed7e428972418a9e49e508f2 SHA1 9f677b2763f3f40711915b61ce91d1b57da0da64 SHA256 4748e16c9363ca0c7ad168ea9c8a198e42277696ae7508d5dc867b30974326d3
 EBUILD xia2-0.2.7.0.ebuild 1027 RMD160 9b2f9c3ac1a4acab90222b5b2360fc4eb48d08ec SHA1 613bb40a4b5870a6491e5121e3433f0eb219f69a SHA256 a82f9c41a846b363de46140ddf435e8a8c5604623c390d61c27280664a1061e1
-MISC ChangeLog 287 RMD160 10c7365f69e08e62bf5643feffcc386d79d013f2 SHA1 5a2e95e6d895d5d75ad38cd8778095ba152e20ec SHA256 f6f247f1787237b5b875a08ad156085c9cc1337bd59558584bb515d948ab8573
+EBUILD xia2-0.2.7.2.ebuild 1096 RMD160 d9602ac17ba349ad0a50e53f942cd33feb63688f SHA1 2d9179106e85245eec517e8b358a35c1f6fcca09 SHA256 2749aa272edd6435b2272f09317c53d760dfb8cfe2c18a7022931d7cc280cfe0
+MISC ChangeLog 482 RMD160 f8ec59cdfda094d0fa1b1446b4999dad0d2aef22 SHA1 a00e994ae416e19d12b56f0c871871f2b5d79b70 SHA256 528edc2481c2599276381b448c6c46f6d39ebf88ccbccab6549c1ddac0edafb7
 MISC metadata.xml 215 RMD160 bc9c07aa91f2f175542244e4e4522a73558210a1 SHA1 facb283386de1c0b6b938cdcd4dde04d1694298b SHA256 13f32353652adbd3d934d41381cfc2cacc9e1127c508cebc73806cc1026ee80c
diff --git a/sci-chemistry/xia2/files/0.2.7.2-fix-syntax.patch b/sci-chemistry/xia2/files/0.2.7.2-fix-syntax.patch
new file mode 100644
index 000000000..15d1a9b0c
--- /dev/null
+++ b/sci-chemistry/xia2/files/0.2.7.2-fix-syntax.patch
@@ -0,0 +1,44 @@
+--- xia2-0.2.7.2/Experts/DRStrategyExpert.py	2007-01-10 20:57:22.000000000 +0100
++++ xia2-0.2.7.2/Experts/DRStrategyExpert.py.new	2009-03-06 14:04:38.000000000 +0100
+@@ -48,24 +48,24 @@
+     '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']}
+     }
+--- xia2core-0.2.7.2.orig/Python/Examples/CCP4/Cad.py	2008-08-03 21:40:37.000000000 -0700
++++ xia2core-0.2.7.2/Python/Examples/CCP4/Cad.py	2008-08-03 21:45:24.000000000 -0700
+@@ -49,8 +49,8 @@
+             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/xia2-0.2.7.2.ebuild b/sci-chemistry/xia2/xia2-0.2.7.2.ebuild
new file mode 100644
index 000000000..5795adb3d
--- /dev/null
+++ b/sci-chemistry/xia2/xia2-0.2.7.2.ebuild
@@ -0,0 +1,50 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+inherit eutils python
+
+DESCRIPTION="An automated data reduction system for crystallography"
+HOMEPAGE="http://www.ccp4.ac.uk/xia/"
+SRC_URI="${HOMEPAGE}/${P}.tar.bz2"
+LICENSE="ccp4"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+RDEPEND=">=sci-chemistry/ccp4-6.1"
+DEPEND="${RDEPEND}"
+
+src_unpack() {
+	unpack ${A}
+	cd "${S}"
+	rm -rf ${P}/binaries || die
+	find . -name '*.bat' | xargs rm || die
+	sed -i \
+		-e "s:/path/to/xiahome:/usr/share/ccp4/XIAROOT:g" \
+		setup.*
+	epatch "${FILESDIR}"/${PV}-fix-syntax.patch
+}
+
+src_compile() {
+	:
+}
+
+src_install() {
+	insinto /usr/share/ccp4/XIAROOT/
+	doins -r * || die
+
+	# Set programs executable
+# fperms cannot handle wildcards
+	chmod 755 "${D}"/usr/share/ccp4/XIAROOT/${P}/Applications/* || die
+	chmod 644 "${D}"/usr/share/ccp4/XIAROOT/${P}/Applications/*.py || die
+
+	# probably we need so set some ENV --> XIAROOT
+}
+
+pkg_postinst() {
+	python_mod_optimize /usr/share/ccp4/XIAROOT
+}
+
+pkg_postrm() {
+	python_mod_cleanup /usr/share/ccp4/XIAROOT
+}