sci-chemistry/xia2 -- version bump

(Portage version: 2.2_rc49/git/Linux x86_64)
 (Signed Manifest commit)

4 files changed, 131 insertions, 1 deletions

diff --git a/sci-chemistry/xia2/ChangeLog b/sci-chemistry/xia2/ChangeLog
index acca53a58..aae67ff61 100644
--- a/sci-chemistry/xia2/ChangeLog
+++ b/sci-chemistry/xia2/ChangeLog
@@ -2,6 +2,14 @@
 # Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+*xia2-0.3.0.6 (14 Nov 2009)
+
+  14 Nov 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
+  +files/0.3.0.6-fix-syntax.patch, +xia2-0.3.0.6.ebuild:
+  version bump
+  HOMEPAGE changed
+  sci-libs/cctbx as RDEPEND
+
   03 Aug 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
   +xia2-0.3.0.0-r2.ebuild:
   bump for ccp4-6.1.2
diff --git a/sci-chemistry/xia2/Manifest b/sci-chemistry/xia2/Manifest
index 3321e7685..7198902fd 100644
--- a/sci-chemistry/xia2/Manifest
+++ b/sci-chemistry/xia2/Manifest
@@ -1,7 +1,20 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA1
+
 AUX 0.3.0.0-fix-syntax.patch 1872 RMD160 00c585a160acbc9d86b3d5a9ad25b5517b3668d6 SHA1 4bbfd985d7ca712da323ea0d315c89a1c44b9507 SHA256 4457b40ea22fdedd8108e9504602e55733721f30397ab9ca1162394d5a1cd830
 AUX 0.3.0.0-pointless.patch 629 RMD160 a9822d57c51e687031c1a64c5a9c03a75ba1a04c SHA1 5e8541b6fc0e1ed8706ecd2f958c9deade155cfb SHA256 f49f733446351d2e89a7258b9cf48de125bcebd3b25d750d572a4090f5779061
+AUX 0.3.0.6-fix-syntax.patch 2034 RMD160 722e7ab6a97edefe91f6f99645c4877b4c5b9138 SHA1 8711ed3721939b0b1f278307846b02d28e3077a6 SHA256 b62a9194d5bc16c0831ebf82cbcd9a93976834926f2805d0a9aeb023d1b3a37a
 AUX Makefile.chef 760 RMD160 541652e0fa0ded7ec2ab086794b299999dc07dc8 SHA1 115c9fd871dafd1e6eee344e4838e0dd071503d3 SHA256 1f8e61dfab1e96d005bf11b1c6f4b6243727b8e123b15b4acd5fd1a56d3a6231
 DIST xia2-0.3.0.0.tar.bz2 39051902 RMD160 3fbea20bcf0b383b904cad269c80a5a17ff0f3ad SHA1 18b7bb01e1097be0f2e5ef72ac304f1343665c26 SHA256 37520b16c17122f3432a998a3ba938c76d1b4edabd27b278af5d0207b064639d
+DIST xia2-0.3.0.6.tar.bz2 3250749 RMD160 2ad7317e80cce20146065465f46e78b0e8b52e5c SHA1 9b422235dfff6e0d48a9c362f6c9fc3879ee2540 SHA256 207924e59a13b19871a43fcbab0859040707dc88b8689d8d4406831605191078
 EBUILD xia2-0.3.0.0-r3.ebuild 1580 RMD160 4d8791039770d553867ac3857f6713e671a12406 SHA1 eb8150f4f880c6950418fdfc37ee1737dcb6716b SHA256 39c7713a1956a6648672f0394fcf8824c29d7b72a3cf2d497eed70236dcdc274
-MISC ChangeLog 1269 RMD160 80c046074cb435bff68e364b5c9380c0f4d4d226 SHA1 a3eba9fb32de9ab6e7148be61a355a015918d1cb SHA256 926c7c4b85a58881fbebeee917db4f9b16bfa682b802a33598bc706b1f3ceba3
+EBUILD xia2-0.3.0.6.ebuild 1308 RMD160 e64f9e8d5088f89085789440e74570e521853210 SHA1 c2fd41f9d0b1b34ca78900c91e22a95f23ef021f SHA256 e6f8ff92784214520cf63da247ff7a12c8bc4ea0e05aaacead6df7627416f0c2
+MISC ChangeLog 1475 RMD160 51cb522c96440b98be622e66c660f7434d599cc8 SHA1 6398a7028440f00c50f338232786f48db06bee19 SHA256 8209be0babe3f72c68068a9e76378f9f50f2b2f49b70a57350cbf9dcca9d3ae6
 MISC metadata.xml 215 RMD160 bc9c07aa91f2f175542244e4e4522a73558210a1 SHA1 facb283386de1c0b6b938cdcd4dde04d1694298b SHA256 13f32353652adbd3d934d41381cfc2cacc9e1127c508cebc73806cc1026ee80c
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.11 (GNU/Linux)
+
+iEYEARECAAYFAkr+5QYACgkQgAnW8HDreRbCVgCeJo8NORV7PeWnxoyYeIPiqP77
+HF0AoJsNrpH2QDP14F99Euyxgw6KC4bT
+=6pVz
+-----END PGP SIGNATURE-----
diff --git a/sci-chemistry/xia2/files/0.3.0.6-fix-syntax.patch b/sci-chemistry/xia2/files/0.3.0.6-fix-syntax.patch
new file mode 100644
index 000000000..b191fb5c1
--- /dev/null
+++ b/sci-chemistry/xia2/files/0.3.0.6-fix-syntax.patch
@@ -0,0 +1,48 @@
+diff --git a/xia2-0.3.0.6/Experts/DRStrategyExpert.py b/xia2-0.3.0.6/Experts/DRStrategyExpert.py
+index 28b1dc3..dba3ef7 100644
+--- a/xia2-0.3.0.6/Experts/DRStrategyExpert.py
++++ b/xia2-0.3.0.6/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-0.3.0.6/Python/Examples/CCP4/Cad.py b/xia2core-0.3.0.6/Python/Examples/CCP4/Cad.py
+index 88f9218..5fb6f2a 100644
+--- a/xia2core-0.3.0.6/Python/Examples/CCP4/Cad.py
++++ b/xia2core-0.3.0.6/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/xia2-0.3.0.6.ebuild b/sci-chemistry/xia2/xia2-0.3.0.6.ebuild
new file mode 100644
index 000000000..a3f2721fc
--- /dev/null
+++ b/sci-chemistry/xia2/xia2-0.3.0.6.ebuild
@@ -0,0 +1,61 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI="2"
+
+inherit eutils python
+
+DESCRIPTION="An automated data reduction system for crystallography"
+HOMEPAGE="http://www.xia2.org/xia/"
+SRC_URI="${HOMEPAGE}/${P}.tar.bz2"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+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="${RDEPEND}"
+
+src_prepare() {
+	find . -name '*.bat' | xargs rm || die
+
+	epatch "${FILESDIR}"/${PV}-fix-syntax.patch
+}
+
+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 "${D}"/usr/share/ccp4/XIAROOT/${P}/Applications/* || die
+	chmod 644 "${D}"/usr/share/ccp4/XIAROOT/${P}/Applications/*.py || die
+
+	cat >> "${T}"/23XIA <<- EOF
+	XIA2_HOME=/usr/share/ccp4/XIAROOT
+
+	XIA2CORE_ROOT=/usr/share/ccp4/XIAROOT/xia2core-${PV}
+	XIA2_ROOT=/usr/share/ccp4/XIAROOT/xia2-${PV}
+
+	PATH=/usr/share/ccp4/XIAROOT/xia2-${PV}/Applications
+	EOF
+
+	doenvd "${T}"/23XIA
+}
+
+pkg_postinst() {
+	python_mod_optimize /usr/share/ccp4/XIAROOT
+}
+
+pkg_postrm() {
+	python_mod_cleanup /usr/share/ccp4/XIAROOT
+}