Version bump

Package-Manager: portage-2.2_rc67/cvs/Linux x86_64

4 files changed, 142 insertions, 6 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/Manifest b/sci-chemistry/xia2/Manifest
index 310b1e4c9fff..bec2777fbaaf 100644
--- a/sci-chemistry/xia2/Manifest
+++ b/sci-chemistry/xia2/Manifest
@@ -3,16 +3,19 @@ Hash: SHA1
 
 AUX 0.3.1.0-fix-syntax.patch 2586 RMD160 23e70c32e9052ff3a12740b71a02a66a5053b8da SHA1 3fdcad17357908ac923a87c9e93364e92b35190f SHA256 4e95f9e9f26d8b4400481b2542ad9e1ca2adaafb6caedb5c57d149f4e2554285
 AUX 0.3.1.6-fix-syntax.patch 2586 RMD160 184341967258e0734a5614830bfbc97f9381c05e SHA1 5247bb4af94c89c2e3023764a8e5470605964135 SHA256 035cb4b757c1769b277fad57515b47473b425f24c5b07e41973f44b83586ab2a
+AUX 0.3.1.7-fix-syntax.patch 2586 RMD160 2a4e777b3f2329cb7cf00f30cea7e48187b37efb SHA1 29d6306e958f94c85859e560ac2d74b891043d6b SHA256 e6205f5b4576fd15129081e9730d35d1cb8e88a27c57df18d2ef93b37c43550c
 DIST xia2-0.3.1.0.tar.bz2 3389906 RMD160 da2b84535e418c266c316a6fce40dd57b1fb6adc SHA1 ded8f83026af9d44053cb17c91fc6130d63d6777 SHA256 32f1866bc17b093cbf157ec7bc217e47d059957104b20c88ed1b5c3706fc7e28
 DIST xia2-0.3.1.6.tar.bz2 3464982 RMD160 960e61db2d832e9fa930ec975b7a642674b8b5a3 SHA1 878854f593671468f67e96b97438bbe701683505 SHA256 fde814a763e6666a1618d01569c19d574f1bf71d754dc3960beeb13c35dd201f
+DIST xia2-0.3.1.7.tar.bz2 3650285 RMD160 1cf5c3bb0fa452092b2244885a3822dabe7caf08 SHA1 0934def0fad457e6b7e91fe7cef0eb7bdf80bee7 SHA256 54beb26396c4b6ecb343544c777c2505238385f2127482d035d2c47b24a7fcf1
 EBUILD xia2-0.3.1.0.ebuild 1470 RMD160 b97c2b93826b4cf467c34a1924ad53e59b5af43b SHA1 b042d3ef02d9bb916d6edc0dc7dabd4947a5e534 SHA256 ebd563e52c5e9be399f0e2a88f94581db5f4fd9e385d3521fc269b6335bcf63c
 EBUILD xia2-0.3.1.6.ebuild 1608 RMD160 0bac3326e5a84c30e1f93e36d0f772c10e7b7478 SHA1 cd69c94ecd21541220a1dec3d5f9bd5ff38e5ceb SHA256 5c0c63aaeac6a3f2411f1c9008a843e3ac4999df71f81d4c81b12fc4afe88b8d
-MISC ChangeLog 670 RMD160 bbe68b68860ab9fe3ebd6ec6622e0f843a3f11c6 SHA1 d66eb438dd8156218da525fdd38d2558d88e0cf4 SHA256 319788d84f5317d67c7245d4adaaf2d8205168059428ed8eaaa13048a16cea80
+EBUILD xia2-0.3.1.7.ebuild 1608 RMD160 6682085284e291bfd1a635e592d4ce608bf4ae2e SHA1 d421143a054731b2632e8d51dba4b0865cf41ee7 SHA256 013cba3663771d82302fcaae2ff23052ae90f1c2f576196b723a2a08003c3685
+MISC ChangeLog 819 RMD160 8ea41eefc03cbad726ca5b2e2f10e66ed53e53de SHA1 0b602147a1f74c2e1f89f3605e7fd196f9730108 SHA256 063bdadd99f260e8d764c96c8a149360905cd5c5a26ac684e80e4cd64ae964c9
 MISC metadata.xml 215 RMD160 bc9c07aa91f2f175542244e4e4522a73558210a1 SHA1 facb283386de1c0b6b938cdcd4dde04d1694298b SHA256 13f32353652adbd3d934d41381cfc2cacc9e1127c508cebc73806cc1026ee80c
 -----BEGIN PGP SIGNATURE-----
-Version: GnuPG v2.0.14 (GNU/Linux)
+Version: GnuPG v2.0.15 (GNU/Linux)
 
-iEYEARECAAYFAkvQsMkACgkQgAnW8HDreRZ2jgCfXEYzRlsR7D78gDehyryTK8DU
-6l8AoJCOWC43SACl7Ago3DhTFdMtCL8F
-=5Ehl
+iEYEARECAAYFAkxPLCwACgkQgAnW8HDreRaJlQCghA1uwnimk9OG4zSjv2lIoKXA
+xPMAnjwJ9cRkrAk0ti3KPYEFF3S0Bc0R
+=qBVH
 -----END PGP SIGNATURE-----
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
+}