Version BUmp

Package-Manager: portage-2.2.0_alpha41/cvs/Linux x86_64

8 files changed, 165 insertions, 18 deletions

diff --git a/sci-chemistry/xia2/ChangeLog b/sci-chemistry/xia2/ChangeLog
index ef0bb4caf80d..318c7114b50b 100644
--- a/sci-chemistry/xia2/ChangeLog
+++ b/sci-chemistry/xia2/ChangeLog
@@ -1,6 +1,13 @@
 # ChangeLog for sci-chemistry/xia2
 # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/xia2/ChangeLog,v 1.5 2011/01/16 12:22:44 xarthisius Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/xia2/ChangeLog,v 1.6 2011/06/25 18:02:55 jlec Exp $
+
+*xia2-0.3.3.1 (25 Jun 2011)
+
+  25 Jun 2011; Justin Lecher <jlec@gentoo.org> +files/0.3.3.1-fix-syntax.patch,
+  xia2-0.3.1.0.ebuild, xia2-0.3.1.6.ebuild, xia2-0.3.1.7.ebuild,
+  +xia2-0.3.3.1.ebuild, metadata.xml:
+  Version BUmp
 
   16 Jan 2011; Kacper Kowalik <xarthisius@gentoo.org> xia2-0.3.1.7.ebuild:
   marked ~ppc wrt #303931
diff --git a/sci-chemistry/xia2/Manifest b/sci-chemistry/xia2/Manifest
index 7eb9efea9fd2..2a64a9da8162 100644
--- a/sci-chemistry/xia2/Manifest
+++ b/sci-chemistry/xia2/Manifest
@@ -1,11 +1,24 @@
+-----BEGIN PGP SIGNED MESSAGE-----
+Hash: SHA256
+
 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
+AUX 0.3.3.1-fix-syntax.patch 2586 RMD160 84e78d31b120c8d046229547207931af6f23a9cb SHA1 185b3a14a6d83f7a5838a8798f4d0b1b930b8076 SHA256 9d86fa8c210180d857b5cbf56226f1260ab8071e6ea9b69850da0e4357b7a7c1
 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
-EBUILD xia2-0.3.1.7.ebuild 1619 RMD160 2f03ea2c21962abfdd49823558d4a8f289495f0e SHA1 d4e3a40d2da4fb930394fb726643311a9933c690 SHA256 8d87732bbcae3400add4233c86ac0b6d1fe13d5714bb9f3d2860f80a0a4a3dd5
-MISC ChangeLog 927 RMD160 74e7e807e53a2e86828aca2ca42b60157ee1bbd6 SHA1 8e7879c93920c3aa64986f27ad557d1b9d89aff1 SHA256 b53ee4463fc4303d5de3f380c0774fabe28df8a27cc0c70152bc99bc4117ddef
-MISC metadata.xml 215 RMD160 bc9c07aa91f2f175542244e4e4522a73558210a1 SHA1 facb283386de1c0b6b938cdcd4dde04d1694298b SHA256 13f32353652adbd3d934d41381cfc2cacc9e1127c508cebc73806cc1026ee80c
+DIST xia2-0.3.3.1.tar.bz2 3074989 RMD160 3254833b3c74d223bd28d609daef048d842f1631 SHA1 6351dfd20756986e91aa4503733f990094859495 SHA256 f1bf94cd9305f768fea1b541ac53d66917126e92620263a96f9c23923ec829c4
+EBUILD xia2-0.3.1.0.ebuild 1472 RMD160 8d067c6e63f57450c915cbfebb06cb0a760535cb SHA1 a4d46b065857aacdf31bbe31cbc1a7424a15407e SHA256 4ee091c07ff6581d10c7616d6c2bfc192f3d1a11e4427da22b306e582ea5df15
+EBUILD xia2-0.3.1.6.ebuild 1610 RMD160 8efc646fab2d780edf7f5a27a47a80c6276874c7 SHA1 acd7737087e69aea0a214bcfc7e195c851e107eb SHA256 4e5419fbe010169049c95809907a11ce55eb080aae73dafe093274f005b63f14
+EBUILD xia2-0.3.1.7.ebuild 1615 RMD160 3acf9c7d16a3f8afbab1a3a18d3201ae8231edd6 SHA1 dd6cdae475851a7e9364d1d9ecbcebc080bdab19 SHA256 5047947052acf654637ebe1d2a1e0ce32f1df329381e2cc9d21e840a82fe35bb
+EBUILD xia2-0.3.3.1.ebuild 1615 RMD160 0b85a4d66a675651812381909e50e5c2b7b960cc SHA1 737a8829054581a92a354802e013d47d5e350741 SHA256 d99088106d565664594aaa1e781650edf97c71865db359bcb61d06e972701281
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+MISC metadata.xml 218 RMD160 5dcdfc9ffbff78c3625f6ee6cd8242c0130bba48 SHA1 e7d6721263f31430e0dd04b17f16c27ebac78a89 SHA256 45420c665fb7a061ce85d5300ea7ed5a034a812dc286e2c87540b90d1388d79d
+-----BEGIN PGP SIGNATURE-----
+Version: GnuPG v2.0.17 (GNU/Linux)
+
+iEYEAREIAAYFAk4GItQACgkQgAnW8HDreRYE4wCeKhq0L1Lsw+MgtIily9HMxvrZ
+G1IAoM2iEAiZB2HXJJ71fcTKXJ9bRzCW
+=3nEm
+-----END PGP SIGNATURE-----
diff --git a/sci-chemistry/xia2/files/0.3.3.1-fix-syntax.patch b/sci-chemistry/xia2/files/0.3.3.1-fix-syntax.patch
new file mode 100644
index 000000000000..36cf6bb60d1d
--- /dev/null
+++ b/sci-chemistry/xia2/files/0.3.3.1-fix-syntax.patch
@@ -0,0 +1,61 @@
+diff --git a/xia2-0.3.3.0/Applications/xia2find.py b/xia2-0.3.3.0/Applications/xia2find.py
+index 1a3b0e2..e0b8a1e 100755
+--- a/xia2-0.3.3.1/Applications/xia2find.py
++++ b/xia2-0.3.3.1/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/xia2-0.3.3.0/Experts/DRStrategyExpert.py b/xia2-0.3.3.0/Experts/DRStrategyExpert.py
+index 28b1dc3..dba3ef7 100644
+--- a/xia2-0.3.3.1/Experts/DRStrategyExpert.py
++++ b/xia2-0.3.3.1/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-0.3.3.0/Python/Examples/CCP4/Cad.py b/xia2core-0.3.3.0/Python/Examples/CCP4/Cad.py
+index 88f9218..5fb6f2a 100644
+--- a/xia2core-0.3.3.1/Python/Examples/CCP4/Cad.py
++++ b/xia2core-0.3.3.1/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/metadata.xml b/sci-chemistry/xia2/metadata.xml
index efb490d78817..d747d72a25b4 100644
--- a/sci-chemistry/xia2/metadata.xml
+++ b/sci-chemistry/xia2/metadata.xml
@@ -1,8 +1,8 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
 <pkgmetadata>
-<herd>sci</herd>
-<maintainer>
-  <email>sci@gentoo.org</email>
-</maintainer>
+	<herd>sci</herd>
+	<maintainer>
+		<email>sci@gentoo.org</email>
+	</maintainer>
 </pkgmetadata>
diff --git a/sci-chemistry/xia2/xia2-0.3.1.0.ebuild b/sci-chemistry/xia2/xia2-0.3.1.0.ebuild
index 276c76ae4ffa..62cb9f7baa88 100644
--- a/sci-chemistry/xia2/xia2-0.3.1.0.ebuild
+++ b/sci-chemistry/xia2/xia2-0.3.1.0.ebuild
@@ -1,13 +1,13 @@
-# Copyright 1999-2010 Gentoo Foundation
+# Copyright 1999-2011 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/xia2/xia2-0.3.1.0.ebuild,v 1.1 2010/02/06 23:36:47 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/xia2/xia2-0.3.1.0.ebuild,v 1.2 2011/06/25 18:02:55 jlec Exp $
 
 EAPI="3"
 
 inherit eutils python
 
 DESCRIPTION="An automated data reduction system for crystallography"
-HOMEPAGE="http://www.xia2.org/xia/"
+HOMEPAGE="http://www.ccp4.ac.uk/xia/"
 SRC_URI="http://www.ccp4.ac.uk/${PN}/${P}.tar.bz2"
 
 LICENSE="BSD"
diff --git a/sci-chemistry/xia2/xia2-0.3.1.6.ebuild b/sci-chemistry/xia2/xia2-0.3.1.6.ebuild
index 96afaa7a87bc..2808afc7f4f6 100644
--- a/sci-chemistry/xia2/xia2-0.3.1.6.ebuild
+++ b/sci-chemistry/xia2/xia2-0.3.1.6.ebuild
@@ -1,6 +1,6 @@
-# Copyright 1999-2010 Gentoo Foundation
+# Copyright 1999-2011 Gentoo Foundation
 # Distributed under the terms of the GNU General Public License v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/xia2/xia2-0.3.1.6.ebuild,v 1.3 2010/04/22 20:25:40 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/xia2/xia2-0.3.1.6.ebuild,v 1.4 2011/06/25 18:02:55 jlec Exp $
 
 EAPI="3"
 
@@ -9,7 +9,7 @@ PYTHON_DEPEND="2"
 inherit eutils python
 
 DESCRIPTION="An automated data reduction system for crystallography"
-HOMEPAGE="http://www.xia2.org/xia/"
+HOMEPAGE="http://www.ccp4.ac.uk/xia/"
 SRC_URI="http://www.ccp4.ac.uk/${PN}/${P}.tar.bz2"
 
 LICENSE="BSD"
diff --git a/sci-chemistry/xia2/xia2-0.3.1.7.ebuild b/sci-chemistry/xia2/xia2-0.3.1.7.ebuild
index ded77c0aa1d1..423b8bea8c7d 100644
--- a/sci-chemistry/xia2/xia2-0.3.1.7.ebuild
+++ b/sci-chemistry/xia2/xia2-0.3.1.7.ebuild
@@ -1,6 +1,6 @@
 # Copyright 1999-2011 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 1.2 2011/01/16 12:22:44 xarthisius Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/xia2/xia2-0.3.1.7.ebuild,v 1.3 2011/06/25 18:02:55 jlec Exp $
 
 EAPI="3"
 
@@ -9,7 +9,7 @@ PYTHON_DEPEND="2"
 inherit eutils python
 
 DESCRIPTION="An automated data reduction system for crystallography"
-HOMEPAGE="http://www.xia2.org/xia/"
+HOMEPAGE="http://www.ccp4.ac.uk/xia/"
 SRC_URI="http://www.ccp4.ac.uk/${PN}/${P}.tar.bz2"
 
 LICENSE="BSD"
diff --git a/sci-chemistry/xia2/xia2-0.3.3.1.ebuild b/sci-chemistry/xia2/xia2-0.3.3.1.ebuild
new file mode 100644
index 000000000000..da04ad976c3d
--- /dev/null
+++ b/sci-chemistry/xia2/xia2-0.3.3.1.ebuild
@@ -0,0 +1,66 @@
+# Copyright 1999-2011 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/xia2/xia2-0.3.3.1.ebuild,v 1.1 2011/06/25 18:02:55 jlec Exp $
+
+EAPI="3"
+
+PYTHON_DEPEND="2"
+
+inherit eutils python
+
+DESCRIPTION="An automated data reduction system for crystallography"
+HOMEPAGE="http://www.ccp4.ac.uk/xia/"
+SRC_URI="http://www.ccp4.ac.uk/${PN}/${P}.tar.bz2"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~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
+}