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authorJustin Lecher <jlec@gentoo.org>2015-10-26 08:29:56 +0100
committerJustin Lecher <jlec@gentoo.org>2015-10-26 08:32:25 +0100
commit7d62034735e700ca67e977470d79f5571b15b221 (patch)
tree78d45bafd1284caf0c06b4b98131677301303cbb /sci-chemistry/xia2/files
parentadd co-maintainer Coacher to metadata (diff)
downloadgentoo-7d62034735e700ca67e977470d79f5571b15b221.tar.gz
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gentoo-7d62034735e700ca67e977470d79f5571b15b221.zip
Drop "CCP4: Software for Macromolecular Crystallography"
obsoletes: Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=160190 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=324059 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=332485 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=367771 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=367773 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=383227 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=448756 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=460502 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=460504 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=466936 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=467040 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=467048 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=476580 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=478580 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=478586 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=478588 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=478594 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=478604 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=521646 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=528512 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=530878 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=540760 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=555614 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=556498 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=557038 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=561196 Gentoo-Bug: https://bugs.gentoo.org/show_bug.cgi?id=562780 Signed-off-by: Justin Lecher <jlec@gentoo.org>
Diffstat (limited to 'sci-chemistry/xia2/files')
-rw-r--r--sci-chemistry/xia2/files/0.3.1.0-fix-syntax.patch61
-rw-r--r--sci-chemistry/xia2/files/0.3.1.6-fix-syntax.patch61
-rw-r--r--sci-chemistry/xia2/files/0.3.1.7-fix-syntax.patch61
-rw-r--r--sci-chemistry/xia2/files/0.3.3.1-fix-syntax.patch61
-rw-r--r--sci-chemistry/xia2/files/0.3.3.3-fix-syntax.patch28
-rw-r--r--sci-chemistry/xia2/files/0.3.4.0-fix-syntax.patch28
6 files changed, 0 insertions, 300 deletions
diff --git a/sci-chemistry/xia2/files/0.3.1.0-fix-syntax.patch b/sci-chemistry/xia2/files/0.3.1.0-fix-syntax.patch
deleted file mode 100644
index 9d92af7e33ce..000000000000
--- a/sci-chemistry/xia2/files/0.3.1.0-fix-syntax.patch
+++ /dev/null
@@ -1,61 +0,0 @@
-diff --git a/xia2-0.3.1.0/Applications/xia2find.py b/xia2-0.3.1.0/Applications/xia2find.py
-index 1a3b0e2..e0b8a1e 100755
---- a/xia2-0.3.1.0/Applications/xia2find.py
-+++ b/xia2-0.3.1.0/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/xia2-0.3.1.0/Experts/DRStrategyExpert.py b/xia2-0.3.1.0/Experts/DRStrategyExpert.py
-index 28b1dc3..dba3ef7 100644
---- a/xia2-0.3.1.0/Experts/DRStrategyExpert.py
-+++ b/xia2-0.3.1.0/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-0.3.1.0/Python/Examples/CCP4/Cad.py b/xia2core-0.3.1.0/Python/Examples/CCP4/Cad.py
-index 88f9218..5fb6f2a 100644
---- a/xia2core-0.3.1.0/Python/Examples/CCP4/Cad.py
-+++ b/xia2core-0.3.1.0/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/files/0.3.1.6-fix-syntax.patch b/sci-chemistry/xia2/files/0.3.1.6-fix-syntax.patch
deleted file mode 100644
index 7770a53c4451..000000000000
--- a/sci-chemistry/xia2/files/0.3.1.6-fix-syntax.patch
+++ /dev/null
@@ -1,61 +0,0 @@
-diff --git a/xia2-0.3.1.6/Applications/xia2find.py b/xia2-0.3.1.6/Applications/xia2find.py
-index 1a3b0e2..e0b8a1e 100755
---- a/xia2-0.3.1.6/Applications/xia2find.py
-+++ b/xia2-0.3.1.6/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/xia2-0.3.1.6/Experts/DRStrategyExpert.py b/xia2-0.3.1.6/Experts/DRStrategyExpert.py
-index 28b1dc3..dba3ef7 100644
---- a/xia2-0.3.1.6/Experts/DRStrategyExpert.py
-+++ b/xia2-0.3.1.6/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-0.3.1.6/Python/Examples/CCP4/Cad.py b/xia2core-0.3.1.6/Python/Examples/CCP4/Cad.py
-index 88f9218..5fb6f2a 100644
---- a/xia2core-0.3.1.6/Python/Examples/CCP4/Cad.py
-+++ b/xia2core-0.3.1.6/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/files/0.3.1.7-fix-syntax.patch b/sci-chemistry/xia2/files/0.3.1.7-fix-syntax.patch
deleted file mode 100644
index ec8ada48aad1..000000000000
--- a/sci-chemistry/xia2/files/0.3.1.7-fix-syntax.patch
+++ /dev/null
@@ -1,61 +0,0 @@
-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/files/0.3.3.1-fix-syntax.patch b/sci-chemistry/xia2/files/0.3.3.1-fix-syntax.patch
deleted file mode 100644
index 36cf6bb60d1d..000000000000
--- a/sci-chemistry/xia2/files/0.3.3.1-fix-syntax.patch
+++ /dev/null
@@ -1,61 +0,0 @@
-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/files/0.3.3.3-fix-syntax.patch b/sci-chemistry/xia2/files/0.3.3.3-fix-syntax.patch
deleted file mode 100644
index 53cacbb5c681..000000000000
--- a/sci-chemistry/xia2/files/0.3.3.3-fix-syntax.patch
+++ /dev/null
@@ -1,28 +0,0 @@
-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/xia2-0.3.3.3/Applications/xia2find.py
-+++ b/xia2-0.3.3.3/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/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-0.3.3.3/Python/Examples/CCP4/Cad.py
-+++ b/xia2core-0.3.3.3/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/files/0.3.4.0-fix-syntax.patch b/sci-chemistry/xia2/files/0.3.4.0-fix-syntax.patch
deleted file mode 100644
index 9ba4c94495ea..000000000000
--- a/sci-chemistry/xia2/files/0.3.4.0-fix-syntax.patch
+++ /dev/null
@@ -1,28 +0,0 @@
-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/xia2-0.3.4.0/Applications/xia2find.py
-+++ b/xia2-0.3.4.0/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/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-0.3.4.0/Python/Examples/CCP4/Cad.py
-+++ b/xia2core-0.3.4.0/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()
-