r22181 - in /trunk: lib/errors.py lib/warnings.py relax.py status.py

[tlinnet]

Author: tlinnet
Date: Fri Feb 14 10:32:15 2014
New Revision: 22181

URL: http://svn.gna.org/viewcvs/relax?rev=22181view=rev
Log:
Shifted the pedantic flag to escalate flag. The option -p would insted be used 
for the option --prompt.

Fix for sr #3117, (https://gna.org/support/?3117) - Functionality to inspect 
interactively after running script - The equivalence to python -i

Modified:
trunk/lib/errors.py
trunk/lib/warnings.py
trunk/relax.py
trunk/status.py

Modified: trunk/lib/errors.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/lib/errors.py?rev=22181r1=22180r2=22181view=diff
==
--- trunk/lib/errors.py (original)
+++ trunk/lib/errors.py Fri Feb 14 10:32:15 2014
@@ -131,9 +131,9 @@
 def __str__(self):
 Modify the behaviour of the error system.
 
-# Save the state if the pedantic flag is turned on.
+# Save the state if the escalate flag is turned on.
 from status import Status; status = Status()
-if status.pedantic:
+if status.escalate:
 save_state()
 
 # Modify the error message to include 'RelaxError' at the start (using 
coloured text if a TTY).

Modified: trunk/lib/warnings.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/lib/warnings.py?rev=22181r1=22180r2=22181view=diff
==
--- trunk/lib/warnings.py (original)
+++ trunk/lib/warnings.py Fri Feb 14 10:32:15 2014
@@ -39,8 +39,8 @@
 # Add the text 'RelaxWarning: ' to the start of the warning message.
 message = RelaxWarning: %s\n % message
 
-# Print stack-trace in pedantic mode.
-if status.pedantic:
+# Print stack-trace in escalate mode.
+if status.escalate:
 tb = 
 for frame in inspect.stack()[4:]:
 file = frame[1]
@@ -77,7 +77,7 @@
 warnings.formatwarning = format
 
 # Set warning filters.
-if status.pedantic:
+if status.escalate:
 warnings.filterwarnings('error', category=BaseWarning)
 else:
 warnings.filterwarnings('always', category=BaseWarning)

Modified: trunk/relax.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/relax.py?rev=22181r1=22180r2=22181view=diff
==
--- trunk/relax.py (original)
+++ trunk/relax.py Fri Feb 14 10:32:15 2014
@@ -279,7 +279,7 @@
 parser.add_option('--licence', action='store_true', dest='licence', 
default=0, help='display the licence')
 parser.add_option('-t', '--tee', action='store', type='string', 
dest='tee', help='tee relax output to stdout and the file LOG_FILE', 
metavar='LOG_FILE')
 parser.add_option('-g', '--gui', action='store_true', dest='gui', 
default=0, help='launch the relax GUI')
-parser.add_option('-p', '--pedantic', action='store_true', 
dest='pedantic', default=0, help='escalate all warnings to errors')
+parser.add_option('-e', '--escalate', action='store_true', 
dest='escalate', default=0, help='escalate all warnings to errors')
 parser.add_option('--test', action='store_true', dest='test', 
default=0, help='run relax in test mode')
 parser.add_option('-x', '--test-suite', action='store_true', 
dest='test_suite', default=0, help='execute the relax test suite')
 parser.add_option('-s', '--system-tests', action='store_true', 
dest='system_tests', default=0, help='execute the relax system/functional tests 
(part of the test suite)')
@@ -301,9 +301,9 @@
 if options.numpy_raise:
 numpy.seterr(all='raise')
 
-# Pedantic flag.
-if options.pedantic:
-status.pedantic = True
+# escalate flag.
+if options.escalate:
+status.escalate = True
 
 # Logging.
 if options.log:

Modified: trunk/status.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/status.py?rev=22181r1=22180r2=22181view=diff
==
--- trunk/status.py (original)
+++ trunk/status.py Fri Feb 14 10:32:15 2014
@@ -51,7 +51,7 @@
 
 # Initialise some variables.
 self._instance.debug = False
-self._instance.pedantic = False
+self._instance.escalate = False
 self._instance.test_mode = False
 self._instance.uf_intro = False
 self._instance.show_gui = False


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r22182 - in /trunk: relax.py status.py

[tlinnet]

Author: tlinnet
Date: Fri Feb 14 10:32:17 2014
New Revision: 22182

URL: http://svn.gna.org/viewcvs/relax?rev=22182view=rev
Log:
Added the -p --prompt option for running a relax script and inspect 
interactively.

Fix for sr #3117, (https://gna.org/support/?3117) - Functionality to inspect 
interactively after running script - The equivalence to python -i

Modified:
trunk/relax.py
trunk/status.py

Modified: trunk/relax.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/relax.py?rev=22182r1=22181r2=22182view=diff
==
--- trunk/relax.py (original)
+++ trunk/relax.py Fri Feb 14 10:32:17 2014
@@ -280,6 +280,7 @@
 parser.add_option('-t', '--tee', action='store', type='string', 
dest='tee', help='tee relax output to stdout and the file LOG_FILE', 
metavar='LOG_FILE')
 parser.add_option('-g', '--gui', action='store_true', dest='gui', 
default=0, help='launch the relax GUI')
 parser.add_option('-e', '--escalate', action='store_true', 
dest='escalate', default=0, help='escalate all warnings to errors')
+parser.add_option('-p', '--prompt', action='store_true', 
dest='prompt', default=0, help='execute the given script and continue into the 
prompt mode to allow for interactive inspection')
 parser.add_option('--test', action='store_true', dest='test', 
default=0, help='run relax in test mode')
 parser.add_option('-x', '--test-suite', action='store_true', 
dest='test_suite', default=0, help='execute the relax test suite')
 parser.add_option('-s', '--system-tests', action='store_true', 
dest='system_tests', default=0, help='execute the relax system/functional tests 
(part of the test suite)')
@@ -305,6 +306,10 @@
 if options.escalate:
 status.escalate = True
 
+# Script prompt interactive inspection flag.
+if options.prompt:
+status.prompt = True
+
 # Logging.
 if options.log:
 # Exclusive modes.

Modified: trunk/status.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/status.py?rev=22182r1=22181r2=22182view=diff
==
--- trunk/status.py (original)
+++ trunk/status.py Fri Feb 14 10:32:17 2014
@@ -52,6 +52,7 @@
 # Initialise some variables.
 self._instance.debug = False
 self._instance.escalate = False
+self._instance.prompt = False
 self._instance.test_mode = False
 self._instance.uf_intro = False
 self._instance.show_gui = False


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r22183 - /trunk/prompt/interpreter.py

[tlinnet]

Author: tlinnet
Date: Fri Feb 14 11:22:56 2014
New Revision: 22183

URL: http://svn.gna.org/viewcvs/relax?rev=22183view=rev
Log:
Second

Modified:
trunk/prompt/interpreter.py

Modified: trunk/prompt/interpreter.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/prompt/interpreter.py?rev=22183r1=22182r2=22183view=diff
==
--- trunk/prompt/interpreter.py (original)
+++ trunk/prompt/interpreter.py Fri Feb 14 11:22:56 2014
@@ -266,12 +266,16 @@
 readline.parse_and_bind(tab: complete)
 
 # Execute the script file if given.
-if script_file:
+if script_file and not status.prompt:
 # Turn on the user function intro flag.
 status.uf_intro = True
 
 # Run the script.
 return run_script(intro=self.__intro_string, local=locals(), 
script_file=script_file, show_script=self.__show_script, 
raise_relax_error=self.__raise_relax_error)
+
+if script_file and status.prompt:
+run_script(intro=self.__intro_string, local=locals(), 
script_file=script_file, show_script=self.__show_script, 
raise_relax_error=self.__raise_relax_error)
+prompt(intro=None, local=locals())
 
 # Go to the prompt.
 else:
@@ -333,12 +337,13 @@
 sys.path.reverse()
 
 # Execute the script as a module.
-if dep_check.runpy_module:
-runpy.run_module(module, globals)
+#if dep_check.runpy_module:
+#runpy.run_module(module, globals)
 
 # Allow scripts to run under Python = 2.4.
-else:
-exec(compile(open(name).read(), name, 'exec'), globals)
+#else:
+#exec(compile(open(name).read(), name, 'exec'), globals)
+exec(compile(open(name).read(), name, 'exec'), globals)
 
 finally:
 # Switch back to the original working directory.


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r22184 - in /trunk: prompt/interpreter.py relax.py

[tlinnet]

Author: tlinnet
Date: Fri Feb 14 11:22:57 2014
New Revision: 22184

URL: http://svn.gna.org/viewcvs/relax?rev=22184view=rev
Log:
Modified the help text to explain that -p will launch relax in prompt mode 
after running any optionally supplied scripts.

Fix for sr #3117, (https://gna.org/support/?3117) - Functionality to inspect 
interactively after running script - The equivalence to python -i

This is to allow the -p --prompt option to be given without a script. relax 
should support this so that a user doesn't get too confused when
trying to start in prompt mode with the --prompt flag and support the --prompt 
argument without a script being supplied.

Modified:
trunk/prompt/interpreter.py
trunk/relax.py

Modified: trunk/prompt/interpreter.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/prompt/interpreter.py?rev=22184r1=22183r2=22184view=diff
==
--- trunk/prompt/interpreter.py (original)
+++ trunk/prompt/interpreter.py Fri Feb 14 11:22:57 2014
@@ -336,14 +336,18 @@
 # Reverse the system path so that the script path is first.
 sys.path.reverse()
 
-# Execute the script as a module.
-#if dep_check.runpy_module:
-#runpy.run_module(module, globals)
+# Execute the script as a module if the inspect interactively prompt 
flag is not true.
+if dep_check.runpy_module and not status.prompt:
+runpy.run_module(module, globals)
+
+# Execute the script as a module if the inspect interactively prompt 
flag is not true.
+elif dep_check.runpy_module and not status.prompt:
+runpy.run_module(module, globals)
 
 # Allow scripts to run under Python = 2.4.
-#else:
-#exec(compile(open(name).read(), name, 'exec'), globals)
-exec(compile(open(name).read(), name, 'exec'), globals)
+else:
+exec(compile(open(name).read(), name, 'exec'), globals)
+
 
 finally:
 # Switch back to the original working directory.

Modified: trunk/relax.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/relax.py?rev=22184r1=22183r2=22184view=diff
==
--- trunk/relax.py (original)
+++ trunk/relax.py Fri Feb 14 11:22:57 2014
@@ -215,7 +215,7 @@
 # Only import the module in the test modes (to improve program 
start up speeds).
 from test_suite.test_suite_runner import Test_suite_runner
 
-# Load the interpreter and turn intros on.
+# Load the interpreter and turn intros on.launch relax in prompt 
mode after running any optionally supplied scripts
 self.interpreter = interpreter.Interpreter(show_script=False, 
raise_relax_error=True)
 self.interpreter.on()
 
@@ -280,7 +280,7 @@
 parser.add_option('-t', '--tee', action='store', type='string', 
dest='tee', help='tee relax output to stdout and the file LOG_FILE', 
metavar='LOG_FILE')
 parser.add_option('-g', '--gui', action='store_true', dest='gui', 
default=0, help='launch the relax GUI')
 parser.add_option('-e', '--escalate', action='store_true', 
dest='escalate', default=0, help='escalate all warnings to errors')
-parser.add_option('-p', '--prompt', action='store_true', 
dest='prompt', default=0, help='execute the given script and continue into the 
prompt mode to allow for interactive inspection')
+parser.add_option('-p', '--prompt', action='store_true', 
dest='prompt', default=0, help='launch relax in prompt mode after running any 
optionally supplied scripts')
 parser.add_option('--test', action='store_true', dest='test', 
default=0, help='run relax in test mode')
 parser.add_option('-x', '--test-suite', action='store_true', 
dest='test_suite', default=0, help='execute the relax test suite')
 parser.add_option('-s', '--system-tests', action='store_true', 
dest='system_tests', default=0, help='execute the relax system/functional tests 
(part of the test suite)')


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r22185 - in /trunk: prompt/interpreter.py relax.py

[tlinnet]

Author: tlinnet
Date: Fri Feb 14 11:47:33 2014
New Revision: 22185

URL: http://svn.gna.org/viewcvs/relax?rev=22185view=rev
Log:
Manually reverted the temporary change of r22184 and 22183.

The command used was:

svn merge -r22184:r22182 .

.
r22184 | tlinnet | 2014-02-14 11:22:57 +0100 (Fri, 14 Feb 2014) | 6 lines

Modified the help text to explain that -p will launch relax in prompt mode 
after running any optionally supplied scripts.

Fix for sr #3117, (https://gna.org/support/?3117) - Functionality to inspect 
interactively after running script - The equivalence to python -i

This is to allow the -p --prompt option to be given without a script. relax 
should support this so that a user doesn't get too confused when
trying to start in prompt mode with the --prompt flag and support the --prompt 
argument without a script being supplied.

r22183 | tlinnet | 2014-02-14 11:22:56 +0100 (Fri, 14 Feb 2014) | 1 line

Second
.


Modified:
trunk/prompt/interpreter.py
trunk/relax.py

Modified: trunk/prompt/interpreter.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/prompt/interpreter.py?rev=22185r1=22184r2=22185view=diff
==
--- trunk/prompt/interpreter.py (original)
+++ trunk/prompt/interpreter.py Fri Feb 14 11:47:33 2014
@@ -266,16 +266,12 @@
 readline.parse_and_bind(tab: complete)
 
 # Execute the script file if given.
-if script_file and not status.prompt:
+if script_file:
 # Turn on the user function intro flag.
 status.uf_intro = True
 
 # Run the script.
 return run_script(intro=self.__intro_string, local=locals(), 
script_file=script_file, show_script=self.__show_script, 
raise_relax_error=self.__raise_relax_error)
-
-if script_file and status.prompt:
-run_script(intro=self.__intro_string, local=locals(), 
script_file=script_file, show_script=self.__show_script, 
raise_relax_error=self.__raise_relax_error)
-prompt(intro=None, local=locals())
 
 # Go to the prompt.
 else:
@@ -336,18 +332,13 @@
 # Reverse the system path so that the script path is first.
 sys.path.reverse()
 
-# Execute the script as a module if the inspect interactively prompt 
flag is not true.
-if dep_check.runpy_module and not status.prompt:
+# Execute the script as a module.
+if dep_check.runpy_module:
 runpy.run_module(module, globals)
 
-# Execute the script as a module if the inspect interactively prompt 
flag is not true.
-elif dep_check.runpy_module and not status.prompt:
-runpy.run_module(module, globals)
-
 # Allow scripts to run under Python = 2.4.
 else:
 exec(compile(open(name).read(), name, 'exec'), globals)
-
 
 finally:
 # Switch back to the original working directory.

Modified: trunk/relax.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/relax.py?rev=22185r1=22184r2=22185view=diff
==
--- trunk/relax.py (original)
+++ trunk/relax.py Fri Feb 14 11:47:33 2014
@@ -215,7 +215,7 @@
 # Only import the module in the test modes (to improve program 
start up speeds).
 from test_suite.test_suite_runner import Test_suite_runner
 
-# Load the interpreter and turn intros on.launch relax in prompt 
mode after running any optionally supplied scripts
+# Load the interpreter and turn intros on.
 self.interpreter = interpreter.Interpreter(show_script=False, 
raise_relax_error=True)
 self.interpreter.on()
 
@@ -280,7 +280,7 @@
 parser.add_option('-t', '--tee', action='store', type='string', 
dest='tee', help='tee relax output to stdout and the file LOG_FILE', 
metavar='LOG_FILE')
 parser.add_option('-g', '--gui', action='store_true', dest='gui', 
default=0, help='launch the relax GUI')
 parser.add_option('-e', '--escalate', action='store_true', 
dest='escalate', default=0, help='escalate all warnings to errors')
-parser.add_option('-p', '--prompt', action='store_true', 
dest='prompt', default=0, help='launch relax in prompt mode after running any 
optionally supplied scripts')
+parser.add_option('-p', '--prompt', action='store_true', 
dest='prompt', default=0, help='execute the given script and continue into the 
prompt mode to allow for interactive inspection')
 parser.add_option('--test', action='store_true', dest='test', 
default=0, help='run relax in test mode')
 parser.add_option('-x', '--test-suite', action='store_true', 
dest='test_suite', default=0, help='execute the relax test suite')
 parser.add_option('-s', '--system-tests', action='store_true', 
dest='system_tests', default=0, help='execute the relax 

r22186 - /trunk/relax.py

[tlinnet]

Author: tlinnet
Date: Fri Feb 14 11:54:44 2014
New Revision: 22186

URL: http://svn.gna.org/viewcvs/relax?rev=22186view=rev
Log:
Modified the help text to explain that -p will launch relax in prompt mode 
after running any optionally supplied scripts.

Fix for sr #3117, (https://gna.org/support/?3117) - Functionality to inspect 
interactively after running script - The equivalence to python -i

This is to allow the -p --prompt option to be given without a script. relax 
should support this so that a user doesn't get too confused when
trying to start in prompt mode with the --prompt flag and support the --prompt 
argument without a script being supplied.

Modified:
trunk/relax.py

Modified: trunk/relax.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/relax.py?rev=22186r1=22185r2=22186view=diff
==
--- trunk/relax.py (original)
+++ trunk/relax.py Fri Feb 14 11:54:44 2014
@@ -280,7 +280,7 @@
 parser.add_option('-t', '--tee', action='store', type='string', 
dest='tee', help='tee relax output to stdout and the file LOG_FILE', 
metavar='LOG_FILE')
 parser.add_option('-g', '--gui', action='store_true', dest='gui', 
default=0, help='launch the relax GUI')
 parser.add_option('-e', '--escalate', action='store_true', 
dest='escalate', default=0, help='escalate all warnings to errors')
-parser.add_option('-p', '--prompt', action='store_true', 
dest='prompt', default=0, help='execute the given script and continue into the 
prompt mode to allow for interactive inspection')
+parser.add_option('-p', '--prompt', action='store_true', 
dest='prompt', default=0, help='launch relax in prompt mode after running any 
optionally supplied scripts')
 parser.add_option('--test', action='store_true', dest='test', 
default=0, help='run relax in test mode')
 parser.add_option('-x', '--test-suite', action='store_true', 
dest='test_suite', default=0, help='execute the relax test suite')
 parser.add_option('-s', '--system-tests', action='store_true', 
dest='system_tests', default=0, help='execute the relax system/functional tests 
(part of the test suite)')


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r22187 - /trunk/prompt/interpreter.py

[tlinnet]

Author: tlinnet
Date: Fri Feb 14 12:13:05 2014
New Revision: 22187

URL: http://svn.gna.org/viewcvs/relax?rev=22187view=rev
Log:
Finished implementing the functionality of interacting with variables after 
executing a script.

Fix for sr #3117, (https://gna.org/support/?3117) - Functionality to inspect 
interactively after running script - The equivalence to python -i

For getting access to variables after executing a script, the variable should 
be saved under: cdp.X, where X define a container.
The name space issue is discussed in: 
http://thread.gmane.org/gmane.science.nmr.relax.devel/5012

Modified:
trunk/prompt/interpreter.py

Modified: trunk/prompt/interpreter.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/prompt/interpreter.py?rev=22187r1=22186r2=22187view=diff
==
--- trunk/prompt/interpreter.py (original)
+++ trunk/prompt/interpreter.py Fri Feb 14 12:13:05 2014
@@ -266,12 +266,17 @@
 readline.parse_and_bind(tab: complete)
 
 # Execute the script file if given.
-if script_file:
+if script_file and not status.prompt:
 # Turn on the user function intro flag.
 status.uf_intro = True
 
 # Run the script.
 return run_script(intro=self.__intro_string, local=locals(), 
script_file=script_file, show_script=self.__show_script, 
raise_relax_error=self.__raise_relax_error)
+
+# Execute the script and go into prompt if the interactive flag -p 
--prompt is given at startup.
+if script_file and status.prompt:
+run_script(intro=self.__intro_string, local=locals(), 
script_file=script_file, show_script=self.__show_script, 
raise_relax_error=self.__raise_relax_error)
+prompt(intro=None, local=locals())
 
 # Go to the prompt.
 else:


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r22188 - /trunk/prompt/interpreter.py

[tlinnet]

Author: tlinnet
Date: Fri Feb 14 12:28:25 2014
New Revision: 22188

URL: http://svn.gna.org/viewcvs/relax?rev=22188view=rev
Log:
Added Copyright info to modified file.

Fix for sr #3117, (https://gna.org/support/?3117) - Functionality to inspect 
interactively after running script - The equivalence to python -i

Modified:
trunk/prompt/interpreter.py

Modified: trunk/prompt/interpreter.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/prompt/interpreter.py?rev=22188r1=22187r2=22188view=diff
==
--- trunk/prompt/interpreter.py (original)
+++ trunk/prompt/interpreter.py Fri Feb 14 12:28:25 2014
@@ -1,6 +1,7 @@
 ###
 # #
 # Copyright (C) 2003-2014 Edward d'Auvergne   #
+# Copyright (C) 2014 Troels E. Linnet #
 # #
 # This file is part of the program relax (http://www.nmr-relax.com).  #
 # #


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r22189 - /trunk/relax.py

[edward]

Author: bugman
Date: Fri Feb 14 14:24:25 2014
New Revision: 22189

URL: http://svn.gna.org/viewcvs/relax?rev=22189view=rev
Log:
Organisation of the relax command line options into distinct groups.

This follows from the message at 
http://thread.gmane.org/gmane.science.nmr.relax.devel/5024.

The optparse.OptionGroup object is now used to cluster the arguments.  This 
cleans up the output of
'relax -h' and explains the options to the user in a clearer way.


Modified:
trunk/relax.py

Modified: trunk/relax.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/relax.py?rev=22189r1=22188r2=22189view=diff
==
--- trunk/relax.py (original)
+++ trunk/relax.py Fri Feb 14 14:24:25 2014
@@ -41,7 +41,7 @@
 
 # Python modules.
 import numpy
-from optparse import Option, OptionParser
+from optparse import Option, OptionGroup, OptionParser
 from os import F_OK, access, getpid, putenv
 if dep_check.cprofile_module:
 import cProfile as profile
@@ -273,25 +273,43 @@
 # Parser object.
 parser = RelaxParser(self, usage=usage: %prog [options] 
[script_file])
 
-# Recognised command line options.
-parser.add_option('-d', '--debug', action='store_true', dest='debug', 
default=0, help='enable debugging output')
-parser.add_option('-l', '--log', action='store', type='string', 
dest='log', help='log relax output to the file LOG_FILE', metavar='LOG_FILE')
-parser.add_option('--licence', action='store_true', dest='licence', 
default=0, help='display the licence')
-parser.add_option('-t', '--tee', action='store', type='string', 
dest='tee', help='tee relax output to stdout and the file LOG_FILE', 
metavar='LOG_FILE')
-parser.add_option('-g', '--gui', action='store_true', dest='gui', 
default=0, help='launch the relax GUI')
-parser.add_option('-e', '--escalate', action='store_true', 
dest='escalate', default=0, help='escalate all warnings to errors')
-parser.add_option('-p', '--prompt', action='store_true', 
dest='prompt', default=0, help='launch relax in prompt mode after running any 
optionally supplied scripts')
-parser.add_option('--test', action='store_true', dest='test', 
default=0, help='run relax in test mode')
-parser.add_option('-x', '--test-suite', action='store_true', 
dest='test_suite', default=0, help='execute the relax test suite')
-parser.add_option('-s', '--system-tests', action='store_true', 
dest='system_tests', default=0, help='execute the relax system/functional tests 
(part of the test suite)')
-parser.add_option('-u', '--unit-tests', action='store_true', 
dest='unit_tests', default=0, help='execute the relax unit tests (part of the 
test suite)')
-parser.add_option('--gui-tests', action='store_true', 
dest='gui_tests', default=0, help='execute the relax GUI tests (part of the 
test suite)')
-parser.add_option('--time', action='store_true', dest='tt', default=0, 
help='enable the timing of individual tests in the test suite')
-parser.add_option('-i', '--info', action='store_true', dest='info', 
default=0, help='display information about this version of relax')
-parser.add_option('-v', '--version', action='store_true', 
dest='version', default=0, help='show the version number and exit')
-parser.add_option('-m', '--multi', action='store', type='string', 
dest='multiprocessor', default='uni', help='set multi processor method')
-parser.add_option('-n', '--processors', action='store', type='int', 
dest='n_processors', default=-1, help='set number of processors (may be 
ignored)')
-parser.add_option('--numpy-raise', action='store_true', 
dest='numpy_raise', default=0, help='convert numpy warnings to errors')
+# Recognised command line options for the UI.
+group = OptionGroup(parser, 'UI options')
+group.add_option('-p', '--prompt', action='store_true', dest='prompt', 
default=0, help='launch relax in prompt mode after running any optionally 
supplied scripts')
+group.add_option('-g', '--gui', action='store_true', dest='gui', 
default=0, help='launch the relax GUI')
+group.add_option('-i', '--info', action='store_true', dest='info', 
default=0, help='display information about this version of relax')
+group.add_option('-v', '--version', action='store_true', 
dest='version', default=0, help='show the version number and exit')
+group.add_option('--licence', action='store_true', dest='licence', 
default=0, help='display the licence')
+group.add_option('--test', action='store_true', dest='test', 
default=0, help='run relax in test mode')
+parser.add_option_group(group)
+
+# Recognised command line options for the multiprocessor.
+group = OptionGroup(parser, 'Multi-processor options')
+group.add_option('-m', '--multi', action='store', type='string', 
dest='multiprocessor', default='uni', 

r22190 - in /branches/double_rotor: ./ lib/errors.py lib/warnings.py prompt/interpreter.py relax.py status.py

[edward]

Author: bugman
Date: Fri Feb 14 14:32:41 2014
New Revision: 22190

URL: http://svn.gna.org/viewcvs/relax?rev=22190view=rev
Log:
Merged revisions 22181-22189 via svnmerge from 
svn+ssh://bug...@svn.gna.org/svn/relax/trunk


  r22181 | tlinnet | 2014-02-14 10:32:15 +0100 (Fri, 14 Feb 2014) | 3 lines
  
  Shifted the pedantic flag to escalate flag. The option -p would insted be 
used for the option --prompt.
  
  Fix for sr #3117, (https://gna.org/support/?3117) - Functionality to inspect 
interactively after running script - The equivalence to python -i

  r22182 | tlinnet | 2014-02-14 10:32:17 +0100 (Fri, 14 Feb 2014) | 3 lines
  
  Added the -p --prompt option for running a relax script and inspect 
interactively.
  
  Fix for sr #3117, (https://gna.org/support/?3117) - Functionality to inspect 
interactively after running script - The equivalence to python -i

  r22183 | tlinnet | 2014-02-14 11:22:56 +0100 (Fri, 14 Feb 2014) | 1 line
  
  Second

  r22184 | tlinnet | 2014-02-14 11:22:57 +0100 (Fri, 14 Feb 2014) | 6 lines
  
  Modified the help text to explain that -p will launch relax in prompt mode 
after running any optionally supplied scripts.
  
  Fix for sr #3117, (https://gna.org/support/?3117) - Functionality to inspect 
interactively after running script - The equivalence to python -i
  
  This is to allow the -p --prompt option to be given without a script. relax 
should support this so that a user doesn't get too confused when
  trying to start in prompt mode with the --prompt flag and support the 
--prompt argument without a script being supplied.

  r22185 | tlinnet | 2014-02-14 11:47:33 +0100 (Fri, 14 Feb 2014) | 22 lines
  
  Manually reverted the temporary change of r22184 and 22183.
  
  The command used was:
  
  svn merge -r22184:r22182 .
  
  .
  r22184 | tlinnet | 2014-02-14 11:22:57 +0100 (Fri, 14 Feb 2014) | 6 lines
  
  Modified the help text to explain that -p will launch relax in prompt mode 
after running any optionally supplied scripts.
  
  Fix for sr #3117, (https://gna.org/support/?3117) - Functionality to inspect 
interactively after running script - The equivalence to python -i
  
  This is to allow the -p --prompt option to be given without a script. relax 
should support this so that a user doesn't get too confused when
  trying to start in prompt mode with the --prompt flag and support the 
--prompt argument without a script being supplied.
  
  r22183 | tlinnet | 2014-02-14 11:22:56 +0100 (Fri, 14 Feb 2014) | 1 line
  
  Second
  .

  r22186 | tlinnet | 2014-02-14 11:54:44 +0100 (Fri, 14 Feb 2014) | 6 lines
  
  Modified the help text to explain that -p will launch relax in prompt mode 
after running any optionally supplied scripts.
  
  Fix for sr #3117, (https://gna.org/support/?3117) - Functionality to inspect 
interactively after running script - The equivalence to python -i
  
  This is to allow the -p --prompt option to be given without a script. relax 
should support this so that a user doesn't get too confused when
  trying to start in prompt mode with the --prompt flag and support the 
--prompt argument without a script being supplied.

  r22187 | tlinnet | 2014-02-14 12:13:05 +0100 (Fri, 14 Feb 2014) | 6 lines
  
  Finished implementing the functionality of interacting with variables after 
executing a script.
  
  Fix for sr #3117, (https://gna.org/support/?3117) - Functionality to inspect 
interactively after running script - The equivalence to python -i
  
  For getting access to variables after executing a script, the variable should 
be saved under: cdp.X, where X define a container.
  The name space issue is discussed in: 
http://thread.gmane.org/gmane.science.nmr.relax.devel/5012

  r22188 | tlinnet | 2014-02-14 12:28:25 +0100 (Fri, 14 Feb 2014) | 3 lines
  
  Added Copyright info to modified file.
  
  Fix for sr #3117, (https://gna.org/support/?3117) - Functionality to inspect 
interactively after running script - The equivalence to python -i

  r22189 | bugman | 2014-02-14 14:24:25 +0100 (Fri, 14 Feb 2014) | 8 lines
  
  Organisation of the relax command line options into distinct groups.
  
  This follows from the message at 
http://thread.gmane.org/gmane.science.nmr.relax.devel/5024.
  
  The optparse.OptionGroup object is now used to cluster the arguments.  This 
cleans up the output of
  'relax -h' and explains the options to the user in a clearer way.


Modified:
branches/double_rotor/   (props changed)
branches/double_rotor/lib/errors.py
branches/double_rotor/lib/warnings.py
branches/double_rotor/prompt/interpreter.py
branches/double_rotor/relax.py
branches/double_rotor/status.py

Propchange: branches/double_rotor/
--
--- svnmerge-integrated (original)
+++ svnmerge-integrated Fri Feb 14 

r22191 - /trunk/prompt/interpreter.py

[tlinnet]

Author: tlinnet
Date: Fri Feb 14 15:19:58 2014
New Revision: 22191

URL: http://svn.gna.org/viewcvs/relax?rev=22191view=rev
Log:
Fix for the user function intro flag.

Fix for sr #3117, (https://gna.org/support/?3117) - Functionality to inspect 
interactively after running script - The equivalence to python -i

It should be turned on for the script so you see the relax messages, and 
then turned off again for the prompt so that
the user function text and relax is not printed out twice.

Modified:
trunk/prompt/interpreter.py

Modified: trunk/prompt/interpreter.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/prompt/interpreter.py?rev=22191r1=22190r2=22191view=diff
==
--- trunk/prompt/interpreter.py (original)
+++ trunk/prompt/interpreter.py Fri Feb 14 15:19:58 2014
@@ -276,7 +276,16 @@
 
 # Execute the script and go into prompt if the interactive flag -p 
--prompt is given at startup.
 if script_file and status.prompt:
+# Turn on the user function intro flag.
+status.uf_intro = True
+
+# Run the script.
 run_script(intro=self.__intro_string, local=locals(), 
script_file=script_file, show_script=self.__show_script, 
raise_relax_error=self.__raise_relax_error)
+
+# Turn off the user function intro flag.
+status.uf_intro = False
+
+# Go to the prompt.
 prompt(intro=None, local=locals())
 
 # Go to the prompt.


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r22192 - in /branches/double_rotor/test_suite/system_tests/scripts/frame_order/cam: base_script.py rotor.py

[edward]

Author: bugman
Date: Fri Feb 14 17:25:00 2014
New Revision: 22192

URL: http://svn.gna.org/viewcvs/relax?rev=22192view=rev
Log:
Converted the Frame_order.test_cam_rotor system script test to use the new 
rotor model parameters.

The rotor frame order parameters {P_alpha, P_beta, P_gamma, T_x, T_y, T_z, 
E_theta, E_phi, p_x, p_y,
p_z}, where P_i are the Euler angles defining the average domain position, T_i 
are the translations
defining the average domain position, E_i are the Eigenframe angles defining 
the rotation axis, and
p_i are the pivot point coordinates, will be converted to {P_alpha, P_beta, 
P_gamma, T_x, T_y, T_z,
Ax_alpha, p_x, p_y, p_z}.  Ax_alpha is the new parameter which defines the 
rotation axis together
with the pivot using the minimal parameter set {p_x, p_y, p_z, Ax_alpha}.


Modified:

branches/double_rotor/test_suite/system_tests/scripts/frame_order/cam/base_script.py

branches/double_rotor/test_suite/system_tests/scripts/frame_order/cam/rotor.py

Modified: 
branches/double_rotor/test_suite/system_tests/scripts/frame_order/cam/base_script.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/double_rotor/test_suite/system_tests/scripts/frame_order/cam/base_script.py?rev=22192r1=22191r2=22192view=diff
==
--- 
branches/double_rotor/test_suite/system_tests/scripts/frame_order/cam/base_script.py
 (original)
+++ 
branches/double_rotor/test_suite/system_tests/scripts/frame_order/cam/base_script.py
 Fri Feb 14 17:25:00 2014
@@ -129,6 +129,8 @@
 self._execute_uf(uf_name='value.set', val=self.AXIS_THETA, 
param='axis_theta')
 if self.AXIS_PHI != None:
 self._execute_uf(uf_name='value.set', val=self.AXIS_PHI, 
param='axis_phi')
+if self.AXIS_ALPHA != None:
+self._execute_uf(uf_name='value.set', val=self.AXIS_ALPHA, 
param='axis_alpha')
 if self.CONE_THETA_X != None:
 self._execute_uf(uf_name='value.set', val=self.CONE_THETA_X, 
param='cone_theta_x')
 if self.CONE_THETA_Y != None:

Modified: 
branches/double_rotor/test_suite/system_tests/scripts/frame_order/cam/rotor.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/double_rotor/test_suite/system_tests/scripts/frame_order/cam/rotor.py?rev=22192r1=22191r2=22192view=diff
==
--- 
branches/double_rotor/test_suite/system_tests/scripts/frame_order/cam/rotor.py 
(original)
+++ 
branches/double_rotor/test_suite/system_tests/scripts/frame_order/cam/rotor.py 
Fri Feb 14 17:25:00 2014
@@ -22,8 +22,12 @@
 # Module docstring.
 Script for optimising the rotor frame order test model of CaM.
 
+# Python module imports
+from numpy import arcsin, array, dot, float64, zeros
+
 # relax module imports.
 from base_script import Base_script
+from lib.geometry.coord_transform import spherical_to_cartesian
 
 
 class Analysis(Base_script):
@@ -31,10 +35,14 @@
 # Set up some class variables.
 DIRECTORY = 'rotor'
 MODEL = 'rotor'
-AXIS_THETA = 0.9600799785953431
-AXIS_PHI = 4.0322755062196229
 CONE_SIGMA_MAX = 30.0 / 360.0 * 2.0 * pi
 
+# Translate the system.
+axis_theta = 0.9600799785953431
+axis_phi = 4.0322755062196229
+r_ax = zeros(3, float64)
+spherical_to_cartesian([1, axis_theta, axis_phi], r_ax)
+AXIS_ALPHA = arcsin(dot(r_ax, array([0, 0, 1], float64)))
 
 # Execute the analysis.
 Analysis(self._execute_uf)


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r22193 - in /branches/double_rotor/specific_analyses/frame_order: api.py parameters.py

[edward]

Author: bugman
Date: Fri Feb 14 17:26:33 2014
New Revision: 22193

URL: http://svn.gna.org/viewcvs/relax?rev=22193view=rev
Log:
Added support for the new axis_alpha frame order parameter to the 
specific_analyses.frame_order package.


Modified:
branches/double_rotor/specific_analyses/frame_order/api.py
branches/double_rotor/specific_analyses/frame_order/parameters.py

Modified: branches/double_rotor/specific_analyses/frame_order/api.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/double_rotor/specific_analyses/frame_order/api.py?rev=22193r1=22192r2=22193view=diff
==
--- branches/double_rotor/specific_analyses/frame_order/api.py (original)
+++ branches/double_rotor/specific_analyses/frame_order/api.py Fri Feb 14 
17:26:33 2014
@@ -71,6 +71,7 @@
 self.PARAMS.add('eigen_gamma', scope='global', units='rad', desc='The 
Eigenframe gamma Euler angle', py_type=float, set='params', err=True, sim=True)
 self.PARAMS.add('axis_theta', scope='global', units='rad', desc='The 
cone axis polar angle (for the isotropic cone model)', py_type=float, 
set='params', err=True, sim=True)
 self.PARAMS.add('axis_phi', scope='global', units='rad', desc='The 
cone axis azimuthal angle (for the isotropic cone model)', py_type=float, 
set='params', err=True, sim=True)
+self.PARAMS.add('axis_alpha', scope='global', units='rad', desc='The 
rotor axis alpha angle (the rotation angle out of the xy plane)', 
py_type=float, set='params', err=True, sim=True)
 self.PARAMS.add('cone_theta_x', scope='global', units='rad', desc='The 
pseudo-ellipse cone opening half-angle for the x-axis', py_type=float, 
set='params', err=True, sim=True)
 self.PARAMS.add('cone_theta_y', scope='global', units='rad', desc='The 
pseudo-ellipse cone opening half-angle for the y-axis', py_type=float, 
set='params', err=True, sim=True)
 self.PARAMS.add('cone_theta', scope='global', units='rad', desc='The 
isotropic cone opening half-angle', py_type=float, set='params', err=True, 
sim=True)
@@ -420,7 +421,7 @@
 upper = 5
 
 # Linear angle grid from 0 to one inc before 2pi.
-if cdp.params[i] in ['ave_pos_alpha', 'ave_pos_gamma', 
'eigen_alpha', 'eigen_gamma', 'axis_phi']:
+if cdp.params[i] in ['ave_pos_alpha', 'ave_pos_gamma', 
'eigen_alpha', 'eigen_gamma', 'axis_phi', 'axis_alpha']:
 lower = 0.0
 upper = 2*pi * (1.0 - 1.0/incs[i])
 
@@ -544,6 +545,10 @@
 
 # Axis spherical coordinate phi.
 if param == 'axis_phi':
+return [0.0, 2*pi]
+
+# Axis alpha angle.
+if param == 'axis_alpha':
 return [0.0, 2*pi]
 
 # Cone angle.

Modified: branches/double_rotor/specific_analyses/frame_order/parameters.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/double_rotor/specific_analyses/frame_order/parameters.py?rev=22193r1=22192r2=22193view=diff
==
--- branches/double_rotor/specific_analyses/frame_order/parameters.py (original)
+++ branches/double_rotor/specific_analyses/frame_order/parameters.py Fri Feb 
14 17:26:33 2014
@@ -86,7 +86,7 @@
 param_vect.append(cdp.eigen_gamma)
 
 # Frame order eigenframe - the isotropic cone axis.
-elif cdp.model in ['iso cone', 'free rotor', 'iso cone, torsionless', 
'iso cone, free rotor', 'rotor', 'double rotor']:
+elif cdp.model in ['iso cone', 'free rotor', 'iso cone, torsionless', 
'iso cone, free rotor', 'double rotor']:
 param_vect.append(cdp.axis_theta)
 param_vect.append(cdp.axis_phi)
 
@@ -94,6 +94,10 @@
 if cdp.model in ['double rotor']:
 param_vect.append(cdp.axis_theta_2)
 param_vect.append(cdp.axis_phi_2)
+
+# Frame order eigenframe - the rotor axis alpha angle.
+if cdp.model in ['rotor']:
+param_vect.append(cdp.axis_alpha)
 
 # Cone parameters - pseudo-elliptic cone parameters.
 if cdp.model in ['pseudo-ellipse', 'pseudo-ellipse, torsionless', 
'pseudo-ellipse, free rotor']:
@@ -138,7 +142,7 @@
 param_vect.append(cdp.eigen_gamma_sim[sim_index])
 
 # Frame order eigenframe - the isotropic cone axis.
-elif cdp.model in ['iso cone', 'free rotor', 'iso cone, torsionless', 
'iso cone, free rotor', 'rotor', 'double rotor']:
+elif cdp.model in ['iso cone', 'free rotor', 'iso cone, torsionless', 
'iso cone, free rotor', 'double rotor']:
 param_vect.append(cdp.axis_theta_sim[sim_index])
 param_vect.append(cdp.axis_phi_sim[sim_index])
 
@@ -146,6 +150,10 @@
 if cdp.model in ['double rotor']:
 param_vect.append(cdp.axis_theta_sim_2[sim_index])
 param_vect.append(cdp.axis_phi_sim_2[sim_index])
+
+# Frame order eigenframe - the rotor axis alpha angle.
+

r22194 - in /branches/double_rotor: specific_analyses/frame_order/optimisation.py target_functions/frame_order.py

[edward]

Author: bugman
Date: Fri Feb 14 17:54:31 2014
New Revision: 22194

URL: http://svn.gna.org/viewcvs/relax?rev=22194view=rev
Log:
Implemented the new frame order rotor model parameters in the target function.

The parameters {axis_theta, axis_phi} have been replaced by the single 
axis_alpha.  To support the
new model construct, the CoM of the entire system is now passed into the target 
function.


Modified:
branches/double_rotor/specific_analyses/frame_order/optimisation.py
branches/double_rotor/target_functions/frame_order.py

Modified: branches/double_rotor/specific_analyses/frame_order/optimisation.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/double_rotor/specific_analyses/frame_order/optimisation.py?rev=22194r1=22193r2=22194view=diff
==
--- branches/double_rotor/specific_analyses/frame_order/optimisation.py 
(original)
+++ branches/double_rotor/specific_analyses/frame_order/optimisation.py Fri Feb 
14 17:54:31 2014
@@ -683,14 +683,18 @@
 if not hasattr(cdp, 'num_int_pts'):
 cdp.num_int_pts = 20
 
+# The centre of mass, for use in the rotor models.
+com = pipe_centre_of_mass(verbosity=0)
+com = array(com, float64)
+
 # The centre of mass of the moving domain - to use as the centroid for the 
average domain position rotation.
 if cdp.ave_pos_pivot == 'com':
-com = pipe_centre_of_mass(atom_id=domain_moving(), verbosity=0)
+ave_pos_pivot = pipe_centre_of_mass(atom_id=domain_moving(), 
verbosity=0)
 ave_pos_piv_sync = False
 
 # The centre of mass of the moving domain - to use as the centroid for the 
average domain position rotation.
 if cdp.ave_pos_pivot == 'motional':
-com = pivot
+ave_pos_pivot = pivot
 ave_pos_piv_sync = True
 
 # Print outs.
@@ -709,7 +713,7 @@
 sys.stdout.write(Base data: %s\n % repr(base_data))
 
 # Set up the optimisation function.
-target = frame_order.Frame_order(model=cdp.model, 
init_params=param_vector, full_tensors=full_tensors, 
full_in_ref_frame=full_in_ref_frame, rdcs=rdcs, rdc_errors=rdc_err, 
rdc_weights=rdc_weight, rdc_vect=rdc_vect, dip_const=rdc_const, pcs=pcs, 
pcs_errors=pcs_err, pcs_weights=pcs_weight, atomic_pos=atomic_pos, temp=temp, 
frq=frq, paramag_centre=paramag_centre, scaling_matrix=scaling_matrix, 
ave_pos_pivot=com, ave_pos_piv_sync=ave_pos_piv_sync, 
translation_opt=translation_opt, pivot=pivot, pivot2=pivot2, 
pivot_opt=pivot_opt, num_int_pts=cdp.num_int_pts, quad_int=cdp.quad_int)
+target = frame_order.Frame_order(model=cdp.model, 
init_params=param_vector, full_tensors=full_tensors, 
full_in_ref_frame=full_in_ref_frame, rdcs=rdcs, rdc_errors=rdc_err, 
rdc_weights=rdc_weight, rdc_vect=rdc_vect, dip_const=rdc_const, pcs=pcs, 
pcs_errors=pcs_err, pcs_weights=pcs_weight, atomic_pos=atomic_pos, temp=temp, 
frq=frq, paramag_centre=paramag_centre, scaling_matrix=scaling_matrix, com=com, 
ave_pos_pivot=ave_pos_pivot, ave_pos_piv_sync=ave_pos_piv_sync, 
translation_opt=translation_opt, pivot=pivot, pivot2=pivot2, 
pivot_opt=pivot_opt, num_int_pts=cdp.num_int_pts, quad_int=cdp.quad_int)
 
 # Return the data.
 return target, param_vector, data_types, scaling_matrix

Modified: branches/double_rotor/target_functions/frame_order.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/double_rotor/target_functions/frame_order.py?rev=22194r1=22193r2=22194view=diff
==
--- branches/double_rotor/target_functions/frame_order.py (original)
+++ branches/double_rotor/target_functions/frame_order.py Fri Feb 14 17:54:31 
2014
@@ -25,7 +25,7 @@
 # Python module imports.
 from copy import deepcopy
 from math import acos, pi, sqrt
-from numpy import array, dot, float32, float64, ones, transpose, uint8, zeros
+from numpy import array, cross, dot, float32, float64, ones, transpose, uint8, 
zeros
 from numpy.linalg import norm
 
 # relax module imports.
@@ -46,7 +46,7 @@
 from lib.frame_order.pseudo_ellipse_torsionless import 
compile_2nd_matrix_pseudo_ellipse_torsionless, 
pcs_numeric_int_pseudo_ellipse_torsionless, 
pcs_numeric_int_pseudo_ellipse_torsionless_qrint
 from lib.frame_order.rotor import compile_2nd_matrix_rotor, 
pcs_numeric_int_rotor, pcs_numeric_int_rotor_qrint
 from lib.geometry.coord_transform import spherical_to_cartesian
-from lib.geometry.rotations import euler_to_R_zyz, two_vect_to_R
+from lib.geometry.rotations import axis_angle_to_R, euler_to_R_zyz, 
two_vect_to_R
 from lib.linear_algebra.kronecker_product import kron_prod
 from lib.order import order_parameters
 from lib.physical_constants import pcs_constant
@@ -56,7 +56,7 @@
 class Frame_order:
 Class containing the target function of the optimisation of Frame Order 
matrix components.
 
-def __init__(self, model=None, init_params=None, full_tensors=None, 
full_in_ref_frame=None, rdcs=None, rdc_errors=None,