relax SVN archive

Merged revisions 26067-26068 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26067 | bugman | 2014-09-26 17:34:15 +0200 (Fri, 26 Sep 2014) | 11 lines

Fix for the experimental information data pipe object when converting to XML state and results files.

This is a partial fix for bug #22704 (https://gna.org/bugs/?22704), the corrupted relax state files
after setting the relax references via the bmrb.software, bmrb.display, or bmrb.write user
functions.

The names and descriptions for the software, citation and script list objects were incorrectly set.
These have been fixed so that the name of the data structure and the real description is present in
the XML state or results file instead of <relax_list desc='relax list container'>.
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r26068 | bugman | 2014-09-26 17:44:48 +0200 (Fri, 26 Sep 2014) | 11 lines

Fix for the experimental information data pipe object when converting to XML state and results files.

This is a partial fix for bug #22704 (https://gna.org/bugs/?22704), the corrupted relax state files
after setting the relax references via the bmrb.software, bmrb.display, or bmrb.write user
functions.

The names and descriptions for the software, citation and script list objects were incorrectly set.
These have been fixed so that the name of the data structure and the real description is present in
the XML state or results file instead of <relax_list desc='relax list container'>.
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Merged revisions 26065-26066 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26065 | tlinnet | 2014-09-26 17:29:39 +0200 (Fri, 26 Sep 2014) | 3 lines

Implemented getting the statistics for parameters and comparing to init NI.

Task #7826 (https://gna.org/task/index.php?7826): Write an python class for the repeated analysis of dispersion data.
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r26066 | tlinnet | 2014-09-26 17:29:49 +0200 (Fri, 26 Sep 2014) | 3 lines

Implemented writing and plotting of statistics for individual and clustered fitting, compararing to full NI.

Task #7826 (https://gna.org/task/index.php?7826): Write an python class for the repeated analysis of dispersion data.
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Merged revisions 26064 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26064 | bugman | 2014-09-26 16:46:20 +0200 (Fri, 26 Sep 2014) | 3 lines

Removed a debugging printout fatal for Python 3.
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Merged revisions 26063 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26063 | bugman | 2014-09-26 16:36:13 +0200 (Fri, 26 Sep 2014) | 6 lines

Created the Bmrb.test_bug_22704_corrupted_state_file system test.

This is to catch bug #22704 (https://gna.org/bugs/?22704), the corrupted relax state files after
setting the relax references via the bmrb.software, bmrb.display, or bmrb.write user functions.
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Merged revisions 26058-26062 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26058 | bugman | 2014-09-26 14:38:48 +0200 (Fri, 26 Sep 2014) | 6 lines

Fixes for the lib.checks.Check object.

The __call__() method keyword arguments **kargs needs to be processed inside the method to strip out
the escalate argument.
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r26059 | bugman | 2014-09-26 14:45:05 +0200 (Fri, 26 Sep 2014) | 5 lines

The default value of the escalate argument of the Check.__call__() method is now 2.

This will cause the calls to the check_*() function/objects to default to raising RelaxErrors.
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r26060 | bugman | 2014-09-26 15:06:55 +0200 (Fri, 26 Sep 2014) | 16 lines

Reverted r26053, as this is no longer the case.

The command used was:
svn merge -r26053:r26052 .

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r26053 | bugman | 2014-09-26 11:44:00 +0200 (Fri, 26 Sep 2014) | 5 lines
Changed paths:
M /trunk/test_suite/system_tests/bmrb.py

Updated the Bmrb.test_bug_22703_display_empty system/GUI test.

The RelaxError type is now different.
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r26061 | bugman | 2014-09-26 15:17:39 +0200 (Fri, 26 Sep 2014) | 6 lines

Changed the behaviour of the lib.checks.Check object again.

This time the registered function is stored rather than converted into a class instance method.
That way the check_*() function-like objects do not need to accept the unused 'self' argument.
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r26062 | bugman | 2014-09-26 15:29:07 +0200 (Fri, 26 Sep 2014) | 5 lines

The data pipe testing function has been converted to the strategy design pattern of the Check object.

The function pipe_control.pipes.test() has also been renamed to check_pipe().
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Merged revisions 26057 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26057 | tlinnet | 2014-09-26 13:06:40 +0200 (Fri, 26 Sep 2014) | 3 lines

Implemented the writing out of parameter values between comparison of NI level.

Task #7826 (https://gna.org/task/index.php?7826): Write an python class for the repeated analysis of dispersion data.
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Merged revisions 26044-26046,26048-26056 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26044 | bugman | 2014-09-26 09:52:37 +0200 (Fri, 26 Sep 2014) | 7 lines

Created the pipe_control.spectrometer.check_setup() function.

This follows the design on the wiki page http://wiki.nmr-relax.com/Relax_source_design.

This is for checking if spectrometer information has been set up.
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r26045 | bugman | 2014-09-26 09:55:10 +0200 (Fri, 26 Sep 2014) | 3 lines

Created the RelaxNoFrqWarning warning class for warning that no spectrometer information is present.
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r26046 | bugman | 2014-09-26 10:00:58 +0200 (Fri, 26 Sep 2014) | 5 lines

Renamed the pipe_control.spectrometer.check_setup() function to check_spectrometer_setup().

This is so it can be used without confusion outside of the module.
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r26048 | bugman | 2014-09-26 10:05:42 +0200 (Fri, 26 Sep 2014) | 3 lines

Fix for a broken elif block in the new pipe_control.spectrometer.check_spectrometer_setup() function.
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r26049 | bugman | 2014-09-26 10:06:58 +0200 (Fri, 26 Sep 2014) | 5 lines

The model-free bmrb_write() API method now checks for spectrometer information.

This is via a call to the pipe_control.spectrometer.check_spectrometer_setup() function.
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r26050 | bugman | 2014-09-26 10:09:18 +0200 (Fri, 26 Sep 2014) | 3 lines

Modified the Bmrb.test_bug_22703_display_empty system/GUI test to catch the RelaxNoFrqError.
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r26051 | bugman | 2014-09-26 11:31:29 +0200 (Fri, 26 Sep 2014) | 6 lines

Created a special Check class based on the strategy design pattern.

This is in the new lib.checks module. The class will be used to simplify and unify all of the
check_*() functions in the pipe_control and specific_analyses packages.
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r26052 | bugman | 2014-09-26 11:43:15 +0200 (Fri, 26 Sep 2014) | 6 lines

Converted the pipe_control.spectrometer.check_*() functions to the strategy design pattern.

These are now passed into the lib.checks.Check object, and the original functions are now instances
of this class.
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r26053 | bugman | 2014-09-26 11:44:00 +0200 (Fri, 26 Sep 2014) | 5 lines

Updated the Bmrb.test_bug_22703_display_empty system/GUI test.

The RelaxError type is now different.
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r26054 | bugman | 2014-09-26 12:15:23 +0200 (Fri, 26 Sep 2014) | 3 lines

Alphabetical ordering of all functions in the pipe_control.pipes module.
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r26055 | bugman | 2014-09-26 12:40:16 +0200 (Fri, 26 Sep 2014) | 9 lines

Changed the design of the Check object in lib.checks.

The design of the checking function to call has been modified - it should now return either None if
the check passes or an instantiated RelaxError object if not. This is then used to determine if the
__call__() method should return True (when None is received). Otherwise if escalate is set to 1,
the text from the RelaxError object is sent into a RelaxWarning and False is returned. And if
escalate is set to 2, then the error object is simply raised.
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r26056 | bugman | 2014-09-26 12:41:06 +0200 (Fri, 26 Sep 2014) | 3 lines

Updated the pipe_control.spectrometer.check_*_func() functions to use the new design.
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Merged revisions 26043 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r26043 | bugman | 2014-09-26 09:37:41 +0200 (Fri, 26 Sep 2014) | 9 lines

Created the Bmrb.test_bug_22703_display_empty system and GUI test.

This system test catches bug #22703 (https://gna.org/bugs/?22703), the failure of the bmrb.display
user function with an AttributeError when no data is present.

It is simultaneously a system and GUI test, as the GUI test class inherits directly from the system
test class.
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Implemented the cdp.exp_info.from_xml() method to correctly restore the experimental info structure.

This fixes bug #22704 (https://gna.org/bugs/?22704), the corrupted relax state files after setting
the relax references via the bmrb.software, bmrb.display, or bmrb.write user functions.

This custom ExpInfo.from_xml() method is required to properly recreate the software, script and
citation list data structures of the cdp.exp_info data structure, as these are special RelaxListType
objects populated by Element objects (both from data_store.data_classes).

Fix for the cdp.exp_info.software data structure setup.

This is a partial fix for bug #22704 (https://gna.org/bugs/?22704), the corrupted relax state files
after setting the relax references via the bmrb.software, bmrb.display, or bmrb.write user
functions.

The Element data container name was being replaced by the software name, making it impossible to
restore from the XML.