relax SVN archive

Copied unit test _lib/_dispersion/* to be reused for other models.

Merged revisions 23336-23337,23340,23343,23345,23352,23360,23362 via svnmerge from
svn+ssh://tlinnet@.../svn/relax/trunk

........
r23336 | bugman | 2014-05-22 15:39:21 +0200 (Thu, 22 May 2014) | 6 lines

Created the Structure.test_bug_22070_structure_superimpose_after_deletion system test.

This is to catch bug #22070 (https://gna.org/bugs/index.php?22070), the failure of the
structure.superimpose user function after deleting atoms with structure.delete.
........
r23337 | bugman | 2014-05-22 16:09:50 +0200 (Thu, 22 May 2014) | 6 lines

Added some checks to the Structure.test_bug_22070_structure_superimpose_after_deletion system test.

These tests reveal the real problem - that the atoms of the second model have not been removed by
the structure.delete user function.
........
r23340 | bugman | 2014-05-22 17:21:05 +0200 (Thu, 22 May 2014) | 11 lines

Important bug fix for the structure.delete user function when multiple models are present.

This is to fix bug #22070 (https://gna.org/bugs/index.php?22070), the failure of the
structure.superimpose user function after deleting atoms with structure.delete.

The problem is that structure.delete was removing the atoms from the first model but none of the
others. This is because it was using the structural object atom_loop() method to find the atoms to
be deleted, but this method operates on the first model. So when the second model is reached, the
atoms are already gone.
........
r23343 | bugman | 2014-05-22 18:10:32 +0200 (Thu, 22 May 2014) | 4 lines

Added git-svn support for the relax version information module.

This allows the subversion revision number and repository URL to be displayed on program startup, so
that it is stored in log files. This is very useful for debugging purposes.
........
r23345 | bugman | 2014-05-22 18:18:27 +0200 (Thu, 22 May 2014) | 3 lines

Improvements for the git-svn support in the relax version module.

Python 3 is now correctly handled and the URL is properly extracted from the git repository.
........
r23352 | bugman | 2014-05-22 18:31:35 +0200 (Thu, 22 May 2014) | 3 lines

Removed a debugging printout.
........
r23360 | bugman | 2014-05-22 19:39:22 +0200 (Thu, 22 May 2014) | 6 lines

Improvement for the unit test printouts when run with the --time command line option.

The full unit test name is now printed out, reverting to the old behaviour (prior to r21965).
However the shortened test names are preserved for the other test suite categories.
........
r23362 | bugman | 2014-05-22 19:55:47 +0200 (Thu, 22 May 2014) | 9 lines

Created the test_ns_cpmg_2site_expanded_no_rex8() relaxation dispersion unit test.

This is a demonstration commit, showing the 'NS CPMG 2-site expanded' model with no exchange when
kex = 1e5. I.e. when the motion is too fast for exchange to be observed. This test should be used
for all dispersion models to make sure that they model this edge case correctly as well.

This follows from http://article.gmane.org/gmane.science.nmr.relax.devel/5906.
........

Created the test_ns_cpmg_2site_expanded_no_rex8() relaxation dispersion unit test.

This is a demonstration commit, showing the 'NS CPMG 2-site expanded' model with no exchange when
kex = 1e5. I.e. when the motion is too fast for exchange to be observed. This test should be used
for all dispersion models to make sure that they model this edge case correctly as well.

This follows from http://article.gmane.org/gmane.science.nmr.relax.devel/5906.

Merged revisions 23360 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

........
r23360 | bugman | 2014-05-22 19:39:22 +0200 (Thu, 22 May 2014) | 6 lines

Improvement for the unit test printouts when run with the --time command line option.

The full unit test name is now printed out, reverting to the old behaviour (prior to r21965).
However the shortened test names are preserved for the other test suite categories.
........

Improvement for the unit test printouts when run with the --time command line option.

The full unit test name is now printed out, reverting to the old behaviour (prior to r21965).
However the shortened test names are preserved for the other test suite categories.

Unit test _lib/_dispersion/test_b14.py copied to _lib/_dispersion/test_cr72.py.

They are both of CPMG type, and can be re-used.

Removed unnecessary math domain checking in model B14.

They are slowing down the code.

There is now protection for edge cases, and a last final check, before returning values.

That should be sufficient.

Critical fix for the math domain catching of model B14.

This was discovered with the added 7 unit tests demonstrating edge case 'no Rex' failures.

This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858.
This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

This is to implement catching of math domain errors, before they occur.

Added 7 unit tests demonstrating edge case 'no Rex' failures of the model 'B14'.

This follows from the ideas in the post http://article.gmane.org/gmane.science.nmr.relax.devel/5858.
This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

This is to implement catching of math domain errors, before they occur.

These tests cover all parameter value combinations which result in no exchange:

- dw = 0.0,
- pA = 1.0,
- kex = 0.0,
- dw = 0.0 and pA = 1.0,
- dw = 0.0 and kex = 0.0,
- pA = 1.0 and kex = 0.0,
- dw = 0.0, pA = 1.0, and kex = 0.0.

The average domain rotation centroid is printed out when setting up the frame order target functions.

This is to help the user understand what is happening in the analysis.