relax SVN archive

Merged revisions 23368-23370 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r23368 | bugman | 2014-05-23 10:06:32 +0200 (Fri, 23 May 2014) | 11 lines

Changed most default dispersion parameter values to avoid edge cases where there is no exchange.

The dw parameters were all 0.0 and kex 1e5, both of which result in no exchange. If this is ever
used for an optimisation starting point - which it never should, apart from development, test suite,
and debugging purposes - then the optimisation algorithm will have a very hard time recovering. The
pA parameter has been changed to 0.90 to set it to a reasonable value while still staying far away
from the no exchange condition of pA = 1.0.

This follows from http://article.gmane.org/gmane.science.nmr.relax.devel/5917.
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r23369 | bugman | 2014-05-23 10:10:46 +0200 (Fri, 23 May 2014) | 10 lines

Fixes for 3 dispersion system tests for the change in default parameter values.

The default values are used in the auto-analysis in the test suite to avoid the grid search. The
changed values affected the optimisation of two spins from Flemming Hansen's data located at
test_suite/shared_data/dispersion/Hansen/, residue 4 used as an example of no exchange and residue
70 used as an example where data is only available at one field. The system test
Relax_disp.test_set_grid_r20_from_min_r2eff_cpmg was also modified as it was directly checking these
default values.
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r23370 | bugman | 2014-05-23 10:18:37 +0200 (Fri, 23 May 2014) | 7 lines

Fix for the Relax_disp.test_cpmg_synthetic_dx_map_points system test.

This uses the default parameter values to start the optimisation, therefore the recent change away
from edge case 'no Rex' values allows the parameter values stored in ds.dx_clust_val to be correctly
optimised.
........

Fix for the Relax_disp.test_cpmg_synthetic_dx_map_points system test.

This uses the default parameter values to start the optimisation, therefore the recent change away
from edge case 'no Rex' values allows the parameter values stored in ds.dx_clust_val to be correctly
optimised.

Fixes for 3 dispersion system tests for the change in default parameter values.

The default values are used in the auto-analysis in the test suite to avoid the grid search. The
changed values affected the optimisation of two spins from Flemming Hansen's data located at
test_suite/shared_data/dispersion/Hansen/, residue 4 used as an example of no exchange and residue
70 used as an example where data is only available at one field. The system test
Relax_disp.test_set_grid_r20_from_min_r2eff_cpmg was also modified as it was directly checking these
default values.

Changed most default dispersion parameter values to avoid edge cases where there is no exchange.

The dw parameters were all 0.0 and kex 1e5, both of which result in no exchange. If this is ever
used for an optimisation starting point - which it never should, apart from development, test suite,
and debugging purposes - then the optimisation algorithm will have a very hard time recovering. The
pA parameter has been changed to 0.90 to set it to a reasonable value while still staying far away
from the no exchange condition of pA = 1.0.

This follows from http://article.gmane.org/gmane.science.nmr.relax.devel/5917.

Merged revisions 23362,23365-23366 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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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.
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r23365 | bugman | 2014-05-23 09:03:27 +0200 (Fri, 23 May 2014) | 7 lines

Attempt at fixing bug #22071, the relax unit test and system test not functioning.

This is reported at https://gna.org/bugs/?22071.

The fix here is that the git commands to show the current subversion revision number only works when
run from the relax base directory, or one of the subdirectories. This should now be fixed, as the
pipe running the command will first 'cd' to the relax base directory.
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r23366 | bugman | 2014-05-23 09:18:34 +0200 (Fri, 23 May 2014) | 6 lines

Another attempt at fixing bug #22071, the relax unit test and system test not functioning.

This is reported at https://gna.org/bugs/?22071.

This time the complicated shell command "cd %s; git svn find-rev $(git rev-parse HEAD)" has been
replaced with "cd %s; git svn info".
........

Another attempt at fixing bug #22071, the relax unit test and system test not functioning.

This is reported at https://gna.org/bugs/?22071.

This time the complicated shell command "cd %s; git svn find-rev $(git rev-parse HEAD)" has been
replaced with "cd %s; git svn info".

Attempt at fixing bug #22071, the relax unit test and system test not functioning.

This is reported at https://gna.org/bugs/?22071.

The fix here is that the git commands to show the current subversion revision number only works when
run from the relax base directory, or one of the subdirectories. This should now be fixed, as the
pipe running the command will first 'cd' to the relax base directory.

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

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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.
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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.
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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.
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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.
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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.
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r23352 | bugman | 2014-05-22 18:31:35 +0200 (Thu, 22 May 2014) | 3 lines

Removed a debugging printout.
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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.
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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.