relax SVN archive

Fix for bug #22102, the point argument of the dx.map user function failing in the GUI.

This is reported at https://gna.org/bugs/?22102.

The Sequence_2D GUI element used for all list of lists arguments in the user function GUI windows
now correctly handles variable length lists. The first column which shows a count of the elements
is now properly taken into account in the SetValue(), GetValue() and add_item() methods, via a new
self.offset variable. The self.variable_length variable has also been fixed so it is not
overwritten by the parent Sequence GUI element.

Merged revisions 23542,23545,23547 via svnmerge from
svn+ssh://tlinnet@.../svn/relax/trunk

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r23542 | bugman | 2014-05-28 17:47:00 +0200 (Wed, 28 May 2014) | 3 lines

Fixes for the frame order PDB presentation in the frame_order.pdb_model user function backend.
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r23545 | bugman | 2014-05-28 17:51:34 +0200 (Wed, 28 May 2014) | 3 lines

Fix for a previous commit (r23532).
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r23547 | bugman | 2014-05-28 17:56:10 +0200 (Wed, 28 May 2014) | 6 lines

Expanded the User_functions.test_dx_map GUI test once again.

The new test is to set 2 valid points in the wizard, open and close the Sequence_2D window (twice),
and check that the points come back.
........

FIx for incorrectly svnmerge command.

To complete the full reverse, I should have gone one reversion number down.

The command used was:
svn merge -r23526:23504 .

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r23526 | tlinnet | 2014-05-28 16:49:00 +0200 (Wed, 28 May 2014) | 13 lines

Added the default value lower grid value to be set for the pA parameter.

This is added in the collected table of specific_analysis/relax_disp/parameter_object.py

This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
Discussed in post http://thread.gmane.org/gmane.science.nmr.relax.devel/5986.

In any function, these default values can get accessed by:

from specific_analyses.relax_disp.parameter_object import Relax_disp_params
PARAMS = Relax_disp_params()
PARAMS.default_value('pA')
PARAMS.grid_lower('pA')
------------------------------------------------------------------------
.....

Fix for differences in systemtests which are different from trunk.

These were found with the command:
diff -bur disp_speed/test_suite/ relax_trunk/test_suite/ | grep -v "Binary files" > diff.txt

Expanded the User_functions.test_dx_map GUI test once again.

The new test is to set 2 valid points in the wizard, open and close the Sequence_2D window (twice),
and check that the points come back.

Reverted r23531-23526 as this would prevent a clean merge back into the trunk.

The parameter_object changes should be perfomed in its own branch.
And there was not a clean separation with the unit tests.

The command used was:
svn merge -r23531:23526 .

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r23531 | tlinnet | 2014-05-28 16:49:08 +0200 (Wed, 28 May 2014) | 15 lines

Added 9th and 10th unit test case for model B14.

These tests are setup, to check how the function behaves under conditions of the grid-seach.

Two tests are setup, which either use the default lower or upper bound of the parameters for the grid search.

The return of the values are not checked, but the behaving of the function can be found when adding the --numpy-raise to run relax.

This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.

These tests are implemented to show bug cases related to:
Bug #22032: (bug #22032: Minimisation explodes when using Grid_INC=None) Minimisation explodes when using Grid_INC=None

The function can return nan or inf values, which are not handled by the minimisation algorithm, causing it to stop.
There needs to be mechanism to catch these cases.
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r23530 | tlinnet | 2014-05-28 16:49:06 +0200 (Wed, 28 May 2014) | 16 lines

Added all the default values for the lower/upper bounds which is set for the parameters in the grid search.

This is added in the collected table of specific_analysis/relax_disp/parameter_object.py.
The values were extracted from: specific_analysis/relax_disp/optimisation.py in grid_search_setup().

This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
Discussed in post http://thread.gmane.org/gmane.science.nmr.relax.devel/5986.

In any function, these default values can get accessed by:

from specific_analyses.relax_disp.parameter_object import Relax_disp_params
PARAMS = Relax_disp_params()
PARAMS.default_value('pA')
PARAMS.grid_upper('pA')

This provides a good look-up table, when stress testing the different lib/dispersion/* functions.
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r23529 | tlinnet | 2014-05-28 16:49:05 +0200 (Wed, 28 May 2014) | 4 lines

Added grid_upper to be handled in specific_analyses/parameter_object.py.

This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
Discussed in post http://thread.gmane.org/gmane.science.nmr.relax.devel/5986.
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r23528 | tlinnet | 2014-05-28 16:49:03 +0200 (Wed, 28 May 2014) | 13 lines

Added the default value upper grid value to be set for the pA parameter.

This is added in the collected table of specific_analysis/relax_disp/parameter_object.py.

This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
Discussed in post http://thread.gmane.org/gmane.science.nmr.relax.devel/5986.

In any function, these default values can get accessed by:

from specific_analyses.relax_disp.parameter_object import Relax_disp_params
PARAMS = Relax_disp_params()
PARAMS.default_value('pA')
PARAMS.grid_upper('pA')
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r23527 | tlinnet | 2014-05-28 16:49:02 +0200 (Wed, 28 May 2014) | 4 lines

Added grid_lower to be handled in specific_analyses/parameter_object.py.

This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
Discussed in post http://thread.gmane.org/gmane.science.nmr.relax.devel/5986.
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r23526 | tlinnet | 2014-05-28 16:49:00 +0200 (Wed, 28 May 2014) | 13 lines

Added the default value lower grid value to be set for the pA parameter.

This is added in the collected table of specific_analysis/relax_disp/parameter_object.py

This is related to: task #7793: (https://gna.org/task/?7793) Speed-up of dispersion models.
Discussed in post http://thread.gmane.org/gmane.science.nmr.relax.devel/5986.

In any function, these default values can get accessed by:

from specific_analyses.relax_disp.parameter_object import Relax_disp_params
PARAMS = Relax_disp_params()
PARAMS.default_value('pA')
PARAMS.grid_lower('pA')
------------------------------------------------------------------------
.....

Fix for a previous commit (r23532).

Attempt to speed up the pseudo-elliptic frame order models.

The quasi-random numerical integration of the PCS for the pseudo-ellipse has been modified so that
the torsion angle check for each Sobol' point is preformed before the tmax_pseudo_ellipse() function
call. A new check that the tilt angle is less than cone_theta_y, the larger of the two cone angles,
has also been added to avoid tmax_pseudo_ellipse() when the theta tilt angle is outside of an
isotropic cone defined by cone_theta_y.

Merged revisions 23542 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r23542 | bugman | 2014-05-28 17:47:00 +0200 (Wed, 28 May 2014) | 3 lines

Fixes for the frame order PDB presentation in the frame_order.pdb_model user function backend.
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Fixes for the frame order PDB presentation in the frame_order.pdb_model user function backend.