relax SVN archive

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')
------------------------------------------------------------------------
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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.
........

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

Merged revisions 23532 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r23532 | bugman | 2014-05-28 17:00:48 +0200 (Wed, 28 May 2014) | 3 lines

Modified the User_functions.test_dx_map GUI test to catch another problem with the Sequence_2D element.
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Merged revisions 23521 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r23521 | bugman | 2014-05-28 16:32:01 +0200 (Wed, 28 May 2014) | 7 lines

Created the User_functions.test_dx_map GUI test.

This extensively checks the 'point' argument for the dx.map user function GUI window. This is to
catch bug #22102 (https://gna.org/bugs/?22102), the point argument of the dx.map user function being
incorrect in the GUI.
........

Merged revisions 23510-23520 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r23510 | bugman | 2014-05-28 14:01:13 +0200 (Wed, 28 May 2014) | 5 lines

Simplified the User_functions GUI tests.

The exec_uf_pipe_create() method has been created to simplify the data pipe creation in the tests.
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r23511 | bugman | 2014-05-28 14:25:20 +0200 (Wed, 28 May 2014) | 7 lines

Expanded the User_functions.test_structure_rotate GUI test.

The rotation matrix argument checks for the Sequence_2D GUI element have been expanded to check that
setting nothing (blank element) returns nothing (None). The other checks have also been slightly
modified.
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r23512 | bugman | 2014-05-28 14:36:46 +0200 (Wed, 28 May 2014) | 6 lines

Expanded the User_functions.test_structure_rotate GUI test to catch more problems.

Now the rotation matrix value in the user function window is set to a series of invalid values to
test if the Sequence_2D GUI element will handle the rubbish input. This is to mimic user errors.
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r23513 | bugman | 2014-05-28 14:39:27 +0200 (Wed, 28 May 2014) | 7 lines

Bug fix for the Sequence_2D GUI element.

This is used for the user function windows in the GUI for setting lists of lists or matrices. The
GUI element GetValue() method will now return None if nothing is set. This prevents a list of lists
of None being added to the main user function window.
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r23514 | tlinnet | 2014-05-28 15:05:21 +0200 (Wed, 28 May 2014) | 17 lines

Reverted r23508-23507 as the correct is dimensions (None, 3) for x,y,x positions.

The command used was:
svn merge -r23508:23507 .

.....
Modified the dim dimensions to (None, 4) to allow the user to change number of points in the GUI.

THe first dimension was used as a counter, the last 3 dimensions is for x,y,z position.

This is for the user function dx.map.

Modified:
trunk/user_functions/dx.py
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r23515 | bugman | 2014-05-28 15:32:39 +0200 (Wed, 28 May 2014) | 3 lines

Created the is_list() and is_list_of_lists() functions for the lib.check_types module.
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r23516 | bugman | 2014-05-28 15:34:19 +0200 (Wed, 28 May 2014) | 3 lines

Copyright update.
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r23517 | bugman | 2014-05-28 15:40:32 +0200 (Wed, 28 May 2014) | 6 lines

Clean up of the User_functions.test_structure_rotate GUI test.

The invalid value check is simpler and the Sequence_2D GUI object return value is now checked to be
None.
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r23518 | bugman | 2014-05-28 15:45:36 +0200 (Wed, 28 May 2014) | 7 lines

Expanded the User_functions.test_structure_rotate GUI once more.

This time the setting of invalid values in the Sequence_2D element itself is now checked. For
example for the rotation matrix of the structure.rotate user function, if a matrix element is set to
a string, a NameError is raised.
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r23519 | bugman | 2014-05-28 15:48:29 +0200 (Wed, 28 May 2014) | 7 lines

Fixes for the Sequence and Sequence_2D GUI elements for handling invalid input data.

These elements used by the user function windows previously raised all sorts of errors if the data
was not what they expected (lists or lists of lists respectively). These situations are now caught
and the input data is ignored, so blank Sequence and Sequence_2D elements are presented to the user.
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r23520 | bugman | 2014-05-28 16:04:38 +0200 (Wed, 28 May 2014) | 7 lines

Bug fix for the Sequence_2D GUI element.

This is used for handling list of lists user function arguments in the user function GUI windows.
The setting of invalid values directly in the Sequence_2D GUI element is now detected. These values
are now replaced with None.
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