relax SVN archive

Renamed the function 'self._update_object()' to the private function 'self.__update_object()'.

Fix for bug #7979 (https://gna.org/bugs/?7979).

A large number of changes were required. Two private functions 'self.__update_sim_append()' and
'self.__update_sim_set()' have been added to the DiffTensorElement class. These are used to
automatically update the Monte Carlo simulation parameter lists.

The name 'dependencies' is now properly spelt.

The unused Monte Carlo simulation code in the function 'self._update_object()' has been deleted.

The object DiffTensorSimList has been modifed to handle the two new private functions.

Modifications to the DiffTensorSimList object.

The self.__setitem__() function now sets the value and the parent DiffTensorElement is now passed
into the DiffTensorSimList object.

Created the generator function 'dependency_generator()'.

This generator is for looping over the list of target parameters to update when a parameter is set.
It replaces all the self._update_object() calls and simplifies the code. It will also be used for
updating the Monte Carlo simulation data structures.

Modified the diffusion tensor data structure unit test for setting the tm parameter.

Now the spherical diffusion tensor type is initially set.

Small changes to the 'DiffTensorSimList' object.

Renamed the object 'base_name' to 'param_name'.

Blocked revisions 2993-3011 via svnmerge

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r2993 | bugman | 2007-01-12 16:02:08 +1100 (Fri, 12 Jan 2007) | 12 lines

Ported r2982 from the 1.2.10 tag using the command:
svn merge -r2981:2982 svn+ssh://bugman@.../svn/relax/tags/1.2.10

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r2982 | bugman | 2007-01-12 13:54:15 +1100 (Fri, 12 Jan 2007) | 3 lines
Changed paths:
M /tags/1.2.10/docs/CHANGES

Updated the CHANGES file for relax version 1.2.10.
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r2994 | bugman | 2007-01-13 15:11:00 +1100 (Sat, 13 Jan 2007) | 10 lines

Rearrangement of the diffusion tensor parameter calculation functions.

These changes are part of the solution for bug #7979 (https://gna.org/bugs/?7979).

The 'self._calc_x()' methods of the DiffTensorElement class, where x is a diffusion tensor
parameter, vector, or matrix, have been shifted from the 'data' directory to the diffusion tensor
code of the 'generic_fns' directory. The methods have also been converted into module functions.
The 'self._update_object()' method calls in the 'self.__setattr__()' method have been modified so
that the type of diffusion is passed into the necessary 'calc_x()' functions.
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r2995 | bugman | 2007-01-13 15:20:50 +1100 (Sat, 13 Jan 2007) | 7 lines

Changed the diffusion tensor MC sim objects from lists to the ListType 'DiffTensorSimList'.

These changes are part of the solution for bug #7979 (https://gna.org/bugs/?7979).

The 'append()' and '__setattr__()' methods of 'DiffTensorSimList' have been set to dummy functions.
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r2996 | bugman | 2007-01-13 16:51:55 +1100 (Sat, 13 Jan 2007) | 3 lines

Added an initial unit test framework for testing of the diffusion tensor objects.
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r2997 | bugman | 2007-01-13 17:03:35 +1100 (Sat, 13 Jan 2007) | 3 lines

Set the executable bit on the diffusion tensor data structure test module.
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r2998 | bugman | 2007-01-13 17:39:38 +1100 (Sat, 13 Jan 2007) | 3 lines

Spell check of the 'unit_test_runner' module.
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r2999 | bugman | 2007-01-13 17:46:48 +1100 (Sat, 13 Jan 2007) | 6 lines

Modified the system/functional + unit test running code so that only the true unit tests are run.

The current setup was looking for unit tests throughout the relax source tree and accidentally
running the code in the file 'minimise/line_search/test_functions.py'.
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r3000 | bugman | 2007-01-13 18:09:15 +1100 (Sat, 13 Jan 2007) | 3 lines

Completed the 'test_set_Diso()' and 'test_set_tm()' unit tests.
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r3001 | bugman | 2007-01-13 18:26:12 +1100 (Sat, 13 Jan 2007) | 3 lines

Modified the 'test_set_Diso' and 'test_set_tm' unit tests to use the proper assert functions.
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r3002 | bugman | 2007-01-13 18:32:59 +1100 (Sat, 13 Jan 2007) | 6 lines

Modified the 'test_set_Diso' unit test.

Rather than testing the RelaxError message string, the 'self.assertRaises()' function is called to
assert that a RelaxError must occur.
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r3003 | bugman | 2007-01-13 18:37:06 +1100 (Sat, 13 Jan 2007) | 6 lines

Modification of the 'test_set_tm' diffusion tensor data structure unit test.

After setting the tm parameter, the automatically generated Diso parameter is tested to see if it is
correctly set.
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r3004 | bugman | 2007-01-13 21:00:17 +1100 (Sat, 13 Jan 2007) | 7 lines

Changes to the output formatting functions of the test suite.

The methods 'self.heading()' and 'self.summary_line()' have been converted to functions and have
been shifted from the file 'test_suite/system_tests/main.py' into the new file
'test_suite/formatting.py'. The final printout by 'test_suite/runner.py' now used these functions.
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r3005 | bugman | 2007-01-13 21:21:47 +1100 (Sat, 13 Jan 2007) | 5 lines

Added the '--unit-test' command line argument.

Supplying this argument to relax will cause solely the unit tests of the test suite to be run.
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r3006 | bugman | 2007-01-13 23:20:29 +1100 (Sat, 13 Jan 2007) | 6 lines

Added the diffusion tensor data structure unit test 'test_set_prolate_params'.

This test checks that all the parameters, vectors, and matrices associated with the prolate
spheroidal diffusion tensor are set up correctly.
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r3007 | bugman | 2007-01-13 23:23:37 +1100 (Sat, 13 Jan 2007) | 3 lines

Renamed the unit test 'test_set_prolate_params' to 'test_set_spheroid_params'.
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r3008 | bugman | 2007-01-13 23:31:39 +1100 (Sat, 13 Jan 2007) | 6 lines

Shifted the calculation of the diffusion objects from the 'test_set_spheroid_params' unit test.

These are now calculated by the method 'self.calc_spheroid_objects()' so that it can be used by
unit tests for the setting of spheroidal errors and simulation values.
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r3009 | bugman | 2007-01-13 23:40:07 +1100 (Sat, 13 Jan 2007) | 3 lines

Added the diffusion tensor object unit test 'test_set_spheroid_errors'.
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r3010 | bugman | 2007-01-13 23:52:49 +1100 (Sat, 13 Jan 2007) | 6 lines

Added the unit test 'test_append_spheroid_sim'.

This test checks that the appending of Monte Carlo simulation spheroidal diffusion tensor parameters
works OK.
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r3011 | bugman | 2007-01-14 00:03:07 +1100 (Sun, 14 Jan 2007) | 7 lines

Added the unit test 'test_set_spheroid_sim'.

This test checks the setting of Monte Carlo simulation spheroidal diffusion tensor parameters making
sure that the diffusion tensor objects are correctly created and that the previous values have been
properly overwritten.
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Added the unit test 'test_set_spheroid_sim'.

This test checks the setting of Monte Carlo simulation spheroidal diffusion tensor parameters making
sure that the diffusion tensor objects are correctly created and that the previous values have been
properly overwritten.

Added the unit test 'test_append_spheroid_sim'.

This test checks that the appending of Monte Carlo simulation spheroidal diffusion tensor parameters
works OK.