relax SVN archive

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r4146 | bugman | 2007-12-09 17:41:47 +0100 (Sun, 09 Dec 2007) | 3 lines

Added the infrastructure for the user function arg unit tests of prompt.value.
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r4147 | bugman | 2007-12-09 18:05:13 +0100 (Sun, 09 Dec 2007) | 3 lines

Implemented the val unit test for the value.set() user function.
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r4148 | bugman | 2007-12-09 18:06:37 +0100 (Sun, 09 Dec 2007) | 6 lines

Bug fix.

The value argment to the value.set() user function has been changed to 'val'. The argument was
clashing with the modules because the names were the same.
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r4149 | bugman | 2007-12-09 18:10:31 +0100 (Sun, 09 Dec 2007) | 3 lines

Implemented the param unit test for the value.set() user function.
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r4150 | bugman | 2007-12-09 18:16:21 +0100 (Sun, 09 Dec 2007) | 3 lines

Implemented the spin_id unit test for the value.set() user function.
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r4151 | bugman | 2007-12-09 18:47:22 +0100 (Sun, 09 Dec 2007) | 3 lines

Converted the set() class method into a module function.
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r4152 | bugman | 2007-12-09 18:52:14 +0100 (Sun, 09 Dec 2007) | 3 lines

Shifted all the specific_fns class imports and initialisations from main.py to __init__.py.
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r4153 | bugman | 2007-12-09 18:56:59 +0100 (Sun, 09 Dec 2007) | 5 lines

Big bug fixes.

The structures 'self.relax.specific' and 'self.relax.specific_setup' no longer exist!
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r4154 | bugman | 2007-12-09 19:02:59 +0100 (Sun, 09 Dec 2007) | 5 lines

Shifted the Specific_setup class into the __init__ module.

This class will be replaced by the specific_setup() function but has been kept here for reference.
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r4155 | bugman | 2007-12-09 19:08:17 +0100 (Sun, 09 Dec 2007) | 5 lines

Added a stub of the function get_specific_fn() to specific_fns/__init__.py.

The function generic_fns.value.set() now calls this instead.
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r4156 | bugman | 2007-12-09 19:10:22 +0100 (Sun, 09 Dec 2007) | 3 lines

Added the relaxation curve fitting module to the __init__.__all__ array.
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r4157 | bugman | 2007-12-09 19:13:57 +0100 (Sun, 09 Dec 2007) | 3 lines

Added a docstring for the specific_fns module.
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r4158 | bugman | 2007-12-09 19:16:38 +0100 (Sun, 09 Dec 2007) | 3 lines

Fixed the specific_fns docstring. It should be at the top and it is a package not a module.
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r4159 | bugman | 2007-12-09 19:24:08 +0100 (Sun, 09 Dec 2007) | 3 lines

Converted the get_string() class method into a module function.
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r4160 | bugman | 2007-12-09 19:28:06 +0100 (Sun, 09 Dec 2007) | 3 lines

Created the get_instance() function to return the appropriate class instance.
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r4161 | bugman | 2007-12-09 19:34:57 +0100 (Sun, 09 Dec 2007) | 3 lines

Implemented the get_specific_fn() function.
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r4162 | bugman | 2007-12-09 19:38:56 +0100 (Sun, 09 Dec 2007) | 3 lines

Deleted the Specific_setup class.
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r4163 | bugman | 2007-12-09 21:45:08 +0100 (Sun, 09 Dec 2007) | 3 lines

Converted the sort_params() class method into a function and renamed it to partition_params().
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r4164 | bugman | 2007-12-09 21:46:36 +0100 (Sun, 09 Dec 2007) | 3 lines

Updated the call to partition_params().
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r4165 | bugman | 2007-12-09 21:48:53 +0100 (Sun, 09 Dec 2007) | 3 lines

Passed the val and param args into partition_params() and changed all references to value to val.
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r4166 | bugman | 2007-12-09 21:50:56 +0100 (Sun, 09 Dec 2007) | 3 lines

Added the framework for adding unit tests of the generic_fns.value module.
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r4167 | bugman | 2007-12-09 21:57:46 +0100 (Sun, 09 Dec 2007) | 3 lines

Wrote 4 unit tests for the generic_fns.value.partition_params() function.
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r4168 | bugman | 2007-12-09 21:59:30 +0100 (Sun, 09 Dec 2007) | 5 lines

Bug fix for the partition_params() function.

The structure self.relax.generic does not exist.
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r4169 | bugman | 2007-12-09 22:01:33 +0100 (Sun, 09 Dec 2007) | 3 lines

Bug fix for 2 of the unit tests for the generic_fns.value.partition_params() function.
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r4170 | bugman | 2007-12-09 22:04:13 +0100 (Sun, 09 Dec 2007) | 5 lines

Bug fix for the partition_params() function.

The RelaxUnknownParamError was being thrown when any parameter was not a diffusion tensor parameter!
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r4171 | bugman | 2007-12-09 22:08:44 +0100 (Sun, 09 Dec 2007) | 5 lines

Bug fix for the partition_params() function.

The specific return_data_names function is now passed into it.
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r4172 | bugman | 2007-12-09 22:09:25 +0100 (Sun, 09 Dec 2007) | 5 lines

Updated the unit tests of generic_fns.value.partition_params().

The model-free return_data_name function is passed into it.
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r4173 | bugman | 2007-12-09 22:11:46 +0100 (Sun, 09 Dec 2007) | 3 lines

Added 2 more unit tests for the generic_fns.value.partition_params() function.
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r4174 | bugman | 2007-12-09 22:12:23 +0100 (Sun, 09 Dec 2007) | 3 lines

Removed the unused RelaxError import.
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r4175 | bugman | 2007-12-09 22:17:55 +0100 (Sun, 09 Dec 2007) | 3 lines

Updated the docstring of the generic_fns.value.set() function.
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r4223 | bugman | 2007-12-20 16:56:03 +0100 (Thu, 20 Dec 2007) | 3 lines

Removed some debugging code which was causing problems.
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r4241 | bugman | 2008-01-02 11:53:55 +0100 (Wed, 02 Jan 2008) | 5 lines

Bug fix in the generic_fns.value.set() function.

The diff_params variable is now called tensor_params.
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r4242 | bugman | 2008-01-02 11:56:41 +0100 (Wed, 02 Jan 2008) | 5 lines

Bug fix in the generic_fns.value.set() function.

The self.relax.generic data structure no longer exists.
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r4243 | bugman | 2008-01-02 12:22:57 +0100 (Wed, 02 Jan 2008) | 7 lines

Implemented the generic_fns.minimise.reset_min_stats() function using the new relax design.

This was copied from the old reset_min_stats() class method but has had a few significant changes
made to it. Now both the sequence specific and global min stats are reset all together by one call
to the function.
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r4244 | bugman | 2008-01-02 12:36:52 +0100 (Wed, 02 Jan 2008) | 5 lines

Bug fix for the value.set() user function.

Empty lists are now caught.
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r4245 | bugman | 2008-01-02 14:51:28 +0100 (Wed, 02 Jan 2008) | 5 lines

Updated the val arg unit test of the value.set() user function.

The unit test now properly checks the arg when a list is passed into it.
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r4246 | bugman | 2008-01-02 14:59:35 +0100 (Wed, 02 Jan 2008) | 6 lines

Updated the value.set() user function.

More comments were added to the code, and empty lists passed in as the param argument are now
checked for.
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r4247 | bugman | 2008-01-02 15:01:17 +0100 (Wed, 02 Jan 2008) | 5 lines

Bug fix for the val arg unit test of the value.set() user function.

An elif loop was incorrect.
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r4248 | bugman | 2008-01-02 15:09:46 +0100 (Wed, 02 Jan 2008) | 5 lines

Bug fix for the param arg unit test of the value.set() user function.

Lists are now properly checked.
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r4249 | bugman | 2008-01-02 15:14:37 +0100 (Wed, 02 Jan 2008) | 5 lines

Bug fix for the generic_fns.value.set() function.

The diff_values variable is now called tensor_values.
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r4250 | bugman | 2008-01-02 15:20:44 +0100 (Wed, 02 Jan 2008) | 3 lines

Fixes to the docstring of the generic_fns.diffusion_tensor.set() function.
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r4251 | bugman | 2008-01-02 15:25:43 +0100 (Wed, 02 Jan 2008) | 6 lines

Bug fix for the generic_fns.diffusion_tensor.set() function.

If no diffusion tensor exists, then a RelaxError is thrown when trying to set the parameters. It's
not possible to create a tensor from scratch as the tensor type is unknown.
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r4252 | bugman | 2008-01-02 15:27:23 +0100 (Wed, 02 Jan 2008) | 5 lines

Fixes to the docstring of the generic_fns.diffusion_tensor.set() function.

The fact that the function cannot be used to initialise a tensor is now stated.
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r4253 | bugman | 2008-01-02 16:11:16 +0100 (Wed, 02 Jan 2008) | 5 lines

Bug fix for the param arg unit test of the value.set() user function.

Lists of params with a single value are allowed!
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r4255 | bugman | 2008-01-02 16:28:34 +0100 (Wed, 02 Jan 2008) | 3 lines

A few small changes to prepare the Value_base_class for unit tests.
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r4256 | bugman | 2008-01-02 16:31:26 +0100 (Wed, 02 Jan 2008) | 3 lines

Updated the main relax copyright notices (including those printed).
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r4257 | bugman | 2008-01-02 16:39:54 +0100 (Wed, 02 Jan 2008) | 5 lines

More changes to prepare the Value_base_class for unit tests.

Spin systems are now set up for the molecule.
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r4258 | bugman | 2008-01-02 16:59:36 +0100 (Wed, 02 Jan 2008) | 3 lines

Added 10 unit tests for the setting of spin specific model-free parameter values.
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r4259 | bugman | 2008-01-02 17:03:51 +0100 (Wed, 02 Jan 2008) | 5 lines

Added 10 more unit tests for the setting of spin specific model-free parameter values.

These are simply the 10 previous tests but applied to all spins rather than a single selected spin.
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r4260 | bugman | 2008-01-02 17:05:18 +0100 (Wed, 02 Jan 2008) | 5 lines

Bug fix for the ten unit tests of setting the model-free parameter values for a given spin.

Missing brackets!
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r4261 | bugman | 2008-01-02 17:13:58 +0100 (Wed, 02 Jan 2008) | 5 lines

Added 10 more unit tests for the setting of model-free parameter values.

These tests check the default parameter values if the val arg is not supplied.
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r4262 | bugman | 2008-01-02 17:23:19 +0100 (Wed, 02 Jan 2008) | 3 lines

Added 5 unit tests for the setting of multiple model-free parameter values at once.
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r4264 | bugman | 2008-01-02 17:38:50 +0100 (Wed, 02 Jan 2008) | 5 lines

Removed the RelaxError from generic_fns.diffusion_tensor.return_data_name() if there is no match.

This relatively new RelaxError was causing failures all across relax.
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r4265 | bugman | 2008-01-02 17:41:23 +0100 (Wed, 02 Jan 2008) | 5 lines

Bug fix for the unit test of the generic_fns.diffusion_tensor.return_data_names() function.

No RelaxError is now raised.
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r4266 | bugman | 2008-01-03 11:57:32 +0100 (Thu, 03 Jan 2008) | 3 lines

Wrote 20 unit tests for the setting of RSDM parameters.
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r4267 | bugman | 2008-01-03 13:59:44 +0100 (Thu, 03 Jan 2008) | 6 lines

Fixed some docstring indentation.

8 spaces of indentation were used in a few functions to make these line up with the user function
docstrings when appended to them.
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r4268 | bugman | 2008-01-03 15:16:00 +0100 (Thu, 03 Jan 2008) | 6 lines

Wrote 57 unit tests for the setting of diffusion tensor parameters.

This should cover all valid parameters and parameter combinations. A number of invalid combinations
are also tested. All tests are run twice by the prompt and generic_fns diffusion tensor code.
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r4269 | bugman | 2008-01-03 15:20:29 +0100 (Thu, 03 Jan 2008) | 6 lines

Bug fix for the generic_fns.diffusion_tensor.set() function.

The setting of alpha, beta, and gamma is now forbidden for the spheroidal diffusion tensor. The
setting of theta and phi are also now forbidden for the ellipsoidal diffusion tensor.
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r4270 | bugman | 2008-01-03 15:21:13 +0100 (Thu, 03 Jan 2008) | 3 lines

Fixed the RelaxError message for the ellipsoidal diff tensor when setting theta or phi.
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r4272 | bugman | 2008-01-03 15:52:24 +0100 (Thu, 03 Jan 2008) | 5 lines

Finished converting generic_fns.value.set() to the new relax design.

The function is now considerably simpler.
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r4273 | bugman | 2008-01-03 15:57:05 +0100 (Thu, 03 Jan 2008) | 5 lines

Fixed 2 of the diffusion tensor parameter setting unit tests.

These are the invalid parameter combinations, where the RelaxUnknownParamCombError is thrown.
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r4274 | bugman | 2008-01-03 15:59:55 +0100 (Thu, 03 Jan 2008) | 5 lines

Bug fix for the generic_fns.diffusion_tensor.set() function.

For detecting the parameter combination {Dpar, Dper}, Dpar was being checked twice!
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r4276 | bugman | 2008-01-03 16:12:47 +0100 (Thu, 03 Jan 2008) | 3 lines

Updated the return_value() method of the Common_functions base class to the new relax design.
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r4277 | bugman | 2008-01-03 17:18:57 +0100 (Thu, 03 Jan 2008) | 3 lines

Updated the set() method of the Common_functions base class to the new relax design.
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r4278 | bugman | 2008-01-03 17:19:57 +0100 (Thu, 03 Jan 2008) | 3 lines

Updated the set_update() dummy method of the Common_functions base class to the new relax design.
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r4279 | bugman | 2008-01-03 17:22:13 +0100 (Thu, 03 Jan 2008) | 3 lines

Updated the set_update() method of the Model_free class to the new relax design.
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r4280 | bugman | 2008-01-03 17:28:19 +0100 (Thu, 03 Jan 2008) | 3 lines

Updated the docstrings for epydoc for the set() and set_update() class methods recently updated.
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r4281 | bugman | 2008-01-03 17:39:12 +0100 (Thu, 03 Jan 2008) | 5 lines

Bug fix in the model-free parameter setting code (in the default_value() method).

The parameter checking should have looked for lower case parameter names!
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r4282 | bugman | 2008-01-03 17:43:17 +0100 (Thu, 03 Jan 2008) | 3 lines

Updated the model-free code to use the default CSA and bond length vals in phyical_constants.py.
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r4283 | bugman | 2008-01-03 17:48:10 +0100 (Thu, 03 Jan 2008) | 5 lines

Bug fix for all the spin specific unit tests of the value setting function.

The spin_id should have started with the atom identifier '@' rather than the residue identifier ':'.
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r4284 | bugman | 2008-01-03 17:49:51 +0100 (Thu, 03 Jan 2008) | 5 lines

Another bug fix for the spin specific unit tests of the value setting function.

No spin data was being set up for the reduced spectral density mapping parameter tests.
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r4285 | bugman | 2008-01-03 18:00:02 +0100 (Thu, 03 Jan 2008) | 3 lines

Updated the set() method of the Jw_mapping class to the new relax design.
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r4286 | bugman | 2008-01-03 18:03:57 +0100 (Thu, 03 Jan 2008) | 6 lines

Set __docformat__ for all model-free docstrings which are appended to the user function docstrings.

The line added at the end of the docstring was:
__docformat__ = "plaintext"
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r4287 | bugman | 2008-01-03 18:04:59 +0100 (Thu, 03 Jan 2008) | 6 lines

Set __docformat__ for all jw mapping docstrings which are appended to the user function docstrings.

The line added at the end of the docstring was:
__docformat__ = "plaintext"
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r4288 | bugman | 2008-01-03 18:06:21 +0100 (Thu, 03 Jan 2008) | 3 lines

Slackened the testing of floats in a parameter setting unit test.
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r4289 | bugman | 2008-01-03 18:08:36 +0100 (Thu, 03 Jan 2008) | 5 lines

Bug fix in the specific_fns.jw_mapping.default_value() function.

The CSA parameter check should have been for lower case.
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r4290 | bugman | 2008-01-03 18:09:25 +0100 (Thu, 03 Jan 2008) | 3 lines

Slackened the testing of floats in a parameter setting unit test.
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r4291 | bugman | 2008-01-03 18:19:58 +0100 (Thu, 03 Jan 2008) | 6 lines

Bug fix for the jw mapping parameter setting function specific_fns.jw_mapping.set().

The J(w) parameters do not have default values and now a new RelaxError, RelaxParamSetError, is
raised if these params are set. All the relevent unit tests have been updated for this change.
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r4293 | bugman | 2008-01-04 10:15:11 +0100 (Fri, 04 Jan 2008) | 5 lines

Changed the name of all the diffusion tensor parameter setting unit tests.

This is to prepare for unit tests checking the default values.
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r4294 | bugman | 2008-01-04 10:31:01 +0100 (Fri, 04 Jan 2008) | 3 lines

Wrote the unit tests for the settubg if default diffusion tensor parameter values.
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r4295 | bugman | 2008-01-04 10:35:22 +0100 (Fri, 04 Jan 2008) | 6 lines

Bug fix for the generic_fns.diffusion_tensor.set() function.

When setting a default value, the non-existant array 'object_names' was being accessed. The array
is actually 'params'!
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r4297 | bugman | 2008-01-04 10:41:38 +0100 (Fri, 04 Jan 2008) | 6 lines

Bug fixes for the unit tests of the setting of default values of the diff params.

The correct default values are now being checked, and some tests were made less stringent (using
assertAlmostEqual).
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r4298 | bugman | 2008-01-04 10:57:32 +0100 (Fri, 04 Jan 2008) | 6 lines

Bug fix for the generic_fns.diffusion_tensor.default_values() function.

For each parameter which defaults to zero, None was being returned instead!!! This bug was caught
by the unit tests of the setting of default diffusion tensor parameter values.
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r4300 | bugman | 2008-01-04 11:00:19 +0100 (Fri, 04 Jan 2008) | 3 lines

Slackened the testing of floats in a diff parameter setting unit test.
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r4302 | bugman | 2008-01-04 11:19:35 +0100 (Fri, 04 Jan 2008) | 3 lines

Added 14 unit tests for the setting of relaxation curve fitting parameter values.
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r4303 | bugman | 2008-01-04 11:22:24 +0100 (Fri, 04 Jan 2008) | 3 lines

Renamed all the previous unit tests from 'test_set_relax_data_xxx' to 'test_set_relax_fit_xxx'.
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r4304 | bugman | 2008-01-04 11:26:36 +0100 (Fri, 04 Jan 2008) | 3 lines

Converted specific_fns.relax_fit.data_init() to the new relax design.
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r4305 | bugman | 2008-01-04 11:28:07 +0100 (Fri, 04 Jan 2008) | 5 lines

Bug fix for the specific_fns.relax_fit.default_value() function.

The Iinf parameter was being checked for as 'te'!!!
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r4307 | bugman | 2008-01-04 11:47:21 +0100 (Fri, 04 Jan 2008) | 7 lines

Modified the structure of the model-free classes containing the model-free specific functions.

One parent, but empty, class called Model_free now inherits all model-free specific functions from
the other classes. The Molmol specific class has also been shifted into its own module as the
initial step for splitting up the original, massive 'model_free.py' file.
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r4308 | bugman | 2008-01-04 11:51:04 +0100 (Fri, 04 Jan 2008) | 3 lines

Prepended 'molmol_' to the start of all the Molmol functions.
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r4309 | bugman | 2008-01-04 13:53:24 +0100 (Fri, 04 Jan 2008) | 3 lines

Updated all of the model-free specific Molmol macro function to the new relax design.
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r4310 | bugman | 2008-01-04 13:56:47 +0100 (Fri, 04 Jan 2008) | 3 lines

Converted the module from being dependent on Numeric to using numpy.
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r4311 | bugman | 2008-01-04 13:57:34 +0100 (Fri, 04 Jan 2008) | 3 lines

Updated 2 comments relating to the change from Numeric to numpy.
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r4312 | bugman | 2008-01-04 14:06:10 +0100 (Fri, 04 Jan 2008) | 3 lines

Converted all the class methods of the colour module to functions.
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r4313 | bugman | 2008-01-04 14:08:24 +0100 (Fri, 04 Jan 2008) | 3 lines

Removed all of the imports of the now non-existant 'Colour' class.
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r4314 | bugman | 2008-01-04 14:10:10 +0100 (Fri, 04 Jan 2008) | 5 lines

Fixed the appending of the molmol_classic_style docstring.

The function used to be called simply classic.
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r4315 | bugman | 2008-01-04 14:15:01 +0100 (Fri, 04 Jan 2008) | 3 lines

Updated the copyright notice and added some comments.
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r4316 | bugman | 2008-01-04 14:15:56 +0100 (Fri, 04 Jan 2008) | 3 lines

Updated the copyright notice and added some comments.
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r4317 | bugman | 2008-01-04 14:16:47 +0100 (Fri, 04 Jan 2008) | 3 lines

Updated the copyright notice by adding the date the file was originally created.
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r4318 | bugman | 2008-01-04 14:18:38 +0100 (Fri, 04 Jan 2008) | 3 lines

Removed the import of the now non-existant 'Colour' class.
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r4319 | bugman | 2008-01-04 14:32:41 +0100 (Fri, 04 Jan 2008) | 3 lines

Added the command line option --system-tests to run solely the relax system/functional tests.
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r4320 | bugman | 2008-01-04 14:34:59 +0100 (Fri, 04 Jan 2008) | 5 lines

Changed the --unit-test command line option to --unit-tests.

The old option still works thanks to the optparse package.
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r4321 | bugman | 2008-01-04 14:42:16 +0100 (Fri, 04 Jan 2008) | 5 lines

Bug fix for running solely the system/functional tests.

The interpeter, which is essential for the tests, is now loaded.
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r4322 | bugman | 2008-01-04 15:34:14 +0100 (Fri, 04 Jan 2008) | 6 lines

A temporary fix for catching stdout during the execution of all unit tests.

The aim is to eventually have stdout collected for each test run and appended to the failure or
error message if the test was unsuccessful.
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r4323 | bugman | 2008-01-04 16:04:53 +0100 (Fri, 04 Jan 2008) | 5 lines

Update for the generic_fns.sequence.display() function.

Now the function operates correctly with IO redirection of stdout.
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r4324 | bugman | 2008-01-04 16:09:52 +0100 (Fri, 04 Jan 2008) | 3 lines

Replaced the insecure os.tempnam() with tempfile.mktemp().
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r4325 | bugman | 2008-01-04 17:26:07 +0100 (Fri, 04 Jan 2008) | 6 lines

Created the framework for a new unittest runner to replace TextTestRunner.

The point it to capture STDOUT during each test and only print it in the reports for failures and
errors.
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r4326 | bugman | 2008-01-04 17:33:45 +0100 (Fri, 04 Jan 2008) | 5 lines

Shifted the IO redirection into the RelaxTestRunner.run() method.

This is a temporary change.
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r4327 | bugman | 2008-01-04 17:39:20 +0100 (Fri, 04 Jan 2008) | 5 lines

Created the _RelaxTestResult class as a replacement for _TextTestResult.

This is where the capture of STDOUT should occur.
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r4328 | bugman | 2008-01-04 17:44:32 +0100 (Fri, 04 Jan 2008) | 5 lines

Shifted the STDOUT redirection into the startTest() and stopTest() methods.

These methods are overrides for those in TestResult and _TextTestResult.
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r4329 | bugman | 2008-01-04 17:45:21 +0100 (Fri, 04 Jan 2008) | 3 lines

Restored the run() method accidentally renamed to run2() in the last commit.
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r4330 | bugman | 2008-01-04 17:49:45 +0100 (Fri, 04 Jan 2008) | 3 lines

Added a deliberate unit test failure for implementing the new RelaxTestRunner code.
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r4331 | bugman | 2008-01-04 17:50:17 +0100 (Fri, 04 Jan 2008) | 3 lines

The normal startTest() code is now run as well.
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r4332 | bugman | 2008-01-04 18:22:42 +0100 (Fri, 04 Jan 2008) | 3 lines

Completed the STDOUT capture and prepending by added an override for _TextTestResult.addError().
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r4333 | bugman | 2008-01-04 18:24:29 +0100 (Fri, 04 Jan 2008) | 3 lines

Removed the RelaxTestRunner.run() method as it was doing nothing.
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r4334 | bugman | 2008-01-04 18:28:05 +0100 (Fri, 04 Jan 2008) | 6 lines

Reverted the debugging code of r4330.

The command used was:
svn merge -r4330:4329 svn+ssh://bugman@.../svn/relax/1.3
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r4335 | bugman | 2008-01-04 18:30:19 +0100 (Fri, 04 Jan 2008) | 3 lines

The RelaxTestRunner is used now with the --unit-tests command line option.
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r4338 | bugman | 2008-01-05 17:09:45 +0100 (Sat, 05 Jan 2008) | 3 lines

Converted the pipe creation functional test to use the unittest framework.
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r4339 | bugman | 2008-01-05 17:10:10 +0100 (Sat, 05 Jan 2008) | 3 lines

Removed the pipe creation test from the old system/functional test framework.
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r4340 | bugman | 2008-01-05 17:20:36 +0100 (Sat, 05 Jan 2008) | 6 lines

Created a class called System_test_runner for executing the system/functional tests.

Whether this is replaced by Gary's Unit_test_runner, invokes Unit_test_runner, or is independent of
Unit_test_runner is not yet known.
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r4341 | bugman | 2008-01-05 17:24:27 +0100 (Sat, 05 Jan 2008) | 3 lines

Renamed the pipe creation module to start with 'test_'.
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r4342 | bugman | 2008-01-05 17:37:41 +0100 (Sat, 05 Jan 2008) | 5 lines

Added some code to execute the new system/functional tests.

This just runs the System_test_runner.run() method which doesn't do anything yet.
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r4343 | bugman | 2008-01-05 17:50:15 +0100 (Sat, 05 Jan 2008) | 3 lines

Added the ability to run the new system/functional tests based on the unittest framework.
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r4344 | bugman | 2008-01-05 17:52:24 +0100 (Sat, 05 Jan 2008) | 6 lines

Bug fix for the pipe creation system test.

The __init__ function should not be overwritten! The relax instance must be passed in by some other
method.
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r4345 | bugman | 2008-01-05 18:01:08 +0100 (Sat, 05 Jan 2008) | 5 lines

Placed the relax namespace into the new system tests.

The relax namespace will now be available to all new TestCase class instances.
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r4346 | bugman | 2008-01-05 18:01:50 +0100 (Sat, 05 Jan 2008) | 3 lines

Removed the unused 'runner' argument to System_test_runner.run().
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r4347 | bugman | 2008-01-05 18:03:00 +0100 (Sat, 05 Jan 2008) | 3 lines

Fixed the reference to the now non-existent 'pipe' variable.
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r4348 | bugman | 2008-01-05 18:04:53 +0100 (Sat, 05 Jan 2008) | 3 lines

System_test_runner.run() is no longer called with the runner argument.
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r4349 | bugman | 2008-01-05 18:06:32 +0100 (Sat, 05 Jan 2008) | 3 lines

Added the missing import of the relax data storage object into the pipe creation system test.
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r4350 | bugman | 2008-01-05 18:09:29 +0100 (Sat, 05 Jan 2008) | 3 lines

Shifted to RelaxTestRunner for the new system/functional tests to catch STDOUT.
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r4351 | bugman | 2008-01-05 18:10:35 +0100 (Sat, 05 Jan 2008) | 3 lines

Added a missing newline.
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r4352 | bugman | 2008-01-05 18:12:16 +0100 (Sat, 05 Jan 2008) | 3 lines

The results of the new system/functional test framework is now returned.
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r4353 | bugman | 2008-01-05 18:27:07 +0100 (Sat, 05 Jan 2008) | 3 lines

Renamed the test suite running module to test_suite_runner.
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r4354 | bugman | 2008-01-05 18:41:07 +0100 (Sat, 05 Jan 2008) | 5 lines

Split the Test_suite_runner.__init__() method into many smaller methods.

This is part of a clean up of the messy base structure of the relax test suite.
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r4355 | bugman | 2008-01-05 18:45:36 +0100 (Sat, 05 Jan 2008) | 6 lines

Clean up of the operation of the --unit-tests and --system-tests command line options.

These now use the Test_suite_runner methods so that the 'relax' file need not deal with the
implementation details of the various test suite categories.
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r4356 | bugman | 2008-01-05 19:02:54 +0100 (Sat, 05 Jan 2008) | 5 lines

Started to convert the model-free system tests to the new unittest framework.

The relaxation data reading test has been converted, but no other tests are currently functional.
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r4357 | bugman | 2008-01-05 19:09:42 +0100 (Sat, 05 Jan 2008) | 5 lines

Bug fix for the new system/functional test framework.

Now all tests from all TestCase instances are run.
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r4358 | bugman | 2008-01-05 19:13:30 +0100 (Sat, 05 Jan 2008) | 3 lines

Converted the CSA value setting test to the new framework.
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r4359 | bugman | 2008-01-05 19:16:20 +0100 (Sat, 05 Jan 2008) | 3 lines

Converted the Bond length value setting test to the new system test framework.
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r4360 | bugman | 2008-01-05 19:19:01 +0100 (Sat, 05 Jan 2008) | 3 lines

Converted the CSA and bond length value setting test to the new system test framework.
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r4361 | bugman | 2008-01-05 20:09:19 +0100 (Sat, 05 Jan 2008) | 3 lines

Converted all of the model-free system/functional tests to the new unittest framework.
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r4362 | bugman | 2008-01-05 20:19:57 +0100 (Sat, 05 Jan 2008) | 3 lines

Converted all of the diffusion tensor system/functional tests to the new unittest framework.
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r4363 | bugman | 2008-01-05 20:25:44 +0100 (Sat, 05 Jan 2008) | 3 lines

Converted all of the angle system/functional tests to the new unittest framework.
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r4364 | bugman | 2008-01-05 20:32:06 +0100 (Sat, 05 Jan 2008) | 3 lines

Converted all of the generic system/functional tests to the new unittest framework.
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r4365 | bugman | 2008-01-05 20:39:03 +0100 (Sat, 05 Jan 2008) | 3 lines

Converted all of the model selection system/functional tests to the new unittest framework.
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r4366 | bugman | 2008-01-05 20:44:13 +0100 (Sat, 05 Jan 2008) | 3 lines

Converted all of the relaxation curve fitting system/functional tests to the new unittest framework.
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r4367 | bugman | 2008-01-05 20:58:57 +0100 (Sat, 05 Jan 2008) | 3 lines

Converted all the remaining system/functional tests to the new unittest framework.
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r4368 | bugman | 2008-01-05 21:02:22 +0100 (Sat, 05 Jan 2008) | 3 lines

Removed all last remnants of the old system/functional test runner.
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r4369 | bugman | 2008-01-05 21:04:54 +0100 (Sat, 05 Jan 2008) | 3 lines

Fixed the call to the residue_loop iterator in the Jw mapping system tests.
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r4370 | bugman | 2008-01-05 21:06:44 +0100 (Sat, 05 Jan 2008) | 3 lines

The sequence system/functional tests are now run.
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r4371 | bugman | 2008-01-05 21:08:14 +0100 (Sat, 05 Jan 2008) | 3 lines

Renamed the test_pipe_create module and class back to pipe_create.
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r4372 | bugman | 2008-01-05 23:27:48 +0100 (Sat, 05 Jan 2008) | 3 lines

Bug fix in the angles calculation system test.
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r4374 | bugman | 2008-01-05 23:33:38 +0100 (Sat, 05 Jan 2008) | 5 lines

Bug fix for the system tests calling the state.load() user function.

The 'file' argument is now called 'state'.
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r4375 | bugman | 2008-01-05 23:35:55 +0100 (Sat, 05 Jan 2008) | 5 lines

Another bug fix for the system tests calling the state.load() user function.

The 'dir' argument is now called 'dir_name'.
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r4376 | bugman | 2008-01-05 23:58:30 +0100 (Sat, 05 Jan 2008) | 3 lines

Shifted all the gyromagnetic ratio values into the physical constants file.
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r4377 | bugman | 2008-01-06 00:22:00 +0100 (Sun, 06 Jan 2008) | 6 lines

Wrote 12 unit tests for using the value setting functions to set the hetero and homonuclei.

This is in preparation for replacing the nuclei() user function with the more powerful value.set().
The values also need to now be spin specific.
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r4378 | bugman | 2008-01-06 00:36:43 +0100 (Sun, 06 Jan 2008) | 3 lines

Updated the model-free code to handle a spin system specific 'nucleus' variable.
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r4379 | bugman | 2008-01-06 00:37:50 +0100 (Sun, 06 Jan 2008) | 3 lines

Removed all the setting of the homonucleus unit tests.
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r4380 | bugman | 2008-01-06 00:40:49 +0100 (Sun, 06 Jan 2008) | 5 lines

Fixed all the unit tests of setting the heteronucleus type.

The variable will be called 'nucleus' and not 'heteronuc'.
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r4381 | bugman | 2008-01-06 00:45:50 +0100 (Sun, 06 Jan 2008) | 3 lines

The specific value setting function, of the base class, now handles string values.
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r4382 | bugman | 2008-01-06 00:54:34 +0100 (Sun, 06 Jan 2008) | 3 lines

Updated the J(w) mapping code to handle a spin system specific 'nucleus' variable.
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r4383 | bugman | 2008-01-06 01:01:41 +0100 (Sun, 06 Jan 2008) | 5 lines

Renamed the J(w) mapping specific set() method to set_doc().

The base class method set() is used instead.
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r4384 | bugman | 2008-01-06 01:03:45 +0100 (Sun, 06 Jan 2008) | 3 lines

Updated the value.set() user function to use the correct J(w) mapping value setting docstring.
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r4385 | bugman | 2008-01-06 01:05:05 +0100 (Sun, 06 Jan 2008) | 5 lines

Bug fix for the base class value setting method set().

If no default value exists, this is now caught and a RelaxError is thrown.
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r4386 | bugman | 2008-01-06 01:10:34 +0100 (Sun, 06 Jan 2008) | 5 lines

Updated the value.set() user function to accept string values of the 'value' variable.

Two new RelaxErrors have been created for this.
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r4387 | bugman | 2008-01-06 01:12:58 +0100 (Sun, 06 Jan 2008) | 3 lines

Updated the value arg unit test of the value.set() user function to use the new RelaxError.
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r4388 | bugman | 2008-01-06 01:18:12 +0100 (Sun, 06 Jan 2008) | 3 lines

Added a missing RelaxError import.
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r4389 | bugman | 2008-01-06 01:20:11 +0100 (Sun, 06 Jan 2008) | 3 lines

Updated the value arg unit test of the value.set() user function to use another new RelaxError.
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r4390 | bugman | 2008-01-06 01:26:47 +0100 (Sun, 06 Jan 2008) | 5 lines

Bug fix for the value arg unit test of the value.set() user function.

The valid str arg types are now being caught and skipped.
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r4391 | bugman | 2008-01-06 12:03:56 +0100 (Sun, 06 Jan 2008) | 3 lines

Converted all the 'structure' user functions to the new relax design.
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r4392 | bugman | 2008-01-06 12:28:55 +0100 (Sun, 06 Jan 2008) | 5 lines

Modified the structure.vectors() user function to use the spin_id string.

It was previously using the residue number and name id system.
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r4393 | bugman | 2008-01-06 12:32:25 +0100 (Sun, 06 Jan 2008) | 3 lines

Wrote 16 unit tests for all args of all structure user functions.
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r4394 | bugman | 2008-01-06 12:34:38 +0100 (Sun, 06 Jan 2008) | 5 lines

Bug fix for the model arg unit test of the structure.read_pdb() user function.

The value is a str, not an int.
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r4395 | bugman | 2008-01-06 12:36:58 +0100 (Sun, 06 Jan 2008) | 5 lines

Bug fix for the structure.read_pdb() user function.

The incorrect RelaxError was being raised for the model argument.
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r4396 | bugman | 2008-01-06 12:39:37 +0100 (Sun, 06 Jan 2008) | 5 lines

Bug fix for the model arg unit test of the structure.read_pdb() user function.

Bin args are now caught as well.
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r4397 | bugman | 2008-01-06 12:49:35 +0100 (Sun, 06 Jan 2008) | 5 lines

Bug fix for the scale arg unit test of the structure.create_diff_tensor_pdb() user function.

Bin args are now caught as well.
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r4398 | bugman | 2008-01-06 20:37:51 +0100 (Sun, 06 Jan 2008) | 3 lines

Added a missing RelaxError import.
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r4402 | bugman | 2008-01-07 10:58:02 +0100 (Mon, 07 Jan 2008) | 3 lines

Converted all of the minimise user functions to the new relax design.
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r4403 | bugman | 2008-01-07 11:05:40 +0100 (Mon, 07 Jan 2008) | 3 lines

Created the base class for the unit tests of the prompt and generic_fns minimisation functions.
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r4404 | bugman | 2008-01-07 11:06:06 +0100 (Mon, 07 Jan 2008) | 3 lines

Wrote the print_flag arg unit test of the minimise.calc() user function.
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r4405 | bugman | 2008-01-07 11:40:38 +0100 (Mon, 07 Jan 2008) | 3 lines

Wrote 5 unit tests for the arguments of the minimise.grid_search() user function.
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r4406 | bugman | 2008-01-07 11:48:17 +0100 (Mon, 07 Jan 2008) | 3 lines

Added string tuples as a new data type for the user function argument unit tests.
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r4407 | bugman | 2008-01-07 12:01:40 +0100 (Mon, 07 Jan 2008) | 5 lines

Wrote a unit test for the arguments to the minimise() user function.

This is for the variable argument list for the minimisation algorithm and its options.
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r4408 | bugman | 2008-01-07 12:03:33 +0100 (Mon, 07 Jan 2008) | 5 lines

Bug fix for the minimise() user function.

All arguments are now checked if they are strings.
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r4409 | bugman | 2008-01-07 13:12:28 +0100 (Mon, 07 Jan 2008) | 5 lines

Simplified the non-keyword argument test of the minimise() user function.

Nested looping is not necessary to test all combinations.
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r4410 | bugman | 2008-01-07 13:13:40 +0100 (Mon, 07 Jan 2008) | 5 lines

Fixed the docstrings of the calc() and grid_search() arg unit tests.

The user functions were incorrectly named with 'minimisation.' prepended.
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r4411 | bugman | 2008-01-07 13:14:22 +0100 (Mon, 07 Jan 2008) | 3 lines

Removed an unnecessary comment.
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r4412 | bugman | 2008-01-07 13:16:08 +0100 (Mon, 07 Jan 2008) | 3 lines

More tidying up of the unit test comments.
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r4413 | bugman | 2008-01-07 13:19:05 +0100 (Mon, 07 Jan 2008) | 3 lines

Wrote a unit test to check the behaviour of minimise() user function with a bad keyword arg.
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r4414 | bugman | 2008-01-07 13:31:37 +0100 (Mon, 07 Jan 2008) | 3 lines

Wrote 6 unit tests for the rest of the minimise() user function keyword arguments.
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r4415 | bugman | 2008-01-07 13:32:55 +0100 (Mon, 07 Jan 2008) | 5 lines

Bug fix for the minimise() user function.

The maximum number of iterations should be an integer. A float should not be accepted!
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r4416 | bugman | 2008-01-07 13:35:00 +0100 (Mon, 07 Jan 2008) | 3 lines

Updated a copyright statement.
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r4417 | bugman | 2008-01-07 13:37:30 +0100 (Mon, 07 Jan 2008) | 5 lines

Bug fix for the grid_search() user function.

Empty lists for the lower, upper, and inc args now throw a RelaxError.
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r4418 | bugman | 2008-01-07 13:40:55 +0100 (Mon, 07 Jan 2008) | 3 lines

Bug fix for the lower and upper args to the grid_search() user function.
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r4419 | bugman | 2008-01-07 13:43:42 +0100 (Mon, 07 Jan 2008) | 5 lines

Bug fix for the params arg unit test of the diffusion_tensor.init() user function.

The new str tuples are now properly handled.
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r4424 | bugman | 2008-01-07 14:26:57 +0100 (Mon, 07 Jan 2008) | 3 lines

Added the missing import of the minimise module.
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r4426 | bugman | 2008-01-07 15:22:29 +0100 (Mon, 07 Jan 2008) | 3 lines

Converted all class methods of generic_fns.minimise() into functions following the new relax design.
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r4427 | bugman | 2008-01-07 15:26:46 +0100 (Mon, 07 Jan 2008) | 5 lines

Removed all of the modules for setting the nucleus type.

This has been shifted into the value.set() user function instead.
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r4428 | bugman | 2008-01-07 15:30:32 +0100 (Mon, 07 Jan 2008) | 6 lines

Bug fixes for all the system tests trying to set the nucleus type.

The call to self.relax.interpreter._Nuclei.nuclei() has been replaced with a call to
self.relax.interpreter._Value.set().
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r4430 | bugman | 2008-01-07 15:52:55 +0100 (Mon, 07 Jan 2008) | 5 lines

Bug fix for the read() and test_labels() methods of the specific_fns.relax_data.Rx_data class.

The arguments are not placed into self!
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r4431 | bugman | 2008-01-07 15:58:52 +0100 (Mon, 07 Jan 2008) | 5 lines

Many fixes for the specific_fns.relax_data.find_index() function.

This function now fits into the new relax design.
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r4432 | bugman | 2008-01-07 16:01:23 +0100 (Mon, 07 Jan 2008) | 3 lines

Bug fix. Updated all the calls to self.find_index().
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r4433 | bugman | 2008-01-07 16:06:07 +0100 (Mon, 07 Jan 2008) | 6 lines

Bug fix for the J(w) mapping system tests trying to set the nucleus type.

The call to self.relax.interpreter._Nuclei.nuclei() has been replaced with a call to
self.relax.interpreter._Value.set().
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r4440 | bugman | 2008-01-07 17:36:57 +0100 (Mon, 07 Jan 2008) | 3 lines

Created a directory for user scripts to be used as system/functional tests.
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r4447 | bugman | 2008-01-07 17:59:23 +0100 (Mon, 07 Jan 2008) | 5 lines

Added the quit argument to the run() class method.

This is to allow the system/functional tests to run this method and to ask relax not to quit.
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r4449 | bugman | 2008-01-07 18:09:07 +0100 (Mon, 07 Jan 2008) | 5 lines

Created a script containing the commands used in the system test for creating a model-free model.

The system test executes the script instead of running the commands itself.
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r4450 | bugman | 2008-01-07 18:15:09 +0100 (Mon, 07 Jan 2008) | 5 lines

The script file is now passed into the interpreter run() method.

This change is like to break many things!!!
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r4452 | bugman | 2008-01-07 18:19:07 +0100 (Mon, 07 Jan 2008) | 3 lines

Fixed the running of the script for the model-free m4 model creating system test.
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r4453 | bugman | 2008-01-07 18:28:57 +0100 (Mon, 07 Jan 2008) | 3 lines

Completely changed how the relax program introduction is handled.
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r4454 | bugman | 2008-01-07 18:35:50 +0100 (Mon, 07 Jan 2008) | 3 lines

Added the ability to turn off the printing out of the script prior to its execution.
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r4455 | bugman | 2008-01-07 18:36:51 +0100 (Mon, 07 Jan 2008) | 3 lines

Turned off the printing of the script prior to its execution in the system tests.
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r4456 | bugman | 2008-01-07 18:42:18 +0100 (Mon, 07 Jan 2008) | 5 lines

Shifted the quit option from run() to __init__().

This will remove the need for all system tests using a script to ask the interpreter to not exit.
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r4457 | bugman | 2008-01-07 18:42:52 +0100 (Mon, 07 Jan 2008) | 3 lines

Made the 'intro_string', 'quit', and 'show_script' variables private.
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r4458 | bugman | 2008-01-07 18:43:35 +0100 (Mon, 07 Jan 2008) | 3 lines

Passed the quit flag into the prompt mode of operation.
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r4461 | semor | 2008-01-07 18:58:13 +0100 (Mon, 07 Jan 2008) | 3 lines

Fixed a typo in an import statement.
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