Author: semor
Date: Fri Jan 4 23:02:41 2008
New Revision: 4337
URL: http://svn.gna.org/viewcvs/relax?rev=4337&view=rev
Log:
Merged revisions
4241-4253,4255-4262,4264-4270,4272-4274,4276-4291,4293-4295,4297-4298,4300,4302-4305,4307-4335
via svnmerge from
svn+ssh://semor@xxxxxxxxxxx/svn/relax/1.3
........
r4241 | bugman | 2008-01-02 05:53:55 -0500 (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 05:56:41 -0500 (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 06:22:57 -0500 (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 06:36:52 -0500 (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 08:51:28 -0500 (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 08:59:35 -0500 (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 09:01:17 -0500 (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 09:09:46 -0500 (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 09:14:37 -0500 (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 09:20:44 -0500 (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 09:25:43 -0500 (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 09:27:23 -0500 (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 10:11:16 -0500 (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 10:28:34 -0500 (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 10:31:26 -0500 (Wed, 02 Jan 2008) | 3 lines
Updated the main relax copyright notices (including those printed).
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r4257 | bugman | 2008-01-02 10:39:54 -0500 (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 10:59:36 -0500 (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 11:03:51 -0500 (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 11:05:18 -0500 (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 11:13:58 -0500 (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 11:23:19 -0500 (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 11:38:50 -0500 (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 11:41:23 -0500 (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 05:57:32 -0500 (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 07:59:44 -0500 (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 09:16:00 -0500 (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 09:20:29 -0500 (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 09:21:13 -0500 (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 09:52:24 -0500 (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 09:57:05 -0500 (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 09:59:55 -0500 (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 10:12:47 -0500 (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 11:18:57 -0500 (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 11:19:57 -0500 (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 11:22:13 -0500 (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 11:28:19 -0500 (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 11:39:12 -0500 (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 11:43:17 -0500 (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 11:48:10 -0500 (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 11:49:51 -0500 (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 12:00:02 -0500 (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 12:03:57 -0500 (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 12:04:59 -0500 (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 12:06:21 -0500 (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 12:08:36 -0500 (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 12:09:25 -0500 (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 12:19:58 -0500 (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 04:15:11 -0500 (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 04:31:01 -0500 (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 04:35:22 -0500 (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 04:41:38 -0500 (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 04:57:32 -0500 (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 05:00:19 -0500 (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 05:19:35 -0500 (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 05:22:24 -0500 (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 05:26:36 -0500 (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 05:28:07 -0500 (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 05:47:21 -0500 (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 05:51:04 -0500 (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 07:53:24 -0500 (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 07:56:47 -0500 (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 07:57:34 -0500 (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 08:06:10 -0500 (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 08:08:24 -0500 (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 08:10:10 -0500 (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 08:15:01 -0500 (Fri, 04 Jan 2008) | 3 lines
Updated the copyright notice and added some comments.
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r4316 | bugman | 2008-01-04 08:15:56 -0500 (Fri, 04 Jan 2008) | 3 lines
Updated the copyright notice and added some comments.
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r4317 | bugman | 2008-01-04 08:16:47 -0500 (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 08:18:38 -0500 (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 08:32:41 -0500 (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 08:34:59 -0500 (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 08:42:16 -0500 (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 09:34:14 -0500 (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 10:04:53 -0500 (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 10:09:52 -0500 (Fri, 04 Jan 2008) | 3 lines
Replaced the insecure os.tempnam() with tempfile.mktemp().
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r4325 | bugman | 2008-01-04 11:26:07 -0500 (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 11:33:45 -0500 (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 11:39:20 -0500 (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 11:44:32 -0500 (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 11:45:21 -0500 (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 11:49:45 -0500 (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 11:50:17 -0500 (Fri, 04 Jan 2008) | 3 lines
The normal startTest() code is now run as well.
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r4332 | bugman | 2008-01-04 12:22:42 -0500 (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 12:24:29 -0500 (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 12:28:05 -0500 (Fri, 04 Jan 2008) | 6 lines
Reverted the debugging code of r4330.
The command used was:
svn merge -r4330:4329 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
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r4335 | bugman | 2008-01-04 12:30:19 -0500 (Fri, 04 Jan 2008) | 3 lines
The RelaxTestRunner is used now with the --unit-tests command line option.
........
Added:
branches/consistency_tests_1.3/specific_fns/model_free/molmol.py
- copied unchanged from r4335, 1.3/specific_fns/model_free/molmol.py
branches/consistency_tests_1.3/test_suite/relax_test_runner.py
- copied unchanged from r4335, 1.3/test_suite/relax_test_runner.py
Modified:
branches/consistency_tests_1.3/ (props changed)
branches/consistency_tests_1.3/colour.py
branches/consistency_tests_1.3/generic_fns/diffusion_tensor.py
branches/consistency_tests_1.3/generic_fns/minimise.py
branches/consistency_tests_1.3/generic_fns/sequence.py
branches/consistency_tests_1.3/generic_fns/value.py
branches/consistency_tests_1.3/prompt/molmol.py
branches/consistency_tests_1.3/prompt/pymol.py
branches/consistency_tests_1.3/prompt/value.py
branches/consistency_tests_1.3/relax
branches/consistency_tests_1.3/relax_errors.py
branches/consistency_tests_1.3/specific_fns/base_class.py
branches/consistency_tests_1.3/specific_fns/jw_mapping.py
branches/consistency_tests_1.3/specific_fns/model_free/__init__.py
branches/consistency_tests_1.3/specific_fns/model_free/model_free.py
branches/consistency_tests_1.3/specific_fns/relax_fit.py
branches/consistency_tests_1.3/test_suite/runner.py
branches/consistency_tests_1.3/test_suite/unit_tests/_generic_fns/test_diffusion_tensor.py
[... 70 lines stripped ...]
r4337 - in /branches/consistency_tests_1.3: ./ generic_fns/ prompt/ specific_fns/ specific_fns/model_free/ test_suite/ test_...