Author: semor
Date: Mon Jan 7 17:43:43 2008
New Revision: 4442
URL: http://svn.gna.org/viewcvs/relax?rev=4442&view=rev
Log:
Merged revisions 4338-4372,4374-4398,4402-4419,4424,4426-4428,4430-4433 via
svnmerge from
svn+ssh://semor@xxxxxxxxxxx/svn/relax/1.3
........
r4338 | bugman | 2008-01-05 11:09:45 -0500 (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 11:10:10 -0500 (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 11:20:36 -0500 (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 11:24:27 -0500 (Sat, 05 Jan 2008) | 3 lines
Renamed the pipe creation module to start with 'test_'.
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r4342 | bugman | 2008-01-05 11:37:41 -0500 (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 11:50:15 -0500 (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 11:52:24 -0500 (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 12:01:08 -0500 (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 12:01:50 -0500 (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 12:03:00 -0500 (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 12:04:53 -0500 (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 12:06:32 -0500 (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 12:09:29 -0500 (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 12:10:35 -0500 (Sat, 05 Jan 2008) | 3 lines
Added a missing newline.
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r4352 | bugman | 2008-01-05 12:12:16 -0500 (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 12:27:07 -0500 (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 12:41:07 -0500 (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 12:45:36 -0500 (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 13:02:54 -0500 (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 13:09:42 -0500 (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 13:13:30 -0500 (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 13:16:20 -0500 (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 13:19:01 -0500 (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 14:09:19 -0500 (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 14:19:57 -0500 (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 14:25:44 -0500 (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 14:32:06 -0500 (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 14:39:03 -0500 (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 14:44:13 -0500 (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 14:58:57 -0500 (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 15:02:22 -0500 (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 15:04:54 -0500 (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 15:06:44 -0500 (Sat, 05 Jan 2008) | 3 lines
The sequence system/functional tests are now run.
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r4371 | bugman | 2008-01-05 15:08:14 -0500 (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 17:27:48 -0500 (Sat, 05 Jan 2008) | 3 lines
Bug fix in the angles calculation system test.
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r4374 | bugman | 2008-01-05 17:33:38 -0500 (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 17:35:55 -0500 (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 17:58:30 -0500 (Sat, 05 Jan 2008) | 3 lines
Shifted all the gyromagnetic ratio values into the physical constants file.
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r4377 | bugman | 2008-01-05 18:22:00 -0500 (Sat, 05 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 | 2008-01-05 18:36:43 -0500 (Sat, 05 Jan 2008) | 3 lines
Updated the model-free code to handle a spin system specific 'nucleus'
variable.
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r4379 | bugman | 2008-01-05 18:37:50 -0500 (Sat, 05 Jan 2008) | 3 lines
Removed all the setting of the homonucleus unit tests.
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r4380 | bugman | 2008-01-05 18:40:49 -0500 (Sat, 05 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 | 2008-01-05 18:45:50 -0500 (Sat, 05 Jan 2008) | 3 lines
The specific value setting function, of the base class, now handles string
values.
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r4382 | bugman | 2008-01-05 18:54:34 -0500 (Sat, 05 Jan 2008) | 3 lines
Updated the J(w) mapping code to handle a spin system specific 'nucleus'
variable.
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r4383 | bugman | 2008-01-05 19:01:41 -0500 (Sat, 05 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 | 2008-01-05 19:03:45 -0500 (Sat, 05 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 | 2008-01-05 19:05:05 -0500 (Sat, 05 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 | 2008-01-05 19:10:34 -0500 (Sat, 05 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 | 2008-01-05 19:12:58 -0500 (Sat, 05 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 | 2008-01-05 19:18:12 -0500 (Sat, 05 Jan 2008) | 3 lines
Added a missing RelaxError import.
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r4389 | bugman | 2008-01-05 19:20:11 -0500 (Sat, 05 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 | 2008-01-05 19:26:47 -0500 (Sat, 05 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 06:03:56 -0500 (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 06:28:55 -0500 (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 06:32:25 -0500 (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 06:34:38 -0500 (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 06:36:58 -0500 (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 06:39:37 -0500 (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 06:49:35 -0500 (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 14:37:51 -0500 (Sun, 06 Jan 2008) | 3 lines
Added a missing RelaxError import.
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r4402 | bugman | 2008-01-07 04:58:02 -0500 (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 05:05:40 -0500 (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 05:06:06 -0500 (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 05:40:38 -0500 (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 05:48:17 -0500 (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 06:01:40 -0500 (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 06:03:33 -0500 (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 07:12:28 -0500 (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 07:13:40 -0500 (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 07:14:22 -0500 (Mon, 07 Jan 2008) | 3 lines
Removed an unnecessary comment.
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r4412 | bugman | 2008-01-07 07:16:08 -0500 (Mon, 07 Jan 2008) | 3 lines
More tidying up of the unit test comments.
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r4413 | bugman | 2008-01-07 07:19:05 -0500 (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 07:31:37 -0500 (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 07:32:55 -0500 (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 07:35:00 -0500 (Mon, 07 Jan 2008) | 3 lines
Updated a copyright statement.
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r4417 | bugman | 2008-01-07 07:37:30 -0500 (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 07:40:55 -0500 (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 07:43:42 -0500 (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 08:26:57 -0500 (Mon, 07 Jan 2008) | 3 lines
Added the missing import of the minimise module.
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r4426 | bugman | 2008-01-07 09:22:29 -0500 (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 09:26:46 -0500 (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 09:30:32 -0500 (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().
........
r4430 | bugman | 2008-01-07 09:52:55 -0500 (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 09:58:52 -0500 (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 10:01:23 -0500 (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 10:06:07 -0500 (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().
........
Added:
branches/consistency_tests_1.3/test_suite/test_suite_runner.py
- copied unchanged from r4433, 1.3/test_suite/test_suite_runner.py
branches/consistency_tests_1.3/test_suite/unit_tests/_prompt/test_minimisation.py
- copied unchanged from r4433,
1.3/test_suite/unit_tests/_prompt/test_minimisation.py
branches/consistency_tests_1.3/test_suite/unit_tests/_prompt/test_structure.py
- copied unchanged from r4433,
1.3/test_suite/unit_tests/_prompt/test_structure.py
branches/consistency_tests_1.3/test_suite/unit_tests/minimisation_testing_base.py
- copied unchanged from r4433,
1.3/test_suite/unit_tests/minimisation_testing_base.py
branches/consistency_tests_1.3/test_suite/unit_tests/structure_testing_base.py
- copied unchanged from r4433,
1.3/test_suite/unit_tests/structure_testing_base.py
Removed:
branches/consistency_tests_1.3/generic_fns/nuclei.py
branches/consistency_tests_1.3/prompt/nuclei.py
branches/consistency_tests_1.3/test_suite/runner.py
branches/consistency_tests_1.3/test_suite/system_tests/main.py
Modified:
branches/consistency_tests_1.3/ (props changed)
branches/consistency_tests_1.3/generic_fns/minimise.py
branches/consistency_tests_1.3/physical_constants.py
branches/consistency_tests_1.3/prompt/grace.py
branches/consistency_tests_1.3/prompt/interpreter.py
branches/consistency_tests_1.3/prompt/minimisation.py
branches/consistency_tests_1.3/prompt/structure.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/model_free.py
branches/consistency_tests_1.3/specific_fns/relax_data.py
branches/consistency_tests_1.3/test_suite/system_tests/__init__.py
branches/consistency_tests_1.3/test_suite/system_tests/angles.py
branches/consistency_tests_1.3/test_suite/system_tests/diffusion_tensor.py
branches/consistency_tests_1.3/test_suite/system_tests/generic.py
branches/consistency_tests_1.3/test_suite/system_tests/jw_mapping.py
branches/consistency_tests_1.3/test_suite/system_tests/model_free.py
branches/consistency_tests_1.3/test_suite/system_tests/model_selection.py
branches/consistency_tests_1.3/test_suite/system_tests/pipe_create.py
branches/consistency_tests_1.3/test_suite/system_tests/relax_fit.py
branches/consistency_tests_1.3/test_suite/system_tests/sequence.py
branches/consistency_tests_1.3/test_suite/unit_tests/_prompt/data_types.py
branches/consistency_tests_1.3/test_suite/unit_tests/_prompt/test_diffusion_tensor.py
branches/consistency_tests_1.3/test_suite/unit_tests/_prompt/test_value.py
branches/consistency_tests_1.3/test_suite/unit_tests/value_testing_base.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/consistency_tests_1.3/generic_fns/minimise.py
URL:
http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.3/generic_fns/minimise.py?rev=4442&r1=4441&r2=4442&view=diff
Removed: branches/consistency_tests_1.3/generic_fns/nuclei.py
URL:
http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.3/generic_fns/nuclei.py?rev=4441&view=auto
Modified: branches/consistency_tests_1.3/physical_constants.py
[... 86 lines stripped ...]
r4442 - in /branches/consistency_tests_1.3: ./ generic_fns/ prompt/ specific_fns/ specific_fns/model_free/ test_suite/ test_...