Author: bugman
Date: Mon Jan 7 13:53:09 2008
New Revision: 4421
URL: http://svn.gna.org/viewcvs/relax?rev=4421&view=rev
Log:
Merged revisions 4372-4419 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
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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.
........
Added:
branches/N_state_model/test_suite/unit_tests/_prompt/test_minimisation.py
- copied unchanged from r4419,
1.3/test_suite/unit_tests/_prompt/test_minimisation.py
branches/N_state_model/test_suite/unit_tests/_prompt/test_structure.py
- copied unchanged from r4419,
1.3/test_suite/unit_tests/_prompt/test_structure.py
branches/N_state_model/test_suite/unit_tests/minimisation_testing_base.py
- copied unchanged from r4419,
1.3/test_suite/unit_tests/minimisation_testing_base.py
branches/N_state_model/test_suite/unit_tests/structure_testing_base.py
- copied unchanged from r4419,
1.3/test_suite/unit_tests/structure_testing_base.py
Modified:
branches/N_state_model/ (props changed)
branches/N_state_model/generic_fns/nuclei.py
branches/N_state_model/physical_constants.py
branches/N_state_model/prompt/minimisation.py
branches/N_state_model/prompt/structure.py
branches/N_state_model/prompt/value.py
branches/N_state_model/relax_errors.py
branches/N_state_model/specific_fns/base_class.py
branches/N_state_model/specific_fns/jw_mapping.py
branches/N_state_model/specific_fns/model_free/model_free.py
branches/N_state_model/test_suite/system_tests/angles.py
branches/N_state_model/test_suite/system_tests/model_free.py
branches/N_state_model/test_suite/system_tests/relax_fit.py
branches/N_state_model/test_suite/unit_tests/_prompt/data_types.py
branches/N_state_model/test_suite/unit_tests/_prompt/test_diffusion_tensor.py
branches/N_state_model/test_suite/unit_tests/_prompt/test_value.py
branches/N_state_model/test_suite/unit_tests/value_testing_base.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/N_state_model/generic_fns/nuclei.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/generic_fns/nuclei.py?rev=4421&r1=4420&r2=4421&view=diff
Modified: branches/N_state_model/physical_constants.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/physical_constants.py?rev=4421&r1=4420&r2=4421&view=diff
Modified: branches/N_state_model/prompt/minimisation.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/prompt/minimisation.py?rev=4421&r1=4420&r2=4421&view=diff
Modified: branches/N_state_model/prompt/structure.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/prompt/structure.py?rev=4421&r1=4420&r2=4421&view=diff
Modified: branches/N_state_model/prompt/value.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/prompt/value.py?rev=4421&r1=4420&r2=4421&view=diff
Modified: branches/N_state_model/relax_errors.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/relax_errors.py?rev=4421&r1=4420&r2=4421&view=diff
Modified: branches/N_state_model/specific_fns/base_class.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/specific_fns/base_class.py?rev=4421&r1=4420&r2=4421&view=diff
Modified: branches/N_state_model/specific_fns/jw_mapping.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/specific_fns/jw_mapping.py?rev=4421&r1=4420&r2=4421&view=diff
Modified: branches/N_state_model/specific_fns/model_free/model_free.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/specific_fns/model_free/model_free.py?rev=4421&r1=4420&r2=4421&view=diff
Modified: branches/N_state_model/test_suite/system_tests/angles.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/test_suite/system_tests/angles.py?rev=4421&r1=4420&r2=4421&view=diff
Modified: branches/N_state_model/test_suite/system_tests/model_free.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/test_suite/system_tests/model_free.py?rev=4421&r1=4420&r2=4421&view=diff
Modified: branches/N_state_model/test_suite/system_tests/relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/test_suite/system_tests/relax_fit.py?rev=4421&r1=4420&r2=4421&view=diff
Modified: branches/N_state_model/test_suite/unit_tests/_prompt/data_types.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/test_suite/unit_tests/_prompt/data_types.py?rev=4421&r1=4420&r2=4421&view=diff
Modified:
branches/N_state_model/test_suite/unit_tests/_prompt/test_diffusion_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/test_suite/unit_tests/_prompt/test_diffusion_tensor.py?rev=4421&r1=4420&r2=4421&view=diff
Modified: branches/N_state_model/test_suite/unit_tests/_prompt/test_value.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/test_suite/unit_tests/_prompt/test_value.py?rev=4421&r1=4420&r2=4421&view=diff
Modified: branches/N_state_model/test_suite/unit_tests/value_testing_base.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/test_suite/unit_tests/value_testing_base.py?rev=4421&r1=4420&r2=4421&view=diff
r4421 - in /branches/N_state_model: ./ generic_fns/ prompt/ specific_fns/ specific_fns/model_free/ test_suite/system_tests/ ...