Blocked revisions 3121-3171 via svnmerge
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r3121 | bugman | 2007-03-08 18:00:29 +1100 (Thu, 08 Mar 2007) | 3 lines
Updated the __repr__ method of the PipeContainer object.
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r3122 | bugman | 2007-03-08 18:23:25 +1100 (Thu, 08 Mar 2007) | 5 lines
Bug fix.
Removed the call to getattr for 'add' to prevent a recursion issue.
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r3123 | bugman | 2007-03-08 18:26:01 +1100 (Thu, 08 Mar 2007) | 3 lines
Renamed the PipeContainer object 'pdb' to 'structure'.
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r3124 | bugman | 2007-03-08 18:26:56 +1100 (Thu, 08 Mar 2007) | 3 lines
Removed the 'run_names' object from the PipeContainer.
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r3125 | bugman | 2007-03-08 18:27:54 +1100 (Thu, 08 Mar 2007) | 3 lines
Converted the 'run_types' array to the variable 'pipe_type'.
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r3126 | bugman | 2007-03-08 18:28:55 +1100 (Thu, 08 Mar 2007) | 3 lines
Converted the global minimisation statistic objects from empty dictionaries to None.
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r3127 | bugman | 2007-03-08 19:36:23 +1100 (Thu, 08 Mar 2007) | 13 lines
Addition of the molecule-residue-spin data classes.
The following classes have been created:
MoleculeList
MoleculeContainer
ResidueList
ResidueContainer
SpinList
SpinContainer
These were modified from the original Residue and ResidueList classes.
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r3128 | varioustoxins | 2007-03-08 20:42:53 +1100 (Thu, 08 Mar 2007) | 3 lines
incorrect interpretation of test_module corrected, unit tests work from
relax command line again
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r3129 | bugman | 2007-03-09 17:25:17 +1100 (Fri, 09 Mar 2007) | 3 lines
Deleted the unused Data.__init__() method.
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r3130 | bugman | 2007-03-09 18:46:41 +1100 (Fri, 09 Mar 2007) | 6 lines
Converted the residue specific data container into the molecule list 'mol' in the pipe container.
The old residue specific container was located at 'self.relax.data.res' whereas the molecule list
object is located at D[pipe].mol where D is the relax data storage singleton.
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r3131 | bugman | 2007-03-09 19:00:51 +1100 (Fri, 09 Mar 2007) | 7 lines
Bug fix.
The __repr__ method of the PipeContainer was failing because of the call to getattr() for the 'mol'
object. Now the 'mol', 'diff', and 'structure' objects are not sent to getattr(), rather a special
description is given rather than the object's attribute.
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r3132 | bugman | 2007-03-09 19:02:25 +1100 (Fri, 09 Mar 2007) | 3 lines
Fixed an incorrect comment in the PipeContainer.
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r3133 | bugman | 2007-03-09 19:06:52 +1100 (Fri, 09 Mar 2007) | 3 lines
Fixed the __repr__() method of the MoleculeList class.
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r3134 | bugman | 2007-03-09 19:11:56 +1100 (Fri, 09 Mar 2007) | 6 lines
Added the variable name = None to the MoleculeContainer class namespace.
This variable is the name of the molecule, which if specified should correspond to a molecule or
chain identifier in the 3D structure file.
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r3135 | bugman | 2007-03-09 19:12:42 +1100 (Fri, 09 Mar 2007) | 3 lines
Two fixes for the MoleculeList class method __repr__().
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r3136 | bugman | 2007-03-09 20:14:13 +1100 (Fri, 09 Mar 2007) | 3 lines
Fixed the __repr__() method of the MoleculeContainer class.
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r3137 | bugman | 2007-03-09 20:27:38 +1100 (Fri, 09 Mar 2007) | 3 lines
Deleted the add_list() method and added the ResidueList object to the MoleculeContainer class.
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r3138 | bugman | 2007-03-09 20:29:42 +1100 (Fri, 09 Mar 2007) | 5 lines
Reversed the order of all the classes in the 'data.mol_res_spin' module.
This is to fix the problem of missing classes during instantiation.
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r3139 | bugman | 2007-03-09 20:34:53 +1100 (Fri, 09 Mar 2007) | 3 lines
Removed a print debugging statement.
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r3140 | bugman | 2007-03-09 20:36:12 +1100 (Fri, 09 Mar 2007) | 3 lines
Removed an extra newline character from the MoleculeContainer.__repr__() string.
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r3141 | bugman | 2007-03-10 10:42:21 +1100 (Sat, 10 Mar 2007) | 12 lines
Completion of the core of the molecule-residue-spin data structures.
All of the initialisation of the class variables and objects in all six classes have been shifted
into __init__() methods so that new copies of the objects are created when molecules, residues, or
spins are added to the structure.
The __repr__() methods of all classes have been updated and return a proper text representation of
the objects.
The XList class docstrings have been updated.
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r3142 | bugman | 2007-03-10 11:08:41 +1100 (Sat, 10 Mar 2007) | 3 lines
Updated the 'data_model_redesign' document to state that the redesign of 'self.relax.data' is complete.
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r3143 | bugman | 2007-03-10 11:28:20 +1100 (Sat, 10 Mar 2007) | 7 lines
Renamed 'run' to 'pipe' in the 'run' user function class.
The file 'prompt/run.py' was renamed to 'prompt/pipe.py' and all instances of 'run' renamed to
'pipe'. The placing of the user function class into the interpreter namespace was also updated.
The docstrings of all the user functions where modified to use the new terminology.
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r3144 | bugman | 2007-03-10 12:04:14 +1100 (Sat, 10 Mar 2007) | 6 lines
Renamed 'run' to 'pipe' in the 'generic_fns.runs' module.
The file 'generic_fns/run.py' was renamed to 'generic_fns/pipe.py' and all instances of 'run'
renamed to 'pipe'.
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r3145 | bugman | 2007-03-10 12:05:17 +1100 (Sat, 10 Mar 2007) | 3 lines
Updated the data model redesign document to say that point 8 of the preparation is complete.
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r3146 | bugman | 2007-03-10 12:07:39 +1100 (Sat, 10 Mar 2007) | 3 lines
Deleted the Pipes class and converted all its methods into module functions.
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r3147 | bugman | 2007-03-10 12:14:25 +1100 (Sat, 10 Mar 2007) | 3 lines
Added the 'generic_fns/' directory to the unit test hierarchy.
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r3148 | bugman | 2007-03-10 12:28:28 +1100 (Sat, 10 Mar 2007) | 13 lines
Removed the ability for stand alone execution of the diffusion tensor data structure unit tests.
Stand alone execution is unnecessary as the command:
$ ./unit_test_runner.py data/test_diff_tensor.py
will run the tests.
Three things have been changed. Firstly the system path modifications have been removed. Secondly
the 'if __name__ == "__main__":' block has been deleted. Finally the 'svn:executable' property has
been removed from the repository.
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r3149 | bugman | 2007-03-10 12:29:29 +1100 (Sat, 10 Mar 2007) | 3 lines
Added a docstring to the Test_diff_tensor class.
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r3150 | bugman | 2007-03-10 12:31:23 +1100 (Sat, 10 Mar 2007) | 3 lines
Updated the import statements, removing many unused imports.
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r3151 | bugman | 2007-03-10 13:03:28 +1100 (Sat, 10 Mar 2007) | 3 lines
Updated the docstring of 'generic_fns.pipes.create' to be in Epydoc format.
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r3152 | bugman | 2007-03-13 13:58:01 +1100 (Tue, 13 Mar 2007) | 2 lines
Added unit tests for the functions of the module 'generic_fns.pipes'.
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r3153 | bugman | 2007-03-13 14:08:53 +1100 (Tue, 13 Mar 2007) | 2 lines
Added unit tests for the methods of the classes of the module 'data.mol_res_spin'.
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r3154 | bugman | 2007-03-13 14:32:48 +1100 (Tue, 13 Mar 2007) | 4 lines
Bug fix.
The import statement for the pipes module has been removed from 'generic_fns.main'.
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r3155 | bugman | 2007-03-13 14:34:03 +1100 (Tue, 13 Mar 2007) | 7 lines
Fixed the problems with the classes of the 'data.mol_res_spin' module.
The add_item() methods of the list type classes have been modified. For the MoleculeList class the
'mol_name' argument has been added and the MoleculeContainer.__init__() method accepts this argument
as well. The 'res_name', 'res_num', 'spin_name', 'spin_num', and 'select' have similarily been
added.
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r3156 | bugman | 2007-03-13 14:34:49 +1100 (Tue, 13 Mar 2007) | 2 lines
Added unit tests for the relax data storage singleton class Data from the 'data' module.
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r3157 | bugman | 2007-03-13 14:36:45 +1100 (Tue, 13 Mar 2007) | 9 lines
Fixed the function generic_fns.pipes.create().
The relax data store singleton method 'add()' has been deleted as the method required the first
argument to be the singleton instance. Instead the functionality has been shifted into the
generic_fns.pipes.create() function. The unit tests have been modified for the new setup.
All references to 'run' in the file 'test_suite/unit_tests/generic_fns/test_pipes.py' have been
replaced with 'pipe'.
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r3158 | bugman | 2007-03-13 14:37:42 +1100 (Tue, 13 Mar 2007) | 5 lines
Added a tearDown() method to the 'test_suite/unit_tests/generic_fns/test_pipes.py' file.
The relax data storage object is reset as the data added to it from different tests was clashing.
The method allows the 'test_creation_fail' unit test to pass.
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r3159 | bugman | 2007-03-13 14:38:11 +1100 (Tue, 13 Mar 2007) | 2 lines
Rewrote the 'generic_fns.pipes.delete()' function.
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r3160 | bugman | 2007-03-13 14:38:54 +1100 (Tue, 13 Mar 2007) | 4 lines
Fixed the 'test_deletion_fail()' unit test.
The error throw was RelaxNoRunError and not RelaxError.
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r3161 | bugman | 2007-03-13 14:40:20 +1100 (Tue, 13 Mar 2007) | 5 lines
Fixed the setting of the current data pipe so that the 'test_creation()' unit test passes.
The current data pipe was not being set to the new data pipe created by the function
'generic_fns.pipes.create()'.
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r3162 | bugman | 2007-03-13 14:41:19 +1100 (Tue, 13 Mar 2007) | 5 lines
Fixed the setting of the current data pipe so that the 'test_deletion()' unit test passes.
The current data pipe was not being set to None by the 'generic_fns.pipes.delete()' if the deleted
pipe is the current pipe.
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r3163 | bugman | 2007-03-13 14:41:54 +1100 (Tue, 13 Mar 2007) | 5 lines
Removed the functions not used by relax from the 'generic_fns.pipes' module.
The functions 'eliminate_unused_pipes()' and 'list_of_pipes()' have been deleted as they are not
used anywhere within relax. The unit test for the 'eliminate_unused_pipes()' has also been deleted.
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r3164 | bugman | 2007-03-13 14:43:51 +1100 (Tue, 13 Mar 2007) | 6 lines
The pipe.create() user function now works!
The prompt.pipe module now import the 'generic_fns.pipes' module and executes the create() function.
The system/functional test for this user function now passes and has been updated with runs renamed
to pipes.
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r3165 | bugman | 2007-03-13 14:45:17 +1100 (Tue, 13 Mar 2007) | 2 lines
Created the new pipe.current() user function.
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r3166 | bugman | 2007-03-13 14:45:47 +1100 (Tue, 13 Mar 2007) | 4 lines
Created the pipe.switch() user function for switching between data pipes.
Two unit tests were created for the new code - test_switch() and test_switch_fail().
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r3167 | bugman | 2007-03-13 14:46:31 +1100 (Tue, 13 Mar 2007) | 2 lines
Created the pipe.list() user function for printing a list of all the data pipes.
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r3168 | bugman | 2007-03-13 14:47:39 +1100 (Tue, 13 Mar 2007) | 5 lines
Created a prototype design pattern as a base class with the __copy__() method.
The prototype __copy__() method simply returns a deepcopy of the object. The PipeContainer,
SpinContainer, ResidueContainer, and MoleculeContainer classes now inherit from the prototype class.
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r3169 | bugman | 2007-03-13 14:48:03 +1100 (Tue, 13 Mar 2007) | 2 lines
Updated and fixed the 'pipe.delete()' user function.
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r3170 | bugman | 2007-03-13 14:48:29 +1100 (Tue, 13 Mar 2007) | 5 lines
Implemented the 'pipe.copy()' user function.
The 'generic_fns.pipes.copy()' function and the three unit tests 'test_copy', 'test_copy_current',
'test_copy_fail' have been added.
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r3171 | bugman | 2007-03-13 18:49:52 +1100 (Tue, 13 Mar 2007) | 12 lines
Bug fix for the prototype copying.
These changes cause the 'test_copy' and 'test_copy_current' unit tests of 'test_pipe.py' to pass.
The prototype '__copy__()' method has been renamed to '__clone__()' as '__copy__()' is reserved as a
replacement method for the 'copy' method of the 'copy' module. As the 'deepcopy' method was not
copying all of the objects of the pipe container correctly, the '__deepcopy__() replacement method
has been added to the prototype base class.
All subclassing of 'ListType' and 'DictType' have been replaced by 'list' and 'dict'.
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