relax SVN archive

The specific_fns.n_state_model module is now imported.

Modified the 5-state system test.

The SVD and matrix angles user functions have been shifted back to the align_tensor user function
base class. To compensate, the 'tensors' arg has been added so that a select set of tensors can be
operated on.

Added the n_state_model user function class. No functions are implemented yet.

Yet another design change for the N-state model (as coded in the 5-state system test)!

Merged revisions 4523-4527,4529-4547,4549-4551 via svnmerge from
svn+ssh://semor@.../svn/relax/1.3

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r4523 | bugman | 2008-01-09 04:50:39 -0500 (Wed, 09 Jan 2008) | 5 lines

Renamed 'print_flag' to 'verbosity' in the calc(), grid_search(), and minimise() user functions.

This arg is not really a flag, and it is the verbosity level, so this makes more sense.
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r4524 | bugman | 2008-01-09 04:53:06 -0500 (Wed, 09 Jan 2008) | 3 lines

Created a new error type for booleans - RelaxBoolError.
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r4525 | bugman | 2008-01-09 04:57:51 -0500 (Wed, 09 Jan 2008) | 3 lines

Converted all the bin args (0/1) to bool args (True/False) in the minimisation user functions.
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r4526 | bugman | 2008-01-09 05:25:14 -0500 (Wed, 09 Jan 2008) | 3 lines

Changed all references to 'print_flag' to 'verbosity' in the user function arg unit tests.
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r4527 | bugman | 2008-01-09 05:26:16 -0500 (Wed, 09 Jan 2008) | 3 lines

Changed all the bin minimisation arg unit tests to tests for boolean args.
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r4529 | bugman | 2008-01-09 05:37:04 -0500 (Wed, 09 Jan 2008) | 6 lines

Removal of all the old threading code!!!

This will all eventually be replaced by Gary Thompson's multi_processor code, once it is ported to
the new relax design. This threading code was broken, buggy, and not fault tolerant anyway.
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r4530 | bugman | 2008-01-09 05:46:51 -0500 (Wed, 09 Jan 2008) | 6 lines

Updated the relax_io.extract_data() function.

The compression flag has been dropped as it is automatically determined and updated the docstring to
epydoc format.
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r4531 | bugman | 2008-01-09 05:48:33 -0500 (Wed, 09 Jan 2008) | 5 lines

Updated the relax_io.get_file_path() function.

The docstring has been updated to epydoc format.
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r4532 | bugman | 2008-01-09 05:50:27 -0500 (Wed, 09 Jan 2008) | 3 lines

Added the return info to the relax_io.extract_data() function docstring.
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r4533 | bugman | 2008-01-09 05:54:11 -0500 (Wed, 09 Jan 2008) | 6 lines

Updated the relax_io.log() function.

The compression flag has been dropped as it is automatically determined, changed the 'print_flag'
arg to 'verbosity', and updated the docstring to epydoc format.
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r4534 | bugman | 2008-01-09 05:56:14 -0500 (Wed, 09 Jan 2008) | 5 lines

Updated the relax_io.mkdir_nofail() function.

Changed the 'print_flag' arg to 'verbosity' and updated the docstring to epydoc format.
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r4535 | bugman | 2008-01-09 05:58:30 -0500 (Wed, 09 Jan 2008) | 5 lines

Updated the relax_io.open_read_file() function.

Changed the 'print_flag' arg to 'verbosity' and updated the docstring to epydoc format.
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r4536 | bugman | 2008-01-09 06:06:00 -0500 (Wed, 09 Jan 2008) | 5 lines

Spun out the compression determining code of open_read_file() into its own function.

The new function is called determine_compression().
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r4537 | bugman | 2008-01-09 06:06:46 -0500 (Wed, 09 Jan 2008) | 3 lines

Converted the devnull_import variable from a bin value to a boolean.
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r4538 | bugman | 2008-01-09 06:26:39 -0500 (Wed, 09 Jan 2008) | 6 lines

Updated the relax_io.open_write_file() function.

The docstring has been updated for epydoc, the 'print_flag' arg changed to 'verbosity', and a
printed warning shifted to using a RelaxWarning.
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r4539 | bugman | 2008-01-09 08:10:13 -0500 (Wed, 09 Jan 2008) | 3 lines

Updated the docstring of the relax_io.open_write_file() function for epydoc.
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r4540 | bugman | 2008-01-09 08:12:14 -0500 (Wed, 09 Jan 2008) | 3 lines

Bug fix. The compress_type arg is no longer accepted.
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r4541 | bugman | 2008-01-09 08:13:07 -0500 (Wed, 09 Jan 2008) | 3 lines

Bug fix. The compress_type arg is no longer accepted.
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r4542 | bugman | 2008-01-09 08:16:22 -0500 (Wed, 09 Jan 2008) | 6 lines

Updated the generic_fns.state.load_state() function.

The compression flag has been dropped as it is automatically determined and the docstring has been
converted to epydoc format.
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r4543 | bugman | 2008-01-09 08:19:47 -0500 (Wed, 09 Jan 2008) | 5 lines

Updated the generic_fns.state.save_state() function.

The docstring has been converted to epydoc format and the 'force' arg converted to a bool.
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r4544 | bugman | 2008-01-09 08:24:45 -0500 (Wed, 09 Jan 2008) | 3 lines

Bug fix. The relax_io.determine_compression() function now returns the full file path.
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r4545 | bugman | 2008-01-09 08:28:24 -0500 (Wed, 09 Jan 2008) | 3 lines

Changed the 'force' arg of the state.save() user function too a boolean.
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r4546 | bugman | 2008-01-09 08:29:21 -0500 (Wed, 09 Jan 2008) | 3 lines

Fixed a RelaxError import.
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r4547 | bugman | 2008-01-09 08:30:40 -0500 (Wed, 09 Jan 2008) | 5 lines

Updated the force arg unit test of the state.save() user function.

The arg is now a boolean.
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r4549 | bugman | 2008-01-09 08:38:00 -0500 (Wed, 09 Jan 2008) | 3 lines

Changed all instances of the 'print_flag' arg to 'verbosity' in the generic_fns.minimise module.
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r4550 | bugman | 2008-01-09 08:39:09 -0500 (Wed, 09 Jan 2008) | 3 lines

Removed some unused imports.
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r4551 | bugman | 2008-01-09 08:41:03 -0500 (Wed, 09 Jan 2008) | 3 lines

Changed all the 'constraints' and 'scaling' args to be of bool type.
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Changed the 'label' arg back to the original 'tensor' arg.

Another design change for the N-state model (as coded in the 5-state system test).

Complete change of the 5-state system test for the N-state model.

The current design for integrating the N-state model into relax was not workable. This system test
introduces a new design for this model.

Added a stub for the assemble_param_vector() method. It doesn't create the vector yet.

Merged revisions 4549-4551 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3

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r4549 | bugman | 2008-01-09 14:38:00 +0100 (Wed, 09 Jan 2008) | 3 lines

Changed all instances of the 'print_flag' arg to 'verbosity' in the generic_fns.minimise module.
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r4550 | bugman | 2008-01-09 14:39:09 +0100 (Wed, 09 Jan 2008) | 3 lines

Removed some unused imports.
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r4551 | bugman | 2008-01-09 14:41:03 +0100 (Wed, 09 Jan 2008) | 3 lines

Changed all the 'constraints' and 'scaling' args to be of bool type.
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