Merged revisions 4618-4701 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3
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r4618 | bugman | 2008-01-10 21:40:40 +0100 (Thu, 10 Jan 2008) | 17 lines
Ported r4617 from the 1.2 line.
The command used was:
svn merge -r4616:4617 svn+ssh://bugman@.../svn/relax/1.2
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r4617 | bugman | 2008-01-10 21:37:22 +0100 (Thu, 10 Jan 2008) | 6 lines
Changed paths:
M /1.2/sample_scripts/full_analysis.py
Modified the full_analysis.py script to be usable when no structure is available.
This is in response to Sebastien's post at
https://mail.gna.org/public/relax-users/2008-01/msg00006.html.
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r4621 | semor | 2008-01-11 04:41:34 +0100 (Fri, 11 Jan 2008) | 3 lines
Initialized merge tracking via "svnmerge" with revisions "1-2505" from
svn+ssh://semor@.../svn/relax/1.2
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r4622 | semor | 2008-01-11 04:43:05 +0100 (Fri, 11 Jan 2008) | 20 lines
Merged revisions 4619-4620 via svnmerge from
svn+ssh://semor@.../svn/relax/1.2
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r4619 | semor | 2008-01-10 16:38:09 -0500 (Thu, 10 Jan 2008) | 7 lines
Modified the full_analysis.py script so it can handle cases when no residues need to be excluded.
This change was proposed in a post at:
https://mail.gna.org/public/relax-users/2008-01/msg00008.html (Message-id:
<47868730.1030205@...>)
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r4620 | semor | 2008-01-10 16:43:29 -0500 (Thu, 10 Jan 2008) | 6 lines
Corrected a mistake.
The inverse of what was wanted was produced concerning the possibility of not giving a file for
unresolved residues.
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r4623 | bugman | 2008-01-11 09:24:03 +0100 (Fri, 11 Jan 2008) | 9 lines
Reverted r4621, the setting up of svnmerge properties from 1.2 to 1.3.
The following command did not work:
svn merge -r4621:4620 .
So instead the following command was used:
svn propdel svnmerge-integrated
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r4659 | bugman | 2008-01-11 21:31:18 +0100 (Fri, 11 Jan 2008) | 6 lines
An import change to fix a circular import issue uncovered in the consistency_tests_1.3 branch.
This was uncovered by Seb. See the thread starting at
https://mail.gna.org/public/relax-devel/2008-01/msg00042.html.
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r4662 | bugman | 2008-01-13 12:07:18 +0100 (Sun, 13 Jan 2008) | 3 lines
Started to convert the model-free user functions to the new relax design.
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r4663 | bugman | 2008-01-13 12:09:22 +0100 (Sun, 13 Jan 2008) | 6 lines
Deleted the model_free.copy() user function.
This function was not used anywhere within relax and the model-free specific copy() method was
complete rubbish anyway (ancient, unused, broken code).
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r4664 | bugman | 2008-01-13 12:15:02 +0100 (Sun, 13 Jan 2008) | 3 lines
Removed the run argument from all model-free user functions.
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r4665 | bugman | 2008-01-13 12:16:34 +0100 (Sun, 13 Jan 2008) | 3 lines
Copyright update.
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r4666 | bugman | 2008-01-13 12:26:29 +0100 (Sun, 13 Jan 2008) | 3 lines
Converted all the res_num args to spin_id in the model-free user functions.
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r4667 | bugman | 2008-01-13 12:31:20 +0100 (Sun, 13 Jan 2008) | 3 lines
Added the framework for unit tests of the model-free user function args.
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r4668 | bugman | 2008-01-13 12:41:52 +0100 (Sun, 13 Jan 2008) | 3 lines
Wrote 7 unit tests for all args of the model-free user functions.
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r4669 | bugman | 2008-01-13 12:43:02 +0100 (Sun, 13 Jan 2008) | 3 lines
Fix for the spin_id arg of the model_free.select_model() user function.
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r4670 | bugman | 2008-01-13 12:44:04 +0100 (Sun, 13 Jan 2008) | 3 lines
Fix for the spin_id arg of the model_free.create_model() user function.
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r4671 | bugman | 2008-01-13 12:45:07 +0100 (Sun, 13 Jan 2008) | 3 lines
Fix for the spin_id arg of the model_free.remove_tm() user function.
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r4673 | bugman | 2008-01-13 12:48:43 +0100 (Sun, 13 Jan 2008) | 5 lines
Bug fix for the model arg of the model_free.select_model() user function.
The testing of this arg started with and elif statement!!!
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r4674 | bugman | 2008-01-13 12:53:06 +0100 (Sun, 13 Jan 2008) | 5 lines
Bug fixes for the model-free user function arg unit tests.
Some args had to be supplied in the unit tests to prevent RelaxErrors from reaching the correct arg.
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r4675 | bugman | 2008-01-13 12:57:32 +0100 (Sun, 13 Jan 2008) | 5 lines
Bug fix for the params arg of the model_free.create_model() user function.
This arg is now properly checked.
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r4676 | bugman | 2008-01-13 13:01:10 +0100 (Sun, 13 Jan 2008) | 3 lines
Removed the Model_free_main.__init__() method and converted its docstring to that of the class.
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r4677 | bugman | 2008-01-13 17:31:48 +0100 (Sun, 13 Jan 2008) | 5 lines
Renamed all the instantiated classes in specific_fns.__init__.
This is to avoid name clashes and the overwriting of the module names.
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r4678 | bugman | 2008-01-13 17:37:05 +0100 (Sun, 13 Jan 2008) | 3 lines
Imported the specific_fns.model_free_obj object.
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r4679 | bugman | 2008-01-13 18:19:08 +0100 (Sun, 13 Jan 2008) | 3 lines
Converted the create_model() model-free method to the new relax design.
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r4680 | bugman | 2008-01-13 18:22:22 +0100 (Sun, 13 Jan 2008) | 3 lines
Converted the model_setup() model-free method to the new relax design.
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r4681 | bugman | 2008-01-13 18:25:13 +0100 (Sun, 13 Jan 2008) | 3 lines
Converted the data_init() model-free method to the new relax design.
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r4682 | bugman | 2008-01-13 18:26:20 +0100 (Sun, 13 Jan 2008) | 3 lines
Updated the docstring of the model_setup() model-free method to be in epydoc format.
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r4683 | bugman | 2008-01-13 18:28:09 +0100 (Sun, 13 Jan 2008) | 5 lines
Added the missing import of the spin_loop.
The model 'm4' construction system test now passes.
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r4684 | bugman | 2008-01-13 18:29:44 +0100 (Sun, 13 Jan 2008) | 3 lines
Fixes for all the unit tests of the generic_fns.value.partition_params() function.
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r4685 | bugman | 2008-01-13 18:32:16 +0100 (Sun, 13 Jan 2008) | 3 lines
Converted the select_model() model-free method to the new relax design.
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r4686 | bugman | 2008-01-13 18:39:35 +0100 (Sun, 13 Jan 2008) | 3 lines
Converted the overfit_deselect() model-free method to the new relax design.
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r4687 | bugman | 2008-01-13 18:43:26 +0100 (Sun, 13 Jan 2008) | 3 lines
Cleaned up the code of the overfit_deselect() model-free method.
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r4688 | bugman | 2008-01-13 19:00:31 +0100 (Sun, 13 Jan 2008) | 5 lines
Converted the grid_search() model-free method to the new relax design.
The grid_search_setup() method has been merged into this method.
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r4689 | bugman | 2008-01-13 19:03:55 +0100 (Sun, 13 Jan 2008) | 5 lines
Bug fix for the system test of AIC model selection between two diffusion tensors.
The diffusion tensor was not been properly set up.
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r4690 | bugman | 2008-01-13 19:16:07 +0100 (Sun, 13 Jan 2008) | 3 lines
Shifted all of the model-free optimisation related methods into a separate module.
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r4691 | bugman | 2008-01-13 19:16:32 +0100 (Sun, 13 Jan 2008) | 3 lines
Renamed the module to avoid a name clash.
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r4692 | bugman | 2008-01-13 19:50:36 +0100 (Sun, 13 Jan 2008) | 3 lines
Converted the assemble_param_names() model-free method to the new relax design.
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r4693 | bugman | 2008-01-13 20:02:17 +0100 (Sun, 13 Jan 2008) | 3 lines
Converted the assemble_param_vector() model-free method to the new relax design.
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r4698 | semor | 2008-01-14 02:26:39 +0100 (Mon, 14 Jan 2008) | 3 lines
Added comments to the imports.
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r4699 | semor | 2008-01-14 05:25:19 +0100 (Mon, 14 Jan 2008) | 3 lines
Added more comments to the imports.
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r4700 | semor | 2008-01-14 05:31:50 +0100 (Mon, 14 Jan 2008) | 3 lines
Added somemore comments to the imports.
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r4701 | semor | 2008-01-14 15:49:41 +0100 (Mon, 14 Jan 2008) | 3 lines
Added some comments to the imports and ordered imports alphabetically.
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