Author: bugman Date: Mon Jan 14 17:57:47 2008 New Revision: 4704 URL: http://svn.gna.org/viewcvs/relax?rev=4704&view=rev Log: Merged revisions 4618-4701 via svnmerge from svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3 ................ 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@xxxxxxxxxxx/svn/relax/1.2 ..... 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. ..... ................ 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@xxxxxxxxxxx/svn/relax/1.2 ................ 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@xxxxxxxxxxx/svn/relax/1.2 ........ 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@xxxxxxxxx>) ........ 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. ........ ................ 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 ................ 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. ................ 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. ................ 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). ................ 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. ................ r4665 | bugman | 2008-01-13 12:16:34 +0100 (Sun, 13 Jan 2008) | 3 lines Copyright update. ................ 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. ................ 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. ................ 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. ................ 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. ................ 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. ................ 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. ................ 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!!! ................ 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. ................ 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. ................ 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. ................ 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. ................ r4678 | bugman | 2008-01-13 17:37:05 +0100 (Sun, 13 Jan 2008) | 3 lines Imported the specific_fns.model_free_obj object. ................ 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. ................ 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. ................ 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. ................ 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. ................ 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. ................ 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. ................ 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. ................ 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. ................ 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. ................ 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. ................ 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. ................ 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. ................ r4691 | bugman | 2008-01-13 19:16:32 +0100 (Sun, 13 Jan 2008) | 3 lines Renamed the module to avoid a name clash. ................ 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. ................ 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. ................ r4698 | semor | 2008-01-14 02:26:39 +0100 (Mon, 14 Jan 2008) | 3 lines Added comments to the imports. ................ r4699 | semor | 2008-01-14 05:25:19 +0100 (Mon, 14 Jan 2008) | 3 lines Added more comments to the imports. ................ r4700 | semor | 2008-01-14 05:31:50 +0100 (Mon, 14 Jan 2008) | 3 lines Added somemore comments to the imports. ................ 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. ................ Added: branches/N_state_model/specific_fns/model_free/mf_minimise.py - copied unchanged from r4701, 1.3/specific_fns/model_free/mf_minimise.py branches/N_state_model/test_suite/unit_tests/_prompt/test_model_free.py - copied unchanged from r4701, 1.3/test_suite/unit_tests/_prompt/test_model_free.py branches/N_state_model/test_suite/unit_tests/model_free_testing_base.py - copied unchanged from r4701, 1.3/test_suite/unit_tests/model_free_testing_base.py Modified: branches/N_state_model/ (props changed) branches/N_state_model/generic_fns/pipes.py branches/N_state_model/maths_fns/chi2.py branches/N_state_model/maths_fns/correlation_time.py branches/N_state_model/maths_fns/direction_cosine.py branches/N_state_model/maths_fns/jw_mapping.py branches/N_state_model/maths_fns/jw_mf.py branches/N_state_model/maths_fns/jw_mf_comps.py branches/N_state_model/maths_fns/mf.py branches/N_state_model/maths_fns/ri.py branches/N_state_model/maths_fns/ri_comps.py branches/N_state_model/maths_fns/weights.py branches/N_state_model/minimise/bfgs.py branches/N_state_model/minimise/cauchy_point.py branches/N_state_model/minimise/constraint_linear.py branches/N_state_model/minimise/coordinate_descent.py branches/N_state_model/minimise/dogleg.py branches/N_state_model/minimise/exact_trust_region.py branches/N_state_model/minimise/fletcher_reeves_cg.py branches/N_state_model/minimise/generic.py branches/N_state_model/minimise/grid.py branches/N_state_model/minimise/hessian_mods/cholesky.py branches/N_state_model/minimise/hessian_mods/eigenvalue.py branches/N_state_model/minimise/hessian_mods/gmw81.py branches/N_state_model/minimise/hessian_mods/gmw81_old.py branches/N_state_model/minimise/hessian_mods/se99.py branches/N_state_model/minimise/hestenes_stiefel_cg.py branches/N_state_model/minimise/levenberg_marquardt.py branches/N_state_model/minimise/line_search/backtrack.py branches/N_state_model/minimise/line_search/grace.py branches/N_state_model/minimise/line_search/interpolate.py branches/N_state_model/minimise/line_search/more_thuente.py branches/N_state_model/minimise/line_search/nocedal_wright_interpol.py branches/N_state_model/minimise/line_search/nocedal_wright_wolfe.py branches/N_state_model/minimise/line_search/test_functions.py branches/N_state_model/minimise/method_of_multipliers.py branches/N_state_model/minimise/ncg.py branches/N_state_model/minimise/newton.py branches/N_state_model/minimise/polak_ribiere_cg.py branches/N_state_model/minimise/polak_ribiere_plus_cg.py branches/N_state_model/minimise/simplex.py branches/N_state_model/minimise/steepest_descent.py branches/N_state_model/minimise/steihaug_cg.py branches/N_state_model/prompt/angles.py branches/N_state_model/prompt/command.py branches/N_state_model/prompt/dasha.py branches/N_state_model/prompt/eliminate.py branches/N_state_model/prompt/fix.py branches/N_state_model/prompt/grace.py branches/N_state_model/prompt/help.py branches/N_state_model/prompt/interpreter.py branches/N_state_model/prompt/jw_mapping.py branches/N_state_model/prompt/model_free.py branches/N_state_model/prompt/model_selection.py branches/N_state_model/prompt/monte_carlo.py branches/N_state_model/prompt/noe.py branches/N_state_model/prompt/palmer.py branches/N_state_model/prompt/relax_fit.py branches/N_state_model/prompt/results.py branches/N_state_model/prompt/tab_completion.py branches/N_state_model/prompt/unselect.py branches/N_state_model/prompt/view.py branches/N_state_model/prompt/vmd.py branches/N_state_model/sample_scripts/full_analysis.py branches/N_state_model/sample_scripts/remap.py branches/N_state_model/specific_fns/__init__.py branches/N_state_model/specific_fns/model_free/__init__.py branches/N_state_model/specific_fns/model_free/model_free.py branches/N_state_model/test_suite/system_tests/model_selection.py branches/N_state_model/test_suite/unit_tests/_generic_fns/test_value.py [This mail would be too long, it was shortened to contain the URLs only.] Modified: 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