Author: bugman Date: Tue Dec 1 09:45:36 2009 New Revision: 10035 URL: http://svn.gna.org/viewcvs/relax?rev=10035&view=rev Log: Merged revisions 9998-10032 via svnmerge from svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3 ........ r9998 | bugman | 2009-11-27 16:00:04 +0100 (Fri, 27 Nov 2009) | 3 lines Added the analysis specific API method is_spin_param() to the frame order module. ........ r9999 | bugman | 2009-11-27 17:16:08 +0100 (Fri, 27 Nov 2009) | 3 lines Docstring fixes for the value.set() user function. ........ r10000 | bugman | 2009-11-27 17:39:31 +0100 (Fri, 27 Nov 2009) | 5 lines Renamed the 'prompt.check' module to the base relax directory module 'arg_check'. This makes the module more available to other parts of relax that requires argument type checking. ........ r10001 | bugman | 2009-11-27 17:53:43 +0100 (Fri, 27 Nov 2009) | 3 lines Removed 'check' from the __all__ list. ........ r10002 | bugman | 2009-11-27 18:03:11 +0100 (Fri, 27 Nov 2009) | 3 lines Fixed all the calls to the renamed 'arg_check' module. ........ r10003 | bugman | 2009-11-27 18:09:39 +0100 (Fri, 27 Nov 2009) | 5 lines Specific analysis API clean up. The get_param_name and get_param_value methods are returned by asking directly for these names. ........ r10004 | bugman | 2009-11-27 18:29:15 +0100 (Fri, 27 Nov 2009) | 7 lines Redesigned the specific analysis API for setting parameter values. Now the set_param_values() method is to be provided. It is for setting single parameter values. This will be followed by a complete redesign of the value.set() user function back end (which is currently a mess). ........ r10005 | bugman | 2009-11-27 18:31:04 +0100 (Fri, 27 Nov 2009) | 3 lines Added the set_param_values() method to the base API (matching the changes of r9986). ........ r10006 | bugman | 2009-11-27 18:32:47 +0100 (Fri, 27 Nov 2009) | 6 lines Massive simplification of the generic_fns.value.set() function. This code was previously a mess, spread randomly across the generic code and specific code. This is a complete refactorization which will cause breakages for a little while. ........ r10007 | bugman | 2009-11-27 18:34:19 +0100 (Fri, 27 Nov 2009) | 5 lines Deletion of the set_non_spin_params() method. This mess is no longer in the base API. ........ r10008 | bugman | 2009-11-27 18:35:09 +0100 (Fri, 27 Nov 2009) | 3 lines Fixed a typo in the new generic_fns.value.set() function. ........ r10009 | bugman | 2009-11-27 18:47:52 +0100 (Fri, 27 Nov 2009) | 3 lines Fix for the call to set_param_values(). ........ r10010 | bugman | 2009-11-28 20:23:51 +0100 (Sat, 28 Nov 2009) | 7 lines Added 'HH' and 'HZ' to the amino acid atom names in __det_pdb_element(). This is in response to Tiago Pais's <tpais att itqb dot unl dot pt> post at https://mail.gna.org/public/relax-users/2009-11/msg00002.html (Message-id: <AF0E494FAE984C0BB8D4C8CE521D621D@Mercurio>). ........ r10011 | bugman | 2009-11-29 15:01:19 +0100 (Sun, 29 Nov 2009) | 3 lines Created a module for storing API methods common to different analysis types. ........ r10012 | bugman | 2009-11-29 15:02:14 +0100 (Sun, 29 Nov 2009) | 3 lines Added the api_common module to the __all__ list. ........ r10013 | bugman | 2009-11-29 15:20:13 +0100 (Sun, 29 Nov 2009) | 5 lines Created the common API method _set_param_values_spin(). A number of modules are now using this method. ........ r10014 | bugman | 2009-11-29 15:23:13 +0100 (Sun, 29 Nov 2009) | 6 lines Fix for the generic_fns.value.set() method. The return_data_name() specific API method should have been used to send the correct string into default_value(). ........ r10015 | bugman | 2009-11-30 10:16:38 +0100 (Mon, 30 Nov 2009) | 3 lines Created the arg_check.is_list() function. ........ r10016 | bugman | 2009-11-30 10:18:47 +0100 (Mon, 30 Nov 2009) | 3 lines Added a unit test test_set_n_state_model_rx() for checking value.set() with the N-state model. ........ r10017 | bugman | 2009-11-30 10:24:41 +0100 (Mon, 30 Nov 2009) | 5 lines The base analysis API set_param_values() arguments have been changed. The param and value args now must be lists. Only the docstring has been modified. ........ r10018 | bugman | 2009-11-30 10:27:24 +0100 (Mon, 30 Nov 2009) | 3 lines Modified the analysis API common method _set_param_values_spin() to accepts lists as args. ........ r10019 | bugman | 2009-11-30 10:28:55 +0100 (Mon, 30 Nov 2009) | 6 lines Analysis API fixes. The param_names() and param_values() methods are now called get_param_names() and get_param_values(). ........ r10020 | bugman | 2009-11-30 10:29:47 +0100 (Mon, 30 Nov 2009) | 3 lines Created the set_param_values() API method for the N-state model. ........ r10021 | bugman | 2009-11-30 10:30:47 +0100 (Mon, 30 Nov 2009) | 3 lines Created the set_param_values() API method for model-free analysis. ........ r10022 | bugman | 2009-11-30 10:32:06 +0100 (Mon, 30 Nov 2009) | 5 lines Fixes for the value.set() back-end to match the analysis API arg changes. The param and value args should be lists. ........ r10023 | bugman | 2009-11-30 10:39:02 +0100 (Mon, 30 Nov 2009) | 3 lines Modified the minimisation set() method to better match that of the analysis API. ........ r10024 | bugman | 2009-11-30 14:32:58 +0100 (Mon, 30 Nov 2009) | 3 lines Added a system test for the OpenDX space mapping for Euler angle frame order parameters. ........ r10025 | bugman | 2009-11-30 14:36:37 +0100 (Mon, 30 Nov 2009) | 5 lines Set all col args to None so that there are no automatic defaults. The automatic defaults make it very difficult for users to debug scripts!!! ........ r10026 | bugman | 2009-11-30 14:44:05 +0100 (Mon, 30 Nov 2009) | 3 lines Created the common method _set_param_values_global() for the analysis API. ........ r10027 | bugman | 2009-11-30 14:46:01 +0100 (Mon, 30 Nov 2009) | 3 lines Wrote the arg_check.is_none() testing function. ........ r10028 | bugman | 2009-11-30 14:46:32 +0100 (Mon, 30 Nov 2009) | 3 lines The frame order theory is now using the common _set_param_values_global() analysis API method. ........ r10029 | bugman | 2009-11-30 15:16:05 +0100 (Mon, 30 Nov 2009) | 3 lines Shifted the path of the new OpenDX frame order mapping system test. ........ r10030 | bugman | 2009-11-30 22:03:47 +0100 (Mon, 30 Nov 2009) | 3 lines Significantly decreased the time required for the frame order mapping system test. ........ r10031 | bugman | 2009-11-30 23:50:43 +0100 (Mon, 30 Nov 2009) | 6 lines Converted all of the analysis API base methods into prototype methods. These all now raise RelaxImplementError when called. All the analyses now alias methods from the api_common module (which were the original base methods). ........ r10032 | bugman | 2009-12-01 00:12:25 +0100 (Tue, 01 Dec 2009) | 3 lines Added checks for spin specific, analysis API common methods to see if model_info is a SpinContainer. ........ Added: branches/j_couplings/arg_check.py - copied unchanged from r10032, 1.3/arg_check.py branches/j_couplings/specific_fns/api_common.py - copied unchanged from r10032, 1.3/specific_fns/api_common.py branches/j_couplings/test_suite/system_tests/scripts/frame_order/opendx_euler_angle_map.py - copied unchanged from r10032, 1.3/test_suite/system_tests/scripts/frame_order/opendx_euler_angle_map.py Removed: branches/j_couplings/prompt/check.py Modified: branches/j_couplings/ (props changed) branches/j_couplings/generic_fns/eliminate.py branches/j_couplings/generic_fns/minimise.py branches/j_couplings/generic_fns/structure/internal.py branches/j_couplings/generic_fns/value.py branches/j_couplings/prompt/__init__.py branches/j_couplings/prompt/align_tensor.py branches/j_couplings/prompt/command.py branches/j_couplings/prompt/consistency_tests.py branches/j_couplings/prompt/dasha.py branches/j_couplings/prompt/deselect.py branches/j_couplings/prompt/diffusion_tensor.py branches/j_couplings/prompt/dx.py branches/j_couplings/prompt/eliminate.py branches/j_couplings/prompt/fix.py branches/j_couplings/prompt/frame_order.py branches/j_couplings/prompt/frq.py branches/j_couplings/prompt/grace.py branches/j_couplings/prompt/jw_mapping.py branches/j_couplings/prompt/minimisation.py branches/j_couplings/prompt/model_free.py branches/j_couplings/prompt/model_selection.py branches/j_couplings/prompt/molecule.py branches/j_couplings/prompt/molmol.py branches/j_couplings/prompt/monte_carlo.py branches/j_couplings/prompt/n_state_model.py branches/j_couplings/prompt/noe.py branches/j_couplings/prompt/palmer.py branches/j_couplings/prompt/pcs.py branches/j_couplings/prompt/pipe.py branches/j_couplings/prompt/pymol.py branches/j_couplings/prompt/rdc.py branches/j_couplings/prompt/relax_data.py branches/j_couplings/prompt/relax_fit.py branches/j_couplings/prompt/residue.py branches/j_couplings/prompt/results.py branches/j_couplings/prompt/select.py branches/j_couplings/prompt/sequence.py branches/j_couplings/prompt/spectrum.py branches/j_couplings/prompt/spin.py branches/j_couplings/prompt/state.py branches/j_couplings/prompt/structure.py branches/j_couplings/prompt/temperature.py branches/j_couplings/prompt/value.py branches/j_couplings/prompt/vmd.py branches/j_couplings/specific_fns/__init__.py branches/j_couplings/specific_fns/api_base.py branches/j_couplings/specific_fns/consistency_tests.py branches/j_couplings/specific_fns/frame_order.py branches/j_couplings/specific_fns/jw_mapping.py branches/j_couplings/specific_fns/model_free/__init__.py branches/j_couplings/specific_fns/model_free/main.py branches/j_couplings/specific_fns/n_state_model.py branches/j_couplings/specific_fns/noe.py branches/j_couplings/specific_fns/relax_fit.py branches/j_couplings/specific_fns/setup.py branches/j_couplings/test_suite/system_tests/frame_order.py branches/j_couplings/test_suite/unit_tests/value_testing_base.py [This mail would be too long, it was shortened to contain the URLs only.] Modified: branches/j_couplings/generic_fns/eliminate.py URL: http://svn.gna.org/viewcvs/relax/branches/j_couplings/generic_fns/eliminate.py?rev=10035&r1=10034&r2=10035&view=diff Modified: branches/j_couplings/generic_fns/minimise.py URL: http://svn.gna.org/viewcvs/relax/branches/j_couplings/generic_fns/minimise.py?rev=10035&r1=10034&r2=10035&view=diff Modified: branches/j_couplings/generic_fns/structure/internal.py URL: http://svn.gna.org/viewcvs/relax/branches/j_couplings/generic_fns/structure/internal.py?rev=10035&r1=10034&r2=10035&view=diff Modified: branches/j_couplings/generic_fns/value.py URL: http://svn.gna.org/viewcvs/relax/branches/j_couplings/generic_fns/value.py?rev=10035&r1=10034&r2=10035&view=diff Modified: branches/j_couplings/prompt/__init__.py URL: http://svn.gna.org/viewcvs/relax/branches/j_couplings/prompt/__init__.py?rev=10035&r1=10034&r2=10035&view=diff Modified: branches/j_couplings/prompt/align_tensor.py URL: 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