Author: semor Date: Thu Jan 17 20:35:31 2008 New Revision: 4840 URL: http://svn.gna.org/viewcvs/relax?rev=4840&view=rev Log: Merged revisions 4796,4799,4802,4804,4815-4819,4821-4834,4839 via svnmerge from svn+ssh://semor@xxxxxxxxxxx/svn/relax/1.3 ........ r4796 | bugman | 2008-01-16 11:31:48 -0500 (Wed, 16 Jan 2008) | 3 lines Shifted the model-free disassemble_param_vector() method as it is specific to minimisation. ........ r4799 | bugman | 2008-01-16 12:00:59 -0500 (Wed, 16 Jan 2008) | 3 lines Converted the model-free code from Numeric to numpy. ........ r4802 | semor | 2008-01-16 13:00:11 -0500 (Wed, 16 Jan 2008) | 3 lines Removed a trailing whitespace. ........ r4804 | bugman | 2008-01-17 04:19:47 -0500 (Thu, 17 Jan 2008) | 5 lines Created a base class method num_instances() to check the sequence and return the number of spins. The J(w) mapping and relaxation curve fitting num_instances() methods have been removed. ........ r4815 | bugman | 2008-01-17 09:08:15 -0500 (Thu, 17 Jan 2008) | 8 lines Updated the generic_fns.value module functions set() and partition_params() to be more general. The updating is not complete, but works for most of the current codebase. The assumption of a data analysis type having a diffusion or other tensor has been removed. This has been replaced by the concept that the params are now partitioned into those that are spin specific and those that are not. The diffusion tensor stuff will be moved into the model-free code. ........ r4816 | bugman | 2008-01-17 09:18:56 -0500 (Thu, 17 Jan 2008) | 5 lines Removed some useless code in the partition_params() function. Because of the main if-else loop, this code will never be executed! ........ r4817 | bugman | 2008-01-17 09:21:56 -0500 (Thu, 17 Jan 2008) | 3 lines Fixed all of the unit tests of the generic_fns.value.partition_params() function. ........ r4818 | bugman | 2008-01-17 09:28:16 -0500 (Thu, 17 Jan 2008) | 3 lines Removed some debugging code which is now covered by the unit tests. ........ r4819 | bugman | 2008-01-17 09:34:31 -0500 (Thu, 17 Jan 2008) | 5 lines More fixes for the unit tests of the generic_fns.value.partition_params() function. The current data pipe needed to be changed back to a model-free pipe. ........ r4821 | semor | 2008-01-17 09:57:43 -0500 (Thu, 17 Jan 2008) | 3 lines Converted the maths_fns.jw_mapping module from Numeric to numpy. ........ r4822 | bugman | 2008-01-17 10:07:22 -0500 (Thu, 17 Jan 2008) | 7 lines Big refactorisation of the value setting code. Expect breakages as the changes aren't complete! The parameter setting set() base class method has been shifted from the specific code to the generic_fns.value module (and has been converted to a function). This method simply sets spin specific functions and hence has been renamed to the set_spin_params() function. ........ r4823 | bugman | 2008-01-17 10:11:21 -0500 (Thu, 17 Jan 2008) | 5 lines Added a few more functions to be returned by get_specific_fn(). These include data_init(), default_value(), and set_update(). ........ r4824 | bugman | 2008-01-17 10:13:14 -0500 (Thu, 17 Jan 2008) | 3 lines Shifted the RelaxParamSetError import to the generic_fns.value module. ........ r4825 | bugman | 2008-01-17 10:19:55 -0500 (Thu, 17 Jan 2008) | 3 lines Removed the Numeric and Scientific packages from the relax prompt namespace. ........ r4826 | bugman | 2008-01-17 10:23:02 -0500 (Thu, 17 Jan 2008) | 3 lines Converted the data.diff_tensor code from Numeric to numpy. ........ r4827 | semor | 2008-01-17 10:34:33 -0500 (Thu, 17 Jan 2008) | 3 lines Converted more maths_fns modules from Numeric to numpy. ........ r4828 | semor | 2008-01-17 10:37:25 -0500 (Thu, 17 Jan 2008) | 3 lines Converted another maths_fns module from Numeric to numpy. ........ r4829 | bugman | 2008-01-17 10:56:35 -0500 (Thu, 17 Jan 2008) | 3 lines Removed the cdp aliases as they are not used very often. ........ r4830 | bugman | 2008-01-17 11:02:50 -0500 (Thu, 17 Jan 2008) | 3 lines Converted the generic_fns.value code from Numeric to numpy. ........ r4831 | bugman | 2008-01-17 11:10:28 -0500 (Thu, 17 Jan 2008) | 6 lines Changed the call to diffusion_tensor.set() to the new specific function set_nonspin_params(). The code for setting parameters that are non-spin specific is very much dependent on the analysis type, and hence this has been shifted into a call into specific_fns. ........ r4832 | bugman | 2008-01-17 11:16:22 -0500 (Thu, 17 Jan 2008) | 5 lines Implemented the base class method set_non_spin_params(). This throws a RelaxError if anything is sent into the function. ........ r4833 | bugman | 2008-01-17 11:21:11 -0500 (Thu, 17 Jan 2008) | 5 lines Wrote the model-free specific set_non_spin_params() method. This simply calls the diffusion tensor setting code. ........ r4834 | bugman | 2008-01-17 11:35:05 -0500 (Thu, 17 Jan 2008) | 5 lines Big inheritance bug fix for the model-free code. The base class methods were being used instead of the model-free methods! ........ r4839 | bugman | 2008-01-17 12:20:36 -0500 (Thu, 17 Jan 2008) | 6 lines Modified the partition_params() function to better handle when no parameter name is supplied. This situation is used for setting the parameter values of the model. The function now returns the model_values list to be used later on. ........ Modified: branches/consistency_tests_1.3/ (props changed) branches/consistency_tests_1.3/data/diff_tensor.py branches/consistency_tests_1.3/generic_fns/value.py branches/consistency_tests_1.3/maths_fns/direction_cosine.py branches/consistency_tests_1.3/maths_fns/jw_mapping.py branches/consistency_tests_1.3/maths_fns/jw_mf.py branches/consistency_tests_1.3/maths_fns/jw_mf_comps.py branches/consistency_tests_1.3/maths_fns/ri_comps.py branches/consistency_tests_1.3/maths_fns/weights.py branches/consistency_tests_1.3/prompt/interpreter.py branches/consistency_tests_1.3/relax_io.py branches/consistency_tests_1.3/specific_fns/__init__.py branches/consistency_tests_1.3/specific_fns/base_class.py branches/consistency_tests_1.3/specific_fns/jw_mapping.py branches/consistency_tests_1.3/specific_fns/model_free/__init__.py branches/consistency_tests_1.3/specific_fns/model_free/mf_minimise.py branches/consistency_tests_1.3/specific_fns/model_free/model_free.py branches/consistency_tests_1.3/specific_fns/relax_fit.py branches/consistency_tests_1.3/test_suite/unit_tests/_generic_fns/test_value.py [This mail would be too long, it was shortened to contain the URLs only.] Modified: branches/consistency_tests_1.3/data/diff_tensor.py URL: http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.3/data/diff_tensor.py?rev=4840&r1=4839&r2=4840&view=diff Modified: branches/consistency_tests_1.3/generic_fns/value.py URL: http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.3/generic_fns/value.py?rev=4840&r1=4839&r2=4840&view=diff Modified: branches/consistency_tests_1.3/maths_fns/direction_cosine.py URL: http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.3/maths_fns/direction_cosine.py?rev=4840&r1=4839&r2=4840&view=diff Modified: branches/consistency_tests_1.3/maths_fns/jw_mapping.py URL: http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.3/maths_fns/jw_mapping.py?rev=4840&r1=4839&r2=4840&view=diff Modified: branches/consistency_tests_1.3/maths_fns/jw_mf.py URL: http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.3/maths_fns/jw_mf.py?rev=4840&r1=4839&r2=4840&view=diff Modified: branches/consistency_tests_1.3/maths_fns/jw_mf_comps.py URL: http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.3/maths_fns/jw_mf_comps.py?rev=4840&r1=4839&r2=4840&view=diff Modified: branches/consistency_tests_1.3/maths_fns/ri_comps.py URL: http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.3/maths_fns/ri_comps.py?rev=4840&r1=4839&r2=4840&view=diff Modified: branches/consistency_tests_1.3/maths_fns/weights.py URL: http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.3/maths_fns/weights.py?rev=4840&r1=4839&r2=4840&view=diff Modified: branches/consistency_tests_1.3/prompt/interpreter.py URL: http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.3/prompt/interpreter.py?rev=4840&r1=4839&r2=4840&view=diff Modified: branches/consistency_tests_1.3/relax_io.py URL: http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.3/relax_io.py?rev=4840&r1=4839&r2=4840&view=diff Modified: branches/consistency_tests_1.3/specific_fns/__init__.py URL: http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.3/specific_fns/__init__.py?rev=4840&r1=4839&r2=4840&view=diff Modified: branches/consistency_tests_1.3/specific_fns/base_class.py URL: http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.3/specific_fns/base_class.py?rev=4840&r1=4839&r2=4840&view=diff Modified: branches/consistency_tests_1.3/specific_fns/jw_mapping.py URL: http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.3/specific_fns/jw_mapping.py?rev=4840&r1=4839&r2=4840&view=diff Modified: branches/consistency_tests_1.3/specific_fns/model_free/__init__.py URL: http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.3/specific_fns/model_free/__init__.py?rev=4840&r1=4839&r2=4840&view=diff Modified: branches/consistency_tests_1.3/specific_fns/model_free/mf_minimise.py URL: http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.3/specific_fns/model_free/mf_minimise.py?rev=4840&r1=4839&r2=4840&view=diff Modified: branches/consistency_tests_1.3/specific_fns/model_free/model_free.py URL: http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.3/specific_fns/model_free/model_free.py?rev=4840&r1=4839&r2=4840&view=diff Modified: branches/consistency_tests_1.3/specific_fns/relax_fit.py URL: http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.3/specific_fns/relax_fit.py?rev=4840&r1=4839&r2=4840&view=diff Modified: branches/consistency_tests_1.3/test_suite/unit_tests/_generic_fns/test_value.py URL: http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.3/test_suite/unit_tests/_generic_fns/test_value.py?rev=4840&r1=4839&r2=4840&view=diff