Author: semor
Date: Thu Mar 27 00:55:10 2008
New Revision: 5234
URL: http://svn.gna.org/viewcvs/relax?rev=5234&view=rev
Log:
Merged revisions 5117,5136-5233 via svnmerge from
svn+ssh://semor@xxxxxxxxxxx/svn/relax/1.3
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r5117 | bugman | 2008-03-21 08:49:16 -0400 (Fri, 21 Mar 2008) | 6 lines
Fix for bug #11004 (https://gna.org/bugs/?11004).
The division by zero is now caught and avoided, but this bug has been
triggered by a deeper problem
which is likely to uncover additional bugs.
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r5136 | bugman | 2008-03-22 10:12:47 -0400 (Sat, 22 Mar 2008) | 3 lines
assemble_param_vector() now calls determine_param_set_type() to get the
model type.
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r5137 | bugman | 2008-03-22 10:22:52 -0400 (Sat, 22 Mar 2008) | 3 lines
Updated the model-free determine_param_set_type() method to the new relax
design.
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r5138 | bugman | 2008-03-22 10:25:06 -0400 (Sat, 22 Mar 2008) | 3 lines
Bug fix for determine_param_set_type(), the diff_data_exists() function is
properly called.
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r5139 | bugman | 2008-03-22 10:28:21 -0400 (Sat, 22 Mar 2008) | 6 lines
Another bug fix for determine_param_set_type().
The structure cdp.diff_tensor should have been accessed, not cdp.diff.
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r5140 | bugman | 2008-03-22 13:17:32 -0400 (Sat, 22 Mar 2008) | 3 lines
Created a new function count_selected_spins() for counting selected spins.
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r5141 | bugman | 2008-03-22 13:23:13 -0400 (Sat, 22 Mar 2008) | 3 lines
Converted the model-free minimise() method to the new relax design.
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r5142 | bugman | 2008-03-22 13:25:26 -0400 (Sat, 22 Mar 2008) | 3 lines
Bug fix in the minimise() method for the call to diff_data_exists().
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r5143 | bugman | 2008-03-22 13:26:10 -0400 (Sat, 22 Mar 2008) | 3 lines
Missing import of return_spin().
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r5144 | bugman | 2008-03-22 13:36:01 -0400 (Sat, 22 Mar 2008) | 3 lines
Created the new function generic_fns.selection.return_spin_from_index().
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r5145 | bugman | 2008-03-22 13:38:47 -0400 (Sat, 22 Mar 2008) | 3 lines
Modified the model-free minimise() method to use the new
return_spin_from_index() function.
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r5146 | bugman | 2008-03-22 13:41:24 -0400 (Sat, 22 Mar 2008) | 5 lines
Bug fix in the test_opt_constr_sd_back_S2_0_970_te_2048_Rex_0_149() system
test.
'spin.chi2' was being accessed as 'spin.chi'.
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r5147 | bugman | 2008-03-22 13:48:19 -0400 (Sat, 22 Mar 2008) | 3 lines
Changed 'unselected' to 'deselected'.
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r5148 | bugman | 2008-03-22 13:53:48 -0400 (Sat, 22 Mar 2008) | 3 lines
Modified all the model-free optimisation system tests to check if the spins
are properly selected.
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r5149 | bugman | 2008-03-22 14:03:06 -0400 (Sat, 22 Mar 2008) | 3 lines
Converted the model-free overfit_deselect() method to use booleans.
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r5150 | bugman | 2008-03-22 14:42:42 -0400 (Sat, 22 Mar 2008) | 3 lines
Modified all the model-free optimisation system tests to compare 'select'
to bools.
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r5151 | bugman | 2008-03-22 14:45:43 -0400 (Sat, 22 Mar 2008) | 5 lines
Bug fix for the model-free overfit_deselect() method.
The spin.xh_vect structure should only be checked for if structural info is
required.
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r5152 | bugman | 2008-03-22 17:08:39 -0400 (Sat, 22 Mar 2008) | 3 lines
Converted the copySign() docstring to epydoc format.
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r5153 | bugman | 2008-03-22 17:10:11 -0400 (Sat, 22 Mar 2008) | 3 lines
Fix for the copySign() docstring - incorrect parameter name.
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r5154 | bugman | 2008-03-22 17:14:07 -0400 (Sat, 22 Mar 2008) | 3 lines
Fixed the epytext '@raise' syntax in two docstrings.
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r5155 | bugman | 2008-03-22 17:15:49 -0400 (Sat, 22 Mar 2008) | 3 lines
Updated the isNegInf() docstring.
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r5156 | bugman | 2008-03-22 17:48:29 -0400 (Sat, 22 Mar 2008) | 3 lines
Updated all the float function docstrings to epydoc format.
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r5157 | bugman | 2008-03-22 17:49:35 -0400 (Sat, 22 Mar 2008) | 3 lines
Renamed all 'nan' to 'NaN' in docstrings and comments.
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r5158 | bugman | 2008-03-22 18:03:16 -0400 (Sat, 22 Mar 2008) | 3 lines
Updated the float module docstring for epydoc.
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r5159 | bugman | 2008-03-22 18:08:49 -0400 (Sat, 22 Mar 2008) | 3 lines
Fixed the epydoc part of the getFloatClass() docstring.
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r5160 | bugman | 2008-03-22 18:12:10 -0400 (Sat, 22 Mar 2008) | 3 lines
Replaced all '@type return:' with '@rtype:' in the docstrings.
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r5161 | bugman | 2008-03-22 18:19:30 -0400 (Sat, 22 Mar 2008) | 3 lines
The Noe calculate() method maths in the docstring has been converted to
epydoc format.
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r5162 | bugman | 2008-03-22 18:22:43 -0400 (Sat, 22 Mar 2008) | 3 lines
Better epydoc support for the equations of the fold_angles() function.
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r5163 | bugman | 2008-03-22 18:23:33 -0400 (Sat, 22 Mar 2008) | 3 lines
Better epydoc support for the equations of the kappa() function.
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r5164 | bugman | 2008-03-22 18:24:11 -0400 (Sat, 22 Mar 2008) | 3 lines
Fix for the map_labels() docstring.
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r5165 | bugman | 2008-03-22 18:25:04 -0400 (Sat, 22 Mar 2008) | 3 lines
Better epydoc support for the equations of the svd() function.
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r5166 | bugman | 2008-03-22 18:27:00 -0400 (Sat, 22 Mar 2008) | 3 lines
Replaced all '@return type:' with '@rtype:'.
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r5167 | bugman | 2008-03-22 18:29:03 -0400 (Sat, 22 Mar 2008) | 3 lines
Better epydoc support for the equations of the fold_angles() function.
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r5168 | bugman | 2008-03-22 18:31:54 -0400 (Sat, 22 Mar 2008) | 3 lines
Better epydoc support for the equations and title of the unit_axes()
function.
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r5169 | bugman | 2008-03-22 20:18:50 -0400 (Sat, 22 Mar 2008) | 6 lines
Started the break up of the insanely complex model-free minimisation
methods in specific_fns.
The configuration of the spin specific part of the grid search has been
shifted into its own
function.
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r5170 | bugman | 2008-03-22 20:22:16 -0400 (Sat, 22 Mar 2008) | 3 lines
The diffusion tensor grid search configuration has been shifted into its
own function.
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r5171 | bugman | 2008-03-22 20:23:39 -0400 (Sat, 22 Mar 2008) | 3 lines
Whoops, removal of the old code which was shifted into a new function in
r5170.
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r5172 | bugman | 2008-03-22 20:42:29 -0400 (Sat, 22 Mar 2008) | 3 lines
Shifted the grid search limits, diagonal scaling, and grid size test into
new separate methods.
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r5173 | bugman | 2008-03-22 20:55:05 -0400 (Sat, 22 Mar 2008) | 3 lines
Shifted all the setting up of data for model-free minimisation into its own
function.
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r5174 | bugman | 2008-03-22 21:03:03 -0400 (Sat, 22 Mar 2008) | 3 lines
Split up the grid search function, reverting back to the structure as in
the 1.2 line.
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r5175 | bugman | 2008-03-23 08:07:49 -0400 (Sun, 23 Mar 2008) | 5 lines
The model-free grid search args are now passed into the minimise() method.
These will later be passed into the grid search configuration functions.
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r5176 | bugman | 2008-03-23 08:14:52 -0400 (Sun, 23 Mar 2008) | 3 lines
Updated the model-free assemble_param_vector() to accept spin containers.
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r5177 | bugman | 2008-03-23 08:18:50 -0400 (Sun, 23 Mar 2008) | 3 lines
Changed all epydoc '@param' to '@keyword' for all keyword args in the
mf_minimise module.
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r5178 | bugman | 2008-03-23 08:31:02 -0400 (Sun, 23 Mar 2008) | 3 lines
Updated the model-free assemble_scaling_matrix() method to the new relax
design.
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r5179 | bugman | 2008-03-23 08:42:32 -0400 (Sun, 23 Mar 2008) | 3 lines
Converted the num_params keyword arg in assemble_scaling_matrix() to a
normal arg.
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r5180 | bugman | 2008-03-23 08:43:43 -0400 (Sun, 23 Mar 2008) | 3 lines
Passed the number of params into the assemble_scaling_matrix() method.
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r5181 | bugman | 2008-03-23 08:46:58 -0400 (Sun, 23 Mar 2008) | 3 lines
The param_set variable is now passed into assemble_scaling_matrix().
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r5182 | bugman | 2008-03-23 09:36:11 -0400 (Sun, 23 Mar 2008) | 3 lines
Bug fix, 'if scaling_matrix:' cannot be used on a numpy object.
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r5183 | bugman | 2008-03-23 09:44:00 -0400 (Sun, 23 Mar 2008) | 3 lines
A number of modifications to get the grid_search_config() method to work.
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r5184 | bugman | 2008-03-23 09:46:28 -0400 (Sun, 23 Mar 2008) | 3 lines
Passed the lower, upper, and inc variables into grid_search_config().
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r5185 | bugman | 2008-03-23 09:47:10 -0400 (Sun, 23 Mar 2008) | 3 lines
Added the missing self arg to a number of grid search methods.
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r5186 | bugman | 2008-03-23 09:47:42 -0400 (Sun, 23 Mar 2008) | 3 lines
Added the missing self arg to test_grid_size().
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r5187 | bugman | 2008-03-23 09:51:05 -0400 (Sun, 23 Mar 2008) | 3 lines
Passed the scaling matrix into the grid_search_config() method.
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r5188 | bugman | 2008-03-23 09:51:59 -0400 (Sun, 23 Mar 2008) | 3 lines
Fix in the assemble_scaling_matrix() docstring.
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r5189 | bugman | 2008-03-23 10:05:06 -0400 (Sun, 23 Mar 2008) | 3 lines
Converted the model-free linear_constraints() method to the new relax
design.
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r5190 | bugman | 2008-03-23 10:16:39 -0400 (Sun, 23 Mar 2008) | 3 lines
Updated the return_spin_from_index() function to return the spin_id string
if asked.
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r5191 | bugman | 2008-03-23 10:18:37 -0400 (Sun, 23 Mar 2008) | 3 lines
Modified the model-free minimise() function to print out the spin_id rather
than res name and num.
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r5192 | bugman | 2008-03-23 10:27:16 -0400 (Sun, 23 Mar 2008) | 3 lines
Modified generate_spin_id() to handle None and int entries in the data
array.
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r5193 | bugman | 2008-03-23 10:33:19 -0400 (Sun, 23 Mar 2008) | 3 lines
Shifted the grid size print out to the test_grid_size() method.
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r5194 | bugman | 2008-03-23 10:35:21 -0400 (Sun, 23 Mar 2008) | 5 lines
minimise_data_setup() is now called and the data stored.
The self arg has also been added.
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r5195 | bugman | 2008-03-23 10:43:52 -0400 (Sun, 23 Mar 2008) | 3 lines
Passed all the necessary data into minimise_data_setup().
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r5196 | bugman | 2008-03-23 10:52:53 -0400 (Sun, 23 Mar 2008) | 3 lines
Started some code to get minimise_data_setup() to return the gyromagnetic
ratios.
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r5197 | bugman | 2008-03-23 10:57:11 -0400 (Sun, 23 Mar 2008) | 3 lines
Converted many physical constant comments to docstrings.
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r5198 | bugman | 2008-03-23 11:24:16 -0400 (Sun, 23 Mar 2008) | 3 lines
Shifted the variable docstrings to the correct position below the variable.
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r5199 | bugman | 2008-03-23 11:30:08 -0400 (Sun, 23 Mar 2008) | 3 lines
Wrote the return_gyromagnetic_ratio() for returning the desired value.
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r5200 | bugman | 2008-03-23 11:34:45 -0400 (Sun, 23 Mar 2008) | 3 lines
Wrote the return_atomic_mass() function for returning the desired atomic
mass.
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r5201 | bugman | 2008-03-23 11:38:34 -0400 (Sun, 23 Mar 2008) | 3 lines
Modified generic_fns.align_tensor.kappa() to use the new
return_gyromagnetic_ratio() function.
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r5202 | bugman | 2008-03-23 11:44:37 -0400 (Sun, 23 Mar 2008) | 3 lines
Completed the gyromagnetic ratio part of the model-free
minimise_data_setup() method.
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r5203 | bugman | 2008-03-23 11:49:00 -0400 (Sun, 23 Mar 2008) | 3 lines
Added a module docstring.
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r5204 | bugman | 2008-03-23 11:53:05 -0400 (Sun, 23 Mar 2008) | 3 lines
Added a package docstring for the OpenDX code.
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r5205 | bugman | 2008-03-23 11:55:34 -0400 (Sun, 23 Mar 2008) | 3 lines
Added a package docstring for the maths_fns package.
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r5206 | bugman | 2008-03-23 12:00:20 -0400 (Sun, 23 Mar 2008) | 3 lines
Added a package docstring for the docs/ directory.
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r5207 | bugman | 2008-03-23 12:00:45 -0400 (Sun, 23 Mar 2008) | 3 lines
Shifted the module docstring to the correct location (the very start).
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r5208 | bugman | 2008-03-23 12:03:05 -0400 (Sun, 23 Mar 2008) | 3 lines
Added module docstrings for the RelaxErrors and RelaxWarnings.
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r5209 | bugman | 2008-03-23 12:12:16 -0400 (Sun, 23 Mar 2008) | 5 lines
Updated the specific_fns.model_free package __init__ module.
A module docstring has been added, as well as the __all__ list.
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r5210 | bugman | 2008-03-23 12:14:23 -0400 (Sun, 23 Mar 2008) | 3 lines
The specific_fns.model_free package is now being included in the API
documentation.
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r5211 | bugman | 2008-03-23 12:17:43 -0400 (Sun, 23 Mar 2008) | 3 lines
All packages in the specific_fns and test_suite directories are now being
included in the API docs.
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r5212 | bugman | 2008-03-23 13:02:43 -0400 (Sun, 23 Mar 2008) | 3 lines
Fixed indentation in the Unit_test_runner.__init__ docstring to allow the
API docs to be compiled.
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r5213 | bugman | 2008-03-23 13:08:08 -0400 (Sun, 23 Mar 2008) | 3 lines
Removed all the subdirectories of test_suite and model_free from the API
docs.
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r5214 | bugman | 2008-03-23 13:10:32 -0400 (Sun, 23 Mar 2008) | 5 lines
Updated the test_suite package __init__ module.
A package docstring was added, and the __all__ list completed.
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r5215 | bugman | 2008-03-23 13:13:42 -0400 (Sun, 23 Mar 2008) | 5 lines
Updated the test_suite.system_tests package __init__ module.
A package docstring was added, and the __all__ list completed.
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r5216 | bugman | 2008-03-23 13:17:28 -0400 (Sun, 23 Mar 2008) | 5 lines
Updated the test_suite.unit_tests package __init__ module.
A package docstring was added, and the __all__ list completed.
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r5217 | bugman | 2008-03-23 13:20:08 -0400 (Sun, 23 Mar 2008) | 3 lines
Removed a duplicated entry in __all__.
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r5218 | bugman | 2008-03-23 13:26:53 -0400 (Sun, 23 Mar 2008) | 3 lines
Updated the epydoc compilation of the API docs to include all unit tests.
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r5219 | bugman | 2008-03-23 13:34:07 -0400 (Sun, 23 Mar 2008) | 3 lines
Added some missing imports of physical constants.
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r5220 | bugman | 2008-03-23 13:47:06 -0400 (Sun, 23 Mar 2008) | 6 lines
Modified the model-free default_value() and return_data_name() methods.
The heteronucleus type is now stored in 'spin.heteronuc_type'. The proton
type has also been added,
and is located in 'spin.proton_type'.
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r5221 | bugman | 2008-03-23 13:56:10 -0400 (Sun, 23 Mar 2008) | 3 lines
Modified the unit tests due to the changed of r5220.
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r5222 | bugman | 2008-03-23 13:57:30 -0400 (Sun, 23 Mar 2008) | 3 lines
Typo fix.
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r5223 | bugman | 2008-03-23 14:02:28 -0400 (Sun, 23 Mar 2008) | 3 lines
Changes to the J(w) mapping code to reflect the model-free changes of r5220.
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r5224 | bugman | 2008-03-23 14:05:14 -0400 (Sun, 23 Mar 2008) | 3 lines
Modified the model-free optimisation test suite script for the new
value.set() behaviour.
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r5225 | bugman | 2008-03-23 14:07:45 -0400 (Sun, 23 Mar 2008) | 3 lines
Fixed the initialisation of the model-free maths_fns code.
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r5226 | bugman | 2008-03-23 14:18:37 -0400 (Sun, 23 Mar 2008) | 3 lines
Renamed all 'num_res' to 'num_spins'.
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r5227 | bugman | 2008-03-23 14:19:28 -0400 (Sun, 23 Mar 2008) | 3 lines
The gyromagnetic ratios are now properly handled.
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r5228 | bugman | 2008-03-23 14:20:41 -0400 (Sun, 23 Mar 2008) | 5 lines
Fix for the testing of the presence of the scaling matrix.
Again a numpy problem.
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r5229 | bugman | 2008-03-23 14:24:11 -0400 (Sun, 23 Mar 2008) | 3 lines
Updated copyright statement.
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r5230 | bugman | 2008-03-23 14:42:31 -0400 (Sun, 23 Mar 2008) | 5 lines
Updated the model-free disassemble_param_vector() method to the new relax
design.
Many model-free optimisation system tests now pass!!!
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r5231 | bugman | 2008-03-23 14:43:30 -0400 (Sun, 23 Mar 2008) | 3 lines
Added missing epydoc entries in the assemble_param_vector() method
docstring.
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r5232 | bugman | 2008-03-23 14:49:26 -0400 (Sun, 23 Mar 2008) | 3 lines
The min_options object is now returned by the grid_search_config() method.
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r5233 | bugman | 2008-03-26 06:28:53 -0400 (Wed, 26 Mar 2008) | 3 lines
Comment fixes in the N-state model maths fns.
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Modified:
branches/consistency_tests_1.3/ (props changed)
branches/consistency_tests_1.3/docs/__init__.py
branches/consistency_tests_1.3/dx/__init__.py
branches/consistency_tests_1.3/float.py
branches/consistency_tests_1.3/generic_fns/align_tensor.py
branches/consistency_tests_1.3/generic_fns/diffusion_tensor.py
branches/consistency_tests_1.3/generic_fns/minimise.py
branches/consistency_tests_1.3/generic_fns/monte_carlo.py
branches/consistency_tests_1.3/generic_fns/pipes.py
branches/consistency_tests_1.3/generic_fns/selection.py
branches/consistency_tests_1.3/generic_fns/value.py
branches/consistency_tests_1.3/maths_fns/__init__.py
branches/consistency_tests_1.3/maths_fns/mf.py
branches/consistency_tests_1.3/maths_fns/n_state_model.py
branches/consistency_tests_1.3/physical_constants.py
branches/consistency_tests_1.3/relax_errors.py
branches/consistency_tests_1.3/relax_io.py
branches/consistency_tests_1.3/relax_warnings.py
branches/consistency_tests_1.3/scons/manuals.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/noe.py
branches/consistency_tests_1.3/specific_fns/relax_data.py
branches/consistency_tests_1.3/test_suite/__init__.py
branches/consistency_tests_1.3/test_suite/system_tests/__init__.py
branches/consistency_tests_1.3/test_suite/system_tests/model_free.py
branches/consistency_tests_1.3/test_suite/system_tests/scripts/opt_setup_S2_0_970_te_2048_Rex_0_149.py
branches/consistency_tests_1.3/test_suite/unit_tests/__init__.py
branches/consistency_tests_1.3/test_suite/unit_tests/unit_test_runner.py
branches/consistency_tests_1.3/test_suite/unit_tests/value_testing_base.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/consistency_tests_1.3/docs/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.3/docs/__init__.py?rev=5234&r1=5233&r2=5234&view=diff
Modified: branches/consistency_tests_1.3/dx/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.3/dx/__init__.py?rev=5234&r1=5233&r2=5234&view=diff
Modified: branches/consistency_tests_1.3/float.py
URL:
http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.3/float.py?rev=5234&r1=5233&r2=5234&view=diff
Modified: branches/consistency_tests_1.3/generic_fns/align_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.3/generic_fns/align_tensor.py?rev=5234&r1=5233&r2=5234&view=diff
Modified: branches/consistency_tests_1.3/generic_fns/diffusion_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.3/generic_fns/diffusion_tensor.py?rev=5234&r1=5233&r2=5234&view=diff
Modified: branches/consistency_tests_1.3/generic_fns/minimise.py
URL:
http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.3/generic_fns/minimise.py?rev=5234&r1=5233&r2=5234&view=diff
[... 78 lines stripped ...]
r5234 - in /branches/consistency_tests_1.3: ./ docs/ dx/ generic_fns/ maths_fns/ scons/ specific_fns/ specific_fns/model_fre...