Author: bugman
Date: Tue Jun 29 23:44:28 2010
New Revision: 11268
URL: http://svn.gna.org/viewcvs/relax?rev=11268&view=rev
Log:
Merged revisions
9871-9875,9891-9986,9998-10032,10038-10041,10047-10084,10086-10091,10094-10102,10108-10110,10117,10157,10178-10188,10197,10204-10205,10240,10242-10245,10267,10296-10302,10304-10326,10330,10404,10431-10435,10443,10450,10461-10462,10611-10612,10626-10631,10645,10652,10668-10671,10674,10676,10680,10684,10688-10689,10691,10694,10699,10703-10704,10708-10754,10766-10789,10794-10829,10838,10841-10842,10845-10860,10862,10865,10878-10879,10881-10884,10937-10958,10961-10990,10999-11002,11004-11050,11053-11059,11070-11071,11085,11087-11099,11144-11175,11185-11189,11206-11210,11223-11224,11230-11233,11236,11240,11243-11246,11248-11263
via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
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r9871 | semor | 2009-11-18 15:20:42 +0100 (Wed, 18 Nov 2009) | 6 lines
Added references to the consistency tests code.
In particular, the reference for this newly published paper was added:
Morin & Gagne (2009) JBNMR, 45: 361-372.
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r9872 | semor | 2009-11-18 16:58:50 +0100 (Wed, 18 Nov 2009) | 7 lines
Added references and instructions in the sample script for consistency
testing.
This is as proposed by Edward in a post at:
https://mail.gna.org/public/relax-devel/2009-11/msg00034.html
(Message-id: <7f080ed10911180653w6b59b40dn1e8f715d9b718fd5@xxxxxxxxxxxxxx>)
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r9873 | semor | 2009-11-18 17:58:39 +0100 (Wed, 18 Nov 2009) | 5 lines
Added DOI links to the citations and corrected a fused f and i character.
This was proposed by Edward.
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r9874 | semor | 2009-11-18 18:29:02 +0100 (Wed, 18 Nov 2009) | 3 lines
Corrected other strange characters causing failures...
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r9875 | bugman | 2009-11-19 10:37:23 +0100 (Thu, 19 Nov 2009) | 3 lines
Converted the 'Branches' subsection of the development chapter into a
proper section.
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r9891 | bugman | 2009-11-24 09:24:48 +0100 (Tue, 24 Nov 2009) | 3 lines
Fixes for the dx.map() user function interface.
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r9892 | bugman | 2009-11-24 10:05:30 +0100 (Tue, 24 Nov 2009) | 10 lines
Added the methods necessary for the dx.map() user function.
These include:
__assemble_param_vector()
map_bounds()
model_statistics()
return_data_name()
return_units()
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r9893 | bugman | 2009-11-24 10:17:37 +0100 (Tue, 24 Nov 2009) | 5 lines
Fix for the base class return_conversion_factor() method.
The spin_id arg is now accepted.
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r9894 | bugman | 2009-11-24 10:32:01 +0100 (Tue, 24 Nov 2009) | 6 lines
Created unit tests for the specific_fns API.
This checks the consistency of methods across the API, using method names
and arg checks. Only the
frame order theories are currently checked.
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r9895 | bugman | 2009-11-24 10:46:05 +0100 (Tue, 24 Nov 2009) | 3 lines
Renamed specific_fns.base_class.Common_functions to
specific_fns.api_base.API_base.
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r9896 | bugman | 2009-11-24 10:55:57 +0100 (Tue, 24 Nov 2009) | 3 lines
The entirety of the specific_fns API is now checked.
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r9897 | bugman | 2009-11-24 10:57:13 +0100 (Tue, 24 Nov 2009) | 3 lines
Updated for the __all__ list for the base_class to api_base rename.
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r9898 | bugman | 2009-11-24 11:07:36 +0100 (Tue, 24 Nov 2009) | 3 lines
Alphabetical ordering of the functions.
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r9899 | bugman | 2009-11-24 11:14:08 +0100 (Tue, 24 Nov 2009) | 3 lines
Removed the back_calc() method from the specific analysis API.
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r9900 | bugman | 2009-11-24 11:20:24 +0100 (Tue, 24 Nov 2009) | 3 lines
Removed the copy() method from the specific analysis API.
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r9901 | bugman | 2009-11-24 11:21:53 +0100 (Tue, 24 Nov 2009) | 3 lines
Added a prototype calculate() method to the API.
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r9902 | bugman | 2009-11-24 11:42:53 +0100 (Tue, 24 Nov 2009) | 3 lines
Removed assemble_param_vector() and disassemble_param_vector() from the
specific analysis API.
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r9903 | bugman | 2009-11-24 11:45:10 +0100 (Tue, 24 Nov 2009) | 3 lines
Removed assemble_scaling_matrix() from the specific analysis API.
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r9904 | bugman | 2009-11-24 11:52:38 +0100 (Tue, 24 Nov 2009) | 3 lines
Removed back_calc() from the specific analysis API.
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r9905 | bugman | 2009-11-24 11:53:20 +0100 (Tue, 24 Nov 2009) | 3 lines
Completed removal of back_calc() from the specific analysis API.
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r9906 | bugman | 2009-11-24 11:56:47 +0100 (Tue, 24 Nov 2009) | 3 lines
Added create_mc_data() to the specific analysis API.
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r9907 | bugman | 2009-11-24 12:18:58 +0100 (Tue, 24 Nov 2009) | 5 lines
Added data_names() to the specific analysis API.
General docstring clean ups as well.
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r9908 | bugman | 2009-11-24 12:39:49 +0100 (Tue, 24 Nov 2009) | 3 lines
Fix for the unit test for the N-state model _assemble_param_vector() method.
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r9909 | bugman | 2009-11-24 12:40:39 +0100 (Tue, 24 Nov 2009) | 3 lines
Fix for the unit test for the N-state model _disassemble_param_vector()
method.
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r9910 | bugman | 2009-11-24 12:56:22 +0100 (Tue, 24 Nov 2009) | 15 lines
A large number of method and documentation variables to the specific
analysis API.
These include:
default_value_doc
default_value()
grid_search()
minimise()
return_data_name_doc
return_data_name()
return_grace_string()
return_units()
set_doc
sim_pack_data()
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r9911 | bugman | 2009-11-24 12:58:24 +0100 (Tue, 24 Nov 2009) | 10 lines
Converted a number of methods to being private, removing them from the API.
These include:
_grid_search_setup()
_linear_constraints()
_model_setup()
_relax_time()
_select_model()
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r9912 | bugman | 2009-11-24 12:59:22 +0100 (Tue, 24 Nov 2009) | 3 lines
Converted the _select_model() method to be private, removing it from the
API.
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r9913 | bugman | 2009-11-24 13:05:29 +0100 (Tue, 24 Nov 2009) | 5 lines
Clean up of the create_mc_data() API method across the board.
The spin_id keyword is now accepted by all, and is a keyword.
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r9914 | bugman | 2009-11-24 13:21:18 +0100 (Tue, 24 Nov 2009) | 3 lines
Docstring update to return_grace_string().
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r9915 | bugman | 2009-11-24 13:22:09 +0100 (Tue, 24 Nov 2009) | 5 lines
Fixes for the relaxation curve fitting API.
The fixes are for the return_data_name(), return_grace_string(), and
return_units() methods.
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r9916 | bugman | 2009-11-24 13:25:52 +0100 (Tue, 24 Nov 2009) | 3 lines
Alphabetical ordering of methods, and separation of the private from the
API methods.
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r9917 | bugman | 2009-11-24 13:47:33 +0100 (Tue, 24 Nov 2009) | 3 lines
Docstring and default arg changes.
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r9918 | bugman | 2009-11-24 13:47:58 +0100 (Tue, 24 Nov 2009) | 3 lines
Removed duplicated epydoc tags.
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r9919 | bugman | 2009-11-24 13:48:37 +0100 (Tue, 24 Nov 2009) | 3 lines
Clean up of the entire NOE API.
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r9920 | bugman | 2009-11-24 13:49:42 +0100 (Tue, 24 Nov 2009) | 3 lines
Alphabetical ordering of methods, and separation of the private from the
API methods.
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r9921 | bugman | 2009-11-24 14:04:23 +0100 (Tue, 24 Nov 2009) | 5 lines
Removed the check of the default values from the specific analysis API arg
checks.
The defaults keyword values can be set to anything by the specific code!
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r9922 | bugman | 2009-11-24 14:52:52 +0100 (Tue, 24 Nov 2009) | 3 lines
Fixes for the string printout creation in the __check_method_args() method.
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r9923 | bugman | 2009-11-24 15:04:25 +0100 (Tue, 24 Nov 2009) | 5 lines
Removed the unused _read() method.
This has been superseded by the spectrum.read_intensities() user function.
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r9924 | bugman | 2009-11-24 15:26:08 +0100 (Tue, 24 Nov 2009) | 3 lines
Added model_statistics() to the specific analysis API.
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r9925 | bugman | 2009-11-24 15:30:49 +0100 (Tue, 24 Nov 2009) | 3 lines
Clean up of the entire N-state model specific API.
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r9926 | bugman | 2009-11-24 15:32:47 +0100 (Tue, 24 Nov 2009) | 3 lines
Converted all self.__*() private methods to self._*() non-API methods.
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r9927 | bugman | 2009-11-24 15:40:14 +0100 (Tue, 24 Nov 2009) | 3 lines
Alphabetical ordering of methods, and separation of the private from the
API methods.
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r9928 | bugman | 2009-11-24 15:50:02 +0100 (Tue, 24 Nov 2009) | 3 lines
Added duplicate_data() to the specific analysis API.
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r9929 | bugman | 2009-11-24 16:46:59 +0100 (Tue, 24 Nov 2009) | 3 lines
Removed some unused methods from the API.
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r9930 | bugman | 2009-11-24 16:48:38 +0100 (Tue, 24 Nov 2009) | 17 lines
Added a number of methods to the specific analysis API.
These include:
deselect()
get_param_names()
get_param_values()
map_bounds()
model_desc()
model_type()
molmol_macro()
read_columnar_results()
return_data_desc()
skip_function()
The API base class should now be complete.
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r9931 | bugman | 2009-11-24 16:59:08 +0100 (Tue, 24 Nov 2009) | 3 lines
Clean up of the entire model-free analysis specific API.
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r9932 | bugman | 2009-11-24 17:05:36 +0100 (Tue, 24 Nov 2009) | 3 lines
Converted all the model-free results methods from private to non-API.
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r9933 | bugman | 2009-11-24 17:08:00 +0100 (Tue, 24 Nov 2009) | 3 lines
Added an empty eliminate_doc variable to the specific analysis API.
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r9934 | bugman | 2009-11-24 17:51:20 +0100 (Tue, 24 Nov 2009) | 5 lines
More fixes for the __format_method() method.
The methods with args and keywords are now properly formatted!
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r9935 | bugman | 2009-11-24 18:02:38 +0100 (Tue, 24 Nov 2009) | 3 lines
Fixes for the eliminate() and model_statistics() API prototype methods.
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r9936 | bugman | 2009-11-24 18:03:08 +0100 (Tue, 24 Nov 2009) | 3 lines
Fix for the N-state model model_statistics() API method.
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r9937 | bugman | 2009-11-24 18:05:40 +0100 (Tue, 24 Nov 2009) | 3 lines
Update for the return_conversion_factor() API prototype method.
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r9938 | bugman | 2009-11-24 18:15:06 +0100 (Tue, 24 Nov 2009) | 3 lines
Shifted many of the model-free specific methods out of the API.
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r9939 | bugman | 2009-11-24 18:35:49 +0100 (Tue, 24 Nov 2009) | 3 lines
Converted the specific analysis base API to use the model_info arg,
returned from model_loop().
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r9940 | bugman | 2009-11-24 18:39:15 +0100 (Tue, 24 Nov 2009) | 3 lines
Updated the N-state model model_statistics() method to the model_info arg.
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r9941 | bugman | 2009-11-24 18:40:39 +0100 (Tue, 24 Nov 2009) | 3 lines
Fixes for the model-free unit tests. The model_index arg is now called
model_info.
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r9942 | bugman | 2009-11-24 18:41:28 +0100 (Tue, 24 Nov 2009) | 3 lines
Converted many of the model-free methods to use model_info rather than
model_index.
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r9943 | bugman | 2009-11-24 19:08:56 +0100 (Tue, 24 Nov 2009) | 3 lines
Fix for the specific analysis base API set_selected_sim() method.
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r9944 | bugman | 2009-11-24 19:18:23 +0100 (Tue, 24 Nov 2009) | 5 lines
Fix for the analysis specific base API sim_return_selected() method.
The model_info arg is now being used.
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r9945 | bugman | 2009-11-24 19:26:08 +0100 (Tue, 24 Nov 2009) | 3 lines
Converted the private __compare_objects() method to the non-API
_compare_objects() method.
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r9946 | bugman | 2009-11-24 19:30:09 +0100 (Tue, 24 Nov 2009) | 3 lines
Alphabetical ordering of model-free methods, and separation of the private
from the API methods.
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r9947 | bugman | 2009-11-24 19:58:18 +0100 (Tue, 24 Nov 2009) | 3 lines
A number of fixes for the model-free analysis specific API methods.
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r9948 | bugman | 2009-11-24 19:58:49 +0100 (Tue, 24 Nov 2009) | 3 lines
Changes to the args for the base API data_init() method.
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r9949 | bugman | 2009-11-24 19:59:32 +0100 (Tue, 24 Nov 2009) | 3 lines
Updates to the methods of the reduced spectral density mapping API.
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r9950 | bugman | 2009-11-25 09:05:00 +0100 (Wed, 25 Nov 2009) | 3 lines
Updated the data_init() method for API consistency.
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r9951 | bugman | 2009-11-25 09:15:40 +0100 (Wed, 25 Nov 2009) | 3 lines
Converted many of the J(w) mapping methods to use the model_info arg rather
than spin.
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r9952 | bugman | 2009-11-25 09:19:52 +0100 (Wed, 25 Nov 2009) | 3 lines
Docstring updates for returned values.
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r9953 | bugman | 2009-11-25 09:21:38 +0100 (Wed, 25 Nov 2009) | 3 lines
Alphabetical ordering of J(w) mapping methods, and separation of the
private from the API methods.
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r9954 | bugman | 2009-11-25 09:26:19 +0100 (Wed, 25 Nov 2009) | 3 lines
Docstring fix.
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r9955 | bugman | 2009-11-25 09:31:52 +0100 (Wed, 25 Nov 2009) | 3 lines
Updated the hybrid analysis API to match the base API.
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r9956 | bugman | 2009-11-25 09:38:44 +0100 (Wed, 25 Nov 2009) | 3 lines
Separation of the private and API methods in the hybrid specific analysis.
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r9957 | bugman | 2009-11-25 09:39:48 +0100 (Wed, 25 Nov 2009) | 3 lines
Converted the frame order private methods into non-API methods.
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r9958 | bugman | 2009-11-25 09:44:55 +0100 (Wed, 25 Nov 2009) | 3 lines
Separation of all the non-API frame order specific methods.
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r9959 | bugman | 2009-11-25 09:46:39 +0100 (Wed, 25 Nov 2009) | 3 lines
Epydoc docstring fix.
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r9960 | bugman | 2009-11-25 09:56:56 +0100 (Wed, 25 Nov 2009) | 3 lines
Updated all the frame order specific analysis API methods to match the base
API.
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r9961 | bugman | 2009-11-25 10:02:26 +0100 (Wed, 25 Nov 2009) | 3 lines
Fixes for the frame order user functions.
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r9962 | bugman | 2009-11-25 10:02:55 +0100 (Wed, 25 Nov 2009) | 3 lines
Removal of set_frq() from the consistency testing analysis specific API.
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r9963 | bugman | 2009-11-25 10:07:09 +0100 (Wed, 25 Nov 2009) | 3 lines
Docstring fixes.
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r9964 | bugman | 2009-11-25 10:17:49 +0100 (Wed, 25 Nov 2009) | 3 lines
More docstring updates.
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r9965 | bugman | 2009-11-25 10:18:38 +0100 (Wed, 25 Nov 2009) | 3 lines
Updated all the consistency testing analysis specific API methods to match
the base API.
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r9966 | bugman | 2009-11-25 10:43:32 +0100 (Wed, 25 Nov 2009) | 3 lines
Fix for the consistency testing return_units() method for the arg name
changes.
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r9967 | bugman | 2009-11-25 10:57:19 +0100 (Wed, 25 Nov 2009) | 3 lines
Epydoc docstring fix.
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r9968 | bugman | 2009-11-25 10:59:05 +0100 (Wed, 25 Nov 2009) | 3 lines
Epydoc docstring fix and reformatting of generic_fns.pcs.read().
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r9969 | bugman | 2009-11-25 12:55:17 +0100 (Wed, 25 Nov 2009) | 5 lines
Decreased the user function docstring size in the relax manual.
This was changed from normal size to \scriptsize to decrease the number of
pages in the manual.
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r9970 | bugman | 2009-11-25 13:06:03 +0100 (Wed, 25 Nov 2009) | 5 lines
The user function descriptions in the relax manual are now in columns.
This shrinks the manual even further.
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r9971 | bugman | 2009-11-25 13:11:52 +0100 (Wed, 25 Nov 2009) | 5 lines
Removed the \newpage command from the user function descriptions.
This cuts the manual size by over 100 pages!!!
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r9972 | bugman | 2009-11-25 13:18:28 +0100 (Wed, 25 Nov 2009) | 3 lines
Added '()' to the end of the user functions in the relax manual.
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r9973 | bugman | 2009-11-25 15:41:03 +0100 (Wed, 25 Nov 2009) | 3 lines
Turned all tables from the user functions in the relax manual into floating
tables.
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r9974 | bugman | 2009-11-25 15:46:58 +0100 (Wed, 25 Nov 2009) | 5 lines
Clean up of the minimisation docstring.
This no longer causes problems in the relax manual.
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r9975 | bugman | 2009-11-25 15:54:01 +0100 (Wed, 25 Nov 2009) | 3 lines
Switched from the multicols package to just using \twocolumn and \onecolumn.
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r9976 | bugman | 2009-11-25 15:54:36 +0100 (Wed, 25 Nov 2009) | 3 lines
Fixes for the align_tensor.svd() docstring for the relax manual.
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r9977 | bugman | 2009-11-25 16:52:44 +0100 (Wed, 25 Nov 2009) | 3 lines
Added rules to break the user function subsections in the manual apart.
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r9978 | bugman | 2009-11-25 17:18:32 +0100 (Wed, 25 Nov 2009) | 3 lines
Modified the spin ID string documentation to be better presented in the
relax manual.
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r9979 | bugman | 2009-11-26 09:09:29 +0100 (Thu, 26 Nov 2009) | 6 lines
User function call examples in the relax manual are now better formatted.
They are allowed to break after '.', '(', and '='. This is for the
examples and the Defaults
subsubsection.
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r9980 | bugman | 2009-11-26 10:22:06 +0100 (Thu, 26 Nov 2009) | 3 lines
Allowed for hyphenation in the user function subsection titles.
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r9981 | bugman | 2009-11-26 12:20:26 +0100 (Thu, 26 Nov 2009) | 3 lines
Massive tables in the relax manual are now being split using the longtable
package.
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r9982 | bugman | 2009-11-26 12:27:18 +0100 (Thu, 26 Nov 2009) | 3 lines
The tables in the user function chapter now have the same font size as the
rest of the text.
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r9983 | bugman | 2009-11-26 12:33:35 +0100 (Thu, 26 Nov 2009) | 3 lines
Better formatting of the user function chapter by using \raggedbottom.
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r9984 | bugman | 2009-11-26 12:50:58 +0100 (Thu, 26 Nov 2009) | 3 lines
Fixed the boolean selection table to be nicer to the automatic manual
compilation.
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r9985 | bugman | 2009-11-26 13:16:37 +0100 (Thu, 26 Nov 2009) | 3 lines
The longtables are now properly labelled.
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r9986 | bugman | 2009-11-26 18:36:27 +0100 (Thu, 26 Nov 2009) | 3 lines
Removed the checking of sequence data from generic_fns.value.set().
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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.
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r9999 | bugman | 2009-11-27 17:16:08 +0100 (Fri, 27 Nov 2009) | 3 lines
Docstring fixes for the value.set() user function.
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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.
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r10001 | bugman | 2009-11-27 17:53:43 +0100 (Fri, 27 Nov 2009) | 3 lines
Removed 'check' from the __all__ list.
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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.
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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.
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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).
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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).
[... 3677 lines stripped ...]
r11268 - in /branches/relax_disp: ./ auto_analyses/ data/ docs/ docs/latex/ generic_fns/ generic_fns/structure/ maths_fns/ o...