relax SVN archive

Major change to the grid search user function.

The minimise.grid_search user function now accepts the skip_preset flag. When True, the grid search
will skip any parameters with a preset value. This allows the user to set parameters via the
value.set user function and then have these parameters skipped in the grid search.

The new skip_preset argument is passed into the pipe_control.minimise.grid_setup() function in the
backend. This then sets both the grid lower and upper bounds to the preset parameter value and sets
the number of increments to 1 for that parameter so that it is essentially skipped in the grid
search.

Shifted the constraints boolean argument to the end of the grid_search() function argument list.

Epydoc docstring fixes for the keyword arguments of the pipe_control.minimise module.

Changes to the minimise.grid_search user function front end.

The Boolean constraints argument has been shifted to the end, and empty lines have been removed.

Merged revisions 24521,24526-24528,24535-24536,24543,24549-24550,24562 via svnmerge from
svn+ssh://tlinnet@.../svn/relax/trunk

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r24521 | bugman | 2014-07-11 10:39:52 +0200 (Fri, 11 Jul 2014) | 6 lines

Updated the minfx version in the release checklist document to 1.0.8.

This version has not been released yet, but it will include important fixes and additions for
constrained parallelised grid searches.
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r24526 | bugman | 2014-07-11 16:19:49 +0200 (Fri, 11 Jul 2014) | 3 lines

Fix for a broken link in the development chapter of the relax manual.
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r24527 | bugman | 2014-07-11 16:25:35 +0200 (Fri, 11 Jul 2014) | 6 lines

Fixes for dead hyperlinks in the relaxation dispersion chapter of the relax manual.

The B14 model links to http://www.nmr-relax.com/api/3.2/lib.dispersion.b14-module.html were broken
as the B in B14 was capitalised.
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r24528 | bugman | 2014-07-11 16:43:26 +0200 (Fri, 11 Jul 2014) | 6 lines

Sent in the verbosity argument value to the minfx.grid.grid_split() function.

The minfx function in the next release (1.0.8) will now be more verbose, so this will help with user
feedback when running the model-free analysis on a cluster or multi-core system using MPI.
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r24535 | bugman | 2014-07-15 12:36:47 +0200 (Tue, 15 Jul 2014) | 5 lines

Created the time user function.

This is just a shortcut for printing out the output of the time.asctime() function.
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r24536 | bugman | 2014-07-15 12:38:40 +0200 (Tue, 15 Jul 2014) | 3 lines

The time user function now uses the chronometer Oxygen icon in the GUI.
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r24543 | bugman | 2014-07-16 20:34:10 +0200 (Wed, 16 Jul 2014) | 3 lines

Added the missing timing module to the relax library package __all__ list.
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r24549 | bugman | 2014-07-17 14:56:24 +0200 (Thu, 17 Jul 2014) | 5 lines

Removed the line wrapping in the epydoc parameter section of the optimisation function docstrings.

This is for the pipe_control.minimise module.
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r24550 | bugman | 2014-07-17 14:57:01 +0200 (Thu, 17 Jul 2014) | 3 lines

More docstring line wrapping removal from pipe_control.minimise.
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r24562 | bugman | 2014-07-18 10:58:56 +0200 (Fri, 18 Jul 2014) | 7 lines

Bug fix for the parameter units descriptions.

This only affects a few rare parameters. The specific analysis API parameter object units() method
was incorrectly checking if the units value is a function - it was checking the parameter conversion
factor instead.
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The relaxation dispersion API now uses the MODEL_R2EFF variable for identifying the R2eff model.

The grid search setup function now uses the prefix argument to the print_model_title() API function.

This is simply set to 'Grid search setup:'.

Modified the new print_model_title() specific analysis API method.

This now accepts the prefix argument for creating different titles independently of the specific
analysis.

The grid search setup printout now also included the number of increments for each parameter.

The grid search setup function now prints out the grid search bounds to be used.

This is in the pipe_control.minimise.grid_setup() function, hence it is analysis independent. This
is useful feedback for the user to know what the grid search is doing. And it will be even more
useful for the zooming grid search to understand what is happening.