relax SVN archive

Redesign of the setup of the names spaces for the user functions.

All the user functions and other objects located in the run() method namespace have been shifted
into the interpreter self._locals dictionary. These are then placed into the run() method namespace
by looping over the keys and using the 'locals()[key] = object' syntax. There may be better ways to
do this.

This has no visible effect on the prompt or script based interfaces. It will change how this is
seen by other modules though, and will allow the namespace to be more easily accessed.

Merged revisions 10296-10302 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3

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r10296 | bugman | 2010-01-25 11:13:06 +0100 (Mon, 25 Jan 2010) | 14 lines

Spun out the automatic model-free protocol code from the full_analysis.py script.

This is discussed in the post https://mail.gna.org/public/relax-devel/2010-01/msg00075.html.

The aim is to have a single code base for the automatic protocols for all UI designs (prompt,
script, GUI, web interface, etc.). The API interface will be via class initialisations. The
automatic model-free protocol has been placed into the dAuvergne_protocol class.

Future aims of this code is to have the UI fill a single data pipe with all the data required for
the analysis, and then to pass in this pipe into the protocol. Then the auto-analysis will copy
this info into any other data pipes it requires. This will allow for better GUI interaction, data
display, etc.
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r10297 | bugman | 2010-01-25 11:33:22 +0100 (Mon, 25 Jan 2010) | 3 lines

Removed all the now unused imports and a useless comment.
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r10298 | bugman | 2010-01-25 11:34:54 +0100 (Mon, 25 Jan 2010) | 3 lines

Updated the copyright notice.
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r10299 | bugman | 2010-01-25 11:37:25 +0100 (Mon, 25 Jan 2010) | 3 lines

Fixed the import of the dAuvergne_protocol class.
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r10300 | bugman | 2010-01-25 12:13:59 +0100 (Mon, 25 Jan 2010) | 3 lines

Modifications to the phthalic_acid_noes.py system test script to allow for standalone operation.
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r10301 | bugman | 2010-01-25 12:40:54 +0100 (Mon, 25 Jan 2010) | 5 lines

Fixes for the N-state model for when only NOEs are present.

This fixes a bug introduced at r10243.
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r10302 | bugman | 2010-01-25 12:54:34 +0100 (Mon, 25 Jan 2010) | 5 lines

Bug fix for the bug fix of r10301!

The bug fix actually introduced a bug, and this commit fixes that!
........

Bug fix for the bug fix of r10301!

The bug fix actually introduced a bug, and this commit fixes that!

Fixes for the N-state model for when only NOEs are present.

This fixes a bug introduced at r10243.

Modifications to the phthalic_acid_noes.py system test script to allow for standalone operation.

Fixed the import of the dAuvergne_protocol class.

Updated the copyright notice.

Removed all the now unused imports and a useless comment.

Spun out the automatic model-free protocol code from the full_analysis.py script.

This is discussed in the post https://mail.gna.org/public/relax-devel/2010-01/msg00075.html.

The aim is to have a single code base for the automatic protocols for all UI designs (prompt,
script, GUI, web interface, etc.). The API interface will be via class initialisations. The
automatic model-free protocol has been placed into the dAuvergne_protocol class.

Future aims of this code is to have the UI fill a single data pipe with all the data required for
the analysis, and then to pass in this pipe into the protocol. Then the auto-analysis will copy
this info into any other data pipes it requires. This will allow for better GUI interaction, data
display, etc.

Insanely massive clean up of all of the Bieri GUI code base.

Not much code has been unaffected by this change. The changes include:

- Important fixes for the whitespace rule violations. There were identified by the
'scripts/code_validator' script. The number of spaces used for indentation was almost random and
hence impossible to work with. Spacing between functions was not following the 2 empty line rule.
Non-arg assignments with '=' sometimes had no space or 2 spaces. Comma separated elements (lists,
tuples, function args, etc.) often didn't have a space after the comma. A few tab characters were
being used whereas '\t' should have been used. There was trailing whitespace everywhere.

- All functions have been shifted to be before classes.

- All functions/methods have been alphabetically ordered. This is important to follow the code.

- Classes were not always capitalised.

- Removed the executable properties from gui_bieri/analyses/select_model_calc.py.