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Changed the dauvergne_protocol LST tags.
* The XML formatted results and save files has been redesigned (it has improved, is more accurate, is easier to read in Python version 2.7.3 and above, and contains more metadata) and is now at version 2.
* The printouts of spin specific data has improved with the addition of an automatic column width algorithm.
* The addition of a new concept called data pipe bundles - related data pipes can now be grouped together into bundles. For example in the dauvergne_protocol model-free auto-analysis[d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, 20082008b], all internally generated data pipes are grouped together in the same bundle.
* Each GUI analysis tab is now associated with a unique data pipe bundle rather than a dedicated data pipe. This allows for better data pipe handling.
* Improved BMRB support. The 'File->Export for BMRB deposition' menu has been added to the GUI which opens a special BMRB export window.
* Increased the default size of the GUI user functions.
* Spacing and layout improvements for the GUI user function descriptions.
* The dauvergne_protocol sample script[d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, 20082008b] initial pipe name has been modified to include the pipe bundle.
* The GUI now sends the pipe bundle name into the relax_fit and noe auto-analyses.
* The relax_fit and noe auto-analyses now centre around the pipe bundle rather than data pipe name.
* Added a set of roman fonts to the gui.fonts module - this will be used by the about dialogs.
* Font size improvements for Mac OS X - the fonts are now roughly the same size as on GNU/Linux and MS Windows. An operating system specific font scaling is now used, with the Mac OS X fonts each being increased by 2 pixels.
* The dauvergne_protocol auto-analysis[d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, 20082008b] now adds the pipe bundle name to all created pipes as a suffix. This is to uniquely identify the data pipes, and to allow more than one model-free analysis to be executed per relax instance (useful for the GUI).
* The analysis wizard now suggests the starting data pipe to be named 'origin - ' + pipe_bundle - this allows unique data pipe names for each analysis.
* Temporarily disabled the Mac OS X task bar icon as it is currently horribly broken in wxPython 2.8 and 2.9.
* The relax save and results XML files now include subversion details in the <relax> tag. This indicates the repository version and the URL, allowing for better debugging.
* The 'relax --version' print out now includes the full subversion info, if it is a checked out copy.
* Improvement for the model-free auto-analysis in the GUI. After execution, the main data pipe of the analysis tab is now set to the 'final' data pipe generated by the dauvergne_protocol[d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, 20082008b]. This means that when switching between analysis tabs, that going back to the model-free tab will make the 'final' data pipe the current one, rather than the data pipe used to initialise the analysis.
* Better handling of the GUI wizard termination. The _handler_close() method is now handling the close events and together with the _ok() method,both now execute the current page's on_next() method. This means that on_next() is called for all avenues for exiting the wizard. This allows the user function pages to unregister themselves with the observer objects.
* The wizard window _cancel() method now calls the current page's on_next() method. This allows the page to clean itself up.
* The 'bundle' arg is now functional in the model_selection user function back end.
* Added the 'bundle_to' arg to the pipe.copy user function back end. This arg is now functional.
* The dauverge_protocol auto-analysis[d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, 20082008b] now uses the new 'bundle' user function args. This is used in the pipe copying to place the newly created pipe and in the model selection, both so that all pipes created during the analysis are located within the pipe bundle reserved for that analysis.
* The GUI user function window titles are now set to the 'title_short' value. This is because the long title can be far too long for a GUI window title!
* The long title or synopsis is now added to the GUI user function description text as italic text.
* Added some backwards compatibility code for old GUI state files missing pipe bundles.
* Created a GUI test for loading an old relax 1.3 save state containing GUI analyses.
* Updated the dauvergne_protocol auto-analysis[d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, 20082008b] to spawn all pipes into the named bundle.
* The generic_fns.pipes.pipe_names() function now can restrict the list of names to a specific bundle.
* The pipe editor window now handles the pipe bundling concept. There is a new button for the pipe.bundle user function, a new column showing the pipe bundles, and the pop up menu allows pipes to be associated with bundles if not already bundled.
* The pipe.create user function now creates pipe bundles in the back end. The new ds.pipe_bundles dictionary is used to hold lists of pipes associated with the pipe bundle name as the dictionary keys. The 'bundle' arg is passed into the ds.add() method for storage.
* Added the 'bundle' keyword arg to the pipe.create user function definition.
* Preparation for the implementation of pipe bundle concept - addition of system and GUI tests. This new pipe bundling concept is simply a way of grouping data pipes together. This will be useful for: grouping and categorisation of data pipes when multiple analyses are performed, the model-free dauvergne_protocol auto-analysis[d'Auvergne and Gooley, 2007][d'Auvergne and Gooley, 20082008b] will place all the data pipes it creates into one bundle, for the GUI mode analyses will be linked to pipe bundles rather than data pipes. This will allow switching data pipes to activate the correct analysis.
* The 'verbatim' user function description elements are now properly formatted in the GUI. These elements now use the font.modern_small formatting to have fixed-width characters.
* Table formatting improvements for the GUI user function descriptions.
<section start=references/>
* [*d'Auvergne and Gooley, 2007] d'Auvergne, E. J. and Gooley, P. R. (2007). Set theory formulation of the model-free problem and the diffusion seeded model-free paradigm. ''Mol. BioSyst.'', '''3'''(7), 483–494. (DOI: [http://dx.doi.org/10.1039/b702202f 10.1039/b702202f).
* [*d'Auvergne and Gooley, 20082008b] d'Auvergne, E. J. and Gooley, P. R. (2008). Optimisation of NMR dynamic models II. A new methodology for the dual optimisation of the model-free parameters and the Brownian rotational diffusion tensor. ''J. Biomol. NMR'', '''40'''(2), 121-133. (DOI: [http://dx.doi.org/10.1007/s10858-007-9213-3 10.1007/s10858-007-9213-3]).
<section end=references/>
<HarvardReferences />
