relax SVN archive

Finally, a real fix to bug #5746.

The bug report is located at https://gna.org/bugs/?func=detailitem&item_id=5746 and is discussed in
the thread starting at https://mail.gna.org/public/relax-devel/2006-04/msg00018.html.

The fix follows from an idea in the post located at
https://mail.gna.org/public/relax-devel/2006-04/msg00021.html. Firstly the model-free calculate()
function was modified so that when self.param_set is equal to 'all' or 'diff' (global statistics)
then the chi-squared value calculated is summed and placed in the global data structure
self.relax.data.chi2 rather than the residue specific data structure.

This change allowed the 'combined' flag to be eliminated from the self.model_statistics() function
of 'specific_fns/model_free.py'. This flag was the source of all the problems and it's removal
allowed chunks of obscure code to be axed. The statistics only need to refer to the self.param_set
value to determine which stats should be returned.

Fix to bug #6389.

The bug is located at https://gna.org/bugs/index.php?func=detailitem&item_id=6389.

The fix was simply to change a single line so that the data structure 'tm' is referred to rather
than 'local_tm'.

Fix to bug #6388.

The bug is located at https://gna.org/bugs/?func=detailitem&item_id=6388.

The problem was simply that the model-free parameters were not set in the OpenDX mapping test of the
test-suite.

Fix to bug #6384.

The bug is located at https://gna.org/bugs/index.php?func=detailitem&item_id=6384.

The function for sorting global from local parameters in the generic_fns/value.py file has been
simplified thanks to the change of the previous revision whereby the local tm parameter is now
referred to as 'local_tm' rather than 'tm'. Hence no algorithms are required to distinguish
between the global 'tm' parameter and the local 'tm' parameter.

Changing of the local tm parameter name of 'tm' to 'local_tm'.

This is a large scale change in preparation for the fixing of bug #6384
(https://gna.org/bugs/?func=detailitem&item_id=6384). The distinction between the global tumbling
time 'tm' and the residue specific 'local tm' parameter has always been problematic. With this
change all these problems should disappear. However as the changes are large, new bugs are almost
guaranteed to appear.

Fix to bug #5806.

The bug is located at https://gna.org/bugs/?func=detailitem&item_id=5806.

To remove the bug, tests for the presence of relaxation data have been added to the
model_statistics() functions. This may cause future bugs!

Added a test (AIC model selection between diffusion tensors) to the relax test-suite.

This test triggers the problem reported by Chris MacRaild at
https://mail.gna.org/public/relax-devel/2006-04/msg00020.html. The test has been added to aid in
the removal of bug #5746 located at https://gna.org/bugs/?func=detailitem&item_id=5746.

Fix to bug #6383.

The bug report is located at https://gna.org/bugs/?func=detailitem&item_id=6383.

The global flag is now set to the default of 0 for residue specific data on initialisation. Also,
the delete function now explicitly sets the global flag.

Fix to bug #6288.

The report is located at https://gna.org/bugs/?func=detailitem&item_id=6288.

The fix was to catch the value of None and hence not preform the 'float()' operation on it.

Spell check of the development chapter of the relax manual.