relax SVN archive

relax version 1.2.8.

This is a major bug fix release. All users who encounter problems are recommended to upgrade to
this version. Optimisation tests have also been added to the test suite.

Ported r2738 from the 1.2 line.

The command used was:
svn merge -r2737:2738 svn+ssh://bugman@.../svn/relax/1.2

This fixes the massively important bug #7616 (https://gna.org/bugs/index.php?7616) which is the
failure of the model selection between the global diffusion models when the local tm models are
included.

Fix for bug #7616 (https://gna.org/bugs/index.php?7616).

This fixes the failure of the model selection between the global diffusion models when the local tm
models are included. This is a very important bug fix.

The 'model_statistics()' function in the model-free and hybrid files have been modified. The
'min_instances' argument to the function was not being utilised at all since r2516
(https://mail.gna.org/public/relax-commits/2006-07/msg00010.html) which introduced this bug. The
argument has been renamed to 'global_stats'. This 'global_stats' argument is feed in solely by the
model selection code. That code decides if global statistics (which are summed for the local tm
models) should be utilised using the test:

if self.num_instances[j] > self.min_instances or self.num_instances[j] == 1:

The model selection function, if the global stats argument is 1 and 'self.param_set' is equal to
'local_tm', will sum the chi2 values of the individual local tm models and return that value.

To fix an issue with the OpenDX code causing a failure of the test suite, the 'min_instances'
argument in the call to the model statistics function has been dropped.

Ported r2736 from the 1.2 line to fix bug #7587 (https://gna.org/bugs/index.php?7587).

The command used was:
svn merge -r2735:2736 svn+ssh://bugman@.../svn/relax/1.2

Fix for bug #7587 (https://gna.org/bugs/index.php?7587).

A simple loop has been added to the model-free results reading function to rename any parameters of
the parameter vector called 'tm' to 'local_tm'.

Fixed the call to by the PyMOL cartoon function to the function 'file_root()' of 'io.py'.

This fixes a bug whereby the function 'io.file_root()' was being called yet it didn't exist. The
change which introduced the problem was announced at
https://mail.gna.org/public/relax-devel/2006-10/msg00228.html (Message-id:
<1162314647.3525.182.camel@...>). The fix was to call 'self.relax.IO.file_root()'.

Changed 5.55e5 to 5.56e5 in the 'pdb.create_tensor_pdb()' user function.

Ported r2731 from the 1.2 line.

The command used was:
svn merge -r2730:2731 svn+ssh://bugman@.../svn/relax/1.2

This updates the release checklist file. The freshmeat announcment has been added and the point
about the changes file has been moved.

Creation of a planning document for the relax data model redesign.

This is still in draft form and will need a lot of work, including the addition of URLs to the
mailing list archives.

Updated the release checklist to include the freshmeat announcment and a shift of the CHANGES file.

The part about updating the CHANGES file has been shifted to be after the creation of the tag.