relax SVN archive

relax version 1.2.6.

A quick release to fix the fatal 'devnull' ImportError (bug #6403). This bug effects those using
Python versions < 2.4 and prevents relax from starting up. The solution was to import the object
using a try statement to allow execution of the program. However if relax ever attempts to use
'devnull' a RelaxError is thrown, a message saying to upgrade to Python >= 2.4 is printed, and the
program terminates. This is currently only a problem in the test-suite.

The full list of changes is:

Features:
N/A

Changes:
N/A

Bugfixes:
* Added the missing PDB file used by one of the OpenDX tests of the relax test-suite. (bug
#6404)
* Fixed the fatal devnull import failure for Python versions < 2.4. (bug #6403)

Updated the CHANGES file for relax version 1.2.6, the fatal devnull import failure fix.

Fix to bug #6403.

The bug is located at https://gna.org/bugs/?func=detailitem&item_id=6403.

The problem is that relax will not start due to an ImportError when trying to import the object
'devnull'. The solution was to import the object using a try statement to allow execution of the
program. However if relax ever attempts to use 'devnull' a RelaxError is thrown, a message saying
to upgrade to Python >= 2.4 is printed, and the program terminates. This is currently only a
problem in the test-suite.

Added the missing PDB file used by some of the relax test-suite.

Fixed the Clore 1990 reference in the manual, changed the rsync command in the release checklist,
and updated the manual.

Updated the manual and changed the version number to 1.2.5.

relax version 1.2.5.

This is mainly a bugfix release. A large number of bugs have been eliminated including bug #5977,
bug #6288, bug #6383, bug #5806, bug #6384, bug #6388, bug #6389, and bug #5746. These are
described in more detail below. To fix a few of these bugs large disruptive changes were required.
This included the change of the local tm parameter name from 'tm' to 'local_tm' and the
simplification of the model-free model_statistics() function and modification of the model-free
calculate() function. Therefore regressions and new bugs may appear in this release, most likely
when the local tm parameter is encountered or during model selection.

The full list of changes is:

Features:
* The data analysis chapter has been split into four: The NOE, relaxation curve-fitting,
model-free, and reduced spectral density mapping chapters.
* A section called the 'The core design of relax' has been added to the the development
chapter of the manual.
* The 'Values, gradients, and Hessians' chapter of the manual is now complete. These are
all the equations used during optimisation.
* The Hessian kite diagram and the gradient construction diagram have been added to the
'Values, gradients, and Hessians' chapter of the manual.

Changes:
* The distribution archives now unpack to the directory 'relax-x.x.x' rather than just'
'relax', where x.x.x is the version number.
* All chapters of the manual have been edited and proofed.
* The Sparky and XEasy peak intensity reading functions have been split to allow the easy
addition of new peak intensity file types.
* Test of AIC model selection between diffusion tensors added to the test suite. (To catch
bug #5746)
* Changing of the local tm parameter name of 'tm' to 'local_tm' to distinguish it from the
global tumbling time 'tm'. (Preparation for fixing bug #6384)

Bugfixes:
* Fix of bug where self.relax.data.select_sim was treated as a list. (bug #5977)
* The value.copy() function now handles the value of None. (bug #6288)
* The global flag is now set by the relax_data.delete() function. (bug #6383)
* The model-free model_statistics() function now tests for the presence of relaxation data.
(bug #5806)
* Sorting of global from local parameters in 'generic_fns/value.py' simplified and fixed by
changing the parameter name 'tm' to 'local_tm'. (bug #6384)
* Model-free parameters now set in the OpenDX mapping test of the test-suite. (bug #6388)
* Failure of model elimination because of a 'local_tm' and 'tm' mix up. (bug #6389)
* Modification of the model-free calculate() function and elimination of the 'combined' flag
from the self.model_statistics() function. (bug #5746)

Added an entry to the changes file for relax version 1.2.5 (r2490-r2518).

Modified the release checklist to include updating the 'CHANGES' file.

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.