relax SVN archive

A fix for the error when trying to plot MC sim data with reduced spectral density mapping.

This problem was reported by Daniel Perez (daniel dot perez at mol dot biol dot ethz dot ch) in the
post at https://mail.gna.org/public/relax-users/2006-10/msg00043.html (Message-id:
<453C7154.4040603@...>).

In case this fix isn't for the same problem (no traceback was provided), the error message that this
solves is reproduced at https://mail.gna.org/public/relax-users/2006-10/msg00045.html (Message-id:
<7f080ed10610230104w3a873225hd5481581886efacf@...>).

The problem was the the function 'return_values' in the file 'specific_fns/jw_mapping.py' was
a copy of an ancient function which did not support MC simulation data. All other types of analysis
were using the function from their common base class. By deleting this ancient code, the base class
function is utilised and the grace.write() user function now works with simulation data.

Ported r2658 from the 1.2 line.

The command used was:
$ svn merge -r2657:2658 svn+ssh://bugman@.../svn/relax/1.2

These changes complete task #4002 (https://gna.org/task/index.php?4002), the implementation of the
'grace.write()' user function for reduced spectral density mapping.

Completion of task #4002 (https://gna.org/task/index.php?4002).

This task was created in response to Daniel Perez's (daniel dot perez at mol dot biol dot ethz dot
ch) post at https://mail.gna.org/public/relax-users/2006-10/msg00040.html (Message-id:
<4539BABA.80204@...>).

Three things were required:

1. The pre-existing function self.relax.specific.jw_mapping.return_conversion_factor was added to
the specific setup interface in 'specific_fns/specific_setup.py'.

2. The string 'J(0)' was not being recognised by the function
'self.relax.specific.jw_mapping.return_data_name' as the round brackets needed to be commented out
for the 'search' function to work.

3. The specific setup interface was returning the wrong 'return_grace_string' function. The
problem was that the model-free version of the function was being returned instead. The function
'return_units' was also that of model-free analysis instead of reduced spectral density mapping.

Removal of apply(func, args) calls from the minimisation code

As discussed at relax-devel:
https://mail.gna.org/public/relax-devel/2006-10/msg00103.html

New branch of the 1.3 line for the removal of apply(func, args) calls

See the relax-devel discussion at:
https://mail.gna.org/public/relax-devel/2006-10/msg00103.html

This fixes a bug in the compile re function.

The bug was reported by Alex Hansen at https://mail.gna.org/public/relax-devel/2006-10/msg00112.html
(Message-id: <481156b20610190725ud6bab67w1f8fbbdf849da52c@...>). The simple fix is
described at https://mail.gna.org/public/relax-devel/2006-10/msg00113.html (Message-id:
<7f080ed10610190738g7df6566fl13b74d9217071924@...>).

Ported r2646 to r2647 from the 1.2 line.

The command used was:
$ svn merge -r2645:2647 svn+ssh://bugman@.../svn/relax/1.2

This adds a number of model-free optimisation tests to the test suite.

Ported r2643 from the 1.2 line.

The command used was:
$ svn merge -r2642:2643 svn+ssh://bugman@.../svn/relax/1.2

This includes a few small formatting changes to the model-free file.

Ported r2642 and r2644 of the 1.2 line (r2643 is not included).

The commands used were:
$ svn merge -r2641:2642 svn+ssh://bugman@.../svn/relax/1.2
$ svn merge -r2643:2644 svn+ssh://bugman@.../svn/relax/1.2

These changes include improvements to the infrastructure chapter of the relax user manual, and a
large expansion of the relax development chapter.

Ported r2641 from the 1.2 line.

The command used was:
$ svn merge -r2640:2641 svn+ssh://bugman@.../svn/relax/1.2

This fixes documentation bug #7402 (https://gna.org/bugs/?7402).