relax SVN archive

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).

Ported r2637 to r2640 from the 1.2 line.

The command used was:
$ svn merge -r2636:2640 svn+ssh://bugman@.../svn/relax/1.2

This includes a number of changes to the Scons system including fixes for the distribution target
functions, the creation of the new module 'scons.install', and a restructure of the base
'sconstruct' file.