relax SVN archive

Ported r2635 from the 1.2 line.

The command used was:
$ svn merge -r2634:2635 svn+ssh://bugman@.../svn/relax/1.2

This involves a few functions moving to the new Scons module file 'scons/distrib.py'.

A fix for the function which loads the sequence from the PDB file.

This fixes two tests of the test suite. The changes already exist within the 1.3 line.

Speed ups for the optimisation tests in the test suite.

The grid search of each optimisation algorithm test has been replaced by the value setting function
as the results of the grid search are the same for each of the tests. As the grid search is
computationally expensive, this significantly speeds up the tests.

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

These tests use the synthetic data back calculated for the model-free parameter values of {S2=0.970,
te=2048, Rex=0.149}.

The following optimisation techniques are currently tested:
Grid search.
Steepest descent, backtracking line search.
Steepest descent, More and Thuente line search.
Coordinate descent, backtracking line search.
Coordinate descent, More and Thuente line search.
BFGS, backtracking line search.
BFGS, More and Thuente line search.
Newton, GMW Hessian modification, backtracking line search.
Newton, GMW Hessian modification, More and Thuente line search.

Fixes for a number of bugs caused by the changes for task #3838.

Task #3838 is located at https://gna.org/task/?3838 and more information is given at
https://mail.gna.org/public/relax-users/2006-10/msg00002.html (Message-id:
<7f080ed10610032153o4571935bq138d2739f55ca3bd@...>).

Part of the problem, the failure of two of the tests of the test suite was reported by Alex Hansen
(viochemist _at_ gmail _dot_ com) in the post located at
https://mail.gna.org/public/relax-devel/2006-10/msg00095.html (Message-id:
<481156b20610130720u39a93e30k6d4603efd8730c96@...>). Another failure was reported by
Alex at https://mail.gna.org/public/relax-devel/2006-10/msg00096.html (Message-id:
<481156b20610130728jb6aa76ag3d9487a20397391b@...).

The first fix, which was a missing run argument, is described at
https://mail.gna.org/public/relax-devel/2006-10/msg00099.html (Message-id:
<7f080ed10610130741j146721c8w512ba61bac3644c7@...>).

The second problem was that the residue number and residue name was being referred to as 'num' and
'name' when they should have been 'res_num' and 'res_name'.

The third problem was an index for selecting the residue. Rather than using the real index 'i', the
index 'j' was being used.

A large expansion of the relax development chapter.

The title has been changed from 'Development of relax' to 'relax development'.

Many sections have been edited/modified.

The section on relax's coding conventions has been re-written. The docstring subsection has been
itemized and examples added. Examples have been added to the 'Variable, function, and class names'
subsection and a subsubsection titled 'Long names' has been added. A subsection called 'Whitespace'
has been added with examples. And finally a subsection called 'Comments' has also been added.

The commit log format section has been itemized and a number of examples given.

The SCons help system which displays the target descriptions is now described.

The subsection titled 'Compilation of the API documentation (HTML version)' has been added to the
SCons section.

Three completely new sections have been added to the end. These include 'The mailing lists', 'The
bug, task, and support request trackers', and 'Links, links, and more links'.

Two small formatting changes to the model-free file.

Modified the infrastructure chapter of the user manual.

Each mailing list has been given their own subsections.

A warning about the thread breaking caused by changing the email subject when using Gmail has been
added.

Fix for the documentation bug #7402 (https://gna.org/bugs/?7402).

This fixes the sigma(NOE) equations in section 8.8.1 of the relax user manual. Alex Hansen reported
that the equations incorrect as one of the spectral density terms were multiplied by a factor of 6
when there should be nothing. This problem does not affect the code, the equations there are
correct.

Removal of the installation targets and changing of the initialisation of the system path variables.

The installation target functions 'self.install()' and 'self.uninstall()' have been deleted as they
are now located in the 'scons.install' module.

The 'self.paths()' function has been removed. All the paths, environmental variables, etc. are now
initialised at the top of the 'sconstruct' file.