relax SVN archive

Fixed a bug in the 'self.package()' target function.

The variable 'file_name' was being accessed when the variable should have been called
env['DIST_FILE'].

A number of large changes to the Scons system.

The package initialisation file '__init__.py' has been added to the 'scons' directory.

The 'sconstruct' script has been split in half. The script was copied to 'scons/manuals.py' and
only the manual compilation functions remain in this file. The class structure has been eliminated
from 'scons/manuals.py' so 'sconstruct' now imports each function from this module. This means that
4 spaces have been removed from the indentation. All the manual compilation Environment setups,
custom BUILDERS actions, and Depends statements have been shifted to the 'self.__init__()' function
of the 'sconstruct' script.

The default values of None for the target functions have been removed as they are always passed to
the functions. For example
def dummy(self, target=None, source=None, env=None):
has been changed to
def dummy(self, target, source, env):

Environmental variables such as LATEX_DIR, SYSTEM, BIN_PATH, etc. (all the variables created in
'self.paths()') are now placed in the Scons Build Environments. The Environment is passed into each
function as 'env' so the variables are accessed by typing, for example, env['LATEX_DIR']. The
variable 'self.system' has been renamed to 'self.SYSTEM'.

The 'self.gpg_bin_sign()' and 'self.gpg_src_sign()' target functions have been merged into the
single function 'self.gpg_sign()'.

Ported r2616 from the 1.2 line.

The command used was:
$ svn merge -r2615:2616 svn+ssh://bugman@.../svn/relax/1.2

This removes the ancient unused file 'maths_fns/test.c_chi.py'.

Deletion of the file 'maths_fns/test.c_chi.py'.

This file is an ancient file last touched in 2004. It serves no purpose so has been removed.

The user function 'pdb.read()' still was accepting the arguements heteronuc='N' and proton='H'.

The code of the user function was not using these or passing them on. They have now been removed.

Ported r2612 from the 1.2 line.

The command used was:
$ svn merge -r2611:2612 svn+ssh://bugman@.../svn/relax/1.2

This completes the fixing of bug #7241 (https://gna.org/bugs/?7241).

Ported r2611 from the 1.2 line.

The command used was:
$ svn merge -r2610:2611 svn+ssh://bugman@.../svn/relax/1.2

This adds the directory for Scons Python modules for the Builder functions.

Fixing the rest of bug #7241 (https://gna.org/bugs/?7241).

Bug #7241 was thought to be fixed in in r2591 and r2593, the commit messages describing the solution
being located at https://mail.gna.org/public/relax-commits/2006-09/msg00064.html (Message-id:
<E1GTgBi-0000R6-4h@...>) for r2591 and
https://mail.gna.org/public/relax-commits/2006-10/msg00001.html (Message-id:
<E1GTt6C-0005rk-8q@...>) for r2593.

However this was not the only place that the Scientific Python PDB data structure peptide_chains was
being accessed. The chains were being accessed in the file 'generic_fns/sequence.py' when the
sequence was being read out of the PDB file. This has now been modified with changes similar to
r2591 and r2593.

Created the directory 'scons' for splitting up the 'sconstruct' script into multiple Python modules.

Fix for bug #7336 (https://gna.org/bugs/index.php?7336).

The user function 'pdb.vectors()' was not set up properly. It was expecting the residue number to
be an integer and the residue name to be a string. However the default is that both are set to
None. This was causing a RelaxError.