relax SVN archive

relax version 1.2.9.

This release includes r2742 to r2780 of the 1.2 line. This is a quick bugfix release which fixes
bug #7641 (http://gna.org/bugs/?7641), the infinite chi-squared RelaxError when the chi-squared
value is zero.

Ported r2780 from the 1.2 line.

The command used was:
svn merge -r2779:2780 svn+ssh://bugman@.../svn/relax/1.2

This changes the interpreter from '/usr/bin/python' to '/usr/bin/env python'.

Changed the interpreter from '/usr/bin/python' to '/usr/bin/env python'.

This changes the first line of the 'relax' file. The change was suggested by Douglas Kojetin
(douglas dot kojetin at gmail dot com) in the post located at
https://mail.gna.org/public/relax-devel/2006-11/msg00098.html (Message-id:
<0E180DBB-896A-45F6-B19D-D6A02FD2BA4A@...>).

The change allows relax to run on Mac OS X by just typing 'relax'. This is because the python
binary is located at '/sw/bin/python'.

Ported r2745, r2746, and r2778 from the 1.2 line.

The commands used were:
svn merge -r2744:2746 svn+ssh://bugman@.../svn/relax/1.2
svn merge -r2777:2778 svn+ssh://bugman@.../svn/relax/1.2

This includes editing of the release checklist file, a spell check of the CHANGES file, and the fix
to bug #7677 (https://gna.org/bugs/index.php?7677).

Fix for bug #7677 (https://gna.org/bugs/index.php?7677).

The fix was simply to add the dummy keyword argument "status=0" to the end of the argument list of
the 'print_stats()' statistics sorting and printing function.

Added tests for isZero & isPositive & id based dicts and subset removal

Preliminary implimentation of auto-scaling for viewing tensors.

As discussed at:
https://mail.gna.org/public/relax-devel/2006-10/msg00204.html

This revision provides a simple scaling based on molecular mass.
This option is selected with the scale='mass' option to the
pdb.create_tensor_pdb() command

Restoring revision 2656. This removes usage of apply() from minimisation
code.

svn merge -r 2656:2657 svn+ssh://macraild@.../svn/relax/1.3

This introduces the changes made and tested in the apply branch.

initial checkin of a unit test runner

note this version only runs one test test_float.py!

Added hybrid run support for the 'pdb.create_tensor_pdb()' user function.

The function 'self.create_tensor_pdb()' in the file 'generic_fns/pdb.py' has been modified to loop
over an array of runs. This array is normally the single standard run. However when a hybrid run
is encountered, the runs of the hybrid are looped over.

The chain ID letter is now taken from the 'string.ascii_uppercase' string. The letter is extracted
using the run index.

All atom IDs have had the chain ID appended to the end to make then unique when multiple chains
exist.

The data structure 'self.atomic_data' of 'generic_fns/pdb.py' has been modified to include the
record name (ATOM, HETATM, or TER) at position 1. Hence all other elements have been shifted by
one. This is to allow multiple TER records one at the end of each chain, each having their own atom
number.

The 'het_data' array in 'self.write_pdb_file()' is no longer sorted as it already is sorted because
of the sorting of atomic data arrays. This allows the HET records to be sorted first by chain ID
then by residue number.

The HETNAM and FORMUL records are now only created if the residue has not been previously
encountered. This avoids duplicated records.

All the atomic coordinate records (ATOM, HETATM, or TER) are now created sequentially by looping
over the atomic data sorted by atom number.