relax SVN archive

Bug fix for the alignment tensor unit tests. AlignTensorData initialisation requires a tensor name!

The generic_fns.align_tensor.init() function now initialises the alignment tensor structure properly.

Recreated the AlignTensorData.__init__() method to allow the tensor name to be set.

Wrote the AlignTensorList class for storing all of the alignment tensors for a single data pipe.

Removed the empty AlignTensorData.__init__() method and shifted its docstring to that of the class.

Merged revisions 4575-4586 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3

........
r4575 | semor | 2008-01-09 19:20:33 +0100 (Wed, 09 Jan 2008) | 10 lines

Changed almost all instances of the 'print_flag' arg to 'verbosity' in the specific_fns directory.

Exceptions were made for instances in generic_minimise() functions where 'print_flag=print_flag'
becomes 'print_flag=verbosity'.

This was pointed out in a post by Edward d'Auvergne at :
https://mail.gna.org/public/relax-devel/2008-01/msg00021.html (Message-id:
<7f080ed10801090840s341431f2nb75b15b137b46176@...>)
........
r4576 | semor | 2008-01-09 19:28:21 +0100 (Wed, 09 Jan 2008) | 10 lines

Completed the changes from the previous commit (4575) as the model_free directory had been skipped.

Changed almost all instances of the 'print_flag' arg to 'verbosity' in the specific_fns/model_free
directory. Exceptions were made for instances in generic_minimise() functions where
'print_flag=print_flag' becomes 'print_flag=verbosity'.

This was pointed out in a post by Edward d'Auvergne at :
https://mail.gna.org/public/relax-devel/2008-01/msg00021.html (Message-id:
<7f080ed10801090840s341431f2nb75b15b137b46176@...>)
........
r4577 | semor | 2008-01-09 19:32:12 +0100 (Wed, 09 Jan 2008) | 3 lines

Changed all instances of the 'print_flag' arg to 'verbosity' in 'relax_io.py'.
........
r4579 | semor | 2008-01-09 19:41:37 +0100 (Wed, 09 Jan 2008) | 3 lines

Fixed a typo that was introduced in the 4576 commit.
........
r4585 | bugman | 2008-01-10 14:35:02 +0100 (Thu, 10 Jan 2008) | 22 lines

Manually ported r4584 from the 1.2 line - the fix to bug #8997 (https://gna.org/bugs/?8997).

The command used was:
svn merge -r4583:4584 svn+ssh://bugman@.../svn/relax/1.2

.....
r4584 | bugman | 2008-01-10 14:30:10 +0100 (Thu, 10 Jan 2008) | 11 lines
Changed paths:
M /1.2/generic_fns/palmer.py

Fix for bug #8997 (https://gna.org/bugs/index.php?8997).

This bug was reported by Carl Diehl (carl dot diehl at bpc dot lu dot se).

The problem was because of a change between relax versions 1.0 and 1.2. Previously the residue
number was being searched for, but the changes used the absolute position to significantly speed up
the code. But the absolute positions are different in a Modelfree 'mfout' file if simulations are
run. The absolute position in this situation is now properly calculated and the test data attached
to the bug report by Seb now works.
.....
........
r4586 | bugman | 2008-01-10 15:54:12 +0100 (Thu, 10 Jan 2008) | 3 lines

Removed a few empty __init__() class methods and shifted their docstrings to the class docstring.
........

Removed a few empty __init__() class methods and shifted their docstrings to the class docstring.

Manually ported r4584 from the 1.2 line - the fix to bug #8997 (https://gna.org/bugs/?8997).

The command used was:
svn merge -r4583:4584 svn+ssh://bugman@.../svn/relax/1.2

.....
r4584 | bugman | 2008-01-10 14:30:10 +0100 (Thu, 10 Jan 2008) | 11 lines
Changed paths:
M /1.2/generic_fns/palmer.py

Fix for bug #8997 (https://gna.org/bugs/index.php?8997).

This bug was reported by Carl Diehl (carl dot diehl at bpc dot lu dot se).

The problem was because of a change between relax versions 1.0 and 1.2. Previously the residue
number was being searched for, but the changes used the absolute position to significantly speed up
the code. But the absolute positions are different in a Modelfree 'mfout' file if simulations are
run. The absolute position in this situation is now properly calculated and the test data attached
to the bug report by Seb now works.
.....

Fix for bug #8997 (https://gna.org/bugs/index.php?8997).

This bug was reported by Carl Diehl (carl dot diehl at bpc dot lu dot se).

The problem was because of a change between relax versions 1.0 and 1.2. Previously the residue
number was being searched for, but the changes used the absolute position to significantly speed up
the code. But the absolute positions are different in a Modelfree 'mfout' file if simulations are
run. The absolute position in this situation is now properly calculated and the test data attached
to the bug report by Seb now works.

Started the shifting of the consistency tests code to the new relax design.

Followed the tips by Edward d'Auvergne in the post at:
https://mail.gna.org/public/relax-devel/2008-01/msg00012.html (Message-id:
<1199821867.8905.7.camel@...>)