relax SVN archive

Modified the specific base class method return_value() to handle peak heights by spectrum id.

Merged revisions 8026-8028,8061,8064 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3

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r8026 | bugman | 2008-11-26 18:02:05 +0100 (Wed, 26 Nov 2008) | 3 lines

Wrote 8 system tests for reading various PDB files using the internal and Scientific python objects.
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r8027 | bugman | 2008-11-27 09:57:19 +0100 (Thu, 27 Nov 2008) | 3 lines

Added a lactose PDB file and 2 system tests reading this file.
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r8028 | bugman | 2008-11-27 10:12:55 +0100 (Thu, 27 Nov 2008) | 5 lines

Fix for the __atom_index() method. This is a partial fix for bug #12637 (https://gna.org/bugs/?12637).

The struct_index of None is now handled.
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r8061 | bugman | 2008-11-29 17:53:30 +0100 (Sat, 29 Nov 2008) | 14 lines

Manually ported the CHANGES file changes to the 1.3 line.

The command used was:
svn merge -r8059:8060 svn+ssh://bugman@.../svn/relax/tags/1.3.3 .

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r8060 | bugman | 2008-11-29 17:51:50 +0100 (Sat, 29 Nov 2008) | 3 lines
Changed paths:
M /tags/1.3.3/docs/CHANGES

Updated the CHANGES file for relax 1.3.3.
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r8064 | bugman | 2008-11-29 18:32:37 +0100 (Sat, 29 Nov 2008) | 14 lines

Manually ported the user manual fixes of r8063 from the 1.3.3 tag.

The command used was:
svn merge -r8062:8063 svn+ssh://bugman@.../svn/relax/tags/1.3.3 .

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r8063 | bugman | 2008-11-29 18:31:20 +0100 (Sat, 29 Nov 2008) | 3 lines
Changed paths:
M /tags/1.3.3/docs/latex/relax.tex

Fixed the spacing in the table of contents of the user manual.
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Merged revisions 7971-7973,7975-7983,7991-7992,7996,8014,8016,8026-8028,8061,8064 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3

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r7971 | bugman | 2008-11-10 23:17:17 +0100 (Mon, 10 Nov 2008) | 6 lines

Added a missing RelaxError import.

This was discovered when trying to replicate bug #12582 (https://gna.org/bugs/index.php?12582)
reported by Chris Brosey (chris dot a dot brosey att vanderbilt dot edu).
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r7972 | bugman | 2008-11-10 23:31:18 +0100 (Mon, 10 Nov 2008) | 3 lines

Added a system test for replicating bug #12582.
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r7973 | bugman | 2008-11-10 23:36:36 +0100 (Mon, 10 Nov 2008) | 9 lines

Fix for bug #12582 (https://gna.org/bugs/index.php?12582).

This was reported by Chris Brosey (chris dot a dot brosey att vanderbilt dot edu).

The problem was that the frq_labels data structure in the SpinContainer was sometimes set to []
rather than the data structure being missing. Now the structure is being tested if it is either
None or [] before being accessed in the model-free return_units() method.
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r7975 | bugman | 2008-11-12 15:57:25 +0100 (Wed, 12 Nov 2008) | 3 lines

Converted some ints to bools.
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r7976 | bugman | 2008-11-12 20:57:14 +0100 (Wed, 12 Nov 2008) | 3 lines

Modified the system test to additionally catch bug #12591 (https://gna.org/bugs/index.php?12591).
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r7977 | bugman | 2008-11-12 20:59:05 +0100 (Wed, 12 Nov 2008) | 3 lines

Renamed the system test script.
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r7978 | bugman | 2008-11-12 20:59:27 +0100 (Wed, 12 Nov 2008) | 3 lines

Deleted the old system test script.
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r7979 | bugman | 2008-11-12 21:00:37 +0100 (Wed, 12 Nov 2008) | 3 lines

Fixes for the system test script rename of the previous commits.
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r7980 | bugman | 2008-11-12 21:18:03 +0100 (Wed, 12 Nov 2008) | 9 lines

Partial fix for bug #12591 (https://gna.org/bugs/index.php?12591).

This was reported by Chris Brosey (chris dot a dot brosey att vanderbilt dot edu).

If no model is ever selected in the model_selection.select() function, then relax no longer fails.
The failure is however caused by another problem elsewhere within relax, so this fix is not
complete.
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r7981 | bugman | 2008-11-12 21:21:39 +0100 (Wed, 12 Nov 2008) | 9 lines

Final fix for bug #12591 (https://gna.org/bugs/index.php?12591).

This bug was reported by Chris Brosey (chris dot a dot brosey att vanderbilt dot edu).

The problem was that the global_index counter in the model-free model_loop() method was supposed to
be incremented at the start of the loop. The deselected spin skipping code was located before this
though, causing the counter to not be incremented!
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r7982 | bugman | 2008-11-12 21:35:26 +0100 (Wed, 12 Nov 2008) | 5 lines

Created a very simple system test to catch bug #12588 (https://gna.org/bugs/index.php?12588).

This bug was reported by Tyler Reddy (treddy at dal dot ca).
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r7983 | bugman | 2008-11-12 21:49:03 +0100 (Wed, 12 Nov 2008) | 8 lines

Fix for bug #12588 (https://gna.org/bugs/index.php?12588).

This bug was reported by Tyler Reddy (treddy at dal dot ca).

The problem was that the results.read() user function was not handling the directory name being part
of the file name argument. This can now be handled.
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r7991 | bugman | 2008-11-20 22:53:30 +0100 (Thu, 20 Nov 2008) | 5 lines

Added a catch for bug #12607 (https://gna.org/bugs/?12607) to the bugs_12582_12591.py script.

This bug was reported by Chris Brosey (chris dot a dot brosey att vanderbilt dot edu).
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r7992 | bugman | 2008-11-20 23:23:56 +0100 (Thu, 20 Nov 2008) | 8 lines

Fix for bug #12607 (https://gna.org/bugs/?12607).

This bug was reported by Chris Brosey (chris dot a dot brosey att vanderbilt dot edu).

The problem was that the fixed flag was being checked for all spins. However deselected spins
should be ignored.
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r7996 | bugman | 2008-11-21 09:45:57 +0100 (Fri, 21 Nov 2008) | 3 lines

Renamed the bugs_12582_12591.py system test script to include bug #12607.
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r8014 | bugman | 2008-11-21 18:35:42 +0100 (Fri, 21 Nov 2008) | 3 lines

The structure.load_spins() user function now tests if a structure has been loaded.
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r8016 | bugman | 2008-11-21 18:38:37 +0100 (Fri, 21 Nov 2008) | 3 lines

Added a missing RelaxError import.
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r8026 | bugman | 2008-11-26 18:02:05 +0100 (Wed, 26 Nov 2008) | 3 lines

Wrote 8 system tests for reading various PDB files using the internal and Scientific python objects.
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r8027 | bugman | 2008-11-27 09:57:19 +0100 (Thu, 27 Nov 2008) | 3 lines

Added a lactose PDB file and 2 system tests reading this file.
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r8028 | bugman | 2008-11-27 10:12:55 +0100 (Thu, 27 Nov 2008) | 5 lines

Fix for the __atom_index() method. This is a partial fix for bug #12637 (https://gna.org/bugs/?12637).

The struct_index of None is now handled.
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r8061 | bugman | 2008-11-29 17:53:30 +0100 (Sat, 29 Nov 2008) | 14 lines

Manually ported the CHANGES file changes to the 1.3 line.

The command used was:
svn merge -r8059:8060 svn+ssh://bugman@.../svn/relax/tags/1.3.3 .

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r8060 | bugman | 2008-11-29 17:51:50 +0100 (Sat, 29 Nov 2008) | 3 lines
Changed paths:
M /tags/1.3.3/docs/CHANGES

Updated the CHANGES file for relax 1.3.3.
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r8064 | bugman | 2008-11-29 18:32:37 +0100 (Sat, 29 Nov 2008) | 14 lines

Manually ported the user manual fixes of r8063 from the 1.3.3 tag.

The command used was:
svn merge -r8062:8063 svn+ssh://bugman@.../svn/relax/tags/1.3.3 .

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r8063 | bugman | 2008-11-29 18:31:20 +0100 (Sat, 29 Nov 2008) | 3 lines
Changed paths:
M /tags/1.3.3/docs/latex/relax.tex

Fixed the spacing in the table of contents of the user manual.
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Merged revisions 8026-8028,8061,8064 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3

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r8026 | bugman | 2008-11-26 18:02:05 +0100 (Wed, 26 Nov 2008) | 3 lines

Wrote 8 system tests for reading various PDB files using the internal and Scientific python objects.
........
r8027 | bugman | 2008-11-27 09:57:19 +0100 (Thu, 27 Nov 2008) | 3 lines

Added a lactose PDB file and 2 system tests reading this file.
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r8028 | bugman | 2008-11-27 10:12:55 +0100 (Thu, 27 Nov 2008) | 5 lines

Fix for the __atom_index() method. This is a partial fix for bug #12637 (https://gna.org/bugs/?12637).

The struct_index of None is now handled.
........
r8061 | bugman | 2008-11-29 17:53:30 +0100 (Sat, 29 Nov 2008) | 14 lines

Manually ported the CHANGES file changes to the 1.3 line.

The command used was:
svn merge -r8059:8060 svn+ssh://bugman@.../svn/relax/tags/1.3.3 .

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r8060 | bugman | 2008-11-29 17:51:50 +0100 (Sat, 29 Nov 2008) | 3 lines
Changed paths:
M /tags/1.3.3/docs/CHANGES

Updated the CHANGES file for relax 1.3.3.
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r8064 | bugman | 2008-11-29 18:32:37 +0100 (Sat, 29 Nov 2008) | 14 lines

Manually ported the user manual fixes of r8063 from the 1.3.3 tag.

The command used was:
svn merge -r8062:8063 svn+ssh://bugman@.../svn/relax/tags/1.3.3 .

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r8063 | bugman | 2008-11-29 18:31:20 +0100 (Sat, 29 Nov 2008) | 3 lines
Changed paths:
M /tags/1.3.3/docs/latex/relax.tex

Fixed the spacing in the table of contents of the user manual.
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Manually updated the relax_fit.py sample script to match the equivalent system test script.

Another fix for the relax_fit.py system test script.

The state.save() user function has no 'file' arg.

Fix for the relax_fit.py system test script. The 'ave_int' value type is no more!

The proper spin specific peak intensity errors are now input into the relax-fit minimise() method.

Fixed the setting of the spin specific peak intensity errors in __errors_repl().

This should be an array equal to cdp.sigma_I.

Some whitespace cleanups.