Author: bugman
Date: Mon Dec 1 16:01:37 2008
New Revision: 8083
URL: http://svn.gna.org/viewcvs/relax?rev=8083&view=rev
Log:
Merged revisions
7971-7973,7975-7983,7991-7992,7996,8014,8016,8026-8028,8061,8064 via svnmerge
from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
........
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).
........
r7972 | bugman | 2008-11-10 23:31:18 +0100 (Mon, 10 Nov 2008) | 3 lines
Added a system test for replicating bug #12582.
........
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.
........
r7975 | bugman | 2008-11-12 15:57:25 +0100 (Wed, 12 Nov 2008) | 3 lines
Converted some ints to bools.
........
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).
........
r7977 | bugman | 2008-11-12 20:59:05 +0100 (Wed, 12 Nov 2008) | 3 lines
Renamed the system test script.
........
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.
........
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.
........
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!
........
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).
........
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.
........
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).
........
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.
........
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.
........
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.
........
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@xxxxxxxxxxx/svn/relax/tags/1.3.3 .
.....
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.
.....
........
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@xxxxxxxxxxx/svn/relax/tags/1.3.3 .
.....
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.
.....
........
Added:
branches/multi_processor_merge/test_suite/shared_data/structures/lactose_MCMM4_S1_1.pdb
- copied unchanged from r8064,
1.3/test_suite/shared_data/structures/lactose_MCMM4_S1_1.pdb
branches/multi_processor_merge/test_suite/system_tests/scripts/bugs_12582_12591_12607.py
- copied unchanged from r8064,
1.3/test_suite/system_tests/scripts/bugs_12582_12591_12607.py
Modified:
branches/multi_processor_merge/ (props changed)
branches/multi_processor_merge/docs/CHANGES
branches/multi_processor_merge/docs/latex/relax.tex
branches/multi_processor_merge/generic_fns/model_selection.py
branches/multi_processor_merge/generic_fns/pipes.py
branches/multi_processor_merge/generic_fns/results.py
branches/multi_processor_merge/generic_fns/sequence.py
branches/multi_processor_merge/generic_fns/structure/internal.py
branches/multi_processor_merge/generic_fns/structure/main.py
branches/multi_processor_merge/specific_fns/model_free/main.py
branches/multi_processor_merge/test_suite/system_tests/model_free.py
branches/multi_processor_merge/test_suite/system_tests/structure.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/multi_processor_merge/docs/CHANGES
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/docs/CHANGES?rev=8083&r1=8082&r2=8083&view=diff
Modified: branches/multi_processor_merge/docs/latex/relax.tex
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/docs/latex/relax.tex?rev=8083&r1=8082&r2=8083&view=diff
Modified: branches/multi_processor_merge/generic_fns/model_selection.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/generic_fns/model_selection.py?rev=8083&r1=8082&r2=8083&view=diff
Modified: branches/multi_processor_merge/generic_fns/pipes.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/generic_fns/pipes.py?rev=8083&r1=8082&r2=8083&view=diff
Modified: branches/multi_processor_merge/generic_fns/results.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/generic_fns/results.py?rev=8083&r1=8082&r2=8083&view=diff
Modified: branches/multi_processor_merge/generic_fns/sequence.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/generic_fns/sequence.py?rev=8083&r1=8082&r2=8083&view=diff
Modified: branches/multi_processor_merge/generic_fns/structure/internal.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/generic_fns/structure/internal.py?rev=8083&r1=8082&r2=8083&view=diff
Modified: branches/multi_processor_merge/generic_fns/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/generic_fns/structure/main.py?rev=8083&r1=8082&r2=8083&view=diff
Modified: branches/multi_processor_merge/specific_fns/model_free/main.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/specific_fns/model_free/main.py?rev=8083&r1=8082&r2=8083&view=diff
Modified: branches/multi_processor_merge/test_suite/system_tests/model_free.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/test_suite/system_tests/model_free.py?rev=8083&r1=8082&r2=8083&view=diff
Modified: branches/multi_processor_merge/test_suite/system_tests/structure.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/test_suite/system_tests/structure.py?rev=8083&r1=8082&r2=8083&view=diff
r8083 - in /branches/multi_processor_merge: ./ docs/ docs/latex/ generic_fns/ generic_fns/structure/ specific_fns/model_free...