Author: semor
Date: Mon Dec 17 18:41:25 2007
New Revision: 4199
URL: http://svn.gna.org/viewcvs/relax?rev=4199&view=rev
Log:
Merged revisions
3343,3347-3349,3353-3354,3356-3358,3362,3368,3373-3374,3525-3527,3530,3534,4142-4143
via svnmerge from
svn+ssh://semor@xxxxxxxxxxx/svn/relax/1.2
................
r3343 | bugman | 2007-07-22 12:07:13 -0400 (Sun, 22 Jul 2007) | 9 lines
Application of Seb's patch
'patch__specific_fns__jw_mapping__trailing_spaces__l1.2_r3342'.
The patch is attached to the post
https://mail.gna.org/public/relax-devel/2007-07/msg00056.html.
This patch 'patch__specific_fns__jw_mapping__trailing_spaces__l1.2_r3342'
fixes
a formating issue (trailing whitespaces) in the 1.2 line (revision 3342) for
the file 'specific_fns/jw_mapping.py'.
................
r3347 | bugman | 2007-07-22 12:31:17 -0400 (Sun, 22 Jul 2007) | 33 lines
Blocked revisions 3339-3340,3342 via svnmerge
........
r3339 | bugman | 2007-07-10 19:43:27 +0200 (Tue, 10 Jul 2007) | 7 lines
Application of Sebastien Morin's 'patch__trailing_whitespace_good' patch.
The file 'dx/isosurface_3D.py' was excluded from the patch set just to be
on the safe side - the
changes to this file could cause the OpenDX programs to fail. See the
post at
https://mail.gna.org/public/relax-devel/2007-07/msg00031.html for details.
........
r3340 | bugman | 2007-07-12 11:34:48 +0200 (Thu, 12 Jul 2007) | 8 lines
Application of Sebastien Morin's patch 'patch__indentation__r3339'.
See the post at
https://mail.gna.org/public/relax-devel/2007-07/msg00030.html for details.
This patch fixes the indentation issues - violations of the 4 spaces for
a tab - within the 1.3
line.
........
r3342 | bugman | 2007-07-17 18:42:08 +0200 (Tue, 17 Jul 2007) | 11 lines
Application of Sebastien Morin's 'patch__function_spacing__1.3_r3341'
patch.
See the post at
https://mail.gna.org/public/relax-devel/2007-07/msg00037.html for the patch.
This patch (patch__function_spacing__1.3_r3341) fixes function spacing
formating
issues in the 1.3 line (r3341). The convention is to leave two empty lines
before a function definition. The issues were found with the
code_validator
script and filtered so that when a function definition followed a class
docstring or class variable, only one empty line is left instead of two.
........
................
r3348 | bugman | 2007-07-22 12:32:38 -0400 (Sun, 22 Jul 2007) | 16 lines
Merged revisions 3345 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
........
r3345 | bugman | 2007-07-22 18:19:33 +0200 (Sun, 22 Jul 2007) | 10 lines
Fix for bug #9562 (http://gna.org/bugs/?9562).
This bug was reported and fixed by Sebastien Morin (sebastien dot morin
dot 1 at ulaval dot ca) by
the patch 'patch__specific_fns__jw_mapping__l1.3_r3342' attached to the
bug report.
In the 1.3 line, revision 3342, there is a typo in the 'set()' function
of the file
'specific_fns/jw_mapping.py'. The string 'csa' is used twice on line
398. The string 'csa' should
be used first and, then, the string 'r'.
........
................
r3349 | bugman | 2007-07-22 12:33:35 -0400 (Sun, 22 Jul 2007) | 15 lines
Blocked revisions 3346 via svnmerge
........
r3346 | bugman | 2007-07-22 18:25:39 +0200 (Sun, 22 Jul 2007) | 10 lines
Application of Seb's patch 'patch__empty_line_after_docstring__1.3_r3342'.
The patch is located at
https://mail.gna.org/public/relax-devel/2007-07/msg00047.html.
This patch (patch__empty_line_after_docstring__1.3_r3342) fixes formating
issues concerning missing
empty lines after docstrings as found using the code_validator script.
Two other small changes are
also made in the 'float.py' file where a docstring was introduced with 4
' symbols ('''') instead of
3 (''') and where there was no space between a # symbol and the following
text (a comment).
........
................
r3353 | bugman | 2007-08-06 07:32:06 -0400 (Mon, 06 Aug 2007) | 14 lines
Blocked revisions 3352 via svnmerge
........
r3352 | bugman | 2007-08-06 13:28:05 +0200 (Mon, 06 Aug 2007) | 9 lines
Application of Sebastien Morin's patch creating the N15_CSA and
NH_BOND_LENGTH constants.
For the patch, see the post at
https://mail.gna.org/public/relax-devel/2007-07/msg00060.html.
The patch 'patch__default_csa_r__l1.3_r3351' makes uniform the use of the
CSA value (now -172 ppm
everywhere) and fixes the test-suite (in jw_mapping) to account for this
change. It also adds two
constants for the CSA and NH bond length default values.
........
................
r3354 | bugman | 2007-08-06 07:36:02 -0400 (Mon, 06 Aug 2007) | 8 lines
Application of Sebastien Morin's patch to convert all default CSA values to
-172 ppm.
For the patch, see the post at
https://mail.gna.org/public/relax-devel/2007-07/msg00060.html.
The patch 'patch__default_csa__l1.2_r3351' makes uniform the use of the CSA
value (now -172 ppm
everywhere) and fixes the test-suite (in jw_mapping) to account for this
change.
................
r3356 | bugman | 2007-08-30 04:42:37 -0400 (Thu, 30 Aug 2007) | 14 lines
Hand ported r3355 from the 1.3 line.
.....
Fix for bug #9892 (https://gna.org/bugs/?9892).
This bug was reported by Douglas Kojetin <douglas dot kojetin at gmail
dot com>, and was first
discussed in the post
https://mail.gna.org/public/relax-users/2007-08/msg00008.html (Message-id:
<1E05882B-96B3-4875-B11B-0A6FEF423937@xxxxxxxxx>).
The fix was to simply test for the presence of the data structures. If
these spin system specific
structures - 'model' and 'params' - were missing, then the bug will arise.
.....
................
r3357 | bugman | 2007-08-30 04:45:03 -0400 (Thu, 30 Aug 2007) | 15 lines
Blocked revisions 3355 via svnmerge
........
r3355 | bugman | 2007-08-30 10:41:32 +0200 (Thu, 30 Aug 2007) | 10 lines
Fix for bug #9892 (https://gna.org/bugs/?9892).
This bug was reported by Douglas Kojetin <douglas dot kojetin at gmail
dot com>, and was first
discussed in the post
https://mail.gna.org/public/relax-users/2007-08/msg00008.html (Message-id:
<1E05882B-96B3-4875-B11B-0A6FEF423937@xxxxxxxxx>).
The fix was to simply test for the presence of the data structures. If
these spin system specific
structures - 'model' and 'params' - were missing, then the bug will arise.
........
................
r3358 | bugman | 2007-10-21 11:59:42 -0400 (Sun, 21 Oct 2007) | 9 lines
Doug's patch for fixing bug #10022 (https://gna.org/bugs/?10022).
The patch by Douglas Kojetin (https://gna.org/users/dkojetin) labelled as
'patch2' and attached to
the bug report has been applied without modification.
This change fixes the convergence test in the 'full_analysis.py' script
which fails when one residue
has the model None associated with it. These situations are now caught and
skipped.
................
r3362 | bugman | 2007-10-21 13:43:37 -0400 (Sun, 21 Oct 2007) | 12 lines
Ported r3360 from the 1.2.11 tag using the command:
svn merge -r3360:3361 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/tags/1.2.11
.....
r3361 | bugman | 2007-10-21 19:40:36 +0200 (Sun, 21 Oct 2007) | 3 lines
Changed paths:
M /tags/1.2.11/docs/CHANGES
Updated the CHANGES file for relax version 1.2.11.
.....
................
r3368 | bugman | 2007-10-21 16:54:32 -0400 (Sun, 21 Oct 2007) | 3 lines
A few fixes to the CHANGES file for version 1.2.11.
................
r3373 | bugman | 2007-10-25 04:10:32 -0400 (Thu, 25 Oct 2007) | 57 lines
Blocked revisions 3359,3369 via svnmerge
........
r3359 | bugman | 2007-10-21 18:04:59 +0200 (Sun, 21 Oct 2007) | 20 lines
Manually ported r3358 from the 1.2 line - the fix to bug #10022
(https://gna.org/bugs/?10022).
The command used was:
svn merge -r3357:3358 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.2
.....
r3358 | bugman | 2007-10-21 17:59:42 +0200 (Sun, 21 Oct 2007) | 9 lines
Changed paths:
M /1.2/sample_scripts/full_analysis.py
Doug's patch for fixing bug #10022 (https://gna.org/bugs/?10022).
The patch by Douglas Kojetin (https://gna.org/users/dkojetin) labelled
as 'patch2' and attached to
the bug report has been applied without modification.
This change fixes the convergence test in the 'full_analysis.py' script
which fails when one residue
has the model None associated with it. These situations are now caught
and skipped.
.....
........
r3369 | bugman | 2007-10-21 23:00:02 +0200 (Sun, 21 Oct 2007) | 31 lines
Manually ported the changes to the CHANGES file for relax 1.2.11.
The command used was:
svn merge -r3361:3368 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.2
.....
r3368 | bugman | 2007-10-21 22:54:32 +0200 (Sun, 21 Oct 2007) | 3 lines
Changed paths:
M /1.2/docs/CHANGES
A few fixes to the CHANGES file for version 1.2.11.
.....
r3362 | bugman | 2007-10-21 19:43:37 +0200 (Sun, 21 Oct 2007) | 12 lines
Changed paths:
M /1.2/docs/CHANGES
Ported r3360 from the 1.2.11 tag using the command:
svn merge -r3360:3361 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/tags/1.2.11
.....
r3361 | bugman | 2007-10-21 19:40:36 +0200 (Sun, 21 Oct 2007) | 3
lines
Changed paths:
M /tags/1.2.11/docs/CHANGES
Updated the CHANGES file for relax version 1.2.11.
.....
.....
........
................
r3374 | bugman | 2007-10-25 04:11:30 -0400 (Thu, 25 Oct 2007) | 14 lines
Merged revisions 3372 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
........
r3372 | bugman | 2007-10-25 10:09:20 +0200 (Thu, 25 Oct 2007) | 8 lines
Fix for bug #10189 (https://gna.org/bugs/?10189).
This bug was reported by Douglas Kojetin (douglas dot kojetin att gmail
dot com).
The problem was that the 'latex_mf_table.py' sample script was trying to
write to the results file
the 'res' variable which was not defined anywhere in the script!!!
........
................
r3525 | bugman | 2007-11-13 16:19:54 -0500 (Tue, 13 Nov 2007) | 8 lines
Fix for bug #10323 (https://gna.org/bugs/?10323).
This bug was reported by Douglas Kojetin <douglas dot kojetin at gmail dot
com>.
The fix was to simply use the same fix which went into the equivalent
model-free code years and
years ago!
................
r3526 | bugman | 2007-11-13 16:22:07 -0500 (Tue, 13 Nov 2007) | 8 lines
Fix for bug #10323 (https://gna.org/bugs/?10323).
This bug was reported by Douglas Kojetin <douglas dot kojetin at gmail dot
com>.
This change adds another test for the 'num_ri' structure to the model-free
code, just in case. The
additional test is in the writing of simulation model-free results file.
................
r3527 | bugman | 2007-11-13 16:39:40 -0500 (Tue, 13 Nov 2007) | 640 lines
Blocked revisions 3379,3382-3524 via svnmerge
........
r3379 | bugman | 2007-10-28 18:55:32 +0100 (Sun, 28 Oct 2007) | 8 lines
Fix for bug #9389 (https://gna.org/bugs/?9389).
This bug was caused by the move away from using the __builtin__
namespace. As the file is now
treated as a module from which errors must be imported, the
AllRelaxErrors object was not being
created. The solution was to add the function 'all_errors()' which
returns a list of all the
RelaxError objects.
........
r3382 | bugman | 2007-10-28 20:29:06 +0100 (Sun, 28 Oct 2007) | 3 lines
Added two unit tests for the, as of yet, non-existent
'generic_fns.residue.rename()' function.
........
r3383 | bugman | 2007-10-28 20:32:32 +0100 (Sun, 28 Oct 2007) | 7 lines
Removed the 'residue.merge()' from the data model redesign document.
I cannot see the purpose of this function, as it would probably duplicate
the functionality of
'residue.copy()' function. It was first mentioned by Chris MacRaild in
the post at
https://mail.gna.org/public/relax-devel/2006-10/msg00061.html.
........
r3384 | bugman | 2007-10-29 15:02:21 +0100 (Mon, 29 Oct 2007) | 3 lines
Added a unit test for renaming multiple residues simultaneously through
'residue.rename()'.
........
r3385 | bugman | 2007-10-29 15:03:53 +0100 (Mon, 29 Oct 2007) | 3 lines
Fixed a bug in the 'test_rename' unit test.
........
r3386 | bugman | 2007-10-29 15:07:45 +0100 (Mon, 29 Oct 2007) | 3 lines
Added 3 unit tests for the non-existant residue.renumber() function.
........
r3387 | bugman | 2007-11-03 14:09:28 +0100 (Sat, 03 Nov 2007) | 3 lines
Created the generic_fns.residue.rename() function and fixed the
corresponding unit tests.
........
r3388 | bugman | 2007-11-03 16:04:48 +0100 (Sat, 03 Nov 2007) | 3 lines
Implemented the generic_fns.residue.renumber() function and fixed its
unit tests.
........
r3389 | bugman | 2007-11-03 17:46:41 +0100 (Sat, 03 Nov 2007) | 3 lines
Added the rudimentary beginnings of the molecule user function class.
........
r3390 | bugman | 2007-11-03 18:36:21 +0100 (Sat, 03 Nov 2007) | 3 lines
Alphabetical arrangement of the residue user functions.
........
r3391 | bugman | 2007-11-03 18:37:32 +0100 (Sat, 03 Nov 2007) | 3 lines
Spelling correction.
........
r3392 | bugman | 2007-11-03 19:25:57 +0100 (Sat, 03 Nov 2007) | 6 lines
More unit tests for the generic_fns.residue.copy() function.
The current test was renamed. Two new tests were added for copying
between molecules and copying
between data pipes.
........
r3393 | bugman | 2007-11-03 23:37:13 +0100 (Sat, 03 Nov 2007) | 5 lines
A large number of changes to make the residue.copy() user function fully
functional.
Now residue data can be copied within a single molecule, between
molecules, and between data pipes.
........
r3394 | bugman | 2007-11-04 11:55:51 +0100 (Sun, 04 Nov 2007) | 6 lines
Added a test for the failure of the
generic_fns.selection.return_residue() function.
This tests the failure of asking for a non-existent data pipe and the
function has been fixed to
fail appropriately.
........
r3395 | bugman | 2007-11-04 13:15:18 +0100 (Sun, 04 Nov 2007) | 3 lines
Added another unit test for the generic_fns.selection.return_residue()
function.
........
r3396 | bugman | 2007-11-04 13:19:36 +0100 (Sun, 04 Nov 2007) | 5 lines
Added two unit tests for the generic_fns.selection.return_molecule()
function.
Also made the function fail properly when no data pipe exists.
........
r3397 | bugman | 2007-11-04 13:27:15 +0100 (Sun, 04 Nov 2007) | 3 lines
Added two unit tests for the
generic_fns.selection.return_single_residue_info() function.
........
r3398 | bugman | 2007-11-04 13:36:57 +0100 (Sun, 04 Nov 2007) | 3 lines
Renamed all instances of RelaxNoRunError to RelaxNoPipeError, and updated
the error message.
........
r3399 | bugman | 2007-11-04 13:39:20 +0100 (Sun, 04 Nov 2007) | 3 lines
Renamed all instances of RelaxRunError with RelaxPipeError, and modified
the error message.
........
r3400 | bugman | 2007-11-04 13:42:08 +0100 (Sun, 04 Nov 2007) | 3 lines
Replaced all mention of 'run' from the RelaxError system and replaced it
with 'pipe'.
........
r3401 | bugman | 2007-11-04 13:51:00 +0100 (Sun, 04 Nov 2007) | 3 lines
Removed dud user functions from 'residue' which remained from the copy of
'sequence'.
........
r3402 | bugman | 2007-11-04 13:51:37 +0100 (Sun, 04 Nov 2007) | 3 lines
Updated the docstring modifications of the 'residue' user function class.
........
r3403 | bugman | 2007-11-04 13:57:38 +0100 (Sun, 04 Nov 2007) | 3 lines
Added the residue.rename() user function.
........
r3404 | bugman | 2007-11-04 14:01:46 +0100 (Sun, 04 Nov 2007) | 3 lines
Created the residue.renumber() user function.
........
r3405 | bugman | 2007-11-04 14:37:59 +0100 (Sun, 04 Nov 2007) | 6 lines
Created the residue.display() user function.
This has been added to the data model redesign document. Two unit tests
have also been created for
the function.
........
r3406 | bugman | 2007-11-04 14:39:34 +0100 (Sun, 04 Nov 2007) | 3 lines
Fixed a typo in the docstrings of the unit tests for the
generic_fns.residue functions.
........
r3407 | bugman | 2007-11-04 14:49:55 +0100 (Sun, 04 Nov 2007) | 3 lines
Modified the data model redesign document to show that the residue user
function class is finished.
........
r3408 | bugman | 2007-11-04 14:56:03 +0100 (Sun, 04 Nov 2007) | 3 lines
Removed junk code, left over from the copy from 'generic_fns/sequence.py'.
........
r3409 | bugman | 2007-11-04 14:58:41 +0100 (Sun, 04 Nov 2007) | 3 lines
Removed some no longer used RelaxError imports.
........
r3410 | bugman | 2007-11-04 15:38:46 +0100 (Sun, 04 Nov 2007) | 3 lines
Added a module docstring.
........
r3411 | bugman | 2007-11-04 15:40:29 +0100 (Sun, 04 Nov 2007) | 3 lines
Spacing.
........
r3412 | bugman | 2007-11-04 15:41:08 +0100 (Sun, 04 Nov 2007) | 3 lines
Created the module docstring.
........
r3413 | bugman | 2007-11-04 15:42:22 +0100 (Sun, 04 Nov 2007) | 3 lines
Added the setUp and tearDown functions for the generic_fns.molecule
function unit tests.
........
r3414 | bugman | 2007-11-04 15:43:40 +0100 (Sun, 04 Nov 2007) | 5 lines
Replace the contents of 'generic_fns/molecule.py' with those of
'generic_fns/residue.py'.
The file originated from 'generic_fns/residue.py' but was unmodified and
out of date.
........
r3415 | bugman | 2007-11-04 17:14:57 +0100 (Sun, 04 Nov 2007) | 3 lines
Updated the module names in '__init__.py'.
........
r3416 | bugman | 2007-11-04 17:28:45 +0100 (Sun, 04 Nov 2007) | 6 lines
Created the molecule.create() user function.
The user function and the function generic_fns.molecule.create() have
been written. Two unit tests
for the function have been created.
........
r3417 | bugman | 2007-11-04 17:30:29 +0100 (Sun, 04 Nov 2007) | 3 lines
Removed the useless molecule user functions remaining from the copy from
'prompt/sequence.py'.
........
r3418 | bugman | 2007-11-04 17:31:34 +0100 (Sun, 04 Nov 2007) | 3 lines
Renamed the user function 'molecule.add()' to 'molecule.create()' in the
redesign doc.
........
r3419 | bugman | 2007-11-04 17:58:21 +0100 (Sun, 04 Nov 2007) | 3 lines
Added a unit test for the copying of the molecule data between different
data pipes.
........
r3420 | bugman | 2007-11-04 18:00:03 +0100 (Sun, 04 Nov 2007) | 6 lines
Added the 'return_single_molecule_info()' function and fixed the
'return_molecule()' function.
The 'return_molecule()' function was returning a molecule container when
no molecule selection was
given. Now None is returned.
........
r3421 | bugman | 2007-11-04 18:01:59 +0100 (Sun, 04 Nov 2007) | 6 lines
Modified the 'generic_fns.residue.copy()' function to work with the
modified 'return_molecule()' fn.
Five unit test were failing due to the previous commit. This was because
of a problem in
'generic_fns.residue.copy()' that wasn't previously detected.
........
r3422 | bugman | 2007-11-04 18:04:22 +0100 (Sun, 04 Nov 2007) | 3 lines
Another fix for the 'return_molecule()' function.
........
[... 2750 lines stripped ...]
r4199 - in /branches/consistency_tests_1.2: ./ docs/ prompt/ sample_scripts/ specific_fns/ test_suite/