Author: semor
Date: Tue Dec 18 18:34:43 2007
New Revision: 4208
URL: http://svn.gna.org/viewcvs/relax?rev=4208&view=rev
Log:
Merged revisions
3333,3339-3340,3342,3345-3346,3352,3355,3359,3369,3372,3379,3382-3524,3528-3529,3540-3691,3695,3697-3713,3715-3719,3721-3728,3730-3731,3733-3755,3757,3773-3807,3809-3833,3836-3838,3840-3869,3872-3905,3907-3974,3976-3986,4004,4014-4015,4018-4021,4027-4031,4061-4102,4104-4114,4137-4139,4141,4144-4175
via svnmerge from
svn+ssh://semor@xxxxxxxxxxx/svn/relax/1.3
........
r3333 | bugman | 2007-07-09 16:57:15 -0400 (Mon, 09 Jul 2007) | 17 lines
Manually ported r3332 from the 1.2 line - the addition of Grace plotting to
the jw_mapping script.
The command used was:
svn merge -r3331:3332 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.2
.....
r3332 | bugman | 2007-07-09 22:48:18 +0200 (Mon, 09 Jul 2007) | 6 lines
Changed paths:
M /1.2/sample_scripts/jw_mapping.py
Application of Sebastien Morin's patch
'patch_sample_scripts_consistency_tests'.
See the post located at
https://mail.gna.org/public/relax-devel/2007-07/msg00015.html for
details.
.....
........
r3339 | bugman | 2007-07-10 13:43:27 -0400 (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 05:34:48 -0400 (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 12:42:08 -0400 (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.
........
r3345 | bugman | 2007-07-22 12:19:33 -0400 (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'.
........
r3346 | bugman | 2007-07-22 12:25:39 -0400 (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).
........
r3352 | bugman | 2007-08-06 07:28:05 -0400 (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.
........
r3355 | bugman | 2007-08-30 04:41:32 -0400 (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.
........
r3359 | bugman | 2007-10-21 12:04:59 -0400 (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 17:00:02 -0400 (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.
.....
.....
........
r3372 | bugman | 2007-10-25 04:09:20 -0400 (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!!!
........
r3379 | bugman | 2007-10-28 13:55:32 -0400 (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 15:29:06 -0400 (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 15:32:32 -0400 (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 10:02:21 -0400 (Mon, 29 Oct 2007) | 3 lines
Added a unit test for renaming multiple residues simultaneously through
'residue.rename()'.
........
r3385 | bugman | 2007-10-29 10:03:53 -0400 (Mon, 29 Oct 2007) | 3 lines
Fixed a bug in the 'test_rename' unit test.
........
r3386 | bugman | 2007-10-29 10:07:45 -0400 (Mon, 29 Oct 2007) | 3 lines
Added 3 unit tests for the non-existant residue.renumber() function.
........
r3387 | bugman | 2007-11-03 09:09:28 -0400 (Sat, 03 Nov 2007) | 3 lines
Created the generic_fns.residue.rename() function and fixed the
corresponding unit tests.
........
r3388 | bugman | 2007-11-03 11:04:48 -0400 (Sat, 03 Nov 2007) | 3 lines
Implemented the generic_fns.residue.renumber() function and fixed its unit
tests.
........
r3389 | bugman | 2007-11-03 12:46:41 -0400 (Sat, 03 Nov 2007) | 3 lines
Added the rudimentary beginnings of the molecule user function class.
........
r3390 | bugman | 2007-11-03 13:36:21 -0400 (Sat, 03 Nov 2007) | 3 lines
Alphabetical arrangement of the residue user functions.
........
r3391 | bugman | 2007-11-03 13:37:32 -0400 (Sat, 03 Nov 2007) | 3 lines
Spelling correction.
........
r3392 | bugman | 2007-11-03 14:25:57 -0400 (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 18:37:13 -0400 (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 05:55:51 -0500 (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 07:15:18 -0500 (Sun, 04 Nov 2007) | 3 lines
Added another unit test for the generic_fns.selection.return_residue()
function.
........
r3396 | bugman | 2007-11-04 07:19:36 -0500 (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 07:27:15 -0500 (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 07:36:57 -0500 (Sun, 04 Nov 2007) | 3 lines
Renamed all instances of RelaxNoRunError to RelaxNoPipeError, and updated
the error message.
........
r3399 | bugman | 2007-11-04 07:39:20 -0500 (Sun, 04 Nov 2007) | 3 lines
Renamed all instances of RelaxRunError with RelaxPipeError, and modified
the error message.
........
r3400 | bugman | 2007-11-04 07:42:08 -0500 (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 07:51:00 -0500 (Sun, 04 Nov 2007) | 3 lines
Removed dud user functions from 'residue' which remained from the copy of
'sequence'.
........
r3402 | bugman | 2007-11-04 07:51:37 -0500 (Sun, 04 Nov 2007) | 3 lines
Updated the docstring modifications of the 'residue' user function class.
........
r3403 | bugman | 2007-11-04 07:57:38 -0500 (Sun, 04 Nov 2007) | 3 lines
Added the residue.rename() user function.
........
r3404 | bugman | 2007-11-04 08:01:46 -0500 (Sun, 04 Nov 2007) | 3 lines
Created the residue.renumber() user function.
........
r3405 | bugman | 2007-11-04 08:37:59 -0500 (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 08:39:34 -0500 (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 08:49:55 -0500 (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 08:56:03 -0500 (Sun, 04 Nov 2007) | 3 lines
Removed junk code, left over from the copy from 'generic_fns/sequence.py'.
........
r3409 | bugman | 2007-11-04 08:58:41 -0500 (Sun, 04 Nov 2007) | 3 lines
Removed some no longer used RelaxError imports.
........
r3410 | bugman | 2007-11-04 09:38:46 -0500 (Sun, 04 Nov 2007) | 3 lines
Added a module docstring.
........
r3411 | bugman | 2007-11-04 09:40:29 -0500 (Sun, 04 Nov 2007) | 3 lines
Spacing.
........
r3412 | bugman | 2007-11-04 09:41:08 -0500 (Sun, 04 Nov 2007) | 3 lines
Created the module docstring.
........
r3413 | bugman | 2007-11-04 09:42:22 -0500 (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 09:43:40 -0500 (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 11:14:57 -0500 (Sun, 04 Nov 2007) | 3 lines
Updated the module names in '__init__.py'.
........
r3416 | bugman | 2007-11-04 11:28:45 -0500 (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 11:30:29 -0500 (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 11:31:34 -0500 (Sun, 04 Nov 2007) | 3 lines
Renamed the user function 'molecule.add()' to 'molecule.create()' in the
redesign doc.
........
r3419 | bugman | 2007-11-04 11:58:21 -0500 (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 12:00:03 -0500 (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 12:01:59 -0500 (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 12:04:22 -0500 (Sun, 04 Nov 2007) | 3 lines
Another fix for the 'return_molecule()' function.
........
r3423 | bugman | 2007-11-04 12:10:46 -0500 (Sun, 04 Nov 2007) | 3 lines
A few more fixes to the 'return_molecule()' function.
........
r3424 | bugman | 2007-11-04 12:11:21 -0500 (Sun, 04 Nov 2007) | 3 lines
Wrote the generic_fns.molecule.copy() function.
........
r3425 | bugman | 2007-11-04 12:14:20 -0500 (Sun, 04 Nov 2007) | 3 lines
Added a unit test to test the failure of copying molecule data to a
non-existent data pipe.
........
r3426 | bugman | 2007-11-04 12:23:47 -0500 (Sun, 04 Nov 2007) | 3 lines
Added two more unit tests for the generic_fns.molecule.copy() function.
........
r3427 | bugman | 2007-11-04 12:53:24 -0500 (Sun, 04 Nov 2007) | 3 lines
Created the molecule.copy() user function interface.
........
r3428 | bugman | 2007-11-04 12:54:23 -0500 (Sun, 04 Nov 2007) | 3 lines
A few changes to the residue.copy() user function RelaxError messages.
........
r3429 | bugman | 2007-11-04 13:02:46 -0500 (Sun, 04 Nov 2007) | 3 lines
Added a unit test for the generic_fns.molecule.delete() function.
........
r3430 | bugman | 2007-11-04 13:07:43 -0500 (Sun, 04 Nov 2007) | 3 lines
Added a unit test for the deletion of all molecules.
........
r3431 | bugman | 2007-11-04 13:10:12 -0500 (Sun, 04 Nov 2007) | 3 lines
Added a unit test for the failure of the generic_fns.molecule.delete()
function.
........
r3432 | bugman | 2007-11-04 13:16:58 -0500 (Sun, 04 Nov 2007) | 3 lines
Implemented the generic_fns.molecule.delete() function.
........
r3433 | bugman | 2007-11-04 13:17:35 -0500 (Sun, 04 Nov 2007) | 3 lines
Fixed a problem in the 'test_delete_all()' unit test.
........
r3434 | bugman | 2007-11-04 13:20:18 -0500 (Sun, 04 Nov 2007) | 3 lines
Added 2 unit tests for the generic_fns.molecule.display() function.
........
r3435 | bugman | 2007-11-04 13:26:18 -0500 (Sun, 04 Nov 2007) | 3 lines
A small change to a generic_fns.molecule.display() unit test.
........
r3436 | bugman | 2007-11-04 13:26:42 -0500 (Sun, 04 Nov 2007) | 3 lines
Wrote the generic_fns.molecule.display() function.
........
r3437 | bugman | 2007-11-04 13:28:43 -0500 (Sun, 04 Nov 2007) | 3 lines
Debugged the generic_fns.molecule.display() function.
........
r3438 | bugman | 2007-11-04 13:29:34 -0500 (Sun, 04 Nov 2007) | 3 lines
Removed some debugging print statements.
........
r3439 | bugman | 2007-11-04 13:33:54 -0500 (Sun, 04 Nov 2007) | 3 lines
Implemented the molecule.delete() user function.
........
r3440 | bugman | 2007-11-04 13:36:00 -0500 (Sun, 04 Nov 2007) | 3 lines
Implemented the molecule.display() user function.
........
r3441 | bugman | 2007-11-04 13:38:07 -0500 (Sun, 04 Nov 2007) | 3 lines
Modified the molecule user functions to include the identification string
documentation.
........
r3442 | bugman | 2007-11-04 13:38:59 -0500 (Sun, 04 Nov 2007) | 3 lines
Added a missing import statement.
........
r3443 | bugman | 2007-11-04 13:41:53 -0500 (Sun, 04 Nov 2007) | 3 lines
Added a unit test for the generic_fns.molecule.rename() function.
........
r3444 | bugman | 2007-11-04 13:47:00 -0500 (Sun, 04 Nov 2007) | 3 lines
Implemented the generic_fns.molecule.rename() function.
........
r3445 | bugman | 2007-11-04 13:50:28 -0500 (Sun, 04 Nov 2007) | 3 lines
Implemented the molecule.rename() user function.
........
r3446 | bugman | 2007-11-04 13:56:29 -0500 (Sun, 04 Nov 2007) | 3 lines
Added 2 unit tests for the failure of the generic_fns.molecule.rename()
function.
........
r3447 | bugman | 2007-11-04 13:57:43 -0500 (Sun, 04 Nov 2007) | 3 lines
Fixed a bug in generic_fns.molecule.rename() found using the previously
committed unit tests.
........
r3448 | bugman | 2007-11-04 13:58:53 -0500 (Sun, 04 Nov 2007) | 3 lines
Renamed the user function molecule.info() to molecule.display() in the
redesign document.
........
r3449 | bugman | 2007-11-04 13:59:34 -0500 (Sun, 04 Nov 2007) | 3 lines
Added the molecule.rename() user function to the redesign document.
........
r3450 | bugman | 2007-11-04 14:12:54 -0500 (Sun, 04 Nov 2007) | 3 lines
Updated the redesign document to show that the molecule user functions are
all implemented.
........
r3451 | bugman | 2007-11-04 14:13:24 -0500 (Sun, 04 Nov 2007) | 3 lines
Removed some unused imports.
........
r3452 | bugman | 2007-11-04 14:14:23 -0500 (Sun, 04 Nov 2007) | 3 lines
Removed some unused imports.
........
r3453 | bugman | 2007-11-04 14:15:11 -0500 (Sun, 04 Nov 2007) | 3 lines
Removed some unused imports.
[... 3119 lines stripped ...]
r4208 - in /branches/consistency_tests_1.3: ./ data/ docs/ docs/latex/ generic_fns/ maths_fns/ minimise/ minimise/line_searc...