Author: bugman
Date: Sun Dec 9 12:56:40 2007
New Revision: 4142
URL: http://svn.gna.org/viewcvs/relax?rev=4142&view=rev
Log:
Blocked revisions
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
via svnmerge
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r3528 | bugman | 2007-11-13 22:49:05 +0100 (Tue, 13 Nov 2007) | 19 lines
Manually ported r3525 from the 1.2 line - the fix to bug #10323
(https://gna.org/bugs/?10323).
The command used was:
svn merge -r3524:3525 svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.2
.....
r3525 | bugman | 2007-11-13 22:19:54 +0100 (Tue, 13 Nov 2007) | 8 lines
Changed paths:
M /1.2/specific_fns/jw_mapping.py
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!
.....
........
r3529 | bugman | 2007-11-13 22:57:03 +0100 (Tue, 13 Nov 2007) | 19 lines
Manually ported r3526 from the 1.2 line.
The command used was:
svn merge -r3525:3526
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.2/specific_fns/model_free.py
specific_fns/model_free/model_free.py
.....
r3526 | bugman | 2007-11-13 22:22:07 +0100 (Tue, 13 Nov 2007) | 8 lines
Changed paths:
M /1.2/specific_fns/model_free.py
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.
.....
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r3540 | bugman | 2007-11-18 19:37:41 +0100 (Sun, 18 Nov 2007) | 3 lines
Wrote a unit test for the renaming of spins.
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r3541 | bugman | 2007-11-18 19:40:19 +0100 (Sun, 18 Nov 2007) | 3 lines
Added a few more remanings to the spin renaming unit test.
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r3542 | bugman | 2007-11-18 19:42:43 +0100 (Sun, 18 Nov 2007) | 3 lines
Implemented the generic_fns.spin.rename() function.
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r3543 | bugman | 2007-11-18 19:43:42 +0100 (Sun, 18 Nov 2007) | 3 lines
Fixes for the spin renaming unit test.
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r3544 | bugman | 2007-11-18 19:50:35 +0100 (Sun, 18 Nov 2007) | 3 lines
Added a description of the data setup for all the spin unit tests.
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r3545 | bugman | 2007-11-18 19:52:20 +0100 (Sun, 18 Nov 2007) | 3 lines
Added a unit test for renaming many spins simultaneously.
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r3546 | bugman | 2007-11-18 19:54:11 +0100 (Sun, 18 Nov 2007) | 3 lines
Added checks to the spin renaming unit test to make sure other spins are
not renamed.
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r3547 | bugman | 2007-11-18 19:55:05 +0100 (Sun, 18 Nov 2007) | 3 lines
A comment fix.
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r3548 | bugman | 2007-11-18 19:55:32 +0100 (Sun, 18 Nov 2007) | 3 lines
And another comment fix (fixing the last fix).
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r3549 | bugman | 2007-11-18 19:59:15 +0100 (Sun, 18 Nov 2007) | 3 lines
Added a unit test for renumbering spins.
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r3550 | bugman | 2007-11-18 20:02:39 +0100 (Sun, 18 Nov 2007) | 3 lines
Implemented the generic_fns.spin.renumber() function.
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r3551 | bugman | 2007-11-18 20:03:34 +0100 (Sun, 18 Nov 2007) | 3 lines
A docstring and comment correction.
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r3552 | bugman | 2007-11-18 20:05:19 +0100 (Sun, 18 Nov 2007) | 3 lines
Fixed the unit test for renumbering spins.
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r3553 | bugman | 2007-11-18 20:08:29 +0100 (Sun, 18 Nov 2007) | 3 lines
Merged the data setup method setup_data() into setUp().
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r3554 | bugman | 2007-11-18 20:09:58 +0100 (Sun, 18 Nov 2007) | 3 lines
Removed all the calls to setup_data() from the spin unit tests to make them
work!
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r3555 | bugman | 2007-11-18 20:13:23 +0100 (Sun, 18 Nov 2007) | 3 lines
Added a unit test for the failure of spin renumbering when multiple spins
are renumbered at once.
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r3556 | bugman | 2007-11-18 20:15:24 +0100 (Sun, 18 Nov 2007) | 3 lines
A few docstring fixes.
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r3557 | bugman | 2007-11-18 20:16:14 +0100 (Sun, 18 Nov 2007) | 3 lines
Removed the unused and useless generic_fns.molecule.renumber() function.
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r3558 | bugman | 2007-11-18 20:19:52 +0100 (Sun, 18 Nov 2007) | 3 lines
A few comment fixes.
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r3559 | bugman | 2007-11-18 20:21:31 +0100 (Sun, 18 Nov 2007) | 3 lines
Removed a few unused imported functions.
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r3560 | bugman | 2007-11-18 20:26:28 +0100 (Sun, 18 Nov 2007) | 3 lines
Implemented the spin.copy() user function.
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r3561 | bugman | 2007-11-18 21:01:13 +0100 (Sun, 18 Nov 2007) | 3 lines
Implemented the spin.create() user function.
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r3562 | bugman | 2007-11-18 21:02:57 +0100 (Sun, 18 Nov 2007) | 3 lines
Implemented the spin.delete() user function.
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r3563 | bugman | 2007-11-18 21:03:57 +0100 (Sun, 18 Nov 2007) | 3 lines
Reordered the user functions in prompt/molecule.py.
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r3564 | bugman | 2007-11-18 21:04:56 +0100 (Sun, 18 Nov 2007) | 3 lines
Implemented the spin.display() user function.
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r3565 | bugman | 2007-11-18 21:07:36 +0100 (Sun, 18 Nov 2007) | 3 lines
Implemented the spin.rename() user function.
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r3566 | bugman | 2007-11-18 21:10:26 +0100 (Sun, 18 Nov 2007) | 3 lines
Implemented the spin.renumber() user function.
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r3567 | bugman | 2007-11-18 21:12:56 +0100 (Sun, 18 Nov 2007) | 3 lines
Updated the identification string documentation for the spin user function
class.
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r3568 | bugman | 2007-11-18 21:15:04 +0100 (Sun, 18 Nov 2007) | 3 lines
Added the spin.rename() and spin.renumber() user functions to the redesign
document.
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r3569 | bugman | 2007-11-18 21:15:53 +0100 (Sun, 18 Nov 2007) | 3 lines
Marked the spin user function class as completed within the data model
redesign document.
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r3570 | bugman | 2007-11-18 21:19:06 +0100 (Sun, 18 Nov 2007) | 3 lines
Removed an unused import from the spin unit tests.
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r3571 | bugman | 2007-11-18 21:20:20 +0100 (Sun, 18 Nov 2007) | 3 lines
Added a directory for adding units tests of the modules in the 'prompt/'
directory.
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r3572 | bugman | 2007-11-18 21:21:39 +0100 (Sun, 18 Nov 2007) | 3 lines
Copied the __init__.py file.
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r3573 | bugman | 2007-11-18 21:28:15 +0100 (Sun, 18 Nov 2007) | 3 lines
Copied the spin unit tests for the generic_fns directory to the prompt
directory.
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r3574 | bugman | 2007-11-18 21:37:52 +0100 (Sun, 18 Nov 2007) | 3 lines
The spin user function unit tests now test these functions rather than
those of generic_fns.spin.
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r3575 | bugman | 2007-11-18 21:43:39 +0100 (Sun, 18 Nov 2007) | 3 lines
Fix to allow the pipes to be set to None in the spin.copy() user function.
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r3576 | bugman | 2007-11-18 21:45:38 +0100 (Sun, 18 Nov 2007) | 3 lines
Fix to allow the spin to target to be set to None in the spin.copy() user
function.
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r3577 | bugman | 2007-11-18 21:47:19 +0100 (Sun, 18 Nov 2007) | 3 lines
Fixed a bug in the spin.renumber() user function.
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r3578 | bugman | 2007-11-18 21:48:31 +0100 (Sun, 18 Nov 2007) | 5 lines
Fixed another bug in the spin.renumber() user function.
The spin number was been checked if it was a string whereas the check
should have been for an int.
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r3579 | bugman | 2007-11-18 21:49:50 +0100 (Sun, 18 Nov 2007) | 6 lines
Fixed a bug in the spin.rename() user function.
The spin ID string was been checked if it was an int whereas the check
should have been for a
string.
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r3580 | bugman | 2007-11-18 21:52:37 +0100 (Sun, 18 Nov 2007) | 5 lines
Fixed a bug in the spin.diplay() user function.
The spin ID string was been checked if it was a string. It can also be
None!
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r3581 | bugman | 2007-11-18 21:54:13 +0100 (Sun, 18 Nov 2007) | 5 lines
Fixed a bug in the spin.create() user function.
The residue ID string was been checked if it was a string. It can also be
None!
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r3582 | bugman | 2007-11-18 22:00:16 +0100 (Sun, 18 Nov 2007) | 5 lines
Big, big bug fix!
The prompt.spin module was importing the residue rather than spin module
from 'generic_fns/'.
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r3583 | bugman | 2007-11-18 22:04:48 +0100 (Sun, 18 Nov 2007) | 6 lines
Bug fix for the spin.renumber() user function.
The generic_fns.spin.create() function was being called instead and the
non-existent spin_num
argument was being passed into it.
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r3584 | bugman | 2007-11-18 22:05:49 +0100 (Sun, 18 Nov 2007) | 6 lines
Bug fix for the spin.rename() user function.
The generic_fns.spin.create() function was being called instead and the
non-existent spin_num
argument was being passed into it.
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r3585 | bugman | 2007-11-18 22:06:42 +0100 (Sun, 18 Nov 2007) | 3 lines
Fixed the printout of the spin.rename() user function.
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r3586 | bugman | 2007-11-18 22:07:15 +0100 (Sun, 18 Nov 2007) | 3 lines
Fixed the printout of the spin.renumber() user function.
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r3587 | bugman | 2007-11-18 22:07:40 +0100 (Sun, 18 Nov 2007) | 3 lines
Fixed the printout of the spin.create() user function.
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r3588 | bugman | 2007-11-18 22:10:12 +0100 (Sun, 18 Nov 2007) | 3 lines
Copied test_suite/unit_tests/generic_fns/test_spin.py to create a base
class for the prompt as well.
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r3589 | bugman | 2007-11-18 22:13:18 +0100 (Sun, 18 Nov 2007) | 3 lines
Preparation of the prompt.spin and generic_fns.spin base class.
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r3590 | bugman | 2007-11-18 22:14:45 +0100 (Sun, 18 Nov 2007) | 3 lines
Updated the __init__.py module with the test_spin module name.
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r3591 | bugman | 2007-11-18 22:24:41 +0100 (Sun, 18 Nov 2007) | 3 lines
Updated the spin user function unit tests to inherit Spin_base_class.
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r3592 | bugman | 2007-11-18 22:38:26 +0100 (Sun, 18 Nov 2007) | 6 lines
Fixed the relax data store import problem/clash in the spin_base_class
module.
The singleton is now imported into the data.__init__ module as Data, and
hence it can be
subsequently imported by the base class. A bit of a kludge, but it works
for now!
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r3593 | bugman | 2007-11-18 22:44:09 +0100 (Sun, 18 Nov 2007) | 7 lines
Fixed all the spin user function unit tests.
All the unit tests in the spin base class are calling functions from within
the object
self.spin_fns. In the spin user function unit test module, this has been
set to the
prompt.spin.Spin instantiated class.
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r3594 | bugman | 2007-11-18 22:46:22 +0100 (Sun, 18 Nov 2007) | 3 lines
Updated the unit tests for the generic_fns.spin module to use the spin base
class.
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r3595 | bugman | 2007-11-18 22:51:06 +0100 (Sun, 18 Nov 2007) | 3 lines
Updated the docstrings of all the unit tests now located in the spin base
class.
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r3596 | bugman | 2007-11-18 23:08:09 +0100 (Sun, 18 Nov 2007) | 6 lines
Wrote a function for returning all different types of data as an array.
This data will be used to test the proper behaviour of the user functions
to the handling of their
arguments.
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r3597 | bugman | 2007-11-18 23:13:44 +0100 (Sun, 18 Nov 2007) | 3 lines
Shifted the return_data_types() function into its own module for all prompt
tests to use.
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r3598 | bugman | 2007-11-18 23:36:43 +0100 (Sun, 18 Nov 2007) | 3 lines
Fixed the spin.copy() user function printout.
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r3599 | bugman | 2007-11-18 23:41:06 +0100 (Sun, 18 Nov 2007) | 5 lines
Fix for the return_data_types() function.
The reference to self has been removed.
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r3600 | bugman | 2007-11-18 23:42:27 +0100 (Sun, 18 Nov 2007) | 3 lines
Wrote a unit test for the proper failure of the spin.copy() user function
pipe_from argument.
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r3601 | bugman | 2007-11-18 23:44:12 +0100 (Sun, 18 Nov 2007) | 3 lines
Bug fix, RelaxNoneStrError is now imported.
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r3602 | bugman | 2007-11-18 23:46:49 +0100 (Sun, 18 Nov 2007) | 3 lines
Bug fix for the unit test of the pipe_from argument of the spin.copy() user
function.
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r3603 | bugman | 2007-11-18 23:52:05 +0100 (Sun, 18 Nov 2007) | 5 lines
Fixed the unit test of the pipe_from argument of the spin.copy() user
function.
The valid None and str arguments are being skipped to avoid the
assertRaises() method.
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r3604 | bugman | 2007-11-18 23:54:55 +0100 (Sun, 18 Nov 2007) | 3 lines
Wrote a unit test for the proper failure of the spin.copy() user function
spin_from argument.
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r3605 | bugman | 2007-11-18 23:55:54 +0100 (Sun, 18 Nov 2007) | 3 lines
Wrote a unit test for the proper failure of the spin.copy() user function
pipe_to argument.
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r3606 | bugman | 2007-11-19 00:00:18 +0100 (Mon, 19 Nov 2007) | 3 lines
Wrote a unit test for the proper failure of the spin.copy() user function
spin_to argument.
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r3607 | bugman | 2007-11-19 00:01:53 +0100 (Mon, 19 Nov 2007) | 5 lines
Fix for the last commit.
This is the spin.copy() unit test for the failure of the spin_to argument.
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r3608 | bugman | 2007-11-19 00:06:10 +0100 (Mon, 19 Nov 2007) | 3 lines
Fix for the spin.copy() unit test for the failure of the spin_to argument.
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r3609 | bugman | 2007-11-20 10:00:10 +0100 (Tue, 20 Nov 2007) | 3 lines
Created, by copying, a base class for testing both the generic_fns and
prompt molecule modules.
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r3610 | bugman | 2007-11-20 10:03:59 +0100 (Tue, 20 Nov 2007) | 3 lines
Updated the generic_fns.test_molecule unit test module to use the newly
created base class.
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r3611 | bugman | 2007-11-20 10:04:45 +0100 (Tue, 20 Nov 2007) | 3 lines
Removed a problematic and unused import.
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r3612 | bugman | 2007-11-20 10:05:17 +0100 (Tue, 20 Nov 2007) | 3 lines
Fixed a small bug.
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r3613 | bugman | 2007-11-20 10:06:43 +0100 (Tue, 20 Nov 2007) | 3 lines
Set up the residue functions to be used by the molecule unit tests (this is
a bad design)!
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r3614 | bugman | 2007-11-20 10:13:10 +0100 (Tue, 20 Nov 2007) | 3 lines
Added a unit test for the proper failure of the spin.create() user function
for the spin_num arg.
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r3615 | bugman | 2007-11-20 10:14:45 +0100 (Tue, 20 Nov 2007) | 3 lines
Added a unit test for the proper failure of the spin.create() user function
for the spin_name arg.
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r3616 | bugman | 2007-11-20 10:15:51 +0100 (Tue, 20 Nov 2007) | 3 lines
Fixed the spin.create() user function unit test of the spin_num arg.
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r3617 | bugman | 2007-11-20 10:17:52 +0100 (Tue, 20 Nov 2007) | 3 lines
Added a unit test for the proper failure of the spin.create() user function
for the res_id arg.
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r3618 | bugman | 2007-11-20 10:21:46 +0100 (Tue, 20 Nov 2007) | 3 lines
Fixed the spin.create() user function unit test of the res_id arg.
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r3619 | bugman | 2007-11-20 10:24:07 +0100 (Tue, 20 Nov 2007) | 3 lines
Added a unit test for the proper failure of the spin.delete() user function
for the spin_id arg.
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r3620 | bugman | 2007-11-20 10:25:38 +0100 (Tue, 20 Nov 2007) | 3 lines
Added a unit test for the proper failure of the spin.display() user
function for the spin_id arg.
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r3621 | bugman | 2007-11-20 10:27:14 +0100 (Tue, 20 Nov 2007) | 3 lines
Added Booleans to the data types passed into the user function argument
unit tests.
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r3622 | bugman | 2007-11-20 10:36:38 +0100 (Tue, 20 Nov 2007) | 3 lines
Added a unit test for the proper failure of the spin.rename() user function
for the spin_id arg.
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r3623 | bugman | 2007-11-20 10:37:28 +0100 (Tue, 20 Nov 2007) | 3 lines
Added a unit test for the proper failure of the spin.rename() user function
for the new_name arg.
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r3624 | bugman | 2007-11-20 10:39:18 +0100 (Tue, 20 Nov 2007) | 3 lines
Added a unit test for the proper failure of the spin.renumber() user
function for the spin_id arg.
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r3625 | bugman | 2007-11-20 10:41:43 +0100 (Tue, 20 Nov 2007) | 3 lines
Added a unit test for the proper failure of the spin.renumber() user
function for the new_number arg.
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r3626 | bugman | 2007-11-20 10:45:28 +0100 (Tue, 20 Nov 2007) | 3 lines
Set 'sys.ps3' in the prompt.spin unit tests to make them pass when using
unit_test_runner.py.
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r3627 | bugman | 2007-11-20 10:49:40 +0100 (Tue, 20 Nov 2007) | 3 lines
Created by copying a rudimentary set of user function argment tests for
prompt.molecule().
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r3628 | bugman | 2007-11-20 10:53:23 +0100 (Tue, 20 Nov 2007) | 4 lines
Implemented the pipe_from arg unit test for the molecule.copy() user
function.
M test_suite/unit_tests/prompt/test_molecule.py
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r3629 | bugman | 2007-11-20 10:54:56 +0100 (Tue, 20 Nov 2007) | 3 lines
Fixed a bug in the molecule.copy() user function caused by the pipe_from
argument.
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r3630 | bugman | 2007-11-20 10:56:42 +0100 (Tue, 20 Nov 2007) | 3 lines
Implemented the mol_from arg unit test for the molecule.copy() user
function.
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r3631 | bugman | 2007-11-20 10:57:49 +0100 (Tue, 20 Nov 2007) | 3 lines
Implemented the pipe_to arg unit test for the molecule.copy() user function.
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r3632 | bugman | 2007-11-20 10:58:44 +0100 (Tue, 20 Nov 2007) | 3 lines
Fixed a bug in the molecule.copy() user function, the pipe_to argument can
be None.
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r3633 | bugman | 2007-11-20 11:00:43 +0100 (Tue, 20 Nov 2007) | 3 lines
Implemented the mol_to arg unit test for the molecule.copy() user function.
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r3634 | bugman | 2007-11-20 11:03:28 +0100 (Tue, 20 Nov 2007) | 3 lines
Implemented the mol_name arg unit test for the molecule.create() user
function.
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r3635 | bugman | 2007-11-20 11:04:27 +0100 (Tue, 20 Nov 2007) | 3 lines
Implemented the mol_id arg unit test for the molecule.delete() user
function.
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r3636 | bugman | 2007-11-20 11:21:27 +0100 (Tue, 20 Nov 2007) | 3 lines
Implemented the mol_id arg unit test for the molecule.display() user
function.
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r3637 | bugman | 2007-11-20 11:22:17 +0100 (Tue, 20 Nov 2007) | 3 lines
Bug fix for the molecule.display() user function - mol_id can be None!
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r3638 | bugman | 2007-11-20 11:24:23 +0100 (Tue, 20 Nov 2007) | 3 lines
Implemented the mol_id arg unit test for the molecule.rename() user
function.
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r3639 | bugman | 2007-11-20 11:25:18 +0100 (Tue, 20 Nov 2007) | 3 lines
Bug fix for the molecule.rename() user function - mol_id should be a str
not an int!
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r3640 | bugman | 2007-11-20 11:26:09 +0100 (Tue, 20 Nov 2007) | 3 lines
Implemented the new_name arg unit test for the molecule.rename() user
function.
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r3641 | bugman | 2007-11-20 11:27:32 +0100 (Tue, 20 Nov 2007) | 3 lines
Removed the 2 molecule.renumber() tests (currently spin.renumber()) as
molecules aren't numbered.
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r3642 | bugman | 2007-11-20 11:30:08 +0100 (Tue, 20 Nov 2007) | 5 lines
Bug fix in the molecule.rename() user function.
The mol_num argument does not exist, it should be mol_id!
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r3643 | bugman | 2007-11-20 11:30:40 +0100 (Tue, 20 Nov 2007) | 3 lines
Fixes and improvements to the docstring of the molecule.rename() user
function.
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r3644 | bugman | 2007-11-20 11:31:28 +0100 (Tue, 20 Nov 2007) | 5 lines
Another bug fix for the molecule.rename() user function.
The function generic_fns.molecule.create() was being called!!!
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r3645 | bugman | 2007-11-20 11:34:25 +0100 (Tue, 20 Nov 2007) | 4 lines
[... 1735 lines stripped ...]
r4142 - /1.2/