relax SVN archive

Bug fix.

The value argment to the value.set() user function has been changed to 'val'. The argument was
clashing with the modules because the names were the same.

Implemented the val unit test for the value.set() user function.

Added the infrastructure for the user function arg unit tests of prompt.value.

Fixed the program intro catch Windows Vista.

Manually merged r4140 of the 1.2.12 tag.

The command used was:
svn merge -r4139:4140 svn+ssh://bugman@.../svn/relax/tags/1.2.12

.....
r4140 | bugman | 2007-12-09 12:33:01 +0100 (Sun, 09 Dec 2007) | 3 lines
Changed paths:
M /tags/1.2.12/sconstruct

Fixed the 'sconstruct' file to handle Windows Vista.
.....

Manually merged r4140 of the 1.2.12 tag.

The command used was:
svn merge -r4139:4140 svn+ssh://bugman@.../svn/relax/tags/1.2.12

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r4140 | bugman | 2007-12-09 12:33:01 +0100 (Sun, 09 Dec 2007) | 3 lines
Changed paths:
M /tags/1.2.12/sconstruct

Fixed the 'sconstruct' file to handle Windows Vista.
.....

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@.../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!
.....
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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@.../svn/relax/1.2/specific_fns/model_free.py specific_fns/model_free/model_free.py

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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

generic_fns.residue is now placed into the namespace of the prompt.molecule unit tests.
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r3646 | bugman | 2007-11-20 11:38:13 +0100 (Tue, 20 Nov 2007) | 5 lines

Bug fix in the molecule.display() user function.

The test for None or a str should use 'and', not 'or'!
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r3647 | bugman | 2007-11-20 11:40:37 +0100 (Tue, 20 Nov 2007) | 5 lines

Bug fix for the molecule.copy() user function.

The arg 'mol_to' can be None!
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r3648 | bugman | 2007-11-20 11:46:34 +0100 (Tue, 20 Nov 2007) | 5 lines

Bug fix for the mol_to arg unit test of the molecule.copy() user function.

The relax_data_store data required was not being setup.
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r3649 | bugman | 2007-11-20 11:48:03 +0100 (Tue, 20 Nov 2007) | 5 lines

Bug fix for the mol_to arg unit test of the molecule.copy() user function.

The mol_to arg can be None!
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r3650 | bugman | 2007-11-20 11:48:56 +0100 (Tue, 20 Nov 2007) | 3 lines

Fixed the printout of the molecule.copy() user function.
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r3651 | bugman | 2007-11-20 11:49:25 +0100 (Tue, 20 Nov 2007) | 3 lines

Fixed the printout of the molecule.rename() user function.
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r3652 | bugman | 2007-11-20 12:03:03 +0100 (Tue, 20 Nov 2007) | 3 lines

Created, by copying, the base class for the generic_fns and prompt residue module unit tests.
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r3653 | bugman | 2007-11-20 13:25:41 +0100 (Tue, 20 Nov 2007) | 3 lines

Updated the generic_fns.test_residue unit test module to use the newly created base class.
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r3654 | bugman | 2007-11-20 13:28:06 +0100 (Tue, 20 Nov 2007) | 3 lines

A number of fixes to the base class for residue unit tests so that the tests now all work.
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r3655 | bugman | 2007-11-20 13:31:25 +0100 (Tue, 20 Nov 2007) | 3 lines

Created by copying the base for the unit tests of the residue user functions.
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r3656 | bugman | 2007-11-20 13:32:15 +0100 (Tue, 20 Nov 2007) | 3 lines

Fixed the docstring for the TestCase subclass for the prompt.molecule unit tests.
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r3657 | bugman | 2007-11-20 13:32:33 +0100 (Tue, 20 Nov 2007) | 3 lines

Fixed the docstring for the TestCase subclass for the prompt.spin unit tests.
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r3658 | bugman | 2007-11-20 13:35:21 +0100 (Tue, 20 Nov 2007) | 3 lines

Implemented the pipe_from arg unit test for the residue.copy() user function.
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r3659 | bugman | 2007-11-20 13:35:57 +0100 (Tue, 20 Nov 2007) | 3 lines

Implemented the res_from arg unit test for the residue.copy() user function.
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r3660 | bugman | 2007-11-20 13:36:43 +0100 (Tue, 20 Nov 2007) | 3 lines

Implemented the pipe_to arg unit test for the residue.copy() user function.
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r3661 | bugman | 2007-11-20 13:37:17 +0100 (Tue, 20 Nov 2007) | 3 lines

Implemented the res_to arg unit test for the residue.copy() user function.
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r3662 | bugman | 2007-11-20 13:38:28 +0100 (Tue, 20 Nov 2007) | 3 lines

Implemented the res_num arg unit test for the residue.create() user function.
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r3663 | bugman | 2007-11-20 13:38:51 +0100 (Tue, 20 Nov 2007) | 3 lines

Implemented the res_name arg unit test for the residue.create() user function.
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r3664 | bugman | 2007-11-20 13:39:55 +0100 (Tue, 20 Nov 2007) | 3 lines

Implemented the mol_id arg unit test for the residue.create() user function.
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r3665 | bugman | 2007-11-20 13:40:35 +0100 (Tue, 20 Nov 2007) | 3 lines

Implemented the res_id arg unit test for the residue.create() user function.
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r3666 | bugman | 2007-11-20 13:42:34 +0100 (Tue, 20 Nov 2007) | 3 lines

Implemented the res_id arg unit test for the residue.display() user function.
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r3667 | bugman | 2007-11-20 13:43:37 +0100 (Tue, 20 Nov 2007) | 3 lines

Implemented the res_id arg unit test for the residue.rename() user function.
........
r3668 | bugman | 2007-11-20 13:44:02 +0100 (Tue, 20 Nov 2007) | 3 lines

Implemented the new_name arg unit test for the residue.rename() user function.
........
r3669 | bugman | 2007-11-20 13:44:42 +0100 (Tue, 20 Nov 2007) | 3 lines

Implemented the res_id arg unit test for the residue.renumber() user function.
........
r3670 | bugman | 2007-11-20 13:45:32 +0100 (Tue, 20 Nov 2007) | 3 lines

Implemented the new_number arg unit test for the residue.renumber() user function.
........
r3671 | bugman | 2007-11-20 13:46:09 +0100 (Tue, 20 Nov 2007) | 5 lines

Bug fix for the new_number arg unit test for the residue.renumber() user function.

The test was named incorrectly.
........
r3672 | bugman | 2007-11-20 13:46:37 +0100 (Tue, 20 Nov 2007) | 5 lines

Bug fix for the new_number arg unit test for the spin.renumber() user function.

The test was named incorrectly.
........
r3673 | bugman | 2007-11-20 13:49:33 +0100 (Tue, 20 Nov 2007) | 5 lines

Bug fix for the residue.renumber() user function.

The res_id was being tested as an int and the new_number as a str. This is the wrong way around!
........
r3674 | bugman | 2007-11-20 13:56:17 +0100 (Tue, 20 Nov 2007) | 6 lines

Another bug fix for the residue.renumber() user function.

The non-existent variable 'res_num' was being passed on to the generic code, whereas 'res_id' should
have been.
........
r3675 | bugman | 2007-11-20 13:58:05 +0100 (Tue, 20 Nov 2007) | 5 lines

Yet another bug fix for residue.renumber().

This one was because generic_fns.residue.create() was being called!!!
........
r3676 | bugman | 2007-11-20 13:58:48 +0100 (Tue, 20 Nov 2007) | 3 lines

residue.rename() user function docstring whitespace fix.
........
r3677 | bugman | 2007-11-20 16:04:19 +0100 (Tue, 20 Nov 2007) | 5 lines

Bug fix for the residue.copy() user function.

The pipe_from argument can be None.
........
r3678 | bugman | 2007-11-20 16:05:08 +0100 (Tue, 20 Nov 2007) | 5 lines

Bug fix for the residue.copy() user function.

The pipe_to argument can also be None.
........
r3679 | bugman | 2007-11-20 16:06:53 +0100 (Tue, 20 Nov 2007) | 5 lines

Bug fix for the residue.rename() user function.

The res_id argument was being tested as an int whereas it is a str.
........
r3680 | bugman | 2007-11-20 16:08:06 +0100 (Tue, 20 Nov 2007) | 5 lines

Bug fix for the residue.rename() user function.

The variable 'res_num' was been used when it should have been 'res_id'.
........
r3681 | bugman | 2007-11-20 16:08:53 +0100 (Tue, 20 Nov 2007) | 5 lines

Bug fix for the residue.rename() user function.

The function generic_fns.residue.create() was being called instead!
........
r3682 | bugman | 2007-11-20 16:09:55 +0100 (Tue, 20 Nov 2007) | 5 lines

Bug fix for the residue.display() user function.

The res_id argument is allowed to be None.
........
r3683 | bugman | 2007-11-20 16:10:28 +0100 (Tue, 20 Nov 2007) | 3 lines

Added the missing import of RelaxNoneStrError.
........
r3684 | bugman | 2007-11-20 16:13:31 +0100 (Tue, 20 Nov 2007) | 5 lines

Bug fix for the residue.copy() user function.

The res_to argument can be None.
........
r3685 | bugman | 2007-11-20 16:22:56 +0100 (Tue, 20 Nov 2007) | 5 lines

Bug fix for the RelaxNoPipeError error class.

The pipe argument of 0 was not being caught.
........
r3686 | bugman | 2007-11-20 16:47:43 +0100 (Tue, 20 Nov 2007) | 5 lines

Bug fix for the residue.copy() user function.

In the test for 'pipe_to' being None, the 'pipe_from' argument was being checked instead!
........
r3687 | bugman | 2007-11-20 16:51:39 +0100 (Tue, 20 Nov 2007) | 5 lines

Bug fix for the residue.create() user function.

Added the missing 'mol_id' argument to the residue.create() user function.
........
r3688 | bugman | 2007-11-20 16:52:51 +0100 (Tue, 20 Nov 2007) | 3 lines

Fixed the print out of the residue.renumber() user function.
........
r3689 | bugman | 2007-11-20 16:53:14 +0100 (Tue, 20 Nov 2007) | 3 lines

Fixed the print out of the residue.copy() user function.
........
r3690 | bugman | 2007-11-20 16:53:58 +0100 (Tue, 20 Nov 2007) | 3 lines

Fixed the print out of the residue.create() user function.
........
r3691 | bugman | 2007-11-20 16:54:38 +0100 (Tue, 20 Nov 2007) | 3 lines

Fixed the print out of the residue.rename() user function.
........
r3695 | bugman | 2007-11-20 17:30:44 +0100 (Tue, 20 Nov 2007) | 3 lines

Made the 'Debug' flag accessible to the functions of the relax interpreter module.
........
r3697 | bugman | 2007-11-20 17:38:03 +0100 (Tue, 20 Nov 2007) | 3 lines

Bug fix to make the test suite work again.
........
r3698 | bugman | 2007-11-20 17:41:59 +0100 (Tue, 20 Nov 2007) | 3 lines

Added the framework for implementing unit tests for the generic_fns.state module.
........
r3699 | bugman | 2007-11-20 17:48:38 +0100 (Tue, 20 Nov 2007) | 3 lines

Added a unit test for the generic_fns.state.save() function.
........
r3700 | bugman | 2007-11-20 17:50:41 +0100 (Tue, 20 Nov 2007) | 6 lines

Change of the internal structure of the generic_fns.state module.

The State class has been eliminated and its methods load() and save() have been converted to module
functions.
........
r3701 | bugman | 2007-11-20 17:51:52 +0100 (Tue, 20 Nov 2007) | 3 lines

Removed the old State class from the namespace of 'self.relax.generic'.
........
r3702 | bugman | 2007-11-20 17:55:36 +0100 (Tue, 20 Nov 2007) | 3 lines

Renamed the relax io module to relax_io as it clashes with the Python io module.
........
r3703 | bugman | 2007-11-20 17:57:19 +0100 (Tue, 20 Nov 2007) | 5 lines

Modified the unit tests for generic_fns.state to import from relax_io.

The function open_write_file is now imported (although it doesn't currently exist).
........
r3704 | bugman | 2007-11-20 17:57:47 +0100 (Tue, 20 Nov 2007) | 3 lines

The open_read_file function is now imported as well.
........
r3705 | bugman | 2007-11-20 17:59:04 +0100 (Tue, 20 Nov 2007) | 3 lines

Added some comments for the import statements.
........
r3706 | bugman | 2007-11-20 18:03:16 +0100 (Tue, 20 Nov 2007) | 6 lines

Fix for the renaming of io.py to relax_io.py.

The module renaming has been taken into account as well as the eventual removal of the IO class and
the conversion from class methods to module functions.
........
r3707 | bugman | 2007-11-20 18:07:13 +0100 (Tue, 20 Nov 2007) | 3 lines

Added a simple docstring to the relax_io module.
........
r3708 | bugman | 2007-11-20 18:08:21 +0100 (Tue, 20 Nov 2007) | 3 lines

Converted the log class method to a function.
........
r3709 | bugman | 2007-11-20 18:09:41 +0100 (Tue, 20 Nov 2007) | 3 lines

Converted the open_read_file class method to a function.
........
r3710 | bugman | 2007-11-20 18:12:07 +0100 (Tue, 20 Nov 2007) | 3 lines

Converted the open_write_file class method into a module function.
........
r3711 | bugman | 2007-11-20 18:20:22 +0100 (Tue, 20 Nov 2007) | 3 lines

Renamed relax_io.mkdir to relax_io.mkdir_nofail and converted it from a class method to a function.
........
r3712 | bugman | 2007-11-20 18:22:06 +0100 (Tue, 20 Nov 2007) | 3 lines

Renamed the file_path class method to the get_file_path module function.
........
r3713 | bugman | 2007-11-20 18:24:30 +0100 (Tue, 20 Nov 2007) | 3 lines

Bug fix for both generic_fns.state unit tests.
........
r3715 | bugman | 2007-11-20 18:49:27 +0100 (Tue, 20 Nov 2007) | 3 lines

A temporary fix to the broken pickling of the relax data storage singleton.
........
r3716 | bugman | 2007-11-20 19:09:37 +0100 (Tue, 20 Nov 2007) | 3 lines

Added a unit test for the generic_fns.state.load() function.
........
r3717 | bugman | 2007-11-20 19:11:18 +0100 (Tue, 20 Nov 2007) | 3 lines

Fix for the generic_fns.state.load() function.
........
r3718 | bugman | 2007-11-20 19:13:42 +0100 (Tue, 20 Nov 2007) | 3 lines

Improved the docstring of the generic_fns.state.load() unit test.
........
r3719 | bugman | 2007-11-20 19:14:17 +0100 (Tue, 20 Nov 2007) | 3 lines

Improved the docstring of the generic_fns.state.save() unit test.
........
r3721 | bugman | 2007-11-20 19:23:32 +0100 (Tue, 20 Nov 2007) | 3 lines

Added a framework for the unit tests of the relax_io module.
........
r3722 | bugman | 2007-11-20 19:28:44 +0100 (Tue, 20 Nov 2007) | 3 lines

Added a unit test to check that some file paths are unmodified by relax_io.get_file_path().
........
r3723 | bugman | 2007-11-20 19:32:19 +0100 (Tue, 20 Nov 2007) | 3 lines

Unit test for the modification of file paths by relax_io.get_file_path when a directory is supplied.
........
r3724 | bugman | 2007-11-20 19:32:55 +0100 (Tue, 20 Nov 2007) | 3 lines

Improved the docstring of the unit test for relax_io.get_file_path().
........
r3725 | bugman | 2007-11-20 19:35:34 +0100 (Tue, 20 Nov 2007) | 3 lines

Added a unit test for relax_io.get_file_path when '~' is present in the path.
........
r3726 | bugman | 2007-11-20 19:39:07 +0100 (Tue, 20 Nov 2007) | 3 lines

Renamed the load() and save() functions of generic_fns.state to load_state() and save_state().
........
r3727 | bugman | 2007-11-20 19:41:01 +0100 (Tue, 20 Nov 2007) | 5 lines

Fixed the tearDown() method of the generic_fns.state unit tests.

The method no longer fails if the file 'test.bz2' does not exist.
........
r3728 | bugman | 2007-11-20 19:42:44 +0100 (Tue, 20 Nov 2007) | 3 lines

Fixed the unit tests of generic_fns.state to use the newly renamed methods of that module.
........
r3730 | bugman | 2007-11-20 23:01:11 +0100 (Tue, 20 Nov 2007) | 3 lines

Added one additional object to the data storage singleton for testing.
........
r3731 | bugman | 2007-11-20 23:17:56 +0100 (Tue, 20 Nov 2007) | 6 lines

Fixed the generic_fns.state.load_state() function.

The relax data storage singleton is new being, object by object, recreated from the initial state
as cleared by its __reset__ method.
........
r3733 | bugman | 2007-11-20 23:26:38 +0100 (Tue, 20 Nov 2007) | 3 lines

Created by copying a base class for testing both the prompt.state and generic_fns.state modules.
........
r3734 | bugman | 2007-11-20 23:36:39 +0100 (Tue, 20 Nov 2007) | 3 lines

The generic_fns.state module unit test code is now using the base class.
........
r3735 | bugman | 2007-11-20 23:41:25 +0100 (Tue, 20 Nov 2007) | 6 lines

Renamed all the unit test directories to start with an underscore.

This is to fix issues with the importing of modules. These directories were clashing with the real
relax directories, making the relax modules in them inaccessible to certain unit tests.
........
r3736 | bugman | 2007-11-20 23:42:48 +0100 (Tue, 20 Nov 2007) | 3 lines

Removed some unused imports.
........
r3737 | bugman | 2007-11-20 23:43:19 +0100 (Tue, 20 Nov 2007) | 3 lines

Removed some more unused imports.
........
r3738 | bugman | 2007-11-20 23:49:43 +0100 (Tue, 20 Nov 2007) | 3 lines

A few more unused imported eliminated.
........
r3739 | bugman | 2007-11-20 23:58:12 +0100 (Tue, 20 Nov 2007) | 5 lines

Added the framework for the unit tests of the prompt.state module.

This inherits 2 unit tests already (which pass).
........
r3740 | bugman | 2007-11-21 00:05:14 +0100 (Wed, 21 Nov 2007) | 3 lines

Implemented the file arg unit test for the state.load() user function.
........
r3741 | bugman | 2007-11-21 00:08:36 +0100 (Wed, 21 Nov 2007) | 3 lines

Implemented the dir arg unit test for the state.load() user function.
........
r3742 | bugman | 2007-11-21 00:09:32 +0100 (Wed, 21 Nov 2007) | 3 lines

Fix for the previously committed unit test.
........
r3743 | bugman | 2007-11-21 00:11:15 +0100 (Wed, 21 Nov 2007) | 3 lines

Shifted the prompt.state.State class instance into the unit test class namespace.
........
r3744 | bugman | 2007-11-21 00:13:29 +0100 (Wed, 21 Nov 2007) | 3 lines

Placed the generic.state module into the unit test class namespace.
........
r3745 | bugman | 2007-11-21 00:14:05 +0100 (Wed, 21 Nov 2007) | 3 lines

Incorrect comment fix.
........
r3746 | bugman | 2007-11-21 00:22:26 +0100 (Wed, 21 Nov 2007) | 3 lines

Updated the prompt.state and generic_fns.state unit tests to test the correct functions.
........
r3747 | bugman | 2007-11-21 00:24:12 +0100 (Wed, 21 Nov 2007) | 3 lines

Fixed the argument unit tests for the state.load() user function.
........
r3748 | bugman | 2007-11-21 00:27:28 +0100 (Wed, 21 Nov 2007) | 3 lines

Fixed the state.load() and state.save() user functions to properly call the generic_fns functions.
........
r3749 | bugman | 2007-11-21 00:36:42 +0100 (Wed, 21 Nov 2007) | 3 lines

Converted the arguments into keyword arguments to try to fix these unit tests.
........
r3750 | bugman | 2007-11-21 00:49:24 +0100 (Wed, 21 Nov 2007) | 3 lines

Fix for the nasty function argument bug!
........
r3751 | bugman | 2007-11-21 00:51:39 +0100 (Wed, 21 Nov 2007) | 3 lines

Implemented the file arg unit test for the state.save() user function.
........
r3752 | bugman | 2007-11-21 00:52:40 +0100 (Wed, 21 Nov 2007) | 5 lines

Implemented the dir arg unit test for the state.save() user function.

And a fix for the file arg unit test of state.save().
........
r3753 | bugman | 2007-11-21 00:56:43 +0100 (Wed, 21 Nov 2007) | 3 lines

Implemented the force arg unit test for the state.save() user function.
........
r3754 | bugman | 2007-11-21 00:57:08 +0100 (Wed, 21 Nov 2007) | 3 lines

Changed the int data types so none would be 0 or 1 (the bin types).
........
r3755 | bugman | 2007-11-21 01:00:41 +0100 (Wed, 21 Nov 2007) | 3 lines

Implemented the compress_type arg unit test for the state.save() user function.
........
r3757 | bugman | 2007-11-21 12:33:10 +0100 (Wed, 21 Nov 2007) | 3 lines

Added dictionaries to the list of diverse objects for testing the behaviour of user function args.
........
r3773 | bugman | 2007-11-21 23:42:04 +0100 (Wed, 21 Nov 2007) | 5 lines

Removed the user function sequence.delete() from the redesign document.

This function is redundant and is of no use. It's just a reset.
........
r3774 | bugman | 2007-11-21 23:54:27 +0100 (Wed, 21 Nov 2007) | 3 lines

For the test suite, the Ap4Aase NOE data collected at 600 MHz has been added to the repository.
........
r3775 | bugman | 2007-11-21 23:57:08 +0100 (Wed, 21 Nov 2007) | 3 lines

Added the base class for the unit tests of the prompt.sequence and generic_fns.sequence modules.
........
r3776 | bugman | 2007-11-22 00:00:01 +0100 (Thu, 22 Nov 2007) | 3 lines

Added the framework and TestCase class for the unit tests of the prompt.sequence module.
........
r3777 | bugman | 2007-11-22 00:01:27 +0100 (Thu, 22 Nov 2007) | 3 lines

Fixed the base class name!
........
r3778 | bugman | 2007-11-22 00:03:47 +0100 (Thu, 22 Nov 2007) | 11 lines

Removed all the user functions of prompt.sequence which are not in the redesign document.

The axed user functions are:
sequence.add()
sequence.copy()
sequnece.delete()
sequence.sort()

These no longer have any use.
........
r3779 | bugman | 2007-11-22 00:40:09 +0100 (Thu, 22 Nov 2007) | 6 lines

Converted the sequence.read() user function to the new relax design.

This function now allows for sequences of molecules, residues, and spins to be read into the
program.
........
r3780 | bugman | 2007-11-22 00:48:50 +0100 (Thu, 22 Nov 2007) | 3 lines

Added a unit test for the reading of the amino acid sequence out of a protein NOE data file.
........
r3781 | bugman | 2007-11-22 00:49:57 +0100 (Thu, 22 Nov 2007) | 3 lines

Bug fix for the prompt.sequence module, the correct RelaxErrors are now imported.
........
r3782 | bugman | 2007-11-22 00:51:05 +0100 (Thu, 22 Nov 2007) | 3 lines

A bug fix for the sequence.read() user function argument checking code.
........
r3783 | bugman | 2007-11-22 00:53:24 +0100 (Thu, 22 Nov 2007) | 3 lines

Implemented the file arg unit test for the sequence.read() user function.
........
r3784 | bugman | 2007-11-22 00:56:07 +0100 (Thu, 22 Nov 2007) | 3 lines

Implemented the dir arg unit test for the sequence.read() user function.
........
r3785 | bugman | 2007-11-22 00:59:21 +0100 (Thu, 22 Nov 2007) | 3 lines

Implemented the mol_name_col arg unit test for the sequence.read() user function.
........
r3786 | bugman | 2007-11-22 01:00:07 +0100 (Thu, 22 Nov 2007) | 3 lines

Implemented the res_num_col arg unit test for the sequence.read() user function.
........
r3787 | bugman | 2007-11-22 01:00:40 +0100 (Thu, 22 Nov 2007) | 3 lines

Implemented the res_name_col arg unit test for the sequence.read() user function.
........
r3788 | bugman | 2007-11-22 01:01:22 +0100 (Thu, 22 Nov 2007) | 3 lines

Implemented the spin_num_col arg unit test for the sequence.read() user function.
........
r3789 | bugman | 2007-11-22 01:02:19 +0100 (Thu, 22 Nov 2007) | 3 lines

Implemented the spin_name_col arg unit test for the sequence.read() user function.
........
r3790 | bugman | 2007-11-22 01:03:06 +0100 (Thu, 22 Nov 2007) | 3 lines

Bug fix for the argument checking of the sequence.read() user function.
........
r3791 | bugman | 2007-11-22 01:05:15 +0100 (Thu, 22 Nov 2007) | 3 lines

Implemented the sep arg unit test for the sequence.read() user function.
........
r3792 | bugman | 2007-11-22 01:14:22 +0100 (Thu, 22 Nov 2007) | 3 lines

Added the framework for the unit tests of the generic_fns.sequence module.
........
r3793 | bugman | 2007-11-22 10:23:43 +0100 (Thu, 22 Nov 2007) | 6 lines

Modified the state.load() and state.save() unit tests to use a tmp file descriptor.

Currently these functions only allow a string file name and don't handle file descriptors, but this
will be changed.
........
r3794 | bugman | 2007-11-22 10:30:34 +0100 (Thu, 22 Nov 2007) | 5 lines

Created the RelaxStrFileError.

This is for when an argument can either be a string or file descriptor.
........
r3795 | bugman | 2007-11-22 10:36:30 +0100 (Thu, 22 Nov 2007) | 3 lines

Modified both state.load() and state.save() to accept file descriptor objects.
........
r3796 | bugman | 2007-11-22 10:37:49 +0100 (Thu, 22 Nov 2007) | 3 lines

Modified the arg unit tests of state.load() and state.save() to use 'state' rather than 'file'.
........
r3797 | bugman | 2007-11-22 10:39:53 +0100 (Thu, 22 Nov 2007) | 3 lines

Modified the base class unit tests of state.load() and state.save() to use the arg 'state'.
........
r3798 | bugman | 2007-11-22 10:41:48 +0100 (Thu, 22 Nov 2007) | 3 lines

More fixes for the state.load() and state.save() arg unit tests.
........
r3799 | bugman | 2007-11-22 10:43:31 +0100 (Thu, 22 Nov 2007) | 3 lines

Changed the 'file' arg to 'state' in the functions of the generic_fns.state module.
........
r3800 | bugman | 2007-11-22 10:49:32 +0100 (Thu, 22 Nov 2007) | 3 lines

Modified open_read_file() and open_write_file() to handle file descriptors, by returning the arg.
........
r3801 | bugman | 2007-11-22 11:01:34 +0100 (Thu, 22 Nov 2007) | 3 lines

Created a simple saved program state file for the state.load() unit tests.
........
r3802 | bugman | 2007-11-22 11:06:46 +0100 (Thu, 22 Nov 2007) | 5 lines

Modified the state base class unit tests to use the new saved state file.

This file is located in test_suite/shared_data/saved_states/.
........
r3803 | bugman | 2007-11-22 11:09:55 +0100 (Thu, 22 Nov 2007) | 3 lines

Changed all the 'dir' args to 'dir_name' in the state.load() and state.save() user functions.
........
r3804 | bugman | 2007-11-22 11:10:42 +0100 (Thu, 22 Nov 2007) | 3 lines

Changed all the 'dir' args to 'dir_name' in the generic_fns.state module.
........
r3805 | bugman | 2007-11-22 11:11:21 +0100 (Thu, 22 Nov 2007) | 3 lines

Fix for the load of program state unit test to use the 'dir_name' arg instead of 'dir'.
........
r3806 | bugman | 2007-11-22 11:12:27 +0100 (Thu, 22 Nov 2007) | 3 lines

Fixed the arg unit tests of state.load() and state.save() to use 'dir_name' rather than 'dir'.
........
r3807 | bugman | 2007-11-22 11:14:25 +0100 (Thu, 22 Nov 2007) | 3 lines

Fixed the directory path for the saved program state (too many '..').
........
r3809 | bugman | 2007-11-22 11:24:17 +0100 (Thu, 22 Nov 2007) | 5 lines

Removed the return_data_types() function and converted data_types into a permanent module constant.

This is in preparation to add file descriptors to the list.
........
r3810 | bugman | 2007-11-22 11:26:04 +0100 (Thu, 22 Nov 2007) | 3 lines

Added the tmpfile() file descriptor to the 'DATA_TYPES' array.
........
r3811 | bugman | 2007-11-22 11:27:39 +0100 (Thu, 22 Nov 2007) | 3 lines

Alphabetically sorted the initialisation of DATA_TYPES to bring some order to the chaos.
........
r3812 | bugman | 2007-11-22 11:31:00 +0100 (Thu, 22 Nov 2007) | 3 lines

Fixed all user function arg unit tests to use the new DATA_TYPES module array.
........
r3813 | bugman | 2007-11-22 11:37:47 +0100 (Thu, 22 Nov 2007) | 3 lines

Updated the sequence.write() user function for the new relax design.
........
r3814 | bugman | 2007-11-22 11:40:59 +0100 (Thu, 22 Nov 2007) | 3 lines

Added unit tests for all arguments of the sequence.write() user function.
........
r3815 | bugman | 2007-11-22 12:11:30 +0100 (Thu, 22 Nov 2007) | 3 lines

Wrote a unit test for the writing of an amino acid sequence to file.
........
r3816 | bugman | 2007-11-22 12:21:41 +0100 (Thu, 22 Nov 2007) | 3 lines

Added a new RelaxError for invalid sequence data.
........
r3817 | bugman | 2007-11-22 12:22:21 +0100 (Thu, 22 Nov 2007) | 3 lines

Small fix for RelaxInvalidSeqError.
........
r3818 | bugman | 2007-11-22 12:36:59 +0100 (Thu, 22 Nov 2007) | 3 lines

Started to implement the read, sequence_exists, and valid_sequence functions.
........
r3819 | bugman | 2007-11-22 12:39:37 +0100 (Thu, 22 Nov 2007) | 3 lines

Updated the extract_data() for the new relax design (converted from a class method to a function).
........
r3820 | bugman | 2007-11-22 17:16:52 +0100 (Thu, 22 Nov 2007) | 3 lines

Fixed the path in the unit test for reading a protein sequence.
........
r3821 | bugman | 2007-11-22 17:18:45 +0100 (Thu, 22 Nov 2007) | 3 lines

Added the missing import of relax_io.strip.
........
r3822 | bugman | 2007-11-22 17:19:25 +0100 (Thu, 22 Nov 2007) | 3 lines

Converted the strip class method to a module function.
........
r3823 | bugman | 2007-11-22 17:25:44 +0100 (Thu, 22 Nov 2007) | 3 lines

Fix for the generic_fns.sequence.read() function.
........
r3824 | bugman | 2007-11-22 17:40:25 +0100 (Thu, 22 Nov 2007) | 2 lines

Renamed valid_sequence() to validate_sequence() and called it from within the read() fn.
........
r3825 | bugman | 2007-11-22 17:49:25 +0100 (Thu, 22 Nov 2007) | 3 lines

Completed the generic_fns.sequence.read() function.
........
r3826 | bugman | 2007-11-22 17:50:39 +0100 (Thu, 22 Nov 2007) | 3 lines

Bug fix for the generic_fns.sequence.validate_sequence() function.
........
r3827 | bugman | 2007-11-22 17:52:41 +0100 (Thu, 22 Nov 2007) | 5 lines

Another bug fix for the generic_fns.sequence.validate_sequence() function.

The mol, res, and spin column numbers are now passed into it.
........
r3828 | bugman | 2007-11-22 17:55:19 +0100 (Thu, 22 Nov 2007) | 3 lines

Updated the docstring of the generic_fns.sequence.validate_sequence() function.
........
r3829 | bugman | 2007-11-22 18:01:07 +0100 (Thu, 22 Nov 2007) | 3 lines

Updated the docstring of generic_fns.sequence.read(). This is now in the epydoc format.
........
r3830 | bugman | 2007-11-22 18:02:47 +0100 (Thu, 22 Nov 2007) | 3 lines

Fix for the unit test of reading of the amino acid sequence out of a protein NOE data file.
........
r3831 | bugman | 2007-11-22 18:09:57 +0100 (Thu, 22 Nov 2007) | 5 lines

Bug fix for the generic_fns.sequence.read() function, it's now functional!

The empty first containers are now taken into account.
........
r3832 | bugman | 2007-11-22 18:11:35 +0100 (Thu, 22 Nov 2007) | 3 lines

Actually the read() function was not functional!!! So this is another fix.
........
r3833 | bugman | 2007-11-22 18:14:04 +0100 (Thu, 22 Nov 2007) | 3 lines

Final fix for the unit test of reading of the amino acid sequence out of a protein NOE data file.
........
r3836 | bugman | 2007-11-22 18:31:25 +0100 (Thu, 22 Nov 2007) | 6 lines

Bug fix for the unit test for reading of the amino acid sequence out of a protein NOE data file.

The path has been changed to a relative path so that the unit tests can be run by themselves or as
part of relax.
........
r3837 | bugman | 2007-11-22 18:33:00 +0100 (Thu, 22 Nov 2007) | 6 lines

Bug fix for the unit test for the unpickling and restoration of the relax data storage singleton.

The path has been changed to a relative path so that the unit tests can be run by themselves or as
part of relax.
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r3838 | bugman | 2007-11-22 19:07:07 +0100 (Thu, 22 Nov 2007) | 3 lines

A temporary fix for the RelaxWarning message formatting.
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r3840 | bugman | 2007-11-23 13:52:34 +0100 (Fri, 23 Nov 2007) | 3 lines

Fixed the system test for loading the of amino acid sequence data.
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r3841 | bugman | 2007-11-23 13:53:55 +0100 (Fri, 23 Nov 2007) | 3 lines

Updated the system test of loading a sequence from a PDB file to use the new relax design.
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r3842 | bugman | 2007-11-23 13:55:04 +0100 (Fri, 23 Nov 2007) | 3 lines

Updated the copyright notice.
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r3843 | bugman | 2007-11-23 15:16:25 +0100 (Fri, 23 Nov 2007) | 3 lines

Updated all the system tests to use the new relax design!
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r3844 | bugman | 2007-11-23 15:28:27 +0100 (Fri, 23 Nov 2007) | 3 lines

Removed the now useless methods of the generic_fns.sequence.Sequence class.
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r3845 | bugman | 2007-11-23 15:29:47 +0100 (Fri, 23 Nov 2007) | 3 lines

Converted the diplay() class method to a module function.
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r3846 | bugman | 2007-11-23 15:31:22 +0100 (Fri, 23 Nov 2007) | 3 lines

Converted the write() class method to a module function.
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r3847 | bugman | 2007-11-23 15:32:23 +0100 (Fri, 23 Nov 2007) | 3 lines

Converted the load_PDB_sequence() class method to a module function.
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r3848 | bugman | 2007-11-23 15:33:37 +0100 (Fri, 23 Nov 2007) | 3 lines

Removed the import of the now non-existant Sequence class.
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r3849 | bugman | 2007-11-23 15:38:54 +0100 (Fri, 23 Nov 2007) | 3 lines

The display() function now works (although not fully).
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r3850 | bugman | 2007-11-23 15:41:40 +0100 (Fri, 23 Nov 2007) | 3 lines

Fixes for the write() function.
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r3851 | bugman | 2007-11-23 15:42:34 +0100 (Fri, 23 Nov 2007) | 3 lines

Added the import for the count_spins() function.
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r3852 | bugman | 2007-11-23 15:48:05 +0100 (Fri, 23 Nov 2007) | 3 lines

Wrote the count_spins() function.
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r3853 | bugman | 2007-11-23 15:50:07 +0100 (Fri, 23 Nov 2007) | 3 lines

Added the missing import of the open_write_file() function.
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r3854 | bugman | 2007-11-23 15:50:48 +0100 (Fri, 23 Nov 2007) | 3 lines

Added the missing import of the spin_loop() function.
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r3855 | bugman | 2007-11-23 16:04:22 +0100 (Fri, 23 Nov 2007) | 3 lines

Fix for the unit test for writing an amino acid sequence.
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r3856 | bugman | 2007-11-23 16:04:44 +0100 (Fri, 23 Nov 2007) | 3 lines

A fix for the write() function.
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r3857 | bugman | 2007-11-23 16:06:30 +0100 (Fri, 23 Nov 2007) | 3 lines

Another fix for the unit test for writing an amino acid sequence.
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r3858 | bugman | 2007-11-23 16:19:15 +0100 (Fri, 23 Nov 2007) | 3 lines

And another fix for the unit test for writing an amino acid sequence.
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r3859 | bugman | 2007-11-23 16:29:32 +0100 (Fri, 23 Nov 2007) | 3 lines

Big improvements to the write() function.
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r3860 | bugman | 2007-11-23 16:30:11 +0100 (Fri, 23 Nov 2007) | 5 lines

Final fix for the unit test for writing an amino acid sequence.

The md5sum has been added to the test.
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r3861 | bugman | 2007-11-23 16:32:14 +0100 (Fri, 23 Nov 2007) | 3 lines

Removal of debugging code from the write() function and an update to the md5sum in its unit test.
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r3862 | bugman | 2007-11-23 16:38:19 +0100 (Fri, 23 Nov 2007) | 3 lines

Updated the docstring of the write() function.
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r3863 | bugman | 2007-11-23 17:08:49 +0100 (Fri, 23 Nov 2007) | 6 lines

Split the write() function in half.

The two new functions are write() and write_body(). The write() function calls write_body(). This
write_body() is designed to be used by the display() function.
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r3864 | bugman | 2007-11-23 17:11:39 +0100 (Fri, 23 Nov 2007) | 3 lines

Implemented the display() function.
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r3865 | bugman | 2007-11-23 17:13:41 +0100 (Fri, 23 Nov 2007) | 3 lines

Implemented all the arg unit tests for the sequence.display() user function.
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r3866 | bugman | 2007-11-23 17:15:00 +0100 (Fri, 23 Nov 2007) | 3 lines

Bug fix for all the arg unit tests for the sequence.display() user function.
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r3867 | bugman | 2007-11-23 17:17:10 +0100 (Fri, 23 Nov 2007) | 3 lines

Implemented a unit test to test the display of an amino acid sequence.
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r3868 | bugman | 2007-11-23 17:27:40 +0100 (Fri, 23 Nov 2007) | 3 lines

Implemented the sequence.display() user function.
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r3869 | bugman | 2007-11-23 17:39:55 +0100 (Fri, 23 Nov 2007) | 3 lines

A few improvements to the unit test for the display of an amino acid sequence.
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r3872 | bugman | 2007-11-24 12:00:37 +0100 (Sat, 24 Nov 2007) | 3 lines

Added a unit test for the generic_fns.selection.count_spins() function.
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r3873 | bugman | 2007-11-24 12:02:36 +0100 (Sat, 24 Nov 2007) | 3 lines

Added a unit test for the generic_fns.selection.count_spins() function, for when there is no data.
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r3874 | bugman | 2007-11-24 12:05:20 +0100 (Sat, 24 Nov 2007) | 3 lines

Added a unit test for the proper operation of the spin loop when no data is present.
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r3875 | bugman | 2007-11-24 12:06:44 +0100 (Sat, 24 Nov 2007) | 3 lines

Added a unit test for the proper operation of the molecule loop when no data is present.
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r3876 | bugman | 2007-11-24 12:07:46 +0100 (Sat, 24 Nov 2007) | 3 lines

Added a unit test for the proper operation of the residue loop when no data is present.
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r3877 | bugman | 2007-11-24 12:16:30 +0100 (Sat, 24 Nov 2007) | 3 lines

Created the test() function for testing the existence of the current or given data pipe.
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r3878 | bugman | 2007-11-24 12:17:33 +0100 (Sat, 24 Nov 2007) | 3 lines

Added the generic_fns.pipes.test() function to the molecule, residue, and spin loop functions.
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r3879 | bugman | 2007-11-24 12:22:24 +0100 (Sat, 24 Nov 2007) | 3 lines

Added a unit test for the proper operation of the residue loop when no data pipe is present.
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r3880 | bugman | 2007-11-24 12:33:06 +0100 (Sat, 24 Nov 2007) | 6 lines

Fixed the unit test of the residue loop with no data pipes present.

The unittest framework couldn't handle the generator function, so an intermediary function was
created!
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r3881 | bugman | 2007-11-24 12:34:21 +0100 (Sat, 24 Nov 2007) | 3 lines

Fixes for the unit tests of the spin and molecule loops when no data is present.
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r3882 | bugman | 2007-11-24 12:35:21 +0100 (Sat, 24 Nov 2007) | 3 lines

Added a unit test for the proper operation of the spin loop when no data pipe is present.
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r3883 | bugman | 2007-11-24 12:36:22 +0100 (Sat, 24 Nov 2007) | 3 lines

Added a unit test for the proper operation of the molecule loop when no data pipe is present.
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r3884 | bugman | 2007-11-24 12:38:02 +0100 (Sat, 24 Nov 2007) | 3 lines

Fix for the test_count_no_spins unit test - a data pipe now exists.
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r3885 | bugman | 2007-11-24 12:40:35 +0100 (Sat, 24 Nov 2007) | 3 lines

Added a unit test, the counting of the number of spins should raise an error when no pipe exists.
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r3886 | bugman | 2007-11-24 20:41:29 +0100 (Sat, 24 Nov 2007) | 5 lines

Wrote the exists_mol_res_spin_data() function.

This function determines if any molecule-residue-spin data exists.
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r3887 | bugman | 2007-11-24 20:49:54 +0100 (Sat, 24 Nov 2007) | 3 lines

Wrote 4 unit tests for the generic_fns.selection.exists_mol_res_spin_data() function.
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r3888 | bugman | 2007-11-24 20:52:11 +0100 (Sat, 24 Nov 2007) | 3 lines

Bug fix for generic_fns.selection.exists_mol_res_spin_data(). No data pipes are now handled.
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r3889 | bugman | 2007-11-24 20:53:59 +0100 (Sat, 24 Nov 2007) | 6 lines

Bug fix.

This is for the unit test for determining if molecule-residue-spin data exists when no data pipe
exists.
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r3890 | bugman | 2007-11-24 20:59:06 +0100 (Sat, 24 Nov 2007) | 5 lines

Bug fix for generic_fns.selection.exists_mol_res_spin_data().

If no spins are selected, the function returns False!
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r3891 | bugman | 2007-11-24 21:03:28 +0100 (Sat, 24 Nov 2007) | 5 lines

Bug fix for generic_fns.selection.exists_mol_res_spin_data().

The testing the presence of data when only a single spin container exists now works.
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r3892 | bugman | 2007-11-24 21:06:20 +0100 (Sat, 24 Nov 2007) | 3 lines

Used the generic_fns.pipes.test() function a bit more.
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r3893 | bugman | 2007-11-24 21:06:56 +0100 (Sat, 24 Nov 2007) | 3 lines

Removed a nasty debugging line.
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r3894 | bugman | 2007-11-24 21:14:14 +0100 (Sat, 24 Nov 2007) | 5 lines

Fixes for the molecule, residue, and spin loops.

The functions do nothing if no molecule-residue-spin data exists.
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r3895 | bugman | 2007-11-24 21:30:18 +0100 (Sat, 24 Nov 2007) | 5 lines

Bug fix for generic_fns.selection.exists_mol_res_spin_data().

Fixed the circular dependence cased by calling the spin_loop() generator function!
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r3896 | bugman | 2007-11-25 11:54:12 +0100 (Sun, 25 Nov 2007) | 3 lines

Updated the data model redesign document. All the sequence user functions are implemented.
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r3897 | bugman | 2007-11-25 12:08:22 +0100 (Sun, 25 Nov 2007) | 3 lines

Wrote 5 unit tests for the generic_fns.selection.exists_mol_res_spin_data() function.
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r3898 | bugman | 2007-11-25 12:12:43 +0100 (Sun, 25 Nov 2007) | 3 lines

Big bug fix for the generic_fns.selection.exists_mol_res_spin_data() function.
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r3899 | bugman | 2007-11-25 12:17:02 +0100 (Sun, 25 Nov 2007) | 5 lines

Removed the selection argument to the generic_fns.selection.exists_mol_res_spin_data() function.

The associated unit test has also been removed.
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r3900 | bugman | 2007-11-25 15:08:29 +0100 (Sun, 25 Nov 2007) | 3 lines

Removed the run argument from the diffusion_tensor.init() user function.
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r3901 | bugman | 2007-11-25 15:11:49 +0100 (Sun, 25 Nov 2007) | 3 lines

Set up the base class for unit tests of the diffusion_tensor modules.
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r3902 | bugman | 2007-11-25 15:14:00 +0100 (Sun, 25 Nov 2007) | 3 lines

Created the framework for the unit tests of the diffusion_tensor user functions.
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r3903 | bugman | 2007-11-25 15:14:40 +0100 (Sun, 25 Nov 2007) | 3 lines

File rename.
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r3904 | bugman | 2007-11-25 15:21:19 +0100 (Sun, 25 Nov 2007) | 3 lines

A file to be imported by all the prompt user test modules for faking the relax instance structure.
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r3905 | bugman | 2007-11-25 15:29:00 +0100 (Sun, 25 Nov 2007) | 3 lines

Updated all the prompt module unit tests to use the new 'fake_relax' structure.
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r3907 | bugman | 2007-11-25 16:30:00 +0100 (Sun, 25 Nov 2007) | 3 lines

Implemented the params unit test for the diffusion_tensor.init() user function.
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r3908 | bugman | 2007-11-25 16:37:17 +0100 (Sun, 25 Nov 2007) | 3 lines

Removed some unused RelaxError imports.
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r3909 | bugman | 2007-11-25 16:39:50 +0100 (Sun, 25 Nov 2007) | 3 lines

Removed some unused RelaxError imports.
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r3910 | bugman | 2007-11-25 16:43:45 +0100 (Sun, 25 Nov 2007) | 3 lines

Implemented all the arg unit tests for the diffusion_tensor.init() user function.
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r3911 | bugman | 2007-11-25 16:45:03 +0100 (Sun, 25 Nov 2007) | 3 lines

Removed the run argument from the diffusion_tensor.display() user function.
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r3912 | bugman | 2007-11-25 16:54:50 +0100 (Sun, 25 Nov 2007) | 3 lines

Updated all the diffusion tensor user functions to the new relax design.
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r3913 | bugman | 2007-11-25 16:57:12 +0100 (Sun, 25 Nov 2007) | 3 lines

Implemented all the arg unit tests for the diffusion_tensor.copy() user function.
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r3914 | bugman | 2007-11-25 16:59:06 +0100 (Sun, 25 Nov 2007) | 5 lines

Bug fix for the diffusion_tensor.copy() user function.

The pipes can be None.
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r3915 | bugman | 2007-11-25 17:05:46 +0100 (Sun, 25 Nov 2007) | 5 lines

Implemented the test of diffusion_tensor.copy(), that both arguments cannot be None.

A unit test for this has also been added.
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r3916 | bugman | 2007-11-25 17:11:49 +0100 (Sun, 25 Nov 2007) | 3 lines

Added a number of tuples of floats of different sizes for the user function argument unit tests.
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r3917 | bugman | 2007-11-25 17:32:34 +0100 (Sun, 25 Nov 2007) | 3 lines

Fixed the params arg unit test for the diffusion_tensor.init() user function.
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r3918 | bugman | 2007-11-25 17:37:00 +0100 (Sun, 25 Nov 2007) | 3 lines

Another fix for the params arg unit test for the diffusion_tensor.init() user function.
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r3919 | bugman | 2007-11-25 17:38:22 +0100 (Sun, 25 Nov 2007) | 3 lines

Added the import of the generic_fns.diffusion_tensor module.
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r3920 | bugman | 2007-11-25 17:50:26 +0100 (Sun, 25 Nov 2007) | 5 lines

Wrote two unit tests for the diffusion tensor initialisation.

One is for bad angular units, the other is for setting a spherical tensor.
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r3921 | bugman | 2007-11-25 17:58:11 +0100 (Sun, 25 Nov 2007) | 3 lines

Removed the placement of the Diffusion_tensor class instance into generic_fns.
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r3922 | bugman | 2007-11-25 18:02:00 +0100 (Sun, 25 Nov 2007) | 5 lines

Removed all of the generic_fns class instances from the relax namespace.

All these class methods will be converted to module functions.
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r3923 | bugman | 2007-11-25 18:06:16 +0100 (Sun, 25 Nov 2007) | 5 lines

Shifted all the calc_* diffusion tensor functions from generic_fns to data.

This is to break a fatal circular import problem!!!
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r3924 | bugman | 2007-11-25 18:07:39 +0100 (Sun, 25 Nov 2007) | 3 lines

Removed an unused import of pi.
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r3925 | bugman | 2007-11-25 18:15:16 +0100 (Sun, 25 Nov 2007) | 5 lines

Converted all the Diffusion_tensor methods into module functions.

The class no longer exists.
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r3926 | bugman | 2007-11-25 18:18:20 +0100 (Sun, 25 Nov 2007) | 3 lines

Fixed the prompt modules which were importing the Diffusion_tensor class.
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r3927 | bugman | 2007-11-25 18:19:00 +0100 (Sun, 25 Nov 2007) | 3 lines

Updated the copyright notices.
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r3928 | bugman | 2007-11-25 18:24:19 +0100 (Sun, 25 Nov 2007) | 3 lines

Converted the generic_fns.diffusion_tensor.init() function to the new relax design.
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r3929 | bugman | 2007-11-25 18:25:00 +0100 (Sun, 25 Nov 2007) | 3 lines

Docstring fix.
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r3930 | bugman | 2007-11-25 18:30:36 +0100 (Sun, 25 Nov 2007) | 3 lines

Bug fix for the generic_fns.diffusion_tensor.init() function.
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r3931 | bugman | 2007-11-25 18:38:16 +0100 (Sun, 25 Nov 2007) | 3 lines

Added a unit test for the generic_fns.pipes.test() function.
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r3932 | bugman | 2007-11-25 18:42:05 +0100 (Sun, 25 Nov 2007) | 3 lines

Added a unit test for the generic_fns.pipes.current() function.
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r3933 | bugman | 2007-11-25 18:44:10 +0100 (Sun, 25 Nov 2007) | 5 lines

Bug fix for the generic_fns.pipes.current() function.

The function now returns the current pipe rather than printing it!
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r3934 | bugman | 2007-11-25 18:51:13 +0100 (Sun, 25 Nov 2007) | 3 lines

Bug fix for the generic_fns.pipes.test() function.
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r3935 | bugman | 2007-11-25 18:55:57 +0100 (Sun, 25 Nov 2007) | 3 lines

Bug fix for the RelaxTensorError class.
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r3936 | bugman | 2007-11-25 19:05:37 +0100 (Sun, 25 Nov 2007) | 3 lines

Implemented the function generic_fns.diffusion_tensor.diff_data_exists().
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r3937 | bugman | 2007-11-25 19:08:02 +0100 (Sun, 25 Nov 2007) | 3 lines

generic_fns.diffusion_tensor.init() now uses the new function for determining the existence of data.
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r3938 | bugman | 2007-11-25 19:09:28 +0100 (Sun, 25 Nov 2007) | 3 lines

Renamed the pipe container object 'diff' to 'diff_tensor'.
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r3939 | bugman | 2007-11-25 19:22:06 +0100 (Sun, 25 Nov 2007) | 5 lines

Updated the diffusion tensor data structure in the relax data store for the new relax design.

The object is no longer a dictionary type with keys set to the run names. It is simply a container.
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r3940 | bugman | 2007-11-25 19:23:15 +0100 (Sun, 25 Nov 2007) | 3 lines

Bug fix for the generic_fns.diffusion_tensor.diff_data_exists() function.
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r3941 | bugman | 2007-11-25 19:25:12 +0100 (Sun, 25 Nov 2007) | 5 lines

Another bug fix for the generic_fns.diffusion_tensor.diff_data_exists() function.

The white_list object now exists.
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r3942 | bugman | 2007-11-25 19:28:46 +0100 (Sun, 25 Nov 2007) | 3 lines

Updated the save state file as the diffusion tensor object is now different.
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r3943 | bugman | 2007-11-25 19:30:17 +0100 (Sun, 25 Nov 2007) | 5 lines

Bug fix for the generic_fns.diffusion_tensor.init() function.

The new data structure is taken into account.
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r3944 | bugman | 2007-11-25 19:35:26 +0100 (Sun, 25 Nov 2007) | 3 lines

Updated all the functions to handle the new diff tensor data structure.
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r3945 | bugman | 2007-11-25 19:42:30 +0100 (Sun, 25 Nov 2007) | 3 lines

Updated the generic_fns.diffusion_tensor.sphere() function.
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r3946 | bugman | 2007-11-25 19:52:48 +0100 (Sun, 25 Nov 2007) | 3 lines

Converted the docstring of generic_fns.diffusion_tensor.init() to the epydoc format.
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r3947 | bugman | 2007-11-25 19:55:07 +0100 (Sun, 25 Nov 2007) | 3 lines

Sent a number of variables into the sphere, spheroid, and ellipsoid functions.
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r3948 | bugman | 2007-11-25 19:57:08 +0100 (Sun, 25 Nov 2007) | 3 lines

Removed all the references to self in generic_fns.diffusion_tensor.set().
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r3949 | bugman | 2007-11-25 19:58:33 +0100 (Sun, 25 Nov 2007) | 3 lines

Removed all the references to self in generic_fns.diffusion_tensor.return_data_name().
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r3950 | bugman | 2007-11-25 20:00:06 +0100 (Sun, 25 Nov 2007) | 5 lines

Bug fix for generic_fns.diffusion_tensor.set().

The current data pipe is now aliased.
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r3951 | bugman | 2007-11-25 20:02:01 +0100 (Sun, 25 Nov 2007) | 5 lines

Bug fix for generic_fns.diffusion_tensor.test_params().

Removed self and added the cdp alias.
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r3952 | bugman | 2007-11-25 20:04:10 +0100 (Sun, 25 Nov 2007) | 3 lines

Bug fixes for the unit test of setting up of a spherical diffusion tensor.
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r3953 | bugman | 2007-11-25 20:08:07 +0100 (Sun, 25 Nov 2007) | 3 lines

Removed all references to self from the generic_fns.diffusion_tensor module.
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r3954 | bugman | 2007-11-25 20:14:15 +0100 (Sun, 25 Nov 2007) | 3 lines

Wrote a unit test for the setting up of a spheroidal diffusion tensor.
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r3955 | bugman | 2007-11-25 20:22:13 +0100 (Sun, 25 Nov 2007) | 3 lines

Fixes for generic_fns.diffusion_tensor.spheroid().
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r3956 | bugman | 2007-11-25 20:26:46 +0100 (Sun, 25 Nov 2007) | 3 lines

Fixes to generic_fns.diffusion_tensor.fold_angles().
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r3957 | bugman | 2007-11-25 20:28:23 +0100 (Sun, 25 Nov 2007) | 3 lines

Converted all the methods of the Angles class into module functions.
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r3958 | bugman | 2007-11-25 20:36:11 +0100 (Sun, 25 Nov 2007) | 3 lines

Removal of references to self and run, and an update to the new data storage object.
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r3959 | bugman | 2007-11-25 20:37:39 +0100 (Sun, 25 Nov 2007) | 3 lines

Fixed all calls to generic_fns.angles.wrap_angles().
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r3960 | bugman | 2007-11-25 20:50:07 +0100 (Sun, 25 Nov 2007) | 3 lines

Fixes to the unit test for the setting up of a spheroidal diffusion tensor.
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r3961 | bugman | 2007-11-25 21:08:44 +0100 (Sun, 25 Nov 2007) | 3 lines

Wrote a unit test for the setting up of an ellipsoidal diffusion tensor.
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r3962 | bugman | 2007-11-25 21:11:58 +0100 (Sun, 25 Nov 2007) | 3 lines

Fixes to all of generic_fns.diffusion_tensor.ellipsoid().
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r3963 | bugman | 2007-11-25 21:15:41 +0100 (Sun, 25 Nov 2007) | 3 lines

Fixed for the unit test for the setting up of a ellipsoid diffusion tensor.
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r3964 | bugman | 2007-11-25 21:16:11 +0100 (Sun, 25 Nov 2007) | 3 lines

Removed some debugging code.
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r3965 | bugman | 2007-11-25 21:17:53 +0100 (Sun, 25 Nov 2007) | 3 lines

Added 2 more checks to the spheroidal tensor unit test.
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r3966 | bugman | 2007-11-25 21:19:15 +0100 (Sun, 25 Nov 2007) | 3 lines

Added one more check to the spherical tensor unit test.
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r3967 | bugman | 2007-11-25 22:04:40 +0100 (Sun, 25 Nov 2007) | 5 lines

Fixed the initialisation of the diffusion tensor system tests.

The diffusion_tensor.init test now passes.
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r3968 | bugman | 2007-11-25 22:15:50 +0100 (Sun, 25 Nov 2007) | 3 lines

Added a unit test for the deletion of diffusion tensor data.
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r3969 | bugman | 2007-11-25 22:17:35 +0100 (Sun, 25 Nov 2007) | 3 lines

Bug fix for generic_fns.diffusion_tensor.delete().
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r3970 | bugman | 2007-11-25 22:21:30 +0100 (Sun, 25 Nov 2007) | 3 lines

Added 2 unit tests for the failure of the diffusion tensor deletion.
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r3971 | bugman | 2007-11-25 22:22:36 +0100 (Sun, 25 Nov 2007) | 3 lines

Bug fix for the generic_fns.diffusion_tensor.delete() function.
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r3972 | bugman | 2007-11-25 22:23:36 +0100 (Sun, 25 Nov 2007) | 3 lines

The last commit, which was supposed to be a bug fix, actually introduced a bug instead!
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r3973 | bugman | 2007-11-25 22:25:27 +0100 (Sun, 25 Nov 2007) | 3 lines

Changed the RelaxError type in the diff tensor failure unit test.
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r3974 | bugman | 2007-11-25 22:26:54 +0100 (Sun, 25 Nov 2007) | 3 lines

Fixed the unit test for the deletion of the diffusion tensor data structure.
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r3976 | bugman | 2007-11-25 23:13:37 +0100 (Sun, 25 Nov 2007) | 3 lines

Bug fix for the RelaxNoTensorError class.
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r3977 | bugman | 2007-11-25 23:15:53 +0100 (Sun, 25 Nov 2007) | 5 lines

Bug fix for the generic_fns.diffusion_tensor.diff_data_exists() function.

The function now works properly.
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r3978 | bugman | 2007-11-25 23:16:57 +0100 (Sun, 25 Nov 2007) | 5 lines

Bug fix for the generic_fns.diffusion_tensor.init() function.

This function now works properly too.
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r3979 | bugman | 2007-11-25 23:23:39 +0100 (Sun, 25 Nov 2007) | 3 lines

Wrote 3 unit tests for displaying spherical, spheroidal, and ellipsoidal diffusion tensors.
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r3980 | bugman | 2007-11-25 23:26:42 +0100 (Sun, 25 Nov 2007) | 5 lines

Wrote 2 unit tests for the failure of generic_fns.diffusion_tensor.display().

This is when there is no data and when there is no data pipe.
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r3981 | bugman | 2007-11-25 23:28:49 +0100 (Sun, 25 Nov 2007) | 3 lines

Fixed the generic_fns.diffusion_tensor.delete() function.
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r3982 | bugman | 2007-11-25 23:40:17 +0100 (Sun, 25 Nov 2007) | 3 lines

Wrote 6 unit tests for the generic_fns.diffusion_tensor.copy() function.
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r3983 | bugman | 2007-11-25 23:49:50 +0100 (Sun, 25 Nov 2007) | 3 lines

Implemented the generic_fns.diffusion_tensor.copy() function.
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r3984 | bugman | 2007-11-25 23:52:27 +0100 (Sun, 25 Nov 2007) | 3 lines

Extended generic_fns.diffusion_tensor.diff_data_exists() to accept an arbitrary data pipe as an arg.
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r3985 | bugman | 2007-11-25 23:53:42 +0100 (Sun, 25 Nov 2007) | 3 lines

A fix for a diffusion tensor copying unit test.
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r3986 | bugman | 2007-11-25 23:58:39 +0100 (Sun, 25 Nov 2007) | 3 lines

Bug fix for generic_fns.diffusion_tensor.copy().
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r4004 | bugman | 2007-11-26 14:26:55 +0100 (Mon, 26 Nov 2007) | 3 lines

Improvement of the RelaxUnknownParamError printout.
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r4014 | bugman | 2007-11-26 15:05:35 +0100 (Mon, 26 Nov 2007) | 3 lines

Wrote a unit test for the generic_fns.diffusion_tensor.return_data_name() function.
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r4015 | bugman | 2007-11-26 15:09:19 +0100 (Mon, 26 Nov 2007) | 6 lines

Bug fix for generic_fns.align_tensor.return_data_name().

The function now checks that a string is passed into it and that it raises a RelaxError when no
parameter matches.
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r4018 | bugman | 2007-11-26 15:19:01 +0100 (Mon, 26 Nov 2007) | 5 lines

Updates to RelaxTensorError and RelaxNoTensorError to allow for multiple types of tensor.

For example a diffusion tensor, alignment tensor, etc.
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r4019 | bugman | 2007-11-26 15:22:47 +0100 (Mon, 26 Nov 2007) | 3 lines

Changed all parts of relax to use the modified RelaxTensorError and RelaxNoTensorError classes.
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r4020 | bugman | 2007-11-26 15:24:27 +0100 (Mon, 26 Nov 2007) | 5 lines

Renamed generic_fns.angles.angles() to generic_fns.angles.angle_diff_frame().

This is to allow for different types of tensors.
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r4021 | bugman | 2007-11-26 15:26:12 +0100 (Mon, 26 Nov 2007) | 3 lines

Removed some unused imports.
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r4027 | bugman | 2007-11-26 15:54:23 +0100 (Mon, 26 Nov 2007) | 5 lines

Removed the empty diff_tensor structure from the PipeContainer.

This will be added after its initialisation.
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r4028 | bugman | 2007-11-26 15:55:56 +0100 (Mon, 26 Nov 2007) | 5 lines

Updated the generic_fns.diffusion_tensor.diff_data_exists() function.

The diff_tensor object is now tested for.
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r4029 | bugman | 2007-11-26 15:57:52 +0100 (Mon, 26 Nov 2007) | 5 lines

Updated the generic_fns.diffusion_tensor.init() function.

The function now adds the DiffTensorData instance as diff_tensor into the PipeContainer.
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r4030 | bugman | 2007-11-26 15:59:48 +0100 (Mon, 26 Nov 2007) | 5 lines

Updated the test_delete() unit test.

The diff_tensor object should be removed by the delete() function.
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r4031 | bugman | 2007-11-26 16:01:21 +0100 (Mon, 26 Nov 2007) | 6 lines

Updated the generic_fns.diffusion_tensor.delete() function.

The DiffTensorData instance is not set up after deletion anymore. The diff_tensor structure should
not exist.
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r4061 | bugman | 2007-11-26 19:35:34 +0100 (Mon, 26 Nov 2007) | 3 lines

Added the base class framework for testing the relaxation data modules.
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r4062 | bugman | 2007-11-26 19:39:51 +0100 (Mon, 26 Nov 2007) | 3 lines

Added the framework for the arg unit tests of the relax_data user functions.
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r4063 | bugman | 2007-11-26 19:53:12 +0100 (Mon, 26 Nov 2007) | 3 lines

Added 13 unit tests for the args of the relax_data.read() user function.
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r4064 | bugman | 2007-11-26 19:58:45 +0100 (Mon, 26 Nov 2007) | 3 lines

Implemented the relax_data.read() user function interface.
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r4065 | bugman | 2007-11-26 20:04:57 +0100 (Mon, 26 Nov 2007) | 3 lines

Bug fixes for the arg unit tests of the relax_data.read() user function.
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r4066 | bugman | 2007-11-26 20:05:49 +0100 (Mon, 26 Nov 2007) | 5 lines

Bug fix for the relax_data.read() user function.

A missing RelaxError import has been added.
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r4067 | bugman | 2007-11-27 10:28:25 +0100 (Tue, 27 Nov 2007) | 6 lines

Bug fix for the docstring of the generic_fns.diffusion_tensor.return_data_name() function.

The docstring, because it is joined onto user function docstrings, must have indentation of 8 spaces
as well!
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r4068 | bugman | 2007-11-27 11:02:21 +0100 (Tue, 27 Nov 2007) | 6 lines

Removed the formatted docstring file from the repository.

This file needs to be regenerated each time and is an automatically created file. Its placement in
the repository is not necessary.
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r4069 | bugman | 2007-11-27 11:06:25 +0100 (Tue, 27 Nov 2007) | 3 lines

Added the last two missing relax base directories for holding unit tests.
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r4070 | bugman | 2007-11-27 11:07:28 +0100 (Tue, 27 Nov 2007) | 3 lines

Turned the 2 new dirs into modules.
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r4071 | bugman | 2007-11-27 11:10:44 +0100 (Tue, 27 Nov 2007) | 3 lines

Copyright label update.
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r4072 | bugman | 2007-11-27 11:23:43 +0100 (Tue, 27 Nov 2007) | 5 lines

Removed the Rx_data class instance from self.relax.specific.

The class instance is now within the module to be imported by who ever wants it.
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r4073 | bugman | 2007-11-27 12:00:32 +0100 (Tue, 27 Nov 2007) | 5 lines

Created the new function generic_fns.selection.generate_spin_id().

This will return an ID string for the spin.
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r4074 | bugman | 2007-11-27 13:17:53 +0100 (Tue, 27 Nov 2007) | 3 lines

Added 5 unit tests for the generic_fns.selection.generate_spin_id() function.
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r4075 | bugman | 2007-11-27 13:21:48 +0100 (Tue, 27 Nov 2007) | 3 lines

Created the RelaxNoSpinError class.
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r4076 | bugman | 2007-11-27 13:23:07 +0100 (Tue, 27 Nov 2007) | 3 lines

Converted the specific_fns.relax_data.read() to the new relax design.
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r4077 | bugman | 2007-11-27 14:53:43 +0100 (Tue, 27 Nov 2007) | 3 lines

Added the missing import of the specific_fns.relax_data module.
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r4078 | bugman | 2007-11-27 14:56:08 +0100 (Tue, 27 Nov 2007) | 3 lines

Added 2 missing imports.
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r4079 | bugman | 2007-11-27 15:07:03 +0100 (Tue, 27 Nov 2007) | 3 lines

Wrote a unit test for the reading of relaxation data.
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r4080 | bugman | 2007-11-27 18:43:14 +0100 (Tue, 27 Nov 2007) | 3 lines

Bug fix for the RelaxNoSequenceError class.
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r4081 | bugman | 2007-11-27 18:50:09 +0100 (Tue, 27 Nov 2007) | 5 lines

Bug fix for the specific_fns.relax_data.read() function.

The use of the dummy function sequence_exists() has been replaced with exists_mol_res_spin_data().
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r4082 | bugman | 2007-11-28 09:01:54 +0100 (Wed, 28 Nov 2007) | 3 lines

Updated the specific_fns.relax_data.test_labels() function to the new relax design.
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r4083 | bugman | 2007-11-28 09:03:01 +0100 (Wed, 28 Nov 2007) | 3 lines

Added a number of missing imports.
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r4084 | bugman | 2007-11-28 09:17:13 +0100 (Wed, 28 Nov 2007) | 5 lines

Rewrote the specific_fns.relax_data.data_init() function.

This was a big simplification!
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r4085 | bugman | 2007-11-28 09:21:34 +0100 (Wed, 28 Nov 2007) | 3 lines

Added a base class for the unit tests of the specific_fns.relax_data module.
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r4086 | bugman | 2007-11-28 09:29:53 +0100 (Wed, 28 Nov 2007) | 3 lines

Wrote 2 unit tests for the specific_fns.relax_data.data_init() function.
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r4087 | bugman | 2007-11-28 09:31:14 +0100 (Wed, 28 Nov 2007) | 3 lines

Bug fix for the read() function.
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r4088 | bugman | 2007-11-28 09:35:54 +0100 (Wed, 28 Nov 2007) | 3 lines

Converted specific_fns.relax_data.update_global_data_structures() to the new relax design.
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r4089 | bugman | 2007-11-28 09:37:03 +0100 (Wed, 28 Nov 2007) | 3 lines

Added some more missing imports.
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r4090 | bugman | 2007-11-28 09:42:33 +0100 (Wed, 28 Nov 2007) | 5 lines

Bug fix for the generic_fns.selection.generate_spin_id() function.

The residue and spin names now always start with the identifier ':' or '@'.
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r4091 | bugman | 2007-11-28 09:43:57 +0100 (Wed, 28 Nov 2007) | 3 lines

Fixes for the unit tests of generic_fns.selection.generate_spin_id().
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r4092 | bugman | 2007-11-28 09:44:48 +0100 (Wed, 28 Nov 2007) | 3 lines

Added the missing import of RelaxNoSpinError.
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r4093 | bugman | 2007-11-28 10:00:08 +0100 (Wed, 28 Nov 2007) | 3 lines

Added 2 unit tests for the generic_fns.selection.return_spin() function.
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r4094 | bugman | 2007-11-28 10:15:55 +0100 (Wed, 28 Nov 2007) | 6 lines

Bug fix to the return_residue() and return_spin() functions.

When a residue or spin is not identified, then this should correspond to all residues or spins and
not none!
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r4095 | bugman | 2007-11-28 10:20:18 +0100 (Wed, 28 Nov 2007) | 5 lines

Big bug fix for the generic_fns.residue.create() function.

The mol_to_cont was being set to a ResidueContainer rather than a MoleculeContainer!!!
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r4096 | bugman | 2007-11-28 10:33:08 +0100 (Wed, 28 Nov 2007) | 9 lines

Split generic_fns.selection.exists_mol_res_spin_data() into 4 new functions.

The new functions are:
exists_mol_res_spin_data()
exists_mol_data()
exists_res_data()
exists_spin_data()
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r4097 | bugman | 2007-11-28 10:36:05 +0100 (Wed, 28 Nov 2007) | 5 lines

Bug fix for the generic_fns.residue.copy() function.

The contents of res_to_cont is now checked for, to see if it is empty.
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r4098 | bugman | 2007-11-28 10:43:17 +0100 (Wed, 28 Nov 2007) | 6 lines

Fixes to the test_return_spin() unit test.

As the setUp() method was modified to add some spin info, the test_spin_loop_no_selection() unit
test had to be updated as well.
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r4099 | bugman | 2007-11-28 10:47:17 +0100 (Wed, 28 Nov 2007) | 3 lines

Bug fix for the generic_fns.spin.create() function.
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r4100 | bugman | 2007-11-28 10:48:45 +0100 (Wed, 28 Nov 2007) | 5 lines

Bug fix for the generic_fns.residue.create() function.

This is the same fix as that for generic_fns.spin.create() in r4099.
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r4101 | bugman | 2007-11-28 10:59:58 +0100 (Wed, 28 Nov 2007) | 3 lines

Bug fix for the generic_fns.spin.copy() function.
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r4102 | bugman | 2007-11-28 11:05:31 +0100 (Wed, 28 Nov 2007) | 5 lines

Bug fix for the generic_fns.spin.copy() function.

The wrong pipe was being used for the destination spin container!
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r4104 | bugman | 2007-11-28 11:14:03 +0100 (Wed, 28 Nov 2007) | 3 lines

Added another unit test for generic_fns.selection.generate_spin_id().
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r4105 | bugman | 2007-11-28 11:16:53 +0100 (Wed, 28 Nov 2007) | 6 lines

Bug fix for the relax_data.read() user function.

The default values for the keyword arguments res_num_col and spin_num_col, and for res_name_col and
spin_name_col, were set to the same thing.
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r4106 | bugman | 2007-11-28 11:23:19 +0100 (Wed, 28 Nov 2007) | 3 lines

Converted specific_fns.relax_data.update_data_structures() to the new relax design.
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r4107 | bugman | 2007-11-28 11:25:29 +0100 (Wed, 28 Nov 2007) | 7 lines

Renaming of the update_data_structures() functions.

The functions have changed to:
update_data_structures() -> update_data_structures_spin()
update_global_data_structures() -> update_data_structures_pipe()
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r4108 | bugman | 2007-11-28 11:39:39 +0100 (Wed, 28 Nov 2007) | 5 lines

Improvements to the test_read_protein_noe_data() unit test.

Now the entire Ap4Aase sequence is checked to see if it has been read in correctly.
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r4109 | bugman | 2007-11-28 11:46:49 +0100 (Wed, 28 Nov 2007) | 5 lines

Big bug fix for generic_fns.sequence.read().

If 2 or more sequential residues had the same name, only the first would be added to the sequence!
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r4110 | bugman | 2007-11-28 11:58:29 +0100 (Wed, 28 Nov 2007) | 3 lines

Updated the test_read() user function to check the pipe relaxation data structures.
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r4111 | bugman | 2007-11-28 12:00:49 +0100 (Wed, 28 Nov 2007) | 6 lines

Bug fix.

Updated all the calls to update_data_structures_pipe(). Now the function arguments are passed in to
it.
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r4112 | bugman | 2007-11-28 12:09:58 +0100 (Wed, 28 Nov 2007) | 3 lines

Updated the test_read() user function to check all the spin relaxation data structures.
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r4113 | bugman | 2007-11-28 12:12:02 +0100 (Wed, 28 Nov 2007) | 6 lines

Bug fix.

Updated all the calls to update_data_structures_spin(). Now the function arguments are passed in to
it.
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r4114 | bugman | 2007-11-28 12:17:13 +0100 (Wed, 28 Nov 2007) | 3 lines

Bug fix for the test_read() unit test.
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r4137 | bugman | 2007-12-09 12:15:34 +0100 (Sun, 09 Dec 2007) | 3 lines

Updated the value.set() user function to the new relax design.
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r4138 | bugman | 2007-12-09 12:17:33 +0100 (Sun, 09 Dec 2007) | 3 lines

Added the base class for the tests of both the 'prompt.value' and 'generic_fns.value' modules.
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r4139 | bugman | 2007-12-09 12:19:58 +0100 (Sun, 09 Dec 2007) | 3 lines

Updated the __init__ file of the base directory of the unit tests.
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Added the message "Copyright (C) 2006-2007 the relax development team" to the relax intro message.

Fixed the 'sconstruct' file to handle Windows Vista.

Updated the __init__ file of the base directory of the unit tests.