Author: bugman
Date: Sun Nov 25 23:01:51 2007
New Revision: 3975
URL: http://svn.gna.org/viewcvs/relax?rev=3975&view=rev
Log:
Merged revisions 3907-3967 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
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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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Added:
branches/N_state_model/test_suite/unit_tests/_generic_fns/test_diffusion_tensor.py
- copied unchanged from r3967,
1.3/test_suite/unit_tests/_generic_fns/test_diffusion_tensor.py
Removed:
branches/N_state_model/generic_fns/main.py
Modified:
branches/N_state_model/ (props changed)
branches/N_state_model/data/diff_tensor.py
branches/N_state_model/data/pipe_container.py
branches/N_state_model/generic_fns/angles.py
branches/N_state_model/generic_fns/diffusion_tensor.py
branches/N_state_model/generic_fns/pipes.py
branches/N_state_model/prompt/diffusion_tensor.py
branches/N_state_model/prompt/dx.py
branches/N_state_model/prompt/value.py
branches/N_state_model/relax
branches/N_state_model/relax_errors.py
branches/N_state_model/test_suite/shared_data/saved_states/basic_single_pipe.bz2
branches/N_state_model/test_suite/system_tests/diffusion_tensor.py
branches/N_state_model/test_suite/unit_tests/_data/test_diff_tensor.py
branches/N_state_model/test_suite/unit_tests/_generic_fns/test_pipes.py
branches/N_state_model/test_suite/unit_tests/_prompt/data_types.py
branches/N_state_model/test_suite/unit_tests/_prompt/test_diffusion_tensor.py
branches/N_state_model/test_suite/unit_tests/_prompt/test_molecule.py
branches/N_state_model/test_suite/unit_tests/_prompt/test_residue.py
branches/N_state_model/test_suite/unit_tests/diffusion_tensor_testing_base.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/N_state_model/data/diff_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/data/diff_tensor.py?rev=3975&r1=3974&r2=3975&view=diff
Modified: branches/N_state_model/data/pipe_container.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/data/pipe_container.py?rev=3975&r1=3974&r2=3975&view=diff
Modified: branches/N_state_model/generic_fns/angles.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/generic_fns/angles.py?rev=3975&r1=3974&r2=3975&view=diff
Modified: branches/N_state_model/generic_fns/diffusion_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/generic_fns/diffusion_tensor.py?rev=3975&r1=3974&r2=3975&view=diff
Removed: branches/N_state_model/generic_fns/main.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/generic_fns/main.py?rev=3974&view=auto
Modified: branches/N_state_model/generic_fns/pipes.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/generic_fns/pipes.py?rev=3975&r1=3974&r2=3975&view=diff
Modified: branches/N_state_model/prompt/diffusion_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/prompt/diffusion_tensor.py?rev=3975&r1=3974&r2=3975&view=diff
Modified: branches/N_state_model/prompt/dx.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/prompt/dx.py?rev=3975&r1=3974&r2=3975&view=diff
Modified: branches/N_state_model/prompt/value.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/prompt/value.py?rev=3975&r1=3974&r2=3975&view=diff
Modified: branches/N_state_model/relax
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/relax?rev=3975&r1=3974&r2=3975&view=diff
Modified: branches/N_state_model/relax_errors.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/relax_errors.py?rev=3975&r1=3974&r2=3975&view=diff
Modified:
branches/N_state_model/test_suite/shared_data/saved_states/basic_single_pipe.bz2
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/test_suite/shared_data/saved_states/basic_single_pipe.bz2?rev=3975&r1=3974&r2=3975&view=diff
Modified: branches/N_state_model/test_suite/system_tests/diffusion_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/test_suite/system_tests/diffusion_tensor.py?rev=3975&r1=3974&r2=3975&view=diff
Modified:
branches/N_state_model/test_suite/unit_tests/_data/test_diff_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/test_suite/unit_tests/_data/test_diff_tensor.py?rev=3975&r1=3974&r2=3975&view=diff
Modified:
branches/N_state_model/test_suite/unit_tests/_generic_fns/test_pipes.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/test_suite/unit_tests/_generic_fns/test_pipes.py?rev=3975&r1=3974&r2=3975&view=diff
Modified: branches/N_state_model/test_suite/unit_tests/_prompt/data_types.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/test_suite/unit_tests/_prompt/data_types.py?rev=3975&r1=3974&r2=3975&view=diff
Modified:
branches/N_state_model/test_suite/unit_tests/_prompt/test_diffusion_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/test_suite/unit_tests/_prompt/test_diffusion_tensor.py?rev=3975&r1=3974&r2=3975&view=diff
Modified:
branches/N_state_model/test_suite/unit_tests/_prompt/test_molecule.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/test_suite/unit_tests/_prompt/test_molecule.py?rev=3975&r1=3974&r2=3975&view=diff
Modified: branches/N_state_model/test_suite/unit_tests/_prompt/test_residue.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/test_suite/unit_tests/_prompt/test_residue.py?rev=3975&r1=3974&r2=3975&view=diff
Modified:
branches/N_state_model/test_suite/unit_tests/diffusion_tensor_testing_base.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/test_suite/unit_tests/diffusion_tensor_testing_base.py?rev=3975&r1=3974&r2=3975&view=diff
r3975 - in /branches/N_state_model: ./ data/ generic_fns/ prompt/ test_suite/shared_data/saved_states/ test_suite/system_tes...