Author: bugman
Date: Mon Sep 14 17:01:33 2009
New Revision: 9527
URL: http://svn.gna.org/viewcvs/relax?rev=9527&view=rev
Log:
Merged revisions 9454,9457-9526 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
........
r9454 | bugman | 2009-09-03 15:23:45 +0200 (Thu, 03 Sep 2009) | 3 lines
Updated the non-dangerous Python3k update command.
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r9457 | bugman | 2009-09-03 17:53:41 +0200 (Thu, 03 Sep 2009) | 3 lines
Created a sub-directory for frame order test scripts.
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r9458 | bugman | 2009-09-03 18:18:51 +0200 (Thu, 03 Sep 2009) | 3 lines
Shifted the rigid frame order system test into the sub-directory.
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r9459 | bugman | 2009-09-03 18:31:23 +0200 (Thu, 03 Sep 2009) | 3 lines
Added another rigid frame order system test.
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r9460 | bugman | 2009-09-03 18:32:10 +0200 (Thu, 03 Sep 2009) | 3 lines
Renamed a frame order system test.
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r9461 | bugman | 2009-09-03 19:05:02 +0200 (Thu, 03 Sep 2009) | 3 lines
Specific architecture and optimisation details are now printed if the frame
order system tests fail.
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r9462 | bugman | 2009-09-03 19:17:08 +0200 (Thu, 03 Sep 2009) | 3 lines
Fix for the new frame order system test - the results file goes to devnull.
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r9463 | bugman | 2009-09-03 19:25:01 +0200 (Thu, 03 Sep 2009) | 3 lines
The beta angle for the tensor rotations is now folded to be between 0 and
pi.
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r9464 | bugman | 2009-09-04 10:24:52 +0200 (Fri, 04 Sep 2009) | 5 lines
Added a function for converting the frame order matrix to the rotational
superoperator.
The function is called daeg_to_rotational_superoperator().
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r9465 | bugman | 2009-09-04 11:21:28 +0200 (Fri, 04 Sep 2009) | 5 lines
Fix for the new daeg_to_rotational_superoperator() function.
The frame order matrix shape is now restored.
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r9466 | bugman | 2009-09-04 16:12:31 +0200 (Fri, 04 Sep 2009) | 5 lines
The print_frame_order_2nd_degree() function now accepts the epsilon arg.
This allows zero to be defined differently making the printout nicer.
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r9467 | bugman | 2009-09-07 19:28:57 +0200 (Mon, 07 Sep 2009) | 6 lines
Improved and expanded the output of the print_frame_order_2nd_degree()
function.
The print out can now be in integer form, dots can replace zeros, and
commas between elements are
now optional. Matrix forms are also converted to array forms.
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r9468 | bugman | 2009-09-07 19:31:49 +0200 (Mon, 07 Sep 2009) | 5 lines
Fix for the __update_model() method.
The theta_axis, phi_axis, and theta_cone params were not being added to the
parameter array!
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r9469 | bugman | 2009-09-08 11:14:08 +0200 (Tue, 08 Sep 2009) | 5 lines
Added some unit tests for the R_euler_zyz() function.
This tests some basic axis rotations.
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r9470 | bugman | 2009-09-08 11:26:37 +0200 (Tue, 08 Sep 2009) | 3 lines
Fixes for the R_euler_zyz() unit tests.
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r9471 | bugman | 2009-09-08 11:27:23 +0200 (Tue, 08 Sep 2009) | 5 lines
Fix for the R_euler_zyz() function.
The rotations were being performed in the opposite direction?!?
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r9472 | bugman | 2009-09-08 14:38:05 +0200 (Tue, 08 Sep 2009) | 3 lines
Removed the incorrect part of the R_euler_zyz() docstring.
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r9473 | bugman | 2009-09-08 14:40:37 +0200 (Tue, 08 Sep 2009) | 5 lines
Bug fix for the R_to_euler_zyz() function.
This matches the important bug fix in the R_euler_zyz() function.
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r9474 | bugman | 2009-09-08 14:43:47 +0200 (Tue, 08 Sep 2009) | 5 lines
Fixes for the test_func3() and test_func4() unit tests.
The rotations were backwards because of the R_euler_zyz() fix!
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r9475 | bugman | 2009-09-08 15:11:17 +0200 (Tue, 08 Sep 2009) | 6 lines
Fix to the frame order system tests.
This corresponds to the fixes in R_euler_zyz() where the rotation matrices
were in the left-handed
universe and hence the rotation was back to front.
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r9476 | bugman | 2009-09-08 16:40:16 +0200 (Tue, 08 Sep 2009) | 3 lines
Created 3 unit tests of the maths_fns.rotation_matrix.quaternion_to_R()
function.
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r9477 | bugman | 2009-09-08 17:07:06 +0200 (Tue, 08 Sep 2009) | 5 lines
Created 3 unit tests of the maths_fns.rotation_matrix.R_axis_angle()
function.
These are almost identical to those of quaternion_to_R().
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r9478 | bugman | 2009-09-08 17:42:48 +0200 (Tue, 08 Sep 2009) | 3 lines
Added a unit test for maths_fns.rotation_matrix.R_to_axis_angle() using R =
I.
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r9479 | bugman | 2009-09-08 17:43:36 +0200 (Tue, 08 Sep 2009) | 5 lines
Bug fix for R_to_axis_angle().
All vector elements were NaN when the angle is 0. Now the zero vector is
not normalised by zero.
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r9480 | bugman | 2009-09-08 17:47:59 +0200 (Tue, 08 Sep 2009) | 3 lines
Added another unit test for maths_fns.rotation_matrix.R_axis_angle().
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r9481 | bugman | 2009-09-08 18:20:08 +0200 (Tue, 08 Sep 2009) | 5 lines
Function renaming and argument order changes in the
maths_fns.rotation_matrix module.
The naming scheme is now more logical (as well as the argument order).
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r9482 | bugman | 2009-09-08 18:27:50 +0200 (Tue, 08 Sep 2009) | 3 lines
Alphabetical reordering of functions.
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r9483 | bugman | 2009-09-08 18:52:54 +0200 (Tue, 08 Sep 2009) | 3 lines
Huge simplifications to the unit tests for the maths_fns.rotation_matrix
package.
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r9484 | bugman | 2009-09-08 19:17:29 +0200 (Tue, 08 Sep 2009) | 5 lines
Created the maths_fns.rotation_matrix.axis_angle_to_quaternion() function.
This is accompanied by 2 unit tests.
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r9485 | bugman | 2009-09-08 19:51:14 +0200 (Tue, 08 Sep 2009) | 5 lines
Created the maths_fns.rotation_matrix.quaternion_to_axis_angle() function.
This is accompanied by 2 unit tests.
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r9486 | bugman | 2009-09-08 20:20:34 +0200 (Tue, 08 Sep 2009) | 5 lines
Created the maths_fns.rotation_matrix.R_to_quaternion() function.
This is accompanied by 2 unit tests.
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r9487 | bugman | 2009-09-08 21:07:41 +0200 (Tue, 08 Sep 2009) | 13 lines
Added a unit test to bounce around all the conversion functions in
maths_fns.rotation_matrix.
This bounces through:
1) euler_zyz_to_R().
2) R_to_axis_angle().
3) axis_angle_to_quaternion().
4) quaternion_to_axis_angle().
5) axis_angle_to_R().
6) R_to_quaternion().
7) quaternion_to_R().
8) R_to_euler_zyz().
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r9488 | bugman | 2009-09-09 16:04:40 +0200 (Wed, 09 Sep 2009) | 5 lines
Added a unit test to check if all the
maths_fns.kronecker_product.transpose_*() functions revert.
Calling the function twice should return the matrix to the original state.
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r9489 | bugman | 2009-09-10 14:33:33 +0200 (Thu, 10 Sep 2009) | 3 lines
Renamed the data pipes system tests module.
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r9490 | bugman | 2009-09-10 16:51:39 +0200 (Thu, 10 Sep 2009) | 3 lines
Wrote a system test for the writing and re-reading of data pipes.
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r9491 | bugman | 2009-09-10 16:53:06 +0200 (Thu, 10 Sep 2009) | 3 lines
Shifted the valid types private function variable into a module variable.
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r9492 | bugman | 2009-09-10 16:54:55 +0200 (Thu, 10 Sep 2009) | 3 lines
The test_write_read_pipes() system test is now using the VALID_TYPES module
variable to get all pipes.
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r9493 | bugman | 2009-09-10 17:01:39 +0200 (Thu, 10 Sep 2009) | 3 lines
Deleted the __init__() class methods as these were empty, and shifted the
docstring to that of the class.
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r9494 | bugman | 2009-09-10 17:02:22 +0200 (Thu, 10 Sep 2009) | 3 lines
Removed an empty line.
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r9495 | bugman | 2009-09-10 17:20:21 +0200 (Thu, 10 Sep 2009) | 5 lines
Added a very basic, and completely empty module and class for SRLS analysis.
This is to allow the data pipe to be created.
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r9496 | bugman | 2009-09-10 17:37:16 +0200 (Thu, 10 Sep 2009) | 3 lines
Updated the specific_fns module __all__ list for the SRLS module.
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r9497 | bugman | 2009-09-10 17:38:20 +0200 (Thu, 10 Sep 2009) | 5 lines
Shifted the test_write_read_pipes() system test to the 'state' test module.
The program state is now being saved as the results file is for just one
data pipe.
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r9498 | bugman | 2009-09-10 18:07:22 +0200 (Thu, 10 Sep 2009) | 3 lines
A few fixes for the test_write_read_pipes() system test.
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r9499 | bugman | 2009-09-10 18:32:31 +0200 (Thu, 10 Sep 2009) | 7 lines
Redesign of the relax state loading for adding support for a XML formatted
state file.
Half of the load_state() is now in load_pickle(), and a new function
load_xml() added.
The determine_format() function will tell if the file is a pickle or XML
file, and then
load_pickle() will run the appropriate loading function.
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r9500 | bugman | 2009-09-10 18:36:40 +0200 (Thu, 10 Sep 2009) | 5 lines
Added the pickle flag to save_state().
This defaults to True to prevent relax failures during the XML file
implementation.
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r9501 | bugman | 2009-09-10 19:01:25 +0200 (Thu, 10 Sep 2009) | 5 lines
The save_state() function now calls the relax data store to_xml() method.
This method is currently only for one data pipe, and is used by the results
writing user function.
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r9502 | bugman | 2009-09-10 19:24:30 +0200 (Thu, 10 Sep 2009) | 6 lines
The relax data store to_xml() method now can add all data pipes to the XML
file (or a subset).
The results.write() method now asks to_xml() for just the current pipe to
be stored, whereas
state.save() supplies no 'pipes' argument to have all pipes stored.
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r9503 | bugman | 2009-09-10 19:26:22 +0200 (Thu, 10 Sep 2009) | 5 lines
Shifted the results.write() force arg to the end.
Bool args should be last!
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r9504 | bugman | 2009-09-10 19:37:33 +0200 (Thu, 10 Sep 2009) | 3 lines
Removed trailing whitespace.
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r9505 | bugman | 2009-09-10 19:56:32 +0200 (Thu, 10 Sep 2009) | 3 lines
Updates to the load_xml() function. This now does something!
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r9506 | bugman | 2009-09-10 20:04:05 +0200 (Thu, 10 Sep 2009) | 3 lines
Created the relax data store is_empty() method.
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r9507 | bugman | 2009-09-11 10:06:05 +0200 (Fri, 11 Sep 2009) | 6 lines
Added the pickle arg to state.save().
This allows the relax state - the contents of the relax data store - to
either be saved as XML or as
a pickled object.
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r9508 | bugman | 2009-09-11 10:07:11 +0200 (Fri, 11 Sep 2009) | 3 lines
Added a warning to the state.save() user function about the pickle format
compatibility.
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r9509 | bugman | 2009-09-11 10:16:04 +0200 (Fri, 11 Sep 2009) | 6 lines
Absorbed the load_xml() function into load_state().
After shifting the data store check to load_state() for all formats, the
function only had one
statement.
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r9510 | bugman | 2009-09-11 10:29:08 +0200 (Fri, 11 Sep 2009) | 3 lines
Docstring clarification of the dir arg.
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r9511 | bugman | 2009-09-11 11:12:30 +0200 (Fri, 11 Sep 2009) | 3 lines
Updated the relax data store from_xml() method for support of the loading
of the XML state file.
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r9512 | bugman | 2009-09-11 11:31:44 +0200 (Fri, 11 Sep 2009) | 5 lines
Added the force flag to the state.load() user function.
When True, this causes the relax data store to be reset prior to state
loading.
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r9513 | bugman | 2009-09-11 11:36:02 +0200 (Fri, 11 Sep 2009) | 5 lines
Duplicated the test_state() system test into test_state_pickle() and
test_state_xml().
This tests both formats.
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r9514 | bugman | 2009-09-11 11:39:53 +0200 (Fri, 11 Sep 2009) | 6 lines
Fixes for load_pickle().
The ds.__reset__() call has been removed because of redundancy and the new
ds.is_empty() has been
blacklisted.
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r9515 | bugman | 2009-09-11 11:48:17 +0200 (Fri, 11 Sep 2009) | 3 lines
Changed the default save state to XML.
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r9516 | bugman | 2009-09-11 13:43:34 +0200 (Fri, 11 Sep 2009) | 3 lines
Added a dir arg to a state.save() call in test_state_pickle().
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r9517 | bugman | 2009-09-11 13:52:36 +0200 (Fri, 11 Sep 2009) | 5 lines
Renamed the state.load() and state.save() directory argument from dir_name
to dir.
This is to bring it in line with the rest of relax.
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r9518 | bugman | 2009-09-11 14:44:41 +0200 (Fri, 11 Sep 2009) | 3 lines
Fixes for print_frame_order_2nd_degree() for when NaN is encountered.
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r9519 | bugman | 2009-09-11 14:46:04 +0200 (Fri, 11 Sep 2009) | 5 lines
Fix for the print_frame_order_2nd_degree().
The NaN fix was partly incorrect.
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r9520 | bugman | 2009-09-11 15:04:15 +0200 (Fri, 11 Sep 2009) | 3 lines
Made the integer printout 4 char wide.
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r9521 | bugman | 2009-09-11 15:31:42 +0200 (Fri, 11 Sep 2009) | 5 lines
Bug fix for the compile_2nd_matrix_iso_cone() function.
The T23 and not T14 transpose should be performed!
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r9522 | bugman | 2009-09-11 15:59:04 +0200 (Fri, 11 Sep 2009) | 2 lines
Reordered the relax debugging save state so that the format is
yyyymmdd_hhmmss rather than yyyyddmm_hhmmss.
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r9523 | bugman | 2009-09-11 17:55:23 +0200 (Fri, 11 Sep 2009) | 3 lines
Added a check for the setting of the domain the tensor corresponds to.
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r9524 | bugman | 2009-09-14 13:59:44 +0200 (Mon, 14 Sep 2009) | 3 lines
Renamed the frame order target function module.
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r9525 | bugman | 2009-09-14 14:07:40 +0200 (Mon, 14 Sep 2009) | 3 lines
Bug fix, the func_iso_cone_elements() method was been replaced with
func_iso_cone().
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r9526 | bugman | 2009-09-14 14:23:10 +0200 (Mon, 14 Sep 2009) | 5 lines
Fix for r9525.
The func_iso_cone() was now not being set up.
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Added:
branches/multi_processor_merge/maths_fns/frame_order.py
- copied unchanged from r9526, 1.3/maths_fns/frame_order.py
branches/multi_processor_merge/specific_fns/srls.py
- copied unchanged from r9526, 1.3/specific_fns/srls.py
branches/multi_processor_merge/test_suite/system_tests/pipes.py
- copied unchanged from r9526, 1.3/test_suite/system_tests/pipes.py
branches/multi_processor_merge/test_suite/system_tests/scripts/frame_order/
- copied from r9526, 1.3/test_suite/system_tests/scripts/frame_order/
Removed:
branches/multi_processor_merge/maths_fns/frame_order_models.py
branches/multi_processor_merge/test_suite/system_tests/pipe_create.py
branches/multi_processor_merge/test_suite/system_tests/scripts/frame_order_rigid_no_rot.py
Modified:
branches/multi_processor_merge/ (props changed)
branches/multi_processor_merge/data/__init__.py
branches/multi_processor_merge/data/pipe_container.py
branches/multi_processor_merge/docs/2to3_checklist
branches/multi_processor_merge/generic_fns/frame_order.py
branches/multi_processor_merge/generic_fns/pipes.py
branches/multi_processor_merge/generic_fns/results.py
branches/multi_processor_merge/generic_fns/state.py
branches/multi_processor_merge/generic_fns/structure/geometric.py
branches/multi_processor_merge/maths_fns/__init__.py
branches/multi_processor_merge/maths_fns/frame_order_matrix_ops.py
branches/multi_processor_merge/maths_fns/n_state_model.py
branches/multi_processor_merge/maths_fns/rotation_matrix.py
branches/multi_processor_merge/prompt/results.py
branches/multi_processor_merge/prompt/state.py
branches/multi_processor_merge/relax_errors.py
branches/multi_processor_merge/specific_fns/__init__.py
branches/multi_processor_merge/specific_fns/consistency_tests.py
branches/multi_processor_merge/specific_fns/frame_order.py
branches/multi_processor_merge/specific_fns/hybrid.py
branches/multi_processor_merge/specific_fns/jw_mapping.py
branches/multi_processor_merge/specific_fns/n_state_model.py
branches/multi_processor_merge/specific_fns/noe.py
branches/multi_processor_merge/specific_fns/setup.py
branches/multi_processor_merge/test_suite/system_tests/__init__.py
branches/multi_processor_merge/test_suite/system_tests/frame_order.py
branches/multi_processor_merge/test_suite/system_tests/relax_fit.py
branches/multi_processor_merge/test_suite/system_tests/results.py
branches/multi_processor_merge/test_suite/system_tests/scripts/1UBQ_relax_fit.py
branches/multi_processor_merge/test_suite/system_tests/scripts/palmer.py
branches/multi_processor_merge/test_suite/system_tests/scripts/palmer_omp.py
branches/multi_processor_merge/test_suite/system_tests/state.py
branches/multi_processor_merge/test_suite/unit_tests/_maths_fns/test_kronecker_product.py
branches/multi_processor_merge/test_suite/unit_tests/_maths_fns/test_n_state_model.py
branches/multi_processor_merge/test_suite/unit_tests/_maths_fns/test_rotation_matrix.py
branches/multi_processor_merge/test_suite/unit_tests/_prompt/test_state.py
branches/multi_processor_merge/test_suite/unit_tests/state_testing_base.py
[This mail would be too long, it was shortened to contain the URLs only.]
Modified: branches/multi_processor_merge/data/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/data/__init__.py?rev=9527&r1=9526&r2=9527&view=diff
Modified: branches/multi_processor_merge/data/pipe_container.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/data/pipe_container.py?rev=9527&r1=9526&r2=9527&view=diff
Modified: branches/multi_processor_merge/docs/2to3_checklist
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/docs/2to3_checklist?rev=9527&r1=9526&r2=9527&view=diff
Modified: branches/multi_processor_merge/generic_fns/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/generic_fns/frame_order.py?rev=9527&r1=9526&r2=9527&view=diff
Modified: branches/multi_processor_merge/generic_fns/pipes.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/generic_fns/pipes.py?rev=9527&r1=9526&r2=9527&view=diff
Modified: branches/multi_processor_merge/generic_fns/results.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/generic_fns/results.py?rev=9527&r1=9526&r2=9527&view=diff
Modified: branches/multi_processor_merge/generic_fns/state.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/generic_fns/state.py?rev=9527&r1=9526&r2=9527&view=diff
Modified: branches/multi_processor_merge/generic_fns/structure/geometric.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/generic_fns/structure/geometric.py?rev=9527&r1=9526&r2=9527&view=diff
Modified: branches/multi_processor_merge/maths_fns/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/maths_fns/__init__.py?rev=9527&r1=9526&r2=9527&view=diff
Modified: branches/multi_processor_merge/maths_fns/frame_order_matrix_ops.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/maths_fns/frame_order_matrix_ops.py?rev=9527&r1=9526&r2=9527&view=diff
Removed: branches/multi_processor_merge/maths_fns/frame_order_models.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/maths_fns/frame_order_models.py?rev=9526&view=auto
Modified: branches/multi_processor_merge/maths_fns/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/maths_fns/n_state_model.py?rev=9527&r1=9526&r2=9527&view=diff
Modified: branches/multi_processor_merge/maths_fns/rotation_matrix.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_processor_merge/maths_fns/rotation_matrix.py?rev=9527&r1=9526&r2=9527&view=diff
Modified: branches/multi_processor_merge/prompt/results.py
[... 77 lines stripped ...]
r9527 - in /branches/multi_processor_merge: ./ data/ docs/ generic_fns/ generic_fns/structure/ maths_fns/ prompt/ specific_f...