relax SVN archive

svn+ssh://bugman@.../svn/relax/1.3

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r9236 | bugman | 2009-07-15 17:38:43 +0200 (Wed, 15 Jul 2009) | 3 lines

The rdc.read() user function now accepts the spin_id arg.
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r9237 | bugman | 2009-07-15 17:39:16 +0200 (Wed, 15 Jul 2009) | 3 lines

Modified return_spin() to handle multiple spin ID strings.
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r9238 | bugman | 2009-07-15 17:45:07 +0200 (Wed, 15 Jul 2009) | 3 lines

The pcs.read() user function also now accepts the spin_id argument.
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r9239 | bugman | 2009-07-15 17:46:36 +0200 (Wed, 15 Jul 2009) | 5 lines

Removed the checks to see if the RDC or PCS data is already loaded.

Now data can be loaded sequentially by a few calls to rdc.read() and pcs.read().
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r9240 | bugman | 2009-07-15 18:00:33 +0200 (Wed, 15 Jul 2009) | 5 lines

Large improvements to the align_tensor.display() user function.

Now much more information is provided.
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r9241 | bugman | 2009-07-15 18:25:39 +0200 (Wed, 15 Jul 2009) | 3 lines

Added the method names() to return a list of alignment tensor names.
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r9242 | bugman | 2009-07-15 18:26:17 +0200 (Wed, 15 Jul 2009) | 5 lines

Removed a check for the presence of the alignment tensor.

Now align_tensor.init() can be used to reset the tensor values.
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r9243 | bugman | 2009-07-15 18:27:37 +0200 (Wed, 15 Jul 2009) | 3 lines

Only add a new tensor object if the tensor doesn't already exist.
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r9244 | bugman | 2009-07-15 19:20:10 +0200 (Wed, 15 Jul 2009) | 3 lines

Fix for the N-state model when N = 1.
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r9245 | bugman | 2009-07-15 20:13:25 +0200 (Wed, 15 Jul 2009) | 3 lines

Added the Saupe element eigenvalues to the align_tensor.display() print out.
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r9246 | bugman | 2009-07-15 20:25:23 +0200 (Wed, 15 Jul 2009) | 3 lines

The matrix_angles() function now avoids NaN problems through arccos of numbers > 1.
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r9248 | bugman | 2009-07-16 19:45:33 +0200 (Thu, 16 Jul 2009) | 5 lines

Bug fix for the write_pdb() method.

The MODEL record is now created for single structures if a model number exists.
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r9249 | bugman | 2009-07-20 01:16:52 +0200 (Mon, 20 Jul 2009) | 11 lines

Created functions for rank-4, 3D tensor transposes (and corresponding unit tests).

The new functions are:
maths_fns.kronecker_product.transpose_12()
maths_fns.kronecker_product.transpose_13()
maths_fns.kronecker_product.transpose_14()
maths_fns.kronecker_product.transpose_23()
maths_fns.kronecker_product.transpose_24()
maths_fns.kronecker_product.transpose_34()
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r9250 | bugman | 2009-07-20 14:02:30 +0200 (Mon, 20 Jul 2009) | 3 lines

Switched to the internal PDB reader for removal of the reliance on Scientific python.
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r9251 | bugman | 2009-07-21 15:09:18 +0200 (Tue, 21 Jul 2009) | 3 lines

Added some MC simulation data and errors for the diffusion tensor system tests.
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r9252 | bugman | 2009-07-21 15:19:03 +0200 (Tue, 21 Jul 2009) | 3 lines

Split the system test of structure.create_diff_tensor_pdb() into 3 tests for each diff type.
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r9253 | bugman | 2009-07-21 15:54:30 +0200 (Tue, 21 Jul 2009) | 3 lines

Removed trailing whitespace.
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r9254 | bugman | 2009-07-21 16:28:02 +0200 (Tue, 21 Jul 2009) | 5 lines

Changed the order of setting the MC simulation data for the diffusion tensor.

This should test things a bit better.
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r9255 | bugman | 2009-07-21 16:57:19 +0200 (Tue, 21 Jul 2009) | 3 lines

Modification of MC sim list elements is now also tested.
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r9256 | bugman | 2009-07-21 16:59:29 +0200 (Tue, 21 Jul 2009) | 6 lines

Bug fixes for the diffusion tensor MC simulation data structure updating.

The MC simulation structures were not being updated at all!!! This now works, allowing the
diffusion tensor PDB representation to be created.
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r9257 | bugman | 2009-07-21 17:03:21 +0200 (Tue, 21 Jul 2009) | 3 lines

The MC sim vectors for the diffusion tensor axes are now being properly created.
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r9258 | bugman | 2009-07-21 17:03:43 +0200 (Tue, 21 Jul 2009) | 3 lines

Removed some debugging code.
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r9259 | bugman | 2009-07-21 17:15:28 +0200 (Tue, 21 Jul 2009) | 5 lines

Bug fix for the creation of the ellipsoid diffusion tensor PDB representation.

The axes are now labelled Dx, Dy, and Dz instead of all Dpar!
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r9260 | bugman | 2009-07-21 17:40:29 +0200 (Tue, 21 Jul 2009) | 5 lines

Bug fix for the creation of the spheroid diff tensor PDB representation.

The simulation vectors should be initialised to a list.
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r9261 | bugman | 2009-07-21 17:47:23 +0200 (Tue, 21 Jul 2009) | 3 lines

The ellipsoid diff tensor PDB file is now being checked, line for line.
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r9262 | bugman | 2009-07-21 21:38:43 +0200 (Tue, 21 Jul 2009) | 3 lines

The diffusion tensor MC sim data is now properly set up.
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r9263 | bugman | 2009-07-21 21:39:44 +0200 (Tue, 21 Jul 2009) | 5 lines

Bug fix for the diffusion tensor MC sim data structures.

All structures are now properly updated when a value for a single simulation changes.
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r9264 | bugman | 2009-07-21 22:31:06 +0200 (Tue, 21 Jul 2009) | 3 lines

The spherical diffusion tensor system tests are now properly set up.
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r9265 | bugman | 2009-07-21 22:32:04 +0200 (Tue, 21 Jul 2009) | 5 lines

Bug fix for the __update_sim_append() method.

Now the diffusion tensor simulation structure appending works if the structure doesn't already exist.
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r9266 | bugman | 2009-07-22 01:10:56 +0200 (Wed, 22 Jul 2009) | 3 lines

Extended the test_copy() system test to properly check if a copy is made, rather than link.
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r9267 | bugman | 2009-07-22 01:20:52 +0200 (Wed, 22 Jul 2009) | 5 lines

Fix for the test_copy() system test.

The wrong indices were being checked.
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r9268 | bugman | 2009-07-22 02:00:13 +0200 (Wed, 22 Jul 2009) | 7 lines

Bug fix for the copying of diffusion tensors data structures.

The DiffTensorSimList objects in DiffTensorData were not being properly copied! This has been fixed
by writing class specific __deepcopy__() methods for both classes. The Element class has also been
subclassed from 'object'.
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r9269 | bugman | 2009-07-22 02:12:55 +0200 (Wed, 22 Jul 2009) | 5 lines

The test_create_diff_tensor_pdb_ellipsoid() system test has been made more vigorous.

The copy operations are now better tested.
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r9270 | bugman | 2009-07-22 09:40:26 +0200 (Wed, 22 Jul 2009) | 3 lines

The diffusion tensor copying system test is now more comprehensive.
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r9271 | bugman | 2009-07-22 11:23:10 +0200 (Wed, 22 Jul 2009) | 5 lines

Added comprehensive checks for the creation of the diffusion tensor PDB representations.

The sphere and spheroid PDB files are now checked, line for line.
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r9276 | bugman | 2009-08-12 13:06:51 +0200 (Wed, 12 Aug 2009) | 3 lines

Made the structure system tests more compatible with non-Unix operating systems.
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r9277 | bugman | 2009-08-12 13:11:27 +0200 (Wed, 12 Aug 2009) | 3 lines

Made get_file_path() and mkdir_nofail() compatible with non-Unix systems.
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r9278 | bugman | 2009-08-12 13:16:06 +0200 (Wed, 12 Aug 2009) | 3 lines

Made the full_analysis.py script more compatible with non-Unix operating systems.
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r9279 | bugman | 2009-08-12 13:18:30 +0200 (Wed, 12 Aug 2009) | 3 lines

Fix for test_load_scientific_results(). The Unix paths are used in the results file!
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r9280 | bugman | 2009-08-12 13:23:15 +0200 (Wed, 12 Aug 2009) | 3 lines

Non-Unix os fix.
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r9281 | bugman | 2009-08-12 13:54:53 +0200 (Wed, 12 Aug 2009) | 3 lines

Modified the unit tests to be more non-Unix operating system compatible.
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r9282 | bugman | 2009-08-12 14:25:49 +0200 (Wed, 12 Aug 2009) | 3 lines

Modified the system tests to be more non-Unix operating system compatible.
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r9283 | bugman | 2009-08-12 14:38:00 +0200 (Wed, 12 Aug 2009) | 4 lines

Modified the shared data scripts to be more non-Unix operating system compatible.
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r9284 | bugman | 2009-08-12 14:53:54 +0200 (Wed, 12 Aug 2009) | 3 lines

Removed the last '/' directory separators to be more non-Unix operating system compatible.
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r9285 | bugman | 2009-08-12 15:02:38 +0200 (Wed, 12 Aug 2009) | 3 lines

Removed a reference to the '..' dir.
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r9286 | bugman | 2009-08-12 15:05:03 +0200 (Wed, 12 Aug 2009) | 3 lines

Redid r9279! This was accidentally reverted by hand in r9282!!!
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r9287 | bugman | 2009-08-12 15:34:50 +0200 (Wed, 12 Aug 2009) | 3 lines

Caught a NaN problem in __q_factors_rdc() causing a system test to fail in Windows.
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r9288 | bugman | 2009-08-12 18:57:21 +0200 (Wed, 12 Aug 2009) | 7 lines

Massive clean up of the float module unit tests.

As a general clean up, the module has been converted to the relax coding conventions. Importantly
the floating point numbers defined as constants for the tests are now properly defined using the
packBytesAsPyFloat() function. This will allow these tests to pass on all machines!
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r9290 | bugman | 2009-08-12 20:04:53 +0200 (Wed, 12 Aug 2009) | 8 lines

Ported the CHANGES file for relax version 1.2.15 to the 1.3 line.

This was obviously forgotten when the release was made.

The command used was:
svn merge -r8033:8034 svn+ssh://bugman@.../svn/relax/tags/1.2.15 .
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r9292 | bugman | 2009-08-13 15:20:47 +0200 (Thu, 13 Aug 2009) | 5 lines

Updated the _off() and _on() user function echoing methods.

The flag is now a boolean, and the message has been reworded.
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r9303 | bugman | 2009-08-14 10:49:12 +0200 (Fri, 14 Aug 2009) | 3 lines

Updated the release checklist document to reflect Gna! and Freshmeat website changes.
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r9304 | bugman | 2009-08-14 10:51:09 +0200 (Fri, 14 Aug 2009) | 3 lines

Converted a number of flags from int to bool.
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r9305 | bugman | 2009-08-14 11:04:30 +0200 (Fri, 14 Aug 2009) | 3 lines

More changes to the release checklist document.
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r9306 | bugman | 2009-08-14 11:06:06 +0200 (Fri, 14 Aug 2009) | 3 lines

Added a script for running the full relax test suite against different Python versions.
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r9307 | bugman | 2009-08-14 11:19:20 +0200 (Fri, 14 Aug 2009) | 3 lines

Fix for the test_opt_constr_newton_gmw_mt_S2_0_970_te_2048_Rex_0_149() system test for Python 2.5.
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r9308 | bugman | 2009-08-14 11:25:29 +0200 (Fri, 14 Aug 2009) | 3 lines

Created a directory for holding miscellaneous scripts for developers.
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r9309 | bugman | 2009-08-14 11:25:55 +0200 (Fri, 14 Aug 2009) | 3 lines

Shifted the python version checking script.
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r9310 | bugman | 2009-08-14 11:28:20 +0200 (Fri, 14 Aug 2009) | 3 lines

Shifted the code validation script from the website hidden location into the scripts directory.
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r9311 | bugman | 2009-08-14 11:37:47 +0200 (Fri, 14 Aug 2009) | 3 lines

Fix for the test_opt_constr_newton_gmw_mt_S2_0_970_te_2048_Rex_0_149() system test for all Python version.
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r9314 | bugman | 2009-08-14 11:44:34 +0200 (Fri, 14 Aug 2009) | 6 lines

Merged the relax 1.3.4 CHANGES file into the 1.3 line.

The command used was:
svn merge -r9296:9297 svn+ssh://bugman@.../svn/relax/tags/1.3.4 .
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