Author: bugman
Date: Thu Aug 7 15:30:09 2008
New Revision: 7078
URL: http://svn.gna.org/viewcvs/relax?rev=7078&view=rev
Log:
Merged revisions
6257-6259,6261-6304,6306,6308,6310-6320,6322-6323,6325-6332,6352-6354,6356-6498,6501-6610,6612-6651,6654,6665,6673,6675-6677,6679,6681,6685-6693,6736-6738,6742-6835,6838,6840,6879,6939-6940,6946-6951,6954,6956,6993-7019,7022-7028,7030-7040,7047-7075
via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
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r6257 | bugman | 2008-05-22 17:27:41 +0200 (Thu, 22 May 2008) | 3 lines
Initialized merge tracking via "svnmerge" with revisions "1-6249" from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/singleton_fixing
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r6258 | bugman | 2008-05-22 17:28:28 +0200 (Thu, 22 May 2008) | 41 lines
Merged revisions 6252-6256 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/singleton_fixing
........
r6252 | bugman | 2008-05-22 16:01:01 +0200 (Thu, 22 May 2008) | 3 lines
Fixed the test_load_and_modify unit test. Key order doesn't matter now.
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r6253 | bugman | 2008-05-22 16:38:44 +0200 (Thu, 22 May 2008) | 6 lines
Fix for the loading of the pickled relax data store.
The blacklisted objects was extended to include all dict objects, data
store specific methods, and
other special objects.
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r6254 | bugman | 2008-05-22 16:55:25 +0200 (Thu, 22 May 2008) | 14 lines
Changed the design of the relax data store singleton.
The singleton saving and loading problem is discussed in the thread
starting at:
https://mail.gna.org/public/relax-devel/2007-11/msg00021.html (Message-id:
<7f080ed10711201001s59a00533pf3c0ee3f88a79edb@xxxxxxxxxxxxxx>). For more
history, see the thread
starting at https://mail.gna.org/public/relax-devel/2007-03/msg00046.html
(Message-id:
<7f080ed10703140609p70d35295ye10ee5939da494a2@xxxxxxxxxxxxxx>) and the
original singleton idea at
https://mail.gna.org/public/relax-devel/2007-03/msg00012.html (Message-id:
<7f080ed10703070006s309a1e1do38e621f48d8f6d9e@xxxxxxxxxxxxxx>).
This reverts to the original singleton behaviour in the last link. Note
that this will be reverted
to the current singleton design once a good solution to the pickling
issues can be found.
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r6255 | bugman | 2008-05-22 17:23:26 +0200 (Thu, 22 May 2008) | 3 lines
Converted all code to use the old singleton design.
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r6256 | bugman | 2008-05-22 17:26:09 +0200 (Thu, 22 May 2008) | 5 lines
Fix for the relax data storage singleton.
The 'instance' class variable is now excluded in the '__repr__()' method.
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r6259 | bugman | 2008-05-22 17:29:10 +0200 (Thu, 22 May 2008) | 3 lines
Removed merge tracking for "svnmerge" for
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/singleton_fixing
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r6261 | bugman | 2008-05-22 17:47:14 +0200 (Thu, 22 May 2008) | 3 lines
Fixed the basic_heights_T2_ncyc1 saved state.
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r6262 | bugman | 2008-05-22 17:52:35 +0200 (Thu, 22 May 2008) | 3 lines
Fixed the test_read_sparky system test.
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r6263 | bugman | 2008-05-22 18:03:57 +0200 (Thu, 22 May 2008) | 3 lines
Shifted all last dependencies from the 'minimise' relax package to the
'minfx' python package.
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r6264 | bugman | 2008-05-22 18:07:50 +0200 (Thu, 22 May 2008) | 6 lines
Deletion of the 'minimise' relax package.
This package has been replaced by the minfx python package (which is
derived from the 'minimise'
code).
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r6265 | bugman | 2008-05-22 18:09:14 +0200 (Thu, 22 May 2008) | 3 lines
Added the missing relax base directories to the unit tests.
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r6266 | bugman | 2008-05-22 18:10:09 +0200 (Thu, 22 May 2008) | 3 lines
Removed the recently added _opendx directory (it already exists as _dx).
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r6267 | bugman | 2008-05-22 18:10:26 +0200 (Thu, 22 May 2008) | 3 lines
Directory rename.
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r6268 | bugman | 2008-05-22 18:11:52 +0200 (Thu, 22 May 2008) | 3 lines
Added an empty package __init__ module.
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r6269 | bugman | 2008-05-22 18:14:11 +0200 (Thu, 22 May 2008) | 3 lines
Added a directory for unit tests of the model-free specific code.
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r6270 | bugman | 2008-05-22 18:15:20 +0200 (Thu, 22 May 2008) | 3 lines
Added an empty package __init__ module.
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r6271 | semor | 2008-05-28 12:59:14 +0200 (Wed, 28 May 2008) | 3 lines
Added a missing import.
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r6272 | semor | 2008-05-28 13:25:43 +0200 (Wed, 28 May 2008) | 3 lines
Numeric to numpy conversion.
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r6273 | bugman | 2008-05-28 20:58:25 +0200 (Wed, 28 May 2008) | 6 lines
Renamed the main model-free module.
The original module was specific_fns.model_free.model_free whereas the new
is
specific_fns.model_free.main.
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r6274 | bugman | 2008-05-28 21:11:18 +0200 (Wed, 28 May 2008) | 3 lines
Split off all the model-free results files methods into their own module.
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r6275 | bugman | 2008-05-28 21:35:55 +0200 (Wed, 28 May 2008) | 3 lines
Wrote a method for determining which relax version the results file belongs
to.
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r6276 | bugman | 2008-05-28 21:39:48 +0200 (Wed, 28 May 2008) | 3 lines
Split the read_columnar_results() method into version specific methods.
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r6277 | bugman | 2008-05-28 21:41:08 +0200 (Wed, 28 May 2008) | 3 lines
Passed the verbosity variable into the __determine_version() method.
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r6278 | bugman | 2008-05-28 21:42:29 +0200 (Wed, 28 May 2008) | 3 lines
Fixes for the verbosity variable.
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r6279 | bugman | 2008-05-28 22:03:01 +0200 (Wed, 28 May 2008) | 3 lines
Fixed the method name.
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r6280 | bugman | 2008-05-28 22:12:21 +0200 (Wed, 28 May 2008) | 3 lines
Modified and renamed read_columnar_col_numbers() to __read_col_numbers().
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r6281 | bugman | 2008-05-28 22:17:40 +0200 (Wed, 28 May 2008) | 3 lines
Changed all references to the dict of column indecies as this is no longer
an instance variable.
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r6282 | bugman | 2008-05-28 22:20:46 +0200 (Wed, 28 May 2008) | 3 lines
Changed some flags to bools in __read_1_2_results().
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r6283 | bugman | 2008-05-28 22:23:25 +0200 (Wed, 28 May 2008) | 3 lines
Shifted a number of variables out of self.
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r6284 | bugman | 2008-05-28 22:25:08 +0200 (Wed, 28 May 2008) | 3 lines
Renamed read_columnar_sequence() to __generate_sequence().
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r6285 | bugman | 2008-05-28 22:40:12 +0200 (Wed, 28 May 2008) | 3 lines
Fixed the sequence generation.
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r6286 | bugman | 2008-05-28 22:47:37 +0200 (Wed, 28 May 2008) | 3 lines
Made the __generate_sequence() method handle all relax versions.
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r6287 | bugman | 2008-05-28 22:49:25 +0200 (Wed, 28 May 2008) | 5 lines
Renamed file_line to spin_line in __generate_sequence().
This is to generalise the method.
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r6288 | bugman | 2008-05-28 22:58:51 +0200 (Wed, 28 May 2008) | 3 lines
Renamed read_columnar_find_index() to __get_spin_container() and converted
it to the new design.
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r6289 | bugman | 2008-05-28 23:07:52 +0200 (Wed, 28 May 2008) | 3 lines
Fixed the setting of the nucleus type.
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r6290 | bugman | 2008-05-28 23:09:38 +0200 (Wed, 28 May 2008) | 3 lines
Renamed __get_spin_container() to __get_spin_id().
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r6291 | bugman | 2008-05-28 23:14:50 +0200 (Wed, 28 May 2008) | 3 lines
Changed the importing and calling of methods from the generic_fns package.
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r6292 | bugman | 2008-05-28 23:15:50 +0200 (Wed, 28 May 2008) | 3 lines
Added a module docstring.
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r6293 | bugman | 2008-05-28 23:19:37 +0200 (Wed, 28 May 2008) | 3 lines
Converted the simulation selection flag to a bool.
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r6294 | bugman | 2008-05-28 23:32:02 +0200 (Wed, 28 May 2008) | 3 lines
Renamed read_columnar_diff_tensor() to __set_diff_tensor() and converted to
the new design.
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r6295 | bugman | 2008-05-28 23:40:11 +0200 (Wed, 28 May 2008) | 3 lines
Renamed read_columnar_param_set() to __fix_params() and converted to the
new design.
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r6296 | bugman | 2008-05-28 23:47:43 +0200 (Wed, 28 May 2008) | 3 lines
Added some additional print outs.
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r6297 | bugman | 2008-05-28 23:49:32 +0200 (Wed, 28 May 2008) | 3 lines
Fixes for the __fix_params() method.
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r6298 | bugman | 2008-05-28 23:56:54 +0200 (Wed, 28 May 2008) | 3 lines
Renamed read_columnar_pdb() to __load_structure() and converted to the new
design.
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r6299 | bugman | 2008-05-29 00:04:23 +0200 (Thu, 29 May 2008) | 3 lines
Renamed read_columnar_xh_vect() to __set_xh_vect() and converted to the new
design.
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r6300 | bugman | 2008-05-29 00:13:15 +0200 (Thu, 29 May 2008) | 3 lines
Renamed read_columnar_relax_data() to __load_relax_data() and converted to
the new design.
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r6301 | bugman | 2008-05-29 00:16:40 +0200 (Thu, 29 May 2008) | 3 lines
Fixed the references to the relax_data object.
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r6302 | bugman | 2008-05-29 01:08:02 +0200 (Thu, 29 May 2008) | 3 lines
Renamed add_residue() to add_data_to_spin() and started to convert it to
the new design.
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r6303 | bugman | 2008-05-29 17:12:32 +0200 (Thu, 29 May 2008) | 3 lines
Fixed an import statement.
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r6304 | bugman | 2008-05-30 10:38:18 +0200 (Fri, 30 May 2008) | 6 lines
Bug fix for the __determine_version() method for identifying a relax 1.2
results file.
For details, see Seb's post at
https://mail.gna.org/public/relax-devel/2008-05/msg00001.html
(Message-id: <483F0716.5080402@xxxxxxxxx>).
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r6306 | bugman | 2008-06-02 13:49:57 +0200 (Mon, 02 Jun 2008) | 9 lines
Added the EXCLUDE variable in full_analysis.py for excluding spins in a
file from the analysis.
This doesn't interfere with the UNRES variable. The idea was proposed by
Seb in the thread starting
at https://mail.gna.org/public/relax-users/2008-05/msg00007.html
(Message-id:
<48275822.3070209@xxxxxxxxx>). The implementation was discussed in
https://mail.gna.org/public/relax-users/2008-05/msg00011.html (Message-id:
<7f080ed10805280653g4d7c6730ic5afa5f08ebcc4aa@xxxxxxxxxxxxxx>).
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r6308 | bugman | 2008-06-02 18:51:04 +0200 (Mon, 02 Jun 2008) | 3 lines
Grammar fixes in the full_analysis.py description.
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r6310 | bugman | 2008-06-02 18:59:18 +0200 (Mon, 02 Jun 2008) | 3 lines
For the new relax design, 'residue' was renamed to 'spin' and 'protein'
renamed to 'molecule'.
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r6311 | bugman | 2008-06-03 21:56:50 +0200 (Tue, 03 Jun 2008) | 3 lines
Changed the Numeric dependency check to a numpy check.
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r6312 | bugman | 2008-06-03 21:59:44 +0200 (Tue, 03 Jun 2008) | 3 lines
Added a check for the minfx python package.
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r6313 | bugman | 2008-06-03 22:14:51 +0200 (Tue, 03 Jun 2008) | 3 lines
Added checks for the Scientific.Visualization.VMD import (because it
requires Numeric).
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r6314 | bugman | 2008-06-04 00:41:06 +0200 (Wed, 04 Jun 2008) | 3 lines
Removed the readline dependence, this is now optional.
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r6315 | semor | 2008-06-04 20:31:35 +0200 (Wed, 04 Jun 2008) | 5 lines
Corrected looping over residues in the consistency_tests system test.
These changes make the system test pass and are based on the jw_mapping
system test.
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r6316 | semor | 2008-06-04 21:14:28 +0200 (Wed, 04 Jun 2008) | 7 lines
Corrected the F_eta and F_R2 values within the system test.
The old values were those for the 1.2 line where the CSA was -170 ppm (now
-172).
The consistency_tests system test now completely passes.
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r6317 | bugman | 2008-06-07 01:10:32 +0200 (Sat, 07 Jun 2008) | 3 lines
Made some tests pass on 32 bit Windows.
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r6318 | bugman | 2008-06-07 01:30:31 +0200 (Sat, 07 Jun 2008) | 3 lines
Removed another Numeric dependence.
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r6319 | bugman | 2008-06-07 01:48:13 +0200 (Sat, 07 Jun 2008) | 3 lines
Added a test for the Scientific PDB parser availability when initialising
the structural object.
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r6320 | bugman | 2008-06-07 19:33:23 +0200 (Sat, 07 Jun 2008) | 7 lines
Bug fix for compilation on Windows with Python 2.5.
The shared library extension should end with '.pyd' in Windows. For Python
versions 2.4 and below,
'.dll' extensions were happily loaded. But with version 2.5, this
extension is no longer
recognised!
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r6322 | bugman | 2008-06-08 00:29:50 +0200 (Sun, 08 Jun 2008) | 3 lines
Shifted the dependency checks into a new module.
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r6323 | bugman | 2008-06-08 00:33:07 +0200 (Sun, 08 Jun 2008) | 3 lines
Deleted the modules after import.
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r6325 | bugman | 2008-06-08 00:42:40 +0200 (Sun, 08 Jun 2008) | 3 lines
Shifted the relaxation curve fitting C module import check into the
dep_check module.
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r6326 | bugman | 2008-06-08 00:48:05 +0200 (Sun, 08 Jun 2008) | 3 lines
Converted a flag to bool.
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r6327 | bugman | 2008-06-08 00:57:01 +0200 (Sun, 08 Jun 2008) | 3 lines
Shifted some dependency checks into the dep_check module.
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r6328 | bugman | 2008-06-08 01:01:00 +0200 (Sun, 08 Jun 2008) | 3 lines
Added a module docstring and rearranged imports in prompt.interpreter.
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r6329 | bugman | 2008-06-08 01:03:35 +0200 (Sun, 08 Jun 2008) | 3 lines
Shifted the readline dependency check into dep_check.
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r6330 | bugman | 2008-06-08 01:10:32 +0200 (Sun, 08 Jun 2008) | 3 lines
Shifted the import check of Scientific.IO.PDB into dep_check.
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r6331 | bugman | 2008-06-08 01:42:45 +0200 (Sun, 08 Jun 2008) | 3 lines
Improved the relaxation curve fitting C module check to differentiate
between missing and bad modules.
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r6332 | bugman | 2008-06-08 01:49:47 +0200 (Sun, 08 Jun 2008) | 3 lines
Shifted the C module import error to after the program introduction string.
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r6352 | bugman | 2008-06-08 15:34:20 +0200 (Sun, 08 Jun 2008) | 3 lines
Initialized merge tracking via "svnmerge" with revisions "1-6332" from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/relax_data_rearrange
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r6353 | bugman | 2008-06-08 15:46:17 +0200 (Sun, 08 Jun 2008) | 77 lines
Merged revisions 6333,6335-6352 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/relax_data_rearrange
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r6333 | bugman | 2008-06-08 12:47:05 +0200 (Sun, 08 Jun 2008) | 3 lines
Created a temporary branch for rearranging the relax_data module.
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r6335 | bugman | 2008-06-08 13:22:29 +0200 (Sun, 08 Jun 2008) | 3 lines
Shifted the relax_data module from specific_fns to generic_fns.
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r6336 | bugman | 2008-06-08 13:24:28 +0200 (Sun, 08 Jun 2008) | 3 lines
Fixed some imports of relax_data.
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r6337 | bugman | 2008-06-08 13:35:43 +0200 (Sun, 08 Jun 2008) | 3 lines
Converted all class methods into module functions.
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r6338 | bugman | 2008-06-08 13:37:28 +0200 (Sun, 08 Jun 2008) | 3 lines
Fixed the relax_data imports again.
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r6339 | bugman | 2008-06-08 14:01:49 +0200 (Sun, 08 Jun 2008) | 3 lines
Wrote the arg unit tests of the relax_data.back_calc() user function.
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r6340 | bugman | 2008-06-08 14:02:37 +0200 (Sun, 08 Jun 2008) | 3 lines
Updated the relax_data.back_calc() user function to the new design.
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r6341 | bugman | 2008-06-08 14:16:34 +0200 (Sun, 08 Jun 2008) | 3 lines
Fixes for the read(), data_init(), and data_name() (now get_data_name())
functions.
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r6342 | bugman | 2008-06-08 14:22:54 +0200 (Sun, 08 Jun 2008) | 3 lines
Shifted the test_relax_data unit test module from _specific_fns to
_generic_fns.
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r6343 | bugman | 2008-06-08 14:25:20 +0200 (Sun, 08 Jun 2008) | 3 lines
Unit test fixes for the shift of relax_data from specific_fns to
generic_fns.
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r6344 | bugman | 2008-06-08 14:25:56 +0200 (Sun, 08 Jun 2008) | 3 lines
Updated a copyright notice.
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r6345 | bugman | 2008-06-08 14:37:30 +0200 (Sun, 08 Jun 2008) | 3 lines
Updated the relax_data.copy() user function interface to the new design.
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r6346 | bugman | 2008-06-08 14:42:28 +0200 (Sun, 08 Jun 2008) | 3 lines
Wrote 4 arg unit tests for the relax_data.copy() user function.
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r6347 | bugman | 2008-06-08 15:05:01 +0200 (Sun, 08 Jun 2008) | 3 lines
Converted all of the relax_data user function interfaces to the new
design.
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r6348 | bugman | 2008-06-08 15:14:26 +0200 (Sun, 08 Jun 2008) | 3 lines
Wrote 9 arg unit tests for the remainder of the relax_data user functions.
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r6349 | bugman | 2008-06-08 15:14:57 +0200 (Sun, 08 Jun 2008) | 3 lines
Added a missing RelaxError import.
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r6350 | bugman | 2008-06-08 15:17:17 +0200 (Sun, 08 Jun 2008) | 3 lines
Fixed the testing of the file arg in the relax_data.write() user function
interface.
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r6351 | bugman | 2008-06-08 15:22:05 +0200 (Sun, 08 Jun 2008) | 3 lines
Finished converting the add_data_to_spin() function to the new design.
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r6354 | bugman | 2008-06-08 15:47:00 +0200 (Sun, 08 Jun 2008) | 3 lines
Removed merge tracking for "svnmerge" for
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/relax_data_rearrange
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r6356 | bugman | 2008-06-22 01:03:18 +0200 (Sun, 22 Jun 2008) | 3 lines
The SpinContainer and not spin_id string is now passed into __set_xh_vect().
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r6357 | bugman | 2008-06-22 01:05:32 +0200 (Sun, 22 Jun 2008) | 3 lines
The SpinContainer and not spin_id string is now passed into
__load_relax_data().
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r6358 | bugman | 2008-06-22 01:19:55 +0200 (Sun, 22 Jun 2008) | 3 lines
Modified the return_conversion_factor() method to accept both the spin
container and spin_id string.
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r6359 | bugman | 2008-06-22 01:27:52 +0200 (Sun, 22 Jun 2008) | 3 lines
Created the new error class RelaxNoSpinSpecError.
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r6360 | bugman | 2008-06-22 01:29:56 +0200 (Sun, 22 Jun 2008) | 3 lines
The return_conversion_factor() method now does error checking for the spin
args.
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r6361 | bugman | 2008-06-22 01:31:58 +0200 (Sun, 22 Jun 2008) | 3 lines
Fixed a call to return_conversion_factor().
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r6362 | bugman | 2008-06-22 01:42:38 +0200 (Sun, 22 Jun 2008) | 5 lines
Converted the read_columnar_model_free_data() to the new relax design.
The method was also renamed to __load_model_free_data().
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r6363 | bugman | 2008-06-22 01:46:07 +0200 (Sun, 22 Jun 2008) | 3 lines
Bug fix for the generic_fns.relax_data.add_data_to_spin() function.
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r6364 | bugman | 2008-06-22 01:49:11 +0200 (Sun, 22 Jun 2008) | 5 lines
Bug fix for the __load_relax_data() method.
All relaxation data was being set as simulation data.
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r6365 | bugman | 2008-06-22 01:50:22 +0200 (Sun, 22 Jun 2008) | 3 lines
Removed a debugging print statement.
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r6366 | bugman | 2008-06-22 01:52:00 +0200 (Sun, 22 Jun 2008) | 3 lines
[... 3159 lines stripped ...]
r7078 - in /branches/multi_processor_merge: ./ data/ docs/latex/ generic_fns/ generic_fns/structure/ maths_fns/ minimise/ op...