Merged revisions 11661,11663-11685,11688,11758,11801,11811-11812,11817,11820-11821,11826-11831,11837-11844,11848-11849,11854-11856,11858-11867,11873,11879,11886,11888,11890-11896,11900,11904-11915,11966-11967,12060,12063,12069-12070,12087-12090,12092-12155,12167-12168,12172-12179,12187,12202,12229-12274,12276-12320 via svnmerge from
svn+ssh://bugman@.../svn/relax/1.3
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r11661 | bugman | 2010-10-25 10:10:42 +0200 (Mon, 25 Oct 2010) | 3 lines
Added 6 system tests for the spheroidal diffusion tensor.
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r11663 | bugman | 2010-11-16 18:07:43 +0100 (Tue, 16 Nov 2010) | 5 lines
Fix for the relatively unused calc_tensor_diag() for oblate tensors.
The eigenvalues were incorrectly ordered for oblate spheroids.
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r11664 | bugman | 2010-11-17 15:04:52 +0100 (Wed, 17 Nov 2010) | 5 lines
Fix for a failing diffusion tensor unit test.
This was testing an unused element of the diffusion tensor data structure incorrectly.
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r11665 | bugman | 2010-11-17 16:03:54 +0100 (Wed, 17 Nov 2010) | 5 lines
The rotation matrix for the spheroidal diffusion tensors is now correctly generated.
Again this is a fix for currently unused code (it will be used for BMRB support though).
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r11666 | bugman | 2010-11-17 16:15:35 +0100 (Wed, 17 Nov 2010) | 5 lines
Fixes for the diffusion tensor system tests.
The spheroidal tensors are now correctly checked.
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r11667 | bugman | 2010-11-17 16:15:57 +0100 (Wed, 17 Nov 2010) | 3 lines
Removed some debugging code.
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r11668 | bugman | 2010-11-17 16:45:32 +0100 (Wed, 17 Nov 2010) | 3 lines
Some rotation matrix check fixes for the diffusion tensor unit tests.
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r11669 | bugman | 2010-11-17 16:48:20 +0100 (Wed, 17 Nov 2010) | 3 lines
Dpar_unit is no longer passed into calc_rotation() for spheroidal diffusion, as it is not needed.
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r11670 | bugman | 2010-11-17 17:01:24 +0100 (Wed, 17 Nov 2010) | 5 lines
Fix for the updating of the rotation and tensor MC sim objects for the spheroidal diffusion.
This problem was only recently introduced.
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r11671 | bugman | 2010-11-17 17:05:46 +0100 (Wed, 17 Nov 2010) | 3 lines
Similar fix as in r11670, but for setting MC sim data.
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r11672 | bugman | 2010-11-17 17:18:29 +0100 (Wed, 17 Nov 2010) | 3 lines
Some more fixes for handling the diffusion tensor data structure 'spheroid_type' variable properly.
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r11673 | bugman | 2010-11-17 19:14:57 +0100 (Wed, 17 Nov 2010) | 5 lines
Fix for the creation of the oblate spheroid geometric object PDB file.
The x and z axes need to be swapped now for the oblate tensor.
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r11674 | bugman | 2010-11-17 19:23:43 +0100 (Wed, 17 Nov 2010) | 6 lines
For some reason, the diffusion tensor PDB file for the oblate tensor now has a slight rotation.
This rotation is about the unique axis of the tensor, so this gives a different PDB file, but the
representation is the same.
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r11675 | bugman | 2010-11-18 13:42:02 +0100 (Thu, 18 Nov 2010) | 3 lines
Some small cosmetic changes to the spheroid diffusion tensor system tests.
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r11676 | bugman | 2010-11-18 13:51:23 +0100 (Thu, 18 Nov 2010) | 3 lines
The hardcoded variables in get_spheroid() are now keyword args.
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r11677 | bugman | 2010-11-18 14:03:01 +0100 (Thu, 18 Nov 2010) | 3 lines
Added 6 system tests for the initialisation of the prolate spheroid diffusion tensor.
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r11678 | bugman | 2010-11-18 16:52:49 +0100 (Thu, 18 Nov 2010) | 6 lines
Fix for the spheroid diffusion tensors for a recently introduced bug.
The oblate and prolate check was failing as the 'spheroid_type' variable was set to None after a
call to diffusion_tensor.init(). 'spheroid_type' is now automatically updated if Da is changed.
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r11679 | bugman | 2010-11-18 17:08:23 +0100 (Thu, 18 Nov 2010) | 5 lines
The tensor is first twisted before rotating to PDB frame in the spheroid diffusion tensor system tests.
The twisting rotation was not being correctly performed.
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r11680 | bugman | 2010-11-18 17:25:40 +0100 (Thu, 18 Nov 2010) | 5 lines
Renamed test_init_spheroid_as_ellipsoid() to test_init_prolate_spheroid_as_ellipsoid().
The print outs of the system test have been slightly improved.
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r11681 | bugman | 2010-11-18 17:38:09 +0100 (Thu, 18 Nov 2010) | 3 lines
Alphabetical ordering of methods, and shifting of the spheroid to ellipsoid checks into a separate method.
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r11682 | bugman | 2010-11-18 18:20:02 +0100 (Thu, 18 Nov 2010) | 3 lines
Added a new system test test_init_oblate_spheroid_as_ellipsoid().
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r11683 | bugman | 2010-11-18 18:25:51 +0100 (Thu, 18 Nov 2010) | 5 lines
Fix for the ellipsoid eigenvalue and rotation matrix reordering for when 2 eigenvalues are the same.
This only affects the (Dxx, Dyy, Dzz, Dxy, Dxz, Dyz) parameter input into diffusion_tensor.init().
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r11684 | bugman | 2010-11-18 18:29:29 +0100 (Thu, 18 Nov 2010) | 5 lines
Fix for the eigenvalue and rotation matrix sorting for (Dxx, Dyy, Dzz, Dxy, Dxz, Dyz).
The eigenvalues were being converted to ints!
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r11685 | bugman | 2010-11-18 18:53:39 +0100 (Thu, 18 Nov 2010) | 6 lines
Final bug fix for the input of (Dxx, Dyy, Dzz, Dxy, Dxz, Dyz) ellipsoidal diffusion parameters.
The numpy eigenvalue decomposition has been replaced by SVD as the eigenvalue decomposition could
generate a proper rotation matrix when 2 eigenvalues are the same. The test suite now passes fully.
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r11688 | bugman | 2010-11-19 14:46:34 +0100 (Fri, 19 Nov 2010) | 3 lines
Improved the diffusion tensor print out.
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r11758 | bugman | 2010-12-10 16:27:22 +0100 (Fri, 10 Dec 2010) | 3 lines
The molecule type can now be specified.
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r11801 | bugman | 2010-12-13 23:51:44 +0100 (Mon, 13 Dec 2010) | 5 lines
The molecule_loop() and residue_loop() methods now accept the return_id flag.
The molecule or residue ID strings are now returned when requested.
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r11811 | bugman | 2010-12-14 11:11:03 +0100 (Tue, 14 Dec 2010) | 8 lines
Added a system test for bug #17276.
This bug (https://gna.org/bugs/index.php?17276) was reported by Leanne Minall <lm7902 att bristol
dot ac dott uk>.
The test passes though as the problem is not in this test data.
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r11812 | bugman | 2010-12-14 11:23:31 +0100 (Tue, 14 Dec 2010) | 3 lines
Bug #17276 is now triggered in the system test.
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r11817 | bugman | 2010-12-14 18:22:33 +0100 (Tue, 14 Dec 2010) | 6 lines
Removed some checks in the generic_fns.mol_res_spin.molecule_loop() function which was triggering bugs.
The old checking code is of no use, as all types of molecule IDs should be accepted! This only
recently became an issue for some unknown reason?!?!
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r11820 | bugman | 2010-12-14 23:47:05 +0100 (Tue, 14 Dec 2010) | 7 lines
An execution lock has been added to the status object.
This allows parts of relax to prevent others from running, which is especially useful in certain
UIs. A special Exec_lock class object has been created to simulate a proper threading.Lock object,
but with certain additional features.
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r11821 | bugman | 2010-12-14 23:47:33 +0100 (Tue, 14 Dec 2010) | 3 lines
All of the auto-analyses now lock relax's execution while they are in operation.
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r11826 | bugman | 2010-12-15 01:33:13 +0100 (Wed, 15 Dec 2010) | 5 lines
The Mf.bug_14941_local_tm_global_selection system test now prints out some status info.
This is to test the status container.
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r11827 | bugman | 2010-12-15 01:35:28 +0100 (Wed, 15 Dec 2010) | 5 lines
Fixes for the status object by renaming __init__() to setup() and calling it only once.
The object was not acting as a singleton because of the presence of __init__(). This is now fixed.
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r11828 | bugman | 2010-12-15 01:36:05 +0100 (Wed, 15 Dec 2010) | 3 lines
The status object is being initialised and setup before execution of the main relax class.
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r11829 | bugman | 2010-12-15 01:36:48 +0100 (Wed, 15 Dec 2010) | 3 lines
The status object is not being initialised on import, to allow controlled setup upon start up.
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r11830 | bugman | 2010-12-15 01:45:19 +0100 (Wed, 15 Dec 2010) | 6 lines
Security fix - execfile() is no longer used to run relax scripts.
Instead a custom function exec_script() is being used to call runpy.run_module(). exec_script()
also locks and releases the relax execution lock before and after operation.
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r11831 | bugman | 2010-12-15 09:41:27 +0100 (Wed, 15 Dec 2010) | 3 lines
The execution lock is released by the interpreter in all Error situations.
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r11837 | bugman | 2010-12-16 11:52:56 +0100 (Thu, 16 Dec 2010) | 6 lines
The debugging flag now disables the execution locking mechanism.
The acquire() and release() calls are also recorded in the 'lock.log' file to help with lock
debugging.
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r11838 | bugman | 2010-12-16 11:53:51 +0100 (Thu, 16 Dec 2010) | 3 lines
Missing module import.
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r11839 | bugman | 2010-12-16 11:56:02 +0100 (Thu, 16 Dec 2010) | 3 lines
Shifted the initialisation of the status object to be after the __main__.debug initialisation.
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r11840 | bugman | 2010-12-16 12:17:36 +0100 (Thu, 16 Dec 2010) | 5 lines
The system and unit tests are placing their names into the status object.
This will be used for debugging.
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r11841 | bugman | 2010-12-16 12:18:14 +0100 (Thu, 16 Dec 2010) | 3 lines
The unit/system test name is being placed into the locking log when debugging.
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r11842 | bugman | 2010-12-16 12:37:36 +0100 (Thu, 16 Dec 2010) | 3 lines
The execution lock mechanism no longer blocks scripts from running within scripts.
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r11843 | bugman | 2010-12-16 12:49:07 +0100 (Thu, 16 Dec 2010) | 3 lines
Nested scripts no longer acquire the execution lock.
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r11844 | bugman | 2010-12-16 15:19:14 +0100 (Thu, 16 Dec 2010) | 5 lines
Better locking support for nested scripts.
The execution lock directly handles the locking of the nesting of scripts.
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r11848 | bugman | 2010-12-17 10:19:50 +0100 (Fri, 17 Dec 2010) | 3 lines
The 'scons clean' target now removes temporary relax save files.
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r11849 | bugman | 2010-12-17 10:36:56 +0100 (Fri, 17 Dec 2010) | 3 lines
Improved execution locking with support for auto analysis and script launching from within a script.
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r11854 | bugman | 2010-12-17 12:05:30 +0100 (Fri, 17 Dec 2010) | 3 lines
Initialized merge tracking via "svnmerge" with revisions "1-11813" from
svn+ssh://bugman@.../svn/relax/branches/peak_list_handling
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r11855 | bugman | 2010-12-17 12:10:03 +0100 (Fri, 17 Dec 2010) | 58 lines
Merged revisions 11815-11816,11819,11832-11835,11847,11850-11853 via svnmerge from
svn+ssh://bugman@.../svn/relax/branches/peak_list_handling
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r11815 | bugman | 2010-12-14 17:51:09 +0100 (Tue, 14 Dec 2010) | 3 lines
Modified the bug_17276 system test data so that there is some noise simulated.
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r11816 | bugman | 2010-12-14 17:52:06 +0100 (Tue, 14 Dec 2010) | 3 lines
Peak intensity data is now stored as a dictionary with the spectrum_id arg as keys.
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r11819 | bugman | 2010-12-14 19:02:59 +0100 (Tue, 14 Dec 2010) | 5 lines
Fix for the Relax_fit.test_read_sparky system test.
This was solely a problem within the test and its data.
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r11832 | bugman | 2010-12-15 12:17:28 +0100 (Wed, 15 Dec 2010) | 3 lines
Switched __errors_repl() to use dictionaries rather than lists.
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r11833 | bugman | 2010-12-15 18:33:22 +0100 (Wed, 15 Dec 2010) | 3 lines
Converted the specific relaxation curve fitting code to use the dictionary data structures.
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r11834 | bugman | 2010-12-15 18:33:44 +0100 (Wed, 15 Dec 2010) | 3 lines
The Monte Carlo simulation code can now handle dictionary type data.
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r11835 | bugman | 2010-12-15 18:51:02 +0100 (Wed, 15 Dec 2010) | 3 lines
The Grace code can now handle dictionary type data.
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r11847 | bugman | 2010-12-17 10:03:04 +0100 (Fri, 17 Dec 2010) | 3 lines
Fixes for the system tests - the data is now in dictionaries.
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r11850 | bugman | 2010-12-17 10:48:25 +0100 (Fri, 17 Dec 2010) | 3 lines
Redesigned the specific API common method _return_value_general() to handle dictionaries.
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r11851 | bugman | 2010-12-17 11:12:52 +0100 (Fri, 17 Dec 2010) | 3 lines
Fix for the API base method _return_value_general() - not all values have errors associated with them.
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r11852 | bugman | 2010-12-17 11:43:27 +0100 (Fri, 17 Dec 2010) | 3 lines
The NOE specific analysis now uses the dictionary type structure for the intensity data structures.
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r11853 | bugman | 2010-12-17 11:44:35 +0100 (Fri, 17 Dec 2010) | 6 lines
The list-type data can also be a numpy array, so the Monte Carlo code can now handle this.
Previously the data was being converted from an ndarray to a list, but now this is explicitly
handled.
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r11856 | bugman | 2010-12-17 12:10:25 +0100 (Fri, 17 Dec 2010) | 3 lines
Removed merge tracking for "svnmerge" for
svn+ssh://bugman@.../svn/relax/branches/peak_list_handling
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r11858 | bugman | 2010-12-17 12:46:00 +0100 (Fri, 17 Dec 2010) | 5 lines
Removed all execfile() calls by switching to the script() user function.
This is for security and for handling the execution locking mechanism properly.
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r11859 | bugman | 2010-12-17 12:57:49 +0100 (Fri, 17 Dec 2010) | 3 lines
Renamed all the frame order scripts so that they have valid module names and can be imported.
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r11860 | bugman | 2010-12-17 13:00:51 +0100 (Fri, 17 Dec 2010) | 3 lines
Fix for running scripts - the '.' character is now disallowed as module import cannot work.
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r11861 | bugman | 2010-12-17 13:04:44 +0100 (Fri, 17 Dec 2010) | 3 lines
More informative nesting information in the execution lock debugging.
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r11862 | bugman | 2010-12-17 13:23:24 +0100 (Fri, 17 Dec 2010) | 3 lines
Modification of the execution lock debugging print outs.
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r11863 | bugman | 2010-12-17 14:11:23 +0100 (Fri, 17 Dec 2010) | 5 lines
Bug fix - the script path is now being removed from sys.path.
This was causing incorrect scripts to be loaded if exec_script() is run multiple times.
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r11864 | bugman | 2010-12-17 14:51:20 +0100 (Fri, 17 Dec 2010) | 6 lines
Fix for the execution locking when an auto-analysis is launched from a script.
The lock is not released and a new one acquired. Instead the mechanism is script, just as it is
for nested scripting.
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r11865 | bugman | 2010-12-17 15:03:00 +0100 (Fri, 17 Dec 2010) | 3 lines
Added a system test for nested scripting.
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r11866 | bugman | 2010-12-17 15:04:02 +0100 (Fri, 17 Dec 2010) | 5 lines
Fix for the Generic.test_nested_scripting() system test.
A data pipe is needed.
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r11867 | bugman | 2010-12-17 15:13:51 +0100 (Fri, 17 Dec 2010) | 5 lines
Nested scripting is now better supported.
The full path of the nested script is not needed if is in the same directory as the parent script.
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r11873 | bugman | 2010-12-17 16:43:21 +0100 (Fri, 17 Dec 2010) | 6 lines
Fix for script execution - the original state is restored if an exception occurs.
The original working directory is restored and the script path is removed in all cases by using a
try-finally setup.
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r11879 | bugman | 2010-12-17 17:10:39 +0100 (Fri, 17 Dec 2010) | 3 lines
Added a check that the script ends in '*.py'.
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r11886 | bugman | 2010-12-17 19:59:11 +0100 (Fri, 17 Dec 2010) | 9 lines
Fix for bug #17343 (https://gna.org/bugs/?17343).
This bug was reported by Vitaly Vostri <vvostri att gmail dott com>, also in the mailing list
message https://mail.gna.org/public/relax-users/2010-12/msg00005.html.
The 'CH2' and 'OT' atoms have been added to the internal PDB reader, for those incomplete PDB files
in which the element column is missing.
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r11888 | bugman | 2010-12-17 20:19:26 +0100 (Fri, 17 Dec 2010) | 3 lines
Fix for script execution - the extension check for '.py' was incorrect!
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r11890 | bugman | 2010-12-17 20:41:01 +0100 (Fri, 17 Dec 2010) | 6 lines
Added test data and a script for testing the reading of CCPN Analysis 2.1 sparky peak lists.
This is data from bug #17341 (https://gna.org/bugs/?17341) submitted by Madeleine Strickland <M dot
Strickland att bristol dot ac dott uk>.
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r11891 | bugman | 2010-12-17 20:51:17 +0100 (Fri, 17 Dec 2010) | 6 lines
Fix for bug #17344 (https://gna.org/bugs/index.php?17344), the broken grace.view() user function.
This has been broken since January, and is released in relax 1.3.5, but no one seems to have
noticed :S
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r11892 | bugman | 2010-12-17 20:51:48 +0100 (Fri, 17 Dec 2010) | 3 lines
The grace executable file is now set to '' in the CCPN analysis peak list system test.
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r11893 | bugman | 2010-12-17 21:11:13 +0100 (Fri, 17 Dec 2010) | 5 lines
Implemented and activated the CCPN Analysis 2.1 peak list reading system test.
This is to catch bug #17341 (https://gna.org/bugs/index.php?17341).
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r11894 | bugman | 2010-12-17 22:59:29 +0100 (Fri, 17 Dec 2010) | 3 lines
Decreased the number of MC sims to speed up the CCPN Analysis peak list reading system test.
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r11895 | bugman | 2010-12-17 22:59:53 +0100 (Fri, 17 Dec 2010) | 3 lines
Bug fix for the CCPN Analysis peak list system test.
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r11896 | bugman | 2010-12-17 23:37:16 +0100 (Fri, 17 Dec 2010) | 6 lines
Added support for CCPN Analysis 2.1 peak lists (exported in Sparky format).
This is a fix for bug #17341 (https://gna.org/bugs/index.php?17341) reported by Madeleine Strickland
<M dott Strickland att bristol dot ac dot uk>.
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r11900 | bugman | 2010-12-19 15:43:54 +0100 (Sun, 19 Dec 2010) | 7 lines
Removed the 2 from CH2 in the atom list in the element determining function.
This is in response to Vitaly Vostrikov's <vvostri att gmail dott com> message at Message-id:
<AANLkTimYA4H7=WbMwzgpxaTJ6_nArKu=ed9VNdXCSuDB@...>,
https://mail.gna.org/public/relax-users/2010-12/msg00013.html.
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r11904 | bugman | 2010-12-20 14:05:59 +0100 (Mon, 20 Dec 2010) | 6 lines
Added a system test for reading relax 1.2.x version results files.
This is from Sebastian Morin's PSE-4 data, truncated, and is to catch the bug of not being able to
handle simulations.
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r11905 | bugman | 2010-12-20 14:18:21 +0100 (Mon, 20 Dec 2010) | 5 lines
Fix for bug #17361 (https://gna.org/bugs/index.php?17361).
The chi2_sim structure should have been initialised to a list, not a dictionary.
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r11906 | bugman | 2010-12-20 14:30:16 +0100 (Mon, 20 Dec 2010) | 6 lines
Another fix for bug #17361 (https://gna.org/bugs/index.php?17361) the loading 1.2.x sim data.
This time the global structures were too large - the lists were being appended to for each spin and
simulation, rather than only each simulation.
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r11907 | bugman | 2010-12-20 14:46:26 +0100 (Mon, 20 Dec 2010) | 3 lines
For the 1.2 results files, the model information is now being setup even if None.
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r11908 | bugman | 2010-12-20 15:06:02 +0100 (Mon, 20 Dec 2010) | 3 lines
Bug fix for the relaxation data add_data_to_spin() function - missing data was not properly eliminated.
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r11909 | bugman | 2010-12-20 15:37:26 +0100 (Mon, 20 Dec 2010) | 3 lines
Completed the test_read_results_1_2_pse() model-free system test for reading relax 1.2.x results.
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r11910 | bugman | 2010-12-20 15:47:46 +0100 (Mon, 20 Dec 2010) | 5 lines
Last fix for bug #17361 (https://gna.org/bugs/index.php?17361) the loading 1.2.x sim data.
The frequency information is now correctly updated when data is missing.
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r11911 | bugman | 2010-12-20 16:02:00 +0100 (Mon, 20 Dec 2010) | 3 lines
Updated some test data for the unit tests.
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r11912 | bugman | 2010-12-20 16:15:19 +0100 (Mon, 20 Dec 2010) | 3 lines
Added a system test to check that relax save files cannot be loaded as results files.
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r11913 | bugman | 2010-12-20 16:15:56 +0100 (Mon, 20 Dec 2010) | 3 lines
Added a check to make sure the relax save states can not be loaded by results.read().
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r11914 | bugman | 2010-12-20 16:28:56 +0100 (Mon, 20 Dec 2010) | 6 lines
Reverted r11913 as this was completely wrong and broke the reading of results files.
The command used was:
svn merge -r11913:11912 .
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r11915 | bugman | 2010-12-20 16:33:45 +0100 (Mon, 20 Dec 2010) | 17 lines
Reverted r11912 as this system test was useless and incorrect.
There is currently no way to see the difference between a save state and a results file unless there
are multiple pipes.
The command used was:
svn merge -r11912:11911 .
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r11912 | bugman | 2010-12-20 16:15:19 +0100 (Mon, 20 Dec 2010) | 3 lines
Changed paths:
M /1.3/test_suite/system_tests/results.py
Added a system test to check that relax save files cannot be loaded as results files.
.....
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r11966 | bugman | 2010-12-27 13:17:01 +0100 (Mon, 27 Dec 2010) | 3 lines
Epydoc docstring fixes.
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r11967 | bugman | 2010-12-27 13:42:03 +0100 (Mon, 27 Dec 2010) | 3 lines
The sample_scripts and scripts directories are no longer parsed for the API documentation.
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r12060 | bugman | 2010-12-31 09:36:09 +0100 (Fri, 31 Dec 2010) | 6 lines
Added Michael Bieri's model-free data extraction script.
This script was attached to Michael's post from back in November 2009 (Message-id:
<4B00A015.30400@...> https://mail.gna.org/public/relax-devel/2009-11/msg00022.html).
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r12063 | bugman | 2010-12-31 11:41:47 +0100 (Fri, 31 Dec 2010) | 6 lines
Back ported the relax version 1.3.6 CHANGES file.
The command used was:
svn merge -r12061:12062 svn+ssh://bugman@.../svn/relax/tags/1.3.6 .
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r12069 | bugman | 2010-12-31 13:10:09 +0100 (Fri, 31 Dec 2010) | 3 lines
Removal of a line accidentally added by copy-and-paste.
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r12070 | bugman | 2010-12-31 13:10:51 +0100 (Fri, 31 Dec 2010) | 3 lines
Updated the release checklist to include the cleaning up of temporary documentation files.
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r12087 | bugman | 2011-01-03 10:26:24 +0100 (Mon, 03 Jan 2011) | 3 lines
Shifted the location of the truncated PSE-4 data for the relax 1.2 results reading system test.
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r12088 | bugman | 2011-01-03 10:29:31 +0100 (Mon, 03 Jan 2011) | 5 lines
Added a system test for reading the final results file from TEM-1.
This file is severely truncated, and is just to trigger a bug.
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r12089 | bugman | 2011-01-03 10:39:15 +0100 (Mon, 03 Jan 2011) | 7 lines
Fix for bug #17417 (https://gna.org/bugs/?17417).
The model_free _model_setup() method should handle no model-free model being set when reading
relax 1.2 results files. The problem was a check for the local_tm parameter in the parameter array,
as this was also set to None.
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r12090 | bugman | 2011-01-03 11:10:21 +0100 (Mon, 03 Jan 2011) | 3 lines
The Mf.test_read_results_1_2_tem1 system test is now checking all of the model-free data correctly.
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r12092 | bugman | 2011-01-03 19:25:44 +0100 (Mon, 03 Jan 2011) | 3 lines
Removed old commented out code.
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r12093 | bugman | 2011-01-03 19:44:32 +0100 (Mon, 03 Jan 2011) | 3 lines
Big clean up of cruft from the Test_finder.scan_paths() method.
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r12094 | bugman | 2011-01-03 19:48:40 +0100 (Mon, 03 Jan 2011) | 3 lines
Removed the PY_UNIT_TEST_PATTERN constant as it is in the Unit_test_runner.test_case_patterns list.
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r12095 | bugman | 2011-01-03 20:18:18 +0100 (Mon, 03 Jan 2011) | 3 lines
Big clean up of the load_test_case() unit test function.
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r12096 | bugman | 2011-01-03 20:23:55 +0100 (Mon, 03 Jan 2011) | 5 lines
Fix for load_test_case() for a bug introduced in r12095.
The import errro test case was not handled correctly.
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r12097 | bugman | 2011-01-03 20:25:32 +0100 (Mon, 03 Jan 2011) | 3 lines
The "testing units..." text is only printed if verbosity is set.
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r12098 | bugman | 2011-01-03 20:32:13 +0100 (Mon, 03 Jan 2011) | 3 lines
Clean up of the unit test runner code for command line usage.
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r12099 | bugman | 2011-01-03 20:34:42 +0100 (Mon, 03 Jan 2011) | 3 lines
Deleted the ExtendedException class as it was doing nothing.
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r12100 | bugman | 2011-01-03 21:01:25 +0100 (Mon, 03 Jan 2011) | 3 lines
Big code clean up in the Unit_test_runner class.
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r12101 | bugman | 2011-01-03 21:19:24 +0100 (Mon, 03 Jan 2011) | 7 lines
Shifted the global relax debug flag from __main__.debug to the relax status singleton.
This allows the flag to be defined even when imported from outside of relax. Also the pedantic flag
is now being directly passed into the relax warning system and hence has been shifted out of
__main__.
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r12102 | bugman | 2011-01-03 21:22:05 +0100 (Mon, 03 Jan 2011) | 3 lines
Removed the status singleton from the main relax class namespace.
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r12103 | bugman | 2011-01-04 08:48:52 +0100 (Tue, 04 Jan 2011) | 3 lines
Made the N_state_model.test_pcs_fit_zero_pos system test less stringent so it passes on 32-bit Linux.
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r12104 | bugman | 2011-01-04 08:53:38 +0100 (Tue, 04 Jan 2011) | 5 lines
Added another set of valid optimisation values to Mf.test_opt_constr_newton_gmw_mt_S2_0_970_te_2048_Rex_0_149.
This is a second set different numbers for 32-bit Linux! The result is the same though.
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r12105 | bugman | 2011-01-04 08:58:39 +0100 (Tue, 04 Jan 2011) | 5 lines
Shifted the relax installation path variable from __main__ into the status singleton object.
This allows relax modules to be imported outside of relax.
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r12106 | bugman | 2011-01-04 09:15:20 +0100 (Tue, 04 Jan 2011) | 7 lines
Changed how the status singleton object is setup - it does it itself!
The status object now sets up itself so that a call to setup() is no longer necessary. setup()
is now private, and relax just overrides the default variables to set the debugging flag or
installation path.
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r12107 | bugman | 2011-01-04 09:16:01 +0100 (Tue, 04 Jan 2011) | 3 lines
Shifted the status object instantiation to the import level.
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r12108 | bugman | 2011-01-04 09:31:02 +0100 (Tue, 04 Jan 2011) | 5 lines
Shifted the status singleton instantiation to the import level in all modules.
This should save execution time.
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r12109 | bugman | 2011-01-04 09:36:28 +0100 (Tue, 04 Jan 2011) | 5 lines
Shifted the status singleton instantiation to the import level in all modules.
This should save execution time. The last commit omitted the main relax directories.
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r12110 | bugman | 2011-01-04 09:44:05 +0100 (Tue, 04 Jan 2011) | 5 lines
Updated 3 optimisation system tests to pass under 32-bit Linux.
Why these optimisation stats are now slightly different must be due to software differences.
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r12111 | bugman | 2011-01-04 10:27:27 +0100 (Tue, 04 Jan 2011) | 3 lines
Updated the copyright statement.
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r12112 | bugman | 2011-01-04 10:28:06 +0100 (Tue, 04 Jan 2011) | 3 lines
Updated the introductory copyright notice.
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r12113 | bugman | 2011-01-04 10:45:41 +0100 (Tue, 04 Jan 2011) | 7 lines
The RelaxTestLoader has been added as a replacement for unittest.TestLoader.
This empty class will in the end handle the skipping of tests when Python packages optional for
relax are not installed. The unit_test_runner uses this class if it can import it, otherwise it
falls back to unittest.TestLoader to allow for non-relax usage.
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r12114 | bugman | 2011-01-04 11:00:32 +0100 (Tue, 04 Jan 2011) | 3 lines
Fixed the import of the RelaxTestLoader.
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r12115 | bugman | 2011-01-04 11:01:17 +0100 (Tue, 04 Jan 2011) | 5 lines
Added a replacment loadTestsFromTestCase() method to RelaxTestLoader.
This method will later be modified to skip certain tests.
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r12116 | bugman | 2011-01-04 11:01:29 +0100 (Tue, 04 Jan 2011) | 3 lines
Fix for the copyright notice.
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r12117 | bugman | 2011-01-04 11:18:08 +0100 (Tue, 04 Jan 2011) | 3 lines
Added an empty list to the relax status object to store info about skipped system and unit tests.
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r12118 | bugman | 2011-01-04 11:21:07 +0100 (Tue, 04 Jan 2011) | 3 lines
System and unit tests can be skipped is the skip flag is set inside the TestCase class.
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r12119 | bugman | 2011-01-04 11:30:38 +0100 (Tue, 04 Jan 2011) | 5 lines
The RelaxTestLoader now skips tests if the are in the status.skipped_test list.
This is instead of the skip flag being set or not.
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r12120 | bugman | 2011-01-04 11:33:58 +0100 (Tue, 04 Jan 2011) | 6 lines
Added __init__() to Test_scientific to skip all tests of this class if the module is not installed.
The method adds the tests to the status.skipped_tests list and executes the base class __init__()
method.
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r12121 | bugman | 2011-01-04 11:35:12 +0100 (Tue, 04 Jan 2011) | 3 lines
Updated the copyright.
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r12122 | bugman | 2011-01-04 11:36:54 +0100 (Tue, 04 Jan 2011) | 3 lines
Docstring fix for the __init__() method.
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r12123 | bugman | 2011-01-04 11:37:16 +0100 (Tue, 04 Jan 2011) | 3 lines
Another docstring fix.
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r12124 | bugman | 2011-01-04 11:40:14 +0100 (Tue, 04 Jan 2011) | 3 lines
The Test_api_base tests requiring Scientific python are now skipped if not installed.
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r12125 | bugman | 2011-01-04 11:44:15 +0100 (Tue, 04 Jan 2011) | 3 lines
The test suite summary is printed out even if not all of the test suite is run.
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r12126 | bugman | 2011-01-04 11:49:13 +0100 (Tue, 04 Jan 2011) | 3 lines
Improvements to the formatting.summary_line() function, and the removal of the indentation.
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r12127 | bugman | 2011-01-04 12:10:35 +0100 (Tue, 04 Jan 2011) | 3 lines
Shortened the test suite formatting.summary_line() default length.
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r12128 | bugman | 2011-01-04 12:13:16 +0100 (Tue, 04 Jan 2011) | 3 lines
The relax test suite now prints out a table of skipped tests.
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r12129 | bugman | 2011-01-04 12:31:09 +0100 (Tue, 04 Jan 2011) | 3 lines
Renamed the relax test suite formatting.heading() function to title() and simplified it.
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r12130 | bugman | 2011-01-04 12:32:35 +0100 (Tue, 04 Jan 2011) | 3 lines
Added a relax test suite formatting.subtitle() function for printing out subtitles.
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r12131 | bugman | 2011-01-04 12:34:21 +0100 (Tue, 04 Jan 2011) | 3 lines
Modified the test suite printout to use the formatting subtitle() and title() functions.
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r12132 | bugman | 2011-01-04 12:35:14 +0100 (Tue, 04 Jan 2011) | 3 lines
Fix for the subtitle() function, the width was too small.
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r12133 | bugman | 2011-01-04 12:37:44 +0100 (Tue, 04 Jan 2011) | 3 lines
Removed the top spacing from the subtitle() function.
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r12134 | bugman | 2011-01-04 12:40:54 +0100 (Tue, 04 Jan 2011) | 3 lines
Alphabetical ordering of functions, and comment updates.
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r12135 | bugman | 2011-01-04 12:41:34 +0100 (Tue, 04 Jan 2011) | 3 lines
Only print out the part of the optional module table when those tests are run.
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r12136 | bugman | 2011-01-04 12:42:27 +0100 (Tue, 04 Jan 2011) | 3 lines
Changed the text of the missing module test suite table print out.
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r12137 | bugman | 2011-01-04 14:04:32 +0100 (Tue, 04 Jan 2011) | 3 lines
The structure system tests involving scientific python are now skipped if the module is not installed.
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r12138 | bugman | 2011-01-04 14:07:46 +0100 (Tue, 04 Jan 2011) | 3 lines
The test suite summary is not longer printed for each category when all tests are run.
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r12139 | bugman | 2011-01-04 14:19:29 +0100 (Tue, 04 Jan 2011) | 3 lines
The unit vector system tests using scientific python are now being skipped if the module is not installed.
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r12140 | bugman | 2011-01-04 14:21:12 +0100 (Tue, 04 Jan 2011) | 3 lines
Missing import.
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r12141 | bugman | 2011-01-04 14:22:27 +0100 (Tue, 04 Jan 2011) | 3 lines
Fix for the system test Unit_vectors.__init__() method - the wrong base class __init__() was being called.
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r12142 | bugman | 2011-01-04 14:24:43 +0100 (Tue, 04 Jan 2011) | 3 lines
The system tests now use the RelaxTestLoader to allow tests to be skipped.
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r12143 | bugman | 2011-01-04 14:29:41 +0100 (Tue, 04 Jan 2011) | 3 lines
Removed a newline in the skipped test table.
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r12144 | bugman | 2011-01-04 14:33:08 +0100 (Tue, 04 Jan 2011) | 3 lines
Added scipy to the relax dependency checking module.
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r12145 | bugman | 2011-01-04 14:35:29 +0100 (Tue, 04 Jan 2011) | 3 lines
relax will now run without the scipy module installed, however the frame order analysis is not usable.
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r12146 | bugman | 2011-01-04 14:43:57 +0100 (Tue, 04 Jan 2011) | 3 lines
The data pipe generic code now uses dep_check to see if the relaxation curve fitting is available.
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r12147 | bugman | 2011-01-04 14:45:49 +0100 (Tue, 04 Jan 2011) | 3 lines
The frame order analysis is disabled if scipy is not installed.
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r12148 | bugman | 2011-01-04 14:49:06 +0100 (Tue, 04 Jan 2011) | 3 lines
The frame order system tests are being skipped if scipy is not installed.
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r12149 | bugman | 2011-01-04 14:49:57 +0100 (Tue, 04 Jan 2011) | 3 lines
Fix for the Frame_order.__init__() system test method - the wrong base class was being called.
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r12150 | bugman | 2011-01-04 14:57:54 +0100 (Tue, 04 Jan 2011) | 3 lines
Updated the copyright.
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r12151 | bugman | 2011-01-04 14:58:19 +0100 (Tue, 04 Jan 2011) | 3 lines
The frame order unit tests are now skipped if scipy is not installed.
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r12152 | bugman | 2011-01-04 15:04:12 +0100 (Tue, 04 Jan 2011) | 3 lines
Missing import.
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r12153 | bugman | 2011-01-04 15:07:32 +0100 (Tue, 04 Jan 2011) | 3 lines
The alignment tensor system test now uses the N-state model rather than frame order so it is always tested.
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r12154 | bugman | 2011-01-04 16:01:15 +0100 (Tue, 04 Jan 2011) | 3 lines
Updated the test suite table print outs to say both packages and modules.
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r12155 | bugman | 2011-01-04 16:06:42 +0100 (Tue, 04 Jan 2011) | 5 lines
The data pipe system test is avoiding the frame order data pipe.
This allows the test to pass without scipy installed.
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r12167 | bugman | 2011-01-05 10:41:39 +0100 (Wed, 05 Jan 2011) | 3 lines
Renamed the full_analysis.py sample script to dauvergne_protocol.py to make it more obvious what it is.
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r12168 | bugman | 2011-01-05 10:43:04 +0100 (Wed, 05 Jan 2011) | 3 lines
Added the file sample_scripts/full_analysis.py with a single line pointing to dauvergne_protocol.py.
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r12172 | bugman | 2011-01-10 12:16:09 +0100 (Mon, 10 Jan 2011) | 9 lines
Added a new system test for the prolate diffusion tensor, this time checking the diffusion type.
A spherical tensor is sent in, triggering the bug found by Vitaly Vostri <vvostri att gmail dott
com> (Message-id: <AANLkTinRO3ZCNwL6GeqWdx0uBvv=PQ=zw6vpdQQeruBW@...>
https://mail.gna.org/public/relax-users/2010-12/msg00014.html).
The problem is that the prolate tensor is changed to an oblate one!?!
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r12173 | bugman | 2011-01-10 13:44:58 +0100 (Mon, 10 Jan 2011) | 3 lines
The type of spheroid is now being checked in all of the oblate and prolate system tests.
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r12174 | bugman | 2011-01-10 14:45:04 +0100 (Mon, 10 Jan 2011) | 12 lines
The diffusion tensor spheroid_type variable is now only updated if it is never explicitly set.
This is to fix the diffusion tensor setting bug found by Vitaly Vostri <vvostri att gmail dott com>
(Message-id: <AANLkTinRO3ZCNwL6GeqWdx0uBvv=PQ=zw6vpdQQeruBW@...>
https://mail.gna.org/public/relax-users/2010-12/msg00014.html).
The result of this bug is that initialising a prolate diffusion tensor with Da set to zero caused
the spheroid_type to be automatically set to 'oblate'. This bug was introduced at exactly r11678,
and was part of changes for better BMRB support. This affects relax version 1.3.6 and the 1.3
repository line from r11678 to 12174.
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r12175 | bugman | 2011-01-10 15:07:29 +0100 (Mon, 10 Jan 2011) | 7 lines
Implemented a system test to catch a bug in the use of volumes for relaxation curve-fitting.
This bug was identified by Maddy Strickland <M.Strickland att bristol dott ac dot uk> in the post
Message-id: <55870.137.222.43.71.1294412799.squirrel@...>
https://mail.gna.org/public/relax-users/2011-01/msg00007.html.
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r12176 | bugman | 2011-01-10 15:11:10 +0100 (Mon, 10 Jan 2011) | 7 lines
The peak volume errors are now calculated for replicated spectra in the relaxation curve-fitting.
This bug was identified by Maddy Strickland <M.Strickland att bristol dott ac dot uk> in the post
Message-id: <55870.137.222.43.71.1294412799.squirrel@...>
https://mail.gna.org/public/relax-users/2011-01/msg00007.html.
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r12177 | bugman | 2011-01-10 15:12:21 +0100 (Mon, 10 Jan 2011) | 3 lines
Fix for the new test_curve_fitting_volume() system test - the intensity type is volume, not height!
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r12178 | bugman | 2011-01-10 15:38:25 +0100 (Mon, 10 Jan 2011) | 3 lines
Decreased the number of simulations to speed up this system test script by a ~ 1/4.
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r12179 | bugman | 2011-01-10 15:40:34 +0100 (Mon, 10 Jan 2011) | 6 lines
Added a check for the peak intensity errors.
This is part of the bug fix for bug r17457 (https://gna.org/bugs/index.php?17457) reported by Maddy
Strickland <M.Strickland att bristol dott ac dot uk>.
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r12187 | bugman | 2011-01-10 18:14:50 +0100 (Mon, 10 Jan 2011) | 6 lines
Merged the relax version 1.3.7 CHANGES file into the main line.
The command used was:
svn merge -r12180:12181 svn+ssh://bugman@.../svn/relax/tags/1.3.7 .
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r12202 | bugman | 2011-01-11 12:58:33 +0100 (Tue, 11 Jan 2011) | 18 lines
Updates for Python 3.0.
The command used from docs/2to3_checklist was:
2to3 -w \
-f buffer \
-f idioms \
-f set_literal \
-f ws_comma \
-x except \
-x import \
-x imports \
-x long \
-x numliterals \
-x xrange \
relax .
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r12229 | bugman | 2011-01-12 11:52:40 +0100 (Wed, 12 Jan 2011) | 3 lines
Created a module to aid in the back-calculation of relaxation data from model-free parameters.
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r12230 | bugman | 2011-01-12 12:00:34 +0100 (Wed, 12 Jan 2011) | 3 lines
Added a new model-free test set, calculated using the new back_calc.py module.
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r12231 | bugman | 2011-01-12 12:18:50 +0100 (Wed, 12 Jan 2011) | 3 lines
Created the test_local_tm_10_S2_0_8_te_40 system test for testing model-free optimisation.
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r12232 | bugman | 2011-01-12 14:17:11 +0100 (Wed, 12 Jan 2011) | 5 lines
Improved the model-free system test value_test() method to handle all types of model-free data.
This includes not checking certain values or statistic unless specifically asked for.
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r12233 | bugman | 2011-01-12 14:20:18 +0100 (Wed, 12 Jan 2011) | 3 lines
The test_local_tm_10_S2_0_8_te_40 model-free system test is now checking the parameter values.
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r12234 | bugman | 2011-01-12 14:20:50 +0100 (Wed, 12 Jan 2011) | 3 lines
Removed a duplicated chi2 test from value_test().
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r12235 | bugman | 2011-01-12 14:23:16 +0100 (Wed, 12 Jan 2011) | 3 lines
Modified the model-free system test method mesg_opt_debug() to handle all model-free models.
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r12236 | bugman | 2011-01-12 14:24:33 +0100 (Wed, 12 Jan 2011) | 3 lines
Added the local_tm parameter to the model-free mesg_opt_debug() system test method.
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r12237 | bugman | 2011-01-12 14:25:44 +0100 (Wed, 12 Jan 2011) | 3 lines
Improved print out from mesg_opt_debug().
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r12238 | bugman | 2011-01-12 14:26:23 +0100 (Wed, 12 Jan 2011) | 3 lines
Newline fix for the mesg_opt_debug() print out.
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r12239 | bugman | 2011-01-12 14:27:54 +0100 (Wed, 12 Jan 2011) | 3 lines
More improvements to the mesg_opt_debug() print out - the correlation times are better reported.
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r12240 | bugman | 2011-01-12 14:29:54 +0100 (Wed, 12 Jan 2011) | 5 lines
Fix for the test_local_tm_10_S2_0_8_te_40() system test.
The te value should be sent in a ps units.
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r12241 | bugman | 2011-01-12 14:31:27 +0100 (Wed, 12 Jan 2011) | 3 lines
Added a directory for holding relaxation data from a grid of model-free values.
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r12242 | bugman | 2011-01-12 14:50:34 +0100 (Wed, 12 Jan 2011) | 3 lines
Created all the relaxation data for the tm2 model-free grid.
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r12243 | bugman | 2011-01-12 15:06:28 +0100 (Wed, 12 Jan 2011) | 3 lines
Shifted all the model-free system test scripts into test_suite/system_tests/scripts/model_free/.
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r12244 | bugman | 2011-01-12 15:20:56 +0100 (Wed, 12 Jan 2011) | 3 lines
Added some more local_tm_10_S2_0_8_te_40 system tests, but this time randomising the Ri data loading.
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r12245 | bugman | 2011-01-12 15:39:41 +0100 (Wed, 12 Jan 2011) | 3 lines
Created the system test for checking the tm2 grid of model-free parameters.
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r12246 | bugman | 2011-01-12 15:42:54 +0100 (Wed, 12 Jan 2011) | 3 lines
The model-free system test value_test() method is now checking the local tm value from a number of tests.
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r12247 | bugman | 2011-01-12 15:44:19 +0100 (Wed, 12 Jan 2011) | 3 lines
Set the initial param values of the test_tm2_grid() system test to the real ones.
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r12248 | bugman | 2011-01-12 15:48:04 +0100 (Wed, 12 Jan 2011) | 6 lines
Bug fix for the module for back-calculating relaxation data from model-free parameters.
The heteronucleus was being ignored when calculating the 5 frequencies of the spectral density
function.
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r12249 | bugman | 2011-01-12 15:50:33 +0100 (Wed, 12 Jan 2011) | 3 lines
Fix for the test_tm2_grid() system test - the correct values of the correlations times are being checked.
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r12250 | bugman | 2011-01-12 16:25:36 +0100 (Wed, 12 Jan 2011) | 3 lines
Newline fix.
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r12251 | bugman | 2011-01-12 16:31:07 +0100 (Wed, 12 Jan 2011) | 3 lines
Created a system test for checking model-free model m2 against the tm2 grid.
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r12252 | bugman | 2011-01-12 16:39:03 +0100 (Wed, 12 Jan 2011) | 3 lines
The same setup script is now used for all of the system tests using the tm2 grid data.
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r12253 | bugman | 2011-01-12 16:40:22 +0100 (Wed, 12 Jan 2011) | 3 lines
Created a system test for checking model-free model m3 against the tm2 grid data.
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r12254 | bugman | 2011-01-12 17:03:09 +0100 (Wed, 12 Jan 2011) | 3 lines
Simplified the 3 system tests based on the model-free tm2 grid by shifting all the code to the script.
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r12255 | bugman | 2011-01-12 17:04:43 +0100 (Wed, 12 Jan 2011) | 3 lines
Fix for the test_tm2_grid system test, the diffusion tensor should not be initialised.
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r12256 | bugman | 2011-01-12 17:08:01 +0100 (Wed, 12 Jan 2011) | 5 lines
The test_m2_grid_vs_m3() system test should really have been against model m4!
Model m3 has no te parameter, so the model does not fit perfectly.
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r12257 | bugman | 2011-01-12 17:09:17 +0100 (Wed, 12 Jan 2011) | 5 lines
Turned constraints off in the tm2 grid system tests to speed up the tests.
Constrained optimisation is not required in these simple models to find the exact solution.
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r12258 | bugman | 2011-01-12 17:27:53 +0100 (Wed, 12 Jan 2011) | 3 lines
The tm2 model parameters are now properly initialised in the tm2 grid system test script.
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r12259 | bugman | 2011-01-12 17:28:54 +0100 (Wed, 12 Jan 2011) | 3 lines
This time really turn off the optimisation constraints!
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r12260 | bugman | 2011-01-12 17:41:01 +0100 (Wed, 12 Jan 2011) | 14 lines
Reverted revision r12259 as this was completely false - it actually undid the previous commit.
The command used was:
svn merge -r12259:12258 .
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r12259 | bugman | 2011-01-12 17:28:54 +0100 (Wed, 12 Jan 2011) | 3 lines
Changed paths:
M /1.3/test_suite/system_tests/scripts/model_free/opt_tm2_grid.py
This time really turn off the optimisation constraints!
.....
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r12261 | bugman | 2011-01-12 17:42:37 +0100 (Wed, 12 Jan 2011) | 5 lines
The initial parameters are now slightly perturbed in the 3 tm2 grid system tests.
This allows the optimisation to be a bit challenged.
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r12262 | bugman | 2011-01-12 17:46:57 +0100 (Wed, 12 Jan 2011) | 3 lines
Te values of zero can now be handled by the spectral_density_mf_orig() model-free method.
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r12263 | bugman | 2011-01-12 18:49:18 +0100 (Wed, 12 Jan 2011) | 5 lines
Chemical exchange relaxation is now handled properly in the relaxation_data() function.
The back-calculated relaxation data is now correct for model-free models with Rex.
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r12264 | bugman | 2011-01-12 18:49:41 +0100 (Wed, 12 Jan 2011) | 3 lines
Changed the S2 parameter to lower case in spectral_density_mf_orig().
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r12265 | bugman | 2011-01-12 19:10:10 +0100 (Wed, 12 Jan 2011) | 3 lines
Converted the rest of the S2 variables to s2.
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r12266 | bugman | 2011-01-12 19:15:25 +0100 (Wed, 12 Jan 2011) | 5 lines
Created the spectral_density_mf_ext() function for the extended model-free theory.
This calculates the spectral density values at the given model-free parameter values.
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r12267 | bugman | 2011-01-12 21:47:04 +0100 (Wed, 12 Jan 2011) | 5 lines
Generated relaxation data for model-free parameters for all of the local tm models.
This can be used for testing both the 10 local tm models and the normal 10 model-free models.
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r12268 | bugman | 2011-01-12 21:55:48 +0100 (Wed, 12 Jan 2011) | 3 lines
Added a system test for the optimisation of the tm0 model-free parameter grid.
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r12269 | bugman | 2011-01-12 21:57:33 +0100 (Wed, 12 Jan 2011) | 3 lines
Added a system test for the optimisation of the m0 model-free model against the tm0 parameter grid.
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r12270 | bugman | 2011-01-12 22:06:00 +0100 (Wed, 12 Jan 2011) | 3 lines
Added system tests of models m1-m4 optimised against the tm0 grid.
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r12271 | bugman | 2011-01-13 09:28:55 +0100 (Thu, 13 Jan 2011) | 5 lines
Split out most of the code from the tm0 grid system test script into a separate module.
This opt_tm_fns will be used for all of the model-free parameter grid system tests.
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r12272 | bugman | 2011-01-13 09:35:42 +0100 (Thu, 13 Jan 2011) | 3 lines
Fix for the opt_and_check() function - the interpreter is in the module namespace.
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r12273 | bugman | 2011-01-13 09:38:47 +0100 (Thu, 13 Jan 2011) | 3 lines
The interpreter now has echoing turned on in the model-free grid system tests.
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r12274 | bugman | 2011-01-13 09:39:47 +0100 (Thu, 13 Jan 2011) | 3 lines
Fix for opt_and_check(), the diffusion tensor object is called cdp.diff_tensor!
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r12276 | bugman | 2011-01-13 10:53:03 +0100 (Thu, 13 Jan 2011) | 3 lines
Modified the value_test() model-free system test method to skip certain parameters if not a float or None.
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r12277 | bugman | 2011-01-13 10:53:38 +0100 (Thu, 13 Jan 2011) | 3 lines
Abstracted opt_and_check() to handle all model-free models and parameter combinations.
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r12278 | bugman | 2011-01-13 10:54:09 +0100 (Thu, 13 Jan 2011) | 3 lines
Fix for the opt_tm0_grid.py script, the parameter values now should be sent in.
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r12279 | bugman | 2011-01-13 11:06:59 +0100 (Thu, 13 Jan 2011) | 5 lines
Converted all the local tm model grids to use 13C.
This is to make the testing easier.
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r12280 | bugman | 2011-01-13 11:07:44 +0100 (Thu, 13 Jan 2011) | 3 lines
Abstracted the 'tm._grid' directory to a function arg and converted the tests to 13C.
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r12281 | bugman | 2011-01-13 11:08:16 +0100 (Thu, 13 Jan 2011) | 3 lines
Modified the module docstring, and passed in the 'tm0_grid' directory to setup_data().
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r12282 | bugman | 2011-01-13 11:08:47 +0100 (Thu, 13 Jan 2011) | 3 lines
Modified the opt_tm2_grid.py model-free system test script to use the abstracted opt_tm_fns.py fns.
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r12283 | bugman | 2011-01-13 11:11:40 +0100 (Thu, 13 Jan 2011) | 5 lines
Fix for the tm0 and tm9 relaxation data grids.
The data was a mixture of 15N spectral densities and 13C relaxation values!
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r12284 | bugman | 2011-01-13 11:15:43 +0100 (Thu, 13 Jan 2011) | 3 lines
Added system tests for the optimisation of all the local tm model-free parameter grids.
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r12285 | bugman | 2011-01-13 11:17:55 +0100 (Thu, 13 Jan 2011) | 3 lines
Added system tests for the optimisation of the normal model-free models against the all the tm parameter grids.
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r12286 | bugman | 2011-01-13 11:21:52 +0100 (Thu, 13 Jan 2011) | 3 lines
Added a system test script for the tm1 grid.
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r12287 | bugman | 2011-01-13 11:25:52 +0100 (Thu, 13 Jan 2011) | 3 lines
Fixes for the tm3 and tm4 relaxation data grids.
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r12288 | bugman | 2011-01-13 11:30:01 +0100 (Thu, 13 Jan 2011) | 3 lines
Added a system test script for the model-free model tm3 relaxation data grid.
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r12289 | bugman | 2011-01-13 11:34:08 +0100 (Thu, 13 Jan 2011) | 3 lines
Fix for the tm3 relaxation data grid - Rex should be scaled by the 1st frq in all cases!
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r12290 | bugman | 2011-01-13 11:34:47 +0100 (Thu, 13 Jan 2011) | 3 lines
The Rex scaling was (2pi)^2 too much - the frequency was already in rad/s!
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r12291 | bugman | 2011-01-13 11:37:47 +0100 (Thu, 13 Jan 2011) | 3 lines
Rex was being scaled the wrong way in opt_and_check().
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r12292 | bugman | 2011-01-13 11:38:19 +0100 (Thu, 13 Jan 2011) | 3 lines
Both Rex values need to be scaled in the model-free value_test() system test method.
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r12293 | bugman | 2011-01-13 11:39:52 +0100 (Thu, 13 Jan 2011) | 3 lines
Fix for the tm4 relaxation data grid - Rex should be scaled by the 1st frq in all cases!
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r12294 | bugman | 2011-01-13 11:40:13 +0100 (Thu, 13 Jan 2011) | 3 lines
Fix for the tm7 relaxation data grid - Rex should be scaled by the 1st frq in all cases!
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r12295 | bugman | 2011-01-13 11:40:31 +0100 (Thu, 13 Jan 2011) | 3 lines
Fix for the tm8 relaxation data grid - Rex should be scaled by the 1st frq in all cases!
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r12296 | bugman | 2011-01-13 11:40:49 +0100 (Thu, 13 Jan 2011) | 3 lines
Fix for the tm9 relaxation data grid - Rex should be scaled by the 1st frq in all cases!
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r12297 | bugman | 2011-01-13 11:42:53 +0100 (Thu, 13 Jan 2011) | 3 lines
Added a system test script for the model-free model tm4 relaxation data grid.
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r12298 | bugman | 2011-01-13 11:50:30 +0100 (Thu, 13 Jan 2011) | 3 lines
Fix for the opt_tm4_grid.py model-free system test script - the tm4 grid should be used!
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r12299 | bugman | 2011-01-13 11:51:50 +0100 (Thu, 13 Jan 2011) | 3 lines
Fix for the opt_tm4_grid.py model-free system test script - the correct number of residues is needed.
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r12300 | bugman | 2011-01-13 11:56:32 +0100 (Thu, 13 Jan 2011) | 3 lines
The te, tf, and ts parameters are now being compared on the picosecond scale.
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r12301 | bugman | 2011-01-13 11:57:10 +0100 (Thu, 13 Jan 2011) | 3 lines
The te, tf, and ts parameters are being scaled to ps in opt_and_check() now.
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r12302 | bugman | 2011-01-13 11:58:57 +0100 (Thu, 13 Jan 2011) | 3 lines
The perturbation to the initial parameter values is an order of magnitude less in opt_and_check() now.
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r12303 | bugman | 2011-01-13 12:03:17 +0100 (Thu, 13 Jan 2011) | 3 lines
Fix for the tm5 relaxation data grid - the parameter is ts, not tf.
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r12304 | bugman | 2011-01-13 12:05:30 +0100 (Thu, 13 Jan 2011) | 3 lines
Added a system test script for the model-free model tm5 relaxation data grid.
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r12305 | bugman | 2011-01-13 12:14:00 +0100 (Thu, 13 Jan 2011) | 3 lines
Loosened the S2f, S2s, ts, and tf checks.
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r12306 | bugman | 2011-01-13 12:14:19 +0100 (Thu, 13 Jan 2011) | 3 lines
The S2s parameter is being calculated from S2 and S2f.
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r12307 | bugman | 2011-01-13 12:22:33 +0100 (Thu, 13 Jan 2011) | 3 lines
Loosened the ts check even further to only 4 significant figs.
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r12308 | bugman | 2011-01-13 12:22:58 +0100 (Thu, 13 Jan 2011) | 3 lines
The initial model-free parameters are no longer perturbed at all - that costs too much time.
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r12309 | bugman | 2011-01-13 12:26:03 +0100 (Thu, 13 Jan 2011) | 3 lines
Fix for the comments, s2 and s2f were being mixed up.
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r12310 | bugman | 2011-01-13 12:28:06 +0100 (Thu, 13 Jan 2011) | 5 lines
Fix for the tm5 relaxation data grid - some of the relaxation data was negative.
The s2 values are now all smaller than s2f to prevent s2s from being > 1.
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r12311 | bugman | 2011-01-13 12:32:54 +0100 (Thu, 13 Jan 2011) | 3 lines
Shortened the tm5 relaxation data grid.
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r12312 | bugman | 2011-01-13 12:34:03 +0100 (Thu, 13 Jan 2011) | 3 lines
Shortened the tm6 relaxation data grid.
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r12313 | bugman | 2011-01-13 12:36:32 +0100 (Thu, 13 Jan 2011) | 5 lines
Loosened the tf check even further to only 4 significant figs.
This now matches the ts check.
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r12314 | bugman | 2011-01-13 12:36:51 +0100 (Thu, 13 Jan 2011) | 3 lines
Added a system test script for the model-free model tm6 relaxation data grid.
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r12315 | bugman | 2011-01-13 12:38:01 +0100 (Thu, 13 Jan 2011) | 3 lines
Fix for the tm7 relaxation data grid - the parameter is ts, not tf.
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r12316 | bugman | 2011-01-13 12:42:57 +0100 (Thu, 13 Jan 2011) | 3 lines
Added a system test script for the model-free model tm7 relaxation data grid.
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r12317 | bugman | 2011-01-13 12:44:05 +0100 (Thu, 13 Jan 2011) | 3 lines
Shortened the tm8 relaxation data grid.
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r12318 | bugman | 2011-01-13 12:50:15 +0100 (Thu, 13 Jan 2011) | 3 lines
Added a system test script for the model-free model tm8 relaxation data grid.
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r12319 | bugman | 2011-01-13 12:51:45 +0100 (Thu, 13 Jan 2011) | 3 lines
Added a system test script for the model-free model tm9 relaxation data grid.
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r12320 | bugman | 2011-01-13 14:18:52 +0100 (Thu, 13 Jan 2011) | 3 lines
The Rex parameters have been made independent of field strength prior to running value_test().
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