mailr8092 - in /1.3: ./ generic_fns/ maths_fns/ prompt/ sample_scripts/ specific_fns/ test_suite/shared_data/saved_states/ test_...


Others Months | Index by Date | Thread Index
>>   [Date Prev] [Date Next] [Thread Prev] [Thread Next]

Header


Content

Posted by edward on December 02, 2008 - 15:17:
Author: bugman
Date: Tue Dec  2 15:16:54 2008
New Revision: 8092

URL: http://svn.gna.org/viewcvs/relax?rev=8092&view=rev
Log:
Merged revisions 
7881-7915,7925,7936,7950-7951,7953-7960,7964,7985-7990,7993-7995,7998-8010,8013,8023-8025,8037-8055,8069-8081,8085-8086,8088-8090
 via svnmerge from 
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/spectral_errors

........
  r7881 | bugman | 2008-10-21 16:01:01 +0200 (Tue, 21 Oct 2008) | 3 lines
  
  Created the empty user function class 'spectrum'.
........
  r7882 | bugman | 2008-10-21 16:03:37 +0200 (Tue, 21 Oct 2008) | 6 lines
  
  Deleted the prompt.spectrum module.
  
  The prompt.noe module will be renamed to this as its only functions are the 
same as the spectrum
  user function class.
........
  r7883 | bugman | 2008-10-21 16:04:32 +0200 (Tue, 21 Oct 2008) | 6 lines
  
  Renamed the noe module to spectrum.
  
  The noe module only contains user functions will are to be merged into the 
spectrum user function
  class, hence will be deleted anyway.
........
  r7884 | bugman | 2008-10-21 16:05:24 +0200 (Tue, 21 Oct 2008) | 3 lines
  
  Renamed the class in the old prompt.noe module.
........
  r7885 | bugman | 2008-10-21 16:06:18 +0200 (Tue, 21 Oct 2008) | 3 lines
  
  Deleted the old NOE user function class from the interpreter namespace.
........
  r7886 | bugman | 2008-10-21 16:31:48 +0200 (Tue, 21 Oct 2008) | 3 lines
  
  Renamed 'spectrum_type' to the more generic 'spectrum_id'.
........
  r7887 | bugman | 2008-10-21 16:38:34 +0200 (Tue, 21 Oct 2008) | 3 lines
  
  Docstring updates for spectrum.read().
........
  r7888 | bugman | 2008-10-21 16:39:01 +0200 (Tue, 21 Oct 2008) | 3 lines
  
  Renamed spectrum.read() to spectrum.read_intensities().
........
  r7889 | bugman | 2008-10-21 16:45:27 +0200 (Tue, 21 Oct 2008) | 5 lines
  
  Deletion of the format argument from the spectrum.read_intensities() user 
function.
  
  To compensate for this, relax will be modified to auto-detect the file 
format.
........
  r7890 | bugman | 2008-10-21 16:49:49 +0200 (Tue, 21 Oct 2008) | 3 lines
  
  Fixed docstrings and user function print outs.
........
  r7891 | bugman | 2008-10-21 16:53:04 +0200 (Tue, 21 Oct 2008) | 3 lines
  
  Switched from calls to noe_obj to generic_fns.intensity.
........
  r7892 | bugman | 2008-10-21 17:22:49 +0200 (Tue, 21 Oct 2008) | 7 lines
  
  Added new arguments and improved the spectrum.read_intensities() docstring.
  
  The mol_name_col, res_num_col, res_name_col, spin_num_col, spin_name_col, 
and sep args have been
  added to support the generic intensity file format.  This format has also 
had a description in the
  docstring written.
........
  r7893 | bugman | 2008-10-21 17:25:06 +0200 (Tue, 21 Oct 2008) | 3 lines
  
  Shifted the relax_fit.mean_and_error() user function interface to 
spectrum.mean_and_error().
........
  r7894 | bugman | 2008-10-21 17:25:43 +0200 (Tue, 21 Oct 2008) | 3 lines
  
  Renamed spectrum.mean_and_error() to spectrum.error_analysis().
........
  r7895 | bugman | 2008-10-21 17:42:29 +0200 (Tue, 21 Oct 2008) | 3 lines
  
  spectrum.error_analysis() now calls generic_fns.intensity.error_analysis().
........
  r7896 | bugman | 2008-10-21 18:34:31 +0200 (Tue, 21 Oct 2008) | 5 lines
  
  Rewrote the spectrum.error_analysis() user function docstring.
  
  This is still missing 3 sections for error analysis with the volume 
integration methods.
........
  r7897 | bugman | 2008-10-21 18:35:59 +0200 (Tue, 21 Oct 2008) | 3 lines
  
  Renamed the generic_fns.intensity module to generic_fns/spectrum.
........
  r7898 | bugman | 2008-10-21 18:37:22 +0200 (Tue, 21 Oct 2008) | 3 lines
  
  Import fix for generic_fns.spectrum.
........
  r7899 | bugman | 2008-10-21 18:38:19 +0200 (Tue, 21 Oct 2008) | 3 lines
  
  Import error fix.
........
  r7900 | bugman | 2008-10-21 18:38:47 +0200 (Tue, 21 Oct 2008) | 3 lines
  
  Another import error fix.
........
  r7901 | bugman | 2008-10-22 10:41:28 +0200 (Wed, 22 Oct 2008) | 3 lines
  
  Finished of the massive docstring of the spectrum.error_analysis() user 
function.
........
  r7902 | bugman | 2008-10-22 10:44:40 +0200 (Wed, 22 Oct 2008) | 3 lines
  
  Created the skeleton module for arg unit tests of the spectrum user 
function class.
........
  r7903 | bugman | 2008-10-22 11:16:31 +0200 (Wed, 22 Oct 2008) | 3 lines
  
  Created the new error class RelaxNoneIntListIntError.
........
  r7904 | bugman | 2008-10-22 11:19:32 +0200 (Wed, 22 Oct 2008) | 3 lines
  
  Wrote 15 arg unit tests for the spectrum user functions.
........
  r7905 | bugman | 2008-10-22 11:20:10 +0200 (Wed, 22 Oct 2008) | 3 lines
  
  Modified the int_col arg to spectrum.read_intensities() to allow for lists 
of integers.
........
  r7906 | bugman | 2008-10-22 11:25:22 +0200 (Wed, 22 Oct 2008) | 3 lines
  
  Renamed spectrum.error() to spectrum.baseplane_rmsd().
........
  r7907 | bugman | 2008-10-22 11:31:14 +0200 (Wed, 22 Oct 2008) | 3 lines
  
  Created the spectrum.integration_points() user function interface.
........
  r7908 | bugman | 2008-10-22 11:33:44 +0200 (Wed, 22 Oct 2008) | 3 lines
  
  Wrote 3 arg unit tests for the spectrum.integration_points() user function.
........
  r7909 | bugman | 2008-10-22 11:35:28 +0200 (Wed, 22 Oct 2008) | 3 lines
  
  Fix for the N arg check of the spectrum.integration_points() user function.
........
  r7910 | bugman | 2008-10-22 11:36:09 +0200 (Wed, 22 Oct 2008) | 3 lines
  
  Fix for 2 arg unit tests of the spectrum.integration_points() user function.
........
  r7911 | bugman | 2008-10-22 11:37:08 +0200 (Wed, 22 Oct 2008) | 3 lines
  
  Fixes for the arg unit tests of the spectrum.baseplane_rmsd() user function.
........
  r7912 | bugman | 2008-10-22 11:56:55 +0200 (Wed, 22 Oct 2008) | 3 lines
  
  Added the int_method arg to the spectrum.read_intensities() user function.
........
  r7913 | bugman | 2008-10-22 12:04:38 +0200 (Wed, 22 Oct 2008) | 3 lines
  
  Wrote the int_method arg unit test of the spectrum.read_intensities() user 
function.
........
  r7914 | bugman | 2008-10-22 12:24:56 +0200 (Wed, 22 Oct 2008) | 3 lines
  
  Fix for the user function class documentation.
........
  r7915 | bugman | 2008-10-22 12:36:21 +0200 (Wed, 22 Oct 2008) | 6 lines
  
  Renamed relax_fit.read() to relax_fit.relax_time() and significantly 
decreased its functionality.
  
  Most of relax_fit.read() is now in spectrum.read_intensities() and hence 
this functionality has been
  axed.  All that is left is the associating of a spectrum to a time point.
........
  r7925 | bugman | 2008-10-22 18:14:40 +0200 (Wed, 22 Oct 2008) | 3 lines
  
  Added 3 arg unit tests for the relax_fit user function class.
........
  r7936 | bugman | 2008-10-22 19:26:53 +0200 (Wed, 22 Oct 2008) | 3 lines
  
  Removed some unused imports.
........
  r7950 | bugman | 2008-10-23 17:09:03 +0200 (Thu, 23 Oct 2008) | 3 lines
  
  Added module docstrings and __docformat__ variables to the 'spectrum' 
prompt module.
........
  r7951 | bugman | 2008-10-23 17:15:19 +0200 (Thu, 23 Oct 2008) | 5 lines
  
  Created a new noe user function class, unrelated to the previously deleted 
one.
  
  This contains the single user function, noe.spectrum_type().
........
  r7953 | bugman | 2008-10-23 17:56:58 +0200 (Thu, 23 Oct 2008) | 3 lines
  
  Fix for the initial spectrum.read_intensities() print out, the int_method 
arg was not being shown.
........
  r7954 | bugman | 2008-10-23 17:58:15 +0200 (Thu, 23 Oct 2008) | 3 lines
  
  Updated the relax_fit.py system test script for the new spectrum user 
function class.
........
  r7955 | bugman | 2008-10-23 17:59:19 +0200 (Thu, 23 Oct 2008) | 5 lines
  
  Expanded the relax_fit.py system test script to include the creation of a 
number of files.
  
  These include files of Rx values, the results file, grace files, and the 
saved state file.
........
  r7956 | bugman | 2008-10-23 18:01:58 +0200 (Thu, 23 Oct 2008) | 5 lines
  
  Updated the relax_fit.py sample script to match the changes of r7954 to the 
system test script.
  
  The script now uses the new spectrum user function class.
........
  r7957 | bugman | 2008-10-23 18:10:59 +0200 (Thu, 23 Oct 2008) | 3 lines
  
  Fixed the args and docstring for the generic_fns.spectrum.read() function.
........
  r7958 | bugman | 2008-10-23 18:23:42 +0200 (Thu, 23 Oct 2008) | 6 lines
  
  The peak list type is now automatically determined.
  
  The new autodetect_format() function was written, and the top half of the 
read() function was
  modified to handle the auto-detection.
........
  r7959 | bugman | 2008-10-23 18:32:08 +0200 (Thu, 23 Oct 2008) | 3 lines
  
  Destroyed assign_func() and shifted all the data storage back to 
generic_fns.spectrum.read().
........
  r7960 | bugman | 2008-10-23 18:57:53 +0200 (Thu, 23 Oct 2008) | 3 lines
  
  Fixes for the peak list system tests, using the new 
spectrum.read_intensities() user function.
........
  r7964 | bugman | 2008-10-24 15:40:05 +0200 (Fri, 24 Oct 2008) | 6 lines
  
  Renamed and converted the read() method to relax_time().
  
  The method now simply creates a structure in the relax data store matching 
cdp.spectrum_ids and
  storing the associated relaxation time periods.
........
  r7985 | bugman | 2008-11-20 21:53:30 +0100 (Thu, 20 Nov 2008) | 5 lines
  
  Changed the default integration method from None to 'height'.
  
  Height integration, when done properly is better than volumes for peak 
intensities ;)
........
  r7986 | bugman | 2008-11-20 21:56:17 +0100 (Thu, 20 Nov 2008) | 3 lines
  
  Cleaned up a warning string.
........
  r7987 | bugman | 2008-11-20 21:58:12 +0100 (Thu, 20 Nov 2008) | 3 lines
  
  Changed the warning message once more.
........
  r7988 | bugman | 2008-11-20 22:05:04 +0100 (Thu, 20 Nov 2008) | 5 lines
  
  Fix for the test_read_sparky() system test.
  
  The relax_fit.read() call was replaced with spectrum.read_intensities().
........
  r7989 | bugman | 2008-11-20 22:09:43 +0100 (Thu, 20 Nov 2008) | 6 lines
  
  Modified the script to create the basic_heights_T2_ncyc1.bz2 saved state 
and regenerated this file.
  
  The spectrum.read_intensities() user function is now used, and the new 
format of the spin specific
  'intensities' data structure is in the saved state.
........
  r7990 | bugman | 2008-11-20 22:18:47 +0100 (Thu, 20 Nov 2008) | 5 lines
  
  Another fix for the test_read_sparky() system test.
  
  This fixes the checking of the new spin specific 'intensities' data 
structure.
........
  r7993 | bugman | 2008-11-20 23:31:32 +0100 (Thu, 20 Nov 2008) | 5 lines
  
  Fixes for the 4 peak list reading system tests.
  
  The spin specific intensities structure is now a simple list.
........
  r7994 | bugman | 2008-11-20 23:39:41 +0100 (Thu, 20 Nov 2008) | 3 lines
  
  Modified the noe.py system test script to use the new 'spectrum' user 
functions.
........
  r7995 | bugman | 2008-11-20 23:40:45 +0100 (Thu, 20 Nov 2008) | 5 lines
  
  Modified the noe.py sample script to use the new 'spectrum' user functions.
  
  This copies the changes of r7994 which were made to the equivalent system 
test.
........
  r7998 | bugman | 2008-11-21 09:54:55 +0100 (Fri, 21 Nov 2008) | 5 lines
  
  Renamed spectrum_type to spectrum_id in the NOE set_error() method.
  
  This method may have to remain for the Monte Carlo simulations?
........
  r7999 | bugman | 2008-11-21 09:57:35 +0100 (Fri, 21 Nov 2008) | 5 lines
  
  Copied the NOE set_error() function to 
generic_fns.spectrum.baseplane_rmsd().
  
  The class method has been converted to a module function.
........
  r8000 | bugman | 2008-11-21 10:03:55 +0100 (Fri, 21 Nov 2008) | 3 lines
  
  Updated the baseplane_rmsd() function to it's new purpose.
........
  r8001 | bugman | 2008-11-21 10:04:45 +0100 (Fri, 21 Nov 2008) | 3 lines
  
  Added a missing bracket.
........
  r8002 | bugman | 2008-11-21 10:06:35 +0100 (Fri, 21 Nov 2008) | 3 lines
  
  The current data pipe is now aliased.
........
  r8003 | bugman | 2008-11-21 10:13:41 +0100 (Fri, 21 Nov 2008) | 3 lines
  
  Fixes for the baseplane_rmsd() function.
........
  r8004 | bugman | 2008-11-21 10:15:04 +0100 (Fri, 21 Nov 2008) | 5 lines
  
  Fix for the noe.py system test script.
  
  The spectrum.baseplane_rmsd() user function was receiving the wrong 
arguments.
........
  r8005 | bugman | 2008-11-21 10:31:10 +0100 (Fri, 21 Nov 2008) | 3 lines
  
  Fix for a RelaxError call in baseplane_rmsd().
........
  r8006 | bugman | 2008-11-21 10:33:31 +0100 (Fri, 21 Nov 2008) | 3 lines
  
  Added some tests to the NOE calculate() method.
........
  r8007 | bugman | 2008-11-21 10:37:46 +0100 (Fri, 21 Nov 2008) | 3 lines
  
  Modified the NOE overfit_deselect() for the new peak intensity data 
structures.
........
  r8008 | bugman | 2008-11-21 10:50:20 +0100 (Fri, 21 Nov 2008) | 5 lines
  
  Created a new warning class, RelaxDeselectWarning.
  
  This is to be used by all overfit_deselect methods!
........
  r8009 | bugman | 2008-11-21 10:51:55 +0100 (Fri, 21 Nov 2008) | 5 lines
  
  Updated the NOE overfit_deselect() method to use RelaxDeselectWarning.
  
  Deselected spins are skipped and the checks are now in an if-elif block.
........
  r8010 | bugman | 2008-11-21 11:22:47 +0100 (Fri, 21 Nov 2008) | 3 lines
  
  Added the spectrum.error_analysis() user fn call to both the NOE sample 
script and system test.
........
  r8013 | bugman | 2008-11-21 13:38:36 +0100 (Fri, 21 Nov 2008) | 3 lines
  
  Initialisation of the error_analysis() function.
........
  r8023 | bugman | 2008-11-25 15:17:22 +0100 (Tue, 25 Nov 2008) | 5 lines
  
  Added a catch for missing data in the grace.write() user function back end.
  
  A RelaxWarning is now thrown saying that an empty file will be created.
........
  r8024 | bugman | 2008-11-25 15:18:51 +0100 (Tue, 25 Nov 2008) | 3 lines
  
  Slight modification to the missing data RelaxWarning message.
........
  r8025 | bugman | 2008-11-26 10:57:42 +0100 (Wed, 26 Nov 2008) | 3 lines
  
  Wrote the interface for the spectrum.replicated() user function.
........
  r8037 | bugman | 2008-11-27 14:02:41 +0100 (Thu, 27 Nov 2008) | 5 lines
  
  Partial implementation of the error_analysis() code
  
  The 2 categories now supported are both peak height and volumes when no 
spectra are replicated.
........
  r8038 | bugman | 2008-11-27 14:06:48 +0100 (Thu, 27 Nov 2008) | 3 lines
  
  Fixes for the volume integration with no replicated spectra.
........
  r8039 | bugman | 2008-11-27 14:12:59 +0100 (Thu, 27 Nov 2008) | 6 lines
  
  Modified the NOE system test to call the noe.spectrum_type() user function.
  
  The spectrum_ids have also been changed to avoid user confusion (when these 
changes are ported to
  the sample script).
........
  r8040 | bugman | 2008-11-27 14:15:42 +0100 (Thu, 27 Nov 2008) | 17 lines
  
  Manually ported r8039 from the system test to the sample script.
  
  The command used was:
  svn merge -r8038:8039 test_suite/system_tests/scripts/noe.py 
sample_scripts/noe.py
  
  .....
  r8039 | bugman | 2008-11-27 14:12:59 +0100 (Thu, 27 Nov 2008) | 6 lines
  Changed paths:
     M /branches/spectral_errors/test_suite/system_tests/scripts/noe.py
  
  Modified the NOE system test to call the noe.spectrum_type() user function.
  
  The spectrum_ids have also been changed to avoid user confusion (when these 
changes are ported to
  the sample script).
  .....
........
  r8041 | bugman | 2008-11-27 14:19:37 +0100 (Thu, 27 Nov 2008) | 3 lines
  
  Activated the 'noe' user function class.
........
  r8042 | bugman | 2008-11-27 14:20:44 +0100 (Thu, 27 Nov 2008) | 5 lines
  
  Fix for the noe.spectrum_type() user function.
  
  The spectrum_type should be a string, not a number.
........
  r8043 | bugman | 2008-11-27 15:05:04 +0100 (Thu, 27 Nov 2008) | 6 lines
  
  Split up the error_analysis() function.
  
  The two functions __errors_height_no_repl() and __errors_volume_no_repl() 
have been created.  The
  other 4 analysis types will be added as functions later.
........
  r8044 | bugman | 2008-11-27 16:22:56 +0100 (Thu, 27 Nov 2008) | 3 lines
  
  Wrote the NOE spectrum_type() method.
........
  r8045 | bugman | 2008-11-27 16:29:02 +0100 (Thu, 27 Nov 2008) | 3 lines
  
  Modified the NOE calculation code for the new spectra setup.
........
  r8046 | bugman | 2008-11-27 17:41:34 +0100 (Thu, 27 Nov 2008) | 3 lines
  
  Added a check for the value of int_method in the 
spectrum.read_intensities() user function.
........
  r8047 | bugman | 2008-11-27 17:47:45 +0100 (Thu, 27 Nov 2008) | 5 lines
  
  Fix for the relax_fit.py system test script.
  
  The spectrum.read_intensities() user function arg int_method was 
incorrectly set.
........
  r8048 | bugman | 2008-11-27 17:49:50 +0100 (Thu, 27 Nov 2008) | 3 lines
  
  Removed some debugging code.
........
  r8049 | bugman | 2008-11-27 18:06:29 +0100 (Thu, 27 Nov 2008) | 5 lines
  
  Fixes for all the peak list reading tests.
  
  The int_method arg to spectrum.read_intensities() was incorrectly set to 
'heights'.
........
  r8050 | bugman | 2008-11-27 18:12:39 +0100 (Thu, 27 Nov 2008) | 3 lines
  
  The duplicated spectra are now specified in the relax_fit.py system test 
script.
........
  r8051 | bugman | 2008-11-27 18:14:00 +0100 (Thu, 27 Nov 2008) | 5 lines
  
  Fixes for the relax_fit.py sample script.
  
  This includes fixes for spectrum.read_intensities() and the use of 
spectrum.replicated().
........
  r8052 | bugman | 2008-11-28 10:48:35 +0100 (Fri, 28 Nov 2008) | 3 lines
  
  Implemented the replicated() function.
........
  r8053 | bugman | 2008-11-28 10:49:01 +0100 (Fri, 28 Nov 2008) | 3 lines
  
  Removed some debugging print outs.
........
  r8054 | bugman | 2008-11-28 14:54:34 +0100 (Fri, 28 Nov 2008) | 3 lines
  
  Fixes for the error_analysis() function.  Replicated spectra are stored in 
'cdp.replicates'.
........
  r8055 | bugman | 2008-11-28 18:02:42 +0100 (Fri, 28 Nov 2008) | 5 lines
  
  Started to implement the __errors_repl() function.
  
  This is a highly modified form of the relaxation curve-fitting 
mean_and_error() method.
........
  r8069 | bugman | 2008-12-01 09:37:13 +0100 (Mon, 01 Dec 2008) | 3 lines
  
  Fix for the calculation of the average variance.
........
  r8070 | bugman | 2008-12-01 10:40:11 +0100 (Mon, 01 Dec 2008) | 5 lines
  
  A number of fixes for the __errors_repl() function.
  
  The variance and sd structures are now correctly created, and the variances 
properly averaged.
........
  r8071 | bugman | 2008-12-01 10:42:42 +0100 (Mon, 01 Dec 2008) | 3 lines
  
  The spin specific error structure intensity_err is now set for each 
selected spin.
........
  r8072 | bugman | 2008-12-01 10:47:02 +0100 (Mon, 01 Dec 2008) | 3 lines
  
  Print out refinement of the __errors_repl() function.
........
  r8073 | bugman | 2008-12-01 10:51:10 +0100 (Mon, 01 Dec 2008) | 3 lines
  
  Removal of the mean_and_error() method.  This is now part of 
generic_fns.spectrum.
........
  r8074 | bugman | 2008-12-01 10:52:19 +0100 (Mon, 01 Dec 2008) | 5 lines
  
  Some fixes for the back_calc() relax-fit method.
  
  Not sure if this method will work yet!
........
  r8075 | bugman | 2008-12-01 10:53:49 +0100 (Mon, 01 Dec 2008) | 3 lines
  
  Replaced all references to 'average peak intensity'.  These are no longer 
averaged.
........
  r8076 | bugman | 2008-12-01 10:59:51 +0100 (Mon, 01 Dec 2008) | 3 lines
  
  Some whitespace cleanups.
........
  r8077 | bugman | 2008-12-01 15:42:53 +0100 (Mon, 01 Dec 2008) | 5 lines
  
  Fixed the setting of the spin specific peak intensity errors in 
__errors_repl().
  
  This should be an array equal to cdp.sigma_I.
........
  r8078 | bugman | 2008-12-01 15:44:30 +0100 (Mon, 01 Dec 2008) | 3 lines
  
  The proper spin specific peak intensity errors are now input into the 
relax-fit minimise() method.
........
  r8079 | bugman | 2008-12-01 15:54:59 +0100 (Mon, 01 Dec 2008) | 3 lines
  
  Fix for the relax_fit.py system test script.  The 'ave_int' value type is 
no more!
........
  r8080 | bugman | 2008-12-01 15:56:39 +0100 (Mon, 01 Dec 2008) | 5 lines
  

[... 138 lines stripped ...]



Related Messages


Powered by MHonArc, Updated Tue Dec 02 15:20:04 2008