Author: bugman
Date: Tue May 31 13:00:10 2011
New Revision: 12838
URL: http://svn.gna.org/viewcvs/relax?rev=12838&view=rev
Log:
Merged revisions
12598-12617,12619-12634,12637-12643,12648,12778-12780,12782-12806,12808-12830
via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
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r12598 | bugman | 2011-02-21 09:54:00 +0100 (Mon, 21 Feb 2011) | 3 lines
Activated the PDC peak intensity type reading, now that the BMRB branch has
been merged.
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r12599 | bugman | 2011-02-21 09:59:38 +0100 (Mon, 21 Feb 2011) | 6 lines
Added the Bruker PDC software info to the exp_info module.
This is from https://mail.gna.org/public/relax-devel/2011-02/msg00056.html
(Message-id:
<4D621CF8.601@xxxxxxxxxxxxxxxxx>).
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r12600 | bugman | 2011-02-21 10:22:55 +0100 (Mon, 21 Feb 2011) | 3 lines
Added the Bruker PDC to the exp_info.software_select() backend.
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r12601 | bugman | 2011-02-21 10:28:39 +0100 (Mon, 21 Feb 2011) | 3 lines
The pdc.read() back end is now reading the PDC version information.
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r12602 | bugman | 2011-02-21 10:30:13 +0100 (Mon, 21 Feb 2011) | 5 lines
The setting of the integration method in pdc.read() now works.
This needed to be done after the packing of the relaxation data.
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r12603 | bugman | 2011-02-21 10:32:41 +0100 (Mon, 21 Feb 2011) | 5 lines
The Bruker PDC software is now added to the experimental information.
This will be included in the BMRB deposition file.
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r12604 | bugman | 2011-02-21 16:40:41 +0100 (Mon, 21 Feb 2011) | 6 lines
Updated the Bruker PDC R1 output file.
This is from https://mail.gna.org/public/relax-devel/2011-02/msg00060.html
(Message-id:
<4D6275CE.6040809@xxxxxxxxxxxxxxxxx>).
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r12605 | bugman | 2011-02-21 16:41:01 +0100 (Mon, 21 Feb 2011) | 3 lines
Updated the conversion script for the new R1 PDC file.
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r12606 | bugman | 2011-02-22 14:56:34 +0100 (Tue, 22 Feb 2011) | 8 lines
Updated the R1 Bruker PDC file to a newer version using "variance
averaging" for the errors.
See https://mail.gna.org/public/relax-devel/2011-02/msg00066.html
(Message-id:
<4D63908C.5060101@xxxxxxxxxxxxxxxxx>).
This is instead of the "worst case per peak scenario" option which over
estimates the errors.
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r12607 | bugman | 2011-02-22 14:59:13 +0100 (Tue, 22 Feb 2011) | 3 lines
Renamed the convert_data Bruker PDC conversion script to indicate it is for
the R1.
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r12608 | bugman | 2011-02-22 15:08:50 +0100 (Tue, 22 Feb 2011) | 3 lines
Updated the convert_data_r1.py to directly read the data out of the Bruker
PDC file.
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r12609 | bugman | 2011-02-22 15:12:57 +0100 (Tue, 22 Feb 2011) | 5 lines
Added a catch for the "worst case per peak scenario" option in the PDC.
This will now throw a RelaxError, telling the user to go back to the PDC
and use the other option.
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r12610 | bugman | 2011-02-22 15:13:15 +0100 (Tue, 22 Feb 2011) | 3 lines
Updated the errors_R1.txt for the new R1 PDC file.
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r12611 | bugman | 2011-02-22 15:13:44 +0100 (Tue, 22 Feb 2011) | 3 lines
Removed a debugging print statement.
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r12612 | bugman | 2011-02-22 15:33:56 +0100 (Tue, 22 Feb 2011) | 3 lines
Convert the pdc.read() back-end to use the \t delimination of the PDC file
for parsing.
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r12613 | bugman | 2011-02-22 15:34:26 +0100 (Tue, 22 Feb 2011) | 3 lines
New relax R1 data file for the new testT1.txt PDC data file.
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r12614 | bugman | 2011-02-22 15:37:13 +0100 (Tue, 22 Feb 2011) | 3 lines
Updated the convert_data_r1.py script for the new R1 PDC data.
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r12615 | bugman | 2011-02-22 15:37:31 +0100 (Tue, 22 Feb 2011) | 3 lines
Updated the Bruker PDC reading system test for the new R1 data.
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r12616 | bugman | 2011-02-22 15:40:05 +0100 (Tue, 22 Feb 2011) | 3 lines
Fixes for the pdc.read() back-end for the NOE PDC file.
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r12617 | bugman | 2011-02-22 16:51:50 +0100 (Tue, 22 Feb 2011) | 3 lines
Updates for the new R1 Bruker PDC file.
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r12619 | bugman | 2011-02-24 12:41:06 +0100 (Thu, 24 Feb 2011) | 6 lines
Updated the Bruker PDC files to the newest versions.
These are taken from the task #7180 (https://gna.org/task/?7180) attached
by Peter Neidig as file
#12537, file #12538, and file #12539.
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r12620 | bugman | 2011-02-24 12:48:03 +0100 (Thu, 24 Feb 2011) | 3 lines
The PDC NOE conversion script is now taking the data directly from the PDC
file.
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r12621 | bugman | 2011-02-24 12:50:14 +0100 (Thu, 24 Feb 2011) | 3 lines
Fix for the pdc.read() back-end for reading NOE data out of the new PDC
files.
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r12622 | bugman | 2011-02-24 12:50:46 +0100 (Thu, 24 Feb 2011) | 3 lines
Fix for the PDC reading system tests, the data now matches the new PDC
files.
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r12623 | bugman | 2011-02-24 12:53:17 +0100 (Thu, 24 Feb 2011) | 3 lines
The R1 value and error are now being read directly from the PDC file.
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r12624 | bugman | 2011-02-24 12:53:48 +0100 (Thu, 24 Feb 2011) | 3 lines
Decreased the accuracy of the PDC reading system test, as the PDC data is
not accurate to 7 places.
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r12625 | bugman | 2011-02-25 14:24:59 +0100 (Fri, 25 Feb 2011) | 9 lines
Removed numpy from the relaxation curve-fitting C module code.
This now expects Python lists as arguments. This should help with
incompatibilities between
different Python versions, as this seems to be due to the numpy C
interface. See for example
the thread started by Min-Kyu <min-kyu dott cho att vanderbilt dot edu>
https://mail.gna.org/public/relax-users/2011-02/msg00000.html (Message-id:
<001f01cbd24f$350042d0$9f00c870$@cho@vanderbilt.edu>).
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r12626 | bugman | 2011-02-25 14:26:23 +0100 (Fri, 25 Feb 2011) | 6 lines
Added wrapper methods to the relaxation curve-fitting specific code for the
new C modules.
These allow the parameter numpy array from minfx to be converted into a
Python list prior to sending
it into the C module.
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r12627 | bugman | 2011-02-25 14:29:07 +0100 (Fri, 25 Feb 2011) | 3 lines
Fix for the back_calc_I C function so that it works under Python 2.5.
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r12628 | bugman | 2011-02-25 14:31:31 +0100 (Fri, 25 Feb 2011) | 3 lines
Added a check for the runpy module.
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r12629 | bugman | 2011-02-25 14:32:27 +0100 (Fri, 25 Feb 2011) | 3 lines
The runpy module is only imported if it exists.
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r12630 | bugman | 2011-02-25 14:33:35 +0100 (Fri, 25 Feb 2011) | 5 lines
Fix for the initialisation of the Bruker_import class.
This allows this module to be loaded in Python 2.4.
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r12631 | bugman | 2011-02-25 14:38:10 +0100 (Fri, 25 Feb 2011) | 3 lines
Scripts can now be run again under Python versions 2.4 or lower.
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r12632 | bugman | 2011-02-25 14:56:04 +0100 (Fri, 25 Feb 2011) | 5 lines
The reference counting appears to not be needed in the C modules.
This allows the modules to be compiled under Python 2.4 or lower.
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r12633 | bugman | 2011-02-25 15:25:42 +0100 (Fri, 25 Feb 2011) | 3 lines
The auto_analyses package modules are now imported by __init__ to force
their existence.
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r12634 | bugman | 2011-02-25 18:46:52 +0100 (Fri, 25 Feb 2011) | 8 lines
Loosened all of the model-free tests so that the minimisation statistics
are no longer checked.
The same result was being obtained on different platforms, different Python
versions, and different
numpy versions, but the minimisation statistics were slightly different.
The iter, f_count, g_count
h_count, and warning variables are no longer checked. This will stop users
from thinking they have
a problem with their version of relax, after running the test suite.
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r12637 | bugman | 2011-03-01 11:35:09 +0100 (Tue, 01 Mar 2011) | 3 lines
Added graphics for the value user function.
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r12638 | bugman | 2011-03-01 11:36:30 +0100 (Tue, 01 Mar 2011) | 3 lines
Added the value user function graphics to the icon paths.
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r12639 | bugman | 2011-03-01 12:08:42 +0100 (Tue, 01 Mar 2011) | 3 lines
Added a wizard graphic for the value user functions.
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r12640 | bugman | 2011-03-01 12:11:24 +0100 (Tue, 01 Mar 2011) | 3 lines
The value user function wizard graphic is now the correct size.
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r12641 | bugman | 2011-03-01 12:13:32 +0100 (Tue, 01 Mar 2011) | 3 lines
Improvements to the value user function wizard graphic - the tensor
background has been deleted.
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r12642 | bugman | 2011-03-01 12:14:53 +0100 (Tue, 01 Mar 2011) | 3 lines
The value wizard graphic is again the wrong size!!!
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r12643 | bugman | 2011-03-01 12:15:43 +0100 (Tue, 01 Mar 2011) | 3 lines
Created an initial value.set() user function GUI element and menu entry.
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r12648 | bugman | 2011-03-01 15:52:19 +0100 (Tue, 01 Mar 2011) | 3 lines
Modified the value.set() user function GUI element so that the parameter
element is an input field.
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r12778 | bugman | 2011-03-03 14:14:22 +0100 (Thu, 03 Mar 2011) | 3 lines
Initialized merge tracking via "svnmerge" with revisions "1-12645" from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/relax_data
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r12779 | bugman | 2011-03-03 14:21:42 +0100 (Thu, 03 Mar 2011) | 583 lines
Merged revisions 12647,12649-12767,12769-12777 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/relax_data
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r12647 | bugman | 2011-03-01 15:36:46 +0100 (Tue, 01 Mar 2011) | 3 lines
Redesigned the relax_data.read() user function front end for handling
data ID strings.
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r12649 | bugman | 2011-03-01 17:04:07 +0100 (Tue, 01 Mar 2011) | 6 lines
Updated the relax_data.read() back end for the new ID string based design.
The update_data_structures_pipe() and data_init() functions have been
deleted and the pack_data()
function highly modified.
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r12650 | bugman | 2011-03-01 17:05:17 +0100 (Tue, 01 Mar 2011) | 3 lines
The model-free code no longer calls the deleted relax_data.data_init()
function.
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r12651 | bugman | 2011-03-01 17:19:26 +0100 (Tue, 01 Mar 2011) | 3 lines
Simplification of the return_value() function.
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r12652 | bugman | 2011-03-01 17:24:07 +0100 (Tue, 01 Mar 2011) | 3 lines
Updates for a number of model-free system tests for the changed
relax_data.read() user function.
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r12653 | bugman | 2011-03-01 17:24:32 +0100 (Tue, 01 Mar 2011) | 3 lines
Simplified the return_data_desc() function.
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r12654 | bugman | 2011-03-01 17:25:20 +0100 (Tue, 01 Mar 2011) | 3 lines
Removal of the test_labels() function, as this was only needed with the
old design.
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r12655 | bugman | 2011-03-01 17:25:29 +0100 (Tue, 01 Mar 2011) | 3 lines
Spacing fix.
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r12656 | bugman | 2011-03-01 17:32:03 +0100 (Tue, 01 Mar 2011) | 3 lines
Deleted the now useless add_data_to_spin() function.
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r12657 | bugman | 2011-03-01 17:56:29 +0100 (Tue, 01 Mar 2011) | 3 lines
Updated the relax_data.back_calc() function for the new design.
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r12658 | bugman | 2011-03-01 18:05:03 +0100 (Tue, 01 Mar 2011) | 3 lines
Converted the relax_data.bmrb_read() function to the new ID string design.
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r12659 | bugman | 2011-03-01 18:09:40 +0100 (Tue, 01 Mar 2011) | 3 lines
Converted the back and front ends of the relax_data.copy() user function
to the new design.
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r12660 | bugman | 2011-03-01 18:13:01 +0100 (Tue, 01 Mar 2011) | 3 lines
Converted RelaxNoRiError and RelaxRiError to the new ID string design.
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r12661 | bugman | 2011-03-01 18:16:32 +0100 (Tue, 01 Mar 2011) | 3 lines
Converted the relax_data.delete() user function back and front end to the
new design.
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r12662 | bugman | 2011-03-01 18:19:09 +0100 (Tue, 01 Mar 2011) | 3 lines
Converted the relax_data.display() user function back and front end to
the new design.
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r12663 | bugman | 2011-03-01 18:20:25 +0100 (Tue, 01 Mar 2011) | 3 lines
Removed the useless find_ri_index() function.
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r12664 | bugman | 2011-03-01 18:23:02 +0100 (Tue, 01 Mar 2011) | 3 lines
Converted the relax_data.peak_intensity_type() user function back and
front end to the new design.
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r12665 | bugman | 2011-03-01 18:25:19 +0100 (Tue, 01 Mar 2011) | 3 lines
Converted the relax_data.temp_calibration() user function back and front
end to the new design.
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r12666 | bugman | 2011-03-01 18:27:24 +0100 (Tue, 01 Mar 2011) | 3 lines
Converted the relax_data.temp_calibration() user function back and front
end to the new design.
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r12667 | bugman | 2011-03-01 18:28:18 +0100 (Tue, 01 Mar 2011) | 3 lines
Fix for the last commit, which should have said relax_data.temp_control().
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r12668 | bugman | 2011-03-01 18:30:27 +0100 (Tue, 01 Mar 2011) | 3 lines
Deletion of the useless update_noe_r1_table() function.
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r12669 | bugman | 2011-03-01 18:33:40 +0100 (Tue, 01 Mar 2011) | 3 lines
Converted the relax_data.write() user function back and front end to the
new design.
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r12670 | bugman | 2011-03-01 18:34:09 +0100 (Tue, 01 Mar 2011) | 3 lines
Removed a non-existent import.
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r12671 | bugman | 2011-03-01 18:39:44 +0100 (Tue, 01 Mar 2011) | 3 lines
Updated the get_data_names() function for the new ID string design.
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r12672 | bugman | 2011-03-01 18:44:44 +0100 (Tue, 01 Mar 2011) | 3 lines
Fix for the relax_data.delete() user function.
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r12673 | bugman | 2011-03-01 18:48:41 +0100 (Tue, 01 Mar 2011) | 3 lines
Spacing fix.
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r12674 | bugman | 2011-03-01 18:51:54 +0100 (Tue, 01 Mar 2011) | 3 lines
Fixes for the pack_data() function.
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r12675 | bugman | 2011-03-01 19:19:47 +0100 (Tue, 01 Mar 2011) | 6 lines
Updated the _minimise_data_setup() method for the new relaxation data ID
string design.
The _relax_data_opt_structs() helper method has been created to convert
the new data structures into
the old ones used in the optimisation code of maths_fns.mf.
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r12676 | bugman | 2011-03-01 19:22:25 +0100 (Tue, 01 Mar 2011) | 3 lines
Updated the model-free overfit_deselect() method for the new relaxation
data structures.
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r12677 | bugman | 2011-03-01 19:28:43 +0100 (Tue, 01 Mar 2011) | 3 lines
Updated the model-free sim_pack_data() method for the new relaxation data
structures.
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r12678 | bugman | 2011-03-01 19:30:28 +0100 (Tue, 01 Mar 2011) | 3 lines
Updated the model-free create_mc_data() method for the new relaxation
data structures.
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r12679 | bugman | 2011-03-01 19:59:45 +0100 (Tue, 01 Mar 2011) | 3 lines
Removed unused code from data_init().
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r12680 | bugman | 2011-03-01 20:12:48 +0100 (Tue, 01 Mar 2011) | 3 lines
Updated the model-free model_statistics() method for the new relaxation
data structures.
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r12681 | bugman | 2011-03-01 20:31:50 +0100 (Tue, 01 Mar 2011) | 3 lines
Updated the model-free calculate() method for the new relaxation data
structures.
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r12682 | bugman | 2011-03-01 20:33:42 +0100 (Tue, 01 Mar 2011) | 3 lines
Updated the model-free minimise() method for the new relaxation data
structures.
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r12683 | bugman | 2011-03-01 21:04:02 +0100 (Tue, 01 Mar 2011) | 3 lines
Typo fix for _relax_data_opt_structs().
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r12684 | bugman | 2011-03-02 09:57:27 +0100 (Wed, 02 Mar 2011) | 3 lines
Removed an incorrect arg to the relax_data.write() user function.
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r12685 | bugman | 2011-03-02 10:03:25 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated all of the unit tests relying on the relax_data user functions
for the new design.
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r12686 | bugman | 2011-03-02 10:08:41 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the front end to the relax_data.back_calc() user function for the
new design.
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r12687 | bugman | 2011-03-02 10:09:50 +0100 (Wed, 02 Mar 2011) | 3 lines
Fix for one of the relax_data unit tests - one of the obligatory args was
missing.
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r12688 | bugman | 2011-03-02 10:13:34 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the BMRB reading and writing system test script for the new relax
data ID string design.
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r12689 | bugman | 2011-03-02 10:18:43 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the Rx back calculation system test script for the new relax data
ID string design.
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r12690 | bugman | 2011-03-02 10:23:46 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated all of the model-free system test scripts for the new relax data
ID string design.
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r12691 | bugman | 2011-03-02 10:34:11 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the test_read_results_1_2 system test to the new relax data ID
string design.
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r12692 | bugman | 2011-03-02 10:43:29 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the test_read_results_1_2_pse4() system test to the new relax
data ID string design.
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r12693 | bugman | 2011-03-02 10:49:28 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the test_read_results_1_2_tem1() system test to the new relax
data ID string design.
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r12694 | bugman | 2011-03-02 10:54:22 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the PDC reading system tests to the new relax data ID string
design.
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r12695 | bugman | 2011-03-02 10:57:34 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the pdc.read() user function to the new relax data ID string
design.
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r12696 | bugman | 2011-03-02 11:13:48 +0100 (Wed, 02 Mar 2011) | 3 lines
Simplified the setup_peak_intensity_type() data.exp_info method for the
new relax data ID string design.
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r12697 | bugman | 2011-03-02 11:15:48 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated temp_calibration_setup() for the new relax data ID string design.
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r12698 | bugman | 2011-03-02 11:17:34 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated temp_control_setup() for the new relax data ID string design.
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r12699 | bugman | 2011-03-02 11:18:19 +0100 (Wed, 02 Mar 2011) | 3 lines
Simple fixes for some of the methods.
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r12700 | bugman | 2011-03-02 11:29:47 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the relaxation data bmrb_write() method for the new relax data ID
string design.
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r12701 | bugman | 2011-03-02 11:30:26 +0100 (Wed, 02 Mar 2011) | 3 lines
Deleted the now useless get_peak_intensity_type(),
get_temp_calibration(), and get_temp_control().
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r12702 | bugman | 2011-03-02 11:35:05 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the test_aic_mod_sel_diff_tensor() system test for the new relax
data ID string design.
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r12703 | bugman | 2011-03-02 11:54:01 +0100 (Wed, 02 Mar 2011) | 3 lines
Updated the Modelfree4 generic_fns.palmer module for the new relax data
ID string design.
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r12704 | bugman | 2011-03-02 11:54:41 +0100 (Wed, 02 Mar 2011) | 3 lines
Syntax fix for the create_mfdata() function.
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[... 1055 lines stripped ...]
r12838 - in /branches/multi_processor_merge: ./ auto_analyses/ data/ docs/ generic_fns/ graphics/relax_icons/16x16/ graphics...