relax SVN archive

Merged revisions 19701-19709 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r19701 | bugman | 2013-05-23 18:35:19 +0200 (Thu, 23 May 2013) | 7 lines

The peak intensity wizard can now function remotely when the spins are not named.

This will be needed for the GUI tests to allow the Question() call to be bypassed and still adding
the spin.name user function as the first page of the wizard. The key for spin.name page has also
been fixed so that the page can be accessed.
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r19702 | bugman | 2013-05-23 18:36:39 +0200 (Thu, 23 May 2013) | 3 lines

Fixes for the Jw.test_calc system test - the spectral density value comparison is now significant.
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r19703 | bugman | 2013-05-23 18:39:09 +0200 (Thu, 23 May 2013) | 8 lines

The timing of individual tests in the relax test suite can now be printed out.

The new command line argument --time has been added which, when supplied with one of the test suite
arguments, will cause the time required to complete each individual test to be displayed. Instead
of just printing the characters '.', 'F', and 'E' for each test, now these characters are postfixed
with the time in seconds, the name of the test and ending in a newline character.
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r19704 | bugman | 2013-05-23 18:40:12 +0200 (Thu, 23 May 2013) | 6 lines

Big speed up of the test suite by skipping a large number of redundant Frame Order system tests.

These are tests of using only PCS or only RDC data. These tests are still active for the
pseudo-ellipse just to make sure that a whole missing data type can be handled.
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r19705 | bugman | 2013-05-23 18:42:08 +0200 (Thu, 23 May 2013) | 3 lines

Suppressed the reporting of skipped tests in the test suite if the module is set to None.
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r19706 | bugman | 2013-05-23 18:42:41 +0200 (Thu, 23 May 2013) | 5 lines

The preview button in the file selection elements of the user function windows can now be disabled.

This is via the new wiz_filesel_preview argument being set to False.
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r19707 | bugman | 2013-05-23 18:43:23 +0200 (Thu, 23 May 2013) | 7 lines

Merged the frq.set and temperature user functions into the new spectrometer user function class.

The frq.set user function is now called spectrometer.frequency and temperature is now
spectrometer.temperature. To match these changes, the cdp.frq variable is now called
cdp.spectrometer_frq.
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r19708 | bugman | 2013-05-23 19:11:08 +0200 (Thu, 23 May 2013) | 7 lines

Modified the spectrometer.frequency user function so that a frequency list and count is stored.

These are the new cdp.spectrometer_frq_list and cdp.spectrometer_frq_count variables. This will
allow various parts of relax which assemble frequency information to be simplified and made more
consistent.
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r19709 | bugman | 2013-05-23 19:13:09 +0200 (Thu, 23 May 2013) | 6 lines

Created basic SVG and PNG graphics for the spectrometer user function class.

The spectrometer is black so as not to offend Bruker, Varian, or Jeol users by avoiding a colour
from one of these companies.
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Created the Relax_disp.test_hansen_trunc_data GUI test for checking the GUI dispersion auto-analysis.

This checks the full operation of the relaxation dispersion GUI analysis, without checking the final
results (to be added later).

A dispersion saved state from the prompt or script UI can now be associated with a GUI analysis.

Added the results from NESSY of the analysis of Flemming Hansen's truncated CPMG data.

This is only for the truncated data of residues 70 and 71. All files, except for the PNG graphics,
have been added to the repository. The 'summary' file has been created to hold the data from
NESSY's summary tab, as this is not stored in the NESSY saved state and is permanently lost after
closing NESSY.

Created a directory for the results of the CPMGFit program using Hansen's truncated CPMG data.

The script 'cpmgfit.py' has been added to create the input files for CPMGFit and execute the
program. The input and batch files have been added to the repository as well.

Created the Relax_disp.test_hansen_cpmgfit_input system test.

This is for checking the operation of the relax_disp.cpmgfit_input user function conversion of
Flemming Hansen's CPMG R2eff values into input files for CPMGFit. A relax state file containing the
results of an analysis of an 'R2eff' model analysis of the truncated data has been added to the test
suite data to speed up the test and to check the loading of dispersion state files.

Added support for interfacing with Art Palmer's CPMGFit program.

The two new user functions relax_disp.cpmgfit_input and relax_disp.cpmgfit_execute have been created
to interface with CPMGFit. The first creates the per spin system CPMGFit input files as well as a
batch script for executing CPMGFit with all the input files. The second bypasses the batch script
and allows CPMGFit to be executed from within relax. This mimics the palmer and dasha user
functions. The back end code is in the new specific_analyses.relax_disp.cpmgfit module.

Fix for the setup of the relaxation dispersion GUI analysis.

The base method add_execute_relax() has been renamed to add_execute_analysis().

Fixes for the LM63 dispersion CPMG model.

The 'r2' model parameter is now an array as there is one R2 value per magnetic field strength. And
the 'rex' parameter has been renamed to 'phi_ex' and is scaled quadratically with the field strength
within the optimisation target function.

Added a script to the test suite shared data for analysing the truncated Hansen CPMG data.