relax SVN archive

Copyright notice update to 2015 for the auto_analyses.frame_order module.

The GUI tests are now skipped for wxPython version <= 2.8 due to bugs causing fatal segfaults.

This follows from http://thread.gmane.org/gmane.science.nmr.relax.devel/7502. These wxPython
versions are simply too buggy.

Updated the wxPython version in the relax manual to be 2.9 or higher.

This is in the section http://www.nmr-relax.com/manual/Dependencies.html.

Added a RelaxWarning printout to the dep_check module if wxPython 2.8 or less is encountered.

This follows from http://thread.gmane.org/gmane.science.nmr.relax.devel/7502. The warning text is
simply written to STDERR as relax starts.

Fix for the frame order auto-analysis when only the 'rigid' model is optimised.

The final summary table printout for the number of Sobol' points used was failing as there were no
models in the table. The table is now only printed out if non rigid models are present in the model
list.

Merged revisions 27200-27230 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r27200 | tlinnet | 2015-01-16 23:19:25 +0100 (Fri, 16 Jan 2015) | 3 lines

Added save state for testing implementation of error analysis.

Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation, where errors are generated with width of standard deviation or residuals.
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r27201 | tlinnet | 2015-01-16 23:19:44 +0100 (Fri, 16 Jan 2015) | 4 lines

Start of implementation of systemtest Relax_disp.test_task_7882_monte_carlo_std_residual, to test doing Monte-Carlo simulations with errors drawn from a
Gauss distribution with a width corresponding to the standard devition of the sum of squares of residuals.

Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation, where errors are generated with width of standard deviation or residuals.
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r27202 | tlinnet | 2015-01-16 23:19:47 +0100 (Fri, 16 Jan 2015) | 3 lines

Implemented target function for relaxation dispersion, which calculate the sum of squares of residuals and the standard deviation of these.

Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation, where errors are generated with width of standard deviation or residuals.
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r27203 | tlinnet | 2015-01-16 23:19:50 +0100 (Fri, 16 Jan 2015) | 3 lines

Implemented storing of sum of squares and the standard deviation of these for relaxation dispersion, when doing a point calculation.

Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation, where errors are generated with width of standard deviation or residuals.
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r27204 | tlinnet | 2015-01-16 23:19:51 +0100 (Fri, 16 Jan 2015) | 3 lines

Stored the sums of squares of the residuals "sos" and standard deviation of this "sos_std" per spin after optimisation.

Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation, where errors are generated with width of standard deviation or residuals.
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r27205 | tlinnet | 2015-01-16 23:19:54 +0100 (Fri, 16 Jan 2015) | 3 lines

Added to systemtest Relax_disp.test_task_7882_monte_carlo_std_residual() that spin.sos and spin.sos_std is stored after grid search.

Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation, where errors are generated with width of standard deviation or residuals.
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r27206 | tlinnet | 2015-01-16 23:19:56 +0100 (Fri, 16 Jan 2015) | 3 lines

Extracted "sos" and "sos_std" after grid search.

Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation, where errors are generated with width of standard deviation or residuals.
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r27207 | tlinnet | 2015-01-16 23:19:58 +0100 (Fri, 16 Jan 2015) | 3 lines

In systemtest Relax_disp.test_task_7882_monte_carlo_std_residual() inserted sanity checks of calculation of degrees of freedom.

Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation, where errors are generated with width of standard deviation or residuals.
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r27208 | tlinnet | 2015-01-16 23:20:01 +0100 (Fri, 16 Jan 2015) | 5 lines

Speed-up of systemtest Relax_disp.test_task_7882_monte_carlo_std_residual() by copying pipe instead of reading results 3 times.

Tested creation of Monte-Carlo data, where errors are generated with width of standard deviation or residuals.

Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation, where errors are generated with width of standard deviation or residuals.
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r27209 | tlinnet | 2015-01-16 23:20:04 +0100 (Fri, 16 Jan 2015) | 3 lines

Extended user function monte_carlo.create_data() to accept 'method="sum_squares"', to create Monte-Carlo data.

Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation, where errors are generated with width of standard deviation or residuals.
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r27210 | tlinnet | 2015-01-16 23:20:06 +0100 (Fri, 16 Jan 2015) | 3 lines

Extended backend in pipe_control.error_analysis.monte_carlo_create_data() to return errors as the standard deviation of the sum of squares of the residual.

Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation, where errors are generated with width of standard deviation or residuals.
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r27211 | tlinnet | 2015-01-16 23:20:08 +0100 (Fri, 16 Jan 2015) | 3 lines

Implemented the api_base method of return_error_sum_squares(), as raising an error if not defined for the api for the pipe_type.

Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation, where errors are generated with width of standard deviation or residuals.
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r27212 | tlinnet | 2015-01-16 23:20:11 +0100 (Fri, 16 Jan 2015) | 3 lines

Implemented in the relaxation dispersion API, the function to return errors as the standard deviation of sums squared residuals.

Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation, where errors are generated with width of standard deviation or residuals.
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r27213 | tlinnet | 2015-01-16 23:20:13 +0100 (Fri, 16 Jan 2015) | 3 lines

Added 'sos' and 'sos_std' as parameter object in relaxation dispersion.

Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation, where errors are generated with width of standard deviation or residuals.
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r27214 | tlinnet | 2015-01-17 14:16:50 +0100 (Sat, 17 Jan 2015) | 17 lines

Reverted range of commits r27213:r27202 as this was a bad implementation.

To get the distribution, one should look at the sum of squares.
But this should be from the weighted sum of squares, which is stored as chi2.
The API provides a method of model_statistics(), to get:
k - number of parameters.
n - number of data points.
chi2 - the chi-squared value.

Then reduced chi2 can be computed. chi2_red = chi2/(n-k)
And the error distribution be drawn from this.

The command used was:
svn merge -r27213:r27201 .

Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation, where errors are generated with width of standard deviation or residuals.
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r27215 | tlinnet | 2015-01-17 17:25:12 +0100 (Sat, 17 Jan 2015) | 3 lines

Simplification of systemtest Relax_disp.test_task_7882_monte_carlo_std_residual, to just test the creation of Monte-Carlo data where errors are drawn from the reduced chi2 distribution.

Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation, where errors are generated with width of standard deviation or residuals.): Implement Monte-Carlo simulation, where errors are generated with width of standard deviation or residuals.
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r27216 | tlinnet | 2015-01-17 17:25:15 +0100 (Sat, 17 Jan 2015) | 3 lines

Extension of the userfunction monte_carlo.create_data, to draw errors from the reduced chi2 gauss distribution as found by best fit.

Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation, where errors are generated with width of standard deviation or residuals.): Implement Monte-Carlo simulation, where errors are generated with width of standard deviation or residuals.
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r27217 | tlinnet | 2015-01-17 17:25:16 +0100 (Sat, 17 Jan 2015) | 3 lines

Adding to back-end of pipe_control.error_analysis(), to modify datapoint as error drawn from the reduced chi2 gauss distribution.

Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation, where errors are generated with width of standard deviation or residuals.): Implement Monte-Carlo simulation, where errors are generated with width of standard deviation or residuals.
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r27218 | tlinnet | 2015-01-17 17:25:18 +0100 (Sat, 17 Jan 2015) | 3 lines

Adding empty API method to return errors from the reduced chi2 distribution.

Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation, where errors are generated with width of standard deviation or residuals.): Implement Monte-Carlo simulation, where errors are generated with width of standard deviation or residuals.
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r27219 | tlinnet | 2015-01-17 17:25:20 +0100 (Sat, 17 Jan 2015) | 3 lines

Added API function in relaxation dispersion to return error structure from the reduced chi2 distribution.

Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation, where errors are generated with width of standard deviation or residuals.): Implement Monte-Carlo simulation, where errors are generated with width of standard deviation or residuals.
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r27220 | tlinnet | 2015-01-18 17:32:37 +0100 (Sun, 18 Jan 2015) | 8 lines

Temporary test of making a confidence interval as described in fitting guide.

This is systemtest Relax_disp.x_test_task_7882_kex_conf, which is not activated by default.

Running the test, interestingely shows, there is a possibility for a lower global kex.
But the value only differ from kex=1826 to kex=1813.

Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation, where errors are generated with width of standard deviation or residuals.): Implement Monte-Carlo simulation, where errors are generated with width of standard deviation or residuals.
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r27221 | tlinnet | 2015-01-19 13:48:41 +0100 (Mon, 19 Jan 2015) | 8 lines

Change to systemtest Relax_disp.x_test_task_7882_kex_conf()

This is just a temporary systemtest, to check for local minima.

This is method in regression book of Graphpad: http://www.graphpad.com/faq/file/Prism4RegressionBook.pdf
Page: 109-111.

Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation, where errors are generated with width of standard deviation or residuals.
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r27222 | tlinnet | 2015-01-19 13:48:44 +0100 (Mon, 19 Jan 2015) | 3 lines

Raising an error, if the R2eff model is used, and drawing errors from the fit.

Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation, where errors are generated with width of standard deviation or residuals.
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r27223 | tlinnet | 2015-01-19 13:48:46 +0100 (Mon, 19 Jan 2015) | 3 lines

To systemtest Relax_disp.test_task_7882_monte_carlo_std_residual(), adding test for raise of errors, if the R2eff model is selected.

Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation, where errors are generated with width of standard deviation or residuals.
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r27224 | tlinnet | 2015-01-20 12:02:01 +0100 (Tue, 20 Jan 2015) | 5 lines

Added test of argument "distribution" in Ãpipe_control.error_analysis.monte_carlo_create_data().

This is to make sure that a wrong argument is not passed into the function.

Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation, where errors are generated with width of standard deviation or residuals.): Implement Monte-Carlo simulation, where errors are generated with width of standard deviation or residuals.
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r27225 | tlinnet | 2015-01-20 12:02:10 +0100 (Tue, 20 Jan 2015) | 5 lines

Extended the user function 'monte_carlo.create_data', to allow for the defition of the STD to use in gauss distribution.

This is for creation of Monte-Carlo simulations, where one has perhaps gained information about the expected errors of the datapoints, which is not measured.

Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation, where errors are generated with width of standard deviation or residuals.): Implement Monte-Carlo simulation, where errors are generated with width of standard deviation or residuals.
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r27226 | tlinnet | 2015-01-20 12:02:12 +0100 (Tue, 20 Jan 2015) | 5 lines

In backend pipe_control.error_analysis.monte_carlo_create_data() added the argument 'fixed_error' to allow for fixed input of error to the gauss distribution.

Inserted a range of checks, to make sure function behaves as expected.

Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation, where errors are generated with width of standard deviation or residuals.): Implement Monte-Carlo simulation, where errors are generated with width of standard deviation or residuals.
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r27227 | tlinnet | 2015-01-20 12:02:14 +0100 (Tue, 20 Jan 2015) | 3 lines

Added to pipe_control.error_analysis.monte_carlo_create_data() the creation of datapoints for a fixed distribution.

Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation, where errors are generated with width of standard deviation or residuals.): Implement Monte-Carlo simulation, where errors are generated with width of standard deviation or residuals.
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r27228 | tlinnet | 2015-01-20 12:02:16 +0100 (Tue, 20 Jan 2015) | 4 lines

To systemtest Relax_disp.test_task_7882_monte_carlo_std_residual(), added tests for creation of Monte-Carlo data
by different methods.

Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation, where errors are generated with width of standard deviation or residuals.): Implement Monte-Carlo simulation, where errors are generated with width of standard deviation or residuals.
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r27229 | tlinnet | 2015-01-20 12:41:21 +0100 (Tue, 20 Jan 2015) | 4 lines

In pipe_control.error_analysis.monte_carlo_create_data(), if data is of list type or ndarray, then modify the datapoint according to the fixed error if
the distribution is set to 'fixed'.

Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation, where errors are generated with width of standard deviation or residuals.): Implement Monte-Carlo simulation, where errors are generated with width of standard deviation or residuals.
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r27230 | tlinnet | 2015-01-20 12:41:23 +0100 (Tue, 20 Jan 2015) | 5 lines

Expanded the STD acronym, to the meaning of Standard deviation.

This is in the user function 'monte_carlo.create_data'.

Task #7882 (https://gna.org/task/?7882): Implement Monte-Carlo simulation, where errors are generated with width of standard deviation or residuals.): Implement Monte-Carlo simulation, where errors are generated with width of standard deviation or residuals.
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Merged revisions 27185-27199 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r27185 | bugman | 2015-01-15 09:26:49 +0100 (Thu, 15 Jan 2015) | 3 lines

Updated my copyright notice on all files changed in 2015.
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r27186 | bugman | 2015-01-15 09:37:14 +0100 (Thu, 15 Jan 2015) | 3 lines

Updated the main relax copyright notices for 2015.
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r27187 | bugman | 2015-01-15 09:39:46 +0100 (Thu, 15 Jan 2015) | 7 lines

The copyright notice in the GUI now uses the info box object.

This is for the status bar at the bottom of the GUI window. This removes one place where copyright
notices needs to be updated each year. This status text will then be updated whenever the info.py
file has been updated.
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r27188 | bugman | 2015-01-15 09:42:02 +0100 (Thu, 15 Jan 2015) | 3 lines

Updated the copyright notice for 2015 in the GUI splash screen graphic.
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r27189 | bugman | 2015-01-15 09:54:55 +0100 (Thu, 15 Jan 2015) | 7 lines

Racing fixes for the General.test_bug_23187_residue_delete_gui GUI test.

Some GUI interpreter flush() calls have been added to avoid racing in the GUI. The GUI tests are so
quick that the asynchronous user function call will be processed at the same time as the spin viewer
window is being created, causing fatal segmentation faults in the test suite.
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r27190 | bugman | 2015-01-15 10:15:50 +0100 (Thu, 15 Jan 2015) | 10 lines

More robustness for the spin viewer GUI window prune_*() methods.

When no spin data exists, the self.tree.GetItemPyData(key) call can return None. This is now being
checked for and such None values are being skipped in the prune_mol(), prune_res() and prune_spin()
methods.

The problem was found in the Mf.test_bug_20479_gui_final_pipe system test when running the command:
for i in {1..10}; do ./relax --gui-tests --time -d &>> gui_tests.log; done
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r27191 | bugman | 2015-01-15 10:17:58 +0100 (Thu, 15 Jan 2015) | 10 lines

More robustness for the spin viewer GUI window update_*() methods.

When no spin data exists, the self.tree.GetItemPyData(key) call can return None. This is now being
checked for and such None values are being skipped in the update_mol(), update_res() and
update_spin() methods.

The problem was found in the Mf.test_bug_20479_gui_final_pipe system test when running the command:
for i in {1..10}; do ./relax --gui-tests --time -d &>> gui_tests.log; done
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r27192 | bugman | 2015-01-15 10:24:37 +0100 (Thu, 15 Jan 2015) | 10 lines

More robustness for the spin viewer GUI window prune_*() methods.

The data returned from the self.tree.GetItemPyData(key) call can in rare racing cases not contain
the 'id' key. This is now being checked for and are being skipped in the prune_mol(), prune_res()
and prune_spin() methods.

The problem was found in the Mf.test_bug_20479_gui_final_pipe system test when running the command:
for i in {1..10}; do ./relax --gui-tests --time -d &>> gui_tests.log; done
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r27193 | bugman | 2015-01-15 10:25:36 +0100 (Thu, 15 Jan 2015) | 10 lines

More robustness for the spin viewer GUI window update_*() methods.

The data returned from the self.tree.GetItemPyData(key) call can in rare racing cases not contain
the 'id' key. This is now being checked for and are being skipped in the update_mol(), update_res()
and update_spin() methods.

The problem was found in the Mf.test_bug_20479_gui_final_pipe system test when running the command:
for i in {1..10}; do ./relax --gui-tests --time -d &>> gui_tests.log; done
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r27194 | bugman | 2015-01-15 14:00:18 +0100 (Thu, 15 Jan 2015) | 5 lines

Created a development document for catching segfaults and other errors in the GUI tests.

This is needed as not all wxPython errors can be caught in the Python unittest framework.
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r27195 | bugman | 2015-01-16 11:44:22 +0100 (Fri, 16 Jan 2015) | 3 lines

Small whitespace formatting fix for the titles printed by the align_tensor.display user function.
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r27196 | bugman | 2015-01-16 17:32:50 +0100 (Fri, 16 Jan 2015) | 5 lines

Improvements for the plots created by the pcs.corr_plot user function.

The axes now have labels, and have the range and number of ticks set to reasonable values.
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r27197 | bugman | 2015-01-16 17:33:56 +0100 (Fri, 16 Jan 2015) | 6 lines

Fix for the rdc.corr_plot user function.

The Y-axis is now set to the measured RDC, as the RDC errors are plotted as dY errors. This matches
the behaviour of the pcs.corr_plot user function.
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r27198 | bugman | 2015-01-16 18:38:10 +0100 (Fri, 16 Jan 2015) | 3 lines

Improvements for the pcs.corr_plot user function - the plot range is now determined by the data.
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r27199 | bugman | 2015-01-16 18:38:19 +0100 (Fri, 16 Jan 2015) | 3 lines

Improvements for the rdc.corr_plot user function - the plot range is now determined by the data.
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Merged revisions 27167 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r27167 | bugman | 2015-01-14 17:00:51 +0100 (Wed, 14 Jan 2015) | 10 lines

Fix for bug #23187 (https://gna.org/bugs/?23187).

This is the problem whereby opening the spin viewer window, deleting a residue, and then reopening
the spin viewer crashes relax.

This change completes the spin viewer update_*() functions. The prune_list variable was initialised
but not used. Now it is used to store the keys of the items to delete, and then the items are
deleted at the end in a new loop so that the loop over the dictionary keys is not corrupted.
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Merged revisions 27165 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r27165 | tlinnet | 2015-01-14 16:10:03 +0100 (Wed, 14 Jan 2015) | 3 lines

Fix in dispersion API, to set error value for clustered values.

Bug #23186 (https://gna.org/bugs/index.php?23186): Error calculation of individual parameter "dw" from Monte-Carlo, is based on first spin.
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Merged revisions 27164 via svnmerge from
svn+ssh://bugman@.../svn/relax/trunk

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r27164 | bugman | 2015-01-14 15:35:01 +0100 (Wed, 14 Jan 2015) | 8 lines

Fix for the showing of the spin viewer window in the GUI tests.

The show_tree() method of the main GUI window class was not calling the custom
self.spin_viewer.Show() method, as required to set up the observer objects required to keep the spin
viewer window updated. The value of status.show_gui was blocking this. Instead the show argument
of this Show() method is being set to status.show_gui to allow the method to always be executed.
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