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* Fix for the parallax shift description in the structure.atomic_fluctuations user function. The parallax shift is not quite orthogonal to the distance fluctuations.
* Implemented ordinary_least_squares function the repeated auto-analysis. Inspection of statistics books, shows that several authors does not recommend using regression through the origin (RTO). From Joseph G. Eisenhauer, Regression through the Origin: RTO residuals will usually have a nonzero mean, because forcing the regression line through the origin is generally inconsistent with the best fit; R square measures (for RTO) the proportion of the variability in the dependent variable "about the origin" explained by regression. This cannot be compared to R square for models which include an intercept. From "Experimental design and data analysis for biologists", G. P. Quinn, M. J. Keough: Minimum observed xi rarely extends to zero, and forcing our regression line through the origin not only involves extrapolating the regression line outside our data range but also assuming the relationship is linear outside this range (Cade & Terrell 1997, Neter et al. 1996); We recommend that it is better to have a model that fits the observed data well than one that goes through the origin but provides a worse fit to the observed data; residuals from the no-intercept model no longer sum to zero; usual partition of SSTotal into SSRegression and SSResidual does not work.
* Added save state for test of bug 23186. Bug #23186 ([https://gna.org/bugs/index.php?23186)Bug #23186: Error calculation of individual parameter "dw" from Monte-Carlo, is based on first spin].* Added the system test Relax_disp.test_bug_23186_cluster_error_calc_dw which shows the failure of Monte Carlo simulations error calculations. Bug #23186 ([https://gna.org/bugs/index.php?23186)Bug #23186: Error calculation of individual parameter "dw" from Monte-Carlo, is based on first spin].* Added additional test for the r2a parameter. Bug #23186 ([https://gna.org/bugs/index.php?23186)Bug #23186: Error calculation of individual parameter "dw" from Monte-Carlo, is based on first spin].* Attempt to implement the GUI test General.test_bug_23187_residue_delete_gui. This will NOT catch the error. Bug #23187 ([https://gna.org/bugs/index.php?23187)Bug #23187: Deleting residue in GUI, and then open spin viewer crashes relax].* Added test for spin independent error of k_AB. Bug #23186 ([https://gna.org/bugs/index.php?23186)Bug #23186: Error calculation of individual parameter "dw" from Monte-Carlo, is based on first spin.
* 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.
* Updated the main relax copyright notices for 2015.
* Improvements for the pcs.corr_plot user function - the plot range is now determined by the data.
* Improvements for the rdc.corr_plot user function - the plot range is now determined by the data.
* Added save state for testing implementation of error analysis. Task #7882 ([https://gna.org/task/?7882)Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals].* Simplification of system test 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)Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals].* Extension of the monte_carlo.create_data user function to draw errors from the reduced chi2 Gauss distribution as found by best fit. Task #7882 ([https://gna.org/task/?7882)Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals].* Adding to backend of pipe_control.error_analysis(), to modify data point as error drawn from the reduced chi2 Gauss distribution. Task #7882 ([https://gna.org/task/?7882)Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals].* Adding empty API method to return errors from the reduced chi2 distribution. Task #7882 ([https://gna.org/task/?7882)Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals].* Added API function in relaxation dispersion to return error structure from the reduced chi2 distribution. Task #7882 ([https://gna.org/task/?7882)Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals].* Temporary test of making a confidence interval as described in fitting guide. This is system test 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)Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals].* Change to system test Relax_disp.x_test_task_7882_kex_conf(). This is just a temporary system test, 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)Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals].* Raising an error, if the R2eff model is used, and drawing errors from the fit. Task #7882 ([https://gna.org/task/?7882)Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals].* To system test 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)Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals].* Added test of argument "distribution" in pipe_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)Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals].* Extended the user function 'monte_carlo.create_data', to allow for the definition 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 data points, which is not measured. Task #7882 ([https://gna.org/task/?7882)Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals].* 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)Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals].* Added to pipe_control.error_analysis.monte_carlo_create_data() the creation of data points for a fixed distribution. Task #7882 ([https://gna.org/task/?7882)Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals].* To system test 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)Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals].* In pipe_control.error_analysis.monte_carlo_create_data(), if data is of list type or ndarray, then modify the data point according to the fixed error if the distribution is set to 'fixed'. Task #7882 ([https://gna.org/task/?7882)Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals].* 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)Task #7882: Implement Monte-Carlo simulation whereby errors are generated with width of standard deviation or residuals].
* 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.
* 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.
<section begin=bugfixes/>
* Bug fix for the lib.arg_check.is_int_list() function for checking a list of lists. This is used to check user function arguments, but was causing a RelaxError to be raised for all integer list of lists user function arguments when a valid value is supplied. The function has been updated to match the is_str_list() function which does not suffer from this bug.
* Fix in dispersion API, to set error value for clustered values. Bug #23186 ([https://gna.org/bugs/index.php?23186)Bug #23186: Error calculation of individual parameter "dw" from Monte-Carlo, is based on first spin.* Fix for bug #23187 ([https://gna.org/bugs/?23187). This is bug #23187, 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.
* 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.
* Bug fix for the printouts from the relax_data.read user function. This problem was introduced in the last relax release. The problem is that the spin ID in the loaded relaxation data printout is the same for all data, being the spin ID of the first spin. This has no effect on how relax runs, it is only incorrect feedback.
