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* Added list of R<sub>1ρ</sub> models, which use R1 in their equations. [https://gna.org/support/?3135 Sr #3135]: Optimisation of the R1 relaxation rate for the off-resonance R<sub>1ρ</sub> relaxation dispersion models. [https://gna.org/bugs/?21788 Bug #21788]: Only Warning is raised for missing loading R1 relaxation rate * Added list of R<sub>1ρ</sub> models, which use R<sub>1</sub> in their equations. [https://gna.org/support/?3135 Sr #3135]: Optimisation of the R<sub>1</sub> relaxation rate for the off-resonance R<sub>1ρ</sub> relaxation dispersion models. [https://gna.org/bugs/?
R1 parameter formatting.
* Trying to move some of the structures into its own part. [https://gna.org/task/?7807 Task #7807]: Speed-up of dispersion models for clustered analysis.
* Fix for forgetting to multiply frqs to power 2. This was found by inspecting all print out before and after implementation. New implementation of [[DPL94]] now passes all system and unit tests. [https://gna.org/task/?7807 Task #7807]: Speed-up of dispersion models for clustered analysis.
* Moved the expansion of the R1 R<sub>1</sub> structure out of the for loops. This is to speed-up the __init__ of the class of the target function. [https://gna.org/task/?7807 Task #7807]: Speed-up of dispersion models for clustered analysis.
* Moved the packing of errors and values out of for loop in the __init__ class of target function. [https://gna.org/task/?7807 Task #7807]: Speed-up of dispersion models for clustered analysis.
* Moved the multi dimensional expansion of inv_relax_times out of for loop. This can be done for all structures, which does not have missing points. [https://gna.org/task/?7807 Task #7807]: Speed-up of dispersion models for clustered analysis.
* Used the new class function: get_back_calc(), to get the data in the right structures when interpolating for graphs. [https://gna.org/task/?7807 Task #7807]: Speed-up of dispersion models for clustered analysis.
* Removed superfluous check, after the returned data is now in right structure. [https://gna.org/task/?7807 Task #7807]: Speed-up of dispersion models for clustered analysis.
* Made changes to the dir argument of system test Relax_disp.test_r1rho_kjaergaard. This is to prepare for: [https://gna.org/support/?3124 sr #3124]: Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub> and [https://gna.org/support/?3138 sr #3138]: Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1]. This is also to test an expected bug, if R1 R<sub>1</sub> is not loaded. [https://gna.org/task/?7807 Task #7807]: Speed-up of dispersion models for clustered analysis.
* The relaxation dispersion target function can now be set up when the optional frqs_H argument is None. This allows the profiling scripts to run.
* More stability fixes for the relaxation dispersion target function initialisation. The target function can now be initialised when the r1 and chemical_shift arguments are None.
* Split system test test_r1rho_kjaergaard into test_r1rho_kjaergaard_auto and test_r1rho_kjaergaard_man. This is to test use of the manual way to analyse. [https://gna.org/task/?7807 Task #7807]: Speed-up of dispersion models for clustered analysis.
* Modified all of Troels' dispersion profiling scripts to work with older relax versions. This is in preparation for obtaining some powerful timing statistics. The calls to the r2eff_*() functions are unnecessary and are the only failure point in the scripts between the current code in the disp_spin_speed branch and trunk or older versions of relax. So these function calls have been eliminated.
* Implemented system test test_r1rho_kjaergaard_missing_r1, for safety check if R1 R<sub>1</sub> data is not loaded. The system test passes, so target function is safe. [https://gna.org/task/?7807 Task #7807]: Speed-up of dispersion models for clustered analysis.
* Python 3 support for the dispersion profiling scripts. The xrange() builtin function does not exist in Python 3, so this is now aliased to range() which is the same thing.
* Replaced double or triple hash-tags "##" with single hash-tags "#". [https://gna.org/task/?7807 Task #7807]: Speed-up of dispersion models for clustered analysis.
* Improved description in GUI text for user function relax_disp.plot_disp_curves(). The improved description now explains the new features. [https://gna.org/support/?3124 Sr #3124]: Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>. [https://gna.org/support/?3138 Sr #3138]: Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].
* Extended graph labelling, file naming and return of data for multiple CPMG graphs types. [https://gna.org/support/?3124 Sr #3124]: Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>. [https://gna.org/support/?3138 Sr #3138]: Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].
* Added system test Relax_disp.test_kteilum_fmpoulsen_makke_check_graphs to check all CPMG graph combinations of: y_axis_types = [Y_AXIS_R2_EFF, Y_AXIS_R2_R1RHO]; x_axis_types = [X_AXIS_DISP, X_AXIS_THETA, X_AXIS_W_EFF]; interpolate_types = [INTERPOLATE_DISP]. This is a total of 6 graphs. The graphs will in most cases be totally equal, since the theta angle is calculated to 90 degrees, and R1 R<sub>1</sub> is returned as 0.0, then R<sub>2</sub>=(R<sub>1ρ</sub> - R1 R<sub>1</sub> cos^2(theta)) / sin^2(theta) = R<sub>1ρ</sub> = R<sub>2eff</sub> for CPMG models. [https://gna.org/support/?3124 Sr #3124]: Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>. [https://gna.org/support/?3138 Sr #3138]: Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].
* Added graphs to check against for system test: Relax_disp.test_kteilum_fmpoulsen_makke_check_graphs. [https://gna.org/support/?3124 Sr #3124]: Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>. [https://gna.org/support/?3138 Sr #3138]: Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].
* Expanded ex. to example in help text for function. [https://gna.org/support/?3124 Sr #3124]: Grace graphs production for R<sub>1ρ</sub> analysis with R<sub>2eff</sub> as function of Ω<sub>eff</sub>. [https://gna.org/support/?3138 Sr #3138]: Interpolating theta through spin-lock offset [Omega], rather than spin-lock field strength [w1].
* Fix to unit tests, after changing the name of matrix_exponential function.
* Added graphs and results for run with MC=2000, for system test Relax_disp.test_r1rho_kjaergaard_auto(). This is to be able to extend graph testing for interpolated R<sub>1ρ</sub> graphs, and to add figures to the latex manual.
* Removed triggering an error in test_r1rho_kjaergaard_missing_r1. There is a bug fetching the standard value of parameter 'r1_fit'.
* Fix for system test Relax_disp.test_r1rho_kjaergaard_missing_r1, running on 64 bit system.
* Added to system test a count of number of headers and values, when issuing a value.write(). [https://gna.org/support/?3121 Sr #3121]: Support request for replacing space in header files for the value.write functions.
* Fix for replacing spaces " " with "_" in header files. [https://gna.org/support/?3121 Sr #3121]: Support request for replacing space in header files for the value.write functions.
* Fix for comment, which mentions R<sub>2</sub> parameter, when it relates to R1 R<sub>1</sub> fit.
* Replaced variable name: MODEL_PARAM_INV_RELAX_TIMES with MODEL_LIST_INV_RELAX_TIMES, to match all of the other MODEL_LIST_* variables. Also added a newline to end of file.
* Replaced remaining variable names: MODEL_PARAM_* with MODEL_LIST_*, to match all of the other MODEL_LIST_* variables.
* Renamed R<sub>1ρ</sub> off resonance models where R1 R<sub>1</sub> is fitted. This removes the "underscore". This is a better representation presented to the user, for example in the GUI model selection list or the relax_disp.select_model user function in all UI.
* Renamed the parameter "r1_fit" to "r1". This naming fits better to all other parameters.
* Split the unit test of specific_analyses.relax_disp.checks.get_times() into its own unit test file.
* Added a "check" function, what will determine if R1 R<sub>1</sub> data is missing for a model to analyse. Also added corresponding unit tests, to test the functionality.
* Modified in documentation, that the [[No Rex]] model have one chemical exchange site, namely itself.
* Copied variables.py to model.py. There should not exist any functions in variables.py. It should only consist of hardcoded variables, and the functions related to model sorting and nesting is split into its own file.
* Removed the unit test regarding model.py in test_variables.py.
* Added unit tests regarding model.py and its functions.
* Removed the auto-sorting of models, when performing auto analysis of Relaxation dispersion. This was discussed in: http://thread.gmane.org/gmane.science.nmr.relax.scm/22733, http://thread.gmane.org/gmane.science.nmr.relax.scm/22734, http://thread.gmane.org/gmane.science.nmr.relax.scm/22737. Through this discussion, it has appeared that the order of how models are sorted for analysis, and hence the possibility for nesting, is a complicated case. The order of analysis should be possible to manually put into the auto analysis. This was not the scope of [https://gna.org/support/?3135 sr #3135]: Optimisation of the R1 R<sub>1</sub> relaxation rate for the off-resonance R<sub>1ρ</sub> relaxation dispersion models to implement such a feature. Such a feature could be implemented for the next version of relax. It could be designed as function to "suggest" an order in the GUI. But this functionality would have to wait.
* Removing the t<sub>ex</sub>->k<sub>ex</sub> conversion, and φ<sub>ex</sub> from δω and p<sub>A</sub>. This solution is not a proper implementation, but these parameters should rather be found by grid search.
* Re-inserted "MODEL_NS_CPMG_2SITE_EXPANDED" to be tested in system test test_hansen_cpmg_data_missing_auto_analysis.
* Added a table for dispersion model nesting in the auto-analysis to the manual. This adds the ideas discussed in the thread http://thread.gmane.org/gmane.science.nmr.relax.devel/6684.
* Added the string 'me' for Methods in Enzymology to the bibtex file for the manual.
* Set the average value of R1 R<sub>1</sub> to 2.0 instead of 5.0. This is "normally" a better guess for R1R<sub>1</sub>.
* Implemented the function, which translates how parameters are copied from a nested model in the auto_analyses for relax_disp. This makes it possible to test the translating code, and makes logic clearer in the auto_analyses.
* Modified the r1rho_off_res_tp02_high_kex dispersion test data. The k<sub>ex</sub> value is now set to 2e<sup>5</sup>.
* Fix for earlier bug fix destroyed functionality. Altering the data-keys to early, meant that data was not fetched correctly. This is related to: https://gna.org/support/?3121 sr #3121: Support request for replacing space in header files for the value.write functions.
* Moved the unit test of specific_analyses.relax_disp.checks.check_missing_r1() from a unit test to a system test. This is because the unit test involved several functions of relax.
* Inserted dictionary, that will convert a R<sub>1ρ</sub> off-resonance without R1R<sub>1</sub>, to the corresponding model which fit R1R<sub>1</sub>.* Inserted to the check of missing R1R<sub>1</sub>, that MODEL_NOREX_R1RHO also depends on R1R<sub>1</sub>.* Implemented function that determine if any model in the list of all models should be replaced or inserted as the correct [[No Rex]] model. It also translate the R<sub>1ρ</sub> off-resonance model to the corresponding 'R1 fit' models, if R1 R<sub>1</sub> is not loaded.
* Inserted system test Relax_disp.test_convert_no_rex_fit_r1, which test the return for the function that will determine if models self.models in the relax_disp should be translated/corrected.
* Fix for unit test, where the standard value of R1 R<sub>1</sub> was lowered from 5.0 to 2.0. Also fixed an import error in another unit test.
* Minimised the dependencies of the version module. This no longer relies on the dep_check module.
* Inserted return of True/False flags from function which convert models. The flag tells if: flag if [[No Rex]] model for R<sub>1ρ</sub> off-resonance was translated; flag if [[No Rex]] model for R<sub>1ρ</sub> off-resonance was inserted; flag if R<sub>1ρ</sub> off-resonance was translated to 'R1 fit' models if no R1 R<sub>1</sub> data was found.
* Changes to system test, after the number of returns from function has been altered.
* Inserted into relax_disp auto_analyses, to convert the input models. This will convert/insert the correct [[No Rex]] to the corresponding [[No Rex]] model for R<sub>1ρ</sub> off-resonance models. It will also translate to the corresponding 'R1 fit' model, if no 'R1 data' has been loaded with relax_data.read() function.
* Lowering of precision in system test Relax_disp.test_r1rho_kjaergaard_missing_r1(). This is due to 64/32-bit issues, between analysing on Linux computer, and testing on Mac computer.
* Made the GUI selection of models for relaxation dispersion more simple. After the implementation of a function which will translate the models, the [[No Rex]] model will be converted to the [[No Rex]] model for R<sub>1ρ</sub> off-resonance. Also the corresponding 'R1 fit' model will be chosen instead, if R1 R<sub>1</sub> data has not been loaded. This makes the model selection easier in the GUI interface.
* Bugfix for Relax_disp.test_bug_21715_clustered_indexerror, where only [[R2eff]], [[No Rex]] is analysed. This special case was not tested in the translating function.
* Shortening the text in the auto_analysis, and raises a warning if R1 R<sub>1</sub> data has not been loaded.
* Rewrote the logic of the key-word 'optimise_r2eff' in the auto-analyses of relax disp. If [[R2eff]] result file exist in the 'pre_run_dir', this is loaded. If the results contain both values, and errors, then no optimisation is performed on the [[R2eff]] model. Unless the 'optimise_r2eff' flag is raised, which is not standard.
* Fixes for the Relax_disp.test_hansen_cpmg_data_missing_auto_analysis system test on MS Windows. This is for 32-bit MS Windows systems where the parameter checks need to be loosened.
* Fixes for the Relax_disp.test_r1rho_kjaergaard_missing_r1 system test on MS Windows. This is for 32-bit MS Windows systems where the parameter checks need to be loosened.
* Created the specific_analyses.relax_disp.data.is_r1_optimsed() function. This follows from an idea for handling R1 R<sub>1</sub> optimisation in the tread at http://thread.gmane.org/gmane.science.nmr.relax.scm/22850/focus=6736. This relaxation dispersion function can be used anywhere that requires the knowledge that R1 R<sub>1</sub> values should be fitted during optimisation or if loaded values should be used.
* Implemented the very basic relax_disp.r1_fit user function. This is as discussed at http://thread.gmane.org/gmane.science.nmr.relax.scm/22850/focus=6737.
* Implemented the specific_analyses.relax_disp.parameters.r1_setup() function. This matches the description at http://thread.gmane.org/gmane.science.nmr.relax.scm/22850/focus=6739 and http://thread.gmane.org/gmane.science.nmr.relax.scm/22850/focus=6736.
* Fixes to unit tests, after parameter conversion have been corrected.
* Replaced that folder names for writing out results should be with replaced with underscores "_". This is for the dispersion auto-analysis.
* Fixes for the relaxation dispersion loop_parameters() function. The R1R<sub>1</sub>, R<sub>2</sub><sup>0</sup>, R<sub>2A</sub><sup>0</sup>, R<sub>2B</sub><sup>0</sup> (and R1rho_prime, R1rho_primeA, R1rho_primeB) parameters are now checked for in each spin container rather than just the first of the cluster. This should make no difference as all spins should have the same model and parameters, but it might be a source of bugs in the future.
* The r1_fit flag is now used to switch between dispersion target functions. This is as described in http://thread.gmane.org/gmane.science.nmr.relax.scm/22850/focus=6736. The change makes the '* R1 fit' models now redundant.
* Removed all of the '* R1 fit' models out of the relax_disp.select_model user function frontend. These models are now redundant as the question of R1 R<sub>1</sub> fitting is now determined internally in relax.* Removed all of the MODEL_*_FIT_R1 dependencies from the specific_analyses.relax_disp package. These models are now redundant as the question of R1 R<sub>1</sub> fitting is now determined internally in relax.
* Fix for the specific_analyses.relax_disp.data.is_r1_optimised() function for on-resonance R<sub>1ρ</sub> data. This function needs to specifically catch these models.
* Fix for the MODEL_LIST_R1RHO variable. Recent changes causes this to not include the on-resonance R<sub>1ρ</sub> dispersion models.
* Import fix for the Relax_disp.test_model_nesting_and_param system test. Somehow the import of the convert_no_rex() function was lost.
* Modified the MODEL_LIST_R1RHO_OFF_RES list to include MODEL_NOREX_R1RHO.
* The specific_analyses.relax_disp.parameters.r1_setup() function is now being called. This happens before the R1 R<sub>1</sub> data is returned in the Disp_minimise_command class.* The dispersion auto-analysis now handles the optional R1 R<sub>1</sub> parameter correctly. The value.set user function was no longer setting the R1 R<sub>1</sub> parameter to the default value when the grid search was deactivated, as it is no longer in MODEL_PARAMS. So instead the new is_r1_optimised() function is being used to decide if the value.set user function should set the 'r1' parameter value.* The dispersion loop_parameter() function now calls r1_setup() to handle R1 R<sub>1</sub> parameters correctly. This allows the R1 R<sub>1</sub> parameter to be removed or added to the parameter list prior to looping over the parameters of the model. The change is required to allow for the dynamic handling of R1 R<sub>1</sub> parameters.* The dispersion back_calc_r2eff() function can now handle the dynamic R1 R<sub>1</sub> parameter. This required a call to r1_setup() to add or remove the parameter, and is_r1_optimised() to obtain the r1_fit flag to be sent into the target function class.* Updated the specific_analyses.relax_disp.model.Model_class class to handle the dynamic R1 R<sub>1</sub> parameter. The class variable self.params now has the 'r1' parameter prepended to the list if is_r1_optimised() returns True.* More changes for specific_analyses.relax_disp.model.Model_class for the dynamic R1 R<sub>1</sub> parameter. The 'r1' parameter is only prepended to self.params if it is not already in the list.* Created the MODEL_LIST_FIT_R1 variable to keep track of dispersion models with R1 R<sub>1</sub> fitting support.* The is_r1_optimised() function now checks MODEL_LIST_FIT_R1. If the model is not in MODEL_LIST_FIT_R1, i.e. R1 R<sub>1</sub> optimisation is not supported, then the function will return False.
* Fix for the test_nesting_param_5 unit test. The 'r1' parameter is now dynamic and hence will not be present in the initial list.
* One final fix for the Model_class.params list with 'r1'. The is_r1_optimised() function is now called with the model name argument, as required.
* Updated the relax_disp.r1_fit user function docstring. This now includes information about which models support R1 R<sub>1</sub> parameter optimisation.
* Removed results files to allow the Relax_disp.test_r1rho_kjaergaard_missing_r1 system test to pass. These are the test_suite/shared_data/dispersion/Kjaergaard_et_al_2013/check_graphs/mc_2000/ results files for the [[No Rex]] and [[DPL94]] models, as well as the final run. This commit is to allow the test to temporarily pass. It can be reverted once a better solution is discussed and decided upon.
* Altered the number of Monte Carlo simulations in test script to 2000.
* Merger of the [[No Rex]] and 'No Rex R1rho off res' models in the specific_analyses.relax_disp package. In the 'variables' module, all *_NOREX_R1RHO variables have simply been deleted and the MODEL_LIST_* structures updated. For the 'data' module, the is_r1_optimised() function was modified to catch the [[No Rex]] model and to then use the cdp.exp_type_list structure to determine if the experiment type is EXP_TYPE_R1RHO. This will be modified in the future by using a function for determining if the current experiment is on or off-resonance. The return_r1_data() and return_r1_err_data() functions have also been modified to check if R1 R<sub>1</sub> values are fit rather than if the model is in MODEL_LIST_R1RHO_OFF_RES. In the 'model' module, in addition to deleting all *_NOREX_R1RHO variables, the convert_no_rex() function has also been deleted as it no longer serves a purpose. In the 'checks' module, all 'No Rex R1rho off res' model references have been replaced with [[No Rex]].
* Updated the dispersion auto-analysis for the universal [[No Rex]] model. The 'No Rex R1rho off res' references have all been deleted. The model conversion logic is also no longer needed and has been deleted.
* Converted the relaxation dispersion GUI interface to the unified [[No Rex]] model. All of the MODEL_NOREX_R1RHO references have simply been deleted.
* Removed all references to the 'No Rex R1rho off res' model in the system tests. In addition, the Relax_disp.test_convert_no_rex system test has been deleted as it no longer has a purpose. For the Relax_disp.test_model_nesting_and_param system test, to allow this to work the cdp.exp_type_list list is set to EXP_TYPE_LIST.
* Removed all references to the 'No Rex R1rho off res' model in the unit tests.
* Updated the [[No Rex]] dispersion model description in the relax manual. The universal nature of the model is now described, including the addition of the off-resonance CPMG and R<sub>1ρ</sub> equations for the absence of chemical exchange. The R1 R<sub>1</sub> parameter optimisation is also shortly covered.* Added a subsection to the dispersion chapter of the manual about R1 R<sub>1</sub> parameter optimisation.* Added the R1 R<sub>1</sub> parameter fitting GUI element to the dispersion GUI tab. This is a simple Boolean toggle element that allows the R1 R<sub>1</sub> optimisation to be turned on. The value is passed into the auto-analysis.* Added the r1_fit argument to the relaxation dispersion auto-analysis. When this is True, the relax_disp.r1_fit user function will be called to turn R1 R<sub>1</sub> parameter fitting on.
* Added the relax_disp.spin_lock_offset user function to the dispersion GUI. This has been added to the pop up menu in the spectrum list GUI element, when the relax_disp_flag has been set. It simply mimics the relax_disp.spin_lock_field functionality already present. This follows from [https://gna.org/task/?7820 task #7820].
* Fix for the relax_disp.spin_lock_offset user function in the dispersion GUI tab. This is in the spectrum list element popup menu.
* Added system test Relax_disp.test_estimate_r2eff_error(). This is to get insight in the error difference between 2000 Monto Carlo simulations and then scipy.optimize.leastsq.
* Add dependency check for scipy.optimize.leastsq. [https://gna.org/task/?7822 Task #7822]: Implement user function to estimate R<sub>2eff</sub> and associated errors for exponential curve fitting.
* Lowering precision in system test Relax_disp.test_r1rho_kjaergaard_missing_r1. This is R1 R<sub>1</sub> estimation with MODEL_NS_R1RHO_2SITE. The lowering of precision is due different system precision.
* Reused the dependency check "scipy_module", since leastsq() has been part of Scipy since 2003.
* Moved target function for curve fitting with scipy into specific_analyses.relax_disp.estimate_r2eff. This will later include the backend specific_analyses.relax_disp.optimisation.estimate_r2eff() function and the code in the target_functions package. The code in target_functions.relax_disp_curve_fit is a lot more than just a target function, so it doesn't really belong in this package. This is also to isolate this experimental feature.
* Formatting changes for the lib.periodic_table module. This is in preparation for extending the information content of this module.
* Modified system test 'test_estimate_r2eff_err_auto', to use the GUI script. It seems to work perfect. This is to test against GUI script: test_r2eff_err_estimate [https://gna.org/task/?7822 Task #7822]: Implement user function to estimate R<sub>2eff</sub> and associated errors for exponential curve fitting.
* Modified test_estimate_r2eff_err_auto, to set r1_fit to False. This still make the system test pass, and fit R1R<sub>1</sub>. So this means R1 R<sub>1</sub> fit button is not functioning properly. [https://gna.org/task/?7822 Task #7822]: Implement user function to estimate R<sub>2eff</sub> and associated errors for exponential curve fitting.
* Fix for warning message in the auto-analyses in the GUI. [https://gna.org/task/?7822 Task #7822]: Implement user function to estimate R<sub>2eff</sub> and associated errors for exponential curve fitting.
* Tried to improve docstring for API documentation. [https://gna.org/task/?7822 Task #7822]: Implement user function to estimate R<sub>2eff</sub> and associated errors for exponential curve fitting.
* Added more print out information, when log(I / I_ref) is negative, and raising errors. This can help the user track back information to the error more easily.
* Improved system test test_bug_negative_intensities_cpmg, by counting number of R<sub>2eff</sub> points. Spin 4, which has one negative intensity, is expected to have one less R<sub>2eff</sub> point. This makes sure, that all CPMG data set can be loaded and analysed, even if some peaks are very weak are fluctuating with error level.
* Fix for also storing 'r1_fit' to cdp even though it is set to False. [https://gna.org/bugs/?22541 Bug #22541]: The R1 R<sub>1</sub> fit flag does not work in the GUI.* Cleanup in GUI test Relax_disp.test_r2eff_err_estimate. This now passes after previous commit. [https://gna.org/bugs/?22541 Bug #22541]: The R1 R<sub>1</sub> fit flag does not work in the GUI.* Added model [[DPL94]], to be tested in GUI test Relax_disp.test_r2eff_err_estimate. This shows that the bug is still there. [https://gna.org/bugs/?22541 Bug #22541]: The R1 R<sub>1</sub> fit flag does not work in the GUI.* Fix for system test test_estimate_r2eff_err and test_r1rho_kjaergaard_missing_r1, where r1_fit=True, needed to be send to Auto_analyses. [https://gna.org/bugs/?22541 Bug #22541]: The R1 R<sub>1</sub> fit flag does not work in the GUI.
* API documentation fixes.
* Moved multifit_covar into lib.statistics, since it is an independent module. [https://gna.org/task/?7822 Task #7822]: Implement user function to estimate R<sub>2eff</sub> and associated errors for exponential curve fitting.
* Initial try to reach constrained methods in minfx through relax. This is in system test Relax_disp.verify_estimate_r2eff_err_compare_mc() This though not seem to be supported.
* Allow R<sub>2eff</sub> model to reach constrained methods in minfx through relax. This is in system test Relax_disp.verify_estimate_r2eff_err_compare_mc() This though not seem to be supported.
* Modified specific_analyses.relax_disp.parameters.r1_setup() to initialise the 'r1' variable. This relates to [https://gna.org/bugs/?22541 bug #22541], the R1 R<sub>1</sub> fit flag does not work in the GUI. This is a hack, as all of the dispersion analysis code assumes that all parameters are initialised. This is a dangerous assumption that will have to be eliminated in the future.* The dispersion get_param_values() API method now calls the r1_setup() function. This relates to [https://gna.org/bugs/?22541 bug #22541], the R1 R<sub>1</sub> fit flag does not work in the GUI. This is to make sure that the parameters are correctly set up prior to obtaining all parameter values. The R1 R<sub>1</sub> parameter is dynamic hence r1_setup() needs to be called at any point model parameters are accessed, as the R1 R<sub>1</sub> parameter can be turned on or off at any time with the relax_disp.r1_fit user function.
* Yet another try to implement constrained method in verify_estimate_r2eff_err_compare_mc.
* Another attempt to reach constrained method in minfx through relax. I would need to specify: l, lower bound constraint vector (l <= x <= u); u, upper bound constraint vector (l <= x <= u); c: user supplied constraint function; dc: user supplied constraint gradient function.
