Changes

| next = 4.1.2| keywords = Dispersion, GUI

* Mac OS X distribution file: Fixes for the DMG file generation. The <code>.git </code> directories are no longer bundled (the check in <code>setup.py </code> was for <code>.svn </code> directories), and the <code>sobol_test.py </code> script contained a bug that blocked the image generation.

* <code>log_converter.py </code> development script: Conversion from SVN to git. A number of spacing bugs have also been removed, simplifying the release process.* relax manual: The [http://www.nmr-relax.com/api/4.1/docs.latex.find_replicate_titles-module.html find_replicate_titles.py script ] can now handle the presence of latex2html. If latex2html had been set up via the <code>docs/devel/latex2html/setup </code> script, then [http://www.nmr-relax.com/api/4.1/docs.latex.find_replicate_titles-module.html find_replicate_titles.py ] would fail due to the presence of <code>*.tex </code> files outside of <code>docs/latex/</code>.* Update from LaTeX2HTML 2008 to 2019. The instructions now point to the latex2html repository fork at SourceForge ([https://sourceforge.net/p/nmr-relax/code-latex2html/ci/master/tree/)latex2html repository fork at SourceForge], with the relax manual specific branches.* GUI tests: Addition of the User_functions.test_bug_2_structure_read_pdb_failure test. This is to catch [httpshttp://sourceforgewww.net/p/nmr-relax.com/ticketsapi/24.1/ bug test_suite.gui_tests.test_user_functions.User_functions-class.html#2test_bug_2_structure_read_pdb_failure User_functions.test_bug_2_structure_read_pdb_failure test], the failure of the structure.read_pdb user function in the GUI.* GUI tests: Addition of the User_functions.test_bug_3_no_argument_validation test. This is to catch [https://sourceforge.net/p/nmr-relax/tickets/32/ bug #32], the absence failure of user the [http://www.nmr-relax.com/manual/structure_read_pdb.html structure.read_pdb user function argument validation within ] in the GUI.* Unit GUI tests: Addition of two tests for specific_analyses.relax_disp.parameters.param_num(). This is to catch [httpsthe [http://sourceforgewww.net/p/nmr-relax.com/ticketsapi/64.1/ bug test_suite.gui_tests.test_user_functions.User_functions-class.html#6test_bug_3_no_argument_validation User_functions.test_bug_3_no_argument_validation test], the failure of the parameter counting for the . This is to catch [https://sourceforge.net/p/nmr-relax/tickets/3-site relaxation dispersion models when spins are clustered. The / bug #3], the absence of user function argument validation within the GUI.* Unit tests: Addition of two unit tests are Test_parametersfor [http://www.test_param_num_clustered_spins and Test_parametersnmr-relax.test_param_num_single_spin in the unit test module _specific_analysescom/api/4._relax_disp1/specific_analyses.test_parametersrelax_disp.* Unit tests: Addition of two tests for parameters-module.html#param_num specific_analyses.relax_disp.parameters.loop_parametersparam_num()]. The two unit tests are Test_parametersThis is to catch [https://sourceforge.test_loop_parameters_clustered_spins and Test_parameters.test_loop_parameters_single_spin in net/p/nmr-relax/tickets/6/ bug #6], the unit test module _specific_analyses._relax_disp.test_parameters. These were added to try to catch failure of the typo error at parameter counting for the end of the function, where the 'dwH_AB' parameter appears twice (the second should be 'dwH_AC')3-site relaxation dispersion models when spins are clustered. However the typo was not caught in the The two unit tests as no currently implemented dispersion model contains the 'dwH_AC' parameterare [http://www. Hence it is a latent bugnmr-relax.com/api/4.1/test_suite.unit_tests._specific_analyses. The tests do catch a minor error with the 'R2eff' model in which the 'i0' parameter is always returned_relax_disp.test_parameters.Test_parameters-class. 'i0' should only be returned when exponential curve data is presenthtml#test_param_num_clustered_spins Test_parameters.test_param_num_clustered_spins] and [http://www. This bug has no apparent affect on the current operation of nmr-relax, so the parameter is probably handled correctly downstream.* Module specific_analysescom/api/4.1/test_suite.unit_tests.relax_disp_specific_analyses.parameters: Fix for loop_parameters() with the 'R2eff' model_relax_disp.test_parameters.Test_parameters-class.html#test_param_num_single_spin Test_parameters. This now only returns test_param_num_single_spin] in the 'i0' parameter when exponential curve data is present[http://www. This fix has no apparent affect on the operation of nmr-relax, so the 'i0' parameter is probably correctly handled in code that calls the loop_parameters() function.* Dispersion: Shift of the model parameters from the parameter loop to libcom/api/4.1/test_suite.unit_tests._specific_analyses._relax_disp.dispersiontest_parameters-module.variableshtml unit test module _specific_analyses. This removes all references to specific model parameters from the loop_parameters() function in the specific_analyses_relax_disp.relax_disptest_parameters].parameters module into lib.dispersion.variables. This simplifies the loop_parameters() function and should minimise latent bugs.* Unit tests: Addition * Unit tests: Addition of two tests for specific_analyses.[http://www.nmr-relax.com/api/4.1/specific_analyses.relax_disp.parameters-module.html#loop_parameters specific_analyses.relax_disp.parameters.linear_constraintsloop_parameters()]. The two unit tests are Test_parameters[http://www.nmr-relax.com/api/4.1/test_suite.test_linear_constraints_clustered_spins and Test_parametersunit_tests.test_linear_constraints_single_spin in the unit test module _specific_analyses._relax_disp.test_parameters. These show that the linear constraints are correctly assembled for single Test_parameters-class.html#test_loop_parameters_clustered_spins Test_parameters.test_loop_parameters_clustered_spins] and clustered spins for all models[http://www.* Module specific_analysesnmr-relax.relax_dispcom/api/4.parameters: Docstring, whitespace, and comment fixes1/test_suite.* Unit tests: Addition of tests for libunit_tests.dispersion_specific_analyses._relax_disp.ns_mmq_3site and libtest_parameters.dispersionTest_parameters-class.ns_r1rho_3sitehtml#test_loop_parameters_single_spin Test_parameters. These are to catch test_loop_parameters_single_spin] in the [httpshttp://sourceforgewww.net/p/nmrnmr-relax.com/ticketsapi/94.1/ bug #9], and specifically test for when pA is 1test_suite.unit_tests._specific_analyses.0 and the other probabilities are zero_relax_disp.test_parameters-module. Two new html unit tests of the _libtest module _specific_analyses._dispersion_relax_disp.test_ns_mmq_3site module include Test_ns_mmq_3sitetest_parameters].test_ns_mmq_3site_mq and Test_ns_mmq_3site.test_ns_mmq_3site_sq_dq_zq, and a single new unit test These were added to try to catch the typo error at the end of the _libfunction, where the {{:deltaomegaHAB}} parameter appears twice (the second should be {{:deltaomegaHAC}})._dispersion.test_ns_r1rho_3site module is Test_ns_r1rho_3site.test_ns_r1rho_3site.* Unit tests However the typo was not caught in the tests as no currently implemented dispersion model contains the {{: Addition of two tests for specific_analysesdeltaomegaHAC}} parameter.relax_disp.parameters.param_conversion() Hence it is a latent bug. The two unit tests are Test_parameters.test_param_conversion_clustered_spins and Test_parameters.test_param_conversion_single_spin in do catch a minor error with the unit test module _specific_analyses._relax_disp.test_parameters'[[R2eff model|R2eff]]' model in which the {{:i0}} parameter is always returned. These tests uncovered that {{:i0}} should only be returned when exponential curve data is present. This bug has no apparent affect on the pC parameter for current operation of relax, so the 3parameter is probably handled correctly downstream.* [http://www.nmr-site R1rho dispersion models 'NS R1rho 3relax.com/api/4.1/specific_analyses.relax_disp.parameters-site' and 'NS R1rho 3-site linear' is not being calculated in the param_conversion() function. This is now reported as module.html Module specific_analyses.relax_disp.parameters]: Fix for [httpshttp://sourceforgewww.net/p/nmr-nmr-relax.com/ticketsapi/114.1/ bug specific_analyses.relax_disp.parameters-module.html#11loop_parameters loop_parameters()].* Unit tests: Creation of with the Test_parameters.test_param_conversion_clustered_spins_sim test'[[R2eff model|R2eff]]' model. This is to check now only returns the specific_analyses.relax_disp.parameters.param_conversion() function for a cluster of 2 spins for Monte Carlo simulations{{:i0}} parameter when exponential curve data is present. It was a failed attempt to catch [httpsThis fix has no apparent affect on the operation of relax, so the {{:i0}} parameter is probably correctly handled in code that calls the [http://sourceforge.net/p/www.nmr-relax.com/ticketsapi/104.1/ bug #10]specific_analyses.relax_disp. The problem probably lies in the Monte Carlo simulation setup functions in the specific analysis API rather than in the parameters-module specific_analyses.relax_disp.parametershtml#loop_parameters loop_parameters() function].* Unit testsDispersion: Test Shift of the dispersion specific analysis API function sim_init_values()model parameters from the parameter loop to [http://www. This is an attempt at catching [https:nmr-relax.com/api/sourceforge4.net1/p/nmrlib.dispersion.variables-relax/tickets/10/ bug #10module.html lib.dispersion.variables], . This removes all references to specific model parameters from the failure of the 3[http://www.nmr-site dispersion models when setting the pC parameter for Monte Carlo simulationsrelax.com/api/4. The failing test however shows that the sim_init_values1/specific_analyses.relax_disp.parameters-module.html#loop_parameters loop_parameters() function probably needs a complete overhaul] in the [http://www.* Dispersion: Improved handling of deselected spins in the loop_parameters() function. This is from the specific_analyses.relax_disp.parameters module. The function nmr-relax.com/api/4.1/specific_analyses.relax_disp.parameters-module.html specific_analyses.relax_disp.parameters module] into [http://www.nmr-relax.com/api/4.1/lib.dispersion.variables-module.html lib.dispersion.variables]. This simplifies the [http://www.nmr-relax.com/api/4.1/specific_analyses.relax_disp.parameters-module.html#loop_parameters loop_parameters() function] and should minimise latent bugs.* Unit tests: Addition of two tests for [http://www.nmr-relax.com/api/4.1/specific_analyses.relax_disp.parameters-module.html#linear_constraints specific_analyses.relax_disp.parameters.linear_constraints()]. The two unit tests are [http://www.nmr-relax.com/api/4.1/test_suite.unit_tests._specific_analyses._relax_disp.test_parameters.Test_parameters-class.html#test_linear_constraints_clustered_spins Test_parameters.test_linear_constraints_clustered_spins] and [http://www.nmr-relax.com/api/4.1/test_suite.unit_tests._specific_analyses._relax_disp.test_parameters.Test_parameters-class.html#test_linear_constraints_single_spin Test_parameters.test_linear_constraints_single_spin] in the [[http://www.nmr-relax.com/api/4.1/test_suite.unit_tests._specific_analyses._relax_disp.test_parameters-module.html unit test module _specific_analyses._relax_disp.test_parameters]. These show that the linear constraints are correctly assembled for single and clustered spins for all models.* [http://www.nmr-relax.com/api/4.1/specific_analyses.relax_disp.parameters-module.html Module specific_analyses.relax_disp.parameters]: Docstring, whitespace, and comment fixes.* Unit tests: Addition of tests for [http://www.nmr-relax.com/api/4.1/lib.dispersion.ns_mmq_3site-module.html lib.dispersion.ns_mmq_3site] and [http://www.nmr-relax.com/api/4.1/lib.dispersion.ns_r1rho_3site-module.html lib.dispersion.ns_r1rho_3site]. These are to catch [https://sourceforge.net/p/nmr-relax/tickets/9/ bug #9], and specifically test for when {{:pA}} is 1.0 and the other probabilities are zero. Two new unit tests of the [http://www.nmr-relax.com/api/4.1/test_suite.unit_tests._lib._dispersion.test_ns_mmq_3site-module.html _lib._dispersion.test_ns_mmq_3site module] include [http://www.nmr-relax.com/api/4.1/test_suite.unit_tests._lib._dispersion.test_ns_mmq_3site.Test_ns_mmq_3site-class.html#test_ns_mmq_3site_mq Test_ns_mmq_3site.test_ns_mmq_3site_mq] and [http://www.nmr-relax.com/api/4.1/test_suite.unit_tests._lib._dispersion.test_ns_mmq_3site.Test_ns_mmq_3site-class.html#test_ns_mmq_3site_sq_dq_zq Test_ns_mmq_3site.test_ns_mmq_3site_sq_dq_zq], and a single new unit test of the [http://www.nmr-relax.com/api/4.1/test_suite.unit_tests._lib._dispersion.test_ns_r1rho_3site-module.html _lib._dispersion.test_ns_r1rho_3site module] is [http://www.nmr-relax.com/api/4.1/test_suite.unit_tests._lib._dispersion.test_ns_r1rho_3site.Test_ns_r1rho_3site-class.html#test_ns_r1rho_3site Test_ns_r1rho_3site.test_ns_r1rho_3site].* Unit tests: Addition of two tests for [http://www.nmr-relax.com/api/4.1/specific_analyses.relax_disp.parameters-module.html#param_conversion specific_analyses.relax_disp.parameters.param_conversion()]. The two unit tests are [http://www.nmr-relax.com/api/4.1/test_suite.unit_tests._specific_analyses._relax_disp.test_parameters.Test_parameters-class.html#test_param_conversion_clustered_spins Test_parameters.test_param_conversion_clustered_spins] and [http://www.nmr-relax.com/api/4.1/test_suite.unit_tests._specific_analyses._relax_disp.test_parameters.Test_parameters-class.html#test_param_conversion_single_spin Test_parameters.test_param_conversion_single_spin] in the [http://www.nmr-relax.com/api/4.1/test_suite.unit_tests._specific_analyses._relax_disp.test_parameters-module.html unit test module _specific_analyses._relax_disp.test_parameters]. These tests uncovered that the {{:pC}} parameter for the 3-site {{:R1rho}} dispersion models '[[NS R1rho 3-site]]' and '[[NS R1rho 3-site linear]]' is not being calculated in the [http://www.nmr-relax.com/api/4.1/specific_analyses.relax_disp.parameters-module.html#param_conversion param_conversion() function]. This is now reported as [https://sourceforge.net/p/nmr-relax/tickets/11/ bug #11].* Unit tests: Creation of the [http://www.nmr-relax.com/api/4.1/test_suite.unit_tests._specific_analyses._relax_disp.test_parameters.Test_parameters-class.html#test_param_conversion_clustered_spins_sim Test_parameters.test_param_conversion_clustered_spins_sim test]. This is to check the [http://www.nmr-relax.com/api/4.1/specific_analyses.relax_disp.parameters-module.html#param_conversion specific_analyses.relax_disp.parameters.param_conversion() function] for a cluster of 2 spins for Monte Carlo simulations. It was a failed attempt to catch [https://sourceforge.net/p/nmr-relax/tickets/10/ bug #10]. The problem probably lies in the Monte Carlo simulation setup functions in the specific analysis API rather than in the [http://www.nmr-relax.com/api/4.1/specific_analyses.relax_disp.parameters-module.html module specific_analyses.relax_disp.parameters].* Unit tests: Test of the [http://www.nmr-relax.com/api/4.1/specific_analyses.relax_disp.api.Relax_disp-class.html#sim_init_values dispersion specific analysis API function sim_init_values()]. This is an attempt at catching [https://sourceforge.net/p/nmr-relax/tickets/10/ bug #10], the failure of the 3-site dispersion models when setting the {{:pC}} parameter for Monte Carlo simulations. The failing test however shows that the [http://www.nmr-relax.com/api/4.1/specific_analyses.relax_disp.api.Relax_disp-class.html#sim_init_values sim_init_values() function] probably needs a complete overhaul.* Dispersion: Improved handling of deselected spins in the [http://www.nmr-relax.com/api/4.1/specific_analyses.relax_disp.parameters-module.html#loop_parameters loop_parameters() function]. This is from the [http://www.nmr-relax.com/api/4.1/specific_analyses.relax_disp.parameters-module.html specific_analyses.relax_disp.parameters module]. The function can now handle the first spins in the cluster being deselected.* FSFCV configuration: Skip some false positive copyrights in the <code>docs/CHANGES </code> file.

* Fix for [https://sourceforge.net/p/nmr-relax/tickets/2/ bug #2], the failure of the [http://www.nmr-relax.com/manual/structure_read_pdb.html structure.read_pdb user function ] in the GUI. The problem was that the file selection argument was being set up incorrectly as two GUI elements - an inactive file selection element and a normal value setting GUI element. Only the second value input GUI element was active (due to the GUI elements being stored in a dictionary, with the first key value being overwritten by the second).* Fix for [https://sourceforge.net/p/nmr-relax/tickets/3/ bug #3], the absence of user function argument validation within the GUI. The code for the user function argument validation in the prompt/script UIs was simply copied and slightly modified to fit into the GUI user function window execution. All arguments are now passed into the new [http://www.nmr-relax.com/api/4.1/lib.arg_check-module.html#validate_arg lib.arg_check.validate_arg() function ] and are checked based on their user function definitions.* Fix for [https://sourceforge.net/p/nmr-relax/tickets/4/ bug #4], the relax controller in the GUI not displaying text when required. Calls to the captured IO stream <code>flush() </code> methods are now been made in a number of places to allow the controller to show the text when required. This includes after printing out the intro text, after any captured and GUI handled errors, after clicking on the "help-<code>help→licence</code>licence" menu entry, after thread exceptions, and after a number of GUI message dialogs. The bug is only present in [[relax 4.1.0]].* Typo fix in the description of the <code>'atomic' </code> argument for the [http://www.nmr-relax.com/manual/structure_rmsd.html structure.rmsd user function].* Fix for [https://sourceforge.net/p/nmr-relax/tickets/5/ bug #5], the incorrect numpy version check in the relaxation dispersion auto-analysis. The [http://www.nmr-relax.com/api/4.1/dep_check-module.html#version_comparison dep_check.version_comparison() function ] is now used for the version comparisons.* Dispersion: Fix for [https://sourceforge.net/p/nmr-relax/tickets/7/ bug #7], the model list containing '[[No Rex]]' twice. The [http://www.nmr-relax.com/api/4.1/lib.dispersion.variables-module.html#MODEL_LIST_FULL MODEL_LIST_FULL variable ] contained the model '[[No Rex]]' twice. The only manifestation of the bug is a RelaxError message showing the full list of models, when a user selects a non-existent dispersion model.* Dispersion: Fix for [https://sourceforge.net/p/nmr-relax/tickets/6/ bug #6], the incorrect parameter counting for 3-site models with spin clustering. The issue was that the list of spin-specific parameters was incomplete. To resolve this, the parameter names have been shifted into the [http://www.nmr-relax.com/api/4.1/lib.dispersion.variables -module .html lib.dispersion.variables module] lists <code>PARAMS_R1</code>, <code>PARAMS_GLOBAL</code>, and <code>PARAMS_SPIN</code>. By removing the parameter names from other parts of relax, the [http://www.nmr-relax.com/api/4.1/lib.dispersion.variables -module .html lib.dispersion.variables module] will serve as a single point of failure and hence it will much easier to maintain the relaxation dispersion code when new models with new parameters are added.* Dispersion: Fix for [https://sourceforge.net/p/nmr-relax/tickets/8/ bug #8], the accidental modification of the hardcoded variables. The <code>MODEL_PARAMS </code> lists in specific_analysis[http://www.nmr-relax.com/api/4.1/lib.dispersion.relax_dispvariables-module.html lib.dispersion.variables ] were accidentally being modified by the [http://www.nmr-relax.com/api/4.1/specific_analyses.relax_disp.model.Model_class-class.html Model_class class ] in the [http://www.nmr-relax.com/api/4.1/specific_analyses.relax_disp.model -module.html specific_analyses.relax_disp.model module]. The list for a given model was being set as the self.params list. This list would then have the <code>'r1' </code> parameter pre-pended to it if that parameter is optimised for a model, and hence the specific_analysis[http://www.nmr-relax.com/api/4.relax_disp1/lib.dispersion.variables-module.html lib.dispersion.variables ] list would be permanently modified. Now <code>copy.deepcopy() </code> is being used for all variables to avoid this issue. This bug was uncovered in the unit tests as the [http://www.nmr-relax.com/api/4.1/test_suite.unit_tests._specific_analyses._relax_disp.test_model-module.html _specific_analyses._relax_disp.test_model tests ] were causing <code>'r1' </code> to be added, and then the later [http://www.nmr-relax.com/api/4.1/test_suite.unit_tests._specific_analyses._relax_disp.test_parameters-module.html _specific_analyses._relax_disp.test_parameters tests ] would fail as <code>'r1' </code> should not be in those lists. This bug is highly unlikely to be encountered by users of relax. You would need to run two analyses, one after the other without closing relax, and the first analysis would need to have '{{:r1' }} optimised and the second not.* Dispersion: Fix for [https://sourceforge.net/p/nmr-relax/tickets/9/ bug #9], the failure of the 3-site dispersion models when {{:pB }} and {{:pC }} are zero. When both are zero, for example during a comprehensive grid search when model nesting is not utilised, a divide by zero error occurs. This is now caught and large values (1e100) are set for the rates instead.* Dispersion: Fix for [https://sourceforge.net/p/nmr-relax/tickets/11/ bug #11], the missing {{:pC }} calculation for the 3-site {{:R1rho }} models. The models '[[NS R1rho 3-site]]' and '[[NS R1rho 3-site linear]]' were simply missing from the list of models for the {{:pC }} parameter.* Dispersion: Fix for [https://sourceforge.net/p/nmr-relax/tickets/10/ bug #10], the 3-site model failure of setting {{:pC }} for Monte Carlo simulations. For this, the [http://www.nmr-relax.com/api/4.1/specific_analyses.relax_disp.api.Relax_disp-class.html#sim_init_values sim_init_values() function ] of [http://www.nmr-relax.com/api/4.1/specific_analyses.relax_disp.api-module.html the relaxation dispersion specific API in specific_analyses.relax_disp.api ] has been completely rewritten. The [http://www.nmr-relax.com/api/4.1/specific_analyses.relax_disp.parameters-module.html#param_conversion specific_analyses.relax_disp.parameters.param_conversion() function ] is now called at the start to generate initial non-model parameters, and at the end to populate the simulation structures. The rest of the function has been stripped down and significantly simplified.

* [https://sourceforge.net/p/nmr-relax/mailman/message/3659347236607157/ Mailing list message].