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[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 bug #2 (https[http://sourceforgewww.net/p/nmr-relax.com/ticketsapi/24.1/), the failure of the structuretest_suite.gui_tests.read_pdb user function in the GUItest_user_functions.* GUI tests: Addition of the User_functions-class.html#test_bug_2_structure_read_pdb_failure User_functions.test_bug_3_no_argument_validation test_bug_2_structure_read_pdb_failure test]. This is to catch bug #3 ([https://sourceforge.net/p/nmr-relax/tickets/32/)bug #2], the absence failure of user function argument validation within the [http://www.nmr-relax.com/manual/structure_read_pdb.html structure.read_pdb user function] in the GUI.* Unit GUI tests: Addition of two tests for specific_analysesthe [http://www.relax_dispnmr-relax.com/api/4.1/test_suite.gui_tests.test_user_functions.User_functions-class.parametershtml#test_bug_3_no_argument_validation User_functions.param_num()test_bug_3_no_argument_validation test]. This is to catch bug #6 ([https://sourceforge.net/p/nmr-relax/tickets/63/)bug #3], the failure absence of user function argument validation within the parameter counting GUI.* Unit tests: Addition of two tests for the 3[http://www.nmr-site relaxation dispersion models when spins are clusteredrelax. The two unit tests are Test_parameterscom/api/4.test_param_num_clustered_spins and Test_parameters1/specific_analyses.relax_disp.test_param_num_single_spin in the unit test parameters-module _specific_analyses._relax_disp.test_parameters.* Unit tests: Addition of two tests for 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 failure of the parameter counting for the unit test module _specific_analyses._relax_disp.test_parameters. 3-site relaxation dispersion models when spins are clustered. These were added to try to catch the typo error at the end of the function, where the 'dwH_AB' parameter appears twice (the second should be 'dwH_AC')The two unit tests are [http://www.nmr-relax. However the typo was not caught in the tests as no currently implemented dispersion model contains the 'dwH_AC' parametercom/api/4.1/test_suite.unit_tests. Hence it is a latent bug_specific_analyses._relax_disp.test_parameters.Test_parameters-class.html#test_param_num_clustered_spins Test_parameters. The tests do catch a minor error with the 'R2eff' model in which the 'i0' parameter is always returnedtest_param_num_clustered_spins] and [http://www.nmr-relax. 'i0' should only be returned when exponential curve data is presentcom/api/4.1/test_suite.unit_tests._specific_analyses._relax_disp.test_parameters. This bug has no apparent affect on the current operation of relax, so the parameter is probably handled correctly downstreamTest_parameters-class.* Module specific_analyseshtml#test_param_num_single_spin Test_parameters.relax_disp.parameterstest_param_num_single_spin] in the [http: Fix for loop_parameters() with the 'R2eff' model//www.nmr-relax.com/api/4. This now only returns the 'i0' parameter when exponential curve data is present1/test_suite.unit_tests._specific_analyses._relax_disp.test_parameters-module. This fix has no apparent affect on the operation html unit test module _specific_analyses._relax_disp.test_parameters].* Unit tests: Addition of two tests for [http://www.nmr-relax, so the 'i0' parameter is probably correctly handled in code that calls the loop_parameters() function.* Dispersion: Shift of the model com/api/4.1/specific_analyses.relax_disp.parameters from the parameter loop to lib-module.html#loop_parameters specific_analyses.relax_disp.dispersionparameters.variablesloop_parameters()]. This removes all references to specific model parameters from the loop_parameters() function in the specific_analysesThe two unit tests are [http://www.relax_dispnmr-relax.parameters module into libcom/api/4.1/test_suite.dispersionunit_tests.variables_specific_analyses. This simplifies the loop_parameters() function and should minimise latent bugs_relax_disp.* Unit tests: Addition of two tests for specific_analysestest_parameters.relax_dispTest_parameters-class.parameters.linear_constraints(). The two unit tests are html#test_loop_parameters_clustered_spins Test_parameters.test_linear_constraints_clustered_spins test_loop_parameters_clustered_spins] and Test_parameters[http://www.nmr-relax.com/api/4.1/test_suite.unit_tests.test_linear_constraints_single_spin in the unit test module _specific_analyses._relax_disp.test_parameters. These show that Test_parameters-class.html#test_loop_parameters_single_spin Test_parameters.test_loop_parameters_single_spin] in the linear constraints are correctly assembled for single 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.ns_mmq_3site and lib_relax_disp.test_parameters-module.html unit test module _specific_analyses.dispersion_relax_disp.ns_r1rho_3sitetest_parameters]. These are were added to try to catch bug #9 (httpsthe typo error at the end of the function, where the {{:deltaomegaHAB}} parameter appears twice (the second should be {{://sourceforgedeltaomegaHAC}}).net/p/nmr-relax/tickets/9/), and specifically test for when pA is 1.0 and However the typo was not caught in the other probabilities are zerotests as no currently implemented dispersion model contains the {{:deltaomegaHAC}} parameter. Hence it is a latent bug. Two new unit The tests of the _lib._dispersion.test_ns_mmq_3site module include Test_ns_mmq_3site.test_ns_mmq_3site_mq and Test_ns_mmq_3site.test_ns_mmq_3site_sq_dq_zq, and do catch a single new unit test of minor error with the _lib._dispersion.test_ns_r1rho_3site module '[[R2eff model|R2eff]]' model in which the {{:i0}} parameter is Test_ns_r1rho_3sitealways returned.test_ns_r1rho_3site.* Unit tests {{: Addition of two tests for specific_analyses.relax_disp.parameters.param_conversion()i0}} should only be returned when exponential curve data is present. The two unit tests are Test_parameters.test_param_conversion_clustered_spins and Test_parameters.test_param_conversion_single_spin in This bug has no apparent affect on the current operation of relax, so the unit test module _specific_analysesparameter is probably handled correctly downstream.* [http://www._relax_dispnmr-relax.test_parameterscom/api/4. These tests uncovered that the pC parameter 1/specific_analyses.relax_disp.parameters-module.html Module specific_analyses.relax_disp.parameters]: Fix for the 3[http://www.nmr-site R1rho dispersion models 'NS R1rho 3relax.com/api/4.1/specific_analyses.relax_disp.parameters-sitemodule.html#loop_parameters loop_parameters()] with the ' and [[R2eff model|R2eff]]'NS R1rho 3-site linear' is not being calculated in the param_conversion() functionmodel. This is now reported as bug #11 (https://sourceforgeonly returns the {{:i0}} parameter when exponential curve data is present.net/p/nmr This fix has no apparent affect on the operation of relax, so the {{:i0}} parameter is probably correctly handled in code that calls the [http://www.nmr-relax.com/ticketsapi/114.1/).* Unit tests: Creation of the Test_parameters.test_param_conversion_clustered_spins_sim test. This is to check the specific_analyses.relax_disp.parameters-module.param_conversionhtml#loop_parameters loop_parameters() function for a cluster ].* Dispersion: Shift of 2 spins for Monte Carlo simulationsthe model parameters from the parameter loop to [http://www. It was a failed attempt to catch bug #10 (https://sourceforge.net/p/nmrnmr-relax.com/ticketsapi/104.1/)lib. The problem probably lies in the Monte Carlo simulation setup functions in the specific analysis API rather than in the dispersion.variables-module specific_analyses.relax_disphtml lib.parametersdispersion.* Unit tests: Test of the dispersion specific analysis API function sim_init_values()variables]. This is an attempt at catching bug #10 (httpsremoves all references to specific model parameters from the [http://sourceforgewww.net/p/nmr-relax.com/ticketsapi/104.1/), the failure of the 3specific_analyses.relax_disp.parameters-site dispersion models when setting module.html#loop_parameters loop_parameters() function] in the pC parameter for Monte Carlo simulations[http://www. The failing test however shows that the sim_init_values() function probably needs a complete overhaulnmr-relax.com/api/4.* Dispersion: Improved handling of deselected spins in the loop_parameters() function. This is from the specific_analyses.relax_disp.parameters module. The function can now handle the 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.

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