Changes

* 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 docs/devel/latex2html/setup 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 *.tex files outside of docs/latex/.

* GUI tests: Addition of the [http://www.nmr-relax.com/api/4.1/test_suite.gui_tests.test_user_functions.User_functions-class.html#test_bug_2_structure_read_pdb_failure User_functions.test_bug_2_structure_read_pdb_failure test]. This is to catch [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.* GUI tests: Addition of the [http://www.nmr-relax.com/api/4.1/test_suite.gui_tests.test_user_functions.User_functions-class.html#test_bug_3_no_argument_validation User_functions.test_bug_3_no_argument_validation test]. This is to catch [https://sourceforge.net/p/nmr-relax/tickets/3/ bug #3], the absence of user function argument validation within the GUI.* Unit tests: Addition of two tests for specific_analyses.relax_disp.parameters.param_num(). This is to catch [https[http://sourceforgewww.net/p/nmr-relax.com/ticketsapi/64.1/ bug specific_analyses.relax_disp.parameters-module.html#6param_num specific_analyses.relax_disp.parameters.param_num()], the failure of the parameter counting for the 3. This is to catch [https://sourceforge.net/p/nmr-site relaxation dispersion models relax/tickets/6/ bug #6], the failure of the parameter counting for the 3-site relaxation dispersion models when spins are clustered. The two unit tests are Test_parameters.test_param_num_clustered_spins and Test_parameters[http://www.nmr-relax.com/api/4.1/test_suite.unit_tests.test_param_num_single_spin in the unit test module _specific_analyses._relax_disp.test_parameters.* Unit tests: Addition of two tests for specific_analysesTest_parameters-class.relax_disphtml#test_param_num_clustered_spins Test_parameters.parameterstest_param_num_clustered_spins] and [http://www.loop_parameters()nmr-relax.com/api/4. The two unit tests are Test_parameters1/test_suite.test_loop_parameters_clustered_spins and Test_parametersunit_tests.test_loop_parameters_single_spin in the unit test module _specific_analyses._relax_disp.test_parameters. These were added to try to catch Test_parameters-class.html#test_param_num_single_spin Test_parameters.test_param_num_single_spin] in the typo error at the end of the function, where the {{:deltaomegaHAB}} parameter appears twice (the second should be {{:deltaomegaHAC}})[http://www.nmr-relax.com/api/4.1/test_suite.unit_tests._specific_analyses._relax_disp.test_parameters-module. However the typo was not caught in the html unit test module _specific_analyses._relax_disp.test_parameters].* Unit tests as no currently implemented dispersion model contains the {{:deltaomegaHAC}} parameterAddition of two tests for [http://www. Hence it is a latent bugnmr-relax. The tests do catch a minor error with the '[[R2eff model|R2eff]]' model in which the {{:i0}} parameter is always returnedcom/api/4. {{:i0}} should only be returned when exponential curve data is present1/specific_analyses.relax_disp.parameters-module. This bug has no apparent affect on the current operation of relax, so the parameter is probably handled correctly downstream.* Module html#loop_parameters specific_analyses.relax_disp.parameters: Fix for .loop_parameters() with the '[[R2eff model|R2eff]]' model. This now only returns the {{The two unit tests are [http:i0}} parameter when exponential curve data is present//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.dispersion_relax_disp.variablestest_parameters. This removes all references to specific model parameters from the loop_parameters() function in the specific_analysesTest_parameters-class.relax_disphtml#test_loop_parameters_clustered_spins Test_parameters.parameters module into libtest_loop_parameters_clustered_spins] and [http://www.nmr-relax.dispersioncom/api/4.variables1/test_suite. This simplifies the loop_parameters() function and should minimise latent bugsunit_tests.* Unit tests: Addition of two tests for specific_analyses_specific_analyses.relax_disp_relax_disp.parameterstest_parameters.linear_constraints(). The two unit tests are Test_parameters-class.test_linear_constraints_clustered_spins and html#test_loop_parameters_single_spin Test_parameters.test_linear_constraints_single_spin test_loop_parameters_single_spin] in the unit test module _specific_analyses[http://www._relax_dispnmr-relax.test_parameterscom/api/4. These show that the linear constraints are correctly assembled for single and clustered spins for all models1/test_suite.unit_tests.* Module specific_analyses_specific_analyses.relax_disp_relax_disp.parameters: Docstring, whitespace, and comment fixestest_parameters-module.* Unit tests: Addition of tests for libhtml unit test module _specific_analyses.dispersion_relax_disp.ns_mmq_3site and lib.dispersion.ns_r1rho_3sitetest_parameters]. These are were added to try to catch [httpsthe typo error at the end of the function, where the {{://sourceforgedeltaomegaHAB}} parameter appears twice (the second should be {{:deltaomegaHAC}}).net/p/nmr-relax/tickets/9/ bug #9], and specifically test for when However the typo was not caught in the tests as no currently implemented dispersion model contains the {{:pAdeltaomegaHAC}} parameter. Hence it is 1.0 and the other probabilities are zeroa 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'[[R2eff model|R2eff]]' model in which the {{:i0}} parameter is always returned._dispersion.test_ns_r1rho_3site module {{:i0}} should only be returned when exponential curve data is Test_ns_r1rho_3sitepresent.test_ns_r1rho_3site.* Unit tests: Addition This bug has no apparent affect on the current operation of two tests for specific_analysesrelax, so the parameter is probably handled correctly downstream.relax_disp.parameters* [http://www.param_conversion()nmr-relax. The two unit tests are Test_parameterscom/api/4.test_param_conversion_clustered_spins and Test_parameters1/specific_analyses.test_param_conversion_single_spin in the unit test relax_disp.parameters-module _specific_analyses._relax_disphtml Module specific_analyses.test_parametersrelax_disp. These tests uncovered that the {{parameters]:pC}} parameter Fix for the 3-site {{[http:R1rho}} dispersion models '[[NS R1rho 3//www.nmr-site]relax.com/api/4.1/specific_analyses.relax_disp.parameters-module.html#loop_parameters loop_parameters()]' and with the '[[NS R1rho 3-site linearR2eff model|R2eff]]' is not being calculated in the param_conversion() functionmodel. This is now reported as [httpsonly returns the {{://sourceforgei0}} 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:/tickets/11www.nmr-relax.com/api/4.1/ bug specific_analyses.relax_disp.parameters-module.html#11loop_parameters loop_parameters() function].* Unit testsDispersion: Creation Shift of the Test_parametersmodel parameters from the parameter loop to [http://www.test_param_conversion_clustered_spins_sim testnmr-relax. This is to check the specific_analysescom/api/4.relax_disp1/lib.parametersdispersion.param_conversion() function for a cluster of 2 spins for Monte Carlo simulationsvariables-module.html lib.dispersion.variables]. It was a failed attempt This removes all references to catch specific model parameters from the [httpshttp://sourceforgewww.net/p/nmrnmr-relax.com/ticketsapi/104.1/ bug specific_analyses.relax_disp.parameters-module.html#10loop_parameters loop_parameters() function]in the [http://www.nmr-relax. The problem probably lies in the Monte Carlo simulation setup functions in the specific analysis API rather than in the com/api/4.1/specific_analyses.relax_disp.parameters-module .html specific_analyses.relax_disp.parametersmodule] into [http://www.nmr-relax.com/api/4.1/lib.* Unit tests: Test of the dispersion specific analysis API function sim_init_values(). variables-module.html lib.dispersion.variables]. This is an attempt at catching simplifies the [httpshttp://sourceforgewww.net/p/nmr-relax.com/ticketsapi/104.1/ bug specific_analyses.relax_disp.parameters-module.html#10loop_parameters loop_parameters() function], the failure and should minimise latent bugs.* Unit tests: Addition of the 3-site dispersion models when setting the {{:pC}} parameter two tests for Monte Carlo simulationsspecific_analyses.relax_disp.parameters. The failing test however shows that the sim_init_valueslinear_constraints() function probably needs a complete overhaul.* Dispersion: Improved handling of deselected spins The two unit tests are Test_parameters.test_linear_constraints_clustered_spins and Test_parameters.test_linear_constraints_single_spin in the loop_parameters() function[[http://www. This is from the specific_analysesnmr-relax.com/api/4.1/test_suite.unit_tests._specific_analyses._relax_disp.relax_disptest_parameters-module.parameters 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.

* 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/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 PARAMS_R1, PARAMS_GLOBAL, and PARAMS_SPIN. 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 MODEL_PARAMS lists in specific_analysis[http://www.relax_dispnmr-relax.com/api/4.1/lib.dispersion.variables-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 'r1' parameter pre-pended to it if that parameter is optimised for a model, and hence the specific_analysis[http://www.nmr-relax.com/api/4.1/lib.dispersion.variables-module.html lib.relax_dispdispersion.variables ] list would be permanently modified. Now copy.deepcopy() 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 'r1' 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 'r1' 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/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.