View source for Relax 4.1.1

{{lowercase title}}

{{infobox relax release
| version  = 4.1.1
| prev     = 4.1.0
| next     = 4.1.2
| keywords = Dispersion, GUI
| type     = Major bugfix
| date     = 8 March 2019
| manual   = yes
}}

== Description ==

<section begin=description/>
This is a major bugfix release.  The release fixes multiple issues with the relax GUI and with the relaxation dispersion analyses.  Please see the notes below for details.
<section end=description/>

== Download ==

<section begin=download/>
The new relax versions can be downloaded from http://www.nmr-relax.com/download.html. If binary distributions are not yet available for your platform and you manage to compile the binary modules, please consider contributing these to the relax project (described in section 3.6 of the relax manual, http://www.nmr-relax.com/manual/relax_distribution_archives.html).
<section end=download/>

== CHANGES file ==

<section begin=metadata/>
Version 4.1.1 <br/>
(8 March 2019, from master) <br/>
https://sourceforge.net/p/nmr-relax/code/ci/4.1.1/tree/
<section end=metadata/>

=== Features ===

<section begin=features/>
* N/A.
<section end=features/>

=== Changes ===

<section begin=changes/>
* 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.
* Release Checklist: Rewrite for the shift to a git repository and to the SourceForge infrastructure.
* Test suite: Temporary file fix for the Bmrb system and GUI tests.  The temporary files normally used by these tests were accidentally removed in a previous commit.  The result was temporary files being placed in the current directory.
* <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 [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 [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 [http://www.nmr-relax.com/api/4.1/specific_analyses.relax_disp.parameters-module.html#param_num specific_analyses.relax_disp.parameters.param_num()].  This is to catch [https://sourceforge.net/p/nmr-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 [http://www.nmr-relax.com/api/4.1/test_suite.unit_tests._specific_analyses._relax_disp.test_parameters.Test_parameters-class.html#test_param_num_clustered_spins Test_parameters.test_param_num_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_num_single_spin Test_parameters.test_param_num_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].
* Unit tests: Addition of two tests for [http://www.nmr-relax.com/api/4.1/specific_analyses.relax_disp.parameters-module.html#loop_parameters specific_analyses.relax_disp.parameters.loop_parameters()].  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_loop_parameters_clustered_spins Test_parameters.test_loop_parameters_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_loop_parameters_single_spin Test_parameters.test_loop_parameters_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 were added to try to catch the typo error at the end of the function, where the {{:deltaomegaHAB}} parameter appears twice (the second should be {{:deltaomegaHAC}}).  However the typo was not caught in the tests as no currently implemented dispersion model contains the {{:deltaomegaHAC}} parameter.  Hence it is a latent bug.  The tests do catch a minor error with the '[[R2eff model|R2eff]]' model in which the {{:i0}} parameter is always returned.  {{:i0}} should only be returned when exponential curve data is present.  This bug has no apparent affect on the current operation of relax, so the parameter is probably handled correctly downstream.
* [http://www.nmr-relax.com/api/4.1/specific_analyses.relax_disp.parameters-module.html Module specific_analyses.relax_disp.parameters]: Fix for [http://www.nmr-relax.com/api/4.1/specific_analyses.relax_disp.parameters-module.html#loop_parameters loop_parameters()] with the '[[R2eff model|R2eff]]' model.  This now only returns the {{:i0}} parameter when exponential curve data is present.  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/api/4.1/specific_analyses.relax_disp.parameters-module.html#loop_parameters loop_parameters() function].
* Dispersion: Shift of the model parameters from the parameter loop to [http://www.nmr-relax.com/api/4.1/lib.dispersion.variables-module.html lib.dispersion.variables].  This removes all references to specific model parameters from the [http://www.nmr-relax.com/api/4.1/specific_analyses.relax_disp.parameters-module.html#loop_parameters loop_parameters() function] in the [http://www.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.
<section end=changes/>

=== Bugfixes ===

<section begin=bugfixes/>
* 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 <code>help→licence</code> 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 [http://www.nmr-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 <code>'r1'</code> parameter pre-pended to it if that parameter is optimised for a model, and hence the [http://www.nmr-relax.com/api/4.1/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] 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.
<section end=bugfixes/>

== Links ==

<section begin=links/>
For reference, the announcement for this release can also be found at following links:

* [http://wiki.nmr-relax.com/Relax_4.1.1 Official release notes on the relax wiki].
* [https://sourceforge.net/p/nmr-relax/mailman/message/36607157/ Mailing list message].
* [https://www.mail-archive.com/nmr-relax-announce@lists.sourceforge.net/msg00002.html The Mail Archive].

{{:Softpedia}}
<section end=links/>

== Announcements ==

{{:relax release announcements}}


== See also ==

* [http://www.nmr-relax.com/api/4.1/ The relax 4.1 API documentation]
{{:relax release see also}}
[[Category:Relaxation dispersion analysis]]