Relax 3.2.0 - Revision history

Bugman: Switch to the {{gna task link}} template to remove dead Gna! links.

2020-10-16T13:58:44Z

Switch to the {{gna task link}} template to remove dead Gna! links.

Show changes

Bugman: Switch to the {{relax developer link}} template to remove dead Gna! links.

2020-10-15T21:37:44Z

Switch to the {{relax developer link}} template to remove dead Gna! links.

Bugman at 21:35, 8 October 2020

2020-10-08T21:35:26Z

Bugman: Fixes for the broken Gna! forum link.

2020-10-08T21:30:16Z

Fixes for the broken Gna! forum link.

Bugman: /* Links */ Fix the broken Gna! forum link by switching to {{gna link}}.

2020-10-08T21:08:56Z

Links: Fix the broken Gna! forum link by switching to {{gna link}}.

Bugman: /* Features */ Minfx link fix.

2020-10-06T18:35:38Z

Features: Minfx link fix.

Bugman: /* Features */ Link fix.

2020-10-06T18:27:06Z

Features: Link fix.

Bugman: /* Description */ Link fix

2020-10-06T08:35:01Z

Description: Link fix

Bugman: /* Description */ Link fix

2020-10-06T07:14:03Z

Description: Link fix

Bugman: Switch to the {{gna link}} template for avoiding dead links.

2020-10-06T07:04:49Z

Switch to the {{gna link}} template for avoiding dead links.

@@ Line 260: / Line 260: @@
 *  The J(w) mapping parameter setting documentation has been shifted into the parameter list object.  This has also been updated to reflect the current design of relax.
 *  The consistency testing parameter setting documentation has been shifted into the parameter list object.  This has also been updated to reflect the current design of relax.
-*  The relaxation dispersion parameter setting documentation has been shifted into the parameter list object.  The documentation has also been rewritten as it originates from [https://gna.org/users/semor Sebastien Morin] back in 2009 and is now very much out of date.
+*  The relaxation dispersion parameter setting documentation has been shifted into the parameter list object.  The documentation has also been rewritten as it originates from {{relax developer link|username=semor|text=Sebastien Morin}} back in 2009 and is now very much out of date.
 *  Deleted the relaxation curve-fitting parameter setting documentation.  This really didn't say anything.
 *  The N-state model parameter setting documentation has been shifted into the parameter list object.
@@ Line 285: / Line 285: @@
 *  Created the new '-r' or '--traceback' relax command line option.  If supplied, stack tracebacks will be shown for all RelaxWarnings and RelaxErrors.  This allows for finer debugging control.
 *  Clean up of the debugging command line options.  The debug flag now will cause stack tracebacks to be printed on all RelaxWarnings.
-*  Created the '--error-state' command line option for saving a pickled state when a RelaxError is raised.  This gives greater control of a powerful feature added to relax by {{gna link|gna.org/users/macraild|text=Chris MacRaild}}.  The pickled state can then be attached to bug reports or can be used to quickly load the state prior to failure when in the scripting UI mode.
+*  Created the '--error-state' command line option for saving a pickled state when a RelaxError is raised.  This gives greater control of a powerful feature added to relax by {{relax developer link|username=macraild|text=Chris MacRaild}}.  The pickled state can then be attached to bug reports or can be used to quickly load the state prior to failure when in the scripting UI mode.
 *  Reordered the debugging command line options and removed the '-r' shortcut.
 *  The lib.errors module is now really independent of relax - the compat module is no longer used.  Instead, the Python 2 and 3 versions of the pickle module are imported using try statements.
@@ Line 675: / Line 675: @@
 *  Fix for [https://gna.org/bugs/?22039 bug #22039, the printing out of Dpar twice by the diffusion_tensor.display user function].  The solution is given in the original bug report.
 *  Fix for [https://gna.org/bugs/?22041 bug #22041, the PDB atom serial number error from the structure.write_pdb user function].  The problem is that the [http://www.nmr-relax.com/manual/structure_write_pdb.html structure.write_pdb user function] preserves the atom numbering from the original structure and uses that for the atom serial number.  However the atom serial number must be replaced with sequential values to produce a valid PDB file.  This is fatal for any CONECT records.
-*  Fix for the chain-reaction failures in the test suite.  This fixes [https://gna.org/bugs/?22055 bug #22055, the processor.run_queue() not cleaning up in uni_processor - chain-reaction failures in the test suite].  The fix was insanely simple, just implementing what was mentioned {{gna link|url=gna.org/users/varioustoxins|text=Gary Thompson's}} FIXME comment in the run_queue() method of the uni-processor object.  The queue execution code has been placed inside a 'try' statement and the queue cleaning up code in a 'finally' statement.  This closes a painfully difficult to find bug that has been in relax since 2006, though only affecting relax developers.
+*  Fix for the chain-reaction failures in the test suite.  This fixes [https://gna.org/bugs/?22055 bug #22055, the processor.run_queue() not cleaning up in uni_processor - chain-reaction failures in the test suite].  The fix was insanely simple, just implementing what was mentioned {{relax developer link|username=varioustoxins|text=Gary Thompson's}} FIXME comment in the run_queue() method of the uni-processor object.  The queue execution code has been placed inside a 'try' statement and the queue cleaning up code in a 'finally' statement.  This closes a painfully difficult to find bug that has been in relax since 2006, though only affecting relax developers.
 <section end=bugfixes/>

@@ Line 340: / Line 340: @@
 *  Shifted all of the dispersion model descriptions and parameter lists to the variables module.  The descriptions and parameter lists which were part of the [http://www.nmr-relax.com/manual/relax_disp_select_model.html relax_disp.select_model user function] backend have been shifted into the specific_analyses.relax_disp.variables module as MODEL_DESC_* and MODEL_PARAMS_* variables.  The descriptions have also all been standardised.  The MODEL_DESC and MODEL_PARAMS dictionaries have also been created to hold all of the descriptions and parameters in one place.
 *  The General.test_bug_21720_pipe_switching_with_tab_closure GUI test now works without compiled C modules.
-*  Updated the release checklist for the new minfx version 1.0.6 release.  See {{gna url|gna.org/forum/forum.php?forum_id=2456}} and https://freecode.com/projects/minfx.
+*  Updated the release checklist for the new minfx version 1.0.6 release.  See {{gna url|1=gna.org/forum/forum.php?forum_id=2456}} and https://freecode.com/projects/minfx.
 *  Fixes for the specific API _set_param_values_spin() method for lists and dictionaries.  This is for the [http://www.nmr-relax.com/manual/value_set.html value.set user function] to allow it to handle parameters of different types.  For example the R<sub>2</sub> parameter in the relaxation dispersion analysis.  This API common method now sets all dictionary elements, list elements, or the variable to the given value.
 *  Created the new specific_analyses.relax_disp.variables.PARAMS_R20 list.  This variable is a list of all R<sub>2</sub><sup>0</sup> parameters of the dispersion models.  It has been shifted out of the parameters module.

@@ Line 340: / Line 340: @@
 *  Shifted all of the dispersion model descriptions and parameter lists to the variables module.  The descriptions and parameter lists which were part of the [http://www.nmr-relax.com/manual/relax_disp_select_model.html relax_disp.select_model user function] backend have been shifted into the specific_analyses.relax_disp.variables module as MODEL_DESC_* and MODEL_PARAMS_* variables.  The descriptions have also all been standardised.  The MODEL_DESC and MODEL_PARAMS dictionaries have also been created to hold all of the descriptions and parameters in one place.
 *  The General.test_bug_21720_pipe_switching_with_tab_closure GUI test now works without compiled C modules.
-*  Updated the release checklist for the new minfx version 1.0.6 release.  See https://gna.org/forum/forum.php?forum_id=2456 and https://freecode.com/projects/minfx.
+*  Updated the release checklist for the new minfx version 1.0.6 release.  See {{gna url|gna.org/forum/forum.php?forum_id=2456}} and https://freecode.com/projects/minfx.
 *  Fixes for the specific API _set_param_values_spin() method for lists and dictionaries.  This is for the [http://www.nmr-relax.com/manual/value_set.html value.set user function] to allow it to handle parameters of different types.  For example the R<sub>2</sub> parameter in the relaxation dispersion analysis.  This API common method now sets all dictionary elements, list elements, or the variable to the given value.
 *  Created the new specific_analyses.relax_disp.variables.PARAMS_R20 list.  This variable is a list of all R<sub>2</sub><sup>0</sup> parameters of the dispersion models.  It has been shifted out of the parameters module.

@@ Line 684: / Line 684: @@
 * [http://wiki.nmr-relax.com/Relax_3.2.0 Official release notes on the relax wiki].
-* [https://gna.org/forum/forum.php?forum_id=2461 Gna! news item].
+* {{gna link|url=gna.org/forum/forum.php?forum_id=2461|text=Gna! news item}}.
 * [http://article.gmane.org/gmane.science.nmr.relax.announce/54 Gmane mailing list archive].
 * [https://mail.gna.org/public/relax-announce/2014-05/msg00000.html Local archives].

@@ Line 43: / Line 43: @@
 *  Expansion of the [http://www.nmr-relax.com/manual/value_set.html value.set user function] to handle parameters which consist of lists of values.  The index argument has been added to allow the index of the list to be specified, and this is then propagated into the specific analysis API.
 *  Improvements for the parameter definitions in all analysis types.  This allows for better output in 2D plots and text files.
-*  Implemented linear constraints for the frame order analysis.  This uses the log-barrier constraint algorithm in the [https://gna.org/projects/minfx/ minfx library] to provide constraints without requiring gradients.
+*  Implemented linear constraints for the frame order analysis.  This uses the log-barrier constraint algorithm in the [{{minfx homepage}} minfx library] to provide constraints without requiring gradients.
 *  Improved and expanded the relax command line options for debugging.
 *  Full independence of the relax library so that it can be used outside of relax.

@@ Line 52: / Line 52: @@
 *  Support for multiple point creation for the [http://www.nmr-relax.com/manual/dx_map.html OpenDX chi-squared space mapping user function].
 *  Automatic determination of reasonable initial contour levels for the [http://www.nmr-relax.com/manual/dx_map.html OpenDX mapping user function].
-*  Addition of a [http://www.nmr-relax.com/manual/N_state_model_or_ensemble_analysis.html new chapter to the manual for the N-state model or ensemble analysis].
+*  Addition of a [http://www.nmr-relax.com/manual/The_N_state_model_or_ensemble_analysis.html new chapter to the manual for the N-state model or ensemble analysis].
 *  Creation of the new [http://www.nmr-relax.com/manual/pymol_frame_order.html pymol.frame_order user function] for visualising results.
 *  Expansion of the Grace 2D data plotting capabilities.

@@ Line 14: / Line 14: @@
 <section begin=description/>
-This is a major feature release.  It includes the addition of the new [[B14]] and [[B14 full]] [[:Category:relaxation dispersion analysis|relaxation dispersion]] models [Baldwin 2014], a complete rearrangement of the module layout of the specific analyses packages, a number of new [http://www.nmr-relax.com/manual/The_list_of_functions.html user functions], documentation improvements including the addition of a [http://www.nmr-relax.com/manual/N_state_model_or_ensemble_analysis.html new chapter to the manual for the N-state model or ensemble analysis], and numerous of other features.  This is also a major bugfix release, so all users are recommended to upgrade.  This is essential if you are using the new relaxation dispersion analysis in relax as a severe bug in the error calculation has been corrected.  See below for a comprehensive list of new features, the rather large number of changes, and the long list of all bugs fixed.
+This is a major feature release.  It includes the addition of the new [[B14]] and [[B14 full]] [[:Category:relaxation dispersion analysis|relaxation dispersion]] models [Baldwin 2014], a complete rearrangement of the module layout of the specific analyses packages, a number of new [http://www.nmr-relax.com/manual/The_list_of_functions.html user functions], documentation improvements including the addition of a [http://www.nmr-relax.com/manual/The_N_state_model_or_ensemble_analysis.html new chapter to the manual for the N-state model or ensemble analysis], and numerous of other features.  This is also a major bugfix release, so all users are recommended to upgrade.  This is essential if you are using the new relaxation dispersion analysis in relax as a severe bug in the error calculation has been corrected.  See below for a comprehensive list of new features, the rather large number of changes, and the long list of all bugs fixed.
 <section end=description/>