Relax 3.3.1 - Revision history

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

2020-10-16T15:04:45Z

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

Show changes

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

2020-10-14T11:19:08Z

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

Bugman: Fixes for the broken Gna! forum link.

2020-10-08T21:28:22Z

Fixes for the broken Gna! forum link.

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

2020-10-08T21:03:34Z

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

Bugman: /* Changes */ Internal links for Dasha and Modelfree4.

2015-12-15T15:23:05Z

Changes: Internal links for Dasha and Modelfree4.

Bugman: Using the HarvardReferences style for the Tollinger01 citation.

2015-11-03T16:43:43Z

Using the HarvardReferences style for the Tollinger01 citation.

Bugman: /* Changes */ Switched to using a labelled section transclusion for the Tollinger01 reference.

2015-11-03T16:36:25Z

Changes: Switched to using a labelled section transclusion for the Tollinger01 reference.

Bugman: Added the 'manual' parameter to {{infobox relax release}}.

2015-10-22T17:01:34Z

Added the 'manual' parameter to {{infobox relax release}}.

Bugman: Increased the sectioning depth.

2015-10-22T17:01:12Z

Increased the sectioning depth.

Bugman: Infobox renaming fix.

2015-10-21T16:52:37Z

Infobox renaming fix.

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 * Epydoc docstring fix for the [http://www.nmr-relax.com/api/3.3/dep_check-module.html#version_comparison dep_check.version_comparison() function].
 * Removed ZZ and HD exchange from the [http://www.nmr-relax.com/manual/Relaxation_dispersion.html dispersion chapter of the relax manual].  These would probably require completely new analysis types added to relax to analyse such data.
-* Updated the 'Announcement' section of the release checklist document.  This now includes details about initially composing the message using the [http://wiki.nmr-relax.com relax wiki], and then how that text and the CHANGES file are used for the [http://news.gmane.org/gmane.science.nmr.relax.announce email announcement] and the [https://gna.org/news/?group=relax Gna! news item].
+* Updated the 'Announcement' section of the release checklist document.  This now includes details about initially composing the message using the [http://wiki.nmr-relax.com relax wiki], and then how that text and the CHANGES file are used for the [http://news.gmane.org/gmane.science.nmr.relax.announce email announcement] and the {{gna link|url=gna.org/news/?group=relax|text=Gna! news item}}.
 * Small changes for the Gna! news item in the release checklist document.
 * Modified the announcement section of the release checklist document.  Text about removing wiki markup has been added.

@@ Line 171: / Line 171: @@
 * Created a basic text based progress meter in the new [http://www.nmr-relax.com/api/3.3/lib.text.progress-module.html lib.text.progress module].  This is taken from the script test_suite/shared_data/frame_order/cam/generate_base.py.
 * Modifications to the [http://www.nmr-relax.com/api/3.3/test_suite.gui_tests.test_user_functions.User_functions-class.html#test_structure_add_atom User_functions.test_structure_add_atom GUI test].  As lists of lists are now accepted by the [http://www.nmr-relax.com/manual/structure_add_atom.html structure.add_atom user function], the operation in the GUI is now significantly different.  Therefore many checks have been removed from the GUI test.
-* Updated the minimum minfx dependency version number from 1.0.9 to 1.0.11 in the [http://www.nmr-relax.com/api/3.3/dep_check-module.html dep_check module].  This [https://gna.org/forum/forum.php?forum_id=2477 newest version handles infinite target function values preventing optimisation from continuing forever].  The [https://gna.org/forum/forum.php?forum_id=2475 1.0.10 version is also useful as there is full support for gradients and Hessians in the log-barrier constraint algorithm].
+* Updated the minimum minfx dependency version number from 1.0.9 to 1.0.11 in the [http://www.nmr-relax.com/api/3.3/dep_check-module.html dep_check module].  This {{gna link|url= newest version handles infinite target function values preventing optimisation from continuing forever].  The {{gna link|url=gna.org/forum/forum.php?forum_id=2475|text=1.0.10 version is also useful as there is full support for gradients and Hessians in the log-barrier constraint algorithm}}.
 * Shifted the [http://www.nmr-relax.com/api/3.2/specific_analyses.relax_disp.variables-module.html specific_analyses.relax_disp.variables module] into [http://www.nmr-relax.com/api/3.3/lib.dispersion.variables-module.html lib.dispersion].  This is both to minimise circular dependencies, as previously the [http://www.nmr-relax.com/api/3.3/specific_analyses.relax_disp-module.html specific_analyses.relax_disp modules] import from [http://www.nmr-relax.com/api/3.2/target_functions.relax_disp-module.html target_functions.relax_disp] and vice-versa, and to allow the relax library functions to have access to these variables.  This follows from a similar change to the frame order analysis in the frame_order_cleanup branch.
 * Dependency fix for the [http://www.nmr-relax.com/api/3.3/auto_analyses.relax_disp_repeat_cpmg-module.html auto_analyses.relax_disp_repeat_cpmg module].  This was causing relax to fail.  SciPy is an optional dependence for relax, but this module caused relax to not start if scipy was not installed.  This was detected by testing relax with PyPy.

@@ Line 315: / Line 315: @@
 * [http://wiki.nmr-relax.com/Relax_3.3.1 Official release notes on the relax wiki].
-* [https://gna.org/forum/forum.php?forum_id=2478 Gna! news item].
+* {{gna link|url=gna.org/forum/forum.php?forum_id=2478|text=Gna! news item}}.
 * [http://article.gmane.org/gmane.science.nmr.relax.announce/59 Gmane mailing list archive].
 * [http://www.mail-archive.com/relax-announce%40gna.org/msg00050.html The Mail Archive].

@@ Line 133: / Line 133: @@
 * Added the [http://www.nmr-relax.com/api/3.3/test_suite.system_tests.relax_disp.Relax_disp-class.html#test_show_apod_rmsd_dir_to_files Relax_disp.test_show_apod_rmsd_dir_to_files system test] to the blacklist.  This is if the showApod program is not installed on the machine and allows the test suite to pass.
 * Extended the printout for the skipped tests in the test suite.  As tests using the NMRPipe showApod software are skipped and listed in this table, the text now includes 'software' in the list.
-* Shifted the checks for the Dasha and Modelfree4 software into the system test __init__() method.  This is to bring this into the same design as the relaxation dispersion tests which require the NMRPipe showApod software.  Now the test suite will list either Dasha or Modelfree4 in the skipped test table if they are not installed.
+* Shifted the checks for the [[Dasha]] and [[Modelfree4]] software into the system test __init__() method.  This is to bring this into the same design as the relaxation dispersion tests which require the NMRPipe showApod software.  Now the test suite will list either [[Dasha]] or [[Modelfree4]] in the skipped test table if they are not installed.
 * Adding another statistic method to plot for multi-data sets.  [https://gna.org/task/?7826 Task #7826: Write a Python class for the repeated analysis of dispersion data].
 * More adding of matplotlib snippets for plotting intermediate data.  [https://gna.org/task/?7826 Task #7826: Write a Python class for the repeated analysis of dispersion data].

@@ Line 209: / Line 209: @@
 * Added checks to the [http://www.nmr-relax.com/api/3.3/test_suite.system_tests.bmrb.Bmrb-class.html#test_bug_22704_corrupted_state_file Bmrb.test_bug_22704_corrupted_state_file system test].  This is to see if the cdp.exp_info data structure has been correctly restored from the save file.
 * Uncommented some checks in the [http://www.nmr-relax.com/api/3.3/test_suite.system_tests.bmrb.Bmrb-class.html#test_bug_22704_corrupted_state_file Bmrb.test_bug_22704_corrupted_state_file system test].
-* For relaxation dispersion, modified that the grid search and linear constraints for parameter k<sub>AB</sub> is between 0-100.  The parameter is only used in the [[TSMFK01]] model.  The k<sub>AB</sub> parameter is only for very slow forward exchange rate.  The expected values should according to the reference paper:   {{#lst:Citations|Tollinger01}}.  The paper concerns values of k<sub>AB</sub> in the region 0.1 to 5.0.  If the exchange rate is any higher value of this, then another model should be used for the analysis.
+* For relaxation dispersion, modified that the grid search and linear constraints for parameter k<sub>AB</sub> is between 0-100.  The parameter is only used in the [[TSMFK01]] model.  The k<sub>AB</sub> parameter is only for very slow forward exchange rate.  The expected values should according to the reference paper:  [Tollinger et al., 2001].  The paper concerns values of k<sub>AB</sub> in the region 0.1 to 5.0.  If the exchange rate is any higher value of this, then another model should be used for the analysis.
 * Set the default insignificance value to 0.0 instead of 1.0.  [https://gna.org/task/?7826 Task #7826: Write a Python class for the repeated analysis of dispersion data].
 * Modified the grid search limits for parameter k<sub>AB</sub> to be between 0.1 and 20.0 rad.s<sup>-1</sup>.  This is for the [[TSMFK01]] model, where values much above 10/20 is not expected.
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 {{:relax release announcements}}

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 | type    = Minor feature and bugfix
 | date    = 9 October 2014
 }}

@@ Line 9: / Line 9: @@
 }}
-= Description =
+== Description ==
 <section begin=description/>
@@ Line 15: / Line 15: @@
 <section end=description/>
-= Download =
+== Download ==
 <section begin=download/>
@@ Line 21: / Line 21: @@
 <section end=download/>
-= CHANGES file =
+== CHANGES file ==
 <section begin=metadata/>
@@ Line 29: / Line 29: @@
 <section end=metadata/>
-== Features ==
+=== Features ===
 <section begin=features/>
@@ Line 47: / Line 47: @@
 <section end=features/>
-== Changes ==
+=== Changes ===
 <section begin=changes/>
@@ Line 288: / Line 288: @@
-== Bugfixes ==
+=== Bugfixes ===
 <section begin=bugfixes/>
@@ Line 309: / Line 309: @@
 <section end=bugfixes/>
-= Links =
+== Links ==
 <section begin=links/>
@@ Line 324: / Line 324: @@
 <section end=links/>
-= Announcements =
+== Announcements ==
 {{:relax release announcements}}
-= See also =
+== See also ==
 * [http://www.nmr-relax.com/api/3.3/ The relax 3.3 API documentation]
 {{:relax release see also}}
 [[Category:Relaxation dispersion analysis]]

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 {{lowercase title}}
-{{relax release infobox
+{{infobox relax release
 | version = 3.3.1
 | prev    = 3.3.0