Difference between revisions of "Relax 3.1.6"

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(Category link updates for the specific analyses.)
(Links to Troels' Gna! page.)
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*  Epydoc docstring fix for the pipe_control.structure.main.load_spins() function.
 
*  Epydoc docstring fix for the pipe_control.structure.main.load_spins() function.
 
*  Created the Mf.test_bug_21615_incomplete_setup_failure GUI tests.  This is designed to catch [https://gna.org/bugs/?21615 bug #21615] as reported by Ivan Leung (ivanhoe dott leung att chem dott ox dot ac dot uk).  Included are the data files Ivan attached to the bug report truncated to two residues.  The GUI test follows exactly the steps outlined by Ivan.
 
*  Created the Mf.test_bug_21615_incomplete_setup_failure GUI tests.  This is designed to catch [https://gna.org/bugs/?21615 bug #21615] as reported by Ivan Leung (ivanhoe dott leung att chem dott ox dot ac dot uk).  Included are the data files Ivan attached to the bug report truncated to two residues.  The GUI test follows exactly the steps outlined by Ivan.
*  Deleted the ancient, unused 'quit' argument of the relax interpreter object.  This code was identified in a post by Troels Linnet at http://thread.gmane.org/gmane.science.nmr.relax.devel/5000/focus=5003.  This argument never worked correctly and has not been used for many, many years.  Many code paths in relax needed to be updated to remove the argument.
+
*  Deleted the ancient, unused 'quit' argument of the relax interpreter object.  This code was identified in a post by [https://gna.org/users/tlinnet Troels Linnet] at http://thread.gmane.org/gmane.science.nmr.relax.devel/5000/focus=5003.  This argument never worked correctly and has not been used for many, many years.  Many code paths in relax needed to be updated to remove the argument.
 
*  Shifted the pedantic flag to escalate flag. The option -p would instead be used for the option --prompt.  Fix for [https://gna.org/support/?3117 sr #3117 - Functionality to inspect interactively after running script - The equivalence to python -i].
 
*  Shifted the pedantic flag to escalate flag. The option -p would instead be used for the option --prompt.  Fix for [https://gna.org/support/?3117 sr #3117 - Functionality to inspect interactively after running script - The equivalence to python -i].
 
*  Added the -p --prompt option for running a relax script and inspect interactively.  Fix for [https://gna.org/support/?3117 sr #3117 - Functionality to inspect interactively after running script - The equivalence to python -i].
 
*  Added the -p --prompt option for running a relax script and inspect interactively.  Fix for [https://gna.org/support/?3117 sr #3117 - Functionality to inspect interactively after running script - The equivalence to python -i].
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*  Added the unit test infrastructure for testing the specific_analyses.relax_disp package.  This currently includes the package __all__ list unit test.
 
*  Added the unit test infrastructure for testing the specific_analyses.relax_disp package.  This currently includes the package __all__ list unit test.
 
*  Updated the specific_analyses.relax_disp package __all__ list.  This was identified in the previously committed unit test.
 
*  Updated the specific_analyses.relax_disp package __all__ list.  This was identified in the previously committed unit test.
*  Added the infrastructure for the unit tests of the specific_analyses.relax_disp.disp_data module.  This is in response to the post http://thread.gmane.org/gmane.science.nmr.relax.scm/19963/focus=5046 by Troels, and is described in my response at http://thread.gmane.org/gmane.science.nmr.relax.scm/19963/focus=5048.
+
*  Added the infrastructure for the unit tests of the specific_analyses.relax_disp.disp_data module.  This is in response to the post http://thread.gmane.org/gmane.science.nmr.relax.scm/19963/focus=5046 by [https://gna.org/users/tlinnet Troels], and is described in my response at http://thread.gmane.org/gmane.science.nmr.relax.scm/19963/focus=5048.
 
*  Created two new LaTeX commands for improving the layout of Python code in the relax manual.  These are \pysep and \pyus which will be used to format the Python module separator character and the Python underscore character respectively.  They are used in the \module{}, \pycode{}, etc.  commands to add the '.\linebreak[0]' and '\_\linebreak[0]' text to allow for improved and consistent line breaking.
 
*  Created two new LaTeX commands for improving the layout of Python code in the relax manual.  These are \pysep and \pyus which will be used to format the Python module separator character and the Python underscore character respectively.  They are used in the \module{}, \pycode{}, etc.  commands to add the '.\linebreak[0]' and '\_\linebreak[0]' text to allow for improved and consistent line breaking.
 
*  Complete reformatting of the base LaTeX files.  The paragraph structure has been changed so that each sentence now starts on a new line.  This is for better tracking of changes (via 'svn diff' for example), for better searchability of certain text elements using command line tools such as 'grep', and for easier easier use of the 'sed' tool.  The change tracking is most important as it allows for finer granularity - a small change will now only be shown as a change in one sentence rather than the whole paragraph, allowing the change to be identified more easily.  It also allows for easier commit maintenance.
 
*  Complete reformatting of the base LaTeX files.  The paragraph structure has been changed so that each sentence now starts on a new line.  This is for better tracking of changes (via 'svn diff' for example), for better searchability of certain text elements using command line tools such as 'grep', and for easier easier use of the 'sed' tool.  The change tracking is most important as it allows for finer granularity - a small change will now only be shown as a change in one sentence rather than the whole paragraph, allowing the change to be identified more easily.  It also allows for easier commit maintenance.

Revision as of 17:38, 12 September 2014


Description

This is a major feature and bugfix release. A comprehensive tutorial has been added to the relaxation dispersion chapter of the manual which shows, step-by-step, the dispersion analysis in the GUI using screenshots. Other changes include improved PDB chain ID support, a new mode for running a relax script and then entering the prompt UI mode, multiple file reading by the spectrum.read_intensities user function, and improvements to the relaxation dispersion analysis. A number of major bugs in the dispersion analysis concerning different relaxation delay times for different experiments and for improved handling of the offset have also been fixed. A number of important GUI bugs have also been fixed. All users are recommended to upgrade to this version of relax.


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).


CHANGES file

Version 3.1.6
(28 February 2014, from /trunk)
http://svn.gna.org/svn/relax/tags/3.1.6


Features

  • Full support for PDB chain IDs in the internal structural object.
  • Improvements for the devel_scripts/python_seek.py for finding all installed Python versions and modules. Individual modules can now be specified on the command line.
  • The pedantic command line option -p, --pedantic has been renamed to -e, --escalate.
  • The new prompt command line option -p, --prompt causes the relax prompt mode to launch after running a script to allow relax to be inspected interactively.
  • Better organisation of the relax command line options into groups, as shown by running 'relax -h'.
  • A tutorial for using the relaxation dispersion analysis in the GUI has been added to the manual. This includes step-by-step instructions with many screenshots.
  • Improvements to the manual including better and consistent line breaking for the GUI menu item text, user functions, file and directory paths, and Python module paths.
  • The spectrum.read_intensities user function can now load multiple files simultaneously, allowing for simplified use in the GUI.
  • Addition of a new GUI window element for loading multiple files.
  • Improvements to the sequence data input GUI window including the item count being displayed and a 'Delete' button to remove the last element.
  • Improvement for the relaxation dispersion auto-analysis - the names of the automatically created data pipes are now unique by appending the name of the data pipe bundle to the end. This allows multiple dispersion auto-analyses to exist simultaneously in the GUI or within one relax state file.
  • The relaxation dispersion analysis now handles deselected spins.
  • Improved colour coding of relax log messages in the relax manual.
  • The relaxation dispersion auto-analysis now creates the chi2.out text file. This is for more easily comparing the chi-squared values between analyses.


Changes


Bugfixes


Links

For reference, the following links are also part of the announcement for this release:


Announcements

If you would like to receive announcements about new relax versions, please subscribe to the relax announcement mailing list. This list only receives ~10 emails per year. It is archived at the SourceForge archives and in The Mail Archive.


See also