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Changes
relax release notes links.
<section begin=features/>
* Initial auto-analysis support for a highly repetitive protocol for analysing relaxation dispersion data.
* Addition of the docs/user_function_changes.txt file which documents all user function changes from [[relax 1.0.1 ]] to [[relax 3.3.1 |3.3.1]] to help with upgrading scripts to newer relax versions.* Updated the translation table used to identify no longer existing user functions and explain what the new user function is called for all relax versions from [[relax 1.3.1|1.3.1 ]] to [[relax 3.3.1|3.3.1]].
* The [http://www.nmr-relax.com/manual/structure_delete.html structure.delete user function can now delete individual models as well as select atoms in individual models].
* Addition of the [http://www.nmr-relax.com/manual/error_analysis_covariance_matrix.html error_analysis.covariance_matrix user function for determining parameter errors via the covariance matrix]. This is currently only implemented for the relaxation curve-fitting analysis.
* Further extended the protocol for repeated dispersion analysis. [https://gna.org/task/?7826 Task #7826: Write a Python class for the repeated analysis of dispersion data].
* Extended the system test for the protocol for repeated dispersion analysis. [https://gna.org/task/?7826 Task #7826: Write a Python class for the repeated analysis of dispersion data].
* Added a relaxation dispersion model profiling log file for relax version [[relax 3.3.0 |3.3.0]] vs. [[relax 3.2.3|3.2.3]]. This is the output from the dispersion model profiling master script. These numbers will be used for the [[relax 3.3.0 ]] release notes (http://wiki.nmr-relax.com/Relax_3.3.0).* Fixes for the [[relax 3.3.0 ]] vs. [[relax 3.2.3|3.2.3 ]] dispersion model profiling log file. The numeric model numbers were incorrectly scaled and a factor of 10 too high.
* Fixes for the scaling factors in the dispersion model super profiling script.
* Editing of the [[relax 3.3.0 ]] features section of the CHANGES file. This will be used for the release notes.
* Added more test data for the repeated analysis. [https://gna.org/task/?7826 Task #7826: Write a Python class for the repeated analysis of dispersion data].
* Updated the Baldwin 2014 reference in the relax manual. The pybliographic software was used to format this BibTeX entry (http://pybliographer.org/). This was updated as volume and page number information is now available.
* Updated the release checklist document, including adding a section about cross-linking. The cross-linking is important for search engine indexing.
* Created a simple script for printing out the names of all user functions.
* Added listings of all user functions from relax version [[relax 2.0.0|2.0.0 ]] all the way to [[relax 3.3.0]]. This will be used to look at how the user function names have changed with time.
* Added a script and log file for comparing relax user function differences between versions.
* Created a document for relax users which follows the changes to the user function names.
* Created a script for printing out relax 1.3 user functions.
* Stripped out all of the relax intro and script printouts from the user function listing files. This allows the diff.py script to be simplified.
* Updated the relax 1.3 user function printout script and added many printouts. The printouts are for relax versions [[relax 1.3.5 |1.3.5]] to [[relax 1.3.16|1.3.16]]. The earlier relax versions used the relax 1.2 user function setup.* Created a script for printing out all user functions for relax 1.2 versions. This also includes the [[relax 1.3.0 ]] to [[relax 1.3.4 ]] versions.* Added the [[relax 1.3.0 ]] to [[relax 1.3.4 ]] user function printouts.
* Changed the behaviour of the script for showing user function difference between relax versions. The relax versions are now reversed so the oldest version is at the bottom of the difference printout.
* Added the [[relax 1.0.1 ]] to [[relax 1.2.15 ]] user function printouts. The diff.log file has also been updated with all of these versions.* Updated the user_function_changes.txt document. This now lists all changes in the user function naming from relax version [[relax |1.0.1 ]] all the way to [[relax 3.3.0]].
* Added all remaining user function ranamings since relax 2.0.0 to the translation table. These were taken directly from the docs/user_function_changes.txt document.
* Added all user function ranamings since [[relax 1.3.1 ]] to the translation table. These were taken directly from the docs/user_function_changes.txt document. Earlier relax versions are far too different, so this will be the earliest relax version for this translation table. The relax 1.2 and earlier (and [[relax 1.3.0|1.3.0]]) versions used the run argument throughout and the scripting was so different, that telling the user how to upgrade to new user functions is pointless. And the release date of [[relax 1.2.15]], the last of these old designs was in November 2008.
* Changed the order of the two relax versions being compared for user function changes. This is in the diff.py script and log file and the user_function_changes.txt document.
* Changed the organisation of the files in the docs/ directory. A new docs/devel directory has been created and the 2to3_checklist, Mac_framework_build_3way, package_layout, and prompt_screenshot.txt documents shifted into it. This is to hide or abstract away the development documents so that relax users do not see them when looking into docs/. This should make the directory less intimidating.
* Critical fix for k_AB not belonging to list of global parameters. k_AB was only changed to the spin of interest, but not for the rest of the cluster. When the parameter vector is assembled, "assemble_param_vector(spins=spins)" it takes the global parameter from spin 0. [https://gna.org/bugs/?22754 Bug #22754: The minimise.calculate user function does not calculate χ<sup>2</sup> value for clustered residues].
* Improvements for PDB creation in the relax library for out of bounds structural coordinates. The lib.structure.pdb_write module atom() and hetatm() functions will now more gracefully handle atomic coordinates which are outside of the PDB limits of [-999.999, 9999.999]. When such coordinates are encountered, instead of producing a too long PDB line which does not pass the validation step, the functions will set the coordinates to the boundary value. This will at least allow a valid PDB file to be created, despite the warping of the coordinates.
* Expanded the list of global dispersion parameters in the set_param_values() API method. This is a quick expansion of Troels' fix for the k_AB parameter to allow for the release of [[relax 3.3.1]]. This is a small part of the discussion at http://thread.gmane.org/gmane.science.nmr.relax.scm/23948/focus=7188.
<section end=bugfixes/>