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More external link formatting, and addition of links to the HTML manual.
* Added .pyc and .so files to be ignored.
* Fix for [http://www.nmr-relax.com/api/4.1/dep_check-module.html dep_check], when packages has an appended release candidate number. For example: numpy 1.8.0rc1.
* Added a script to check for copyright notice compliance to the FSF standard. This standard is from [https://www.gnu.org/prep/maintain/html_node/Copyright-Notices.htmlFSF standard].
* Support for multiple git and svn repositories in the FSF copyright notice compliance checking script.
* Collection of all commits to attribute to other authors. This is for the FSF copyright notice compliance checking script.
* Renamed the LGPLv3 file in the extern.sobol package to COPYING.LESSER.
* Updated all of the minfx project links from Gna! to the SourceForge site.
* Updated all of the relax deployment scripts for the Gna! shutdown. These now use the SourceForge sites for [https://sourceforge.net/projects/nmr-relax/ relax], [https://sourceforge.net/projects/minfx/ minfx], and [https://sourceforge.net/projects/bmrblib/ bmrblib ] instead. The svn to git conversion is also taken into account, and git is used to pull in the latest relax code from the SourceForge mirror.
* Converted a large number of Gna! links to point to the equivalent Web Archive URL. Most of these links should have had a snapshot made in the Internet Archive Wayback Machine.
* Added some hyperlinks to the external programs listed in the intro chapter of the user manual.
* Added relaxation dispersion to the list of all data pipe types in the intro chapter.
* Improvements to the script UI text in the intro chapter.
* Linked to the internal Gna! mailing list archives for the multi-processor announcement. This is for [http://www.nmr-relax.com/mail.gna.org/public/relax-devel/2007-05/msg00000.htmlinternal Gna! mailing list archives for the multi-processor announcement].
* Added new sections to the infrastructure and development chapters about the Gna! shutdown. This is to warn that the information in these chapters of the manual is out of date.
* Updated the NESSY link to point to the new SourceForge location for the project.
* Improved the help to settings in XQuartz when running Docker on a mac and accessing the OpenDX GUI.
* Renamed the extern.sobol.sobol_lib-not_tested module to sobol_lib_untested. This is in preparation for updating to the newest upstream code.
* Updated the extern.sobol package to the latest upstream code. This is the new MIT licensed code (which was previously LGPL licensed) from [http://people.sc.fsu.edu/~jburkardt/py_src/sobol/sobol.htmlnew MIT licensed code] (which was previously LGPL licensed). The licence text has been modified to suit the licence change, and the LGPL copyright notices dropped from all files. The Python 3 updates to the relax version of the package have been transferred into the new code.
* Added the MIT licence with copyright notices to the top of all files. The origin of all code was traced back through the MATLAB sources, FORTRAN90 sources, and FORTRAN77 sources. The original f77 code did not contain any shared lines of code with the f90 code, so no copyright statements for Bennett Fox were added. Comments were added to each function to document the history of all of the code.
* Easier reading of the Dockerfile.
* Updated the general relax copyright notice for 2018. This last copyright year is now stored as info.copyright_final_year.
* Clarified the GPLv3+ licensing in the relax introduction string.
* Manual: Addition of a GPLv3+ copyright notice to a [http://www.nmr-relax.com/manual/index.html second title page].
* Another Oxygen Icon licensing text fix in the README files.
* Improved the LGPLv3+ licensing text for the base directory of the Oxygen Icons.
* Manual: Added the LGPLv3+ copyright notice for the Oxygen Icons to the [http://www.nmr-relax.com/manual/index.html second title page].
* Documentation for the copyright and public domain notices for 3D structures. This is to explain why the strict format text files are not modified to include notices, hence they are placed in the README file, and detailing the public domain nature of the Protein Data Bank repository.
* Updated the script for Docker images.
* Scons: Fixes for the manual compilation. The relax manual cannot be compiled if one of the sys.path values contains a 'docs/' directory. Instead of appending the relax docs/ path to sys.path, it is now prepended. The documentation Python module __all__ lists have also been filled out.
* Renamed the [http://www.nmr-relax.com/api/4.1/version-module.html#version relax default repository version] from "repository checkout" to "repository commit". This general text is more appropriate for a git repository.
* Manual: Removed a Gna! reference in the [http://www.nmr-relax.com/manual/Introduction.html intro chapter].
* Manual: Alias creation for the relax mailing lists. This is to allow for a centralised place for changing the mailing list name, if any changes occur to the mailing list in the future.
* [http://www.nmr-relax.com/manual/Free_software_infrastructure.html Manual, Ch. Infrastructure]: Converted the Gna! shutdown note into a new 'History' section. A lot of the relax free software/open source infrastructure history is now documented.* [http://www.nmr-relax.com/manual/Free_software_infrastructure.html Manual, Ch. Infrastructure]: Removed the Gna! information from the relax website section.* [http://www.nmr-relax.com/manual/Free_software_infrastructure.html Manual, Ch. Infrastructure]: Updated the relax mailing list information from Gna! to SourceForge. This is now all through LaTeX aliases, so infrastructure changes should be easier to deal with in the future.* [http://www.nmr-relax.com/manual/Free_software_infrastructure.html Manual, Ch. Infrastructure]: Abstracted the bug reporting section using aliasing. This removes all Gna! specific links from the chapter, shifting them to SourceForge links in the main relax.tex file.* [http://www.nmr-relax.com/manual/Free_software_infrastructure.html Manual, Ch. Infrastructure]: Abstract the relax repository section and switch from svn to git. This removes all Gna! specific links from the chapter, shifting them to SourceForge links in the main relax.tex file.* [http://www.nmr-relax.com/manual/Free_software_infrastructure.html Manual, Ch. Infrastructure]: Removal of the news section, as this is not supported on SourceForge.* [http://www.nmr-relax.com/manual/Free_software_infrastructure.html Manual, Ch. Infrastructure]: Abstract the distribution archive section and switch from svn to git. This removes all Gna! specific links from the chapter, shifting them to SourceForge links in the main relax.tex file.* [http://www.nmr-relax.com/manual/Installation_instructions.html Manual, Ch. Installation]: Abstraction of the bug tracker links. This replaces the dead Gna! links to the current SourceForge links.* [http://www.nmr-relax.com/manual/The_N_state_model_or_ensemble_analysis.html Manual, Ch. N-state model]: Abstraction of the relax-users mailing list.* [http://www.nmr-relax.com/manual/Relaxation_dispersion.html Manual, Ch. Dispersion]: Dead link and mailing list fixes. The mailing lists are now abstracted using aliases, some old dead links have been removed, and some Gna! support request links have been converted to Internet Archive links.* [http://www.nmr-relax.com/manual/relax_development.html Manual, Ch. Development]: Removal of the note about the Gna! shutdown. The chapter is about to be updated for the switch to SourceForge, so this note is no longer needed.* [http://www.nmr-relax.com/manual/relax_development.html Manual, Ch. Development]: Aliases for the mailing lists and addition of a cross reference.* [http://www.nmr-relax.com/manual/relax_development.html Manual, Ch. Development]: Converted the version control section from SVN to git.* [http://www.nmr-relax.com/manual/relax_development.html Manual, Ch. Development]: Minor edits to the coding conventions section.
* Adding exit codes for the unit and system tests. This is for Travis to fail if these fail. In Windows these can be seen with: echo Exit Code is %errorlevel%
* [http://www.nmr-relax.com/manual/relax_development.html Manual, Ch. Development]: Removal of the section describing creating and submitting patches.* [http://www.nmr-relax.com/manual/relax_development.html Manual, Ch. Development]: Section rearrangement in preparation for new text.* [http://www.nmr-relax.com/manual/relax_development.html Manual, Ch. Development]: svn to git and infrastructure abstraction in the Committers section. All references to svn have been changed to git. And the Gna! infrastructure has been abstracted to aliases in the main relax.tex file so that future infrastructure changes are easier to deal with. In addition, many edits of the text have been made.* [http://www.nmr-relax.com/manual/relax_development.html Manual, Ch. Development]: Expansion of the relax repository section.* [http://www.nmr-relax.com/manual/relax_development.html Manual, Ch. Development]: Minor edits to the relax repository git mirror section.* [http://www.nmr-relax.com/manual/relax_development.html Manual, Ch. Development]: Editing of the source code repository section.* [http://www.nmr-relax.com/manual/relax_development.html Manual, Ch. Development]: Added links to the web interfaces for all relax mirror sites.
* Fixing the return value of execution of unit and system tests.
* [http://www.nmr-relax.com/manual/relax_development.html Manual, Ch. Development]: New subsection and editing of the relax repository section. An initial section describing git version control and listing all relax repositories has been added.* [http://www.nmr-relax.com/manual/Free_software_infrastructure.html Manual, Ch. Infrastructure]: Updated the relax repository section to include the website and demo.* [http://www.nmr-relax.com/manual/relax_development.html Manual, Ch. Development]: Complete rewrite of the 'Submitting changes to the relax project' section. This converts the Subversion instructions to git, and switches from Gna! to the aliased primary relax infrastructure.* [http://www.nmr-relax.com/manual/relax_development.html Manual, Ch. Development]: Converted the SCons section from SVN to git, and removed Gna! references.* [http://www.nmr-relax.com/manual/relax_development.html Manual, Ch. Development]: Major editing of the 'Core design of relax' section. This section is now significantly improved. There was a lot of old information, some dating back to the pre-relax 3.0 designs. And a lot of new information has been added to expand on all of the descriptions.* [http://www.nmr-relax.com/manual/relax_development.html Manual, Ch. Development]: Minor editing of the tracker section.* [http://www.nmr-relax.com/manual/relax_development.html Manual, Ch. Development]: Updated the very out of date links section. This was incredibly out of date. The links have been updated to include everything listed at http://www.nmr-relax.com/links.html.* [http://www.nmr-relax.com/manual/Index.html Manual, Index]: Removed the no longer relevant svnmerge.py entry.
* Simplify Travis file.
* Added travis-ci support for Python 3.7 and OSX. Adding notifications from builds att travis-ci.com to nmr-relax-devel att lists.sourceforge.net. This is after inspiration from https://github.com/WeblateOrg/translation-finder/blob/master/.travis.yml. Windows can not be added due to unknown compile error.
