In doxygen the setting `HTML_COLORSTYLE` has been introduced with as default `AUTO_LIGHT` but due to the current strategy of CGAL in respect to HTML stylesheets the divider between the treeview and the text is not properly visible anymore. Due to the same strategy the setting to `AUTO_LIGHT` does not make sense for CGAL.
When setting `HTML_COLORSTYLE=LIGHT` the divider is properly visible again.
Based on the problems with the line numbers in some warnings, see review of https://github.com/CGAL/cgal/pull/6688 one of the problems was the `ALIASES` for figures, here we have the code `\latexonly ^^ \endlatexonly` though the code in the `\latexonly` part should be LaTeX commands. Here the "attempted" newline is not necessary at all so the `^^` can be removed leaving an empty `\latexonly` part that can be removed as well.
There are a number of other numbering problems found in https://github.com/CGAL/cgal/pull/6688 but they are on the doxygen side as a proposed pull request https://github.com/doxygen/doxygen/pull/9465 has been submitted.
Update of documentation in respect of code fragments
- making code fragments work in footnotes
- placing some words in in code tags
- completing some words to code tags
- removing some `#` as they are not necessary
- don't show obfuscation code in email
In the BGL package we get a warning like:
```
/home/cgal-testsuite/cgal_doc_build/CGAL-5.4-Ic-33/doc/BGL/PackageDescription.txt:29: warning: ignoring \dot command because HAVE_DOT is not set
```
The BGL package uses the `\dot` and has now to use the setting `HAVE_DOT=YES` to see the dot image.
Till now this went OK as the `\dot` command didn't look at the setting of the `HAVE_DOT` setting in the Doxyfile, though by the issue https://github.com/doxygen/doxygen/issues/7273 and the pull request https://github.com/doxygen/doxygen/pull/8663 it is now required that `HAVE_DOT` is set.
The idea of setting `HAVE_DOT` for the BGL project removed the warning (and shows the figure again) though has also as side effect that the inheritance graphs are shown. Until now CGAL shows for the inheritance just the text version.
Doxygen now has for the `CLASS_GRAPH` setting the possibility `TEXT` that does exactly what is required.
Due to the general setting of `HAVE_DOT` also the not needed `graph_legend` was generated and some `INCLUDE_GRAPH`s, by setting this to `NO ` these are no suppressed as well.
```
warning: Tag 'LATEX_SOURCE_CODE' at line 1971 of file '.../doc_dxy/BaseDoxyfile' has become obsolete.
To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
warning: Tag 'RTF_SOURCE_CODE' at line 2061 of file '.../doc_dxy/BaseDoxyfile' has become obsolete.
To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
warning: Tag 'DOCBOOK_PROGRAMLISTING' at line 2166 of file '.../BaseDoxyfile' has become obsolete.
To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
```
these tags have been declared obsolete (in the current master version), so they should be removed..
CGAL doesn't use the involved formats so this has no influence on the CGAL documentation processing.
In pull request #4644 a central MATHJAX_CODEFILE was introduced, but the snap rounding package was omitted, so this is corrected here.
For the MathJax V3 ( see #5707) this change is even mandatory (the current construct doesn't work).
Below the bottom blue block we see for the packages some extra white space. For the Manual page this white space is not present.
The reason is the placing of the "hack.js" code.
Laurent Rineau
Sébastien Loriot
albert-github
Mael Rouxel-Labbé
Dmitry Anisimov
Dmitry Anisimov
Maxime Gimeno