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In the current master the settings
- `DOT_TRANSPARENT` and `FORNULA_TRANSPARENT` are obsolete.
- `DOT_FONTNAME` / `DOT_FONTSIZE` are incorporated into the new `...ATTR` settings
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Ignore complete current build directory when building documentation
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Found the file
```
build/CMakeFiles/ShowIncludes/foo.h
```
during the build of the documentation. The build directory should be excluded.
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In e,g, https://gudhi.inria.fr/doc/latest/struct_coefficient_field.html (in general in `../struct_coefficient_field.html`) we see lines like:
```
#include </home/gailuron/workspace/gudhi/gudhi-devel/build/gudhi.3.5.0/concept/Persistent_cohomology/CoefficientField.h>
```
and
```
The documentation for this struct was generated from the following file:
/home/gailuron/workspace/gudhi/gudhi-devel/build/gudhi.3.5.0/concept/Persistent_cohomology/CoefficientField.h
```
instead of the relative names:
```
#include <src/Persistent_cohomology/concept/CoefficientField.h>
```
and
```
The documentation for this struct was generated from the following file:
src/Persistent_cohomology/concept/CoefficientField.h
```
(the links are pointing to the correct places in all cases.)
This is corrected by stripping the path.
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Doxygen only
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issue #613 [cpp documentation] Footer needs to be generated with a more recent version of doxygen
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recent version of doxygen
The problem was that the update of the treeview was not called in the footer, though after correcting this some new problems occurred in respect to the treeview (the small pointers ran into the text) and with the in page table of cvontents (e.g. in installation.html).
- footer.html: call proper update function by means of `<div>`, as base the 1.9.4 version served but also older version work.
- stylesheet.css, Doxyfile.in: implemented as extra stylesheet and for the "small pointer" problem adjusted the `.arrow` settings
- header.html:
- placed the `<link rel="stylesheet" type="text/css" href="https://gudhi.inria.fr/assets/css/styles_feeling_responsive.css" />` more as an extra stylesheet as otherwise a second scrollbar would occur
- placed the `div id="top">` at the right place
- corrected `<img>` tag so it is properly closed (so XML compliant)
- corrected setting of `data-topbar` to `data-topbar=true` as HTML5 does not allow attributes without values.
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Documentation: Render formulas by means of MathJax 3
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Since doxygen version 1.9.3 the settings `CLASS_DIAGRAMS` and `CLASS_GRAPH` have been integrated into `CLASS_GRAPH` and `CLASS_DIAGRAMS` is now obsolete.
The value of `CLASS+GRAPH` doesn't have to be adjusted, in this case, as it was already set to `NO`.
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Based on review, made a switch between MathJax 2 and MathJax 3 based on the doxygen version
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- create entries in Doxyfile.in for the use of MathJax
- adjust formula so it is properly rendered in MathJax 3 (formula will also work with MathJax 2)
(available in doxygen since doxygen 1.9.2)
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In case we have the files`Bitmap_cubical_complex/Random_bitmap_cubical_complex.cpp` this will be linked to `_random_bitmap_cubical_complex_8cpp-example.html` and this is now hard coded.
When the setting of `CASE_SENSE_NAMES` is set to `YES` the mapping is to `Random_bitmap_cubical_complex_8cpp-example.html` but the hard coded link is still to `_random_bitmap_cubical_complex_8cpp-example.html` so the link cannot be resolved (at runtime!). Same could happen when the `CASE_SENSE_NAMES` is left blank and the the value is system dependent. It is unlikely that this happens but ...
By introducing the `ALIASES` `gudhi_example_link` this can be handled by doxygen in a more transparent way.
Furthermore wit 2 examples there was a double `cpp` in the text part, this has been corrected as well
Notre this solution supersedes #621 and maked #621 obsolete.
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Based on review corrected `EXAMPLE_PATH` and `CITE_BIB_FILES`.
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When running doxygen on the sources we get (a.o.) the following warnings:
```
.../gudhi-devel/src/Contraction/include/gudhi/Edge_contraction.h:214: warning: unbalanced grouping commands
.../gudhi-devel/src/common/doc/examples.h:3: warning: the name 'Examples' supplied as the argument in the \file statement is not an input file
error: bib file .../gudhi-devel/biblio/how_to_cite_gudhi.bib not found!
.../gudhi-devel/src/common/doc/installation.h:271: warning: included file biblio/how_to_cite_gudhi.bib is not found. Check your EXAMPLE_PATH
```
This is corrected in the different files and in the settings in src/Doxyfile.in
Also there are a number of settings that are obsolete like:
```
warning: Tag 'LATEX_SOURCE_CODE' at line 1835 of file '.../gudhi-devel/build_windows_fork/Doxyfile' has become obsolete.
```
This is corrected in the src/Doxyfile.in file
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version required. Modification of documentation accordingly
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instead of geomview.org documentation. Modify data/points/alphacomplexdoc.off in dimension 3 to be used as an example for OFF section in file format.
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module process
Doxyfile.in generates a build/src/Doxyfile that is copied by the user_version target (to avoid file generation in sources)
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ninja_cmake_warning_fix_vincent@3748 636b058d-ea47-450e-bf9e-a15bfbe3eedb
Former-commit-id: 0a5ab637c2db102a59c994f03f0ec7fadbda3780
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