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Spelling corrections
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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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Co-authored-by: Vincent Rouvreau <10407034+VincentRouvreau@users.noreply.github.com>
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Documentation: handling references to examples in a more transparent way
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In my opinion there is no need to copy the `Doxyfile.in` file to the build directory (neither in the User nor the development version).
The usage is:
```
configure_file(${GUDHI_DOXYGEN_SOURCE_PREFIX}/Doxyfile.in "${CMAKE_CURRENT_BINARY_DIR}/Doxyfile" @ONLY)
```
in the file `src/cmake/modules/GUDHI_doxygen_target.cmake` and we see that this uses the file from its original source directory.
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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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Oops left test version in it.
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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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Adding the other examples also with `gudhi_example_link`.
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Documentation: Non persistent links
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Co-authored-by: Marc Glisse <marc.glisse@inria.fr>
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Documentation: Updating redirected links
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Co-authored-by: Marc Glisse <marc.glisse@inria.fr>
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Co-authored-by: Marc Glisse <marc.glisse@inria.fr>
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Co-authored-by: Marc Glisse <marc.glisse@inria.fr>
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Co-authored-by: Marc Glisse <marc.glisse@inria.fr>
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A number of spelling corrections as reported by the codespell (see: https://github.com/codespell-project/codespell) program and lists.
Some remarks:
- not considered are grammatical errors
- not considered are names in the code although there are a number that could be improved (like `childs` -> `children`)
- in the documentation it could be made clearer what are variables and what is running text (e.g. by placing variables in running text between backticks)
- some comments are in the French language, I think it would be better to have them in the English (United States version).
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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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During the link check we found some references to `#title..` in respect to links to CGAL, these links work at the moment but are, by CGAL, generated links during runtime based on the HTML `<H...>` tags.
When a new paragraph or chapter is added these numbers will change and thus will the link point to the wrong place. All these items have also a more persistent reference anchor that is generated based on the `<name>` of the section (e.g. `\section <name> <description>`).
Therefore it is better to used the references based on the `<name>`.
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Updating simple links in documentation sources for which we got during link checking:
```
This is a permanent redirect. The link should be updated.
```
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Made references to boost so that they point to the last released version.
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After review:
- option is now:
```
-DWITH_GUDHI_CPP_DOCUMENTATION_ONLY=ON
```
- added some instructions to the installation description.
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VincentRouvreau/stree_iterator_boundary_and_opposite_vertex
Boundary and its opposite vertex iterator for the simplex tree
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Documentation: Warning about return statement
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Based on review corrected `EXAMPLE_PATH` and `CITE_BIB_FILES`.
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When running doxygen over the sources we get the warnings like:
```
.../gudhi-devel/src/Skeleton_blocker/include/gudhi/Skeleton_blocker_complex.h:1073: warning: found documented return type for Gudhi::skeleton_blocker::Skeleton_blocker_complex::remove_popable_blockers that does not return anything
```
The functions are `void` functions so should not have a return value.
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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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given as an input
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