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Cech optimization
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-Some other minor changes
-Change license to LGPL
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[Alpha] Get extra point using boundary_opposite_vertex_simplex_range
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Fetch datasets
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in alpha
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in cech
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Documentation: Obsolete CLASS_DIAGRAMS
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No need to copy Doxyfile.in
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Fix unbalanced groups and some doxygen typos
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VincentRouvreau/simplex_tree_extended_persistence_enhancement
extended_persistence uses directly get_persistent_pairs
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Spelling corrections
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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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VincentRouvreau/stree_iterator_boundary_and_opposite_vertex
Boundary and its opposite vertex iterator for the simplex tree
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