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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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documentation
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VincentRouvreau/persistence_graphical_tools_improvements
Persistence graphical tools improvements
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option)
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dirname and filename
Modify remote fetching test
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contains the extra point, a bool is enough
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Use Filtration_value instead of double for casting
Use a templated range of points instead of vector in cech constructor
Capitalize sphere_circumradius.h file name and make it private in doc
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cech_complex_example_from_points.cpp
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