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Proposal for how_to_cite_gudhi update
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c++17 as a new standard to compile the library
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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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Cech optimization
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-Some other minor changes
-Change license to LGPL
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doxygen_only
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recent version of doxygen
With the doxygen versions <= 1.9.2 the default setting 'overflow: hidden;' causes problems.
With the commit:
```
Commit: 590198b416cd53313d150428d2f912586065ea0d [590198b]
Date: Wednesday, December 1, 2021 1:37:26 PM
issue #8924 Horizontal scroll bar missing in HTML for wide class="dotgraph" objects
```
for the doxygen 1.9.3 version this has already been corrected but to run properly with the <= 1.9.2 version
this setting is required
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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: handling references to examples in a more transparent way
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Adding the other examples also with `gudhi_example_link`.
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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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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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After review:
- option is now:
```
-DWITH_GUDHI_CPP_DOCUMENTATION_ONLY=ON
```
- added some instructions to the installation description.
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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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remove useless include boost/version.h
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First version of points generation on torus
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distance_functions.h file
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Modify cech test to be more relevant regarding the current algorithm
Do some cleaning
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Enable WITH_NETWORK option in some of the CI platforms (for a minimal testing)
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Test another sphinx themes
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Fix numerical approximations inconsistencies with dim fraction exponent when generating points as grid on torus
Add notes in doc regarding the torus versions use cases
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values: 'grid'(i.e uniform==True) or 'random' (i.e uniform==False)
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