Fix some doxygen warnings in Persistence_matrix

[mglisse]

@hschreiber this reduces a bit the number of doxygen warnings. It is in no way complete, but some of the fixes would be straightforward to apply in more places. It is possible that some of the changes are wrong. Feel free to take over...

[hschreiber]

All doxygen warnings related to the matrix should be corrected now! The only ones remaining are:

dox_warn/src/Simplex_tree/example/mini_simplex_tree.cpp:17: warning: Detected potential recursive class relation between class MyOptions and base class Gudhi::Simplex_tree_options_minimal!
dox_warn/src/Simplex_tree/test/simplex_tree_iostream_operator_unit_test.cpp:24: warning: Detected potential recursive class relation between class MyOptions and base class Gudhi::Simplex_tree_options_minimal!
dox_warn/src/Simplex_tree/test/simplex_tree_remove_unit_test.cpp:23: warning: Detected potential recursive class relation between class MyOptions and base class Gudhi::Simplex_tree_options_minimal!
error: bib file dox_warn/biblio/how_to_cite_gudhi.bib not found!
dox_warn/src/common/doc/installation.h:84: warning: \cite command to 'cgal:eb-19b' does not have an associated number
dox_warn/src/Alpha_complex/doc/Intro_alpha_complex.h:53: warning: \cite command to 'cgal:hdj-t-19b' does not have an associated number
dox_warn/src/Alpha_complex/doc/Intro_alpha_complex.h:54: warning: \cite command to 'cgal:eb-19b' does not have an associated number
dox_warn/src/Alpha_complex/doc/Intro_alpha_complex.h:58: warning: \cite command to 'cgal:s-gkd-19b' does not have an associated number
dox_warn/src/Alpha_complex/include/gudhi/Alpha_complex.h:84: warning: \cite command to 'cgal:s-gkd-19b' does not have an associated number

The first part:

dox_warn/src/Simplex_tree/example/mini_simplex_tree.cpp:17: warning: Detected potential recursive class relation between class MyOptions and base class Gudhi::Simplex_tree_options_minimal!
dox_warn/src/Simplex_tree/test/simplex_tree_iostream_operator_unit_test.cpp:24: warning: Detected potential recursive class relation between class MyOptions and base class Gudhi::Simplex_tree_options_minimal!
dox_warn/src/Simplex_tree/test/simplex_tree_remove_unit_test.cpp:23: warning: Detected potential recursive class relation between class MyOptions and base class Gudhi::Simplex_tree_options_minimal!

is probably just due to MyOptions being redefined in each of these .cpp. I don't know if it is worth changing the names just for that.

And the second part:

error: bib file dox_warn/biblio/how_to_cite_gudhi.bib not found!
dox_warn/src/common/doc/installation.h:84: warning: \cite command to 'cgal:eb-19b' does not have an associated number
dox_warn/src/Alpha_complex/doc/Intro_alpha_complex.h:53: warning: \cite command to 'cgal:hdj-t-19b' does not have an associated number
dox_warn/src/Alpha_complex/doc/Intro_alpha_complex.h:54: warning: \cite command to 'cgal:eb-19b' does not have an associated number
dox_warn/src/Alpha_complex/doc/Intro_alpha_complex.h:58: warning: \cite command to 'cgal:s-gkd-19b' does not have an associated number
dox_warn/src/Alpha_complex/include/gudhi/Alpha_complex.h:84: warning: \cite command to 'cgal:s-gkd-19b' does not have an associated number

just appears in the "developer" version because of how biblio/how_to_cite_gudhi.bib.in is handled. Marc and Vincent are aware of it. @mglisse, should I try to fix this or is it too much work to be worth it?

[mglisse]

is probably just due to MyOptions being redefined in each of these .cpp

I am surprised that doxygen runs on the tests (GUDHI_doxygen_target.cmake explicitly mentions examples but not tests or include).

@mglisse, should I try to fix this or is it too much work to be worth it?

As you want. It isn't a priority since one version works. It probably isn't that much work, but it is unlikely to be fun to work on.

[hschreiber]

is probably just due to MyOptions being redefined in each of these .cpp

I am surprised that doxygen runs on the tests (GUDHI_doxygen_target.cmake explicitly mentions examples but not tests or include).

I think it runs by default everywhere as Doxygen also entered some vscode related folders on my side and gave me weird warnings about it.

@mglisse, should I try to fix this or is it too much work to be worth it?

As you want. It isn't a priority since one version works. It probably isn't that much work, but it is unlikely to be fun to work on.

Ok, I will try then and stop if it takes too much time. It will probably not be much fun, but I will learn something from it as I didn't worked much with cmake yet.