Update doxygen (cont'd)

[ischoegl]

Changes proposed in this pull request

• Restructure doxygen File Input/Output documentation
• Restructure oneD documentation
• Restructure zeroD documentation
• Add tree view

If applicable, fill in the issue number this pull request is fixing

Resolves #1535

If applicable, provide an example illustrating new features this pull request is introducing

Checklist

• The pull request includes a clear description of this code change
• Commit messages have short titles and reference relevant issues
• Build passes (scons build & scons test) and unit tests address code coverage
• Style & formatting of contributed code follows contributing guidelines
• The pull request is ready for review

[codecov]

Codecov Report

Merging #1543 (4354877) into main (25e8e5c) will decrease coverage by 0.02%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##             main    #1543      +/-   ##
==========================================
- Coverage   70.47%   70.46%   -0.02%     
==========================================
  Files         376      379       +3     
  Lines       59081    59080       -1     
  Branches    21222    21222              
==========================================
- Hits        41640    41633       -7     
- Misses      14360    14367       +7     
+ Partials     3081     3080       -1     

Impacted Files	Coverage Δ
include/cantera/base/AnyMap.h	80.00% <ø> (ø)
include/cantera/base/Interface.h	100.00% <ø> (ø)
include/cantera/base/Solution.h	87.50% <ø> (ø)
include/cantera/base/SolutionArray.h	94.44% <ø> (ø)
include/cantera/base/Units.h	90.90% <ø> (ø)
include/cantera/base/YamlWriter.h	100.00% <ø> (ø)
include/cantera/base/ctexceptions.h	60.86% <ø> (ø)
include/cantera/base/global.h	81.81% <ø> (ø)
include/cantera/kinetics/EdgeKinetics.h	100.00% <ø> (ø)
include/cantera/kinetics/ImplicitSurfChem.h	100.00% <ø> (ø)
... and 32 more

... and 14 files with indirect coverage changes

📣 We’re building smart automated test selection to slash your CI/CD build times. Learn more

[speth]

Thanks for working on this, @ischoegl. I had just a few small comments.

[speth]

I see what you're trying to do by adding the class name to the docstring, but the way member functions are shown in Doxygen's "modules" leaves a fair bit to be desired, as I'm sure you've noticed. While I think the two groups touched on in this PR are okay, I'd suggest not going any further in the direction of trying to populate such groups, if you hadn't already come to that conclusion.

[ischoegl]

I tried to collect some spots where Jacobians are evaluated, as they are relevant to the new derivGroup module. I indeed tried to mitigate the lacking presentation. I have no intention to make this more wide-spread.

There is some need to document PreconditionerBase etc, which hopefully will take care of some of these stop-gap entries.

[speth]

breathe may eventually provide us with an opportunity to adjust the presentation, so I think this is fine for now.

[ischoegl]

@speth ... I believe I addressed everything.

[speth]

Thanks, @ischoegl. This looks good to me.