Fix Doxygen Ref issues

[alexander-novo]

Description

The PR #524 was created to fix some error messages Doxygen was giving about refs not being found. It was fixed by removing the refs, but those refs are useful so it would be nice to fix the root issue instead. This PR does that.

Proposed changes

The root of the issue is a quirk with Doxygen - since the docs of CircuitComponent are inherited by PowerElectronicsModel, some of the refs in CircuitComponent docs appear in the PowerElectronicsModel context, but some of these items are re-imported into the PowerElectronicsModel namespace. The re-imports aren't documented and Doxygen can only tell that they refer to the same things if in the code they clearly come from CircuitComponent.

DOXYGEN_EXTRACT_ALL has been set in the normal docs to help with normal docs as well - many items aren't documented, but they should still appear in the documentation. Refs will also be able to resolve for them even if they aren't documented.

EXTRACT_PRIVATE has been set in the Sphinx documentation Doxyfile. Sphinx will strip privates from the doxygen xml, and this will help errors from being generated, since the Doxygen documentation is developer-oriented, it might mention private members in the documentation.

Checklist

• All tests pass.
• Code compiles cleanly with flags -Wall -Wpedantic -Wconversion -Wextra.
• The new code follows GridKit™ style guidelines.
• [N/A] There are unit tests for the new code.
• [N/A] The new code is documented.
• The feature branch is rebased with respect to the target branch.
• I have updated CHANGELOG.md to reflect the changes in this PR. If this is a minor PR that is part of a larger fix already included in the file, state so.

This is part of a previous fix

Further comments

@lukelowry can you verify that this fixes the issue you were having in the previous PR?

[pelesh]

I'm getting folowing error:

/home/user/src/gridkit/GridKit/GridKit/Solver/Dynamic/Rosenbrock.hpp:334: error: unable to resolve reference to 'RHS_first_stage_' for \ref command

*** Doxygen has finished

[alexander-novo]

I'm getting folowing error:

/home/user/src/gridkit/GridKit/GridKit/Solver/Dynamic/Rosenbrock.hpp:334: error: unable to resolve reference to 'RHS_first_stage_' for \ref command

*** Doxygen has finished

Is this when running the GridKitDocs target in cmake, or when running doxygen for the sphinx documentation?

I believe this is due to a bug in Doxygen. My doxygen version is 1.17.0 and I do not have these errors. When I downgrade to 1.9.8, I get similar errors.

[lukelowry]

Error on RTD when I tried to build docs

[rtd-command-info] start-time: 2026-08-13T20:49:59.413892Z, end-time: 2026-08-13T20:50:06.063784Z, duration: 6, exit-code: 1
rm -rf docs/xml && cd docs && doxygen Doxyfile
/home/docs/checkouts/readthedocs.org/user_builds/gridkit/checkouts/alex/GridKit/Solver/Dynamic/Native/InfNorm.hpp:41: error: unable to resolve reference to 'scale_' for \ref command
/home/docs/checkouts/readthedocs.org/user_builds/gridkit/checkouts/alex/GridKit/Solver/Dynamic/Rosenbrock.hpp:453: error: unable to resolve reference to 'RHS_' for \ref command

If you fix those I can run it again until it builds on RTD

[alexander-novo]

Error on RTD when I tried to build docs

[rtd-command-info] start-time: 2026-08-13T20:49:59.413892Z, end-time: 2026-08-13T20:50:06.063784Z, duration: 6, exit-code: 1
rm -rf docs/xml && cd docs && doxygen Doxyfile
/home/docs/checkouts/readthedocs.org/user_builds/gridkit/checkouts/alex/GridKit/Solver/Dynamic/Native/InfNorm.hpp:41: error: unable to resolve reference to 'scale_' for \ref command
/home/docs/checkouts/readthedocs.org/user_builds/gridkit/checkouts/alex/GridKit/Solver/Dynamic/Rosenbrock.hpp:453: error: unable to resolve reference to 'RHS_' for \ref command

If you fix those I can run it again until it builds on RTD

Yes those are exactly what I get with the outdated version of doxygen. This is a doxygen bug - you should try updating.

[lukelowry]

Well that's the unfortunate thing, we can't do that on RTD unless we just use a more recent version of Ubuntu

In .readthedocs.yaml, can you change to:

build:
  os: ubuntu-26.04

[lukelowry]

https://gridkit.readthedocs.io/en/alex/

Take a look, it builds now!