Fix graphs in documentation, update dependencies.

[hvdijk]

Overview

Fix graphs in documentation, update dependencies.

Reason for change

Describe how the current behaviour of the project is causing problems for you
or is otherwise unsatisfactory for your use case.

Description of change

• Generating graphs needs graphviz to be installed.
• A newer versions of Sphinx is needed to support current Python.

Anything else we should know?

If there's any other relevant information we should know that may help us in
understanding and verifying your patch, please include it here.

Checklist

• Read and follow the project Code of Conduct.
• Make sure the project builds successfully with your changes.
• Run relevant testing locally to avoid regressions.
• Run clang-format-20 on all modified code.