Changes to notebooks and documentation

[lmoresi]

Some rewriting of the internal solver documentation in response to JOSS reviews.

Updating notebooks to current codebase (e.g. evalf -> evaluate with rbf argument).

Improving adaptivity example

[Copilot]

Pull Request Overview

This PR focuses on updating notebooks and documentation for the underworld3 codebase. The changes address JOSS review feedback by improving internal solver documentation and updating examples to align with current API usage, particularly replacing deprecated evalf calls with the newer evaluate function. Additionally, a new adaptivity example is improved and dependencies are updated.

• Improved solver documentation with clearer titles and references
• Replaced deprecated evalf= parameter with _evalf= or removed altogether in favor of newer API patterns
• Updated notebook examples to use current API (evaluate instead of evalf)

Reviewed Changes

Copilot reviewed 23 out of 35 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
src/underworld3/visualisation.py	Added meshio fallback for mesh conversion with try/except block
src/underworld3/utilities/_api_tools.py	Minor formatting changes to class definition and markdown headers
src/underworld3/systems/solvers.py	Added documentation headers and updated evalf parameter usage
src/underworld3/systems/ddt.py	Updated evalf reference and improved docstring formatting
src/underworld3/swarm.py	Code cleanup removing outdated comments
src/underworld3/function/expressions.py	Fixed LaTeX rendering escape sequence
src/underworld3/function/_function.pyx	Bug fixes for function evaluation and variable handling
src/underworld3/discretisation.py	Added conditional visualization and improved mesh display
src/underworld3/cython/petsc_generic_snes_solvers.pyx	Updated solver documentation headers
environment.yml	Added new dependencies: rich, meshio, pygmsh
docs/user/_quarto.yml	Updated notebook file references and formatting cleanup
docs/user/Notebooks/	Multiple notebook updates with API changes and improved examples

Comments suppressed due to low confidence (1)

src/underworld3/systems/solvers.py:2128

• [nitpick] The parameter name _evalf with a leading underscore suggests it's private/internal, but it's being used as a public parameter in the function signature. Consider using evalf without the underscore if it's meant to be public.

 _evalf=False,

[lmoresi]

This is documentation updating and modifications to JOSS paper.