Development - synchronise changes to documentation / JOSS

[lmoresi]

No description provided.

[Copilot]

Pull Request Overview

This PR synchronizes changes to documentation and JOSS paper, updating code formatting, docstrings, solver display names, dependencies, and notebooks to align with development improvements.

Key Changes

• Updated solver display names and documentation headers for consistency
• Refactored visualization code to use meshio when available with fallback to PyVista
• Enhanced error handling and removed redundant code comments
• Updated dependencies and notebook formatting

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	Restructured mesh conversion to use meshio as primary method with PyVista fallback
src/underworld3/utilities/_api_tools.py	Updated class definition syntax and markdown header formatting
src/underworld3/systems/solvers.py	Enhanced docstrings with consistent headers and updated parameter naming
src/underworld3/systems/ddt.py	Improved class documentation formatting
src/underworld3/swarm.py	Updated comments and added particle migration cleanup
src/underworld3/function/expressions.py	Fixed LaTeX rendering escape sequence
src/underworld3/function/_function.pyx	Improved iteration and removed redundant code
src/underworld3/discretisation.py	Enhanced mesh viewing with conditional visualization
src/underworld3/cython/petsc_generic_snes_solvers.pyx	Updated solver display names and documentation headers
environment.yml	Added new dependencies (rich, meshio, pygmsh)
docs/user/_quarto.yml	Updated notebook file names and cleaned formatting
docs/user/Notebooks/html5/temperature_plot.html	Updated base64 data for visualization
docs/user/Notebooks/Notebook_Index.ipynb	Updated notebook references and Python version
docs/user/Notebooks/8-Particle_Swarms.ipynb	Improved code formatting and documentation
docs/user/Notebooks/7-Unsteady_Flow.ipynb	Enhanced documentation and code structure

Comments suppressed due to low confidence (1)

src/underworld3/systems/solvers.py:2128

• [nitpick] Parameter name _evalf uses a leading underscore which typically indicates a private/internal parameter, but this appears to be a user-facing API parameter that should use a more descriptive public name.

 _evalf=False,