Update documentation and clean-up code

The documentation for all existing and new modules and the user guide need to be updated. Also, the ruff linter needs to be pleased.

User Guide

• [ ]

API Reference (doc of actual code)

• experiments 09dfc149 (whole module still contains some unlinted parts, see #87 )
  • eigen
  • relax
  • relax_dynamic
  • antenna
• interactions (linted) 048e00ba
• plotting
  • plotly (linted) 5dd2cc49
• sample (linted) bff07c9b
  • material
  • mesh
  • sample
• _logging e71def88
• common (all linted) 1dc41c46
  • bibliography
  • config
  • io
  • math
  • typing
  • utils
• vectorfields.py (linted) e46d3c9b
• materials.py (linted) 173fc6a7
• geometries/ (linted) 25f5c8f3