New visualization options

Added

• A new Escher binding independent of the original one [Escher-custom]
  • This integration is independent of the original and, therefore, does not have the same version conflicts.
• A new Visualization option that displays cobra Objects as a Force Directed Graph
• Introduced Galata as a new test suite
  • Galata automates the testing of visualization as it can compare reference images with outputs created in Jupyter Notebooks

Changed

• cobramod.pathway
  • The visualization function now includes the possibility to choose between different visualization options
• Type checks
  • Reintroduced MyPy as Ruff does not check types according to ruff's FAQ
• GitHub Actions
  • GitHub Actions now run tests on Windows and macOS once again
  • New workflow for the creation of Galata reference images
  • GitHub Action has been divided into smaller sections to provide a better overview of failed steps
• Documentation
  • Now uses Furo as a theme
  • Provides additional live examples of the new visualization options
• Tests
  • Tests no longer check for specific database versions; this is only done in a controlled manner for the db_version module
  • Tests for visualization using Escher now use Escher-Custom
  • Several visualization tests were replaced by an equivalent test using Galata
• environment.yml
  • Some dependencies now use their conda-forge package to reduce build time
  • 'sphinx-autoapi' was set to a dev version to be able to create the documentation using Python 3.12
• Maintenance
  • Several adjustments due to announced deprecations