Switch to uv and poethepoet

[Thijss]

This PR migrates the python package management to uv (https://docs.astral.sh/uv/) and adds poethepoet to simplify/streamline CI/CD checks.

• A uv.lock file is added
• poethepoet is now used to run CI/CD tasks
  • tasks are added to pyproject.toml
• dev-dependencies are moved from optional to group dependencies (following https://docs.astral.sh/uv/concepts/projects/dependencies/)
• Github Actions workflows are simplified and updated to work with uv
  • nigthly action now runs with a uv update command.
• Dependencies are updated since these weren't explicitly locked before.
• Python file changes:
  • Some style/lint issues have been addressed, to accommodate issues raised by new versions of mypy/ruff/etc.
• pre-commit now only runs poe all --check
  • small downside: it now always runs on all files, instead of just staged files.

ToDo

• Possibly mention uv in the README.
• use uv --frozen where possible
• Create test release to check whether extras (e.g. visualizer) are still working correctly

[sonarqubecloud]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
50.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud

[jaapschoutenalliander]

Nice work, let's try how it it works in this setup and if any addition/change is needed we can iterate