Start applying ruff rules to notebooks (ruff 0.6+)

[DimitriPapadopoulos]

Jupyter notebooks are now linted and formatted by default

TODO:

• [ ] Add unit tests and/or doctests in docstrings
• [ ] Add docstrings and API docs for any new/modified user-facing classes and functions
• [ ] New/modified features documented in docs/tutorial.rst
• [ ] Changes documented in docs/release.rst
• [x] GitHub Actions have all passed
• [x] Test coverage is 100% (Codecov passes)

[jhamman]

I'm fine merging this in as is @DimitriPapadopoulos. We may also consider removing these notebooks from the repo as many of them are referencing data that we don't have access to.

[DimitriPapadopoulos]

Let's remove the notebooks then.

[DimitriPapadopoulos]

Superseded by #2897.