Update script to strip numpy typing and re-execute notebooks

[lilyminium]

Fixes #407

This updates the script that generates the default values of topology attrs to strip the NumPy typing, since that doesn't seem very relevant. (Also, np.False_ generates an artificial link when rendered with sphinx.)

Edit: it also re-executes some notebooks to update to reflect the numpy types that now get returned.

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📚 Documentation preview 📚: https://mdanalysisuserguide--408.org.readthedocs.build/en/408/

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[lilyminium]

Re-executed some notebooks to reflect the numpy types that now get returned; the failing ParmEd notebook (which is erroring due to a baked-in incompatibility with numpy >= 2.0 in mda itself) is going to be tricky to resolve without down-pinning numpy currently, seems easier to patch with MDAnalysis/mdanalysis#4883 in the main repo instead.

[lilyminium]

Going to quickly self-merge to fix CI.

[lilyminium]

Never mind, at some point we decided self-merging was a bad idea 😅

[lilyminium]

@RMeli or @MDAnalysis/docteam would any of you have time to take a quick look at this? This will unblock CI for @namiroues's work too :-)

[RMeli]

Thanks for fixing the CI @lilyminium! I had a quick look and looks alright to me.