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Fix linting and notebook errors. PR created automatically by Jules for task 16469324276285694698 started by @sergey9519546

Summary - Onboard notebook-shim at version 0.2.4 Summary by Sourcery Chores: - Add configuration entry for the notebook-shim package at version 0.2.4.
pkg onboarding

... uncertainty demo notebook. Description of Changes This adds a Jupyter notebook (and example mechanism) for running UQ on a surface mechanism. There s also a small bugfix for the uncertainty tool where it ...

Adds basic utilities to load and save FluidFlower snapshots in prescribed format, and a notebook for interaction with data stored in the shared folder.

@AlrauneZ Great work on the notebooks! I have fixed the linting issues and merged your work with mine. If you pull from this branch you should get the updated version without any issues. Also, example_mibitrans_anatrans now contains the diversity model comparison figure we discussed last Monday.
documentation

Description This PR contains DPO and ORPO example notebooks. These notebooks will also serve as integration tests for DPO. Tests Ran the notebooks manually. Checklist Before submitting this PR ...