Update code in notebooks for LLM ingestion #310
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This PR updates various notebooks in the notebook directory of MIRA such that the code in the cells are correct following updates to MIRA (change in project structure, expected data types to be passed to a constructor, etc). Import paths have been updated, initial instantion has been changed to accept an expression rather than a value, other minor errors such as usage of a module that has not been imported or incorrect key errors for dictionaries have also been corrected.
Only the code cells have been changed and no notebooks have been reran to minimize the diff shown on Github. However, for some files the metadata has changed which appears in the diffs. Additionally, for some of the notebooks, a large diff still persists.