Update commit hooks and fix new ruff and mypy issues
#1424
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The following actions uses node12 which is deprecated and will be forced to run on node16: codecov/codecov-action@v1. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/
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The following actions use a deprecated Node.js version and will be forced to run on node20: ts-graphviz/setup-graphviz@v1, codecov/codecov-action@v1. For more info: https://github.blog/changelog/2024-03-07-github-actions-all-actions-will-run-on-node20-instead-of-node16-by-default/
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