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Ruff code formatting fixes #218

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GenevieveBuckley
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This PR updates the version of python used to run the ruff code formatting check (since python 3.8 is nearing end of life), and updates the code for compliance with ruff's linting specifications.

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@GenevieveBuckley
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We should be able to merge this after the CI fixes in #222 are merged

@GenevieveBuckley
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Closed, in favour of #224
This PR has more ruff updates than needed, since we decided to target ruff to python 3.9 instead of python 3.12

@GenevieveBuckley GenevieveBuckley deleted the update-ruff branch June 6, 2024 00:52
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