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Apply Flake8, YamlLint and Black styling to entire repository

Daniel Thomas Murnane requested to merge DM_fix_linting into dev

This is a big merge, but it is purely aesthetic! It simply applies Flake8 and Black styling to every file. It is compatible with the pre-commit hooks that we encourage people to use when git committing.

It passes all linting checks, build check, and pytest checks.

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