Mypy and test fixes, black formatting

[Rigidity]

This fixes mypy errors, type stubs, and formats all of the test files with black. Black formatting is checked in CI as well.

You can review one commit at a time, and mostly ignore the "Black formatting" commit, since no changes were made in it other than formatting and adding CI to enforce the formatting.

[coveralls-official]

Pull Request Test Coverage Report for Build 8569782024

Details

• 0 of 0 changed or added relevant lines in 0 files are covered.
• No unchanged relevant lines lost coverage.
• Overall coverage remained the same at 85.544%

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Totals
Change from base Build 8558009590:	0.0%
Covered Lines:	11350
Relevant Lines:	13268

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💛 - Coveralls

[arvidn]

it all looks good, except the type of the atom property should be Optional[bytes] as far as I can tell