Get *all* python files to pass flake8 checks

[Athanasius]

See #1712 (comment) for why we need this to be the case.

Currently some lines in a lot of files don't pass, because they've never been part of a diff that was checked by flake8 (or have become non-passing due to flake8 changes since they were last 'seen').

[Athanasius]

Reference for alternate run methods: PyCQA/flake8#1760

[Athanasius]

For reference, the flake8 changelogs seem to only be at https://flake8.pycqa.org/en/latest/release-notes/index.html

You have to spot the link to that site in the top-right of the github repo.