Fix linting errors

Currently flake8 is run every time a commit is made and it finds quite a few issues with the code. It would be good to fix the issues and when this is done make linting errors fail the tests, so we can keep the quality of the code in check more easily in the future.

Start by running the existing flake8 check to inventory the reported issues; the payload does not name specific source or test files. Fix the reported linting errors, then make lint failures fail the test process and verify that the check behaves as intended.

Written by the indexing model from the issue text.