Testing: flake8 linting shows errors & warnings but workflow step doesn't fail

[dfornika]

As part of our testing suite, we run flake8 against the parsers and the AntimicrobialResistanceGenomicAnalysisResult class, using GitHub Actions.

We can see in the logs that flake8 is finding issues, but the workflow steps are passing anyways. See:

https://github.com/pha4ge/harmonized-amr-parsers/runs/546839506?check_suite_focus=true#step:4:23

The linting workfow steps should fail if there are linting issues.

[dfornika]

I just noticed this note that explains why the linting step doesn't cause the workflow to fail. It is explicitly made to exit with status 0.

https://github.com/pha4ge/harmonized-amr-parsers/blob/4397bbfff73818776b1787bcd14e55a93f70921a/.github/workflows/pythonpackage.yml#L32

[fmaguire]

Refactor is now flake8 compliant too.