Fix flake8 for all the project

[noviluni]

I saw that we were limiting the flake8 to certain folders. I think it doesn't make sense to exclude some folders, so I removed it and fixed the new flake8 errors.

[codecov]

Codecov Report

Merging #958 (105b728) into master (ad50964) will not change coverage.
The diff coverage is n/a.

@@           Coverage Diff           @@
##           master     #958   +/-   ##
=======================================
  Coverage   98.26%   98.26%           
=======================================
  Files         231      231           
  Lines        2597     2597           
=======================================
  Hits         2552     2552           
  Misses         45       45           

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