track improvements towards pep8 compliance

[JessicaS11]

After updating the GH actions (#475), in order to get the checks to pass we needed to add a lot of ignore codes to the .flake8 config file. This draft PR removes those ignores so PRs moving forward have a spot to look to see if any edited files are out of compliance (but the checks will still pass as we work towards compliance for legacy code).

[github-actions]

👈 Launch a binder notebook on this branch for commit ba8c5b6

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👈 Launch a binder notebook on this branch for commit a2ad04b

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[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 66.59%. Comparing base (948a70b) to head (c021602).

Additional details and impacted files

@@             Coverage Diff              @@
##           development     #493   +/-   ##
============================================
  Coverage        66.59%   66.59%           
============================================
  Files               36       36           
  Lines             3059     3059           
  Branches           534      534           
============================================
  Hits              2037     2037           
  Misses             934      934           
  Partials            88       88           

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