Flake8 fixes

Closes #3583 (closed)

1. Fix some flake8 errors

2. Enforce flake8 except for these errors (to be fixed in the future)

   • E402 module level import not at top of file
   • E722 do not use bare 'except'
   • F821 undefined name '...'
   • F841 local variable '...' is assigned to but never used

One day we will get there.