I’ve figured out a possible solution to this, but there might be something better. If you write a comment that will raise an E501 error, i.e. it is too long, you can append that line with # noqa: E501, and flake8 will ignore it. For example:
# This is a really really long comment that would usually be flagged by flake8 because it is longer than 79 characters
would usually raise an E501, but
# This is a really really long comment that would usually be flagged by flake8 because it is longer than 79 characters # noqa: E501
will not.
documented here.