Document Purpose of PyCharm Directives

[mfleader]

A number of calls to __init__() or private methods are associated with these directives. Their purpose should be documented in the code, or they should be removed

# noinspection PyProtectedMember
# noinspection PyArgumentList

If we're going to disable this warning, we should have a comment here explaining why.

Originally posted by @webbnh in #131 (comment)