I realize I'm being annoyingly late to this suggestion, having already merged the PEP8 test, but perhaps rather than failing on PEP8 violations we should just be tracking their total number.  That's what we do on the `astropy` project, for example.  If a particular large PR increases the number by a large amount, we address it, otherwise, there is always just some background of PEP8 violations we expect to have.

Another alternative might be to just turn off all whitespace-related checks in the automated checking, even though that will let some things through that are uncontroversially bad (such as `function_call ( x )`, for example.  The other whitespace rule that I think is worthy of violating rather frequently is the grouping of operators for precedence, i.e. `x + x**2`.  The fact that PEP8 doesn't encourage this is just a sign of its background in non-scientific programming, IMHO.

If this is becoming too much of a monster to get right, I propose we leave the pep8 test in, but comment out the `assert` statement that actually causes it to fail.