istanbul doesn't cover files that have been proxyquire'd in

Having some bother getting istanbul and proxyquire to play nicely.

If I import a module into my test normally:

import subject from "../src/foo.es6"

Then istanbul covers the module as expected.

Importing with proxyquire works, in that I can stub the things, but istanbul says that file is no longer covered, when it definitely is.

let subject = proxyquire("../src/foo.es6", { /** stubs **/}).default;