How do I configure PyCharm's Coverage checker to recognize .coveragerc?

There is a feature request for this at https://youtrack.jetbrains.com/issue/PY-16945

You can make PyCharm use the .coveragerc by putting it into the working directory you run your tests from.

The feature request from https://youtrack.jetbrains.com/issue/PY-16945 was implemented and works in version 2018.1.

There is a different way to make PyCharm ignore certain files and folders:

In the Settings choose Project: ... - Project Structure. Here you can mark folders as Excluded or exclude files specifically.

PyCharm`s code coverage reports ignores all those exluded files, too.