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Starting with mypy 0.990, when testing a module in a namespace, mypy starts emitting errors when it encounters that module:
error: Source file found twice under different module names: "abode" and "jaraco.abode"
The issue almost certainly has the same root cause as pytest-dev/pytest#3396. Pytest is too reliant on the old assumption that a directory without an __init__.py is not a package, but that assumption doesn't hold since Python 3.3.