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Yep, until we eventually move everything into `pyproject.toml` which is explicitly documented to support `[tool.foo]` config namespaces.

https://www.python.org/dev/peps/pep-0518/

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That's explicitly called out by miedzinski, the PR author, in the discussion [1]--although for some reason it's mentioned as PEP 512 but links to the same page you mentioned.

[1] https://github.com/python/mypy/pull/2761

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