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Notice the function is_python_file in autopep8.py; it's using the file suffix '.py' & shebang line to recognize a python file. So an expediency is to add a shebang line for your .pyi stub files.
But, a better answer is to modify the function and take .pyi suffix into account, I think.
Python Code
N/A
Command Line
autopep8 ./types --in-place --recursive
☝Does not run on
./types/**/*.pyi
filesYour Environment
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