Marcel Plch <gmarcel.p...@gmail.com> added the comment:

I created a PR with fix on this issue - 
https://github.com/python/cpython/pull/4611

This makes Py_EndInterpreter() call atexit callbacks for the subinterpreter it 
is destroying.

It doesn't make Py_Finalize() end all subinterpreters, as the current 
implementation of subinterpreters makes it hard to do so. This is the same as 
the current behaviour: you need to end all subinterpreters before calling 
Py_Finalize().

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<https://bugs.python.org/issue31901>
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