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Since Python 3.7, it's possible to load the atexit module more than once:
commit 776407fe893fd42972c7e3f71423d9d86741d07c
Author: Marcel Plch <gmarcel.plch@gmail.com>
Date: Wed Dec 20 11:17:58 2017 +0100
 bpo-31901: atexit callbacks should be run at subinterpreter shutdown (#4611)
 
 Change atexit behavior and PEP-489 multiphase init support.
Each new import executes the module which overrides PyInterpreterState.pyexitfunc with _Py_PyAtExit().
Example:
---
import sys
atexit1 = sys.modules.pop('atexit', None)
if atexit1 is None:
 import atexit as atexit1
 del sys.modules['atexit']
import atexit as atexit2
atexit1.register(print, "atexit1 callback")
atexit2.register(print, "atexit2 callback")
---
Output:
---
atexit2 callback
---
Either PyInterpreterState should support a list of exit functions, or atexit should raise an exception if it's loaded more than once.
call_ll_exitfuncs() calls a list of functions: _PyRuntimeState.exitfuncs. But these functions are called at the end of Py_Finalize(), whereas atexit functions are called after calling threading._shutdown() in Py_Finalize() and Py_EndInterpreter().

I will take a look :)

I created bpo-40600: "Add an option to disallow creating more than one instance of a module".

@vstineer
I'd like to update PR 19562 not to create more than one instance.
if the PR is updated, would you like to review this PR?

I would prefer a more generic solution, if possible:
> bpo-40600: "Add an option to disallow creating more than one instance of a module".

Fixed by bpo-42639.