Python doesn't understand PYX files in PYTHONPATH

Question

I have included some directories in PYTHONPATH and got and exception

Fatal Python error: Py_Initialize: Unable to get the locale encoding
Traceback (most recent call last):
  File "/usr/lib/python3.6/encodings/__init__.py", line 31, in <module>
  File "/home/dimskraft/MYPATH/library/python/codecs/__init__.py", line 1, in <module>
ModuleNotFoundError: No module named '__codecs'
Aborted (core dumped)

Nevertheless

cat /home/dimskraft/MYPATH/library/python/codecs/__init__.py
from __codecs import loads, dumps, list_all_codecs  # noqa


ls /home/dimskraft/MYPATH/library/python/codecs
__codecs.pyx  gen_corpus  __init__.py  __init__.pyc  __pycache__  test  ya.make

So, it doesn't see __codecs.pyx, which is still there.

How to teach it to see it?