https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1099038

My question is why pytest try to create a file in the modules system library ?

My guess is that it's because the tests are executed from the module 
installation directory.

If you look at the debci output[1], you'll see lots of paths like this:
../../../../usr/lib/python3/dist-packages/silx/app/compare/test

pytest is simply trying to create a cache dir inside the module path.
I'm not sure why it would fail because of that, since those exceptions are 
caught and should only result in a warning. But I may be overlooking something.

You could try to change the cache with this option: [2]

Or perhaps you should look at how pytest is executed, and if it's using the 
correct test location.
Should these unit tests really be installed alongside the module?

[1] https://ci.debian.net/packages/s/silx/testing/amd64/58042493/
[2] https://docs.pytest.org/en/latest/reference/reference.html#confval-cache_dir

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