I have upraded my Linux distro recently. Python 3.5 was replaced by Python 3.6.
All site packages I have installed with pip3 are still in the /usr
I just hit the same problem upgrading from Python 3.6 to Python 3.7, I forgot to run pip freeze before I upgraded to Python 3.7. The solution that worked is to specify the --path option as the old site-packages/ directory (which was not deleted):
pip3 freeze --path /usr/local/lib/python3.6/site-packages/ > python3.6_requirements.txt
pip3 install -r python3.6_requirements.txt