A genius called @ludeeus helped on discord.
Needed to activate the virtual environment and reinstall the latest pip.
sudo -u homeassistant -H -s
cd /srv/homeassistant
python3 -m venv .
source bin/activate
curl https://bootstrap.pypa.io/get-pip.py -o get-pip.py
python get-pip.py
It upgraded from v 9.0.1 to 19.1