Here are the steps to update HA in a venv (old but I think they are still valid):
$ sudo systemctl stop [email protected]
$ sudo su -s /bin/bash homeassistant
$ source /srv/homeassistant/bin/activate
$ pip3 install --upgrade homeassistant
$ exit
$ sudo systemctl start [email protected]
If necessary change the user “homeassistant” in the second line to whatever user you used to install HA.