Thanks. Using qu1ck’s answer this is what we need to do. This solves my issue.
export PYTHONPATH=/usr/lib/kicad-nightly/lib/python3/dist-packages/
export LD_LIBRARY_PATH=/usr/lib/kicad-nightly/lib/python3/dist-packages/
And then if you use this in your python script
import pcbnew
print(pcbnew.GetBuildVersion())
It is going to output this
5.99.0-unknown-b10f156dd0~130~ubuntu21.04.1