First, uninstall nupic completely.
Looks like the README is wrong, pycapnp 0.5.12 is fine. So yes it seems like you’re doing it right. You don’t even need to manually install numpy or pycapnp, they will install when you run pip install -r bindings/py/requirements.txt.
Then hopefully you can just run python setup.py install [--user] to run the cmake build.