In order to run the robot outside of the App, currently you'll still need to calibrate your containers for protocols from within the App. In order to calibrate using the app, you'll need to upload a Python protocol with all of your containers and instruments, including nominal commands using each of these. Once you have the calibration data saved, you'll need to point your Python interpreter to the calibration file. If you are interested in manually locating this file, please refer to this article.
Using Jupyter Notebook
To associate the App's calibration file with Jupyter Notebook, you'll need to run this:
from opentrons.util import environment
environment.refresh() # point jupyter to your App's calibration file
To check if this was successful, run this:
print(environment.get_path('CALIBRATIONS_FILE')) # should print the location of file
If this returns the wrong path, you'll need to run:
and then run:
From here, you'll be able to paste in robot commands and run them through Jupyter Notebook.