Jupyter

Useful Commands

!which python; python -V # check python version

Common Issues & Troubleshooting

ModuleNotFoundError

Jupyter Notebook tends to create path issues that disagree with the python path run locally. To fix this, I use the following troubleshooting methods:

Kernel.json

In the terminal:

# check Jupyter path
$ which -a jupyter
/usr/local/bin/jupyter # sample output

# check default python path
$ which -a python
/usr/bin/python

# check python3 path
$ which -a python3
/usr/local/bin/python3

If there is disagreement between the paths (as shown above), you can redirect the Jupyter kernel to point at the desired directory.

# identify where Jupyter stores kernel information
$ jupyter kernselspec list
Available kernels:
  python3    /usr/local/share/jupyter/kernels/python3

Navigate to the /kernels directory and locate kernel.json

Inside:

{
 "argv": ["python3", 
 "-m", 
 "IPython.kernel",
 "-f", 
 "{connection_file}"],
 "display_name": "Python 3",
 "language": "python"
}

Where it lists "python3" change it to your python path where the libraries are being installed. For example:

{
 "argv": [
  "/usr/local/opt/python/bin/python3.7",
  "-m",
  "ipykernel_launcher",
  "-f",
  "{connection_file}"
 ],
 "display_name": "Python 3",
 "language": "python"
}

The python3 kernel should now be pointing at the correct directory.

iPython Kernel Install

Navigate to the repository where the notebook files live and follow the recommendation in this issue from the Jupyter Github.

ipython kernel install

Check kernel.json to confirm that the path has been updated and that the path matches.

To confirm that your Jupyter notebook is running the same version of python:

In Jupyter notebook:

import sys
sys.executable
'/usr/local/opt/python/bin/python3.7' # this is from kernel.json

In the terminal:

$ python3
import sys
sys.executable
'/usr/local/opt/python/bin/python3.7'
'/Library/Frameworks/Python.framework/Versions/3.7/bin/python3'

Oops! If they don't match, then use the executable path from your locally installed python version to update kernel.json

Restart the notebook to see results.

Uninstall Jupyter

If none of the above methods worked, try uninstalling Jupyter.

pip uninstall jupyter
pip install jupyter