Type-check Jupyter Notebooks with mypy

Question

I have a project containing a bunch of Python modules (.py files) and a bunch of Jupyter Notebooks (.ipynb files) which import things from the Python modules.

I can (assuming I've got __init__.py files in all subfolders) type-check all the .py files by simply running mypy . from the root of the project. But I'd like to also be able to type-check my Jupyter Notebooks.

An ideal solution would:

type check all Python code in my Jupyter Notebooks,
be able to follow imports of .py modules from within Jupyter Notebooks when type-checking, just like imports in .py files,
let me type-check the whole project from the command line, so that I can run type-checking as part of a test suite or a pre-commit hook, and
in some way meaningfully report the locations of type errors within my Notebooks, analogously to how mypy prints line numbers for errors in .py files.

How can I do this?

ignoring_gravity · Accepted Answer · 2022-01-13 13:12:39Z

24

You could use nbQA and do

pip install -U nbqa nbqa mypy your_notebook.ipynb

edited Jan 13, 2022 at 13:12

answered Jul 21, 2020 at 11:21

ignoring_gravity

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2 Comments

erb Over a year ago

This answer is great as it provides a general solution to the problem of running linters/formatters/etc on notebooks. Thanks for writing it @ignoring_gravity!

ignoring_gravity Over a year ago

Thanks @erb , much appreciated! Version 0.7.0 has just come out, it has a few fixes for mypy

Sharukh Rahman · Accepted Answer · 2022-05-21 15:45:28Z

Checkout nb-mypy

Nb Mypy is a facility to automatically run mypy on Jupyter notebook cells as they are executed, whilst retaining information about the execution history.

More details here

E.Serra · Accepted Answer · 2019-11-21 14:05:12Z

You can: Convert all notebooks to python, then run mypy on that (How do I convert a IPython Notebook into a Python file via commandline?).

jupyter nbconvert --to script [YOUR_NOTEBOOK].ipynb

Just write a small script to do this and you are fine :)

Maarten Fabré · Accepted Answer · 2020-06-05 08:07:16Z

I use Jupytext and my IDE for this.

I export a copy in py:percent format, link that to the notebook. I Do the development in the jupyter lab environment, but the .py file is the one that goes in the git repository. Before commiting, I run it throught the usual linters, black, pydocstyle, mypy (with a strict configuration). I then reload the notebook in Jupyter lab, restart the kernel and 'Run All' to make sure the results are still OK, and only then commit the file to the repository

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