To make the version control more efficient, we don’t want git to track the output of jupyter notebooks every time a notebook is committed. If the output is indeed necessary we can always convert an HTML as a report and keep it static.

To clear output automatically after staging, first modify the .git/config file by adding the following lines:

[filter "strip-notebook-output"]
    clean = "jupyter nbconvert --ClearOutputPreprocessor.enabled=True --to=notebook --stdin --stdout --log-level=ERROR %f"

Then create the .gitattributes file under project folder with content:

*.ipynb filter=strip-notebook-output

Note that the .gitattributes file is version controlled while the .git/config file is not, thus collaborators need to manually edit it.

Referenced from this blog post and an update in this stackoverflow post.