How to commit jupyter notebooks without output to git while keeping the notebooks outputs intact locally

commit_jupyter_notebooks_code_to_git_and_keep_output_locally.md

Commit jupyter notebooks code to git and keep output locally

1. Add a filter to git config by running the following command in bash inside the repo:

git config filter.strip-notebook-output.clean 'jupyter nbconvert --ClearOutputPreprocessor.enabled=True --to=notebook --stdin --stdout --log-level=ERROR'  

2. Create a .gitattributes file inside the directory with the notebooks

3. Add the following to that file:

*.ipynb filter=strip-notebook-output  

After that, commit to git as usual. The notebook output will be stripped out in git commits, but it will remain unchanged locally.

Source: StackOverflow

How to override the above for a specific notebook

This is useful if you sometimes want to add specific notebooks with their cell outputs intact to git, while still having the default behavior of clearing out cells.

1. When adding to git a notebook whose cell outputs you want to keep, instead of the usual git add <path to your notebook> command, use this: git -c filter.strip-notebook-output.clean= add <path to your notebook>

Source: StackOverflow

the command you ran will not work

@33eyes It will work, but won't output anything, just freeze. So that means jupyter command is available in PATH. But if running it from git bash gives 'unrecognized command', that means it's not in PATH anymore, so I suspect it's not in global PATH env var and that's how git would run it either when from git bash, cmd.exe, windows terminal or vscode etc. etc.

hi everyone, I solved the issue. it's because I was in a virtual environment and needed to add that specific installation of python to PATH.

1. in Anaconda prompt, type where jupyter or just figure out where your jupyter.exe is stored in your venv

(orf) C:\Users\kyi>where jupyter
C:\Users\kyi\AppData\Local\anaconda3\envs\orf\Scripts\jupyter.exe

2. add this path (without the jupyter.exe part) to a new variable in PATH

@33eyes can you add the 4th step of

4. Run git add --renormalize . to go through all of your existing notebook files and scrub the outputs. Otherwise, you could get heinous merge conflicts later.

PS to people having PATH issues: If you are using VScode, perhaps your issue is caused by vscode running all of the git commands in a weird environment typically different from what you have on the command line.

It works, you're great!

It works but when trying to merge, it breaks the process as merging adds "<<<<<<<", "=======", ">>>>>>>" all over the place in the conflicting files. So if the conflicting file is a *.ipynb, jupyter nbconvert does not recognize the file as a proper JSON. And breaks when executing git mergetool or git diff <*.ipynb file>.
The solution I guess is to avoid executing the filter when running those commands but I'm not sure how to do that.

If i remove the required from .git/config it loads the mergetool but the error still appears so it's not a clean solution.

@konradmb your solution is fantastic. Is there a way to push it so that everyone who clones the repo has the config? As I understand it this is a local solution. Thanks!

@miguel9554

• I don't think that would be possible as that feature would be deemed as unsafe. For example an attacker could add a filter that runs rm for all files.
• Yes, this solution works only locally.
• There's a workaround at https://stackoverflow.com/a/18330114 but it still requires every user to adjust local settings (they discuss the security concerns too).
• An idea: maybe you can add a pre-merge filter step to GitHub Actions that would run on every pull request?