33eyes/commit_jupyter_notebooks_code_to_git_and_keep_output_locally.md

Hello - thanks for this, I really needed it.

On my system (Mac, Python 3.9.9 installed via brew) I needed jupyter-nbconvert instead of jupyter nbconvert.

👍 Interesting, must be a brew thing. My python install was by conda, and everything else's the same.

Wow, this worked a treat!

I tend to run Jupyter in a Docker container. So, if you want to run the Notebook output cleaning preprocessor using a Jupyter container instead, all you need to do is tweak the git config like this:

git config --global filter.strip-notebook-output.clean 'docker run --rm -i -v \"${pwd}:/home/jovyan\" jupyter/datascience-notebook jupyter nbconvert --clear-output --to=notebook --stdin --stdout'

I've set it as a global config parameter, so that it applies to all repos.

Mine one was also conda install and python 3.6. It worked like charm Thanks a lot.

wow, thanks! this is the best!

Based on this StackOverflow answer, I've added required field (git will fail if cleaning errors out) and moved .gitattributes to internal config.

1. Add to .git/config:

   [filter "strip-notebook-output"]
   clean = "jupyter nbconvert --ClearOutputPreprocessor.enabled=True --ClearMetadataPreprocessor.enabled=True --to=notebook --stdin --stdout --log-level=ERROR"
   smudge = "cat"
   required

2. Create .git/info/attributes and add:

   *.ipynb filter=strip-notebook-output

I am having trouble getting the filter to actually activate. Does anyone know what to do in this case? I can only get it working on one device, but not the same repository on a different device, for two different repositories. I am adding the .gitattributes and .git/config on both different devices.

Working on: Python 3.11.4, conda 23.5.2, git 23.9.1.windows.1
Not working on: Python 3.10.11, conda 23.3.1, git 2.41.0.windows.3

Troubleshooting
It’s possible that despite the above changes the “old” data still shows and the filter is not applied. Here are a couple of things I’ve tried:

First, double-check that all steps, names, and paths are correct.

Second, try deleting and restoring the file(s) affected by the filter. I would delete the file directly (e.g. go into the Finder and Trash the file), then use git (e.g. git reset) to restore the file via a git mechanism. This should trigger git’s hook to apply filters.

If there are still problems, or you want to learn more nitty-gritty about git attribute keyword expansion support (what “git smudge and clean” is all about), you can check the official documentation: “Customizing Git Attributes: Keyword Expansion”.

Another source says I have to do git add --renormalize:

Whenever you change the clean filter, you have to renormalise your repository:

$ git add --renormalize .
After these changes, git will run automatically the command to clear output cells on every Jupyter notebook file added to the staging area.

But this didn't work for me, git bash didn't like the jupyter command ('unrecognized command') since git and jupyter are not in the same environment.

@air-kyi Check if you can run jupyter nbconvert command manually. Also remember that filters are not a part of a repository. You need to add them manually on each device.

I did add them manually on each device; I tried running jupyter nbconvert --ClearOutputPreprocessor.enabled=True --to=notebook --stdin --stdout --log-level=ERROR manually in conda and it didn't do anything or loaded forever without error message, and the same command in git bash gave 'unrecognized command' (I wouldn't really expect it to run in git since jupyter is not associated with git?)

It won't do anything because it waits for stdin input.
I don't have experience with conda, but if it works like venv, then that's where the problem is.

You'd need to install jupyter globally (easier) or modify filter to activate environment before running (harder). Try to run pip install nbconvert or python3 -m pip install nbconvert in git bash window. If it doesn't work: install python from python.org and remember to check "add python to PATH" or something similar. Maybe you can do it with conda, but I have zero experience with that.

Hey @air-kyi , sorry you are having trouble with this. Conda includes jupyter, so you should be all set with regard to jupyter installs. You don't need git bash for running non-git related commands (or even for git, for that matter), it just makes using git a bit easier, especially on Windows. For testing out nbconvert from command line, the command you ran will not work because you have a --stdin flag in it which tells it to wait for a notebook file from stdin input, as @konradmb pointed out. You can test running nbconvert from command line with this command instead: jupyter nbconvert --to html notebook.ipynb. It should output an HTML version of your notebook. If it works, then your nbconvert is probably fine.

I wrote the gist above as a little code snippet to use as a starting point that people can modify as needed for their own setup. I wrote it while working on a Mac, and judging from your git version it looks like you are on Windows. If that's the case, then you may need additional steps or some other configuration that is specific to Windows. You are welcome to fork this gist and create your own version for Windows. I would highly recommend posting a question about the errors you are getting on stackoverflow.com, and you'll get a bigger audience of people trying to help you troubleshoot your issues there. Git Gists are primarily for sharing code snippets and not so much for troubleshooting them in-depth. I think someone on StackOverflow will be able to point you in the right direction. Good luck!

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?