How to clear Jupyter Notebook's output in all cells from the Linux terminal?

Question

I have a problem when the output from a notebook is really long and it's saved into the notebook, any time I want to open this particular notebook again the browser crashes and can't display correctly.

To fix this I have to open it with a text editor and delete all output from that cell causing the problem.

I wonder if there is a way to clean all output from the notebook so one can open it again without problem. I want to delete all output since deleting a specific one seems more troublesome.

Answer 1

nbconvert 6.0 should fix --clear-output

The option had been broken for a long time previously, bug report with merged patch: https://github.com/jupyter/nbconvert/issues/822

Usage should be for in-place operation:

jupyter nbconvert --clear-output --inplace my_notebook.ipynb 

Or to save to another file called my_notebook_no_out.ipynb:

jupyter nbconvert --clear-output \   --to notebook --output=my_notebook_no_out my_notebook.ipynb 

This was brought to my attention by Harold in the comments.

Before nbconvert 6.0: --ClearOutputPreprocessor.enabled=True

Same usage as --clear-output:

jupyter nbconvert --ClearOutputPreprocessor.enabled=True --inplace my_notebook.ipynb jupyter nbconvert --ClearOutputPreprocessor.enabled=True \   --to notebook --output=my_notebook_no_out my_notebook.ipynb 

Tested in Jupyter 4.4.0, notebook==5.7.6.

Answer 2

If you create a .gitattributes file, you can run a filter over certain files before they are added to git. This will leave the original file on disk as-is, but commit the "cleaned" version.

For this to work, add this to your local .git/config or global ~/.gitconfig:

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

Then create a .gitattributes file in your directory with notebooks, with this content:

*.ipynb filter=strip-notebook-output 

How this works:

• The attribute tells git to run the filter's clean action on each notebook file before adding it to the index (staging).
• The filter is our friend nbconvert, set up to read from stdin, write to stdout, strip the output, and only speak when it has something important to say.
• When a file is extracted from the index, the filter's smudge action is run, but this is a no-op as we did not specify it. You could run your notebook here to re-create the output (nbconvert --execute).
• Note that if the filter somehow fails, the file will be staged unconverted.

My only minor gripe with this process is that I can commit .gitattributes but I have to tell my co-workers to update their .git/config.

If you want a hackier but much faster version, try JQ:

  clean = "jq '.cells[].outputs = [] | .cells[].execution_count = null | .'"