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

jupyter-notebook

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.

Solution 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.

Solution 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 | .'"

Solution 3:

Use --ClearOutputPreprocessor.enabled=True and --clear-output

Following this command:

jupyter nbconvert --ClearOutputPreprocessor.enabled=True --clear-output *.ipynb

Solution 4:

Use clean_ipynb, which not only clears notebook output but can also clean the code.

Install by pip install clean_ipynb

Run by clean_ipynb hello.ipynb

Solution 5:

To extend the answer from @dirkjot to resolve issue regarding sharing configuration:

Create a local .gitconfig file, rather than modifying .git/config. This makes the command that needs to be run on other machines slightly simpler. You can also create a script to run the git config command:

git config --local include.path ../.gitconfig

Note I have also changed the log level to INFO because I did want to see confirmation that the clean was running.

repo/.gitconfig

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

repo/.gitattributes

*.ipynb filter=strip-notebook-output

repo/git_configure.sh

git config --local include.path ../.gitconfig

Users then just need to run:

$ chmod u+x git_configure.sh
$ ./git_configure.sh