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 | .'"

Answer 3

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

Following this command:

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

Answer 4

nbstripout worked well for me.

Open the Jupyter terminal, navigate to the folder containing your notebook, and then run the following line:

nbstripout my_notebook.ipynb

Answer 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

Answer 6

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

Answer 7

I must say I find jupyer nbconvert painfully slow for the simple job of clearing some sub-arrays and resetting some execution numbers. It’s a superior solution in maintainability because that tool is expected to be updated if there is a change in the notebook source code format. However, the alternate solution below is faster and may also be useful if you don’t have nbconvert 6.0 (I have an environment running 5.6.1 at the moment…)

A very simple jq (a sort of sed for json) script does the trick very fast:

jq 'reduce path(.cells[]|select(.cell_type == "code")) as $cell (.; setpath($cell + ["outputs"]; []) | setpath($cell + ["execution_count"]; null))' notebook.ipynb > out-notebook.ipynb

Very simply, it identifies code cells, and replaces their outputs and execution_count attributes with [] and null respectively.

---

Or if you only want to remove the outputs and keep execution numbers, you can do even simpler:

jq 'del(.cells[]|select(.cell_type == "code").outputs[])' notebook.ipynb > out-notebook.ipynb

Answer 8

As mentioned in one of the previous answers you can use the command-line json processor jq to perform this task notably quicker than with nbconvert. A complete command for getting rid of metadata, outputs and execution counts can be found in this blog post:

jq --indent 1 \
    '
    (.cells[] | select(has("outputs")) | .outputs) = []
    | (.cells[] | select(has("execution_count")) | .execution_count) = null
    | .metadata = {"language_info": {"name":"python", "pygments_lexer": "ipython3"}}
    | .cells[].metadata = {}
    ' 01-parsing.ipynb

If desired, you could modify to just clean a specific part of the output, such as execution counts (recursively wherever they occur in the json), and then add this as a git filter:

[filter "nbstrip"]
    clean = jq --indent 1 '(.. |."execution_count"? | select(. != null)) = null'
    smudge = cat

And add the following to ~/.config/git/attributes to have the filter applied globally to all your local repos:

*.ipynb filter=nbstripout

There is also nbstripout which is made for this purpose, but it's a bit slower.

Answer 9

I suggest using pre-commit approach, using something like:

  - repo: local
    hooks:
      - id: jupyter-nb-clear-output
        name: jupyter-nb-clear-output
        files: \.ipynb$
        stages: [commit]
        language: python
        entry: jupyter nbconvert --ClearOutputPreprocessor.enabled=True --inplace
        additional_dependencies: ['jupyterlab']

also explained more in this blog.

Answer 10

Parse the json:

#LARGE Notebook Clean Make a Copy FIRST and Run this only on the COPY!!!!

import json 
filename = 'COPY_of_Huge_Notebook.ipynb' 
f = open(filename) 
large_ntbk = json.load(f) 
f.close() 
outputs = large_ntbk['cells'] 
for o in outputs:
    if 'outputs' in o:
        outputs['outputs'] = []

small = open('small.ipynb', 'w') 
json.dump(large_ntbk, small, indent = 2) 
small.close()