cgarciae/nbstripout

strip output from Jupyter and IPython notebooks

nbstripout: strip output from Jupyter and IPython notebooks

Opens a notebook, strips its output, and writes the outputless version to the original file.

Useful mainly as a git filter or pre-commit hook for users who don't want to track output in VCS.

This does mostly the same thing as the Clear All Output command in the notebook UI.

Based on https://gist.github.com/minrk/6176788.

Python 3 only

As of version 0.6.1, nbstripout supports Python 3 only. If you need to use Python 2.7, install nbstripout 0.3.10

pip install nbstripout==0.3.10

Screencast

This screencast demonstrates the use and working principles behind the nbstripout utility and how to use it as a Git filter:

Installation

You can download and install the latest version of nbstripout from PyPI, the Python package index, as follows:

pip install --upgrade nbstripout

When using the Anaconda Python distribution, install nbstripout via the conda package manager from conda-forge:

conda install -c conda-forge nbstripout

Usage

Strip output from IPython / Jupyter / Zeppelin notebook (modifies the file in-place):

nbstripout FILE.ipynb [FILE2.ipynb ...]
nbstripout FILE.zpln

Force processing of non .ipynb files:

nbstripout -f FILE.ipynb.bak

For using Zeppelin mode while processing files with other extensions use:

nbstripout -m zeppelin -f <file.ext>

Write to stdout e.g. to use as part of a shell pipeline:

cat FILE.ipynb | nbstripout > OUT.ipynb
cat FILE.zpln | nbstripout -m zeppelin > OUT.zpln

or

nbstripout -t FILE.ipynb | other-command

Set up the git filter and attributes as described in the manual installation instructions below:

nbstripout --install

Set up the git filter using .gitattributes

nbstripout --install --attributes .gitattributes

Specify a different path to the Python interpreter to be used for the git filters (default is the path to the Python interpreter used when nbstripout is installed). This is useful if you have Python installed in different or unusual locations across machines (e.g. /usr/bin/python3 on your machine vs /usr/local/bin/python3 in a container or elsewhere):

# Using just 'python3' lets each machine find its Python itself.
# However, keep in mind that depending on your setup this might not be
# the Python version you want or even fail because an absolute path is required.
nbstripout --install --python python3

Set up the git filter in your global ~/.gitconfig

nbstripout --install --global

Set up the git filter in your system-wide $(prefix)/etc/gitconfig (most installations will require you to sudo)

[sudo] nbstripout --install --system

Remove the git filter and attributes:

nbstripout --uninstall

Remove the git filter from your global ~/.gitconfig and attributes

nbstripout --uninstall --global

Remove the git filter from your system-wide $(prefix)/etc/gitconfig and attributes

[sudo] nbstripout --uninstall --system

Remove the git filter and attributes from .gitattributes:

nbstripout --uninstall --attributes .gitattributes

Check if nbstripout is installed in the current repository (exits with code 0 if installed, 1 otherwise):

nbstripout --is-installed

Print status of nbstripout installation in the current repository and configuration summary of filter and attributes if installed (exits with code 0 if installed, 1 otherwise):

nbstripout --status

Do a dry run and only list which files would have been stripped:

nbstripout --dry-run FILE.ipynb [FILE2.ipynb ...]

Print the version:

nbstripout --version

Show this help page:

nbstripout --help

Configuration files

The following table shows in which files the nbstripout filter and attribute configuration is written to for given extra flags to --install and --uninstall:

flags	filters	attributes
none	.git/config	.git/info/attributes
--global	~/.gitconfig	~/.config/git/attributes
--system	$(prefix)/etc/gitconfig	$(prefix)/etc/gitattributes
--attributes=.gitattributes	.git/config	.gitattributes
--global --attributes=.gitattributes	~/.gitconfig	.gitattributes

Install globally

Usually, nbstripout is installed per repository so you can choose where to use it or not. You can choose to set the attributes in .gitattributes and commit this file to your repository, however there is no way to have git set up the filters automatically when someone clones a repository. This is by design, to prevent you from executing arbitrary and potentially malicious code when cloning a repository.

To install nbstripout for all your repositories such that you no longer need to run the installation once per repository, install as follows:

mkdir -p ~/.config/git  # This folder may not exist
nbstripout --install --global --attributes=~/.config/git/attributes

This will set up the filters and diff driver in your ~/.gitconfig and instruct git to apply them to any .ipynb file in any repository.

Note that you need to uninstall with the same flags:

nbstripout --uninstall --global --attributes=~/.config/git/attributes

Install system-wide

To install nbstripout system-wide so that it applies to all repositories for all users, install as follows (most installations will require you to sudo):

[sudo] nbstripout --install --system

This will set up the filters and diff driver in $(prefix)/etc/gitconfig and instruct git to apply them to any .ipynb file in any repository for any user.

Note that you need to uninstall with the same flags:

[sudo] nbstripout --uninstall --system

Apply retroactively

nbstripout can be used to rewrite an existing Git repository using git filter-branch to strip output from existing notebooks. This invocation uses --index-filter and operates on all ipynb-files in the repo:

git filter-branch -f --index-filter '
    git checkout -- :*.ipynb
    find . -name "*.ipynb" -exec nbstripout "{}" +
    git add . --ignore-removal
'

If the repository is large and the notebooks are in a subdirectory it will run faster with git checkout -- :<subdir>/*.ipynb. You will get a warning for commits that do not contain any notebooks, which can be suppressed by piping stderr to /dev/null.

This is a potentially slower but simpler invocation using --tree-filter:

git filter-branch -f --tree-filter 'find . -name "*.ipynb" -exec nbstripout "{}" +'

Removing empty cells

Drop empty cells i.e. cells where source is either empty or only contains whitespace

nbstripout --drop-empty-cells

Removing init cells

By default nbstripout will keep cells with init_cell: true metadata. To disable this behavior use

nbstripout --strip-init-cells

Removing entire cells

In certain conditions it might be handy to remove not only the output, but the entire cell, e.g. when developing exercises.

To drop all cells tagged with "solution" run:

nbstripout --drop-tagged-cells="solution"

The option accepts a list of tags separated by whitespace.

Keeping some output

Do not strip the execution count/prompt number

nbstripout --keep-count

Do not strip outputs that are smaller that a given max size (useful for removing large outputs like images)

nbstripout --max-size 1k

Do not strip the output

nbstripout --keep-output

To mark special cells so that the output is not stripped, you can either:

1. Set the keep_output tag on the cell. To do this, enable the tags toolbar (View > Cell Toolbar > Tags) and then add the keep_output tag for each cell you would like to keep the output for.

2. Set the "keep_output": true metadata on the cell. To do this, select the "Edit Metadata" Cell Toolbar, and then use the "Edit Metadata" button on the desired cell to enter something like:

   {
     "keep_output": true,
   }
   

You can also keep output for an entire notebook. This is useful if you want to strip output by default in an automated environment (e.g. CI pipeline), but want to be able to keep outputs for some notebooks. To do so, add the option above to the notebook metadata instead. (You can also explicitly remove outputs from a particular cell in these notebooks by adding a cell-level metadata entry.)

Another use-case is to preserve initialization cells that might load customized CSS etc. critical for the display of the notebook. To support this, we also keep output for cells with:

{
  "init_cell": true,
}

This is the same metadata used by the init_cell nbextension.

Stripping metadata

The following metadata is stripped by default:

• Notebook metadata: signature, widgets
• Cell metadata: ExecuteTime, collapsed, execution, scrolled

Additional metadata to be stripped can be configured via either

• git config (--global/--system) filter.nbstripout.extrakeys, e.g.

  git config --global filter.nbstripout.extrakeys '
    metadata.celltoolbar
    metadata.kernelspec
    metadata.language_info.codemirror_mode.version
    metadata.language_info.pygments_lexer
    metadata.language_info.version
    metadata.toc
    metadata.notify_time
    metadata.varInspector
    cell.metadata.heading_collapsed
    cell.metadata.hidden
    cell.metadata.code_folding
    cell.metadata.tags
    cell.metadata.init_cell'
  

• the --extra-keys flag, which takes a space-delimited string as an argument, e.g.

  --extra-keys "metadata.celltoolbar cell.metadata.heading_collapsed"
  

You can keep certain metadata with either

• git config (--global/--system) filter.nbstripout.keepmetadatakeys, e.g.

  git config --global filter.nbstripout.keepmetadatakeys '
    cell.metadata.collapsed
    cell.metadata.scrolled'
  

• the --keep-metadata-keys flag, which takes a space-delimited string as an argument, e.g.

  --keep-metadata-keys "cell.metadata.collapsed cell.metadata.scrolled"
  

Note: Previous versions of Jupyter used metadata.kernel_spec for kernel metadata. Prefer stripping kernelspec entirely: only stripping some attributes inside kernelspec may lead to errors when opening the notebook in Jupyter (see #141).

Excluding files and folders

To exclude specific files or folders from being processed by the nbstripout filters, add the path and exception to your filter specifications defined in .git/info/attributes or .gitattributes:

docs/** filter= diff=

This will disable nbstripout for any file in the docs directory.:

notebooks/Analysis.ipynb filter= diff=

This will disable nbstripout for the file Analysis.ipynb located in the notebooks directory.

To check which attributes a given file has with the current config, run

git check-attr -a -- path/to/file

For a file to which the filter applies you will see the following:

$ git check-attr -a -- foo.ipynb
foo.ipynb: diff: ipynb
foo.ipynb: filter: nbstripout

For a file in your excluded folder you will see the following:

$ git check-attr -a -- docs/foo.ipynb
foo.ipynb: diff:
foo.ipynb: filter:

Manual filter installation

Set up a git filter and diff driver using nbstripout as follows:

git config filter.nbstripout.clean '/path/to/nbstripout'
git config filter.nbstripout.smudge cat
git config filter.nbstripout.required true
git config diff.ipynb.textconv '/path/to/nbstripout -t'

This will add a section to the .git/config file of the current repository.

If you want the filter to be installed globally for your user, add the --global flag to the git config invocations above to have the configuration written to your ~/.gitconfig and apply to all repositories.

If you want the filter to be installed system-wide, add the --system flag to the git config invocations above to have the configuration written to $(prefix)/etc/gitconfig and apply to all repositories for all users.

Create a file .gitattributes (if you want it versioned with the repository) or .git/info/attributes (to apply it only to the current repository) with the following content:

*.ipynb filter=nbstripout
*.ipynb diff=ipynb

This instructs git to use the filter named _nbstripout_ and the diff driver named _ipynb_ set up in the git config above for every .ipynb file in the repository.

If you want the attributes be set for .ipynb files in any of your git repositories, add those two lines to ~/.config/git/attributes. Note that this file and the ~/.config/git directory may not exist.

If you want the attributes be set for .ipynb files in any git repository on your system, add those two lines to $(prefix)/etc/gitattributes. Note that this file may not exist.

Using nbstripout as a pre-commit hook

pre-commit is a framework for managing git pre-commit hooks.

Once you have pre-commit installed, add the following to the .pre-commit-config.yaml in your repository:

repos:
- repo: https://github.com/kynan/nbstripout
  rev: 0.6.1
  hooks:
    - id: nbstripout

Then run pre-commit install to activate the hook.

Warning

In this mode, nbstripout is used as a git hook to strip any .ipynb files before committing. This also modifies your working copy!

In its regular mode, nbstripout acts as a filter and only modifies what git gets to see for committing or diffing. The working copy stays intact.

Troubleshooting

Known issues

Certain Git workflows are not well supported by nbstripout:

• Local changes to notebook files that are made invisible to Git due to the nbstripout filter do still cause conflicts when attempting to sync upstream changes (git pull, git merge etc.). This is because Git has no way of resolving a conflict caused by a non-stripped local file being merged with a stripped upstream file. Addressing this issue is out of scope for nbstripout. Read more and find workarounds in #108.

Show files processed by nbstripout filter

Git has no builtin support for listing files a clean or smudge filter operates on. As a workaround, change the setup of your filter in .git/config, ~/.gitconfig or $(prefix)/etc/gitconfig as follows to see the filenames either filter operates on:

[filter "nbstripout"]
    clean  = "f() { echo >&2 \"clean: nbstripout $1\"; nbstripout; }; f %f"
    smudge = "f() { echo >&2 \"smudge: cat $1\"; cat; }; f %f"
    required = true

Mercurial usage

Mercurial does not have the equivalent of smudge filters. One can use an encode/decode hook but this has some issues. An alternative solution is to provide a set of commands that first run nbstripout, then perform these operations. This is the approach of the mmf-setup package.