nb-clean 3.3.0

Clean Jupyter notebooks for versioning

nb-clean cleans Jupyter notebooks of cell execution counts, metadata, outputs, and (optionally) empty cells, preparing them for committing to version control. It provides both a Git filter and pre-commit hook to automatically clean notebooks before they're staged, and can also be used with other version control systems, as a command line tool, and as a Python library. It can determine if a notebook is clean or not, which can be used as a check in your continuous integration pipelines.

[!NOTE]

nb-clean 2.0.0 introduced a new command line interface to make cleaning notebooks in place easier. If you upgrade from a previous release, you'll need to migrate to the new interface as described under Migrating to nb-clean 2.

Installation

To install the latest release from PyPI, use pip:

python3 -m pip install nb-clean

nb-clean can also be installed with Conda:

conda install -c conda-forge nb-clean

In Python projects using Poetry or PDM for dependency management, add nb-clean as a development dependency with poetry add --group dev nb-clean or pdm add --dev nb-clean. nb-clean requires Python 3.8 or later.

Usage

Checking

You can check if a notebook is clean with:

nb-clean check notebook.ipynb

or by passing the notebook contents on standard input:

nb-clean check < notebook.ipynb

The check can be run with the following flags:

• To check for empty cells use --remove-empty-cells or the short form -e.
• To ignore cell metadata use --preserve-cell-metadata or the short form -m. This will ignore all metadata fields. You can also pass a list of fields to ignore with --preserve-cell-metadata field1 field2 or -m field1 field2. Note that when not passing a list of fields, either the -m or --preserve-cell-metadata flag must be passed after the notebook paths to process, or the notebook paths should be preceded with -- so they are not interpreted as metadata fields.
• To ignore cell outputs use --preserve-cell-outputs or the short form -o.
• To ignore cell execution counts use --preserve-execution-counts or the short form -c.
• To ignore language version notebook metadata use --preserve-notebook-metadata or the short form -n.
• To check the notebook does not contain any notebook metadata use --remove-all-notebook-metadata or the short form -M.

For example, to check if a notebook is clean whilst ignoring notebook metadata:

nb-clean check --preserve-notebook-metadata notebook.ipynb

To check if a notebook is clean whilst ignoring all cell metadata:

nb-clean check --preserve-cell-metadata -- notebook.ipynb

To check if a notebook is clean whilst ignoring only the tags cell metadata field:

nb-clean check --preserve-cell-metadata tags -- notebook.ipynb

nb-clean will exit with status code 0 if the notebook is clean, and status code 1 if it is not. nb-clean will also print details of cell execution counts, metadata, outputs, and empty cells it finds.

Cleaning (interactive)

You can clean a Jupyter notebook with:

nb-clean clean notebook.ipynb

This cleans the notebook in place. You can also pass the notebook content on standard input, in which case the cleaned notebook is written to standard output:

nb-clean clean < original.ipynb > cleaned.ipynb

The cleaning can be run with the following flags:

• To remove empty cells use --remove-empty-cells or the short form -e.
• To preserve cell metadata use --preserve-cell-metadata or the short form -m. This will preserve all metadata fields. You can also pass a list of fields to preserve with --preserve-cell-metadata field1 field2 or -m field1 field2. Note that when not passing a list of fields, either the -m or --preserve-cell-metadata flag must be passed after the notebook paths to process, or the notebook paths should be preceded with -- so they are not interpreted as metadata fields.
• To preserve cell outputs use --preserve-cell-outputs or the short form -o.
• To preserve cell execution counts use --preserve-execution-counts or the short form -c.
• To preserve notebook metadata (such as language version) use --preserve-notebook-metadata or the short form -n.
• To remove all notebook metadata use --remove-all-notebook-metadata or the short form -M.

For example, to clean a notebook whilst preserving notebook metadata:

nb-clean clean --preserve-notebook-metadata notebook.ipynb

To clean a notebook whilst preserving all cell metadata:

nb-clean clean --preserve-cell-metadata -- notebook.ipynb

To clean a notebook whilst preserving only the tags cell metadata field:

nb-clean clean --preserve-cell-metadata tags -- notebook.ipynb

Cleaning (Git filter)

To add a filter to an existing Git repository to automatically clean notebooks when they're staged, run the following from the working tree:

nb-clean add-filter

This will configure a filter to remove cell execution counts, metadata, and outputs. To also remove empty cells, use:

nb-clean add-filter --remove-empty-cells

To preserve cell metadata, such as that required by tools such as papermill, use:

nb-clean add-filter --preserve-cell-metadata

To preserve only specific cell metadata, e.g., tags and special, use:

nb-clean add-filter --preserve-cell-metadata tags special

To preserve cell outputs, use:

nb-clean add-filter --preserve-cell-outputs

To preserve cell execution counts, use:

nb-clean add-filter --preserve-execution-counts

To preserve notebook language_info.version metadata, use:

nb-clean add-filter --preserve-notebook-metadata

By default, nb-clean will not delete all notebook metadata. To completely remove all notebook metadata:

nb-clean add-filter --remove-all-notebook-metadata

nb-clean will configure a filter in the Git repository in which it is run, and won't mutate your global or system Git configuration. To remove the filter, run:

nb-clean remove-filter

Cleaning (pre-commit hook)

nb-clean can also be used as a pre-commit hook. You may prefer this to the Git filter if your project already uses the pre-commit framework.

Note that the Git filter and pre-commit hook work differently, with different effects on your working directory. The pre-commit hook operates on the notebook on disk, cleaning the copy in your working directory. The Git filter cleans notebooks as they are added to the index, leaving the copy in your working directory dirty. This means cell outputs are still visible to you in your local Jupyter instance when using the Git filter, but not when using the pre-commit hook.

After installing pre-commit, add the nb-clean hook by adding the following snippet to .pre-commit-config.yaml in the root of your repository:

repos:
  - repo: https://github.com/srstevenson/nb-clean
    rev: 3.3.0
    hooks:
      - id: nb-clean

You can pass additional arguments to nb-clean with an args array. The following example shows how to preserve only two specific metadata fields. Note that, in the example, the final item -- in the arg list is mandatory. The option --preserve-cell-metadata may take an arbitrary number of field arguments, and the -- argument is needed to separate them from notebook filenames, which pre-commit will append to the list of arguments.

repos:
  - repo: https://github.com/srstevenson/nb-clean
    rev: 3.3.0
    hooks:
      - id: nb-clean
        args:
          - --remove-empty-cells
          - --preserve-cell-metadata
          - tags
          - slideshow
          - --

Run pre-commit install to ensure the hook is installed, and pre-commit autoupdate to update the hook to the latest release of nb-clean.

Preserving all nbformat metadata

To ignore or preserve specifically the metadata defined in the nbformat documentation, use the following options: --preserve-cell-metadata collapsed scrolled deletable editable format name tags jupyter execution.

Migrating to nb-clean 2

The following table maps from the command line interface of nb-clean 1.6.0 to that of nb-clean >=2.0.0.

The examples in the table use long flags, but short flags can also be used instead.

Description	nb-clean 1.6.0	nb-clean >=2.0.0
Clean notebook	nb-clean clean --input notebook.ipynb | sponge notebook.ipynb	nb-clean clean notebook.ipynb
Clean notebook (remove empty cells)	nb-clean clean --input notebook.ipynb --remove-empty	nb-clean clean --remove-empty-cells notebook.ipynb
Clean notebook (preserve all cell metadata)	nb-clean clean --input notebook.ipynb --preserve-metadata	nb-clean clean --preserve-cell-metadata -- notebook.ipynb
Check notebook	nb-clean check --input notebook.ipynb	nb-clean check notebook.ipynb
Check notebook (ignore non-empty cells)	nb-clean check --input notebook.ipynb --remove-empty	nb-clean check --remove-empty-cells notebook.ipynb
Check notebook (ignore all cell metadata)	nb-clean check --input notebook.ipynb --preserve-metadata	nb-clean check --preserve-cell-metadata -- notebook.ipynb
Add Git filter to clean notebooks	nb-clean configure-git	nb-clean add-filter
Remove Git filter	nb-clean unconfigure-git	nb-clean remove-filter

Copyright

Copyright © Scott Stevenson.

nb-clean is distributed under the terms of the ISC license.