nb-clean 6.0.0

nb-clean cleans Jupyter notebooks for version control. It removes cell metadata, execution counts, outputs, and the notebook's language version. It can check notebooks in CI, clean files in place, or run as a Git filter or pre-commit hook.

Installation

Install a published release from PyPI with uv:

uv tool install nb-clean

For a single invocation:

uvx nb-clean check notebooks/

Wheels contain the native executable and require Python 3.10 or later for installation. They are built for macOS and Linux on ARM64 and x86-64, and Windows on x86-64. Linux wheels require glibc 2.17 or later. Use Cargo or binary archives on other platforms.

Install a published release from crates.io with Cargo:

cargo install nb-clean --locked

Building requires Rust 1.88 or later.

Download binary archives from GitHub releases for macOS (Apple Silicon and Intel), Linux (ARM64 and x86-64), and Windows (x86-64). Extract the archive and put nb-clean or nb-clean.exe on your PATH. Linux archives are built on Ubuntu 22.04 and use glibc. Build from source for systems incompatible with those binaries. Running nb-clean does not require a Python installation. Git is needed only for filter configuration.

Checking and cleaning

nb-clean check notebook.ipynb
nb-clean check notebooks/
nb-clean clean notebook.ipynb
nb-clean clean notebooks/ another.ipynb

Directories are searched recursively for .ipynb files, skipping hidden files and directories (such as .ipynb_checkpoints) and paths ignored by Git. Paths supplied explicitly are always processed. Use --no-ignore to disregard Git ignore rules, or --hidden to include hidden files and directories. Pass both to search all directories without either restriction:

nb-clean clean --no-ignore --hidden notebooks/

Overlapping inputs and symlink aliases are processed once. Directory symlinks encountered during recursion are skipped; an explicitly supplied directory symlink is traversed. Notebook file symlinks are followed, and cleaning updates their targets while preserving the links.

check reports unwanted content and exits with status 1 if any notebooks are dirty. Cells are numbered from zero. clean updates changed files while preserving their permissions. Already-clean files are left untouched. If a file fails, remaining files are still processed and the command returns an error status.

With no paths, both commands read stdin. Cleaning writes the notebook to stdout:

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

Clean stdin is passed through unchanged. Changed notebooks are written with sorted keys, one-space indentation, Unicode text, and a trailing newline, following nbformat's JSON layout.

nb-clean supports nbformat 4. It checks the structure needed for cleaning, keeps unknown fields, and does not upgrade notebooks or repair cell IDs. Empty source means an empty string or an array whose strings are all empty. Whitespace-only cells are retained.

Options

These directory search options work with check and clean:

The flags are independent: --no-ignore still skips hidden paths, and --hidden still respects Git ignore rules. Neither flag affects explicitly supplied files or stdin.

These options work with check, clean, and add-filter:

By default, notebook metadata is retained except language_info.version and transient fields. Preserving outputs with -o still clears output execution counts unless -c is also supplied.

For example, preserve cell tags and slideshow settings:

nb-clean clean --preserve-cell-metadata-field tags \
  --preserve-cell-metadata-field slideshow notebook.ipynb

Following nbformat, nb-clean always removes notebook metadata orig_nbformat, orig_nbformat_minor, and signature, and cell metadata trusted. Preservation options do not override this rule. Their presence makes a notebook dirty.

-M conflicts with -n. Preserving all cell metadata conflicts with selecting individual fields. Use nb-clean --help or nb-clean clean --help for help, and nb-clean --version for the version.

Git filter

From a Git working tree:

nb-clean add-filter
# Or configure the filter with cleaning options:
nb-clean add-filter --preserve-cell-metadata-field tags
nb-clean remove-filter

The filter is configured in the local Git configuration and .git/info/attributes. Staging cleans the notebook in the index; the working copy keeps its outputs. Installation and removal are idempotent and preserve unrelated settings and attributes. The executable must be on PATH when Git stages notebooks.

Pre-commit

Add this to .pre-commit-config.yaml:

repos:
  - repo: https://github.com/srstevenson/nb-clean
    rev: v6.0.0
    hooks:
      - id: nb-clean
        args: [--preserve-cell-metadata-field, tags]

Pre-commit builds the executable. The hook cleans notebooks in the working directory, so their outputs are removed on disk.

Jujutsu

Add this to ~/.config/jj/config.toml, then run jj fix:

[fix.tools.nb-clean]
command = ["nb-clean", "clean"]
patterns = ["glob:'**/*.ipynb'"]

Append cleaning options to the command array as needed.

Exit statuses

Errors take precedence over dirty results. If several files fail, the status corresponds to the first error in sorted processing order. Errors go to stderr; check findings go to stdout.

Migrating from nb-clean 5

check and clean now skip hidden files and directories, including .ipynb_checkpoints, and Git-ignored paths when searching directories. Previously, these notebooks were included.

To retain the version 5 directory search behaviour, add both --no-ignore and --hidden:

nb-clean check --no-ignore --hidden notebooks/
nb-clean clean --no-ignore --hidden notebooks/

The flags are independent: --no-ignore disables Git ignore rules, while --hidden includes hidden files and directories. Explicitly supplied files are still processed regardless of either restriction. Stdin, Git filters, and the standard pre-commit hook need no changes.

Migrating from nb-clean 4

nb-clean was ported from Python to Rust in version 5. PyPI wheels install the native executable; the Python library API is removed. The installed command supports Git filters and pre-commit as before.

Use nb-clean --version instead of nb-clean version. To preserve selected metadata, replace --preserve-cell-metadata tags slideshow -- with --preserve-cell-metadata-field tags --preserve-cell-metadata-field slideshow. The bare -m option now accepts no field arguments and can appear before paths.

An execution count of zero is now reported as dirty. Transient metadata is also reported explicitly. Processing errors use the statuses above, and clean files are no longer rewritten just to normalise formatting. Unsupported notebook major versions are rejected.

Development

See the contribution instructions.

Copyright

Copyright Scott Stevenson. Distributed under the ISC licence.