https://github.com/kynan/nbstripout

strip output from Jupyter and IPython notebooks
https://github.com/kynan/nbstripout

filter git hacktoberfest hooks ipython ipython-notebook jupyter jupyter-notebook

Last synced: about 2 months ago
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strip output from Jupyter and IPython notebooks

• Host: GitHub
• URL: https://github.com/kynan/nbstripout
• Owner: kynan
• License: other
• Created: 2015-09-12T23:36:59.000Z (about 9 years ago)
• Default Branch: main
• Last Pushed: 2024-03-24T14:44:18.000Z (6 months ago)
• Last Synced: 2024-06-11T17:32:04.642Z (3 months ago)
• Topics: filter, git, hacktoberfest, hooks, ipython, ipython-notebook, jupyter, jupyter-notebook
• Language: Python
• Homepage:
• Size: 277 KB
• Stars: 1,163
• Watchers: 8
• Forks: 94
• Open Issues: 22
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.md
  • Contributing: CONTRIBUTING.md
  • License: LICENSE.txt
  • Code of conduct: CODE_OF_CONDUCT.md

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• awesome-starred - kynan/nbstripout - strip output from Jupyter and IPython notebooks (jupyter-notebook)

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# nbstripout: strip output from Jupyter and IPython notebooks

Reads a notebook from a file or stdin, strips output and some metadata, and

writes the "cleaned" version of the notebook to the original file or stdout.

Intended to be used as a Git filter or pre-commit hook for users who don't want

to track output in Git.

Roughly equivalent to the "Clear All Output" command in the notebook UI, but

only "visible" to Git: keep your output in the file on disk, but don't commit

the output to Git. This helps minimizing diffs and reduce file size.

Originally based on .

## Python 3 only

As of version 0.4.0, 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:

[![image](https://i.imgur.com/7oQHuJ5.png)](https://www.youtube.com/watch?v=BEMP4xacrVc)

## Installation

You can download and install the latest version of `nbstripout` from the Python

package index [PyPI](https://pypi.org/project/nbstripout/) as follows:

    pip install --upgrade nbstripout

When using the [Anaconda](https://www.anaconda.com/download) Python

distribution, install `nbstripout` via the [conda](https://docs.conda.io)

package manager from [conda-forge](https://conda-forge.org):

    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 

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

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

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

Operate on all `.ipynb` files in the current directory and subdirectories

recursively:

    find . -name '*.ipynb' -exec nbstripout {} +

Print the version:

    nbstripout --version

Show help and usage instructions:

    nbstripout --help

### Using as a Git filter

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.

    nbstripout --install --python python3

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.

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

### 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-repo`](https://github.com/newren/git-filter-repo) to strip output

from existing notebooks. This invocation operates on all ipynb files in the repo:

```sh

    #!/usr/bin/env bash

    # get lint-history with callback from https://github.com/newren/git-filter-repo/pull/542

    ./lint-history.py --relevant 'return filename.endswith(b".ipynb")' --callback '

    import json, warnings, nbformat

    from nbstripout import strip_output

    from nbformat.reader import NotJSONError

    try:

        with warnings.catch_warnings():

            warnings.simplefilter("ignore", category=UserWarning)

            notebook = nbformat.reads(blob.data, as_version=nbformat.NO_CONVERT)

        # customize to your needs

        strip_output(notebook, keep_output=False, keep_count=False, keep_id=False, extra_keys=["metadata.widgets","metadata.execution","cell.attachments"], drop_empty_cells=True,  drop_tagged_cells=[],strip_init_cells=False, max_size=0)

        old_len = len(blob.data)

        blob.data = (nbformat.writes(notebook) + "\n").encode("utf-8")

        if old_len != len(blob.data):

            print(change.blob_id, change.filename, old_len, len(blob.data))

    except NotJSONError as e:

         print("ERROR", type(e), change.blob_id, filename)

    '

```

### Removing empty cells

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

whitespace:

    nbstripout --drop-empty-cells

### Removing [init]{.title-ref} 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

only large outputs like images):

    nbstripout --max-size 1k

Do not strip the output, only metadata:

    nbstripout --keep-output

Do not reassign the cell ids to be sequential (which is the default behavior):

    nbstripout --keep-id

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](https://github.com/ipython-contrib/jupyter_contrib_nbextensions/tree/master/src/jupyter_contrib_nbextensions/nbextensions/init_cell).

### Stripping metadata

The following metadata is stripped by default:

-   Notebook metadata: `signature`, `widgets`

-   Cell metadata: `ExecuteTime`, `collapsed`, `execution`, `heading_collapsed`,

    `hidden`, `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"

Note: Only notebook and cell metadata is currently supported and every key

specified via `filter.nbstripout.extrakeys` or `--extra-keys` must start with

`metadata.` for notebook and `cell.metadata.` for cell metadata.

You can keep certain metadata that would be stripped by default 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](https://github.com/kynan/nbstripout/issues/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](https://pre-commit.com) is a framework for managing git

[pre-commit hooks](https://git-scm.com/docs/githooks).

Once you have [pre-commit](https://pre-commit.com) installed, add the following

to the `.pre-commit-config.yaml` in your repository:

    repos:

    - repo: https://github.com/kynan/nbstripout

      rev: 0.7.1

      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](https://github.com/kynan/nbstripout/issues/108).

### Show files processed by nbstripout filter

Git has [no builtin support](https://stackoverflow.com/a/52065333/396967) 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