Using at the Command Line

Command line conversion

The package provides a jupytext script for command line conversion between the various notebook extensions:

jupytext --to py notebook.ipynb                 # convert notebook.ipynb to a .py file
jupytext --to py:percent notebook.ipynb         # convert notebook.ipynb to a .py file in the double percent format
jupytext --to py:percent --opt comment_magics=false notebook.ipynb   # same as above + do not comment magic commands
jupytext --to markdown notebook.ipynb           # convert notebook.ipynb to a .md file
jupytext --output notebook.ipynb      # convert notebook.ipynb to a file

jupytext --to notebook              # convert to an .ipynb file with no outputs
jupytext --update --to notebook     # update the input cells in the .ipynb file and preserve outputs and metadata

jupytext --to md --test notebook.ipynb          # Test round trip conversion

jupytext --to md --output - notebook.ipynb      # display the markdown version on screen
jupytext --from ipynb --to py:percent           # read ipynb from stdin and write double percent script on stdout

Jupytext has a --sync mode that updates all the paired representations of a notebook based on timestamps:

jupytext --set-formats ipynb,py notebook.ipynb  # Turn notebook.ipynb into a paired ipynb/py notebook
jupytext --sync notebook.ipynb                  # Update whichever of notebook.ipynb/ is outdated

You may also find useful to --pipe the text representation of a notebook into tools like black:

jupytext --sync --pipe black notebook.ipynb    # read most recent version of notebook, reformat with black, save

To reorder the imports in your notebook, use

jupytext --pipe 'isort - --treat-comment-as-code "# %%" --float-to-top' notebook.ipynb

(remove the --float-to-top argument if you prefer to run isort per cell).

For programs that don’t accept pipes, use {} as a placeholder for the name of a temporary file that will contain the text representation of the notebook. For instance, run pytest on your notebook with:

jupytext --check 'pytest {}' notebook.ipynb    # export the notebook in format py:percent in a temp file, run pytest

Read more about running pytest on notebooks in our example Tests in a Note also that on Windows you need to use double quotes instead of single quotes and type e.g. jupytext --check "pytest {}" notebook.ipynb.

Execute jupytext --help to access the full documentation.

Execute notebook cells

For convenience, when creating a notebook from text you can execute it:

jupytext --set-kernel -             # create a YAML header with kernel metadata matching the current python executable
jupytext --set-formats md:myst      # create a YAML header with an explicit jupytext format
jupytext --to notebook --execute    # convert to an .ipynb file and run it

If you wanted to convert a collection of Markdown files to paired notebooks, and execute them in the current Python environment, you could run:

jupytext --set-formats ipynb,md --execute *.md

Advanced usage: error tolerance

If any notebook cell errors, execution will terminate and jupytext will not save the notebook. This can cause headaches as the details of any error would be encoded in the notebook, which would not have been saved. But there’s an error-tolerant way to execute a notebook: jupyter nbconvert has a mode which will still save a notebook if a cell errors, producing something akin to what would happen if you ran all cells manually in Jupyter’s notebook UI.

# First, convert script (py/sh/R/jl etc) -> notebook. May need additional args to define input format etc as above.
jupytext --to ipynb
# Then, execute notebook in place and allowing cells to produce errors
jupyter nbconvert --to ipynb --inplace --execute --allow-errors script.ipynb
# One can also combine these to a single command using jupytext --pipe
jupytext --to ipynb --pipe-fmt ipynb \
  --pipe 'jupyter nbconvert --to ipynb --execute --allow-errors --stdin --stdout' \

In each of the above, jupyter nbconvert could be replaced with any alternative tool to execute a jupyter notebook non-interactively, including papermill which would allow notebook parameterisation (see @mwouts’ post on the topic here).

Notebook and cell metadata filters

If you want to preserve (or filter out) certain notebook or cell metadata, change the value of either notebook_metadata_filter or cell_metadata_filter with the --update-metadata option. For instance, if you wish to convert an .ipynb document to a .md file and preserve all the notebook metadata in that document, run

jupytext --to md --update-metadata '{"jupytext": {"notebook_metadata_filter":"all"}}' notebook.ipynb

Read more on the default and possible values for the metadata filters in this section.

Testing the round-trip conversion

Representing Jupyter notebooks as scripts requires a solid round trip conversion. You don’t want your notebooks (nor your scripts) to be modified because you are converting them to the other form. Our test suite includes a few hundred tests to ensure that round trip conversion is safe.

You can easily test that the round trip conversion preserves your Jupyter notebooks and scripts. Run for instance:

# Test the ipynb -> py:percent -> ipynb round trip conversion
jupytext --test notebook.ipynb --to py:percent

# Test the ipynb -> (py:percent + ipynb) -> ipynb (à la paired notebook) conversion
jupytext --test --update notebook.ipynb --to py:percent

Note that jupytext --test compares the resulting notebooks according to its expectations. If you wish to proceed to a strict comparison of the two notebooks, use jupytext --test-strict, and use the flag -x to report with more details on the first difference, if any.

Please note that

  • Scripts opened with Jupyter have a default metadata filter that prevents additional notebook or cell metadata to be added back to the script. Remove the filter if you want to store Jupytext’s settings, or the kernel information, in the text file.

  • Cell metadata are available in the light and percent formats, as well as in the Markdown and R Markdown formats. R scripts in spin format support cell metadata for code cells only. Sphinx Gallery scripts in sphinx format do not support cell metadata.

  • By default, a few cell metadata are not included in the text representation of the notebook. And only the most standard notebook metadata are exported. Learn more on this in the sections for notebook specific and global settings for metadata filtering.