.. paperpipe:

Papermill Pipeline
==================

The papermill pipeline executes Jupyter notebooks using
`Papermill <https://papermill.readthedocs.io/>`_. Plase read the official
documentation on how to paramaterize the notebooks.

An example pipeline definition file is below (and
can be obtained typing ``owl pdef get papermill``
-- see :ref:`piperun`).

.. code-block:: yaml

    version: 1.2
    name: papermill

    input_dir: /home/user/myDir
    output_dir: /home/user/myDir
    notebook: notebook.ipynb

    paramaters: {}


    # use dask (optional, see docs)
    # use_dask: false

    resources:
      workers: 1
      memory: 8
      threads: 1

The pipeline requires the input and output directories and the name of the 
notebook to execute. The executed notebook will be saved in the output directory
with the name ``notebook_out.ipynb`` in this example.

The parameters required to run the notebook are defined in ``parameters``.
See `Papermill <https://papermill.readthedocs.io/>`_ on information on how
to parameterize notebooks.

The following shows an example output notebook that includes outputs and figures.

.. figure:: paperpipe.png

The notebook :download:`papermill_example.ipynb <./papermill_example.ipynb>` demonstrates
a Papermill notebook example.