Skip to main content

SoS extension for papermill

Project description

PyPI version Build Status

Papermill engine for SoS Notebook

papermill is a tool for parameterizing, executing, and analyzing Jupyter Notebooks. It lets you parameterize and execute notebooks in batch mode.

SoS Notebook is a Jupyter kernel that allows the use of multiple kernels in one Jupyter notebook. Using language modules that understand datatypes of underlying languages (modules sos-bash, sos-r, sos-matlab, etc), SoS Notebook allows data exchange among live kernels of supported languages. SoS Notebook is also a frontend to the SoS Workflow that allows the development and execution of workflows from Jupyter notebooks.

Because the default papermill executor assumes a single kernel for the entire notebook, sos-papermill is provided as a customized engine for the execution of SoS notebooks.

Installation

pip install sos-papermill

or

conda install sos-papermill -c conda-forge

if you are using a conda environment.

Note that you will need to install sos-notebook, all relevant kernels (e.g. bash_kernel, irkernel) and related language modules (e.g. sos-bash, sos-r) to execute notebooks that use these kernels. Please refer to Running SoS for details on how to install SoS Notebook.

Documentation

sos-papermill provides sos engine for papermill. All you need to do is to add option --engine sos to any papermill command that you might use:

papermill --engine sos [other options]

For example, to execute a parametrized notebook with parameter cutoff, you can use command

papermill --engine sos my_experiment.ipynb experiment_cutoff_2.ipynb -y '{"cutoff": 2}'

Please refer to the Papermill documentation for details on the use of papermill.

Note that parameters can be defined in either a SoS or a subkernel cell but in both cases parameters should be passed in Python syntax. Parameters defined in a subkernel will be automatically transferred to the subkernel using a %put magic.

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for sos-papermill, version 0.2.1
Filename, size File type Python version Upload date Hashes
Filename, size sos_papermill-0.2.1-py3-none-any.whl (7.6 kB) File type Wheel Python version py3 Upload date Hashes View
Filename, size sos-papermill-0.2.1.tar.gz (12.0 kB) File type Source Python version None Upload date Hashes View

Supported by

Pingdom Pingdom Monitoring Google Google Object Storage and Download Analytics Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN DigiCert DigiCert EV certificate StatusPage StatusPage Status page