Running an IPython/Jupyter notebook non-interactively

Run and replace original .ipunb file:

jupyter nbconvert --ExecutePreprocessor.timeout=-1 --to notebook --inplace --execute original.ipynb

Until this functionality becomes part of the core, I put together a little command-line app that does just what you want. It's called runipy and you can install it with pip install runipy. The source and readme are on github.

Yes it is possible, and easy, it will (mostly) be in IPython core for 2.0, I would suggest looking at those examples for now.

[edit]

$ jupyter nbconvert --to notebook --execute original.ipynb --output=new.ipynb

It is now in Jupyter NbConvert. NbConvert comes with a bunch of Preprocessors that are disabled by default, two of them (ClearOutputPreprocessor and ExecutePreprocessor) are of interest. You can either enabled them in your (local|global) config file(s) via c.<PreprocessorName>.enabled=True (Uppercase that's python), or on the command line with --ExecutePreprocessor.enabled=True keep the rest of the command as usual.

The --ExecutePreprocessor.enabled=True has convenient --execute alias that can be used on recent version of NbConvert. It can be combine with --inplace if desired

For example, convert to html after running the notebook headless :

$ jupyter nbconvert --to=html --execute RunMe.ipynb

converting to PDF after stripping outputs

$ ipython nbconvert --to=pdf --ClearOutputPreprocessor.enabled=True RunMe.ipynb

This (of course) does work with non-python kernels by spawning a <insert-your-language-here> kernel, if you set --profile=<your fav profile>. The conversion can be really long as it needs to rerun the notebook. You can do notebook to notebook conversion with the --to=notebook option.

There are various other options (timeout, allow errors, ...) that might need to be set/unset depending on use case. See documentation and of course jupyter nbconvert --help, --help-all, or nbconvert online documentation for more information.

To cover some features such as parallel workers, input parameters, e-mail sending or S3 input/output... you can install jupyter-runner

pip install jupyter-runner

Readme on github: https://github.com/omar-masmoudi/jupyter-runner