Home

Notes on scripted execution of notebooks

Using nbconvert:

jupyter nbconvert --to notebook --inplace --execute --ExecutePreprocessor.timeout=1200 notebooks/*

This executes all notebooks in-place, overwriting the previous state of the output cells.

Another option is jupyter-cache (which caches the executed state in a separate location and intelligently determines if that needs to be updated) - this is used by jupyter-book, which is in turn used by nbmake. nbmake is a plugin for pytest, with possibility for parallel execution, and by using jupyter-book, offers some extra control on the generated notebook html using notebook cell metadata.

Currently transitioning display of notebooks to https://swarm.magneticearth.org

Recipe to compile book locally:

git clone https://github.com/Swarm-DISC/Swarm_notebooks.git
cd Swarm_notebooks
docker run -v $(pwd):/home/jovyan -u root -e VIRES_TOKEN=$VIRES_TOKEN \
	registry.gitlab.eox.at/esa/vires_vre_ops/vre-swarm-notebook:0.8.0 \
	bash -c \
	'
	      export CDF_LIB=/opt/conda/lib && \
	      pip install --upgrade viresclient && \
	      viresclient set_token https://vires.services/ows $VIRES_TOKEN && \
	      viresclient set_default_server https://vires.services/ows && \
	      pip install jupyter-book --ignore-installed && \
	      jupyter-book build .
	'

Might need jupyter-book clean . to fix things between builds.

Experiment with using nbmake to benefit from parallelisation:

pip install nbmake[html] pytest-xdist[psutil] jupyter-book
pytest --numprocesses 2 --nbmake --overwrite notebooks/*.ipynb --deselect=notebooks/04c1_Geomag-Ground-Data-FTP.ipynb 

Note that we must overwrite the notebooks with the executed state rather than working in the jupyter-cache. Then use:

jupyter-book build --config _config-testing.yml .

to compile the book using the alternate config (which does not execute the books nor look at the jupyter-cache).

Push the book to Netlify:

netlify deploy --dir=_build/html