Rendering Jupyter notebooks to HTML

How to execute notebooks reproducibly and save the output to the results folder

Rendering Jupyter notebooks to HTML allows notebooks to serve as a reproducible record of the analysis from start to finish.

To do so, add commands* to your main script to execute jupyter nbconvert with the --execute flag listed. This renders the final results into /results as an HTML file.

jupyter nbconvert \  
    --ExecutePreprocessor.allow_errors=True \  
    --ExecutePreprocessor.timeout=-1 \  
    --FilesWriter.build_directory=../results \  
    --execute notebook.ipynb

Notes

• The --ExecutePreprocessor.allow_errors=True flag isn't strictly necessary, but will reveal errors within the notebook, which makes debugging much easier.

• The --ExecutePreprocessor.timeout=-1 flag will disable execution timeouts, allowing each cell to take as much time as it needs to execute.

• If you are using Python 3 you may need to specify the following flag: --ExecutePreprocessor.kernel_name="python3"

• Code Ocean currently strips out the inline results from notebooks in the /code pane. This showcases that all notebooks in the /results have been successfully rendered in the Code Ocean environment.

• See nbconvert's documentation for more details

These commands can also be used to render a Jupyter notebook directly from the command line.