While Jupyter notebooks are commonly used interactively, with cells executed individually, to publish on Code Ocean, we ask that notebooks be executed as a whole. This allows notebooks to serve as a reproducible record of the analysis from start to finish.
To do so, add commands* to your master 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=Trueflag isn't strictly necessary, but will reveal errors within the notebook, which makes debugging much easier.The
--ExecutePreprocessor.timeout=-1flag 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
/codepane. This showcases that all notebooks in the/resultshave been successfully rendered in the Code Ocean environment.See nbconvert's excellent documentation for more details
*These commands can also be used to render a Jupyter notebook directly from the command line.