Rendering Jupyter notebooks to HTML
How to execute notebooks reproducibly and save the output to the results folder
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How to execute notebooks reproducibly and save the output to the results folder
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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.
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 for more details
