While Jupyter notebooks are commonly used interactively, with cells executed individually, on Code Ocean we ask that the notebook be executable as a whole and serve as a reproducible record of the analysis from start to finish. To render a Jupyter notebook from the command-line, or (in this case) from your
run.sh shell script, use the following command:
jupyter nbconvert \
--ExecutePreprocessor.allow_errors=Trueflag isn't strictly necessary, but will reveal errors within the notebook, which makes debugging much easier.
--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:
- See nbconvert's excellent documentation for more details.
For an example of a Jupyter running on Code Ocean, see Fractal Generation with L-Systems.