Run (and time) Jupyter Notebooks for command-line and makefile
Run Jupyter notebooks quietly from command-line
runPyNB is a quick and dirty utility to run (and time) Jupyter notebooks from command-line and makefiles.
Install from PyPI
pip install runpynb
runpynb <notebook(s)> [options] (".ipynb" not required)
runpynb: Run all notebooks in directory.
runpynb <notebook(s)> -q: Run quietly (
$ runpynb hello.ipynb -q
runpynb <notebook(s)> -qs: Run quietly (
-q) as a sequence of workflow (
-s). Errors (eg in
error.ipynb) will break the workflow.
$ runpynb error.ipynb hello.ipynb -qs
runpynb <notebook(s)> -o: Save output as separate notebook (
-o), instead of overwriting existing notebook(s).
$ runpynb hello.ipynb -o
usage: runpynb [-h] [-t TIMEOUT] [-s] [-o] [-v VERSION] [-q] [notebooks ...] Run (and time) Jupyter notebooks silently in command-line. positional arguments: notebooks List of Jupyter notebooks (*.ipynb) to be run (default=all notebooks in path). optional arguments: -h, --help show this help message and exit -t TIMEOUT, --timeout TIMEOUT Seconds until a cell in the notebook timesout, which raises a Timeouterror exception (default is 3000=5 mins). -s, --sequence Sequence implicit in notebook lists. If error occurs somewhere, stop entire pipeline. -o, --output Save output as a separate notebook with "-out"-suffix (e.g. *-out.ipynb) instead of overwriting existing file. -v VERSION, --version VERSION Version of notebook to return (Default=No conversion). Notebook will be converted if necessary. -q, --quiet Be quiet and don't print messages (including run time). Caution: Does not suppress error messages.
My workflow involves using
Jupyter notebooks to clean, and analyze data.
I use this utility to run notebooks silently from the command-line and
Makefiles (without converting from
.ipynb files to
Usage with Makefiles
A minimal workflow where
get-data.ipynb takes 5000 seconds to prepare
data.csv to produce
.DEFAULT_GOAL := output.png data.csv: get-data.ipynb runpynb $^ -t 5000 output.png: analyze.ipynb data.csv runpynb $<
- Build fails with Python 3.6 in Windows OS.
- Notebooks with long execution time will require the
runpynb notebook.ipynb -t 10000).
This package is licensed under the MIT License.
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