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# Run Jupyter notebooks quietly from command-line
[](https://pypi.org/project/runpynb/)
<br>
[](https://pypi.org/project/runpynb/)
<br>
[](https://zenodo.org/badge/latestdoi/520408889)
`runPyNB` is a quick and dirty utility to run (and time) Jupyter notebooks from command-line and makefiles.
<!------------------- Quickstart ------------------->
## Quickstart
Install from PyPI
```bash
pip install runpynb
```
General usage: `runpynb <notebook(s)> [options]` (".ipynb" not required)
* `runpynb`: Run all notebooks in directory.
<pre>
$ runpynb</pre>
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<!------------------------ Usage ---------------------->
## Usage
* `runpynb <notebook(s)> -q`: Run quietly (`-q`).
<pre>
$ runpynb hello.ipynb -q</pre>
* `runpynb <notebook(s)> -qs`: Run quietly (`-q`) as a sequence of workflow (`-s`). Errors (eg in `error.ipynb`) will break the workflow.
<pre>
$ runpynb error.ipynb hello.ipynb -qs</pre>
* `runpynb <notebook(s)> -o`: Save output as separate notebook (`-o`), instead of overwriting existing notebook(s).
<pre>
$ runpynb hello.ipynb -o</pre>
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<!---------------------- Options ---------------------->
## Options
```bash
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.
```
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<!----------------- Project status ----------------->
## Status
[](https://runpynb.readthedocs.io/en/latest/?badge=latest)
<br>
[](https://app.travis-ci.com/LSYS/runPyNB)
<br>
[](https://github.com/LSYS/runPyNB/actions/workflows/tests.yml)
[](https://codecov.io/gh/LSYS/runPyNB)
<br>
[](https://github.com/LSYS/runPyNB/actions/workflows/build.yml)
<br>
[](https://github.com/LSYS/runPyNB/actions/workflows/cli.yml)
<br>
[](https://github.com/LSYS/runPyNB/actions/workflows/doclinks.yml)
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<br>
<!---------------------- About --------------------->
## More on this package
This is a lightweight package that wraps around the official Jupyter [`nbformat`](https://nbformat.readthedocs.io/en/latest/) and [`nbconvert`](https://nbconvert.readthedocs.io/en/latest/) modules.
My workflow involves using [`Jupyter notebooks`](https://jupyter.org/) to clean, and analyze data.
I use this utility to run notebooks silently from the command-line and [`Makefiles`](#usage-with-makefiles) (without converting from `.ipynb` files to `.py` files).
Related packages are [`guoquan/runnb`](https://github.com/guoquan/runnb) and [`vinayak-mehta/nbcommands`](https://github.com/vinayak-mehta/nbcommands) with a planned enhancement `nbtime` to run Jupyter notebooks from command-line.
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<!---------------------- Build --------------------->
## Usage with Makefiles
A minimal workflow where `get-data.ipynb` takes 5000 seconds to prepare `data.csv`.
And where `analyze.ipynb` uses `data.csv` to produce `output.png`.
```makefile
.DEFAULT_GOAL := output.png
data.csv: get-data.ipynb
runpynb $^ -t 5000
output.png: analyze.ipynb data.csv
runpynb $<
```
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<!-------------------- License ------------------->
## License
This package is licensed under the [MIT License](https://github.com/LSYS/runPyNB/blob/main/LICENSE).
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"description": "<div id=\"top\"></div> \n\n# Run Jupyter notebooks quietly from command-line\n[](https://pypi.org/project/runpynb/)\n\n<br>\n[](https://pypi.org/project/runpynb/)\n<br>\n[](https://zenodo.org/badge/latestdoi/520408889)\n\n`runPyNB` is a quick and dirty utility to run (and time) Jupyter notebooks from command-line and makefiles.\n\n<!------------------- Quickstart ------------------->\n## Quickstart\nInstall from PyPI\n```bash\npip install runpynb\n```\n\nGeneral usage: `runpynb <notebook(s)> [options]` (\".ipynb\" not required)\n\n* `runpynb`: Run all notebooks in directory.\n\n <pre>\n $ runpynb</pre>\n \n\n<p align=\"right\">(<a href=\"#top\">back to top</a>)</p>\n\n<!------------------------ Usage ---------------------->\n## Usage\n\n* `runpynb <notebook(s)> -q`: Run quietly (`-q`).\n\n <pre>\n $ runpynb hello.ipynb -q</pre>\n \n \n* `runpynb <notebook(s)> -qs`: Run quietly (`-q`) as a sequence of workflow (`-s`). Errors (eg in `error.ipynb`) will break the workflow.\n\n <pre>\n $ runpynb error.ipynb hello.ipynb -qs</pre>\n \n \n* `runpynb <notebook(s)> -o`: Save output as separate notebook (`-o`), instead of overwriting existing notebook(s).\n\n <pre>\n $ runpynb hello.ipynb -o</pre>\n \n \n<p align=\"right\">(<a href=\"#top\">back to top</a>)</p>\n\n<!---------------------- Options ---------------------->\n## Options\n```bash\nusage: runpynb [-h] [-t TIMEOUT] [-s] [-o] [-v VERSION] [-q] [notebooks ...]\n\nRun (and time) Jupyter notebooks silently in command-line.\n\npositional arguments:\n notebooks List of Jupyter notebooks (*.ipynb) to be run\n (default=all notebooks in path).\n\noptional arguments:\n -h, --help show this help message and exit\n -t TIMEOUT, --timeout TIMEOUT\n Seconds until a cell in the notebook timesout, which\n raises a Timeouterror exception (default is 3000=5\n mins).\n -s, --sequence Sequence implicit in notebook lists. If error occurs\n somewhere, stop entire pipeline.\n -o, --output Save output as a separate notebook with \"-out\"-suffix\n (e.g. *-out.ipynb) instead of overwriting existing\n file.\n -v VERSION, --version VERSION\n Version of notebook to return (Default=No conversion).\n Notebook will be converted if necessary.\n -q, --quiet Be quiet and don't print messages (including run\n time). Caution: Does not suppress error messages.\n```\n<p align=\"right\">(<a href=\"#top\">back to top</a>)</p>\n\n\n<!----------------- Project status ----------------->\n## Status\n[](https://runpynb.readthedocs.io/en/latest/?badge=latest)\n<br>\n[](https://app.travis-ci.com/LSYS/runPyNB)\n<br>\n[](https://github.com/LSYS/runPyNB/actions/workflows/tests.yml)\n[](https://codecov.io/gh/LSYS/runPyNB)\n<br>\n[](https://github.com/LSYS/runPyNB/actions/workflows/build.yml)\n<br>\n[](https://github.com/LSYS/runPyNB/actions/workflows/cli.yml)\n<br>\n[](https://github.com/LSYS/runPyNB/actions/workflows/doclinks.yml)\n<p align=\"right\">(<a href=\"#top\">back to top</a>)</p>\n<br>\n\n\n<!---------------------- About --------------------->\n## More on this package\n\nThis is a lightweight package that wraps around the official Jupyter [`nbformat`](https://nbformat.readthedocs.io/en/latest/) and [`nbconvert`](https://nbconvert.readthedocs.io/en/latest/) modules.\n\nMy workflow involves using [`Jupyter notebooks`](https://jupyter.org/) to clean, and analyze data.\nI use this utility to run notebooks silently from the command-line and [`Makefiles`](#usage-with-makefiles) (without converting from `.ipynb` files to `.py` files). \n\nRelated packages are [`guoquan/runnb`](https://github.com/guoquan/runnb) and [`vinayak-mehta/nbcommands`](https://github.com/vinayak-mehta/nbcommands) with a planned enhancement `nbtime` to run Jupyter notebooks from command-line.\n<p align=\"right\">(<a href=\"#top\">back to top</a>)</p>\n\n<!---------------------- Build --------------------->\n## Usage with Makefiles\nA minimal workflow where `get-data.ipynb` takes 5000 seconds to prepare `data.csv`.\nAnd where `analyze.ipynb` uses `data.csv` to produce `output.png`.\n```makefile\n.DEFAULT_GOAL := output.png\n\ndata.csv: get-data.ipynb\n\trunpynb $^ -t 5000\n\t\noutput.png: analyze.ipynb data.csv\n\trunpynb $< \n```\n<p align=\"right\">(<a href=\"#top\">back to top</a>)</p>\n\n\n<!-------------------- License ------------------->\n## License\nThis package is licensed under the [MIT License](https://github.com/LSYS/runPyNB/blob/main/LICENSE).\n",
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