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README.md

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➤ nbsafety

Checked with mypy License: BSD3 Binder

About

nbsafety adds a layer of protection to computational notebooks by solving the stale dependency problem, a problem which exists due to the fact that notebooks segment execution into "cells" with implicit dependencies amongst themselves. Here's an example in action:

Step 0: modify cell 1 Step 1: rerun cell 1 Step 2: rerun cell 2 Step 3: rerun cell 3

When the first cell is rerun, the second cell now contains a reference to an updated f and is suggested for re-execution with a turquoise highlight. The third cell contains a reference to a stale y -- y is stale due to its dependency on an old value of f. As such, the third cell is marked as unsafe for re-execution with a red highlight. Once the second cell is rerun, it is now suggested to re-execute the third cell in order to refresh its stale output.

nbsafety accomplishes its magic using a combination of a runtime tracer (to build the implicit dependency graph) and a static checker (to provide warnings before running a cell), both of which are deeply aware of Python's data model. In particular, nbsafety requires minimal to no changes in user behavior, opting to get out of the way unless absolutely necessary and letting you use notebooks the way you prefer.

Install

pip install nbsafety

If using JupyterLab, we highly recommend installing the companion extension:

jupyter labextension install jupyterlab-nbsafety  # optional but highly recommended if using JupyterLab

Interface

The JupyterLab extension and bundled Jupyter notebook extension both show cells with unsafe executions (due to uses of variables with stale dependencies) as being annotated with red UI elements, and recommends cells to run (in order to refresh variables with stale dependencies) by displaying them with turquoise UI elements.

Running

Because nbsafety is implemented as a custom Jupyter kernel, it works for both Jupyter notebooks and JupyterLab (if using JupyterLab, the additional labextension is recommended). To run an nbsafety kernel, select "Python 3 (nbsafety)" from the list of notebook types in Jupyter's "New" dropdown dialogue. For JupyterLab, similarly select "Python 3 (nbsafety)" from the list of available kernels in the Launcher tab.

Jupyter Notebook Entrypoint: Jupyter Lab Entrypoint:

Troubleshooting Install

The kernel and nbextension should be installed automatically, but in case the kernel is not available as an option or the UI elements are not showing up, try running the following:

python -m nbsafety.install
jupyter nbextension install --py nbsafety --sys-prefix
jupyter nbextension enable --py nbsafety --sys-prefix

Uninstall

In addition to pip uninstall nbsafety, it is also necessary to deregister the kernel from Jupyter for a full uninstall (as well as the extension from JupyterLab, if using JupyterLab):

jupyter kernelspec uninstall nbsafety
jupyter labextension uninstall jupyterlab-nbsafety

License

Code in this project licensed under the BSD-3-Clause License.

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➤ Contributors

Stephen Macke Ray Gong
Stephen Macke Ray Gong