nbsafety adds a layer of protection to computational notebooks by solving the stale dependency problem when executing cells out-of-order

Overview

-----------------------------------------------------

➤ nbsafety

Checked with mypy License: BSD3 Binder

About

nbsafety adds a layer of protection to computational notebooks by solving the stale dependency problem when executing cells out-of-order. Here's an example in action:

nbsafety example

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

Interface

The kernel ships with an extension that highlights cells with live references to stale symbols using red UI elements. It furthermore uses turquoise highlights for cells with live references to updated symbols, as well as for cells that resolve staleness.

Running

To run an nbsafety kernel in Jupyter, 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:

Uninstall

pip uninstall nbsafety

License

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

-----------------------------------------------------

➤ Contributors

Stephen Macke Ray Gong Shreya Shankar
Stephen Macke Ray Gong Shreya Shankar
Comments
  • "Exception occurred: pop from empty list"

    I don't know how to print the call stack in a Jupyterhub notebook, so unfortunately my explanation may not be super helpful. I'm noticing the error Exception occurred: pop from empty list when running a cell that seems to have acceptable logic, and this error doesn't show up when working with a non-nbsafety / regular Jupyter notebook.

    Screen Shot 2021-01-29 at 1 13 50 AM Screen Shot 2021-01-29 at 1 13 33 AM

    I am still able to do my work if I ignore the error, but I just thought I'd make the issue :)

    opened by shreyashankar 6
  • Bump follow-redirects from 1.14.4 to 1.14.8 in /frontend/test

    Bump follow-redirects from 1.14.4 to 1.14.8 in /frontend/test

    ⚠️ Dependabot is rebasing this PR ⚠️

    Rebasing might not happen immediately, so don't worry if this takes some time.

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    Bumps follow-redirects from 1.14.4 to 1.14.8.

    Commits
    • 3d81dc3 Release version 1.14.8 of the npm package.
    • 62e546a Drop confidential headers across schemes.
    • 2ede36d Release version 1.14.7 of the npm package.
    • 8b347cb Drop Cookie header across domains.
    • 6f5029a Release version 1.14.6 of the npm package.
    • af706be Ignore null headers.
    • d01ab7a Release version 1.14.5 of the npm package.
    • 40052ea Make compatible with Node 17.
    • 86f7572 Fix: clear internal timer on request abort to avoid leakage
    • 2e1eaf0 Keep Authorization header on subdomain redirects.
    • Additional commits viewable in compare view

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    dependencies 
    opened by dependabot[bot] 4
  • liveness-based slicing should detect version of live symbols at the time the cell was run

    liveness-based slicing should detect version of live symbols at the time the cell was run

    Example failure:

    # cell 1
    x = 0
    
    # cell 2
    if True:
        y = 7
    else:
        # even though this branch is not taken,
        # liveness-based usage should detect the
        # version of `x` used at the time it was
        # live, meaning cell 1 should get included
        # in the slice
        print(x)
    
    # cell 3
    x = 5
    
    # cell 4
    print(x + y)
    

    The slice for reconstructing cell 4 should use all of cells 1, 2, 3, and 4, but the current slicer will leave out cell 1, since it will detect the more recent version of x used in cell 3 during liveness checking and therefore leave out the definition in cell 1.

    opened by smacke 4
  • Bump node-fetch from 2.6.1 to 2.6.7 in /frontend/test

    Bump node-fetch from 2.6.1 to 2.6.7 in /frontend/test

    ⚠️ Dependabot is rebasing this PR ⚠️

    Rebasing might not happen immediately, so don't worry if this takes some time.

    Note: if you make any changes to this PR yourself, they will take precedence over the rebase.


    Bumps node-fetch from 2.6.1 to 2.6.7.

    Release notes

    Sourced from node-fetch's releases.

    v2.6.7

    Security patch release

    Recommended to upgrade, to not leak sensitive cookie and authentication header information to 3th party host while a redirect occurred

    What's Changed

    Full Changelog: https://github.com/node-fetch/node-fetch/compare/v2.6.6...v2.6.7

    v2.6.6

    What's Changed

    Full Changelog: https://github.com/node-fetch/node-fetch/compare/v2.6.5...v2.6.6

    v2.6.2

    fixed main path in package.json

    Changelog

    Sourced from node-fetch's changelog.

    Changelog

    All notable changes will be recorded here.

    The format is based on Keep a Changelog, and this project adheres to Semantic Versioning.

    What's Changed

    New Contributors

    Full Changelog: https://github.com/node-fetch/node-fetch/compare/v3.1.0...v3.1.2

    3.1.0

    What's Changed

    ... (truncated)

    Commits
    • 1ef4b56 backport of #1449 (#1453)
    • 8fe5c4e 2.x: Specify encoding as an optional peer dependency in package.json (#1310)
    • f56b0c6 fix(URL): prefer built in URL version when available and fallback to whatwg (...
    • b5417ae fix: import whatwg-url in a way compatible with ESM Node (#1303)
    • 18193c5 fix v2.6.3 that did not sending query params (#1301)
    • ace7536 fix: properly encode url with unicode characters (#1291)
    • 152214c Fix(package.json): Corrected main file path in package.json (#1274)
    • See full diff in compare view
    Maintainer changes

    This version was pushed to npm by endless, a new releaser for node-fetch since your current version.


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    dependencies 
    opened by dependabot[bot] 3
  • Feature request: automatic update of dependent cells

    Feature request: automatic update of dependent cells

    Is there a way to automatically update the dependent cells?

    I am looking for a behavior that is similar to the behavior of reactive observablehq notebooks or akernel:

    https://github.com/davidbrochart/akernel

    Related:

    • https://github.com/davidbrochart/akernel/issues/24
    • https://discourse.jupyter.org/t/dag-based-notebooks/11173/4
    • https://stackoverflow.com/questions/69539309/how-to-monitor-state-of-observales-in-reactive-calculations
    • https://discourse.jupyter.org/t/how-to-get-output-model-for-a-given-cell-in-a-jupyterlab-extension/11342
    enhancement 
    opened by stefaneidelloth 3
  • Bump terser from 5.14.1 to 5.14.2 in /frontend/labextension

    Bump terser from 5.14.1 to 5.14.2 in /frontend/labextension

    Bumps terser from 5.14.1 to 5.14.2.

    Changelog

    Sourced from terser's changelog.

    v5.14.2

    • Security fix for RegExps that should not be evaluated (regexp DDOS)
    • Source maps improvements (#1211)
    • Performance improvements in long property access evaluation (#1213)
    Commits

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    dependencies 
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  • Bump minimist from 1.2.5 to 1.2.6 in /frontend/nbextension

    Bump minimist from 1.2.5 to 1.2.6 in /frontend/nbextension

    Bumps minimist from 1.2.5 to 1.2.6.

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    dependencies 
    opened by dependabot[bot] 2
  • Bump minimist from 1.2.5 to 1.2.6 in /frontend/labextension

    Bump minimist from 1.2.5 to 1.2.6 in /frontend/labextension

    Bumps minimist from 1.2.5 to 1.2.6.

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    dependencies 
    opened by dependabot[bot] 2
  • Bump url-parse from 1.5.3 to 1.5.7 in /frontend/labextension

    Bump url-parse from 1.5.3 to 1.5.7 in /frontend/labextension

    Bumps url-parse from 1.5.3 to 1.5.7.

    Commits
    • 8b3f5f2 1.5.7
    • ef45a13 [fix] Readd the empty userinfo to url.href (#226)
    • 88df234 [doc] Add soft deprecation notice
    • 78e9f2f [security] Fix nits
    • e6fa434 [security] Add credits for incorrect handling of userinfo vulnerability
    • 4c9fa23 1.5.6
    • 7b0b8a6 Merge pull request #223 from unshiftio/fix/at-sign-handling-in-userinfo
    • e4a5807 1.5.5
    • 193b44b [minor] Simplify whitespace regex
    • 319851b [fix] Remove CR, HT, and LF
    • Additional commits viewable in compare view

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    dependencies 
    opened by dependabot[bot] 2
  • Bump follow-redirects from 1.14.4 to 1.14.7 in /frontend/test

    Bump follow-redirects from 1.14.4 to 1.14.7 in /frontend/test

    Bumps follow-redirects from 1.14.4 to 1.14.7.

    Commits
    • 2ede36d Release version 1.14.7 of the npm package.
    • 8b347cb Drop Cookie header across domains.
    • 6f5029a Release version 1.14.6 of the npm package.
    • af706be Ignore null headers.
    • d01ab7a Release version 1.14.5 of the npm package.
    • 40052ea Make compatible with Node 17.
    • 86f7572 Fix: clear internal timer on request abort to avoid leakage
    • 2e1eaf0 Keep Authorization header on subdomain redirects.
    • 2ad9e82 Carry over Host header on relative redirects (#172)
    • See full diff in compare view

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    dependencies 
    opened by dependabot[bot] 2
  • Bump path-parse from 1.0.6 to 1.0.7 in /frontend/labextension

    Bump path-parse from 1.0.6 to 1.0.7 in /frontend/labextension

    Bumps path-parse from 1.0.6 to 1.0.7.

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    dependencies 
    opened by dependabot[bot] 2
  • [feature request] Integrate with ipywidgets

    [feature request] Integrate with ipywidgets

    I just discovered ipyflow, it's really cool !

    I see a huge potential for an integration with ipywidgets. Indeed, if one could simply do:

    import ipywidgets as w
    from magic import widget
    
    slider = w.IntSlider()
    a = 10
    
    b = a + widget(slider, "value")
    

    And then b would update when the widget value changes, it would be awesome !

    enhancement 
    opened by horaceg 1
  • reconsider showing updated highlight if running corresponding cell would give error

    reconsider showing updated highlight if running corresponding cell would give error

    Some cases where we suggest rerunning cell via turquoise highlight but where doing so would give an error.

    Example: x and y are ints, some cell C has x + y, we redefine x as a string 'foo', and now we suggest rerunning C even though doing so would throw an error.

    opened by smacke 0
Owner
null
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