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

Last update: Jan 7, 2023

Related tags

Miscellaneous python jupyter static-code-analysis static-analysis highlighting pypi tracing developer-tools notebooks jupyter-notebooks lineage nbsafety

Overview

➤ nbsafety

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:

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

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.

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
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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.

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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
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
⚠️ Dependabot is rebasing this PR ⚠️

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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

fix: don't forward secure headers to 3th party by @jimmywarting in node-fetch/node-fetch#1453

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

v2.6.6

What's Changed

fix(URL): prefer built in URL version when available and fallback to whatwg by @jimmywarting in node-fetch/node-fetch#1352

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

core: update fetch-blob by @jimmywarting in node-fetch/node-fetch#1371

docs: Fix typo around sending a file by @jimmywarting in node-fetch/node-fetch#1381

core: (http.request): Cast URL to string before sending it to NodeJS core by @jimmywarting in node-fetch/node-fetch#1378

core: handle errors from the request body stream by @mdmitry01 in node-fetch/node-fetch#1392

core: Better handle wrong redirect header in a response by @tasinet in node-fetch/node-fetch#1387

core: Don't use buffer to make a blob by @jimmywarting in node-fetch/node-fetch#1402

docs: update readme for TS @types/node-fetch by @adamellsworth in node-fetch/node-fetch#1405

core: Fix logical operator priority to disallow GET/HEAD with non-empty body by @maxshirshin in node-fetch/node-fetch#1369

core: Don't use global buffer by @jimmywarting in node-fetch/node-fetch#1422

ci: fix main branch by @dnalborczyk in node-fetch/node-fetch#1429

core: use more node: protocol imports by @dnalborczyk in node-fetch/node-fetch#1428

core: Warn when using data by @jimmywarting in node-fetch/node-fetch#1421

docs: Create SECURITY.md by @JamieSlome in node-fetch/node-fetch#1445

core: don't forward secure headers to 3th party by @jimmywarting in node-fetch/node-fetch#1449

New Contributors

@mdmitry01 made their first contribution in node-fetch/node-fetch#1392

@tasinet made their first contribution in node-fetch/node-fetch#1387

@adamellsworth made their first contribution in node-fetch/node-fetch#1405

@maxshirshin made their first contribution in node-fetch/node-fetch#1369

@JamieSlome made their first contribution in node-fetch/node-fetch#1445

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

3.1.0

What's Changed

fix(Body): Discourage form-data and buffer() by @jimmywarting in node-fetch/node-fetch#1212

fix: Pass url string to http.request by @serverwentdown in node-fetch/node-fetch#1268

Fix octocat image link by @lakuapik in node-fetch/node-fetch#1281

fix(Body.body): Normalize Body.body into a node:stream by @jimmywarting in node-fetch/node-fetch#924

docs(Headers): Add default Host request header to README.md file by @robertoaceves in node-fetch/node-fetch#1316

Update CHANGELOG.md by @jimmywarting in node-fetch/node-fetch#1292

Add highWaterMark to cloned properties by @davesidious in node-fetch/node-fetch#1162

Update README.md to fix HTTPResponseError by @thedanfernandez in node-fetch/node-fetch#1135

docs: switch url to URL by @dhritzkiv in node-fetch/node-fetch#1318

fix(types): declare buffer() deprecated by @dnalborczyk in node-fetch/node-fetch#1345

chore: fix lint by @dnalborczyk in node-fetch/node-fetch#1348

refactor: use node: prefix for imports by @dnalborczyk in node-fetch/node-fetch#1346

Bump data-uri-to-buffer from 3.0.1 to 4.0.0 by @dependabot in node-fetch/node-fetch#1319

Bump mocha from 8.4.0 to 9.1.3 by @dependabot in node-fetch/node-fetch#1339

Referrer and Referrer Policy by @tekwiz in node-fetch/node-fetch#1057

Add typing for Response.redirect(url, status) by @c-w in node-fetch/node-fetch#1169

... (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)

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dependencies
opened by dependabot[bot] 3
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
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)

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dependencies
opened by dependabot[bot] 2
Bump minimist from 1.2.5 to 1.2.6 in /frontend/nbextension
Bumps minimist from 1.2.5 to 1.2.6.

Commits

7efb22a 1.2.6

ef88b93 security notice for additional prototype pollution issue

c2b9819 isConstructorOrProto adapted from PR

bc8ecee test from prototype pollution PR

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

Commits

7efb22a 1.2.6

ef88b93 security notice for additional prototype pollution issue

c2b9819 isConstructorOrProto adapted from PR

bc8ecee test from prototype pollution PR

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dependencies
opened by dependabot[bot] 2
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

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dependencies
opened by dependabot[bot] 2
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)

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dependencies
opened by dependabot[bot] 2
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
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

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

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YoutubeViews Free Youtube viewer bot A Bot that adds YouTube views to your video of choice Installation git clone https://github.com/davdtheemonk/Yout

5 Dec 6, 2022

Blender pluggin (python script) that adds a randomly generated tree with random branches and bend orientations

2 Dec 24, 2021

Blender addon that simplifies access to useful operators and adds missing functionality

Quick Menu is a Blender addon that simplifies common tasks Compatible with Blender 3.x.x Install through Edit -> Preferences -> Addons -> Install... -

94 Dec 27, 2022

Adds a Bake node to Blender's shader node system

Bake to Target This Blender Addon adds a new shader node type capable of reducing the texture-bake step to a single button press. Please note that thi

8 Oct 4, 2022

Simple dependency injection framework for Python

A simple, strictly typed dependency injection library.

14 Jun 29, 2022

🗽 Like yarn outdated/upgrade, but for pip. Upgrade all your pip packages and automate your Python Dependency Management.

pipupgrade The missing command for pip Table of Contents Features Quick Start Usage Basic Usage Docker Environment Variables FAQ License Features Upda

529 Dec 31, 2022

edgetest is a tox-inspired python library that will loop through your project's dependencies, and check if your project is compatible with the latest version of each dependency

Bleeding edge dependency testing Full Documentation edgetest is a tox-inspired python library that will loop through your project's dependencies, and

16 Dec 7, 2022

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

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Overview

➤ nbsafety

About

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Interface

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➤ Contributors

Comments

v2.6.7

Security patch release

What's Changed

v2.6.6

What's Changed

v2.6.2

Changelog

What's Changed

New Contributors

3.1.0

What's Changed

v5.14.2

Owner

Identifies the faulty wafer before it can be used for the fabrication of integrated circuits and, in photovoltaics, to manufacture solar cells.

Skull shaped MOSFET cells for the Efabless's 130nm process

Stack BOF Protection Bypass Techniques

Dot Browser is a privacy-conscious web browser with smarts built-in for protection against trackers and advertisments online.

Blender addon for executing the operator in response to the received OSC message.

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Tool that adds githuh profile views to ur acc

A Bot that adds YouTube views to your video of choice

Blender pluggin (python script) that adds a randomly generated tree with random branches and bend orientations

Blender addon that simplifies access to useful operators and adds missing functionality

Adds a Bake node to Blender's shader node system

Simple dependency injection framework for Python

🗽 Like yarn outdated/upgrade, but for pip. Upgrade all your pip packages and automate your Python Dependency Management.

edgetest is a tox-inspired python library that will loop through your project's dependencies, and check if your project is compatible with the latest version of each dependency

Async-first dependency injection library based on python type hints

Pipenv-local-deps-repro - Reproduction of a local transitive dependency on pipenv

A type based dependency injection framework for Python 3.9+

VCM EE1.2 P-layer feature map anchor generation 137th MPEG-VCM