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Open Source Science

https://github.com/cytoscape/cytoscape.js

Graph theory (network) library for visualisation and analysis

https://github.com/cytoscape/cytoscape.js

Science Score: 59.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 1 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: pubmed.ncbi, ncbi.nlm.nih.gov, zenodo.org
  • ✓
    Committers with academic emails
    7 of 153 committers (4.6%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.9%) to scientific vocabulary

Keywords

analysis cytoscapejs graph-theory javascript network visualisation visualization

Keywords from Contributors

bioinformatics systems-biology biology network-visualization diagram profiles cytoscapejs-extension sbgn commonmark pandoc
Last synced: 5 months ago · JSON representation

Repository

Graph theory (network) library for visualisation and analysis

Basic Info
  • Host: GitHub
  • Owner: cytoscape
  • License: mit
  • Language: JavaScript
  • Default Branch: unstable
  • Homepage: https://js.cytoscape.org
  • Size: 82.2 MB
Statistics
  • Stars: 10,613
  • Watchers: 220
  • Forks: 1,649
  • Open Issues: 15
  • Releases: 0
Topics
analysis cytoscapejs graph-theory javascript network visualisation visualization
Created over 14 years ago · Last pushed 6 months ago
Metadata Files
Readme Contributing License Code of conduct Security

README.md

GitHub repo Ask a question with Phind News and tutorials License npm DOI npm installs Automated tests Extensions Cloudflare

Created at the University of Toronto and published in Oxford Bioinformatics (2016, 2023).
Authored by: Max Franz, Christian Lopes, Dylan Fong, Mike Kucera, ..., Gary Bader

Cytoscape.js

Graph theory (network) library for visualisation and analysis : https://js.cytoscape.org

Description

Cytoscape.js is a fully featured graph theory library. Do you need to model and/or visualise relational data, like biological data or social networks? If so, Cytoscape.js is just what you need.

Cytoscape.js contains a graph theory model and an optional renderer to display interactive graphs. This library was designed to make it as easy as possible for programmers and scientists to use graph theory in their apps, whether it's for server-side analysis in a Node.js app or for a rich user interface.

You can get started with Cytoscape.js with one line:

js var cy = cytoscape({ elements: myElements, container: myDiv });

Learn more about the features of Cytoscape.js by reading its documentation.

Example

The Tokyo railway stations network can be visualised with Cytoscape:

A live demo and source code are available for the Tokyo railway stations graph. More demos are available in the documentation.

Documentation

You can find the documentation and downloads on the project website.

Roadmap

Future versions of Cytoscape.js are planned in the milestones of the Github issue tracker. You can use the milestones to see what's currently planned for future releases.

Contributing to Cytoscape.js

Would you like to become a Cytoscape.js contributor? You can contribute in technical roles (e.g. features, testing) or non-technical roles (e.g. documentation, outreach), depending on your interests. Get in touch with us by posting a GitHub discussion.

For the mechanics of contributing a pull request, refer to CONTRIBUTING.md.

Feature releases are made monthly, while patch releases are made weekly. This allows for rapid releases of first- and third-party contributions.

Citation

To cite Cytoscape.js in a paper, please cite the Oxford Bioinformatics issue:

Cytoscape.js: a graph theory library for visualisation and analysis

Franz M, Lopes CT, Huck G, Dong Y, Sumer O, Bader GD

Bioinformatics (2016) 32 (2): 309-311 first published online September 28, 2015 doi:10.1093/bioinformatics/btv557 (PDF)

Build dependencies

Install node and npm. Run npm install before using npm run.

Build instructions

Run npm run <target> in the console. The main targets are:

Building:

  • build: do all builds of the library (umd, min, umd, esm)
  • build:min : do the unminified build with bundled dependencies (for simple html pages, good for novices)
  • build:umd : do the umd (cjs/amd/globals) build
  • build:esm : do the esm (ES 2015 modules) build
  • clean : clean the build directory
  • docs : build the docs into documentation
  • release : build all release artifacts
  • watch : automatically build lib for debugging (with sourcemap, no babel, very quick)
    • good for general testing on debug/index.html
    • served on http://localhost:8080 or the first available port thereafter, with livereload on debug/index.html
  • watch:babel : automatically build lib for debugging (with sourcemap, with babel, a bit slower)
    • good for testing performance or for testing out of date browsers
    • served on http://localhost:8080 or the first available port thereafter, with livereload on debug/index.html
  • watch:umd : automatically build prod umd bundle (no sourcemap, with babel)
    • good for testing cytoscape in another project (with a "cytoscape": "file:./path/to/cytoscape" reference in your project's package.json)
    • no http server
  • dist : update the distribution js for npm etc.

Testing:

The default test scripts run directly against the source code. Tests can alternatively be run on a built bundle. The library can be built on node>=6, but the library's bundle can be tested on node>=0.10.

  • test : run all testing & linting
  • test:js : run the mocha tests on the public API of the lib (directly on source files)
    • npm run test:js -- -g "my test name" runs tests on only the matching test cases
  • test:build : run the mocha tests on the public API of the lib (on a built bundle)
    • npm run build should be run beforehand on a recent version of node
    • npm run test:build -- -g "my test name" runs build tests on only the matching test cases
  • test:modules : run unit tests on private, internal API
    • npm run test:modules -- -g "my test name" runs modules tests on only the matching test cases
  • lint : lint the js sources via eslint
  • benchmark : run all benchmarks
  • benchmark:single : run benchmarks only for the suite specified in benchmark/single

Release instructions

Background

  • Ensure that a milestone exists for the release you want to make, with all the issues for that release assigned in the milestone.
  • Bug fixes should be applied to both the master and unstable branches. PRs can go on either branch, with the patch applied to the other branch after merging.
  • When a patch release is made concurrently with a feature release, the patch release should be made first. Wait 5 minutes after the patch release completes before starting the feature release -- otherwise Zenodo doesn't pick up releases properly.

Patch version

  1. Go to Actions > Patch release
  2. Go to the 'Run workflow' dropdown
  3. [Optional] The 'master' branch should be preselected for you
  4. Press the green 'Run workflow' button
  5. Close the milestone for the release

Feature version

  1. Go to Actions > Feature release
  2. Go to the 'Run workflow' dropdown
  3. [Optional] The 'unstable' branch should be preselected for you
  4. Press the green 'Run workflow' button
  5. Close the milestone for the release
  6. Make the release announcement on the blog

Notes on GitHub Actions UI

  • 'Use workflow from' in the GitHub UI selects the branch from which the workflow YML file is selected. Since the workflow files should usually be the same on the master and unstable branches, it shouldn't matter what's selected.
  • 'Branch to run the action on' in the GitHub UI is preselected for you. You don't need to change it.

Tests

Mocha tests are found in the test directory. The tests can be run in the browser or they can be run via Node.js (npm run test:js).

Owner

  • Name: Cytoscape Consortium
  • Login: cytoscape
  • Kind: organization

GitHub Events

Total
  • Create event: 38
  • Commit comment event: 1
  • Release event: 8
  • Issues event: 121
  • Watch event: 475
  • Delete event: 1
  • Issue comment event: 313
  • Push event: 163
  • Pull request review comment event: 35
  • Pull request review event: 50
  • Pull request event: 67
  • Fork event: 45
Last Year
  • Create event: 38
  • Commit comment event: 1
  • Release event: 8
  • Issues event: 121
  • Watch event: 475
  • Delete event: 1
  • Issue comment event: 313
  • Push event: 163
  • Pull request review comment event: 35
  • Pull request review event: 50
  • Pull request event: 67
  • Fork event: 45

Committers

Last synced: 8 months ago

All Time
  • Total Commits: 6,054
  • Total Committers: 153
  • Avg Commits per committer: 39.569
  • Development Distribution Score (DDS): 0.215
Past Year
  • Commits: 382
  • Committers: 8
  • Avg Commits per committer: 47.75
  • Development Distribution Score (DDS): 0.55
Top Committers
Name Email Commits
Max Franz m****z@g****m 4,755
Mike Kucera m****a@g****m 230
Yue Dong o****o@g****m 152
Akash Mondal a****1@g****m 107
greenkeeper[bot] 2****] 92
Manfred Cheung m****n@u****a 62
EliotRagueneau e****u@e****k 42
dependabot[bot] 4****] 32
Dylan Fong d****g@u****a 31
Gerardo Huck g****k@g****m 29
r-ba r****s@g****m 29
Onur Sumer s****r@g****m 25
Josejulio Martínez j****e@r****m 24
jquery404 j****4@g****m 22
Jan Zak zj@z****z 15
Joseph Stahl j****t@o****m 15
Christian Lopes c****s@g****m 14
Soetji Anto s****i@g****m 14
ayhun a****t@g****m 12
Noah Pedrini n****i@g****m 12
Bogdan Chadkin t****d@y****u 12
Jan Hartmann j****n@b****m 11
tmullen t****n@g****m 10
metincansiper m****5@h****m 10
Chris c****l@g****m 9
Joseph Stahl h****o@j****m 8
Jan Hartmann k****t@j****k 8
Paolo Parlapiano p****o@g****m 7
Mélanie Gauthier m****r@t****m 7
Eli Sherer e****r@g****m 6
and 123 more...
Committer Domains (Top 20 + Academic)
uwaterloo.ca: 2 ebi.ac.uk: 2 infotrack.com.au: 2 skas.io: 1 appdirect.com: 1 arcor.de: 1 ebuchmann.com: 1 codility.com: 1 frontiersin.org: 1 leaksignal.com: 1 moserit.com: 1 doerfler.io: 1 sparkbeyond.com: 1 chlupacek.cz: 1 uni-ulm.de: 1 rambler.ru: 1 wilzbach.me: 1 guimeira.com: 1 caci.com: 1 trisotech.com: 1 gladstone.ucsf.edu: 1 email.arizona.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 253
  • Total pull requests: 143
  • Average time to close issues: 3 months
  • Average time to close pull requests: 16 days
  • Total issue authors: 170
  • Total pull request authors: 43
  • Average comments per issue: 4.72
  • Average comments per pull request: 3.23
  • Merged pull requests: 111
  • Bot issues: 0
  • Bot pull requests: 12
Past Year
  • Issues: 71
  • Pull requests: 78
  • Average time to close issues: 23 days
  • Average time to close pull requests: 15 days
  • Issue authors: 46
  • Pull request authors: 13
  • Average comments per issue: 2.08
  • Average comments per pull request: 2.88
  • Merged pull requests: 59
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • maxkfranz (34)
  • EliotRagueneau (8)
  • mikekucera (8)
  • soetji (6)
  • simCecca (3)
  • jquery404 (3)
  • danprince (3)
  • ghost (3)
  • KonradHoeffner (3)
  • Amanyadav12345 (3)
  • UBarodzich (2)
  • ngkahinkeith (2)
  • rob-gordon (2)
  • Ciappone (2)
  • Rey-Wang (2)
Pull Request Authors
  • maxkfranz (47)
  • mikekucera (19)
  • dependabot[bot] (17)
  • EliotRagueneau (12)
  • soetji (12)
  • jquery404 (6)
  • chrtannus (3)
  • kn1ght (2)
  • ayjayt (2)
  • luke-mckee-ol (2)
  • kinow (2)
  • d2fong (2)
  • hoijui (2)
  • jan-molak (2)
  • AkMo3 (2)
Top Labels
Issue Labels
bug (105) stale (43) pinned (15) browser-bug (4) help-wanted (2) priority-2-medium (2) priority-3-low (2) PR (2) known-issue (1) performance (1) priority-1-high (1)
Pull Request Labels
dependencies (17) stale (8) pinned (6) bug (1)

Packages

  • Total packages: 23
  • Total downloads:
    • npm 6,443,681 last-month
    • nuget 25,927 total
  • Total docker downloads: 1,686,762,931
  • Total dependent packages: 291
    (may contain duplicates)
  • Total dependent repositories: 5,651
    (may contain duplicates)
  • Total versions: 885
  • Total maintainers: 24
npmjs.org: cytoscape

Graph theory (a.k.a. network) library for analysis and visualisation

  • Versions: 264
  • Dependent Packages: 259
  • Dependent Repositories: 5,456
  • Downloads: 6,443,588 Last month
  • Docker Downloads: 1,686,762,861
Rankings
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Downloads: 0.2%
Dependent repos count: 0.3%
Average: 0.6%
Docker downloads count: 0.6%
Forks count: 1.0%
Stargazers count: 1.1%
Maintainers (5)
chrtannus mikekucera cytoscapenpm maxkfranz dylanfong
Last synced: 5 months ago
bower.io: cytoscape

Graph theory (a.k.a. network) library for analysis and visualisation

  • License: MIT
  • Latest release: v3.33.0
    published 7 months ago
  • Versions: 223
  • Dependent Packages: 1
  • Dependent Repositories: 150
Rankings
Forks count: 0.7%
Stargazers count: 0.7%
Dependent repos count: 1.3%
Average: 1.3%
Dependent packages count: 2.6%
Last synced: 5 months ago
proxy.golang.org: github.com/cytoscape/cytoscape.js
  • Versions: 267
  • Dependent Packages: 0
  • Dependent Repositories: 1
Rankings
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Stargazers count: 0.7%
Average: 3.6%
Dependent repos count: 4.8%
Dependent packages count: 8.4%
Last synced: 5 months ago
repo1.maven.org: org.webjars.bower:cytoscape

WebJar for cytoscape

  • Versions: 9
  • Dependent Packages: 13
  • Dependent Repositories: 16
  • Docker Downloads: 35
Rankings
Stargazers count: 3.0%
Forks count: 4.0%
Average: 4.4%
Dependent packages count: 4.7%
Dependent repos count: 6.0%
Last synced: 5 months ago
repo1.maven.org: org.webjars.npm:cytoscape

WebJar for cytoscape

  • Versions: 26
  • Dependent Packages: 6
  • Dependent Repositories: 18
  • Docker Downloads: 35
Rankings
Stargazers count: 3.0%
Forks count: 4.0%
Average: 5.5%
Dependent repos count: 5.7%
Dependent packages count: 9.6%
Last synced: 5 months ago
nuget.org: cytoscape.js

Graph theory (a.k.a. network) library for analysis and visualisation

  • Versions: 12
  • Dependent Packages: 1
  • Dependent Repositories: 2
  • Downloads: 25,927 Total
Rankings
Dependent repos count: 5.1%
Average: 9.3%
Dependent packages count: 10.9%
Downloads: 11.8%
Maintainers (1)
Stalker
Last synced: 5 months ago
npmjs.org: @visallo/cytoscape

Graph theory (a.k.a. network) library for analysis and visualisation

  • Versions: 3
  • Dependent Packages: 1
  • Dependent Repositories: 1
  • Downloads: 1 Last month
Rankings
Forks count: 1.0%
Stargazers count: 1.1%
Average: 10.4%
Dependent repos count: 10.7%
Downloads: 18.2%
Dependent packages count: 21.1%
Maintainers (8)
joeferner stephencorwin strianta visallo-admin jharwig jburke372 kunklejr mwizeman
Last synced: 5 months ago
npmjs.org: cytoscape-universal

Graph theory (a.k.a. network) library for analysis and visualisation

  • Versions: 1
  • Dependent Packages: 1
  • Dependent Repositories: 1
  • Downloads: 7 Last month
Rankings
Forks count: 1.0%
Stargazers count: 1.1%
Dependent repos count: 10.7%
Average: 11.8%
Dependent packages count: 21.1%
Downloads: 25.0%
Maintainers (1)
jaydenlin
Last synced: 5 months ago
npmjs.org: cytoscape-tongbin

Graph theory (a.k.a. network) library for analysis and visualisation

  • Versions: 6
  • Dependent Packages: 1
  • Dependent Repositories: 1
  • Downloads: 14 Last month
Rankings
Forks count: 1.0%
Stargazers count: 1.1%
Dependent repos count: 10.7%
Average: 11.9%
Dependent packages count: 21.1%
Downloads: 25.6%
Maintainers (1)
npm.txu
Last synced: 5 months ago
npmjs.org: @qwoach/cytoscape

Graph theory (a.k.a. network) library for analysis and visualisation

  • Versions: 9
  • Dependent Packages: 2
  • Dependent Repositories: 0
  • Downloads: 36 Last month
Rankings
Forks count: 1.1%
Stargazers count: 1.3%
Dependent packages count: 9.5%
Average: 12.2%
Downloads: 24.0%
Dependent repos count: 25.3%
Maintainers (1)
arthabus
Last synced: 5 months ago
npmjs.org: @l4legenda/cytoscape

Graph theory (a.k.a. network) library for analysis and visualisation

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 2 Last month
Rankings
Forks count: 0.9%
Stargazers count: 1.0%
Average: 12.5%
Downloads: 14.6%
Dependent repos count: 18.8%
Dependent packages count: 27.0%
Maintainers (1)
l4legenda
Last synced: 5 months ago
npmjs.org: cytoscape-bbfe

Graph theory (a.k.a. network) library for analysis and visualisation

  • Versions: 1
  • Dependent Packages: 1
  • Dependent Repositories: 1
  • Downloads: 5 Last month
Rankings
Forks count: 1.0%
Stargazers count: 1.1%
Dependent repos count: 10.7%
Average: 13.6%
Dependent packages count: 21.1%
Downloads: 34.1%
Maintainers (1)
lvliqi
Last synced: 5 months ago
repo1.maven.org: org.webjars.bowergithub.cytoscape:cytoscape.js

WebJar for cytoscape

  • Versions: 6
  • Dependent Packages: 3
  • Dependent Repositories: 0
Rankings
Stargazers count: 2.5%
Forks count: 3.2%
Average: 13.6%
Dependent packages count: 16.9%
Dependent repos count: 32.0%
Last synced: 5 months ago
npmjs.org: cytoscape-bundle

Graph theory (a.k.a. network) library for analysis and visualisation

  • Versions: 1
  • Dependent Packages: 1
  • Dependent Repositories: 1
  • Downloads: 3 Last month
Rankings
Forks count: 1.0%
Stargazers count: 1.1%
Dependent repos count: 10.7%
Average: 13.9%
Dependent packages count: 21.1%
Downloads: 35.7%
Maintainers (1)
hekike
Last synced: 5 months ago
npmjs.org: try-cy

Graph theory (a.k.a. network) library for analysis and visualisation

  • Versions: 2
  • Dependent Packages: 1
  • Dependent Repositories: 1
  • Downloads: 3 Last month
Rankings
Forks count: 1.0%
Stargazers count: 1.1%
Dependent repos count: 10.7%
Average: 16.0%
Dependent packages count: 21.1%
Downloads: 46.2%
Maintainers (1)
sakop
Last synced: 5 months ago
npmjs.org: cytoscape-select

Graph theory (a.k.a. network) library for analysis and visualisation

  • Versions: 9
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 5 Last month
Rankings
Forks count: 1.0%
Stargazers count: 1.1%
Dependent repos count: 10.7%
Average: 16.7%
Downloads: 18.0%
Dependent packages count: 52.6%
Maintainers (1)
alex_w_00
Last synced: 5 months ago
npmjs.org: cytoscape-auto-release-test

Graph theory (a.k.a. network) library for analysis and visualisation

  • Versions: 10
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 10 Last month
Rankings
Forks count: 1.0%
Stargazers count: 1.1%
Downloads: 14.2%
Average: 21.5%
Dependent repos count: 37.5%
Dependent packages count: 54.0%
Maintainers (1)
maxkfranz
Last synced: 5 months ago
repo1.maven.org: org.webjars.npm:github-com-cytoscape-cytoscape-js

WebJar for cytoscape

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Stargazers count: 2.5%
Forks count: 3.2%
Average: 21.6%
Dependent repos count: 32.0%
Dependent packages count: 48.9%
Last synced: 5 months ago
repo1.maven.org: org.webjars.bower:github-com-cytoscape-cytoscape-js

WebJar for cytoscape

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Stargazers count: 2.5%
Forks count: 3.2%
Average: 21.6%
Dependent repos count: 32.0%
Dependent packages count: 48.9%
Last synced: 5 months ago
npmjs.org: try-cytoscape

Graph theory (a.k.a. network) library for analysis and visualisation

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 3 Last month
Rankings
Forks count: 1.0%
Stargazers count: 1.1%
Dependent repos count: 10.7%
Average: 22.3%
Downloads: 46.2%
Dependent packages count: 52.6%
Maintainers (1)
sakop
Last synced: 5 months ago
npmjs.org: cyto-release-auto

Graph theory (a.k.a. network) library for analysis and visualisation

  • Versions: 30
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 0 Last month
Rankings
Forks count: 12.1%
Stargazers count: 15.0%
Dependent repos count: 18.9%
Average: 23.0%
Dependent packages count: 46.1%
Maintainers (1)
akmo_3
Last synced: 5 months ago
npmjs.org: @jquery404/cytoscape

Graph theory (a.k.a. network) library for analysis and visualisation

  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 4 Last month
Rankings
Dependent repos count: 25.0%
Average: 30.6%
Dependent packages count: 36.1%
Maintainers (1)
jquery404
Last synced: 5 months ago
npmjs.org: jquery404-cytoscape

Graph theory (a.k.a. network) library for analysis and visualisation

  • Homepage: http://js.cytoscape.org
  • License: MIT
  • Status: unpublished
  • Latest release: 3.31.0
    published 12 months ago
  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent repos count: 25.0%
Average: 30.6%
Dependent packages count: 36.1%
Maintainers (1)
jquery404
Last synced: 5 months ago

Dependencies

.github/workflows/tests.yml actions
  • actions/checkout v2 composite
package-lock.json npm
  • 742 dependencies
package.json npm
  • @babel/core ^7.3.4 development
  • @babel/preset-env ^7.5.5 development
  • @rollup/plugin-babel ^5.0.0 development
  • @rollup/plugin-commonjs ^11.1.0 development
  • @rollup/plugin-node-resolve ^7.1.3 development
  • @rollup/plugin-replace ^2.3.2 development
  • benchmark ^2.1.4 development
  • bluebird ^3.5.0 development
  • chai ^4.1.2 development
  • cpy-cli ^3.1.1 development
  • cross-env ^7.0.0 development
  • download-cli ^1.0.5 development
  • eslint ^6.0.0 development
  • esm ^3.2.25 development
  • gh-pages ^2.1.1 development
  • handlebars ^4.7.6 development
  • highlight.js ^10.0.0 development
  • http-server ^0.12.3 development
  • jsonlint ^1.6.2 development
  • livereload ^0.9.1 development
  • marked ^4.0.10 development
  • mocha ^7.1.2 development
  • npm-run-all ^4.1.5 development
  • rimraf ^3.0.0 development
  • rollup ^2.8.2 development
  • rollup-plugin-license ^2.3.0 development
  • rollup-plugin-terser ^5.3.0 development
  • heap ^0.2.6
  • lodash ^4.17.21
.github/workflows/feature-release.yml actions
  • JamesIves/github-pages-deploy-action v4 composite
  • actions/checkout v3 composite
  • actions/setup-node v3 composite
  • actions/upload-artifact v3 composite
.github/workflows/patch-release.yml actions
  • JamesIves/github-pages-deploy-action v4 composite
  • actions/checkout v3 composite
  • actions/setup-node v3 composite
  • actions/upload-artifact v3 composite
bower.json bower
documentation/versions.json meteor