https://github.com/theosanderson/taxonium

A tool for exploring very large trees in the browser
https://github.com/theosanderson/taxonium

Keywords

deckgl phylogenetics phylogeny react tree virus

Keywords from Contributors

battery simulator profiles blog pypi virtualization control reporting embedded climate-model

Last synced: 11 months ago
JSON representation

Acceptance Criteria

Revelant topics? true
External users? true
Open source license? true
Active? true
Fork? false

Repository metadata

A tool for exploring very large trees in the browser

Host: GitHub
URL: https://github.com/theosanderson/taxonium
Owner: theosanderson
License: gpl-3.0
Created: 2021-06-24T17:26:34.000Z (almost 4 years ago)
Default Branch: master
Last Pushed: 2024-05-20T20:19:33.000Z (12 months ago)
Last Synced: 2024-06-01T01:58:04.811Z (11 months ago)
Topics: deckgl, phylogenetics, phylogeny, react, tree, virus
Language: JavaScript
Homepage: http://taxonium.org
Size: 251 MB
Stars: 93
Watchers: 7
Forks: 16
Open Issues: 81
Releases: 0
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Citation: CITATION.bib

Owner metadata

Name: Theo Sanderson
Login: theosanderson
Email:
Kind: user
Description: Full stack pathogen geneticist
Website: http://theo.io
Location: London, UK
Twitter: theosanderson
Company: The Francis Crick Institute
Icon url: https://avatars.githubusercontent.com/u/19732295?u=89dff01eb4ac28f55c0e806f9533c1d4408931f4&v=4
Repositories: 143
Last ynced at: 2024-04-18T09:39:04.266Z
Profile URL: https://github.com/theosanderson

Committers metadata

Last synced: 11 months ago

Total Commits: 2,095
Total Committers: 13
Avg Commits per committer: 161.154
Development Distribution Score (DDS): 0.349

Commits in past year: 153
Committers in past year: 4
Avg Commits per committer in past year: 38.25
Development Distribution Score (DDS) in past year: 0.51

Name	Email	Commits
Theo Sanderson	t**o@s**k	1364
theosanderson	t**o@t**o	315
github-actions	4****]	150
theosanderson	t****n	96
pre-commit-ci[bot]	6****]	54
Alex Kramer	a**r@u**u	53
github-actions	g**s@g**m	29
allcontributors[bot]	4****]	15
Alex Kramer	a**e@u**u	13
Richard Goater	r**9@s**k	3
Sehi L'Yi	s**i@g**m	1
Sung Kwon	s**n@t**i	1
Koorous Vargha	3****a	1

Committer domains:

Issue and Pull Request metadata

Last synced: 11 months ago

Total issues: 96
Total pull requests: 157
Average time to close issues: 28 days
Average time to close pull requests: 13 days
Total issue authors: 17
Total pull request authors: 9
Average comments per issue: 2.92
Average comments per pull request: 1.37
Merged pull request: 113
Bot issues: 0
Bot pull requests: 3

Past year issues: 37
Past year pull requests: 84
Past year average time to close issues: 10 days
Past year average time to close pull requests: about 15 hours
Past year issue authors: 13
Past year pull request authors: 6
Past year average comments per issue: 2.38
Past year average comments per pull request: 1.3
Past year merged pull request: 68
Past year bot issues: 0
Past year bot pull requests: 1

More stats: https://issues.ecosyste.ms/repositories/lookup?url=https://github.com/theosanderson/taxonium

Top Issue Authors

theosanderson (40)
corneliusroemer (31)
AngieHinrichs (4)
GuilhemSempere (4)
Sanyukta2001 (3)
UTNK (2)
liamxg (2)
kvargha (1)
daniel-ji (1)
martinghunt (1)
NicolaDM (1)
niemasd (1)
chaoran-chen (1)
singing-scientist (1)
Biophylo2001 (1)

Top Pull Request Authors

theosanderson (142)
amkram (4)
sehilyi (2)
richardgoater (2)
simonbukin (2)
pre-commit-ci[bot] (2)
DLiarakos (1)
allcontributors[bot] (1)
kvargha (1)

Top Issue Labels

help wanted (1)

Top Pull Request Labels

Package metadata

Total packages: 2
Total downloads:
- pypi: 500 last-month
- npm: 75 last-month
Total dependent packages: 0 (may contain duplicates)
Total dependent repositories: 1 (may contain duplicates)
Total versions: 101
Total maintainers: 1

npmjs.org: taxonium-component

React component for exploring large phylogenetic trees in the browser

Homepage: https://github.com/theosanderson/taxonium
Licenses: gpl-3.0
Latest release: 2.0.115 (published over 1 year ago)
Last Synced: 2024-06-01T01:58:33.279Z (11 months ago)
Versions: 18
Dependent Packages: 0
Dependent Repositories: 1
Downloads: 75 Last month
Rankings:
- Stargazers count: 5.283%
- Forks count: 6.007%
- Dependent repos count: 10.353%
- Downloads: 10.392%
- Average: 16.82%
- Dependent packages count: 52.063%
Maintainers (1)
- theosanderson

pypi.org: taxoniumtools

Generate files for taxonium

Homepage: https://github.com/theosanderson/taxonium
Documentation: https://taxoniumtools.readthedocs.io/
Licenses: MIT License
Latest release: 2.0.115 (published over 1 year ago)
Last Synced: 2024-06-01T01:58:32.173Z (11 months ago)
Versions: 83
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 500 Last month
Rankings:
- Stargazers count: 7.763%
- Dependent packages count: 10.052%
- Forks count: 10.16%
- Downloads: 11.871%
- Average: 21.441%
- Dependent repos count: 67.358%
Maintainers (1)
- theosanderson

Dependencies

.github/workflows/docker-publish-backend.yml actions

actions/checkout v3 composite
docker/build-push-action ac9327eae2b366085ac7f6a2d02df8aa8ead720a composite
docker/login-action 28218f9b04b4f3f62068d7b6ce6ca5b26e35336c composite
docker/metadata-action 98669ae865ea3cffbcbaa878cf57c20bbf1c6c38 composite
docker/setup-buildx-action 79abd3f86f79a9d68a23c75a09a9a85889262adf composite
sigstore/cosign-installer d6a3abf1bdea83574e28d40543793018b6035605 composite

.github/workflows/docker-publish-frontend.yml actions

actions/checkout v3 composite
docker/build-push-action ac9327eae2b366085ac7f6a2d02df8aa8ead720a composite
docker/login-action 28218f9b04b4f3f62068d7b6ce6ca5b26e35336c composite
docker/metadata-action 98669ae865ea3cffbcbaa878cf57c20bbf1c6c38 composite
docker/setup-buildx-action 79abd3f86f79a9d68a23c75a09a9a85889262adf composite
sigstore/cosign-installer d6a3abf1bdea83574e28d40543793018b6035605 composite

.github/workflows/electron-build.yml actions

actions/checkout v1 composite
actions/setup-node v1 composite
actions/upload-artifact v1 composite
shogo82148/actions-upload-release-asset v1 composite

.github/workflows/frontend-test.yml actions

actions/checkout v2 composite
actions/setup-node v3 composite
actions/upload-artifact v3 composite

.github/workflows/precommit-checker.yaml actions

actions/checkout v3 composite
actions/setup-python v3 composite
pre-commit/action v3.0.0 composite

.github/workflows/prettier.yml2 actions

actions/checkout v2 composite
creyD/prettier_action v4.2 composite

.github/workflows/python-build.yml actions

actions/checkout master composite
actions/setup-python v1 composite
pypa/gh-action-pypi-publish master composite

.github/workflows/python-format.yaml2 actions

actions/checkout master composite
mritunjaysharma394/autoyapf v2 composite

.github/workflows/python-test.yml actions

LouisBrunner/checks-action v1.1.1 composite
actions/checkout v2 composite
actions/setup-python v2 composite
actions/upload-artifact v3 composite

.github/workflows/selenium-test.yml actions

actions/checkout v3 composite
actions/download-artifact v3 composite
actions/setup-python v3 composite

.devcontainer/Dockerfile docker

mcr.microsoft.com/vscode/devcontainers/javascript-node 0-${VARIANT} build

taxonium_backend/package.json npm

@jsonlines/core ^1.0.2
axios ^0.26.1
commander ^9.1.0
compression ^1.7.4
cors ^2.8.5
express ^4.17.3
express-queue ^0.0.13
node-fetch ^3.2.10
pako ^2.0.4
taxonium_data_handling file:../taxonium_data_handling
xml2js ^0.4.23

taxonium_backend/yarn.lock npm

@jsonlines/core 1.0.2
accepts 1.3.8
array-flatten 1.1.1
axios 0.26.1
body-parser 1.19.2
bytes 3.0.0
bytes 3.1.2
commander 9.1.0
compressible 2.0.18
compression 1.7.4
content-disposition 0.5.4
content-type 1.0.4
cookie 0.4.2
cookie-signature 1.0.6
core-js 3.22.2
cors 2.8.5
data-uri-to-buffer 4.0.0
debug 2.6.9
debug 3.2.7
debug 4.3.4
depd 1.1.2
destroy 1.0.4
ee-first 1.1.1
encodeurl 1.0.2
escape-html 1.0.3
etag 1.8.1
express 4.17.3
express-end 0.0.8
express-queue 0.0.13
fetch-blob 3.2.0
finalhandler 1.1.2
follow-redirects 1.14.9
formdata-polyfill 4.0.10
forwarded 0.2.0
fresh 0.5.2
http-errors 1.8.1
iconv-lite 0.4.24
inherits 2.0.4
ipaddr.js 1.9.1
media-typer 0.3.0
merge-descriptors 1.0.1
methods 1.1.2
mime 1.6.0
mime-db 1.52.0
mime-types 2.1.35
mini-queue 0.0.14
ms 2.0.0
ms 2.1.2
ms 2.1.3
negotiator 0.6.3
node-domexception 1.0.0
node-fetch 3.2.10
object-assign 4.1.1
on-finished 2.3.0
on-headers 1.0.2
pako 2.0.4
parseurl 1.3.3
path-to-regexp 0.1.7
proxy-addr 2.0.7
qs 6.9.7
range-parser 1.2.1
raw-body 2.4.3
readable-stream 3.6.0
readable-web-to-node-stream 3.0.2
safe-buffer 5.1.2
safe-buffer 5.2.1
safer-buffer 2.1.2
sax 1.2.4
send 0.17.2
serve-static 1.14.2
setprototypeof 1.2.0
statuses 1.5.0
string_decoder 1.3.0
taxonium_data_handling 1.0.1
toidentifier 1.0.1
type-is 1.6.18
unpipe 1.0.0
util-deprecate 1.0.2
utils-merge 1.0.1
vary 1.1.2
web-streams-polyfill 3.2.1
xml2js 0.4.23
xmlbuilder 11.0.1

taxonium_data_handling/package.json npm

readable-web-to-node-stream ^3.0.2

taxonium_data_handling/yarn.lock npm

inherits 2.0.4
readable-stream 3.6.0
readable-web-to-node-stream 3.0.2
safe-buffer 5.2.1
string_decoder 1.3.0
util-deprecate 1.0.2

taxonium_electron/package.json npm

@electron-forge/cli ^6.0.0-beta.67 development
@electron-forge/maker-deb ^6.0.0-beta.67 development
@electron-forge/maker-dmg ^6.0.0-beta.67 development
@electron-forge/maker-rpm ^6.0.0-beta.67 development
@electron-forge/maker-squirrel ^6.0.0-beta.67 development
@electron-forge/maker-zip ^6.0.0-beta.67 development
electron ^21.1.0 development
electron-squirrel-startup ^1.0.0
taxonium_backend file:../taxonium_backend

taxonium_electron/yarn.lock npm

553 dependencies

taxonium_web_client/package.json npm

eslint-config-standard ^16.0.3 development
eslint-plugin-node ^11.1.0 development
eslint-plugin-promise ^5.1.0 development
postcss 8 development
@craco/craco ^6.1.2
@fontsource/roboto ^4.5.5
@jbrowse/plugin-data-management ^2.1.4
@jbrowse/react-linear-genome-view ^2.1.4
@tailwindcss/forms ^0.5.2
@testing-library/jest-dom ^5.11.4
@testing-library/react ^11.1.0
@testing-library/user-event ^12.1.10
JSONStream ^1.3.5
autoprefixer ^9
axios ^0.27.2
binary-search ^1.3.6
classnames ^2.3.1
commander ^9.0.0
compression ^1.7.4
cors ^2.8.5
craco ^0.0.3
deck.gl ^8.6.6
jsonl ^1.1.2
lodash ^4.17.21
lzma-native ^8.0.6
node-polyfill-webpack-plugin ^1.1.4
pako ^2.0.4
process ^0.11.10
react ^17.0.2
react-circular-progressbar ^2.0.4
react-debounce-input ^3.2.3
react-dom ^17.0.2
react-hot-toast ^2.2.0
react-icons ^4.6.0
react-modal ^3.15.1
react-router-dom ^5.2.0
react-scripts 5.0.0
react-spinners ^0.11.0
react-tooltip ^4.2.21
readable-web-to-node-stream ^3.0.2
scale-color-perceptual ^1.1.2
tailwindcss >=3.1.0
taxonium_data_handling file:../taxonium_data_handling
web-vitals ^1.0.1
webpack ^5.72.0
yargs ^17.3.1

taxonium_web_client/yarn.lock npm

1853 dependencies

docs/requirements.txt pypi

alive-progress *
biopython *
furo *
google-api-python-client *
myst-parser *
orjson *
pandas *
protobuf <4
sphinx-argparse *
sphinx-book-theme *
sphinx-rtd-theme *
sphinxcontrib-gtagjs *
treeswift *

Score: 14.081846923184166

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