taxonworks

Workbench for biodiversity informatics.

https://github.com/SpeciesFileGroup/taxonworks

Science Score: 36.0%

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
○
Academic publication links
✓
Committers with academic emails
10 of 37 committers (27.0%) from academic institutions
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (10.2%) to scientific vocabulary

Keywords

biodiversity biodiversity-informatics collections describe evolution life nomenclature ruby species taxonomy

Keywords from Contributors

bioinformatics annotation data-manager ontology climate-models autograding energy-system-model optim interactive projection

Last synced: 6 months ago · JSON representation

Repository

Workbench for biodiversity informatics.

Basic Info

Host: GitHub
Owner: SpeciesFileGroup
License: mit
Language: Ruby
Default Branch: development
Homepage: http://taxonworks.org
Size: 99.4 MB

Statistics

Stars: 102
Watchers: 23
Forks: 30
Open Issues: 803
Releases: 142

Topics

biodiversity biodiversity-informatics collections describe evolution life nomenclature ruby species taxonomy

Created over 12 years ago · Last pushed 6 months ago

Metadata Files

Readme Changelog Contributing License Code of conduct

Overview

TaxonWorks is a web-based workbench designed for taxonomists and biodiversity scientists. It provides tools to help you capture, organize, and enhance your data, collaborate with others, and prepare your work for analysis and publication. With TaxonWorks, you can easily manage your research data, share it with colleagues, and streamline the process of analyzing and publishing your findings.

To get more information on the project, its vision, and scope see taxonworks.org and docs.taxonworks.org.

License

TaxonWorks is open source and is presently available under the MIT Open Source License.

Funding

The foundation of TaxonWorks is funded by an endowment of the Species File Group. This project was funded in part by NSF-ABI-1356381. Any opinions, findings and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.

Owner

Name: Species File Group
Login: SpeciesFileGroup
Kind: organization
Location: University of Illinois, INHS

Website: http://speciesfilegroup.org
Repositories: 55
Profile: https://github.com/SpeciesFileGroup

A biodiversity informatics research group.

GitHub Events

Total

Create event: 64
Commit comment event: 12
Release event: 20
Issues event: 459
Watch event: 13
Delete event: 67
Issue comment event: 761
Push event: 989
Pull request review event: 48
Pull request review comment event: 52
Pull request event: 210
Fork event: 4

Last Year

Create event: 64
Commit comment event: 12
Release event: 20
Issues event: 460
Watch event: 13
Delete event: 67
Issue comment event: 761
Push event: 990
Pull request review event: 48
Pull request review comment event: 52
Pull request event: 210
Fork event: 4

Committers

Last synced: 7 months ago

All Time

Total Commits: 26,011
Total Committers: 37
Avg Commits per committer: 703.0
Development Distribution Score (DDS): 0.689

Past Year

Commits: 1,922
Committers: 10
Avg Commits per committer: 192.2
Development Distribution Score (DDS): 0.616

Top Committers

Name	Email	Commits
mjy	d**d@g**m	8,097
José Luis Pereira	p**i@o**m	7,522
Jim Tucker	t**d@u**u	2,700
Hernán Lucas Pereira	e**r@g**m	1,922
jrflood	j**d@i**u	1,465
Dmitry Dmitriev	a**a@g**m	1,431
Tom Klein	t**e@g**m	1,013
mbeckman	m**n@i**u	777
eef	e**f@i**u	302
Dash Peters	3****w	254
Fauzi Kliman	f**n@g**m	225
Geoff Ower	g**r@i**u	92
Dmitry Mozzherin	d**n@g**m	88
dependabot[bot]	4****]	24
Debbie Paul	d**l@i**u	17
eef	e****u	15
proceps	Z****1	14
Lisa Walley	l**y@e**g	13
proceps	v**e@g**m	5
mikemaehr	m**r@g**m	5
W Beecher Baker	w**r@p**u	4
omahs	7****s	3
José Luis Pereira	j**o@M**l	3
lc-art1	0**l@g**m	2
dceades	d**s@i**u	2
daisie_local	d**h@g**m	2
Devarsh Ruparelia	d**a@g**m	2
J Richard Flood	j**d@J**l	2
David C. Eades	d**s@D**l	2
JeGoi	j**d@g**m	1
and 7 more...

Committer Domains (Top 20 + Academic)

illinois.edu: 6 sfg-hackathon.(none): 1 mbp-de-jose.mlp.fcnym.unlp.edu.ar: 1 mbp-de-jose.fibertel.com.ar: 1 hernan.(none): 1 purdue.edu: 1 eol.org: 1 uiuc.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 3,882
Total pull requests: 755
Average time to close issues: 6 months
Average time to close pull requests: 18 days
Total issue authors: 99
Total pull request authors: 20
Average comments per issue: 1.99
Average comments per pull request: 1.56
Merged pull requests: 568
Bot issues: 0
Bot pull requests: 107

Past Year

Issues: 343
Pull requests: 261
Average time to close issues: 7 days
Average time to close pull requests: 6 days
Issue authors: 34
Pull request authors: 8
Average comments per issue: 1.1
Average comments per pull request: 0.99
Merged pull requests: 173
Bot issues: 0
Bot pull requests: 56

View more stats

Top Authors

Issue Authors

mjy (1,319)
proceps (687)
tmcelrath (418)
AntWeb-org (162)
LordFlashmeow (104)
adrik29 (97)
kleintom (78)
mabecabrera (75)
LocoDelAssembly (69)
hhopkins77 (65)
debpaul (65)
kandakoj (60)
jlpereira (59)
gdower (52)
typophyllum (46)

Pull Request Authors

kleintom (236)
LordFlashmeow (117)
dependabot[bot] (107)
LocoDelAssembly (71)
mjy (48)
jlpereira (47)
gdower (34)
Merfoo (31)
TuckerJD (21)
jrflood (19)
neolefty (12)
lc-art1 (4)
Kunyao-Alex (1)
omahs (1)
dshorthouse (1)

Top Labels

Issue Labels

enhancement (1,642) bug (1,379) task (172) model (149) question (147) blocker (146) API (70) idea (65) export (53) soft validation (32) can't replicate (20) needs more information (19) stale (13) good first issue (12) help wanted (7) exemplary issue (6) dependencies (4) deprecation (3) javascript (2) ruby (2) UI (2) AI (1)

Pull Request Labels

dependencies (107) ruby (53) javascript (52)

Dependencies

package-lock.json npm

857 dependencies

package.json npm

@babel/core ^7.18.6 development
@babel/plugin-transform-runtime ^7.18.6 development
@babel/preset-env ^7.18.6 development
@babel/runtime ^7.18.6 development
@vue/compiler-sfc ^3.2.37 development
babel-loader ^8.2.5 development
compression-webpack-plugin ^10.0.0 development
css-loader ^6.7.1 development
css-minimizer-webpack-plugin ^4.0.0 development
eslint ^8.18.0 development
eslint-config-standard ^17.0.0 development
eslint-plugin-import ^2.26.0 development
eslint-plugin-n ^15.2.3 development
eslint-plugin-node ^11.1.0 development
eslint-plugin-promise ^6.0.0 development
eslint-plugin-standard ^4.1.0 development
eslint-plugin-vue ^9.1.1 development
mini-css-extract-plugin ^2.6.1 development
postcss ^8.4.14 development
postcss-flexbugs-fixes ^5.0.2 development
postcss-import ^14.1.0 development
postcss-loader ^7.0.0 development
postcss-preset-env ^7.7.2 development
raw-loader ^4.0.2 development
resolve-url-loader ^5.0.0 development
sass ^1.53.0 development
sass-loader ^13.0.2 development
style-loader ^3.3.1 development
stylus ^0.58.1 development
stylus-loader ^7.0.0 development
terser-webpack-plugin ^5.3.3 development
url ^0.11.0 development
vue-loader ^17.0.0 development
webpack ^5.73.0 development
webpack-assets-manifest ^5.1.0 development
webpack-cli ^4.10.0 development
webpack-dev-server ^4.9.2 development
webpack-merge ^5.8.0 development
worker-loader ^3.0.8 development
@geoman-io/leaflet-geoman-free ^2.13.0
@ibm/plex ^6.0.2
@sfgrp/sled ^1.0.3
@sfgrp/svg-radial-menu ^1.0.7
axios ^0.27.2
chart.js ^3.8.0
d3 ^7.5.0
dompurify ^2.3.8
easymde ^2.16.1
exif-js ^2.3.0
json2csv ^5.0.7
leaflet ^1.8.0
leaflet.pattern ^0.1.0
parse-dms 0.0.5
pdfjs-dist 2.14.305
qs ^6.11.0
shakapacker 6.4.1
v-hotkey ^0.9.0
vue ^3.2.37
vue-handy-scroll ^3.0.1
vue-hotkeys 0.0.1
vue-tippy ^6.0.0-alpha.58
vue-turbolinks ^2.2.2
vuedraggable ^4.1.0
vuex ^4.0.2

.github/docker-tests/docker-image-test/Gemfile rubygems

browsermob-proxy ~> 0.3.1
capybara ~> 3.29
rexml ~> 3.2, >= 3.2.5
rspec ~> 3.8
rspec-steps ~> 2.1, >= 2.1.1
webdrivers ~> 4.5
webrick ~> 1.7

Gemfile rubygems

better_errors ~> 2.9 development
binding_of_caller >= 0 development
brakeman >= 4.6.1, ~> 5.1 development
capybara ~> 3.18 development
codecov ~> 0.6.0 development
database_cleaner ~> 2.0 development
factory_bot_rails ~> 6.2 development
faker ~> 2.10 development
guard-rspec ~> 4.7.3 development
os ~> 1.0, >= 1.0.1 development
parallel_tests >= 0 development
prawn ~> 2.4.0 development
puma ~> 5.5 development
rails-controller-testing ~> 1.0.2 development
rspec ~> 3.6 development
rspec-activemodel-mocks ~> 1.1.0 development
rspec-rails ~> 5.0 development
rubocop ~> 1.20 development
rubocop-faker ~> 1.1 development
rubocop-performance ~> 1.10 development
rubocop-rails ~> 2.4 development
rubocop-rspec ~> 2.6 development
ruby-prof ~> 1.2 development
sdoc ~> 2.2.0 development
seedbank ~> 0.5.0 development
selenium-webdriver ~> 4.2.0 development
simplecov >= 0 development
spring-commands-rspec ~> 1.0.4 development
timecop ~> 0.9.1 development
vcr ~> 6.0 development
web-console ~> 4.0, >= 4.0.1 development
webdrivers ~> 5.0 development
webmock ~> 3.8 development
activerecord-postgis-adapter ~> 7.0
acts_as_list ~> 1.0
amazing_print ~> 1.4.0
barby ~> 0.6.8
bcrypt ~> 3.1.11
best_in_place >= 0
bibtex-ruby ~> 6.0
biodiversity >= 0
bundler ~> 2.0
chartkick ~> 4.0
chronic ~> 0.10.2
chunky_png ~> 1.4.0
citeproc-ruby ~> 1.1.10
closure_tree ~> 7.0
csl ~> 1.6.0
csl-styles ~> 1.0.1.8
daemons ~> 1.4.1
delayed_job_active_record ~> 4.1.3
dropzonejs-rails ~> 0.8.1
dwc-archive >= 0
dwc_agent ~> 3.0
exception_notification ~> 4.4
execjs ~> 2.8.1
ffi-geos ~> 2.3.0
gnfinder ~> 0.16
gpx >= 0
groupdate ~> 5.2
hiredis ~> 0.6.1
indefinite_article ~> 0.2.4
jbuilder ~> 2.7
jquery-rails ~> 4.4
jquery-turbolinks ~> 2.1
jquery-ui-rails ~> 6.0.1
kaminari ~> 1.2.0
logic_tools >= 0
logical_query_parser >= 0
matrix ~> 0.4.2
modularity ~> 3.0.0
namecase ~> 2.0
net-smtp ~> 0.3.1
paper_trail ~> 12.0
paperclip >= 0
paperclip-meta ~> 3.0
passenger ~> 6.0.2
pdf-reader ~> 2.2
pg ~> 1.1
postgresql_cursor ~> 0.6.1
psych ~> 3.3
rack-cors ~> 1.1
rails ~> 6.1
rails-jquery-autocomplete ~> 1.0.3
rails_or ~> 1.1.8
rainbow ~> 3.0.0
rake ~> 13.0
rdf ~> 3.0
redcarpet ~> 3.4
redis ~> 4.5
responders ~> 3.0
rgb ~> 0.1
rgeo ~> 2.2
rgeo-geojson ~> 2.1, >= 2.1.1
rgeo-proj4 ~> 3.0, >= 3.0.1
rmagick ~> 4.2, >= 4.2.2
roo ~> 2.8, >= 2.8.3
roo-xls ~> 1.2
ruby-graphviz ~> 1.2.5
ruby-units ~> 2.3.0
rubyzip ~> 2.3.0
sassc-rails ~> 2.1.0
serrano >= 0
shakapacker ~> 6.3
shortener ~> 0.8.0
sprockets ~> 3.7.2
sprockets-es6 ~> 0.9.2
sprockets-rails ~> 3.2.0
sqed ~> 0.7.0
taxonifi ~> 0.6.0
term-ansicolor ~> 1.6
thor ~> 1.1.0
turbolinks ~> 5.2.0
tzinfo-data ~> 1.2019
uglifier ~> 4.2
validates_timeliness ~> 4.1, >= 4.1.1
waxy ~> 0.1
zaru ~> 0.3.0
zip_tricks ~> 5.6

Gemfile.lock rubygems

268 dependencies

.github/workflows/base-image.yml actions

actions/checkout v2 composite
docker/login-action v1 composite

.github/workflows/build.yml actions

actions/cache v3 composite
actions/checkout v3 composite
actions/setup-node v3 composite
ruby/setup-ruby v1 composite
postgis/postgis 12-3.0 docker

.github/workflows/deliver.yml actions

actions/cache v3 composite
actions/checkout v3 composite
actions/github-script v6 composite
docker/login-action v2 composite

.github/docker-tests/docker-image-taxonworks/Dockerfile docker

sfgrp/taxonworks latest build

.github/docker-tests/docker-image-test/Dockerfile docker

ruby 3.1.2 build

Dockerfile docker

base latest build
sfgrp/taxonworks-base latest build

docker-compose.yml docker

mdillon/postgis 10
postgis/postgis 12-3.0

.github/docker-tests/docker-compose.yml docker

ecosyste.ms

Data

Tools

Indexes

Applications

Experiments

Open Source Science

taxonworks

Science Score: 36.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

Overview

License

Funding

Owner

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Dependencies