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Open Source Science

https://github.com/databio/bedhost

API and UI for BEDbase

https://github.com/databio/bedhost

Science Score: 26.0%

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
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (7.1%) to scientific vocabulary

Keywords

bed bioinformatics fastapi genomic-intervals genomics rest-api server
Last synced: 5 months ago · JSON representation

Repository

API and UI for BEDbase

Basic Info
  • Host: GitHub
  • Owner: databio
  • License: bsd-2-clause
  • Language: TypeScript
  • Default Branch: master
  • Homepage: https://bedbase.org
  • Size: 3.22 MB
Statistics
  • Stars: 2
  • Watchers: 9
  • Forks: 1
  • Open Issues: 25
  • Releases: 21
Topics
bed bioinformatics fastapi genomic-intervals genomics rest-api server
Created over 6 years ago · Last pushed 5 months ago
Metadata Files
Readme License

README.md

bedhost

Code style: black Github badge

bedhost is a Python FastAPI module for the API that powers BEDbase. It needs a path to the bedbase configuration file, which can be provided either via -c/--config argument or read from $BEDBASE_CONFIG environment variable.

Links of interest

Developer quick-start

source environment/production.env BEDBASE_CONFIG=deployment/config/api.bedbase.org.yaml uvicorn bedhost.main:app --reload

UI development: terminal export VITE_API_HOST=http://localhost:8000

Owner

  • Name: Databio
  • Login: databio
  • Kind: organization
  • Location: University of Virginia

Solving problems in computational biology

GitHub Events

Total
  • Create event: 32
  • Release event: 6
  • Issues event: 66
  • Delete event: 23
  • Member event: 3
  • Issue comment event: 68
  • Push event: 173
  • Pull request review comment event: 35
  • Pull request event: 64
  • Pull request review event: 37
Last Year
  • Create event: 32
  • Release event: 6
  • Issues event: 66
  • Delete event: 23
  • Member event: 3
  • Issue comment event: 68
  • Push event: 173
  • Pull request review comment event: 35
  • Pull request event: 64
  • Pull request review event: 37

Issues and Pull Requests

Last synced: 5 months ago

All Time
  • Total issues: 104
  • Total pull requests: 88
  • Average time to close issues: 4 months
  • Average time to close pull requests: 22 days
  • Total issue authors: 10
  • Total pull request authors: 10
  • Average comments per issue: 2.32
  • Average comments per pull request: 0.99
  • Merged pull requests: 71
  • Bot issues: 0
  • Bot pull requests: 15
Past Year
  • Issues: 31
  • Pull requests: 44
  • Average time to close issues: 27 days
  • Average time to close pull requests: 5 days
  • Issue authors: 7
  • Pull request authors: 5
  • Average comments per issue: 0.39
  • Average comments per pull request: 0.98
  • Merged pull requests: 32
  • Bot issues: 0
  • Bot pull requests: 12
View more stats
Top Authors
Issue Authors
  • nsheff (41)
  • khoroshevskyi (30)
  • stolarczyk (9)
  • donaldcampbelljr (7)
  • xuebingjie1990 (5)
  • sanghoonio (4)
  • nleroy917 (3)
  • oddodaoddo (2)
  • jwokaty (2)
  • vjcitn (1)
Pull Request Authors
  • khoroshevskyi (29)
  • xuebingjie1990 (19)
  • dependabot[bot] (15)
  • sanghoonio (7)
  • nsheff (6)
  • nleroy917 (4)
  • stolarczyk (4)
  • oddodaoddo (2)
  • Tobeje (1)
  • jwokaty (1)
Top Labels
Issue Labels
likely-solved (13) solved (6) ui (6) docs (5) enhancement (4) bug (4) priority-low (4) priority-high (2) invalid (1) priority-medium (1) good first issue (1)
Pull Request Labels
dependencies (15) javascript (7)

Dependencies

.github/workflows/black.yaml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
  • psf/black 20.8b1 composite
.github/workflows/deploy-api-dev.yml actions
  • actions/checkout v4 composite
  • aws-actions/amazon-ecr-login v2 composite
  • aws-actions/amazon-ecs-deploy-task-definition v1 composite
  • aws-actions/amazon-ecs-render-task-definition v1 composite
  • aws-actions/configure-aws-credentials v4 composite
.github/workflows/deploy-api.yml actions
  • actions/checkout v4 composite
  • aws-actions/amazon-ecr-login v2 composite
  • aws-actions/amazon-ecs-deploy-task-definition v1 composite
  • aws-actions/amazon-ecs-render-task-definition v1 composite
  • aws-actions/configure-aws-credentials v4 composite
.github/workflows/dockerhub-dev.yaml actions
  • actions/checkout v4 composite
  • docker/build-push-action v5 composite
  • docker/login-action v3 composite
.github/workflows/dockerhub.yaml actions
  • actions/checkout v4 composite
  • docker/build-push-action v5 composite
  • docker/login-action v3 composite
.github/workflows/python-publish.yaml actions
  • actions/checkout v4 composite
  • actions/setup-python v5 composite
  • pypa/gh-action-pypi-publish release/v1 composite
Dockerfile docker
  • python 3.10-slim build
ui/package-lock.json npm
  • 396 dependencies
ui/package.json npm
  • @types/node ^20.11.27 development
  • @types/react ^18.2.64 development
  • @types/react-dom ^18.2.21 development
  • @typescript-eslint/eslint-plugin ^7.1.1 development
  • @typescript-eslint/parser ^7.1.1 development
  • @vitejs/plugin-react ^4.2.1 development
  • eslint ^8.57.0 development
  • eslint-plugin-react-hooks ^4.6.0 development
  • eslint-plugin-react-refresh ^0.4.5 development
  • sass ^1.72.0 development
  • typescript ^5.2.2 development
  • vite ^5.1.6 development
  • @tanstack/react-query ^5.28.0
  • @tanstack/react-query-devtools ^5.28.0
  • @tanstack/react-table ^8.15.3
  • @uidotdev/usehooks ^2.4.1
  • axios ^1.6.7
  • bootstrap ^5.3.3
  • bootstrap-icons ^1.11.3
  • chart.js ^4.4.2
  • chartjs-chart-error-bars ^4.4.0
  • framer-motion ^11.0.20
  • react ^18.2.0
  • react-bootstrap ^2.10.1
  • react-chartjs-2 ^5.2.0
  • react-dom ^18.2.0
  • react-dropzone ^14.2.3
  • react-helmet-async ^2.0.4
  • react-hot-toast ^2.4.1
  • react-markdown ^9.0.1
  • react-router-dom ^6.22.3
  • rehype-highlight ^7.0.0
requirements/requirements-all.txt pypi
  • bbconf >=0.5.1
  • fastapi >=0.103.0
  • logmuse >=0.2.7
  • markdown *
  • pephubclient >=0.4.1
  • psycopg *
  • python-multipart >=0.0.9
  • requests *
  • setuptools *
  • uvicorn *
  • yacman >=0.9.2
requirements/requirements-dev.txt pypi
setup.py pypi