databio/actions

Shared GitHub Actions code for lab repositories. Anything here can be called from any repo, public or private, in any org. This repo is public: it must hold no secrets and nothing private. A called workflow runs inside the calling repo's job and uses the caller's secrets.

GitHub offers two kinds of shared code, and this repo holds both:

• Reusable workflows (.github/workflows/*.yml with on: workflow_call) are whole jobs. Call one from a job: uses: databio/actions/.github/workflows/<name>.yml@master.
• Composite actions (<name>/action.yml) are groups of steps that run inside the caller's job. Call one from a step: uses: databio/actions/<name>@master.

What's here

Name	Kind	What it does
notify-doc-hub.yml	reusable workflow	Tells databio/doc-hubs that a spoke's docs changed, so that site rebuilds
ruff.yml	reusable workflow	Lints a Python repo with ruff (ruff check and ruff format --check), using one org-wide ruff version

notify-doc-hub.yml

A spoke repo adds .github/workflows/notify-docs.yml:

name: Notify docs

on:
  push:
    branches: [master]
    paths:
      - 'docs/**'
      - '.github/workflows/notify-docs.yml'
  workflow_dispatch:

jobs:
  notify:
    uses: databio/actions/.github/workflows/notify-doc-hub.yml@master
    with:
      site: village              # site slug in doc-hubs sites.toml
      spoke: researcher-profiles # spoke slug in hubs/<site>/spokes.toml
    secrets:
      DOCS_DISPATCH_TOKEN: ${{ secrets.DOCS_DISPATCH_TOKEN }}

DOCS_DISPATCH_TOKEN is a databio org secret. Repos in other orgs need it set in their own org. The full spoke checklist (path filters, naming for repos with several spokes) is in the doc-hubs README, "Add a spoke".

Callers use @master, so a change here reaches every caller at once. Keep changes backward compatible with the site / spoke inputs, or update doc-hubs' deploy.yml in step.

ruff.yml

The one lint job for every databio Python repo. A repo's lint workflow is just:

name: Lint

on: [push, pull_request]

jobs:
  lint:
    name: Lint
    uses: databio/actions/.github/workflows/ruff.yml@master

It runs ruff check . and ruff format --check . from the repo root, so the rules come from the repo's own ruff.toml or pyproject.toml. Ruff is installed with astral-sh/ruff-action (a prebuilt binary), so there is no Python setup or pip install, and the job takes a few seconds.

Ruff version. The default version is set once, in ruff.yml. Bump that default to move every repo to a new ruff at once. A repo that must stay on a different version overrides it:

  lint:
    uses: databio/actions/.github/workflows/ruff.yml@master
    with:
      version: "0.17.0"

Skip tests when lint fails. Inside the same workflow file, make the test job wait on lint, so a lint failure does not also spend minutes on tests:

  test:
    needs: lint