rarelens/.github/workflows/ci.yml

name: ci
on:
  pull_request:
  push:
    branches: [main]

jobs:
  api:
    runs-on: ubuntu-latest
    services:
      postgres:
        image: postgres:16-alpine
        env: { POSTGRES_USER: rarelens, POSTGRES_PASSWORD: rarelens, POSTGRES_DB: rarelens }
        ports: ["5432:5432"]
        options: --health-cmd "pg_isready -U rarelens" --health-interval 5s --health-retries 10
    steps:
      - uses: actions/checkout@v4
      - uses: astral-sh/setup-uv@v3
      - run: uv pip install --system -e "api[dev]"
      - run: cd api && ruff check . && mypy app
      - run: cd api && pytest -q
        env:
          DATABASE_URL: postgresql+asyncpg://rarelens:rarelens@localhost:5432/rarelens
          REQUIRE_DB: "1"

  ml:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - uses: astral-sh/setup-uv@v3
      - run: uv pip install --system -e "ml[dev]"
      - run: cd ml && pytest -q

  web:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - uses: actions/setup-node@v4
        with: { node-version: 22, cache: npm, cache-dependency-path: web/package-lock.json }
      - run: cd web && npm ci && npm run check && npm test && npm run build

  pipeline:
    runs-on: ubuntu-latest
    services:
      postgres:
        image: postgres:16-alpine
        env: { POSTGRES_USER: rarelens, POSTGRES_PASSWORD: rarelens, POSTGRES_DB: rarelens }
        ports: ["5432:5432"]
        options: --health-cmd "pg_isready -U rarelens" --health-interval 5s --health-retries 10
    steps:
      - uses: actions/checkout@v4
      - uses: astral-sh/setup-uv@v3
      - run: uv pip install --system -r pipeline/requirements.txt pytest
      - run: cd pipeline && pytest -q tests
        env:
          DATABASE_URL: postgresql://rarelens:rarelens@localhost:5432/rarelens
          REQUIRE_DB: "1"
      - uses: nf-core/setup-nextflow@v2
      # Stub run checks wiring and channel shapes only; no containers or VEP cache needed.
      - run: cd pipeline && nextflow run main.nf -stub-run --vcf tests/data/tiny.vcf

  terraform:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - uses: hashicorp/setup-terraform@v3
      - run: cd infra/terraform && terraform init -backend=false && terraform fmt -check && terraform validate

  images:
    if: github.ref == 'refs/heads/main'
    needs: [api, ml, web, pipeline]
    runs-on: ubuntu-latest
    permissions: { contents: read, id-token: write }
    strategy:
      matrix:
        include:
          - { component: api, context: api, dockerfile: api/Dockerfile }
          - { component: web, context: web, dockerfile: web/Dockerfile }
          - { component: ml, context: ml, dockerfile: ml/Dockerfile }
          - { component: pipeline, context: pipeline, dockerfile: pipeline/Dockerfile }
          - { component: loader, context: pipeline, dockerfile: pipeline/loader.Dockerfile }
    env:
      REGISTRY: europe-west2-docker.pkg.dev/${{ secrets.GCP_PROJECT }}/rarelens
    steps:
      - uses: actions/checkout@v4
      - uses: google-github-actions/auth@v2
        with:
          workload_identity_provider: ${{ secrets.GCP_WIF_PROVIDER }}
          service_account: ${{ secrets.GCP_CI_SA }}
      - run: gcloud auth configure-docker europe-west2-docker.pkg.dev --quiet
      - uses: docker/build-push-action@v6
        with:
          context: ${{ matrix.context }}
          file: ${{ matrix.dockerfile }}
          push: true
          # Only the pipeline driver uses it: pins the loader image from the same commit.
          build-args: LOADER_IMAGE=${{ env.REGISTRY }}/loader:${{ github.sha }}
          tags: ${{ env.REGISTRY }}/${{ matrix.component }}:${{ github.sha }}