pipeline/.github/workflows/check.yaml at a61a313e2b619d4ec73f95a54bb22fd81380d5e9 · opentargets/pipeline · GitHub

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---
name: Check

on:
  pull_request:
    branches:
      - main
  workflow_call:
    inputs:
      packages:
        description: 'A JSON string with the packages to check.'
        required: false
        type: string

jobs:
  matrix:
    name: Compute test matrix
    runs-on: ubuntu-latest
    outputs:
      include: ${{ steps.compute.outputs.include }}
      has_pts: ${{ steps.compute.outputs.has_pts }}
    steps:
      - id: compute
        # pts has far more tests than the other packages, so it's sharded
        # separately across 4 runners with pytest-split to cut CI wall time.
        run: |
          packages='${{ inputs.packages || '["orchestration","pis","pts","croissant"]' }}'
          include=$(jq -c '[.[] | select(. != "pts") | {package: .}]' <<< "$packages")
          has_pts=$(jq -c 'any(. == "pts")' <<< "$packages")
          echo "include=$include" >> "$GITHUB_OUTPUT"
          echo "has_pts=$has_pts" >> "$GITHUB_OUTPUT"

  test:
    needs: matrix
    if: needs.matrix.outputs.include != '[]'
    name: Test ${{ matrix.package }}
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        include: ${{ fromJSON(needs.matrix.outputs.include) }}
    steps:
      - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
      - uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0

      - name: Sync dependencies
        working-directory: ${{ matrix.package }}
        run: uv sync --locked --all-groups --all-extras

      - name: Run tests
        working-directory: ${{ matrix.package }}
        run: uv run --frozen pytest -rxs

      - name: run ty # better to do it here because we have deps installed
        working-directory: ${{ matrix.package }}
        run: uv run --frozen ty check --output-format=github

  test-pts:
    needs: matrix
    if: needs.matrix.outputs.has_pts == 'true'
    name: Test pts (shard ${{ matrix.group }}/4)
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        group: [1, 2, 3, 4]
    steps:
      - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
      - uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0

      - name: Sync dependencies
        working-directory: pts
        run: uv sync --locked --all-groups --all-extras

      - name: Run tests
        working-directory: pts
        run: uv run --frozen pytest -rxs --splits 4 --group ${{ matrix.group }}

      - name: run ty # better to do it here because we have deps installed
        if: matrix.group == 1
        working-directory: pts
        run: uv run --frozen ty check --output-format=github

  test-gate:
    name: Test pts
    # branch protection requires the context "Test pts". Since pts's own
    # result now lives in test-pts (separate from the other packages), this
    # gate reports it under a name that's stable regardless of shard count -
    # and stays green when pts isn't part of this run at all (e.g. a
    # single-package release tag for another package).
    needs: [matrix, test-pts]
    if: always()
    runs-on: ubuntu-latest
    steps:
      - run: |
          if [[ "${{ needs.matrix.outputs.has_pts }}" == "true" ]]; then
            [[ "${{ needs.test-pts.result }}" == "success" ]] || exit 1
          fi

  lint:
    name: Lint all packages
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@9c091bb21b7c1c1d1991bb908d89e4e9dddfe3e0 # v7.0.0
      - uses: astral-sh/setup-uv@fac544c07dec837d0ccb6301d7b5580bf5edae39 # v8.2.0
      - uses: j178/prek-action@bdca6f102f98e2b4c7029491a53dfd366469e33d # v2.0.4
        with:
          extra-args: --all-files --skip ty # we run ty during test