test-and-lint.yml

name: Test and Lint

on: pull_request

# Cancel actions when new commits are pushed to PR
concurrency: 
    group: ${{ github.head_ref }}
    cancel-in-progress: true
env:
  BUCKET_NAME : "bioio-dev-test-resources"
  AWS_REGION : "us-west-2"
permissions:
  id-token: write   # This is required for requesting the JWT
  contents: read    # This is required for actions/checkout

jobs:
  test-core-lib:
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        python-version: [3.9, '3.10', 3.11]
        os: [
          ubuntu-latest,
          windows-latest,
          macos-latest,
        ]
    steps:
      - uses: actions/checkout@v2
        with:
          submodules: true
      - uses: aws-actions/configure-aws-credentials@v3
        with:
          role-to-assume: arn:aws:iam::978220035532:role/bioio_github
          role-session-name: bioio-aicsimageio-${{ github.sha }}
          aws-region: ${{ env.AWS_REGION }}
      - name: Setup Python
        uses: actions/setup-python@v2
        with:
          python-version: ${{ matrix.python-version }}
      - name: Install Dependencies
        run: |
          python -m pip install --upgrade pip
          pip install .[test]
      - uses: actions/cache@v2
        id: cache
        with:
          path: aicsimageio/tests/resources
          key: ${{ hashFiles('scripts/TEST_RESOURCES_HASH.txt') }}
      - name: Download Test Resources
        if: steps.cache.outputs.cache-hit != 'true'
        run: |
          python scripts/download_test_resources.py --debug
      - name: Run tests with Tox
        # Run tox using the version of Python in `PATH`
        run: tox -e py
      - name: Upload codecov
        uses: codecov/codecov-action@v2

  test-readers:
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        python-version: [3.9, '3.10', 3.11]
        os: [
          ubuntu-20.04,
          windows-latest,
          macos-11,
        ]
        tox-env: [
          bioformats,
          czi,
          base-imageio,
          dv,
          lif,
          nd2,
          sldy,
          bfio,
          omezarr,
        ]
    steps:
      - uses: actions/checkout@v2
        with:
          submodules: true
      - uses: aws-actions/configure-aws-credentials@v3
        with:
          role-to-assume: arn:aws:iam::978220035532:role/bioio_github
          role-session-name: bioio-aicsimageio-${{ github.sha }}
          aws-region: ${{ env.AWS_REGION }}
      - name: Setup Python
        uses: actions/setup-python@v2
        with:
          python-version: ${{ matrix.python-version }}
      - uses: actions/setup-java@v2
        with:
          distribution: "temurin"
          java-version: "11"
      - name: Install Dependencies
        run: |
          python -m pip install --upgrade pip
          pip install .[test]
      - uses: actions/cache@v2
        id: cache
        with:
          path: aicsimageio/tests/resources
          key: ${{ hashFiles('scripts/TEST_RESOURCES_HASH.txt') }}
      - name: Download Test Resources
        if: steps.cache.outputs.cache-hit != 'true'
        run: |
          python scripts/download_test_resources.py --debug
      - name: Run tests with Tox
        run: tox -e ${{ matrix.tox-env }}
      - name: Upload codecov
        uses: codecov/codecov-action@v2

  lint:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v2
        with:
          submodules: true
      - name: Set up Python
        uses: actions/setup-python@v1
        with:
          python-version: 3.11
      - name: Install Dependencies
        run: |
          python -m pip install --upgrade pip
          pip install pre-commit
      - name: Lint
        run: pre-commit run --all-files --show-diff-on-failure

  docs:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
        with:
          fetch-depth: 0
          submodules: true
      - name: Set up Python
        uses: actions/setup-python@v4
        with:
          python-version: 3.11
      - name: Install Dependencies
        run: |
          pip install --upgrade pip
          pip install .[dev]
      - name: Generate Docs
        run: |
          gitchangelog
          make gen-docs