starfish-prod-ci.yml

name: starfish-prod-ci

on:

  push:
    branches: [ master ]

  pull_request:
    branches: [ master ]

jobs:

  lint:
    name: Lint
    runs-on: "ubuntu-latest"
    steps:
      - uses: actions/checkout@v2

      - name: Setup Python 3.8
        uses: actions/setup-python@v2
        with:
          python-version: 3.8

      - uses: actions/cache@v2
        with:
          path: ${{ env.pythonLocation }}
          key: ${{ runner.OS }}-${{ env.pythonLocation }}-${{ hashFiles('requirements/REQUIREMENTS-CI.txt') }}

      - name: Install Dependencies
        run: |
          make install-dev

      - name: flake8 linting
        run: |
          make lint mypy

  starfish-fast:
    name: Python-${{ matrix.python-version }}-${{ matrix.os }}
    needs: lint
    strategy:
      matrix:
        os: ["windows-latest", "ubuntu-latest"]
        python-version: ["3.8", "3.9", "3.10"]
      fail-fast: false
    runs-on: ${{ matrix.os }}
    steps:
      - uses: actions/checkout@v2

      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v2
        with:
          python-version: ${{ matrix.python-version }}

      - uses: actions/cache@v2
        with:
          path: ${{ env.pythonLocation }}
          key: ${{ runner.OS }}-${{ env.pythonLocation }}-${{ hashFiles('requirements/REQUIREMENTS-CI.txt') }}

      - name: Install dependencies
        run: |
          make install-dev

      - name: Run tests
        run: |
          make fast-test docs-html

  starfish-slow:
    name: Python-${{ matrix.python-version }}-${{ matrix.os }}
    needs: starfish-fast
    strategy:
      matrix:
        os: ["windows-latest", "ubuntu-latest"]
        python-version: ["3.8", "3.9", "3.10"]
      fail-fast: false
    runs-on: ${{ matrix.os }}
    steps:
      - uses: actions/checkout@v2

      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v2
        with:
          python-version: ${{ matrix.python-version }}

      - uses: actions/cache@v2
        with:
          path: ${{ env.pythonLocation }}
          key: ${{ runner.OS }}-${{ env.pythonLocation }}-${{ hashFiles('requirements/REQUIREMENTS-CI.txt') }}

      - name: Install dependencies
        run: |
          make install-dev

      - name: Run tests
        run: |
          make -j check-notebooks slow-test

  # Disabling napari tests for now since github actions runner has no
  # display so will need to modify tests to have napari run headless maybe?

  # napari-pinned:
  #   name: Napari Pinned
  #   runs-on: "ubuntu-latest"
  #   steps:
  #     - uses: actions/checkout@v2

  #     - name: Install dependencies
  #       run: |
  #         sudo apt-get install -y libgl1-mesa-glx libqt5x11extras5 xvfb
  #         pip install -U pip==21.0.1
  #         pip install -r requirements/REQUIREMENTS-NAPARI-CI.txt
  #         make install-dev
  #         pip freeze
  #         export DISPLAY=:99
  #         Xvfb $DISPLAY -ac -screen 0 1024x768x24 &
  #         sleep 10

  #     - name: Run tests
  #       run: |
  #         python -c "import vispy; print(vispy.sys_info())"
  #         make napari-test

  # napari-latest:
  #   name: Napari Latest
  #   needs: napari-pinned
  #   runs-on: "ubuntu-latest"
  #   steps:
  #     - uses: actions/checkout@v2

  #     - name: Install dependencies
  #       run: |
  #         sudo apt-get install -y libgl1-mesa-glx libqt5x11extras5 xvfb
  #         make install-dev
  #         pip install .[napari] pytest-qt
  #         pip freeze
  #         export DISPLAY=:99
  #         Xvfb $DISPLAY -ac -screen 0 1024x768x24 &
  #         sleep 10

  #     - name: Run tests
  #       run: |
  #         python -c "import vispy; print(vispy.sys_info())"
  #         make napari-test

  docker-smoketest:
    name: Docker Smoketest
    needs: starfish-slow
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v2

      - name: Build Docker Image
        run: |
          docker build -f docker/Dockerfile -t spacetx/starfish .

      - name: Run Docker Smoketest
        run: |
          docker run --rm spacetx/starfish starfish --help

  smfish-notebook:
    name: smFISH Notebook Test
    needs: starfish-slow
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v2

      - name: Setup Python 3.8
        uses: actions/setup-python@v2
        with:
          python-version: 3.8

      - uses: actions/cache@v2
        with:
          path: ${{ env.pythonLocation }}
          key: ${{ runner.OS }}-${{ env.pythonLocation }}-${{ hashFiles('requirements/REQUIREMENTS-CI.txt') }}

      - name: Install Dependencies
        run: |
          make install-dev

      - name: Run Notebook Tests
        run: |
          make notebooks/py/smFISH.py

  merfish-notebook:
    name: MERFISH Notebook Test
    needs: starfish-slow
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v2

      - name: Setup Python 3.8
        uses: actions/setup-python@v2
        with:
          python-version: 3.8

      - uses: actions/cache@v2
        with:
          path: ${{ env.pythonLocation }}
          key: ${{ runner.OS }}-${{ env.pythonLocation }}-${{ hashFiles('requirements/REQUIREMENTS-CI.txt') }}

      - name: Install Dependencies
        run: |
          make install-dev

      - name: Run Notebook Tests
        run: |
          make notebooks/py/MERFISH.py

  osmfish-notebook:
    name: osmFISH Notebook Test
    needs: starfish-slow
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v2

      - name: Setup Python 3.8
        uses: actions/setup-python@v2
        with:
          python-version: 3.8

      - uses: actions/cache@v2
        with:
          path: ${{ env.pythonLocation }}
          key: ${{ runner.OS }}-${{ env.pythonLocation }}-${{ hashFiles('requirements/REQUIREMENTS-CI.txt') }}

      - name: Install Dependencies
        run: |
          make install-dev

      - name: Run Notebook Tests
        run: |
          make notebooks/py/osmFISH.py

  dartfish-notebook:
    name: DARTFISH Notebook Test
    needs: starfish-slow
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v2

      - name: Setup Python 3.8
        uses: actions/setup-python@v2
        with:
          python-version: 3.8

      - uses: actions/cache@v2
        with:
          path: ${{ env.pythonLocation }}
          key: ${{ runner.OS }}-${{ env.pythonLocation }}-${{ hashFiles('requirements/REQUIREMENTS-CI.txt') }}

      - name: Install Dependencies
        run: |
          make install-dev

      - name: Run Notebook Tests
        run: |
          make notebooks/py/DARTFISH.py

  simulation-notebook:
    name: Simulation Notebook Test
    needs: starfish-slow
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v2

      - name: Setup Python 3.8
        uses: actions/setup-python@v2
        with:
          python-version: 3.8

      - uses: actions/cache@v2
        with:
          path: ${{ env.pythonLocation }}
          key: ${{ runner.OS }}-${{ env.pythonLocation }}-${{ hashFiles('requirements/REQUIREMENTS-CI.txt') }}

      - name: Install Dependencies
        run: |
          make install-dev

      - name: Run Notebook Tests
        run: |
          make notebooks/py/Starfish_simulation.py

  iss-notebook:
    name: ISS Notebook Test
    needs: starfish-slow
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v2

      - name: Setup Python 3.8
        uses: actions/setup-python@v2
        with:
          python-version: 3.8

      - uses: actions/cache@v2
        with:
          path: ${{ env.pythonLocation }}
          key: ${{ runner.OS }}-${{ env.pythonLocation }}-${{ hashFiles('requirements/REQUIREMENTS-CI.txt') }}

      - name: Install Dependencies
        run: |
          make install-dev

      - name: Run Notebook Tests
        run: |
          make notebooks/py/ISS.py

  baristaseq-notebook:
    name: BaristaSeq Notebook Test
    needs: starfish-slow
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v2

      - name: Setup Python 3.8
        uses: actions/setup-python@v2
        with:
          python-version: 3.8

      - uses: actions/cache@v2
        with:
          path: ${{ env.pythonLocation }}
          key: ${{ runner.OS }}-${{ env.pythonLocation }}-${{ hashFiles('requirements/REQUIREMENTS-CI.txt') }}

      - name: Install Dependencies
        run: |
          make install-dev

      - name: Run Notebook Tests
        run: |
          make notebooks/py/BaristaSeq.py

  seqfish-notebook:
    name: SeqFISH Notebook Test
    needs: starfish-slow
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v2

      - name: Setup Python 3.8
        uses: actions/setup-python@v2
        with:
          python-version: 3.8

      - uses: actions/cache@v2
        with:
          path: ${{ env.pythonLocation }}
          key: ${{ runner.OS }}-${{ env.pythonLocation }}-${{ hashFiles('requirements/REQUIREMENTS-CI.txt') }}

      - name: Install Dependencies
        run: |
          make install-dev

      - name: Run Notebook Tests
        run: |
          make notebooks/py/SeqFISH.py

  starmap-data-processing-example:
    name: STARmap Notebook Test
    needs: starfish-slow
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v2

      - name: Setpu Python 3.8
        uses: actions/setup-python@v2
        with:
          python-version: 3.8
      
      - uses: actions/cache@v2
        with:
          path: ${{ env.pythonLocation }}
          key: ${{ runner.OS }}-${{ env.pythonLocation }}-${{ hashFiles('requirements/REQUIREMENTS-CI.txt') }}
      
      - name: Install Dependencies
        run: |
          make install-dev

      - name: Run Notebook Tests
        run: |
          make notebooks/py/STARmap.py

  smfish-data-processing-example:
    name: 3D smFISH Data Processing Example
    needs: starfish-slow
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v2

      - name: Setup Python 3.8
        uses: actions/setup-python@v2
        with:
          python-version: 3.8

      - uses: actions/cache@v2
        with:
          path: ${{ env.pythonLocation }}
          key: ${{ runner.OS }}-${{ env.pythonLocation }}-${{ hashFiles('requirements/REQUIREMENTS-CI.txt') }}

      - name: Install Dependencies
        run: |
          make install-dev

      - name: Run Data Processing Example Test
        run: |
          make 3d_smFISH.py

  iss-pipeline-data-processing-example:
    name: iss_pipeline.py Data Processing Example
    needs: starfish-slow
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v2

      - name: Setup Python 3.8
        uses: actions/setup-python@v2
        with:
          python-version: 3.8

      - uses: actions/cache@v2
        with:
          path: ${{ env.pythonLocation }}
          key: ${{ runner.OS }}-${{ env.pythonLocation }}-${{ hashFiles('requirements/REQUIREMENTS-CI.txt') }}

      - name: Install Dependencies
        run: |
          make install-dev

      - name: Run Data Processing Example Test
        run: |
          make TESTING=1 iss_pipeline.py