tests.yaml

# This workflow will install Python dependencies, run tests and lint with a single version of Python
# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions

name: build

on:
  push:
    branches: [master]
  pull_request:
    branches: [master]

concurrency:
  group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
  cancel-in-progress: true

jobs:
  tests:

    runs-on: ubuntu-latest

    strategy:
      matrix:
        python-version: [3.7, 3.8, 3.9, "3.10"]

    steps:
    - uses: actions/checkout@v4

    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v5
      with:
        python-version: ${{ matrix.python-version }}

    - name: Cache pip
      uses: actions/cache@v4
      with:
        # path: ${{ env.pythonLocation }}
        # key: ${{ env.pythonLocation }}-${{ hashFiles('setup.py') }}
        # restore-keys: |
        #   ${{ env.pythonLocation }}-
        # This path is specific to Ubuntu
        path: ~/.cache/pip
        # Look to see if there is a cache hit for the corresponding requirements file
        key: ${{ runner.os }}-pip-${{ hashFiles('setup.py') }}
        restore-keys: |
          ${{ runner.os }}-pip-
          ${{ runner.os }}-

    - name: Install Dependencies
      run: |
        python -m pip install --upgrade pip
        python -m pip install -r requirements.txt -r requirements-test.txt
        python -m pip install .

    - name: PyTest
      run: |
        pytest --cov deepcell_spots

    - name: Coveralls
      if: env.COVERALLS_REPO_TOKEN != null
      env:
        COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}
        COVERALLS_FLAG_NAME: ${{ matrix.python-version }}
        COVERALLS_PARALLEL: true
      run: |
        coveralls --service=github

  test-docker:
    name: Build docker image and run tests
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v4
      - uses: docker/setup-qemu-action@v3
      - uses: docker/setup-buildx-action@v3

      - name: Cache docker layers
        uses: actions/cache@v4
        with:
          path: /tmp/.buildx-cache
          key: ${{ runner.os }}-buildx-${{ github.sha }}
          restore-keys: ${{ runner.os }}-buildx-

      - name: Build image run unit tests
        env:
          IMAGE: ${{ github.repository }}:${{ github.sha }}
          NAME: deepcell-spots-test
        run: |
          docker buildx build --load --tag ${{ env.IMAGE }} .
          docker run -d -it \
            --entrypoint=bash \
            --name ${{ env.NAME }} \
            ${{ env.IMAGE }}
          docker cp requirements-test.txt ${{ env.NAME }}:/opt/deepcell-spots/requirements-test.txt
          docker exec ${{ env.NAME }} pip install -r /opt/deepcell-spots/requirements-test.txt
          docker exec ${{ env.NAME }} pytest /opt/deepcell-spots/deepcell_spots
          docker kill ${{ env.NAME }} && docker rm ${{ env.NAME }}


  coveralls:
    name: Finish Coveralls
    needs: tests
    runs-on: ubuntu-latest
    steps:
    - name: Coveralls Finished
      uses: coverallsapp/github-action@master
      if: env.COVERALLS_REPO_TOKEN != null
      env:
        COVERALLS_REPO_TOKEN: ${{ secrets.COVERALLS_REPO_TOKEN }}
      with:
        github-token: ${{ secrets.GITHUB_TOKEN }}
        parallel-finished: true