test_stardist.yml

name: CellProfiler-Stardist

on:
    push:
      branches:
        - master
    pull_request:
      types: [opened, reopened, synchronize, ready_for_review, review_requested]

jobs:
  build_cellprofiler:
    name: Test CellProfiler-Stardist
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v2
      - uses: actions/setup-python@v2
        with:
          architecture: x64
          python-version: ${{ matrix.python-version }}
      - name: Get pip cache dir
        id: pip-cache-dir
        run: |
          echo "::set-output name=dir::$(pip cache dir)"
      - name: Cache pip
        uses: actions/cache@v3
        id: cache-pip
        with:
          path: ${{ steps.pip-cache-dir.outputs.dir }}
          key: ${{ runner.os }}-${{ env.pythonLocation }}-${{ hashFiles('**/setup.py') }}
      - name: Set up Python
        uses: actions/setup-python@v2
        with:
          python-version: 3.8

      - name: Install CellProfiler dependencies
        run: |
          sudo apt-get update
          sudo apt install -y make gcc build-essential libgtk-3-dev
          sudo apt-get install -y python3-pip openjdk-11-jdk-headless default-libmysqlclient-dev libnotify-dev libsdl2-dev
          export JAVA_HOME=/usr/lib/jvm/java-11-openjdk-amd64
          export PATH=$PATH:/home/ubuntu/.local/bin

      - name: Install CellProfiler
        run: |
          wget https://extras.wxpython.org/wxPython4/extras/linux/gtk3/ubuntu-20.04/wxPython-4.1.0-cp38-cp38-linux_x86_64.whl
          pip install wxPython-4.1.0-cp38-cp38-linux_x86_64.whl
          pip install --upgrade pip setuptools wheel
          pip install numpy
          pip install git+https://github.com/CellProfiler/centrosome.git@cython3
          
      - name: Run stardist plugin pipeline
        run: |
          pip install -e .[stardist]
          python -m cellprofiler -c -r -p ./tests/headless_test/4.2.5_plugins_test_pipeline_STARDIST.cppipe -i ./tests/headless_test/test_pipeline_img -o . --plugins-directory=./active_plugins --log-level=DEBUG 2>&1 | tee logfile
          sh ./tests/headless_test/test_run.sh "module runstardist" logfile