Runilastik module that can use local OR Docker installations #75
Workflow file for this run
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| 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 |