Create an EnforceObjectsOneToOne plugin [WIP] #150
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: Basic plugin testing | |
| on: | |
| push: | |
| branches: | |
| - master | |
| pull_request: | |
| types: [opened, reopened, synchronize, ready_for_review, review_requested] | |
| jobs: | |
| build_cellprofiler: | |
| name: Build CellProfiler | |
| 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: Install basic CellProfiler plugins require | |
| run: | | |
| pip install -e . | |
| - name: Run basic plugin pipeline | |
| run: | | |
| python -m cellprofiler -c -r -p ./tests/headless_test/4.2.5_plugins_test_pipeline_BASIC.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 compensatecolors" logfile | |
| sh ./tests/headless_test/test_run.sh "module distancetransform" logfile | |
| sh ./tests/headless_test/test_run.sh "module enhancedmeasuretexture" logfile | |
| sh ./tests/headless_test/test_run.sh "module histogramequalization" logfile | |
| sh ./tests/headless_test/test_run.sh "module histogrammatching" logfile | |
| sh ./tests/headless_test/test_run.sh "module pixelshuffle" logfile | |