Fxing segfault cause by test showing window but not closing window #1300
Workflow file for this run
This file contains hidden or 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: Python APP | |
| on: [pull_request] | |
| jobs: | |
| fetch_cache: | |
| name: fetch cache | |
| runs-on: 'ubuntu-24.04' | |
| env: | |
| TestDataUrl: 'https://zenodo.org/record/5147737/files/DICOM-RT-02.zip' | |
| steps: | |
| - name: Cache Test Data | |
| id: cache-TestData | |
| uses: actions/cache@v3 | |
| with: | |
| enableCrossOsArchive: true | |
| lookup-only: true | |
| path: DICOM-RT-02.zip | |
| key: ${{ env.TestDataUrl }} | |
| - name: Download Test Data | |
| if: steps.cache-TestData.outputs.cache-hit != 'true' | |
| run: | | |
| sudo apt-get install wget | |
| wget -O DICOM-RT-02.zip $TestDataUrl | |
| build_Linux: | |
| needs: fetch_cache | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python: | |
| - '3.12' | |
| - '3.10' | |
| - '3.11' | |
| os: | |
| # - 'ubuntu-20.04' | |
| - 'ubuntu-24.04' | |
| name: Build - ${{ matrix.os }} - Python ${{ matrix.python }} | |
| runs-on: ${{ matrix.os }} | |
| timeout-minutes: 40 | |
| env: | |
| DISPLAY: ':99.0' | |
| TestDataUrl: 'https://zenodo.org/record/5147737/files/DICOM-RT-02.zip' | |
| # USER_ONKODICOM_HIDDEN: '/tmp/.onkodicom' | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Install Poetry | |
| run: | | |
| curl -sSL https://install.python-poetry.org | python - --version 1.8.5 | |
| poetry --version | |
| - name: Set up Python ${{ matrix.python }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python }} | |
| cache: 'poetry' | |
| - name: Upgrade pip and setuptools | |
| run: | | |
| pip install --upgrade pip wheel setuptools | |
| - name: Install plastimatch | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install plastimatch | |
| - name: Install dependencies | |
| run: | | |
| # python -m pip install --upgrade pip wheel setuptools | |
| poetry install --no-root | |
| # currently having poetry going straight to the github main branch for pyradiomics ~ 3.1.1 | |
| # - name: Workaround Install pyradiomics (no-use-pep517) | |
| # # https://github.com/AIM-Harvard/pyradiomics/issues/653#issuecomment-1245039225 | |
| # # pyradiomics 3.1.0 has a metadata mismatch | |
| # run: | | |
| # poetry run pip install pyradiomics==3.0.1 | |
| - name: Lint with flake8 | |
| run: | | |
| # stop the build if there are Python syntax errors or undefined names | |
| poetry run flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | |
| poetry run flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | |
| - name: Download Cached Test Data | |
| uses: actions/cache@v3 | |
| with: | |
| enableCrossOsArchive: true | |
| fail-on-cache-miss: true | |
| path: DICOM-RT-02.zip | |
| key: ${{ env.TestDataUrl }} | |
| - name: Install test data | |
| run: | | |
| sudo apt-get install unzip | |
| mkdir test/testdata | |
| mkdir test/batchtestdata | |
| unzip DICOM-RT-02.zip -d test/testdata | |
| unzip DICOM-RT-02.zip -d test/batchtestdata | |
| sudo chmod -R 777 test/testdata | |
| sudo chmod -R 777 test/batchtestdata | |
| - name: Testing setup | |
| run: | | |
| # sudo mkdir -p /tmp/.onkodicom | |
| # sudo chmod 777 /tmp/.onkodicom | |
| sudo apt-get update | |
| sudo apt-get install xvfb libxkbcommon-x11-0 herbstluftwm libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-randr0 libxcb-render-util0 libxcb-xinerama0 libxcb-xfixes0 libopengl0 libglut3.12 libglut-dev freeglut3-dev libgeos-c1v5 libgeos++-dev libgeos-dev libxcb-cursor0 | |
| # install everything related to xcb. libxcb-cursor0 is required for Qt >=6.5 and it has numerous dependencies | |
| sudo apt-get install -y libxcb1 libxcb-cursor0 libxcb-glx0 libxcb-icccm4 libxcb-image0 libxcb-keysyms1 libxcb-randr0 libxcb-render0 libxcb-render-util0 libxcb-shape0 libxcb-shm0 libxcb-sync1 libxcb-util1 libxcb-xfixes0 libxcb-xinerama0 libxcb-xkb1 | |
| # sudo Xvfb :1 -screen 0 1024x768x24 </dev/null & | |
| /sbin/start-stop-daemon --start --quiet --pidfile /tmp/custom_xvfb_99.pid --make-pidfile --background --exec /usr/bin/Xvfb -- :99 -screen 0 1920x1200x24 -ac +extension GLX | |
| sleep 3 | |
| herbstluftwm & | |
| sleep 1 | |
| # Check system resources | |
| free -m | |
| ulimit -a | |
| - name: Testing and Coverage with pytest | |
| run: | | |
| # First try single test file without coverage as part of debugging Ubuntu 24.04 build | |
| export QT_DEBUG_PLUGINS=1 | |
| export PYTHONFAULTHANDLER=1 | |
| # export MPLBACKEND=Agg | |
| # poetry run python -m pytest "test/test_machine_learning_preprocessing.py" -v -s | |
| # Append this for fail under x percent "--cov-fail-under=80" | |
| poetry run python -m pytest "test/" -v --durations=10 --cov-config=.coveragerc --cov-report term-missing --cov=. | |
| build_Windows: | |
| needs: fetch_cache | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python: | |
| - '3.12' | |
| - '3.10' | |
| - '3.11' | |
| os: | |
| # - 'windows-2019' | |
| - 'windows-2022' | |
| name: Build - ${{ matrix.os }} - Python ${{ matrix.python }} | |
| runs-on: ${{ matrix.os }} | |
| timeout-minutes: 50 | |
| # Tests on Windows are unstable. We do not want it to fail the entire test result | |
| continue-on-error: true | |
| env: | |
| DISPLAY: ':99.0' # do we need this in Windows? | |
| TestDataUrl: 'https://zenodo.org/record/5147737/files/DICOM-RT-02.zip' | |
| PlastimatchWindowsUrl: 'https://downloads.sourceforge.net/project/plastimatch/Windows%20Binaries/Plastimatch-1.9.0-win64.msi' | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Install Poetry | |
| run: | | |
| (Invoke-WebRequest -Uri https://install.python-poetry.org -UseBasicParsing).Content | py - | |
| Add-Content $env:GITHUB_PATH "$env:APPDATA\Python\Scripts" | |
| - name: Set up Python ${{ matrix.python }} | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python }} | |
| cache: 'poetry' | |
| - name: Upgrade pip and setuptools | |
| run: | | |
| python.exe -m pip install --upgrade pip wheel setuptools | |
| - name: Install plastimatch | |
| run: | | |
| Invoke-WebRequest -Uri ${{ env.PlastimatchWindowsUrl }} -OutFile Plastimatch.msi | |
| Start-Process -Wait msiexec -ArgumentList '/i Plastimatch.msi /passive' | |
| Add-Content $env:GITHUB_PATH "C:\Program Files\Plastimatch" | |
| - name: Install dependencies | |
| run: | | |
| poetry install --no-root | |
| # currently having poetry going straight to the github main branch for pyradiomics ~ 3.1.1 | |
| # - name: Workaround Install pyradiomics (no-use-pep517) | |
| # https://github.com/AIM-Harvard/pyradiomics/issues/653#issuecomment-1245039225 | |
| # run: | | |
| # poetry run pip install pyradiomics==3.0.1 | |
| - name: Lint with flake8 | |
| run: | | |
| # stop the build if there are Python syntax errors or undefined names | |
| poetry run flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | |
| poetry run flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | |
| - name: Download Cached Test Data | |
| uses: actions/cache@v3 | |
| with: | |
| enableCrossOsArchive: true | |
| fail-on-cache-miss: true | |
| path: DICOM-RT-02.zip | |
| key: ${{ env.TestDataUrl }} | |
| - name: Install test data | |
| run: | | |
| 7z x DICOM-RT-02.zip -o${{ github.workspace }}\test\testdata | |
| 7z x DICOM-RT-02.zip -o${{ github.workspace }}\test\batchtestdata | |
| - name: Testing and Coverage with pytest | |
| continue-on-error: true | |
| run: | | |
| # Append this for fail under x percent "--cov-fail-under=80" | |
| # todo: currently in Windows some tests halt. Set timeout (in seconds) as a workaround. | |
| cd ${{ github.workspace }} | |
| poetry run python -m pytest "test/" -v --durations=10 --cov-config=.coveragerc --cov-report term-missing --cov=. --timeout=180 |