test update pyproject.toml: added "user" extras for pymedphys, performed poetry update #961
Workflow file for this run
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| name: Python APP | |
| on: [push, pull_request] | |
| jobs: | |
| fetch_cache: | |
| name: fetch cache | |
| runs-on: 'ubuntu-latest' | |
| 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: | |
| - '3.9' | |
| - '3.10' | |
| os: | |
| - 'ubuntu-20.04' | |
| # - 'ubuntu-22.04' | |
| 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' | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Install Poetry | |
| run: | | |
| curl -sSL https://install.python-poetry.org | python - | |
| 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 | |
| - 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 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 freeglut3 freeglut3-dev | |
| # 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 | |
| - name: Testing and Coverage with pytest | |
| run: | | |
| # 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: | |
| - '3.9' | |
| - '3.10' | |
| 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: | | |
| 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 | |
| - 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 |