Refactoring min-dep tests #25
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| name: tests | ||
|
Check failure on line 1 in .github/workflows/cicd_tests.yml
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| on: | ||
| # quick tests for pull requests and the releasing branches | ||
| push: | ||
| branches: | ||
| - dev | ||
| - main | ||
| - releasing/* | ||
| paths-ignore: # skip if only docs are modified | ||
| - '**.md' | ||
| - '**.rst' | ||
| - 'docs/**' | ||
| pull_request: | ||
| head_ref-ignore: | ||
| - dev | ||
| paths-ignore: # skip if only docs are modified | ||
| - '**.md' | ||
| - '**.rst' | ||
| - 'docs/**' | ||
| concurrency: | ||
| # automatically cancel the previously triggered workflows when there's a newer version | ||
| group: cicd-tests-${{ github.event.pull_request.number || github.ref }} | ||
| cancel-in-progress: true | ||
| env: | ||
| # supported versions of Python | ||
| PYTHON_VER1: '3.10' | ||
| PYTHON_VER2: '3.11' | ||
| PYTHON_VER3: '3.12' | ||
| PYTHON_VER4: '3.13' | ||
| PYTHON_VER5: '3.14' | ||
| # supported versions of PyTorch | ||
| PYTORCH_VER1: '2.8.0' | ||
| PYTORCH_VER2: '2.9.1' | ||
| PYTORCH_VER3: '2.10.0' | ||
| PYTORCH_VER4: '2.11.0' | ||
| TORCHVISION_VER: '0.23.0' # used for testing with lowest PyTorch version | ||
| PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION: python # https://github.com/Project-MONAI/MONAI/issues/4354 | ||
| # These jobs run the CICD tests, type checking, and testing packaging. These use the minimum supported versions of | ||
| # Python and PyTorch in many places using the above environment variables, when support is dropped for a version it is | ||
| # important to update these as appropriate. | ||
| jobs: | ||
| static-checks: # Perform static type and other checks using runtests.sh | ||
| runs-on: ubuntu-latest | ||
| strategy: | ||
| matrix: | ||
| opt: ["codeformat", "pytype", "mypy"] | ||
| steps: | ||
| - name: Clean unused tools | ||
| run: | | ||
| find /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \; | ||
| sudo rm -rf /usr/share/dotnet | ||
| sudo rm -rf /usr/local/lib/android | ||
| sudo rm -rf /opt/ghc /usr/local/.ghcup | ||
| sudo docker system prune -f | ||
| - uses: actions/checkout@v6 | ||
| - name: Set up Python ${{ env.PYTHON_VER1 }} | ||
| uses: actions/setup-python@v6 | ||
| with: | ||
| python-version: ${{ env.PYTHON_VER1 }} | ||
| cache: 'pip' | ||
| - name: Install dependencies | ||
| run: | | ||
| python -m pip install --upgrade pip wheel | ||
| python -m pip install --no-build-isolation -r requirements-dev.txt | ||
| - name: Lint and type check | ||
| run: | | ||
| # clean up temporary files | ||
| $(pwd)/runtests.sh --build --clean | ||
| # Github actions have multiple cores, so parallelize pytype | ||
| $(pwd)/runtests.sh --build --${{ matrix.opt }} -j $(nproc --all) | ||
| min-dep: # Test with minumum dependencies installed for different OS, Python, and PyTorch combinations | ||
| runs-on: ${{ matrix.os }} | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| # Base test cases are to test on all three OSes with the lowest versions of Python and PyTorch, other cases are | ||
| # added below as special cases to cover other Python and PyTorch versions under Ubuntu | ||
| os: [windows-latest, macOS-latest, ubuntu-latest] | ||
| python-version: ${{ env.PYTHON_VER1 }} | ||
| pytorch-version: ${{ env.PYTORCH_VER1 }} | ||
| include: | ||
| # Test Python versions under Ubuntu with lowest PyTorch version supported | ||
| - os: ubuntu-latest | ||
| pytorch-version: ${{ env.PYTORCH_VER1 }} | ||
| python-version: ${{ env.PYTHON_VER2 }} | ||
| - os: ubuntu-latest | ||
| pytorch-version: ${{ env.PYTORCH_VER1 }} | ||
| python-version: ${{ env.PYTHON_VER3 }} | ||
| - os: ubuntu-latest | ||
| pytorch-version: ${{ env.PYTORCH_VER1 }} | ||
| python-version: ${{ env.PYTHON_VER4 }} | ||
| - os: ubuntu-latest | ||
| pytorch-version: ${{ env.PYTORCH_VER1 }} | ||
| python-version: ${{ env.PYTHON_VER5 }} | ||
| # Test PyTorch versions under Ubuntu with lowest Python version supported | ||
| - os: ubuntu-latest | ||
| python-version: ${{ env.PYTHON_VER1 }} | ||
| pytorch-version: ${{ env.PYTORCH_VER2 }} | ||
| - os: ubuntu-latest | ||
| python-version: ${{ env.PYTHON_VER1 }} | ||
| pytorch-version: ${{ env.PYTORCH_VER3 }} | ||
| - os: ubuntu-latest | ||
| python-version: ${{ env.PYTHON_VER1 }} | ||
| pytorch-version: ${{ env.PYTORCH_VER4 }} | ||
| timeout-minutes: 40 | ||
| steps: | ||
| - if: runner.os == 'Linux' | ||
| name: Clean unused tools | ||
| run: | | ||
| find /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \; | ||
| sudo rm -rf /usr/share/dotnet | ||
| sudo rm -rf /usr/local/lib/android | ||
| sudo rm -rf /opt/ghc /usr/local/.ghcup | ||
| sudo docker system prune -f | ||
| - uses: actions/checkout@v6 | ||
| - name: Set up Python ${{ matrix.python-version }} | ||
| uses: actions/setup-python@v6 | ||
| with: | ||
| python-version: ${{ matrix.python-version }} | ||
| cache: 'pip' | ||
| - name: Prepare pip wheel | ||
| run: | | ||
| which python | ||
| python -m pip install --upgrade pip wheel | ||
| python -m pip install --user more-itertools>=8.0 | ||
| - name: Install the minimum dependencies | ||
| run: | | ||
| # min. requirements | ||
| python -m pip install torch==${{ matrix.pytorch-version }} | ||
| python -m pip install -r requirements-min.txt | ||
| python -m pip list | ||
| BUILD_MONAI=0 python setup.py develop # no compile of extensions | ||
| shell: bash | ||
| - if: matrix.os == 'linux-gpu-runner' | ||
| name: Print GPU Info | ||
| run: | | ||
| nvidia-smi | ||
| python -c 'import torch; print(torch.rand(2,2).to("cuda:0"))' | ||
| shell: bash | ||
| - name: Run quick tests | ||
| run: | | ||
| python -c 'import torch; print(torch.__version__); print(torch.rand(5,3))' | ||
| python -c "import monai; monai.config.print_config()" | ||
| # ./runtests.sh --min | ||
| shell: bash | ||
| env: | ||
| QUICKTEST: True | ||
| NGC_API_KEY: ${{ secrets.NGC_API_KEY }} | ||
| NGC_ORG: ${{ secrets.NGC_ORG }} | ||
| NGC_TEAM: ${{ secrets.NGC_TEAM }} | ||
| full-dep: # Test with full dependencies installed for different OS runners | ||
| runs-on: ${{ matrix.os }} | ||
| strategy: | ||
| fail-fast: false | ||
| matrix: | ||
| os: [windows-latest, macOS-latest, ubuntu-latest] | ||
| timeout-minutes: 120 | ||
| env: | ||
| QUICKTEST: True | ||
| steps: | ||
| - if: runner.os == 'Linux' | ||
| name: Clean unused tools | ||
| run: | | ||
| find /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \; | ||
| sudo rm -rf /usr/share/dotnet | ||
| sudo rm -rf /usr/local/lib/android | ||
| sudo rm -rf /opt/ghc /usr/local/.ghcup | ||
| sudo docker system prune -f | ||
| - if: runner.os == 'windows' | ||
| name: Config pagefile (Windows only) | ||
| uses: al-cheb/configure-pagefile-action@v1.5 | ||
| with: | ||
| minimum-size: 8GB | ||
| maximum-size: 16GB | ||
| disk-root: "D:" | ||
| - uses: actions/checkout@v6 | ||
| - name: Set up Python ${{ env.PYTHON_VER1 }} | ||
| uses: actions/setup-python@v6 | ||
| with: | ||
| python-version: ${{ env.PYTHON_VER1 }} | ||
| cache: 'pip' | ||
| - name: Prepare pip wheel | ||
| run: | | ||
| which python | ||
| python -m pip install --upgrade pip wheel | ||
| - if: runner.os == 'windows' | ||
| name: Install torch cpu from pytorch.org (Windows only) | ||
| run: | | ||
| python -m pip install torch==$PYTORCH_VER1 torchvision==$TORCHVISION_VER+cpu --index-url https://download.pytorch.org/whl/cpu | ||
| - if: runner.os == 'Linux' | ||
| name: Install itk pre-release (Linux only) | ||
| run: | | ||
| python -m pip install --pre -U itk | ||
| - name: Install the complete dependencies | ||
| run: | | ||
| python -m pip install --user --upgrade pip wheel | ||
| python -m pip install torch==$PYTORCH_VER1 torchvision==$TORCHVISION_VER | ||
| cat "requirements-dev.txt" | ||
| python -m pip install --no-build-isolation -r requirements-dev.txt | ||
| python -m pip list | ||
| python -m pip install -e . # test no compile installation | ||
| shell: bash | ||
| - name: Run compiled (${{ runner.os }}) | ||
| run: | | ||
| python -m pip uninstall -y monai | ||
| BUILD_MONAI=1 python -m pip install -e . # compile the cpp extensions | ||
| shell: bash | ||
| - name: Run quick tests | ||
| run: | | ||
| python -c 'import torch; print(torch.__version__); print(torch.rand(5,3))' | ||
| python -c "import monai; monai.config.print_config()" | ||
| # python -m unittest -v | ||
| packaging: # Test package generation | ||
| runs-on: ubuntu-latest | ||
| env: | ||
| QUICKTEST: True | ||
| shell: bash | ||
| steps: | ||
| - name: Clean unused tools | ||
| run: | | ||
| find /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \; | ||
| sudo rm -rf /usr/share/dotnet | ||
| sudo rm -rf /usr/local/lib/android | ||
| sudo rm -rf /opt/ghc /usr/local/.ghcup | ||
| sudo docker system prune -f | ||
| - uses: actions/checkout@v6 | ||
| with: | ||
| fetch-depth: 0 | ||
| - name: Set up Python ${{ env.PYTHON_VER1 }} | ||
| uses: actions/setup-python@v6 | ||
| with: | ||
| python-version: ${{ env.PYTHON_VER1 }} | ||
| cache: 'pip' | ||
| - name: Install dependencies | ||
| run: | | ||
| python -m pip install --user --upgrade pip setuptools wheel twine packaging | ||
| # install the latest pytorch for testing | ||
| # however, "pip install monai*.tar.gz" will build cpp/cuda with an isolated | ||
| # fresh torch installation according to pyproject.toml | ||
| python -m pip install torch==$PYTORCH_VER1 torchvision --extra-index-url https://download.pytorch.org/whl/cpu | ||
| - name: Check packages | ||
| run: | | ||
| pip uninstall monai | ||
| pip list | grep -iv monai | ||
| git fetch --depth=1 origin +refs/tags/*:refs/tags/* | ||
| set -e | ||
| # build tar.gz and wheel | ||
| python setup.py check -m -s | ||
| python setup.py sdist bdist_wheel | ||
| python -m twine check dist/* | ||
| - run: echo "pwd=$PWD" >> $GITHUB_OUTPUT | ||
| id: root | ||
| - run: echo "tmp_dir=$(mktemp -d)" >> $GITHUB_OUTPUT | ||
| id: mktemp | ||
| - name: Move packages | ||
| run: | | ||
| printf ${{ steps.root.outputs.pwd }} | ||
| printf ${{ steps.mktemp.outputs.tmp_dir }} | ||
| # move packages to a temp dir | ||
| cp dist/monai* "${{ steps.mktemp.outputs.tmp_dir }}" | ||
| rm -r build dist monai.egg-info | ||
| cd "${{ steps.mktemp.outputs.tmp_dir }}" | ||
| ls -al | ||
| - name: Install wheel file | ||
| working-directory: ${{ steps.mktemp.outputs.tmp_dir }} | ||
| run: | | ||
| # install from wheel | ||
| python -m pip install monai*.whl --extra-index-url https://download.pytorch.org/whl/cpu | ||
| python -c 'import monai; monai.config.print_config()' 2>&1 | grep -iv "unknown" | ||
| python -c 'import monai; print(monai.__file__)' | ||
| python -m pip uninstall -y monai | ||
| rm monai*.whl | ||
| - name: Install source archive | ||
| working-directory: ${{ steps.mktemp.outputs.tmp_dir }} | ||
| run: | | ||
| # install from tar.gz | ||
| name=$(ls *.tar.gz | head -n1) | ||
| echo $name | ||
| python -m pip install $name[all] --extra-index-url https://download.pytorch.org/whl/cpu | ||
| python -c 'import monai; monai.config.print_config()' 2>&1 | grep -iv "unknown" | ||
| python -c 'import monai; print(monai.__file__)' | ||
| - name: Quick test | ||
| working-directory: ${{ steps.mktemp.outputs.tmp_dir }} | ||
| run: | | ||
| # run min tests | ||
| cp ${{ steps.root.outputs.pwd }}/requirements*.txt . | ||
| cp -r ${{ steps.root.outputs.pwd }}/tests . | ||
| ls -al | ||
| python -m pip install --no-build-isolation -r requirements-dev.txt --extra-index-url https://download.pytorch.org/whl/cpu | ||
| python -m unittest -v | ||
| build-docs: | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
| - uses: actions/checkout@v6 | ||
| - name: Set up Python ${{ env.PYTHON_VER1 }} | ||
| uses: actions/setup-python@v6 | ||
| with: | ||
| python-version: ${{ env.PYTHON_VER1 }} | ||
| cache: 'pip' | ||
| - name: Install dependencies | ||
| run: | | ||
| python -m pip install --upgrade pip wheel | ||
| python -m pip install -r docs/requirements.txt --extra-index-url https://download.pytorch.org/whl/cpu | ||
| - name: Make html | ||
| run: | | ||
| cd docs/ | ||
| make clean | ||
| make html 2>&1 | tee tmp_log | ||
| if [[ $(grep -c "ERROR:" tmp_log) != 0 ]]; then echo "found errors"; grep "ERROR:" tmp_log; exit 1; fi | ||
| sed '/WARNING.*pip/d' tmp_log > tmp_log1; mv tmp_log1 tmp_log # monai#7133 | ||
| if [[ $(grep -c "WARNING:" tmp_log) != 0 ]]; then echo "found warnings"; grep "WARNING:" tmp_log; exit 1; fi | ||
| shell: bash | ||
