Refactoring min-dep tests

.github/workflows/cicd_tests.yml

@@ -0,0 +1,339 @@
+name: tests
+
+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
+
+# Supported versions of Python and PyTorch are listed here for use below and as documentation
+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'  # TODO: not compatible with Torchscript, re-enable once Torchscript removed from MONAI
+  # 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_VER1: '0.23.0'  # used for testing with lowest PyTorch version (PYTORCH_VER1), update as needed
+  TORCHVISION_VER2: '0.24.1'  # used for testing with second lowest PyTorch version (PYTORCH_VER2)
+
+  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 but also hard coded where necessary.
+# 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: ['3.10']
+        pytorch-version: ['2.8.0']
+        include:
+        # Test Python versions under Ubuntu with lowest PyTorch version supported
+        - os: ubuntu-latest
+          pytorch-version: '2.8.0'
+          python-version: '3.11'
+        - os: ubuntu-latest
+          pytorch-version: '2.8.0'
+          python-version: '3.12'
+        - os: ubuntu-latest
+          pytorch-version: '2.8.0'
+          python-version: '3.13'
+        # - os: ubuntu-latest
+        #   pytorch-version: '2.9.1'
+        #   python-version: '3.14'
+
+        # Test PyTorch versions under Ubuntu with lowest Python version supported
+        - os: ubuntu-latest
+          python-version: '3.10'
+          pytorch-version: '2.9.1'
+        - os: ubuntu-latest
+          python-version: '3.10'
+          pytorch-version: '2.10.0'
+        - os: ubuntu-latest
+          python-version: '3.10'
+          pytorch-version: '2.11.0'
+
+    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: ${{ env.PYTHON_VER1 }}
+        cache: 'pip'
+    - name: Prepare pip wheel
+      run: |
+        which python
+        python -m pip install --upgrade pip wheel
+    - if: runner.os == 'windows'
+      name: Install torch cpu from pytorch.org (Windows only)
+      run: |
+        # BUG: PyTorch 2.8.0 appears to have a gloo bug under Windows with failing distributed tests
+        python -m pip install torch==${PYTORCH_VER2} torchvision==${TORCHVISION_VER2}+cpu --index-url https://download.pytorch.org/whl/cpu
+      shell: bash
+    - if: runner.os != 'windows'
+      name: Install torch gpu
+      run: |
+        # install the lowest version of PyTorch supported
+        python -m pip install torch==${PYTORCH_VER1} torchvision==${TORCHVISION_VER1}
+      shell: bash
+    - if: runner.os == 'Linux'
+      name: Install itk pre-release (Linux only)
+      run: |
+        python -m pip install --pre -U itk
+      shell: bash
+    - name: Install the complete dependencies
+      run: |
+        python -m pip install --user --upgrade pip wheel pybind11  # TODO: pybind11 added for macOS, may not be needed
+        #python -m pip install torch==${PYTORCH_VER1} torchvision==${TORCHVISION_VER1}
+        cat "requirements-dev.txt"
+        python -m pip install --no-build-isolation -r requirements-dev.txt
+        python -m pip list
+        python -m pip install -e .  # test no compile installation
+      shell: bash
+    - name: Run compiled (${{ 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
+      shell: bash
+
+  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

.github/workflows/conda.yml

@@ -19,7 +19,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        python-version: ["3.9", "3.10"]
+        python-version: ["3.10", "3.11"]
     runs-on: ${{ matrix.os }}
     timeout-minutes: 46 # equal to max + 3*std over the last 600 successful runs
     env:

.github/workflows/cron-ngc-bundle.yml

@@ -18,10 +18,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v6
-    - name: Set up Python 3.9
+    - name: Set up Python 3.10
       uses: actions/setup-python@v6
       with:
-        python-version: '3.9'
+        python-version: '3.10'
     - name: cache weekly timestamp
       id: pip-cache
       run: echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT

.github/workflows/cron.yml

@@ -67,7 +67,7 @@ jobs:
         if pgrep python; then pkill python; fi
       shell: bash
     - name: Upload coverage
-      uses: codecov/codecov-action@v5
+      uses: codecov/codecov-action@v6
       with:
         fail_ci_if_error: false
         files: ./coverage.xml
@@ -115,7 +115,7 @@ jobs:
         if pgrep python; then pkill python; fi
       shell: bash
     - name: Upload coverage
-      uses: codecov/codecov-action@v5
+      uses: codecov/codecov-action@v6
       with:
         fail_ci_if_error: false
         files: ./coverage.xml
@@ -220,7 +220,7 @@ jobs:
         if pgrep python; then pkill python; fi
       shell: bash
     - name: Upload coverage
-      uses: codecov/codecov-action@v5
+      uses: codecov/codecov-action@v6
       with:
         fail_ci_if_error: false
         files: ./coverage.xml