Refactoring min-dep tests

.github/workflows/pythonapp.yml → .github/workflows/cicd_tests.yml

@@ -1,5 +1,4 @@
-# Jenkinsfile.monai-premerge
-name: premerge
+name: tests
 
 on:
   # quick tests for pull requests and the releasing branches
@@ -8,52 +7,176 @@ on:
       - 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: build-${{ github.event.pull_request.number || github.ref }}
+  group: cicd-tests-${{ 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'
+  # 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 but also hard coded where necessary.
+# When support is dropped for a version it is important to update these as appropriate.
+
 jobs:
-  # caching of these jobs:
-  #   - docker-py3-pip- (shared)
-  #   - ubuntu py37 pip-
-  #   - os-latest-pip- (shared)
-  flake8-py3:
+  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 3.9
+    - name: Set up Python ${{ env.PYTHON_VER1 }}
       uses: actions/setup-python@v6
       with:
-        python-version: '3.9'
+        python-version: ${{ env.PYTHON_VER1 }}
         cache: 'pip'
     - name: Install dependencies
       run: |
-        find  /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
         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 2 cores, so parallelize pytype
-        $(pwd)/runtests.sh --build --${{ matrix.opt }} -j 2
+        # 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: '2.9.0'
+          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 }}
 
-  quick-py3:  # full dependencies installed tests for different OS
+  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
@@ -62,10 +185,10 @@ jobs:
         maximum-size: 16GB
         disk-root: "D:"
     - uses: actions/checkout@v6
-    - name: Set up Python 3.9
+    - name: Set up Python ${{ env.PYTHON_VER1 }}
       uses: actions/setup-python@v6
       with:
-        python-version: '3.9'
+        python-version: ${{ env.PYTHON_VER1 }}
         cache: 'pip'
     - name: Prepare pip wheel
       run: |
@@ -74,16 +197,16 @@ jobs:
     - if: runner.os == 'windows'
       name: Install torch cpu from pytorch.org (Windows only)
       run: |
-        python -m pip install torch==2.5.1 torchvision==0.20.1+cpu --index-url https://download.pytorch.org/whl/cpu
+        python -m pip install torch==${PYTORCH_VER1} torchvision==${TORCHVISION_VER}+cpu --index-url https://download.pytorch.org/whl/cpu
+      shell: bash
     - if: runner.os == 'Linux'
       name: Install itk pre-release (Linux only)
       run: |
         python -m pip install --pre -U itk
-        find  /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
-    - name: Install the dependencies
+    - name: Install the complete dependencies
       run: |
         python -m pip install --user --upgrade pip wheel
-        python -m pip install torch==2.5.1 torchvision==0.20.1
+        python -m pip install torch==${PYTORCH_VER1} torchvision==${TORCHVISION_VER}
         cat "requirements-dev.txt"
         python -m pip install --no-build-isolation -r requirements-dev.txt
         python -m pip list
@@ -94,37 +217,41 @@ jobs:
         python -m pip uninstall -y monai
         BUILD_MONAI=1 python -m pip install -e .  # compile the cpp extensions
       shell: bash
-    - name: Run quick tests (CPU ${{ runner.os }})
+    - 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
-      env:
-        QUICKTEST: True
-        PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION: python  # https://github.com/Project-MONAI/MONAI/issues/4354
+        # python -m unittest -v
 
-  packaging:
+  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 3.9
+    - name: Set up Python ${{ env.PYTHON_VER1 }}
       uses: actions/setup-python@v6
       with:
-        python-version: '3.9'
+        python-version: ${{ env.PYTHON_VER1 }}
         cache: 'pip'
     - name: Install dependencies
       run: |
-        find  /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
         python -m pip install --user --upgrade pip setuptools wheel twine packaging
         # install the latest pytorch for testing
         # however, "pip install monai*.tar.gz" will build cpp/cuda with an isolated
         # fresh torch installation according to pyproject.toml
-        python -m pip install torch>=2.5.1 torchvision --extra-index-url https://download.pytorch.org/whl/cpu
+        python -m pip install torch==${PYTORCH_VER1} torchvision --extra-index-url https://download.pytorch.org/whl/cpu
     - name: Check packages
       run: |
         pip uninstall monai
@@ -176,17 +303,15 @@ jobs:
         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
-      env:
-        PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION: python  # https://github.com/Project-MONAI/MONAI/issues/4354
 
   build-docs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v6
-    - name: Set up Python 3.9
+    - name: Set up Python ${{ env.PYTHON_VER1 }}
       uses: actions/setup-python@v6
       with:
-        python-version: '3.9'
+        python-version: ${{ env.PYTHON_VER1 }}
         cache: 'pip'
     - name: Install dependencies
       run: |

.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

.github/workflows/docker.yml

@@ -26,18 +26,18 @@ jobs:
         with:
           ref: dev
           fetch-depth: 0
-      - 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'
       - shell: bash
         run: |
           git describe
           python -m pip install -U pip wheel setuptools
           python setup.py build
           cat build/lib/monai/_version.py
       - name: Upload version
-        uses: actions/upload-artifact@v6
+        uses: actions/upload-artifact@v7
         with:
           name: _version.py
           path: build/lib/monai/_version.py

.github/workflows/pythonapp-gpu.yml

@@ -53,7 +53,7 @@ jobs:
 
         if [ ${{ matrix.environment }} = "PT230+CUDA124" ]
         then
-        PYVER=3.9 PYSFX=3 DISTUTILS=python3-distutils && \
+        PYVER=3.10 PYSFX=3 DISTUTILS=python3-distutils && \
         apt-get update && apt-get install -y --no-install-recommends \
           curl \
           pkg-config \
@@ -125,6 +125,6 @@ jobs:
       shell: bash
     - name: Upload coverage
       if: ${{ github.head_ref != 'dev' && github.event.pull_request.merged != true }}
-      uses: codecov/codecov-action@v5
+      uses: codecov/codecov-action@v6
       with:
         files: ./coverage.xml