cicd_tests.yml

name: tests

on:
  # quick tests for pull requests and the releasing branches
  push:
    branches:
      - dev
      - main
      - releasing/*
  pull_request:
    branches:
      - dev
      - main
      - releasing/*

permissions:
  contents: read

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

  # versions of PyTorch/Torchvision to use for full-dep Windows tests, needed to get around a gloo bug
  WIN_FULLDEP_VER: '2.11.0'
  WIN_FULLDEP_VISION_VER: '0.26.0'

  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:
  # This job will set its output value `skip` to 2 if only documentation was changed, either documentation files or
  # the docstrings of source files. If any source lines are changed, or non-documentation files are changed, the
  # result is 0 which then triggers tests to run. This job works by using the compare_sources.py script to compare
  # changed files to see if they differ in ways other than comments or docstrings.
  test_skip:
    runs-on: ubuntu-latest
    outputs:
      skip: ${{ steps.check-changes.outputs.skip }}
    steps:
    - uses: actions/checkout@v7
      with:
        fetch-depth: 2
    - name: Set up Python ${{ env.PYTHON_VER1 }}
      uses: actions/setup-python@v6
      with:
        python-version: ${{ env.PYTHON_VER1 }}
        cache: 'pip'
    - name: Check File Changes
      id: check-changes
      shell: bash
      run: |
        echo "skip=1" >> $GITHUB_OUTPUT

        mkdir -p /tmp/check_changes
        if ! git diff --name-only HEAD^..HEAD ':!docs' > /tmp/check_changes/changed_files
        then
          echo "skip=0" >> "$GITHUB_OUTPUT"
          exit 0
        fi

        while read i
        do
          echo "Checking for changes: $i"
          if ! git show HEAD^:$i > /tmp/check_changes/$(basename $i)
          then
            echo "New file found, or 'git show' failed, running tests."
          elif ! python monai/utils/compare_sources.py $i /tmp/check_changes/$(basename $i)
          then
            echo "Change found, running tests."
          else
            continue
          fi

          echo "skip=0" >> $GITHUB_OUTPUT
          break
        done < /tmp/check_changes/changed_files

  static-checks:  # Perform static type and other checks using runtests.sh
    runs-on: ubuntu-latest
    strategy:
      matrix:
        opt: ["codeformat", "pyrefly"]
    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@v7
    - 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 .[all,testing]
    - name: Lint and type check
      run: |
        # clean up temporary files
        $(pwd)/runtests.sh --build --clean
        $(pwd)/runtests.sh --build --${{ matrix.opt }}

  min-dep:  # Test with minumum dependencies installed for different OS, Python, and PyTorch combinations
    runs-on: ${{ matrix.os }}
    needs: test_skip
    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:
    - name: Clean unused tools
      if: runner.os == 'Linux' && needs.test_skip.outputs.skip == 0
      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@v7
      if: needs.test_skip.outputs.skip == 0
    - name: Set up Python ${{ matrix.python-version }}
      if: needs.test_skip.outputs.skip == 0
      uses: actions/setup-python@v6
      with:
        python-version: ${{ matrix.python-version }}
        cache: 'pip'
    - name: Prepare pip wheel
      if: needs.test_skip.outputs.skip == 0
      run: |
        which python
        python -m pip install --upgrade pip wheel tomli
    - name: Install the minimum dependencies
      if: needs.test_skip.outputs.skip == 0
      run: |
        # min. requirements
        python -m pip install torch==${{ matrix.pytorch-version }}
        python monai/config/print_dependencies.py build-system | xargs pip install --no-build-isolation
        python -m pip install --no-build-isolation .[testing]
        python -m pip list
      shell: bash
    - name: Run quick tests
      if: needs.test_skip.outputs.skip == 0
      run: |
        nvidia-smi || true
        python monai/config/check_env.py --env --monai
        ./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, ubuntu-latest, macOS-latest]  # macOS-latest is very slow (#8864), testing install only
    timeout-minutes: 120
    needs: test_skip
    env:
      QUICKTEST: True
    steps:
    - name: Clean unused tools
      if: runner.os == 'Linux' && needs.test_skip.outputs.skip == 0
      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
    - name: Config pagefile (Windows only)
      if: runner.os == 'windows' && needs.test_skip.outputs.skip == 0
      uses: al-cheb/configure-pagefile-action@v1.5
      with:
        minimum-size: 8GB
        maximum-size: 16GB
        disk-root: "D:"
    - uses: actions/checkout@v7
      if: needs.test_skip.outputs.skip == 0
    - name: Set up Python ${{ env.PYTHON_VER1 }}
      if: needs.test_skip.outputs.skip == 0
      uses: actions/setup-python@v6
      with:
        python-version: ${{ env.PYTHON_VER1 }}
        cache: 'pip'
    - name: Prepare pip wheel
      if: needs.test_skip.outputs.skip == 0
      run: |
        which python
        python -m pip install --upgrade pip wheel
    - if: runner.os == 'windows' && needs.test_skip.outputs.skip == 0
      name: Install torch cpu from pytorch.org (Windows only)
      run: |
        python -m pip install torch==${WIN_FULLDEP_VER} torchvision==${WIN_FULLDEP_VISION_VER}+cpu --index-url https://download.pytorch.org/whl/cpu
      shell: bash
    - if: runner.os != 'windows' && needs.test_skip.outputs.skip == 0
      name: Install torch gpu
      run: |
        # install the lowest version of PyTorch supported
        python -m pip install torch==${PYTORCH_VER1} torchvision==${TORCHVISION_VER1}
      shell: bash
    - if: runner.os == 'Linux' && needs.test_skip.outputs.skip == 0
      name: Install itk pre-release (Linux only)
      run: |
        python -m pip install --pre -U itk
      shell: bash
    - name: Install the complete dependencies
      if: needs.test_skip.outputs.skip == 0
      run: |
        python -m pip install --user --upgrade pip wheel tomli
        python monai/config/print_dependencies.py build-system | xargs pip install --no-build-isolation
        python -m pip install --no-build-isolation .[all,testing]
        python -m pip list
      shell: bash
    - name: Run compiled (${{ runner.os }})
      if: needs.test_skip.outputs.skip == 0
      run: |
        python -m pip uninstall -y monai
        BUILD_MONAI=1 python -m pip install --no-build-isolation -e .  # compile the cpp extensions
        python -c 'import monai._C' > /dev/null
        nvidia-smi || true
        python monai/config/check_env.py --env --monai
      shell: bash
    - if: runner.os != 'macOS' && needs.test_skip.outputs.skip == 0
      name: Run full tests
      run: |
        python -m unittest -v
      shell: bash
    - if: runner.os == 'macOS' && needs.test_skip.outputs.skip == 0
      name: Run min tests
      run: |
        # TODO: enable large range of macOS tests which don't take a very long time
        ./runtests.sh --min
      shell: bash

  hyena-dep:  # Optional HyenaND dependency + the no-CUDA Hyena tests.
    # nvsubquadratic >= 0.1.1 supports Python >= 3.10 and keeps its CUDA-kernel sdist
    # (subquadratic-ops-torch-cu12) plus the megatron / dali / timm packages in opt-in
    # extras, so it installs on a CPU runner.  We still pass ``--no-deps`` deliberately:
    #   (1) the HyenaND operators import only torch + einops + omegaconf at runtime, so
    #       skipping the (still batteries-included: datasets/lightning/wandb) core deps
    #       keeps this job lean; and
    #   (2) nvsubquadratic pins torch>=2.10,<2.11, which would otherwise upgrade/clash
    #       with the torch this job (and MONAI's matrix) installs.
    # CUDA-required Hyena tests skip cleanly here; the GPU surface is covered by
    # ``.github/workflows/pythonapp-hyena-gpu.yml``.
    runs-on: ubuntu-latest
    timeout-minutes: 30
    needs: test_skip
    if: needs.test_skip.outputs.skip == 0
    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 + nvsubquadratic (no-deps)
      run: |
        python -m pip install --upgrade pip wheel tomli pytest
        # need a specific version of torch for nvsubquadratic
        python monai/config/print_dependencies.py build-system | \
          xargs -d '\n' pip install --no-build-isolation torch==2.10.0 torchvision==0.25.0
        # # nvsubquadratic runtime imports need only torch + einops + omegaconf; install
        # # the package itself without its core dependency tree (see job comment above).
        python -m pip install --no-build-isolation omegaconf
        python -m pip install --no-build-isolation --no-deps 'nvsubquadratic>=0.1.1'
        python -m pip install --no-build-isolation .[hyena,testing]
        python -m pip list
      shell: bash
    - name: Run Hyena tests (CUDA-required cases skip cleanly)
      run: |
        python -c "from monai.networks.blocks.hyena import is_nvsubquadratic_available; \
                   assert is_nvsubquadratic_available(), 'nvsubquadratic must be importable'"
        python -m pytest -v \
          tests/networks/blocks/test_hyena_block.py \
          tests/networks/nets/test_hyena_nd_unetr.py \
          tests/networks/nets/test_swin_unetr.py
      shell: bash

  packaging:  # Test package generation
    runs-on: ubuntu-latest
    env:
      QUICKTEST: True
      INDEX_URL: "https://download.pytorch.org/whl/cpu"
    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@v7
      with:
        fetch-depth: 0
    - name: Set up Python ${{ env.PYTHON_VER1 }}
      uses: actions/setup-python@v6
      with:
        python-version: ${{ env.PYTHON_VER1 }}
        cache: 'pip'
    - name: Install dependencies
      run: |
        python -m pip install --user --upgrade pip setuptools wheel twine packaging tomli
        # install the latest pytorch for testing
        python monai/config/print_dependencies.py build-system all testing | \
            xargs -d '\n' pip install --no-build-isolation torch==${PYTORCH_VER1} --extra-index-url $INDEX_URL
    - name: Check packages
      run: |
        python -m pip uninstall -y monai
        python -m 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 --no-build-isolation monai*.whl --extra-index-url $INDEX_URL
        python -m monai.config
        python -m pip uninstall -y monai
        rm monai*.whl
    - name: Install source archive
      working-directory: ${{ steps.mktemp.outputs.tmp_dir }}
      run: |
        for name in *.tar.gz; do break; done
        echo $name
        python -m pip install --no-build-isolation ${name}[all] --extra-index-url $INDEX_URL
        python -m monai.config
        python -m pip uninstall -y monai
    - name: Install using uv
      working-directory: ${{ steps.root.outputs.pwd }}
      run: |
        pip install uv
        uv pip install --system --no-build-isolation .[all] --extra-index-url $INDEX_URL
        python -m monai.config