pythonapp.yml

# Jenkinsfile.monai-premerge
name: premerge

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

concurrency:
  # automatically cancel the previously triggered workflows when there's a newer version
  group: build-${{ github.event.pull_request.number || github.ref }}
  cancel-in-progress: true

jobs:
  # caching of these jobs:
  #   - docker-py3-pip- (shared)
  #   - ubuntu py37 pip-
  #   - os-latest-pip- (shared)
  flake8-py3:
    runs-on: ubuntu-latest
    strategy:
      matrix:
        opt: ["codeformat", "pytype", "mypy"]
    steps:
    - uses: actions/checkout@v4
    - name: Set up Python 3.9
      uses: actions/setup-python@v5
      with:
        python-version: '3.9'
    - name: cache weekly timestamp
      id: pip-cache
      run: |
        echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
    - name: cache for pip
      uses: actions/cache@v4
      id: cache
      with:
        path: ~/.cache/pip
        key: ${{ runner.os }}-pip-${{ steps.pip-cache.outputs.datew }}
    - 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 -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

  quick-py3:  # full dependencies installed tests for different OS
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        os: [windows-latest, macOS-latest, ubuntu-latest]
    timeout-minutes: 120
    steps:
    - if: runner.os == 'windows'
      name: Config pagefile (Windows only)
      uses: al-cheb/configure-pagefile-action@v1.4
      with:
        minimum-size: 8GB
        maximum-size: 16GB
        disk-root: "D:"
    - uses: actions/checkout@v4
    - name: Set up Python 3.9
      uses: actions/setup-python@v5
      with:
        python-version: '3.9'
    - name: Prepare pip wheel
      run: |
        which python
        python -m pip install --upgrade pip wheel
    - name: cache weekly timestamp
      id: pip-cache
      run: |
        echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
        echo "dir=$(pip cache dir)" >> $GITHUB_OUTPUT
      shell: bash
    - name: cache for pip
      uses: actions/cache@v4
      id: cache
      with:
        path: ${{ steps.pip-cache.outputs.dir }}
        key: ${{ matrix.os }}-latest-pip-${{ steps.pip-cache.outputs.datew }}
    - if: runner.os == 'windows'
      name: Install torch cpu from pytorch.org (Windows only)
      run: |
        python -m pip install torch==1.13.1+cpu torchvision==0.14.1+cpu -f https://download.pytorch.org/whl/torch_stable.html
    - 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
      run: |
        python -m pip install --user --upgrade pip wheel
        python -m pip install torch==1.13.1 torchvision==0.14.1
        cat "requirements-dev.txt"
        python -m pip install -r requirements-dev.txt
        python -m pip list
        python setup.py develop  # test no compile installation
      shell: bash
    - name: Run compiled (${{ runner.os }})
      run: |
        python setup.py develop --uninstall
        BUILD_MONAI=1 python setup.py develop  # compile the cpp extensions
      shell: bash
    - name: Run quick tests (CPU ${{ runner.os }})
      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

  packaging:
    runs-on: ubuntu-latest
    env:
      QUICKTEST: True
      shell: bash
    steps:
    - uses: actions/checkout@v4
      with:
        fetch-depth: 0
    - name: Set up Python 3.9
      uses: actions/setup-python@v5
      with:
        python-version: '3.9'
    - name: cache weekly timestamp
      id: pip-cache
      run: |
        echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
    - name: cache for pip
      uses: actions/cache@v4
      id: cache
      with:
        path: |
          ~/.cache/pip
          ~/.cache/torch
        key: ${{ runner.os }}-pip-${{ steps.pip-cache.outputs.datew }}
    - name: Install dependencies
      run: |
        find  /opt/hostedtoolcache/* -maxdepth 0 ! -name 'Python' -exec rm -rf {} \;
        python -m pip install --user --upgrade pip setuptools wheel twine
        # 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>=1.9 torchvision
    - 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
        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]
        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 -r requirements-dev.txt
        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@v4
    - name: Set up Python 3.9
      uses: actions/setup-python@v5
      with:
        python-version: '3.9'
    - name: cache weekly timestamp
      id: pip-cache
      run: |
        echo "datew=$(date '+%Y-%V')" >> $GITHUB_OUTPUT
    - name: cache for pip
      uses: actions/cache@v4
      id: cache
      with:
        path: |
          ~/.cache/pip
          ~/.cache/torch
        key: ${{ runner.os }}-pip-${{ steps.pip-cache.outputs.datew }}
    - name: Install dependencies
      run: |
        python -m pip install --upgrade pip wheel
        python -m pip install -r docs/requirements.txt
    - 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