pythonapp.yml

name: build

on:
  # quick tests for every pull request
  push:
    branches:
      - dev
  pull_request:

jobs:
  # caching of these jobs:
  #   - docker-py3-pip- (shared)
  #   - ubuntu py37 pip-
  #   - os-latest-pip- (shared)
  flake8-py3:
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v2
    - name: Set up Python 3.8
      uses: actions/setup-python@v2
      with:
        python-version: 3.8
    - name: cache weekly timestamp
      id: pip-cache
      run: |
        echo "::set-output name=datew::$(date '+%Y-%V')"
    - name: cache for pip
      uses: actions/cache@v2
      id: cache
      with:
        path: ~/.cache/pip
        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 requirements-dev.txt
    - name: Lint and type check
      run: |
        # clean up temporary files
        $(pwd)/runtests.sh --clean
        # Git hub actions have 2 cores, so parallize pytype
        $(pwd)/runtests.sh --codeformat -j 2

  quick-py3:  # full dependencies installed tests for different OS
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        os: [windows-latest, macOS-latest, ubuntu-latest]
    timeout-minutes: 60
    steps:
    - if: runner.os == 'windows'
      name: Config pagefile (Windows only)
      uses: al-cheb/configure-pagefile-action@v1.2
      with:
        minimum-size: 8
        maximum-size: 16
        disk-root: "D:"
    - uses: actions/checkout@v2
    - name: Set up Python 3.8
      uses: actions/setup-python@v2
      with:
        python-version: 3.8
    - name: Prepare pip wheel
      run: |
        which python
        python -m pip install --upgrade pip wheel
    - name: cache weekly timestamp
      id: pip-cache
      run: |
        echo "::set-output name=datew::$(date '+%Y-%V')"
        echo "::set-output name=dir::$(pip cache dir)"
      shell: bash
    - name: cache for pip
      uses: actions/cache@v2
      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==1.8.1+cpu torchvision==0.9.1+cpu -f https://download.pytorch.org/whl/torch_stable.html
        # min. requirements for windows instances
        python -c "f=open('requirements-dev.txt', 'r'); txt=f.readlines(); f.close(); print(txt); f=open('requirements-dev.txt', 'w'); f.writelines(txt[1:12]); f.close()"
    - name: Install the dependencies
      run: |
        python -m pip install torch==1.8.1 torchvision==0.9.1
        cat "requirements-dev.txt"
        python -m pip install -r requirements-dev.txt
        python -m pip list
        python setup.py develop  # test no compile installation
        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

  min-dep-os:  # min dependencies installed tests for different OS
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        os: [windows-latest, macOS-latest, ubuntu-latest]
    timeout-minutes: 40
    steps:
    - uses: actions/checkout@v2
    - name: Set up Python 3.8
      uses: actions/setup-python@v2
      with:
        python-version: 3.8
    - name: Prepare pip wheel
      run: |
        which python
        python -m pip install --upgrade pip wheel
    - name: cache weekly timestamp
      id: pip-cache
      run: |
        echo "::set-output name=datew::$(date '+%Y-%V')"
        echo "::set-output name=dir::$(pip cache dir)"
      shell: bash
    - name: cache for pip
      uses: actions/cache@v2
      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==1.8.1+cpu -f https://download.pytorch.org/whl/torch_stable.html
    - name: Install the dependencies
      run: |
        # min. requirements
        python -m pip install torch==1.8.1
        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
    - 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 tests.min_tests
      env:
        QUICKTEST: True

  min-dep-py3:  # min dependencies installed tests for different python
    runs-on: ubuntu-latest
    strategy:
      fail-fast: false
      matrix:
        python-version: [3.6, 3.7, 3.8, 3.9]
    timeout-minutes: 40
    steps:
    - uses: actions/checkout@v2
    - name: Set up Python ${{ matrix.python-version }}
      uses: actions/setup-python@v2
      with:
        python-version: ${{ matrix.python-version }}
    - name: Prepare pip wheel
      run: |
        which python
        python -m pip install --user --upgrade pip setuptools wheel
    - name: cache weekly timestamp
      id: pip-cache
      run: |
        echo "::set-output name=datew::$(date '+%Y-%V')"
        echo "::set-output name=dir::$(pip cache dir)"
      shell: bash
    - name: cache for pip
      uses: actions/cache@v2
      id: cache
      with:
        path: ${{ steps.pip-cache.outputs.dir }}
        key: ubuntu-latest-latest-pip-${{ steps.pip-cache.outputs.datew }}
    - name: Install the dependencies
      run: |
        # min. requirements
        python -m pip install torch==1.8.1
        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
    - 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 tests.min_tests
      env:
        QUICKTEST: True

  GPU-quick-py3:  # GPU with full dependencies
    if: github.repository == 'Project-MONAI/MONAI'
    strategy:
      matrix:
        environment:
          - "PT16+CUDA102"
          - "PT16+CUDA110"
          - "PT17+CUDA102"
          - "PT17+CUDA110"
          - "PT18+CUDA102"
          - "PT18+CUDA112"
        include:
          - environment: PT16+CUDA102
            pytorch: "torch==1.6.0 torchvision==0.7.0"
            base: "nvcr.io/nvidia/cuda:10.2-devel-ubuntu18.04"
          - environment: PT16+CUDA110
            # we explicitly set pytorch to -h to avoid pip install error
            pytorch: "-h"
            base: "nvcr.io/nvidia/pytorch:20.07-py3"
          - environment: PT17+CUDA102
            pytorch: "torch==1.7.1 torchvision==0.8.2"
            base: "nvcr.io/nvidia/cuda:10.2-devel-ubuntu18.04"
          - environment: PT17+CUDA110
            # we explicitly set pytorch to -h to avoid pip install error
            pytorch: "-h"
            base: "nvcr.io/nvidia/pytorch:20.09-py3"
          - environment: PT18+CUDA102
            pytorch: "torch==1.8.1 torchvision==0.9.1"
            base: "nvcr.io/nvidia/cuda:10.2-devel-ubuntu18.04"
          - environment: PT18+CUDA112
            # we explicitly set pytorch to -h to avoid pip install error
            pytorch: "-h"
            base: "nvcr.io/nvidia/pytorch:21.02-py3"
    container:
      image: ${{ matrix.base }}
      options: --gpus all
    runs-on: [self-hosted, linux, x64, common]
    steps:
    - uses: actions/checkout@v2
    - name: apt install
      run: |
        if [ ${{ matrix.environment }} = "PT16+CUDA102" ] || \
           [ ${{ matrix.environment }} = "PT17+CUDA102" ] || \
           [ ${{ matrix.environment }} = "PT18+CUDA102" ]
        then
        PYVER=3.6 PYSFX=3 DISTUTILS=python3-distutils && \
        apt-get update && apt-get install -y --no-install-recommends \
          curl \
          pkg-config \
          python$PYVER \
          python$PYVER-dev \
          python$PYSFX-pip \
          $DISTUTILS \
          rsync \
          swig \
          unzip \
          zip \
          zlib1g-dev \
          libboost-locale-dev \
          libboost-program-options-dev \
          libboost-system-dev \
          libboost-thread-dev \
          libboost-test-dev \
          libgoogle-glog-dev \
          libjsoncpp-dev \
          cmake && \
        rm -rf /var/lib/apt/lists/* && \
        export PYTHONIOENCODING=utf-8 LC_ALL=C.UTF-8 && \
        rm -f /usr/bin/python && \
        rm -f /usr/bin/python`echo $PYVER | cut -c1-1` && \
        ln -s /usr/bin/python$PYVER /usr/bin/python && \
        ln -s /usr/bin/python$PYVER /usr/bin/python`echo $PYVER | cut -c1-1` &&
        curl -O https://bootstrap.pypa.io/get-pip.py && \
        python get-pip.py && \
        rm get-pip.py;
        fi
    - name: Install dependencies
      run: |
        which python
        python -m pip install --upgrade pip wheel
        python -m pip install ${{ matrix.pytorch }}
        python -m pip install -r requirements-dev.txt
        python -m pip list
    - name: Run quick tests (GPU)
      run: |
        nvidia-smi
        export LAUNCH_DELAY=$(python -c "import numpy; print(numpy.random.randint(30) * 10)")
        echo "Sleep $LAUNCH_DELAY"
        sleep $LAUNCH_DELAY
        export CUDA_VISIBLE_DEVICES=$(coverage run -m tests.utils)
        echo $CUDA_VISIBLE_DEVICES
        trap 'if pgrep python; then pkill python; fi;' ERR
        python -c $'import torch\na,b=torch.zeros(1,device="cuda:0"),torch.zeros(1,device="cuda:1");\nwhile True:print(a,b)' > /dev/null &
        python -c "import torch; print(torch.__version__); print('{} of GPUs available'.format(torch.cuda.device_count()))"
        python -c 'import torch; print(torch.rand(5, 3, device=torch.device("cuda:0")))'
        python -c "import monai; monai.config.print_config()"
        # build for the current self-hosted CI Tesla V100
        BUILD_MONAI=1 TORCH_CUDA_ARCH_LIST="7.0" ./runtests.sh --quick --unittests
        if [ ${{ matrix.environment }} = "PT18+CUDA112" ]; then
          # test the clang-format tool downloading once
          coverage run -m tests.clang_format_utils
        fi
        coverage xml
        if pgrep python; then pkill python; fi
      shell: bash
    - name: Upload coverage
      uses: codecov/codecov-action@v1
      with:
        file: ./coverage.xml

  packaging:
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v2
      with:
        fetch-depth: 0
    - name: Set up Python 3.8
      uses: actions/setup-python@v2
      with:
        python-version: 3.8
    - name: cache weekly timestamp
      id: pip-cache
      run: |
        echo "::set-output name=datew::$(date '+%Y-%V')"
    - name: cache for pip
      uses: actions/cache@v2
      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 --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>=1.5 torchvision
    - name: Test source archive and wheel file
      run: |
        git fetch --depth=1 origin +refs/tags/*:refs/tags/*
        root_dir=$PWD
        echo "$root_dir"
        set -e

        # build tar.gz and wheel
        python setup.py check -m -s
        python setup.py sdist bdist_wheel
        python -m twine check dist/*

        # move packages to a temp dir
        tmp_dir=$(mktemp -d)
        cp dist/monai* "$tmp_dir"
        rm -r build dist monai.egg-info
        cd "$tmp_dir"
        ls -al

        # 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

        # install from tar.gz
        python -m pip install monai*.tar.gz
        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*.tar.gz

        # clean up
        cd "$root_dir"
        rm -r "$tmp_dir"

  build-docs:
    runs-on: ubuntu-latest
    steps:
    - uses: actions/checkout@v2
    - name: Set up Python 3.8
      uses: actions/setup-python@v2
      with:
        python-version: 3.8
    - name: cache weekly timestamp
      id: pip-cache
      run: |
        echo "::set-output name=datew::$(date '+%Y-%V')"
    - name: cache for pip
      uses: actions/cache@v2
      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 "WARNING:" tmp_log) != 0 ]]; then echo "found warnings"; grep "WARNING:" tmp_log; exit 1; fi
      shell: bash