testbed/Project-MONAI__MONAI/.github/workflows/pythonapp.yml

name: build

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

jobs:
  # caching of these jobs:
  #   - docker-20-03-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 3.7
      uses: actions/setup-python@v1
      with:
        python-version: 3.7
    - 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 --nounittests --codeformat -j 2

  quick-py3:  # full dependencies installed
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        os: [windows-latest, macOS-latest, ubuntu-latest]
    timeout-minutes: 20
    steps:
    - uses: actions/checkout@v2
    - name: Set up Python 3.x
      uses: actions/setup-python@v1
      with:
        python-version: '3.x'
    - name: Prepare pip wheel
      run: |
        which python
        python -m pip install --upgrade pip wheel
    - name: cache weekly timestamp
      id: pip-cache
      run: |
        echo "::set-output name=datew::$(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==1.4 -f https://download.pytorch.org/whl/cpu/torch_stable.html
        python -m pip install torchvision==0.5.0
        # 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==1.4
        python -m pip install torchvision==0.5.0
        cat "requirements-dev.txt"
        python -m pip install -r requirements-dev.txt
        python -m pip list
        python setup.py develop  # compile the cpp extensions
    - name: Run quick tests (CPU ${{ runner.os }})
      run: |
        python -c 'import torch; print(torch.__version__); print(torch.rand(5,3))'
        python -m unittest -v
      env:
        QUICKTEST: True

  GPU-quick-py3:  # GPU with full dependencies
    strategy:
      matrix:
        environment:
          - "PT15+CUDA101"
          - "PT16+CUDA101"
          - "PT15+CUDA102"
          - "PT16+CUDA102"
          - "PT16+CUDA110"
        include:
          - environment: PT15+CUDA101
            pytorch: "torch==1.5.0+cu101 torchvision==0.6.0+cu101 -f https://download.pytorch.org/whl/torch_stable.html"
            base: "nvcr.io/nvidia/cuda:10.1-devel-ubuntu18.04"
          - environment: PT16+CUDA101
            pytorch: "torch==1.6.0+cu101 torchvision==0.7.0+cu101 -f https://download.pytorch.org/whl/torch_stable.html"
            base: "nvcr.io/nvidia/cuda:10.1-devel-ubuntu18.04"
          - environment: PT15+CUDA102
            pytorch: "torch==1.5.0 torchvision==0.6.0"
            base: "nvcr.io/nvidia/cuda:10.2-devel-ubuntu18.04"
          - environment: PT16+CUDA102
            pytorch: "torch torchvision"
            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"
    container:
      image: ${{ matrix.base }}
      options: --gpus all
    runs-on: [self-hosted, linux, x64]
    steps:
    - uses: actions/checkout@v2
    - name: apt install
      run: |
        if [ ${{ matrix.environment }} != "PT16+CUDA110" ]; then \
        PYVER=3.6 PYSFX=3 DISTUTILS=python3-distutils && \
        apt-get update && apt-get install -y --no-install-recommends \
          curl \
          pkg-config \
          python$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 ${{ matrix.pytorch }}
        python -m pip install -r requirements-dev.txt
    - name: Run quick tests (GPU)
      run: |
        python -m pip list
        nvidia-smi
        export CUDA_VISIBLE_DEVICES=$(python -m tests.utils)
        echo $CUDA_VISIBLE_DEVICES
        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")))'
        ./runtests.sh --quick
        coverage xml
    - 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.x
      uses: actions/setup-python@v1
      with:
        python-version: '3.x'
    - 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 --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>=1.4 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 3.7
      uses: actions/setup-python@v1
      with:
        python-version: 3.7
    - 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 docs/requirements.txt
    - name: Make html
      run: |
        cd docs/
        make html