CI-ubuntu.yml

name: CI Ubuntu 18.04

on:
  push:
    branches: [ master ]
  pull_request:
    branches: [ master ]
  release:
    types: [ published ]
  # Allows you to run this workflow manually from the Actions tab
  workflow_dispatch:

env:
  # Customize the CMake build type here (Release, Debug, RelWithDebInfo, etc.)
  BUILD_TYPE: Release
  ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION: true

jobs:
  build:
    name: Build
    # The CMake configure and build commands are platform agnostic and should work equally
    # well on Windows or Mac.  You can convert this to a matrix build if you need
    # cross-platform coverage.
    # See: https://docs.github.com/en/free-pro-team@latest/actions/learn-github-actions/managing-complex-workflows#using-a-build-matrix
    runs-on: ubuntu-20.04
    container:
      image: ubuntu:18.04

    steps:
    - name: Use node 16
      run: |
          apt update && apt -y install wget
          touch "$HOME/.bashrc"
          wget -qO- https://raw.githubusercontent.com/nvm-sh/nvm/v0.40.1/install.sh | bash
          export NVM_DIR="$HOME/.nvm"
          [ -s "$NVM_DIR/nvm.sh" ] && . "$NVM_DIR/nvm.sh"
          nvm install 16.9.1
          
    - name: Check free space
      run: |
        df -h

    - uses: actions/checkout@v2

    - name: Install dependencies
      run: |
        apt update && apt install -y sudo
        mkdir -p ${{github.workspace}}/artifacts
        # Get a newer version of cmake
        sudo apt install -y gpg wget software-properties-common lsb-release ca-certificates
        wget -O - https://apt.kitware.com/keys/kitware-archive-latest.asc 2>/dev/null | gpg --dearmor - | sudo tee /usr/share/keyrings/kitware-archive-keyring.gpg >/dev/null
        echo 'deb [signed-by=/usr/share/keyrings/kitware-archive-keyring.gpg] https://apt.kitware.com/ubuntu/ bionic main' | sudo tee /etc/apt/sources.list.d/kitware.list >/dev/null
        sudo apt-get update
        sudo rm /usr/share/keyrings/kitware-archive-keyring.gpg
        sudo apt-get install kitware-archive-keyring
        sudo apt install -y cmake
        sudo apt install -y g++ patchelf
        sudo apt install -y '^libxcb.*-dev' libx11-xcb-dev libglu1-mesa-dev libxrender-dev libxi-dev libxkbcommon-dev libxkbcommon-x11-dev
        sudo apt install -y libopenslide-dev libjpeg-turbo8-dev # Needed for WSI module
        sudo apt install -y pkgconf libusb-1.0-0-dev # Needed for realsense
        sudo apt install -y python3 libpython3-dev python3-pip python3-setuptools
        sudo pip3 install --upgrade pip
        pip3 install numpy==1.19.5 pylddwrap==1.2.0 twine wheel==0.37.1
        
    - name: Install CUDA and TensorRT
      run: |
        wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/cuda-ubuntu1804.pin
        sudo mv cuda-ubuntu1804.pin /etc/apt/preferences.d/cuda-repository-pin-600
        sudo apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/3bf863cc.pub
        sudo apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/7fa2af80.pub
        sudo add-apt-repository "deb https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/ /"
        sudo apt-get update
        sudo apt-get install -y cuda-toolkit-11-0 libcudnn8 libnvinfer-dev libnvonnxparsers-dev libnvparsers-dev

    - name: Configure CMake
      run: |
        cmake -B build \
            -DCMAKE_BUILD_TYPE=${{env.BUILD_TYPE}}\
            -DFAST_MODULE_OpenVINO=ON \
            -DFAST_MODULE_Dicom=ON \
            -DFAST_MODULE_WholeSlideImaging=ON \
            -DFAST_MODULE_OpenIGTLink=ON \
            -DFAST_MODULE_Clarius=ON \
            -DFAST_MODULE_TensorFlow=ON \
            -DCUDA_TOOLKIT_ROOT_DIR="/usr/local/cuda/" \
            -DFAST_MODULE_TensorRT=ON \
            -DFAST_MODULE_HDF5=ON \
            -DFAST_MODULE_Plotting=ON \
            -DFAST_MODULE_Python=ON \
            -DFAST_MODULE_RealSense=ON \
            -DFAST_BUILD_EXAMPLES=ON

    - name: Build
      run: cmake --build build --config ${{env.BUILD_TYPE}} -j 4

    - name: Free some space
      run: |
        df -h
        rm -Rf build/external/tensorflow/src/tensorflow/
        rm -Rf build/external/openvino/src/openvino/
        rm -Rf build/external/qt5/src/qt5/
        rm -Rf build/external/clarius/src/clarius/
        df -h

    - name: Build Python wheel
      run: |
        cmake --build build --config ${{env.BUILD_TYPE}} --target python-wheel -j 4
        cp build/python/dist/pyFAST-*.whl build/

    - name: Free some space
      run: |
        df -h
        rm -Rf build/python/
        df -h

    - name: Package
      run: |
        cmake --build build --config ${{env.BUILD_TYPE}} --target package -j 4

    - name: Upload Debian package
      uses: actions/upload-artifact@v3
      with:
        name: Debian package
        path: ${{github.workspace}}/build/fast_*.deb
        if-no-files-found: error

    - name: Upload archive package
      uses: actions/upload-artifact@v3
      with:
        name: Archive package (tar.xz)
        path: ${{github.workspace}}/build/fast_*.tar.xz
        if-no-files-found: error

    - name: Upload Python wheel
      uses: actions/upload-artifact@v3
      with:
        name: Python wheel
        path: ${{github.workspace}}/build/pyFAST-*.whl
        if-no-files-found: error

    - name: Upload Debian package to release
      if: ${{ github.event_name == 'release' }}
      uses: svenstaro/upload-release-action@2.7.0
      with:
        repo_token: ${{ secrets.GITHUB_TOKEN }}
        file: ${{github.workspace}}/build/fast_*.deb
        file_glob: true
        tag: ${{ github.ref }}
        overwrite: true

    - name: Upload archive package to release
      if: ${{ github.event_name == 'release' }}
      uses: svenstaro/upload-release-action@2.7.0
      with:
        repo_token: ${{ secrets.GITHUB_TOKEN }}
        file: ${{github.workspace}}/build/fast_*.tar.xz
        file_glob: true
        tag: ${{ github.ref }}
        overwrite: true

    - name: Upload Python wheel to release
      if: ${{ github.event_name == 'release' }}
      uses: svenstaro/upload-release-action@2.7.0
      with:
        repo_token: ${{ secrets.GITHUB_TOKEN }}
        file: ${{github.workspace}}/build/pyFAST-*.whl
        file_glob: true
        tag: ${{ github.ref }}
        overwrite: true

    - name: Upload Python wheel to PyPi
      if: ${{ github.event_name == 'release' && !contains(github.ref, 'rc') }}
      run: |
        twine upload --username __token__ --password ${{ secrets.PYPI_API_TOKEN }} ${{github.workspace}}/build/pyFAST-*.whl

  test-cpp:
    name: Run C++ Tests
    needs: [build]
    runs-on: [self-hosted, linux]
    steps:
      - name: Download artifacts
        uses: actions/download-artifact@v3
        with:
          name: 'Archive package (tar.xz)'
          path: ${{github.workspace}}/download/
      - name: Extract artifact
        run: |
          mkdir -p ${{github.workspace}}/download/
          cd ${{github.workspace}}/download/
          tar -xf fast_*.tar.xz -C ${{github.workspace}}
      - name: Download test data
        run: |
          cd ${{github.workspace}}
          cd fast*
          cd fast/bin/
          ./downloadTestData
      - name: Run tests
        env:
          DISPLAY: ':1'
        run: |
          cd ${{github.workspace}}
          cd fast_*
          cd fast/bin/
          ./testFAST ~[visual]
      - name: Cleanup
        if: always()
        run: |
          rm -Rf ${{github.workspace}}
          rm -Rf $HOME/FAST/kernel_binaries/*

  test-python:
    name: Run Python Tests
    needs: [build]
    runs-on: [self-hosted, linux]
    steps:
      - uses: actions/checkout@v2
      - name: Download artifacts
        uses: actions/download-artifact@v3
        with:
          name: 'Python wheel'
          path: ${{github.workspace}}/download/
      - name: Create environment and install python packages
        run: |
          cd ${{github.workspace}}
          mkdir tmp
          cd tmp
          virtualenv -p python3 venv
          source venv/bin/activate
          pip3 install pytest
          pip3 install ${{github.workspace}}/download/pyFAST-*.whl
      - name: Run tests
        env:
          DISPLAY: ':1'
        run: |
          cd ${{github.workspace}}/tmp/
          source venv/bin/activate
          pytest ../source/FAST/
      - name: Cleanup
        if: always()
        run: |
          rm -Rf ${{github.workspace}}/download/
          rm -Rf ${{github.workspace}}/tmp/
          rm -Rf $HOME/FAST/kernel_binaries/*