FP-ubuntu.yml

name: FastPathology Ubuntu 18.04

on:
  workflow_dispatch:

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

jobs:
  build:
    name: Build
    runs-on: ubuntu-20.04
    container:
      image: ubuntu:18.04

    steps:
    - uses: actions/checkout@v3
    
    - name: Install dependencies
      run: |
        apt update && apt install -y sudo
        # Get a newer version of cmake
        sudo apt install -y gpg wget software-properties-common lsb-release
        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

    - 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
      # Configure CMake in a 'build' subdirectory. `CMAKE_BUILD_TYPE` is only required if you are using a single-configuration generator such as make.
      # See https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TYPE.html?highlight=cmake_build_type
      run: |
        cmake -B build \
            -DCMAKE_BUILD_TYPE=${{env.BUILD_TYPE}}\
            -DFAST_MODULE_OpenVINO=ON \
            -DFAST_MODULE_Dicom=OFF \
            -DFAST_MODULE_WholeSlideImaging=ON \
            -DFAST_MODULE_OpenIGTLink=OFF \
            -DFAST_MODULE_Clarius=OFF \
            -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=OFF \
            -DFAST_MODULE_RealSense=OFF \
            -DFAST_BUILD_TESTS=ON \
            -DFAST_BUILD_EXAMPLES=OFF

    - name: Build
      # Build your program with the given configuration
      run: cmake --build build --config ${{env.BUILD_TYPE}} -j 4

    - name: Package
      run: |
        cmake --build build --config ${{env.BUILD_TYPE}} --target package -j 4
        mv build/fast_*.tar.xz build/fast_ubuntu18.04.tar.xz

    - name: Upload archive package
      uses: actions/upload-artifact@v3
      with:
        name: Archive package (tar.xz)
        path: ${{github.workspace}}/build/fast_ubuntu18.04.tar.xz
        if-no-files-found: error

    - name: Upload package to external repo release
      uses: svenstaro/upload-release-action@v2.7.0
      with:
        repo_name: AICAN-Research/FAST-Pathology-dependencies
        repo_token: ${{ secrets.FAST_PATHOLOGY_PUSH_TOKEN }}
        file: ${{github.workspace}}/build/fast_ubuntu18.04.tar.xz
        asset_name: fast_ubuntu18.04.tar.xz
        file_glob: true
        tag: v1.0.0
        overwrite: true

  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/*