Update Python WSI tutorial documentation (#206) #587
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| # This is a basic workflow to help you get started with Actions | |
| name: CI Windows | |
| # Controls when the action will run. | |
| on: | |
| # Triggers the workflow on push or pull request events but only for the master branch | |
| 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 | |
| jobs: | |
| 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: windows-2019 | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Install dependencies | |
| run: | | |
| pip3 install --upgrade pip | |
| pip3 install numpy==1.19.5 twine | |
| - name: Install CUDA | |
| shell: powershell | |
| run: | | |
| $CUDA_KNOWN_URLS = @{ | |
| "11.0.1" = "http://developer.download.nvidia.com/compute/cuda/11.0.1/network_installers/cuda_11.0.1_win10_network.exe"; | |
| "11.0.2" = "http://developer.download.nvidia.com/compute/cuda/11.0.2/network_installers/cuda_11.0.2_win10_network.exe"; | |
| "11.0.3" = "http://developer.download.nvidia.com/compute/cuda/11.0.3/network_installers/cuda_11.0.3_win10_network.exe"; | |
| "11.1.0" = "https://developer.download.nvidia.com/compute/cuda/11.1.0/network_installers/cuda_11.1.0_win10_network.exe"; | |
| "11.1.1" = "https://developer.download.nvidia.com/compute/cuda/11.1.1/network_installers/cuda_11.1.1_win10_network.exe"; | |
| "11.2.0" = "https://developer.download.nvidia.com/compute/cuda/11.2.0/network_installers/cuda_11.2.0_win10_network.exe"; | |
| "11.2.1" = "https://developer.download.nvidia.com/compute/cuda/11.2.1/network_installers/cuda_11.2.1_win10_network.exe"; | |
| "11.2.2" = "https://developer.download.nvidia.com/compute/cuda/11.2.2/network_installers/cuda_11.2.2_win10_network.exe"; | |
| "11.3.0" = "https://developer.download.nvidia.com/compute/cuda/11.3.0/network_installers/cuda_11.3.0_win10_network.exe" | |
| } | |
| $CUDA_PACKAGES_IN = @( | |
| "nvcc"; | |
| "cudart"; | |
| ) | |
| $CUDA_VERSION_FULL = "11.0.3" | |
| $CUDA_MAJOR=11 | |
| $CUDA_MINOR=0 | |
| $CUDA_PATCH=3 | |
| $CUDA_PACKAGES = "" | |
| Foreach ($package in $CUDA_PACKAGES_IN) { | |
| # Make sure the correct package name is used for nvcc. | |
| if($package -eq "nvcc" -and [version]$CUDA_VERSION_FULL -lt [version]"9.1"){ | |
| $package="compiler" | |
| } elseif($package -eq "compiler" -and [version]$CUDA_VERSION_FULL -ge [version]"9.1") { | |
| $package="nvcc" | |
| } | |
| $CUDA_PACKAGES += " $($package)_$($CUDA_MAJOR).$($CUDA_MINOR)" | |
| } | |
| echo "$($CUDA_PACKAGES)" | |
| $CUDA_REPO_PKG_REMOTE=$CUDA_KNOWN_URLS[$CUDA_VERSION_FULL] | |
| $CUDA_REPO_PKG_LOCAL="cuda_$($CUDA_VERSION_FULL)_win10_network.exe" | |
| Write-Output "Downloading CUDA Network Installer for $($CUDA_VERSION_FULL) from: $($CUDA_REPO_PKG_REMOTE)" | |
| Invoke-WebRequest $CUDA_REPO_PKG_REMOTE -OutFile $CUDA_REPO_PKG_LOCAL | Out-Null | |
| if(Test-Path -Path $CUDA_REPO_PKG_LOCAL){ | |
| Write-Output "Downloading Complete" | |
| } else { | |
| Write-Output "Error: Failed to download $($CUDA_REPO_PKG_LOCAL) from $($CUDA_REPO_PKG_REMOTE)" | |
| exit 1 | |
| } | |
| # Invoke silent install of CUDA (via network installer) | |
| Write-Output "Installing CUDA $($CUDA_VERSION_FULL). Subpackages $($CUDA_PACKAGES)" | |
| Start-Process -Wait -FilePath .\"$($CUDA_REPO_PKG_LOCAL)" -ArgumentList "-s $($CUDA_PACKAGES)" | |
| # Check the return status of the CUDA installer. | |
| if (!$?) { | |
| Write-Output "Error: CUDA installer reported error. $($LASTEXITCODE)" | |
| exit 1 | |
| } | |
| # Store the CUDA_PATH in the environment for the current session, to be forwarded in the action. | |
| $CUDA_PATH = "C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v$($CUDA_MAJOR).$($CUDA_MINOR)" | |
| $CUDA_PATH_VX_Y = "CUDA_PATH_V$($CUDA_MAJOR)_$($CUDA_MINOR)" | |
| # Set environmental variables in this session | |
| $env:CUDA_PATH = "$($CUDA_PATH)" | |
| $env:CUDA_PATH_VX_Y = "$($CUDA_PATH_VX_Y)" | |
| Write-Output "CUDA_PATH $($CUDA_PATH)" | |
| Write-Output "CUDA_PATH_VX_Y $($CUDA_PATH_VX_Y)" | |
| - name: Download cuDNN and TensorRT | |
| uses: robinraju/release-downloader@main | |
| if: ${{ github.event_name != 'pull_request' }} | |
| with: | |
| repository: "smistad/FAST-secret-dependencies" | |
| latest: true | |
| fileName: "*" | |
| token: ${{ secrets.DOWNLOAD_SECRET_DEPENDENCIES }} | |
| - name: Install cuDNN and TensorRT | |
| if: ${{ github.event_name != 'pull_request' }} | |
| shell: powershell | |
| run: | | |
| Expand-Archive -Path ${{github.workspace}}/cudnn-windows-x86_64-8.6.0.163_cuda11-archive.zip -DestinationPath ${{github.workspace}}/cudnn/ | |
| cp ${{github.workspace}}/cudnn/cudnn-windows-x86_64-8.6.0.163_cuda11-archive/bin/*.dll "C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v11.0/bin/" | |
| cp ${{github.workspace}}/cudnn/cudnn-windows-x86_64-8.6.0.163_cuda11-archive/include/cudnn*.h "C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v11.0/include/" | |
| cp ${{github.workspace}}/cudnn/cudnn-windows-x86_64-8.6.0.163_cuda11-archive/lib/cudnn*.lib "C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v11.0/lib/x64/" | |
| Expand-Archive -Path ${{github.workspace}}/TensorRT-8.5.3.1.Windows10.x86_64.cuda-11.8.cudnn8.6.zip -DestinationPath ${{github.workspace}}/trt/ | |
| - name: Configure CMake (with TensorRT) | |
| if: ${{ github.event_name != 'pull_request' }} | |
| # 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 ${{github.workspace}} -B ${{github.workspace}}/build ` | |
| -DCMAKE_BUILD_TYPE=${{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="C:/Program Files/NVIDIA GPU Computing Toolkit/CUDA/v11.0/" ` | |
| -DTensorRT_ROOT="${{github.workspace}}/trt/TensorRT-8.5.3.1/" ` | |
| -DTensorRT_parsers_LIBRARY="${{github.workspace}}/trt/TensorRT-8.5.3.1/lib/nvparsers.lib" ` | |
| -DTensorRT_onnx_parser_LIBRARY="${{github.workspace}}/trt/TensorRT-8.5.3.1/lib/nvonnxparser.lib" ` | |
| -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: Configure CMake (without TensorRT) | |
| if: ${{ github.event_name == 'pull_request' }} | |
| # 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 ${{github.workspace}} -B ${{github.workspace}}/build ` | |
| -DCMAKE_BUILD_TYPE=${{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 ` | |
| -DFAST_MODULE_TensorRT=OFF ` | |
| -DFAST_MODULE_HDF5=ON ` | |
| -DFAST_MODULE_Plotting=ON ` | |
| -DFAST_MODULE_Python=ON ` | |
| -DFAST_MODULE_RealSense=ON ` | |
| -DFAST_BUILD_EXAMPLES=ON | |
| - name: Build | |
| # Build your program with the given configuration | |
| run: cmake --build ${{github.workspace}}/build --config ${{env.BUILD_TYPE}} -j 4 | |
| - name: Build Python wheel | |
| run: cmake --build ${{github.workspace}}/build --config ${{env.BUILD_TYPE}} --target python-wheel -j 4 | |
| - name: Package | |
| run: cmake --build ${{github.workspace}}/build --config ${{env.BUILD_TYPE}} --target package -j 4 | |
| - name: Upload Windows installer | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: Window installer | |
| path: ${{github.workspace}}/build/fast_*.exe | |
| if-no-files-found: error | |
| - name: Upload archive package | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: Archive package (zip) | |
| path: ${{github.workspace}}/build/fast_*.zip | |
| if-no-files-found: error | |
| - name: Upload Python wheel | |
| uses: actions/upload-artifact@v2 | |
| with: | |
| name: Python wheel | |
| path: ${{github.workspace}}/build/python/dist/pyFAST-*.whl | |
| if-no-files-found: error | |
| - name: Upload Windows installer to release | |
| if: ${{ github.event_name == 'release' }} | |
| uses: svenstaro/upload-release-action@v2 | |
| with: | |
| repo_token: ${{ secrets.GITHUB_TOKEN }} | |
| file: ${{github.workspace}}/build/fast_*.exe | |
| file_glob: true | |
| tag: ${{ github.ref }} | |
| overwrite: true | |
| - name: Upload archive package to release | |
| if: ${{ github.event_name == 'release' }} | |
| uses: svenstaro/upload-release-action@v2 | |
| with: | |
| repo_token: ${{ secrets.GITHUB_TOKEN }} | |
| file: ${{github.workspace}}/build/fast_*.zip | |
| file_glob: true | |
| tag: ${{ github.ref }} | |
| overwrite: true | |
| - name: Upload Python wheel to release | |
| if: ${{ github.event_name == 'release' }} | |
| uses: svenstaro/upload-release-action@v2 | |
| with: | |
| repo_token: ${{ secrets.GITHUB_TOKEN }} | |
| file: ${{github.workspace}}/build/python/dist/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/python/dist/pyFAST-*.whl | |