Try to avoid wrong TIFF header being used on Apple #647
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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: 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/* | |