Merge branch 'master' of https://github.com/smistad/FAST #606

Workflow file for this run

.github/workflows/CI-ubuntu.yml at 6b0ac55

	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

	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@v2
	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@v2
	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@v2
	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

	- name: Test PyPi upload
	if: ${{ github.event_name == 'release' && !contains(github.ref, 'rc') }}
	run: \|
	sleep 60
	pip3 install pyfast==${GITHUB_REF#refs/tags/v}
	shell: bash

	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/*

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Merge branch 'master' of https://github.com/smistad/FAST #606

Workflow file

Merge branch 'master' of https://github.com/smistad/FAST #606

Jobs

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Workflow file for this run