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build-test.yml
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name: Build and ctest and recon_test_pack CI
on:
push:
branches: [ master ]
paths-ignore:
- '.appveyor.yml'
- 'CITATION.cff'
- '**/*.md'
- '**/*.html'
- '**/*.htm'
- '**/*.tex'
pull_request:
branches: [ master ]
paths-ignore:
- '.appveyor.yml'
- 'CITATION.cff'
- '**/*.md'
- '**/*.html'
- '**/*.htm'
- '**/*.tex'
workflow_dispatch:
inputs:
debug_enabled:
description: 'Run the build with tmate debugging enabled (https://github.com/marketplace/actions/debugging-with-tmate)'
required: false
default: false
jobs:
build:
runs-on: ${{ matrix.os }}
strategy:
matrix:
include:
- os: ubuntu-latest
compiler: gcc
compiler_version: 9
cuda_version: "0"
BUILD_FLAGS: "-DSTIR_OPENMP=ON"
BUILD_TYPE: "Release"
parallelproj: "ON"
ROOT: "ON"
ITK: "OFF"
- os: ubuntu-latest
compiler: clang
#compiler_version:
cuda_version: "0"
BUILD_FLAGS: "-DSTIR_OPENMP=ON"
BUILD_TYPE: "Release"
parallelproj: "ON"
ROOT: "OFF"
# currently using ITK 5.2 which doesn't like clang 14
ITK: "OFF"
- os: ubuntu-latest
compiler: gcc
compiler_version: 10
cuda_version: "0"
BUILD_FLAGS: "-DSTIR_OPENMP=ON -DCMAKE_CXX_STANDARD=17"
BUILD_TYPE: "Debug"
parallelproj: "OFF"
ROOT: "OFF"
ITK: "ON"
- os: ubuntu-latest
compiler: gcc
compiler_version: 12
cuda_version: "0"
BUILD_FLAGS: "-DSTIR_OPENMP=ON -DCMAKE_CXX_STANDARD=14"
BUILD_TYPE: "RelWithDebInfo"
parallelproj: "ON"
ROOT: "OFF"
ITK: "ON"
- os: ubuntu-latest
compiler: gcc
compiler_version: 12
cuda_version: "12.1.0"
BUILD_FLAGS: "-DSTIR_OPENMP=ON -DCMAKE_CXX_STANDARD=14"
BUILD_TYPE: "Release"
parallelproj: "ON"
ROOT: "OFF"
ITK: "ON"
- os: macOS-latest
compiler: gcc
compiler_version: 11
cuda_version: "0"
BUILD_FLAGS: "-DSTIR_OPENMP=OFF"
parallelproj: "OFF"
BUILD_TYPE: "Debug"
ROOT: "OFF"
ITK: "OFF"
# Currently disabled due to problems with listmode recon, see https://github.com/UCL/STIR/issues/1200
#- os: macOS-latest
# compiler: clang
# compiler_version: 16
# BUILD_FLAGS: "-DSTIR_OPENMP=OFF"
# parallelproj: "OFF"
# BUILD_TYPE: "Release"
# ROOT: "OFF"
# ITK: "OFF"
# let's run all of them, as opposed to aborting when one fails
fail-fast: false
name: ${{ matrix.os }}-${{ matrix.compiler }}-${{ matrix.compiler_version }}-cuda${{ matrix.cuda_version }}-${{ matrix.BUILD_TYPE }}-pp=${{ matrix.parallelproj }}-ROOT=${{ matrix.ROOT }}
steps:
- name: disk space
shell: bash
run: |
case ${{matrix.os}} in
(ubuntu* | macOS*)
df -h
# saves about 2GB
echo removing dotnet
sudo rm -rf /usr/share/dotnet
# saves about 10 GB
echo removing agent_tools
sudo rm -rf "$AGENT_TOOLSDIRECTORY"
# saves about 10 GB
echo removing android files
sudo rm -rf /usr/local/lib/android
df -h
;;
(windows*)
# no idea how to do this
;;
esac
- uses: actions/checkout@v3
with:
submodules: recursive
- name: set_compiler_variables
shell: bash
run: |
set -ex
if test 'XX${{ matrix.compiler }}' = 'XXclang'; then
CC="clang"
CXX="clang++"
elif test 'XX${{ matrix.compiler }}' = 'XXgcc'; then
CC="gcc"
CXX="g++"
fi
if test 'XX${{ matrix.compiler_version }}' != 'XX'; then
CC=${CC}-${{ matrix.compiler_version }}
CXX=${CXX}-${{ matrix.compiler_version }}
fi
if test 'XX${{ matrix.os }}' = 'XXmacOS-latest'; then
# need to force XCode version for the moment due to a linker bug
# see https://github.com/UCL/STIR/issues/1103
echo DEVELOPER_DIR="/Applications/Xcode_14.1.app/Contents/Developer" >> $GITHUB_ENV
if test 'XX${{ matrix.compiler }}' = 'XXclang'; then
brew install llvm@${{ matrix.compiler_version }}
if test XX${HOMEBREW_PREFIX} = XX; then
HOMEBREW_PREFIX=/usr/local
fi
LDFLAGS="-L$HOMEBREW_PREFIX/opt/llvm/lib/c++ -Wl,-rpath,$HOMEBREW_PREFIX/opt/llvm/lib/c++"
# make available to jobs below
echo LDFLAGS="$LDFLAGS" >> $GITHUB_ENV
CC="$HOMEBREW_PREFIX/opt/llvm/bin/clang"
CXX="$HOMEBREW_PREFIX/opt/llvm/bin/clang++"
fi
fi
export CC CXX
# make available to jobs below
echo CC="$CC" >> $GITHUB_ENV
echo CXX="$CXX" >> $GITHUB_ENV
- if: ${{ ! matrix.cuda_version == '0' }}
uses: Jimver/[email protected]
id: cuda-toolkit
with:
cuda: ${{ matrix.cuda_version }}
linux-local-args: '["--toolkit"]'
- name: install_dependencies
shell: bash
run: |
set -ex
# We will install some external dependencies here
CMAKE_INSTALL_PREFIX=${GITHUB_WORKSPACE}/install
case ${{matrix.os}} in
(ubuntu*)
sudo apt update
# install compiler
if test 'XX${{ matrix.compiler }}' = 'XXclang'; then
# package is called clang, need libomp-dev for OpenMP support
sudo apt install $CC libomp-dev
else
sudo apt install $CXX
fi
# other dependencies
sudo apt install libboost-dev libhdf5-serial-dev swig python3-dev nlohmann-json3-dev
if test "${{matrix.ITK}}XX" == "ONXX"; then
sudo apt install libinsighttoolkit5-dev
fi
# free up some disk space
sudo apt clean
PYTHON_EXECUTABLE=$(which python3)
;;
(macOS*)
brew install boost swig python nlohmann-json
PYTHON_EXECUTABLE=$(which python3)
;;
(windows*)
# this compiles the whole thing so takes ages
vcpkg install boost-core hdf5 nlohmann-json
# swig is preinstalled and is currently not in vcpcg
vcpkg list
PYTHON_EXECUTABLE=$(which python3)
;;
esac
echo PYTHON_EXECUTABLE="$PYTHON_EXECUTABLE" >> $GITHUB_ENV
${PYTHON_EXECUTABLE} -m venv ${GITHUB_WORKSPACE}/my-env
source ${GITHUB_WORKSPACE}/my-env/bin/activate
#python -m pip install -U pip
case ${{matrix.os}} in
(macOS*)
# attempt to get round buggy Accelerate builds, see https://github.com/numpy/numpy/issues/15947
# but it didn't work, so commented out
# brew install openblas
# export OPENBLAS=$(brew --prefix openblas)
#python -m pip install --no-cache-dir --no-binary numpy numpy # avoid the cached .whl!
python -m pip install numpy
;;
(*)
python -m pip install numpy
;;
esac
python -m pip install pytest
if test "${{matrix.parallelproj}}XX" == "ONXX"; then
git clone --depth 1 --branch v1.3.7 https://github.com/gschramm/parallelproj
mkdir parallelproj/build
cd parallelproj/build
if test ! "${{matrix.cuda_version}}" == "0"; then
extra_args="-DSKIP_CUDA_LIB:BOOL=ON"
fi
cmake .. -DCMAKE_INSTALL_PREFIX=${CMAKE_INSTALL_PREFIX} "${extra_args}"
cmake --build . --target install --config Release
cd ../..
fi
# Install NiftyPET
if test ! "${{matrix.cuda_version}}" == "0"; then
export PATHTOOLS=${GITHUB_WORKSPACE}/NiftyPET_tools
export HMUDIR=${GITHUB_WORKSPACE}/mmr_hardwareumaps
python -m pip install "nipet>=2"
niftypet_cmake_prefix=${{python -c "from niftypet.nipet import cmake_prefix; print(cmake_prefix)"}}
echo NiftyPET_PREFIX="$niftypet_cmake_prefix" >> $GITHUB_ENV
fi
# Install ROOT (warning: currently only valid on Ubuntu)
if test "${{matrix.ROOT}}XX" == "ONXX"; then
wget https://root.cern/download/root_v6.24.02.Linux-ubuntu20-x86_64-gcc9.3.tar.gz
tar -xzvf root_v6.24.02.Linux-ubuntu20-x86_64-gcc9.3.tar.gz
source root/bin/thisroot.sh
fi
# we'll install some dependencies with shared libraries, so need to let the OS know
# thisroot.sh also modified the path, so save that for the recon_test_pack
case ${{matrix.os}} in
(ubuntu*)
echo LD_LIBRARY_PATH="${CMAKE_INSTALL_PREFIX}/lib:$LD_LIBRARY_PATH" >> $GITHUB_ENV
echo PATH="$PATH" >> $GITHUB_ENV
;;
(macOS*)
echo DYLD_FALLBACK_LIBRARY_PATH="${CMAKE_INSTALL_PREFIX}/lib:$DYLD_FALLBACK_LIBRARY_PATH" >> $GITHUB_ENV
echo PATH="$PATH" >> $GITHUB_ENV
;;
(windows*)
echo PATH="${CMAKE_INSTALL_PREFIX}/lib:${CMAKE_INSTALL_PREFIX}/bin:$PATH" >> $GITHUB_ENV
;;
esac
- name: ccache
uses: hendrikmuhs/ccache-action@v1
with:
key: ${{ matrix.os }}-${{ matrix.compiler }}-${{ matrix.compiler_version }}-cuda${{ matrix.cuda_version }}-${{ matrix.BUILD_TYPE }}
max-size: "2G"
- name: configure
shell: bash
env:
BUILD_TYPE: ${{ matrix.BUILD_TYPE }}
BUILD_FLAGS: ${{ matrix.BUILD_FLAGS }}
run: |
set -ex
source ${GITHUB_WORKSPACE}/my-env/bin/activate
#export PATH="/usr/lib/ccache:/usr/local/opt/ccache/libexec:$PATH"
cmake --version
if test "XX$CC" != "XX"; then
$CC --version
$CXX --version
fi
CMAKE_INSTALL_PREFIX=${GITHUB_WORKSPACE}/install
# make available to jobs below
echo CMAKE_INSTALL_PREFIX="$CMAKE_INSTALL_PREFIX" >> $GITHUB_ENV
EXTRA_BUILD_FLAGS="-DBUILD_SWIG_PYTHON=ON -DPYTHON_EXECUTABLE=`which python`"
EXTRA_BUILD_FLAGS="${EXTRA_BUILD_FLAGS} -DCMAKE_INSTALL_PREFIX=${CMAKE_INSTALL_PREFIX} -DCMAKE_BUILD_TYPE=${BUILD_TYPE}"
EXTRA_BUILD_FLAGS="${EXTRA_BUILD_FLAGS} -DCMAKE_PREFIX_DIR=${NiftyPET_PREFIX}"
EXTRA_BUILD_FLAGS="${EXTRA_BUILD_FLAGS} -DDOWNLOAD_ZENODO_TEST_DATA=ON"
EXTRA_BUILD_FLAGS="${EXTRA_BUILD_FLAGS} -DDISABLE_STIR_LOCAL=OFF -DSTIR_LOCAL=${GITHUB_WORKSPACE}/examples/C++/src"
echo "cmake flags $BUILD_FLAGS $EXTRA_BUILD_FLAGS"
mkdir build
cd build
cmake -S .. ${BUILD_FLAGS} ${EXTRA_BUILD_FLAGS}
# report disk space
case ${{matrix.os}} in
(ubuntu* | macOS*)
df -h
;;
(windows*)
# no idea how to do this
;;
esac
- name: build
shell: bash
env:
BUILD_TYPE: ${{ matrix.BUILD_TYPE }}
run: |
cd ${GITHUB_WORKSPACE}/build;
source ${GITHUB_WORKSPACE}/my-env/bin/activate
cmake --build . -j 2 --config ${BUILD_TYPE}} --target install
- name: ctest
shell: bash
env:
BUILD_TYPE: ${{ matrix.BUILD_TYPE }}
run: |
cd ${GITHUB_WORKSPACE}/build
# don't run all of them in Debug mode as it takes too long
if test ${BUILD_TYPE} = Debug; then
EXCLUDE="-E test_data_processor_projectors|test_export_array|test_ArcCorrection|test_blocks_on_cylindrical_projectors"
fi
ctest --output-on-failure -C ${BUILD_TYPE} ${EXCLUDE}
- name: recon_test_pack
shell: bash
env:
BUILD_FLAGS: ${{ matrix.BUILD_FLAGS }}
BUILD_TYPE: ${{ matrix.BUILD_TYPE }}
run: |
set -ex;
PATH=${CMAKE_INSTALL_PREFIX}/bin:$PATH
cd ${GITHUB_WORKSPACE}/recon_test_pack
./run_tests.sh --nointbp
# don't run all of them in Debug mode as it takes too long
if test ${BUILD_TYPE} != Debug; then
./run_test_simulate_and_recon.sh
./run_test_listmode_recon.sh
./run_test_simulate_and_recon_with_motion.sh
./run_scatter_tests.sh
./run_test_zoom_image.sh
./run_ML_norm_tests.sh
if test "${{matrix.ROOT}}XX" == "ONXX"; then ./run_root_GATE.sh; fi
./run_tests_modelling.sh
cd ${GITHUB_WORKSPACE}/recon_test_pack/SPECT
./run_SPECT_tests.sh
fi
- name: Upload log files for debugging
uses: actions/upload-artifact@v3
if: failure()
with:
name: recon_test_pack_log_files-${{ matrix.os }}-${{ matrix.compiler }}${{ matrix.compiler_version }}-${{ matrix.BUILD_TYPE }}-pp=${{ matrix.parallelproj }}-ROOT=${{ matrix.ROOT }}
path: ${{ github.workspace }}/recon_test_pack/**/*.log
retention-days: 7
# Enable tmate debugging of manually-triggered workflows if the input option was provided
- name: Setup tmate session if triggered
uses: mxschmitt/action-tmate@v3
timeout-minutes: 15
if: ${{ github.event_name == 'workflow_dispatch' && github.event.inputs.debug_enabled }}
- name: examples
shell: bash
run: |
set -ex;
PATH=${CMAKE_INSTALL_PREFIX}/bin:$PATH
# Run examples to see if they work
cd ${GITHUB_WORKSPACE}/examples/PET_simulation
./run_simulation.sh 1> /dev/null
# Run the Demo executables
EXE_LOC=${GITHUB_WORKSPACE}/build/src/examples/C++
cd ${GITHUB_WORKSPACE}/examples/C++/src
generate_image generate_image.par
forward_project sino.hs image.hv small.hs
# Cannot test demo1 or demo2 as they require interactivity. Piping does not work.
${EXE_LOC}/demo3 demo.par --display_off
${EXE_LOC}/demo3 demoPM.par --display_off
${EXE_LOC}/demo4_obj_fun demo4_obj_fun.par
${EXE_LOC}/demo5_line_search demo5_line_search.par
- name: Python
shell: bash
run: |
set -ex
source ${GITHUB_WORKSPACE}/my-env/bin/activate
# Run Python tests, making sure we're using the correct Python interpreter
which python
export PYTHONPATH=${CMAKE_INSTALL_PREFIX}/python
cd ${GITHUB_WORKSPACE}/src
case ${{matrix.os}} in
(macOS*)
echo skipping pytest due to numpy problem for now.
;;
(*)
python -m pytest .
;;
esac