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Merge SHARDRecon into main MRtrix3 codebase #2280

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Merge SHARDRecon into main MRtrix3 codebase

Merge SHARDRecon into main MRtrix3 codebase #2280

Workflow file for this run

.github/workflows/checks.yml at 2172535
name: Checks
on:
pull_request:
types: [opened, synchronize]
branches: [ master, dev]
merge_group:
types: [checks_requested]
branches: [master]
jobs:
linux-clang-build:
runs-on: ubuntu-latest
env:
QT_SELECT: qt6
SCCACHE_GHA_ENABLED: "true"
SCCACHE_CACHE_SIZE: "2G"
steps:
- uses: actions/checkout@v1
with:
submodules: true
- name: install dependencies
run: |
sudo apt-get update
sudo apt-get install clang qt6-base-dev libglvnd-dev zlib1g-dev libfftw3-dev ninja-build python3-distutils python3-numpy
- name: Run sccache-cache
uses: mozilla-actions/[email protected]
- name: Get CMake
uses: lukka/get-cmake@latest
with:
cmakeVersion: '3.16.3'
- name: Print CMake version
run: cmake --version
- name: configure
run: >
cmake
-B build
-G Ninja
-D CMAKE_BUILD_TYPE=Release
-D MRTRIX_BUILD_TESTS=ON
-D MRTRIX_STL_DEBUGGING=ON
-D MRTRIX_WARNINGS_AS_ERRORS=ON
-D CMAKE_C_COMPILER=clang
-D CMAKE_CXX_COMPILER=clang++
- name: build
run: cmake --build build
- name: unit tests
run: cd build && ctest -L unittest --output-on-failure
- name: binary tests
run: cd build && ctest -L binary --output-on-failure
#
# - name: limited script tests
# run: cd build && ctest -L pythonci --output-on-failure
- name: check command documentation
run: ./docs/generate_user_docs.sh --build-dir build && git diff --exit-code docs/
linux-gcc-build:
runs-on: ubuntu-latest
env:
QT_SELECT: qt6
SCCACHE_GHA_ENABLED: "true"
SCCACHE_CACHE_SIZE: "2G"
steps:
- uses: actions/checkout@v1
with:
submodules: true
- name: install dependencies
run: |
sudo apt-get update
sudo apt-get install g++-9 qt6-base-dev libglvnd-dev zlib1g-dev libfftw3-dev ninja-build python3-numpy
- name: Run sccache-cache
uses: mozilla-actions/[email protected]
- name: Get CMake
uses: lukka/get-cmake@latest
with:
cmakeVersion: '3.16.3'
- name: Print CMake version
run: cmake --version
- name: configure
run: >
cmake
-B build
-G Ninja
-D CMAKE_BUILD_TYPE=Release
-D MRTRIX_BUILD_TESTS=ON
-D MRTRIX_STL_DEBUGGING=ON
-D MRTRIX_WARNINGS_AS_ERRORS=ON
- name: build
run: cmake --build build
- name: unit tests
run: cd build && ctest -L unittest --output-on-failure
- name: binary tests
run: cd build && ctest -L binary --output-on-failure
#
# - name: limited script tests
# run: cd build && ctest -L pythonci --output-on-failure
macos-build:
runs-on: macos-latest
env:
SCCACHE_GHA_ENABLED: "true"
SCCACHE_CACHE_SIZE: "2G"
steps:
- uses: actions/checkout@v1
with:
submodules: true
- name: install dependencies
run: |
brew bundle --file=${{ github.workspace }}/.brewfile
brew link --force qt
brew install numpy
- name: Run sccache-cache
uses: mozilla-actions/[email protected]
- name: Get CMake
uses: lukka/get-cmake@latest
with:
cmakeVersion: '3.21.0'
- name: Print CMake version
run: cmake --version
- name: configure
run: >
export PATH=/usr/local/opt/qt/bin:$PATH;
cmake
-B build
-G Ninja
-D CMAKE_BUILD_TYPE=Release
-D MRTRIX_BUILD_TESTS=ON
-D MRTRIX_STL_DEBUGGING=ON
-D MRTRIX_USE_PCH=OFF
-D MRTRIX_WARNINGS_AS_ERRORS=ON
- name: build
run: cmake --build build
- name: unit tests
run: cd build && ctest -L unittest --output-on-failure
- name: binary tests
run: cd build && ctest -L binary --output-on-failure
#
# - name: limited script tests
# run: cd build && ctest -L pythonci --output-on-failure
windows-build:
runs-on: windows-latest
defaults:
run:
shell: msys2 {0}
env:
CHERE_INVOKING: enabled_from_arguments
MINGW_PACKAGE_PREFIX: mingw-w64-ucrt-x86_64
SCCACHE_GHA_ENABLED: "true"
SCCACHE_CACHE_SIZE: "2G"
SCCACHE_DIR: ${{ github.workspace }}/.sccache
steps:
- uses: actions/checkout@v1
with:
submodules: true
- uses: msys2/setup-msys2@v2
with:
msystem: UCRT64
release: false
install: |
git
python
${{env.MINGW_PACKAGE_PREFIX}}-bc
${{env.MINGW_PACKAGE_PREFIX}}-cmake
${{env.MINGW_PACKAGE_PREFIX}}-diffutils
${{env.MINGW_PACKAGE_PREFIX}}-fftw
${{env.MINGW_PACKAGE_PREFIX}}-gcc
${{env.MINGW_PACKAGE_PREFIX}}-ninja
${{env.MINGW_PACKAGE_PREFIX}}-pkg-config
${{env.MINGW_PACKAGE_PREFIX}}-qt6-base
${{env.MINGW_PACKAGE_PREFIX}}-qt6-svg
${{env.MINGW_PACKAGE_PREFIX}}-zlib
- name: Run sccache-cache
uses: mozilla-actions/[email protected]
- name: export sccache to msys2 shell
run: |
export SCCACHE_UNIX_PATH=$(cygpath -u "$SCCACHE_PATH")
echo "SCCACHE_UNIX_PATH=$SCCACHE_UNIX_PATH" >> $GITHUB_ENV
- name: configure
run: >
cmake
-B build
-G Ninja
-D CMAKE_BUILD_TYPE=Release
-D MRTRIX_BUILD_TESTS=ON
-D MRTRIX_STL_DEBUGGING=ON
-D MRTRIX_WARNINGS_AS_ERRORS=ON
-D CMAKE_CXX_COMPILER_LAUNCHER=${{env.SCCACHE_UNIX_PATH}} .
- name: build
run: cmake --build build
- name: unit tests
run: cd build && ctest -L unittest --output-on-failure
- name: binary tests
run: cd build && ctest -L binary --output-on-failure
#
# - name: limited script tests
# run: cd build && ctest -L pythonci --output-on-failure
secondary-checks:
runs-on: ubuntu-latest
env:
QT_SELECT: qt6
steps:
- uses: actions/checkout@v1
- name: install dependencies
run: |
sudo apt-get update
sudo apt-get install pylint python3-sphinx sphinx-rtd-theme-common python3-recommonmark python3-sphinx-rtd-theme python3-pip python3-sphinx-notfound-page
- name: check syntax
run: ./check_syntax || { cat syntax.log; false; }
- name: pylint
run: |
./run_pylint || { cat pylint.log; false; }
- name: check copyright headers
run: ./update_copyright && git diff --exit-code
- name: check building of documentation
run: python3 -m sphinx -n -N -W -w sphinx.log docs/ tmp/
- name: clang-format check
uses: DoozyX/[email protected]
with:
source: '.'
extensions: 'h,cpp'
clangFormatVersion: 16
# Ignore third party headers
exclude: './thirdparty ./_deps'