Initial port of align tool from Avogadro 1.x code #2255
Workflow file for this run
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name: CMake Build Matrix | |
# Many thanks to Cristian Adam for examples | |
# e.g. https://github.com/cristianadam/HelloWorld/blob/master/.github/workflows/build_cmake.yml | |
# https://cristianadam.eu/20191222/using-github-actions-with-c-plus-plus-and-cmake/ | |
on: [push, pull_request, workflow_dispatch] | |
env: | |
QT_VERSION: 5.15.2 | |
# this is different from MACOSX_DEPLOYMENT_TARGET to prevent build problems | |
# we set MACOSX_DEPLOYMENT_TARGET later | |
MACOS_TARGET: 10.12 | |
FEATURES: -DBUILD_GPL_PLUGINS=ON -DWITH_COORDGEN=OFF -DUSE_VTK=ON -DUSE_3DCONNEXION=ON | |
CACHE: -DCMAKE_C_COMPILER_LAUNCHER=sccache -DCMAKE_CXX_COMPILER_LAUNCHER=sccache | |
SCCACHE_GHA_ENABLED: "true" | |
jobs: | |
build: | |
name: ${{ matrix.config.name }} | |
runs-on: ${{ matrix.config.os }} | |
strategy: | |
fail-fast: false | |
matrix: | |
config: | |
- { | |
name: "Ubuntu GCC", artifact: "Ubuntu-Latest.tar.gz", | |
os: ubuntu-latest, | |
cc: "gcc", cxx: "g++", | |
build_type: "Release", | |
cmake_flags: "-G Ninja -DENABLE_TESTING=ON -DTEST_QTGL=OFF -USE_SYSTEM_ZLIB=ON", | |
cpack: "", | |
} | |
- { | |
name: "Ubuntu AppImage", artifact: "Avogadro2.AppImage", | |
os: ubuntu-20.04, | |
cc: "gcc", cxx: "g++", | |
build_type: "Release", | |
cmake_flags: "-G Ninja -DINSTALL_BUNDLE_FILES=ON -USE_SYSTEM_ZLIB=ON", | |
cpack: "", | |
} | |
- { | |
name: "macOS Latest Clang", artifact: "macOS.dmg", | |
os: macos-latest, | |
cc: "clang", cxx: "clang++", | |
build_type: "Release", | |
cmake_flags: "-G Ninja", | |
cpack_flags: "-G DragNDrop", | |
} | |
- { | |
name: "Windows Latest MSVC", artifact: "Win64.exe", | |
os: windows-latest, | |
cc: "cl", cxx: "cl", | |
build_type: "Release", | |
cmake_flags: "-DOPENSSL_ROOT_DIR=D:\\a\\Tools\\OpenSSL\\Win_x64", | |
build_flags: "-j 2", | |
cpack_flags: "-G NSIS", | |
} | |
- { | |
name: "Ubuntu Address Sanitizer", artifact: "", | |
os: ubuntu-20.04, | |
cc: "gcc", cxx: "g++", | |
build_type: "asan", | |
cmake_flags: "-G Ninja -DENABLE_TESTING=ON -DTEST_QTGL=OFF -USE_SYSTEM_ZLIB=ON", | |
cpack: "", | |
} | |
- { | |
name: "Ubuntu Undefined Behavior Sanitizer", artifact: "", | |
os: ubuntu-20.04, | |
cc: "gcc", cxx: "g++", | |
build_type: "ubsan", | |
cmake_flags: "-G Ninja -DENABLE_TESTING=ON -DTEST_QTGL=OFF -USE_SYSTEM_ZLIB=ON", | |
cpack: "", | |
} | |
steps: | |
- name: Install Dependencies (Linux) | |
if: runner.os == 'Linux' | |
run: | | |
sudo apt-get -qq update | |
sudo apt-get -qq install ninja-build libeigen3-dev libboost-all-dev libglew-dev libxml2-dev | |
sudo apt-get -qq install qtbase5-dev qtchooser qt5-qmake qtbase5-dev-tools libqt5x11extras5-dev libqt5svg5-dev | |
sudo apt-get -qq install libgcc-10-dev libgcc-9-dev | |
- name: Install Dependencies (macOS) | |
if: runner.os == 'macOS' | |
run: | | |
if uname -p | grep -q "arm" ; then | |
export PATH=/opt/homebrew/bin:$PATH | |
else # not self-hosted runner | |
brew install ninja eigen glew | |
fi | |
- name: Install Dependencies (Windows) | |
if: runner.os == 'Windows' | |
run: choco install ninja | |
- name: Checkout openchemistry | |
uses: actions/checkout@v4 | |
with: | |
repository: openchemistry/openchemistry | |
submodules: recursive | |
- name: Checkout avogadroapp | |
uses: actions/checkout@v4 | |
with: | |
repository: openchemistry/avogadroapp | |
path: avogadroapp | |
- name: Checkout molecules | |
uses: actions/checkout@v4 | |
with: | |
repository: openchemistry/molecules | |
path: molecules | |
- name: Checkout i18n | |
uses: actions/checkout@v4 | |
with: | |
repository: openchemistry/avogadro-i18n | |
path: avogadro-i18n | |
- name: Checkout avogadrolibs | |
uses: actions/checkout@v4 | |
with: | |
path: avogadrolibs | |
- name: Install Qt | |
uses: jurplel/install-qt-action@v3 | |
with: | |
cache: True | |
version: ${{ env.QT_VERSION }} | |
- name: Install OpenSSL (Win64) | |
if: runner.os == 'Windows' | |
uses: jurplel/install-qt-action@v3 | |
with: | |
cache: True | |
tools: 'tools_opensslv3_x64' | |
version: ${{ env.QT_VERSION }} | |
host: 'windows' | |
target: 'desktop' | |
arch: 'win64_msvc2019_64' | |
- name: Configure MSVC Command Prompt | |
if: runner.os == 'Windows' | |
uses: ilammy/msvc-dev-cmd@v1 | |
with: | |
arch: x64 | |
- name: Grab cache files | |
uses: actions/cache@v3 | |
if: runner.os != 'Windows' | |
with: | |
path: | | |
${{ runner.workspace }}/build/Downloads | |
key: ${{ matrix.config.name }}-downloads | |
- name: Run sccache-cache | |
uses: mozilla-actions/sccache-action@main | |
- name: Configure | |
run: | | |
if [ ! -d "${{ runner.workspace }}/build" ]; then mkdir "${{ runner.workspace }}/build"; fi | |
cd "${{ runner.workspace }}/build" | |
# won't have any effect except on Mac | |
echo "MACOSX_DEPLOYMENT_TARGET=${{ env.MACOS_TARGET }}" >> $GITHUB_ENV | |
CC=${{matrix.config.cc}} CXX=${{matrix.config.cxx}} cmake $GITHUB_WORKSPACE ${{env.FEATURES}} ${{env.CACHE}} -DCMAKE_BUILD_TYPE=${{matrix.config.build_type}} ${{matrix.config.cmake_flags}} | |
shell: bash | |
- name: Build | |
run: | | |
CC=${{matrix.config.cc}} CXX=${{matrix.config.cxx}} CMAKE_C_COMPILER_LAUNCHER=sccache CMAKE_CXX_COMPILER_LAUNCHER=sccache cmake --build . --config ${{matrix.config.build_type}} ${{matrix.config.build_flags}} | |
shell: bash | |
working-directory: ${{ runner.workspace }}/build | |
- name: Fix Mac plugins | |
if: runner.os == 'macOS' | |
working-directory: ${{ runner.workspace }}/build/prefix/lib/openbabel | |
run: | | |
for plugin in *.so; do | |
for libpath in `otool -L ${plugin} | grep '/Users/runner/work' | awk '{print $1}'`; do | |
export lib=`echo $libpath | cut -d '/' -f 9`; | |
echo "Fixing $plugin $lib $libpath" | |
install_name_tool -change $libpath @executable_path/../Frameworks/$lib $plugin | |
done | |
done | |
cd .. # build/prefix/lib | |
for plugin in libinchi.?.?.?.dylib; do | |
for libpath in `otool -L ${plugin} | grep '/Users/runner/work' | awk '{print $1}'`; do | |
export lib=`echo $libpath | cut -d '/' -f 9`; | |
echo "Fixing $plugin $lib $libpath" | |
install_name_tool -change $libpath @executable_path/../Frameworks/$lib $plugin | |
done | |
done | |
otool -L libinchi.?.?.?.dylib | |
cp -p libinchi* ../Avogadro2.app/Contents/Frameworks/ | |
# finally, fixup the binaries | |
cd ../bin | |
for exe in obabel obmm eht_bind genXrdPattern; do | |
for libpath in `otool -L ${exe} | grep '/Users/runner/work' | awk '{print $1}'`; do | |
export lib=`echo $libpath | cut -d '/' -f 9`; | |
echo "Fixing $exe $lib $libpath" | |
install_name_tool -change $libpath @executable_path/../Frameworks/$lib $exe | |
done | |
done | |
- name: Run tests | |
if: matrix.config.os == 'ubuntu-20.04' | |
shell: cmake -P {0} | |
run: | | |
include(ProcessorCount) | |
ProcessorCount(N) | |
set(ENV{CTEST_OUTPUT_ON_FAILURE} "ON") | |
set(ENV{ASAN_OPTIONS} "new_delete_type_mismatch=0") | |
execute_process( | |
COMMAND ctest -j ${N} | |
WORKING_DIRECTORY ${{ runner.workspace }}/build/avogadrolibs | |
RESULT_VARIABLE result | |
) | |
if (NOT result EQUAL 0) | |
message(FATAL_ERROR "Running tests failed!") | |
endif() | |
- name: Install the Apple certificate | |
# From GitHub docs: https://docs.github.com/en/actions/guides/installing-an-apple-certificate-on-macos-runners-for-xcode-development | |
if: runner.os == 'macOS' | |
working-directory: ${{ runner.workspace }}/build | |
env: | |
BUILD_CERTIFICATE_BASE64: ${{ secrets.BUILD_CERTIFICATE_BASE64 }} | |
P12_PASSWORD: ${{ secrets.P12_PASSWORD }} | |
KEYCHAIN_PASSWORD: ${{ secrets.KEYCHAIN_PASSWORD }} | |
NOTARIZE_USERNAME: ${{ secrets.AC_USERNAME }} | |
NOTARIZE_PASSWORD: ${{ secrets.AC_PASSWORD }} | |
CODESIGN_IDENTITY: ${{ secrets.CODESIGN_ID }} | |
PRODUCT_BUNDLE_IDENTIFIER: cc.avogadro | |
run: | | |
# create variables | |
if [ -n "${P12_PASSWORD}" ]; then | |
CERTIFICATE_PATH=$RUNNER_TEMP/build_certificate.p12 | |
KEYCHAIN_PATH=$RUNNER_TEMP/app-signing.keychain-db | |
# import certificate and provisioning profile from secrets | |
echo -n "$BUILD_CERTIFICATE_BASE64" | base64 --decode --output $CERTIFICATE_PATH | |
# create temporary keychain if the cert is non-zero | |
if [ -s $CERTIFICATE_PATH ]; then | |
security create-keychain -p "$KEYCHAIN_PASSWORD" $KEYCHAIN_PATH | |
security set-keychain-settings -lut 21600 $KEYCHAIN_PATH | |
security unlock-keychain -p "$KEYCHAIN_PASSWORD" $KEYCHAIN_PATH | |
# import certificate to keychain | |
security import $CERTIFICATE_PATH -P "$P12_PASSWORD" -A -t cert -f pkcs12 -k $KEYCHAIN_PATH | |
security list-keychain -d user -s $KEYCHAIN_PATH | |
# signing occurs via avogadroapp cpack instructions | |
fi # certificate exists | |
fi # password exists | |
- name: Create Mac and Windows Packages | |
if: matrix.config.os == 'windows-latest' || matrix.config.os == 'macos-latest' | |
shell: bash | |
run: | | |
if [ -z "${P12_PASSWORD}" ]; then | |
unset CODESIGN_IDENTITY # to prevent cpack failing when trying to sign | |
fi | |
[[ ! "${GITHUB_REF}" =~ "tags" ]] && export SNAPSHOT_DATE=`date -j "+%d-%m-%y"` | |
cpack ${{ matrix.config.cpack_flags }} | |
working-directory: ${{ runner.workspace }}/build/avogadroapp | |
env: | |
P12_PASSWORD: ${{ secrets.P12_PASSWORD }} | |
CODESIGN_IDENTITY: ${{ secrets.CODESIGN_ID }} | |
- name: AppImage | |
if: matrix.config.os == 'ubuntu-20.04' && matrix.config.build_type == 'Release' | |
shell: bash | |
run: | | |
mkdir appdir | |
mv prefix appdir/usr | |
wget -c -nv "https://github.com/probonopd/linuxdeployqt/releases/download/continuous/linuxdeployqt-continuous-x86_64.AppImage" | |
wget -c -nv "https://github.com/AppImage/AppImageKit/releases/download/continuous/appimagetool-x86_64.AppImage" | |
chmod a+x *.AppImage | |
./linuxdeployqt-continuous-x86_64.AppImage appdir/usr/share/applications/*.desktop -bundle-non-qt-libs -extra-plugins=iconengines | |
# add the custom AppRun | |
rm appdir/AppRun | |
cp ../avogadrolibs/avogadrolibs/scripts/AppImage.sh appdir/AppRun | |
chmod a+x appdir/AppRun | |
./appimagetool-x86_64.AppImage appdir | |
mv Avogadro2*.AppImage avogadroapp # for upload | |
working-directory: ${{ runner.workspace }}/build | |
- name: Notarize Mac DMG | |
if: runner.os == 'macOS' | |
run: | | |
# check if we have the password and the username | |
if [ -n "${NOTARIZE_PASSWORD}" ] && [ -n "${NOTARIZE_USERNAME}" ]; then | |
codesign -s "$CODESIGN_IDENTITY" --timestamp Avogadro2*.dmg | |
xcrun notarytool submit Avogadro2*.dmg --apple-id "$NOTARIZE_USERNAME" --team-id "$NOTARIZE_TEAM" --password "$NOTARIZE_PASSWORD" --verbose --wait | |
xcrun stapler staple -v Avogadro2*.dmg | |
fi | |
working-directory: ${{ runner.workspace }}/build/avogadroapp | |
env: | |
NOTARIZE_TEAM: ${{ secrets.AC_TEAM }} | |
NOTARIZE_USERNAME: ${{ secrets.AC_USERNAME }} | |
NOTARIZE_PASSWORD: ${{ secrets.AC_PASSWORD }} | |
CODESIGN_IDENTITY: ${{ secrets.CODESIGN_ID }} | |
continue-on-error: true | |
- name: Setup tmate session | |
if: ${{ failure() }} | |
uses: mxschmitt/action-tmate@v3 | |
- name: Upload | |
if: matrix.config.artifact != 0 | |
uses: actions/upload-artifact@v3 | |
with: | |
path: ${{ runner.workspace }}/build/avogadroapp/Avogadro2*.* | |
name: ${{ matrix.config.artifact }} | |
- name: Cleanup | |
if: ${{ always() }} # To ensure this step runs even when earlier steps fail | |
shell: bash | |
run: | | |
ls -la ./ | |
rm -rf ./* || true | |
rm -rf ./.??* || true | |
ls -la ./ | |