Fix residue not initializing id in default constructor #3487
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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" | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: 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-22.04, | |
| cc: "gcc", cxx: "g++", | |
| build_type: "Release", | |
| cmake_flags: "-G Ninja -DBUILD_MOLEQUEUE=OFF -DINSTALL_BUNDLE_FILES=ON -USE_SYSTEM_ZLIB=ON", | |
| cpack: "", | |
| } | |
| - { | |
| name: "macOS Clang", artifact: "macOS.dmg", | |
| os: macos-13, | |
| cc: "clang", cxx: "clang++", | |
| build_type: "Release", | |
| cmake_flags: "-G Ninja -DBUILD_MOLEQUEUE=OFF", | |
| cpack_flags: "-G DragNDrop", | |
| } | |
| - { | |
| name: "Windows Latest MSVC", artifact: "Win64.exe", | |
| os: windows-latest, | |
| cc: "cl", cxx: "cl", | |
| build_type: "Release", | |
| cmake_flags: "-DBUILD_MOLEQUEUE=OFF", | |
| 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 add-apt-repository -y universe | |
| 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 | |
| sudo apt install libfuse2 | |
| - 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 fragments | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: openchemistry/fragments | |
| path: fragments | |
| - name: Checkout crystals | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: openchemistry/crystals | |
| path: crystals | |
| - 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: | |
| aqtversion: '==3.1.*' | |
| cache: true | |
| version: ${{ env.QT_VERSION }} | |
| - 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@v4 | |
| 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 libopenbabel.?.?.?.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 | |
| otool -L libopenbabel.?.?.?.dylib | |
| cp -p libinchi* ../Avogadro2.app/Contents/Frameworks/ | |
| cp -p libopenbabel* ../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: ${{ secrets.CODESIGN_ID }} | |
| PRODUCT_BUNDLE_IDENTIFIER: cc.avogadro | |
| run: | | |
| # be sure the DMG can be created easily | |
| # https://github.com/actions/runner-images/issues/7522#issuecomment-1556766641 | |
| echo killing...; sudo pkill -9 XProtect >/dev/null || true; | |
| echo waiting...; while pgrep XProtect; do sleep 3; done; | |
| # create variables | |
| if [ -n "${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 -d -o $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 $KEYCHAIN_PATH | |
| # signing occurs via avogadroapp cpack instructions | |
| fi # certificate exists | |
| fi # password exists | |
| - name: Create Mac and Windows Packages | |
| if: matrix.config.os == 'windows-latest' || runner.os == 'macOS' | |
| shell: bash | |
| run: | | |
| if [ -z "${P12_PASSWORD}" ]; then | |
| unset CODESIGN_IDENTITY # to prevent cpack failing when trying to sign | |
| fi | |
| if [ -z "${OPENSSL_ROOT_DIR}" ]; then | |
| unset OPENSSL_ROOT_DIR | |
| fi | |
| [[ ! "${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 }} | |
| OPENSSL_ROOT_DIR: ${{ matrix.config.ssl_env }} | |
| - name: AppImage | |
| if: matrix.config.os == 'ubuntu-22.04' && matrix.config.build_type == 'Release' | |
| shell: bash | |
| run: | | |
| mkdir appdir | |
| mv prefix appdir/usr | |
| export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:appdir/usr/lib | |
| wget -c -nv "https://github.com/linuxdeploy/linuxdeploy/releases/download/continuous/linuxdeploy-x86_64.AppImage" | |
| wget -c -nv "https://github.com/linuxdeploy/linuxdeploy-plugin-qt/releases/download/continuous/linuxdeploy-plugin-qt-x86_64.AppImage" | |
| wget -c -nv "https://github.com/AppImage/AppImageKit/releases/download/continuous/appimagetool-x86_64.AppImage" | |
| chmod a+x *.AppImage | |
| ./linuxdeploy-x86_64.AppImage -d appdir/usr/share/applications/*.desktop --plugin qt --appdir appdir | |
| # 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 Avogadro*.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@v4 | |
| with: | |
| path: ${{ runner.workspace }}/build/avogadroapp/Avogadro*.* | |
| 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 ./ |