Read MBIS charges from ORCA output #3580
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" | |
| 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: "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 | |
| continue-on-error: true | |
| 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: Upload | |
| if: matrix.config.artifact != 0 | |
| id: upload-artifact | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| path: ${{ runner.workspace }}/build/avogadroapp/Avogadro*.* | |
| name: ${{ matrix.config.artifact }} | |
| - name: Sign Windows artifact | |
| if: matrix.config.os == 'windows-latest' && github.ref == 'refs/heads/master' | |
| uses: signpath/github-action-submit-signing-request@v1 | |
| with: | |
| api-token: '${{ secrets.SIGNPATH_API_TOKEN }}' | |
| organization-id: '${{ secrets.SIGNPATH_ORG_ID }}' | |
| project-slug: 'avogadrolibs' | |
| signing-policy-slug: 'test-signing' | |
| github-artifact-id: '${{ steps.upload-artifact.outputs.artifact-id }}' | |
| wait-for-completion: true | |
| output-artifact-directory: '${{ runner.workspace }}/build/avogadroapp' | |
| - name: Notarize Mac DMG | |
| if: matrix.config.os == 'windows-latest' && github.ref == 'refs/heads/master' | |
| run: | | |
| ls -la ./ | |
| working-directory: ${{ runner.workspace }}/build/avogadroapp | |
| - name: Setup tmate session | |
| if: failure() | |
| uses: mxschmitt/action-tmate@v3 | |
| - 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 ./ |