Fix crash when creating ligands from the clipboard -- off-by-one bug #2159
Workflow file for this run
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| name: CMake Self-Hosted | |
| on: [push, pull_request, workflow_dispatch] | |
| env: | |
| # this is different from MACOSX_DEPLOYMENT_TARGET to prevent build problems | |
| # we set MACOSX_DEPLOYMENT_TARGET later | |
| MACOS_TARGET: 10.12 | |
| FEATURES: -DUSE_VTK=ON -DBUILD_GPL_PLUGINS=ON -DBUILD_MOLEQUEUE=OFF -DWITH_COORDGEN=OFF -DUSE_3DCONNEXION=ON | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| build: | |
| name: ${{ matrix.config.name }} | |
| runs-on: ${{ matrix.config.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| - { | |
| name: "macOS ARM", artifact: "macOS-arm64.dmg", | |
| os: [self-hosted, macOS], | |
| cc: "clang", cxx: "clang++", | |
| build_type: "Release", | |
| cmake_flags: "-G Ninja -DCMAKE_PREFIX_PATH=/opt/homebrew/Cellar/qt@5/5.15.5_1/lib/cmake/Qt5", | |
| cpack_flags: "-G DragNDrop", | |
| } | |
| steps: | |
| - name: Install Dependencies (macOS) | |
| if: runner.os == 'macOS' | |
| run: | | |
| if uname -p | grep -q "arm" ; then | |
| export PATH=/opt/homebrew/bin:$PATH | |
| else # not self-hosted runner | |
| brew install ninja eigen glew | |
| fi | |
| - name: 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 avogadrolibs | |
| uses: actions/checkout@v4 | |
| with: | |
| path: avogadrolibs | |
| - name: Checkout i18n | |
| uses: actions/checkout@v4 | |
| with: | |
| repository: openchemistry/avogadro-i18n | |
| path: avogadro-i18n | |
| - name: Configure | |
| run: | | |
| if [ ! -d "${{ runner.workspace }}/build" ]; then mkdir "${{ runner.workspace }}/build"; fi | |
| cd "${{ runner.workspace }}/build" | |
| echo "MACOSX_DEPLOYMENT_TARGET=${{ env.MACOS_TARGET }}" >> $GITHUB_ENV | |
| CC=${{matrix.config.cc}} CXX=${{matrix.config.cxx}} cmake $GITHUB_WORKSPACE ${{env.FEATURES}} -DCMAKE_BUILD_TYPE=${{matrix.config.build_type}} ${{matrix.config.cmake_flags}} | |
| shell: bash | |
| - name: Build | |
| run: | | |
| CC=${{matrix.config.cc}} CXX=${{matrix.config.cxx}} cmake --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' | awk '{print $1}'`; do | |
| export lib=`echo $libpath | cut -d '/' -f 10`; | |
| 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' | awk '{print $1}'`; do | |
| export lib=`echo $libpath | cut -d '/' -f 10`; | |
| 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' | awk '{print $1}'`; do | |
| # export lib=`echo $libpath | cut -d '/' -f 10`; | |
| # echo "Fixing $exe $lib $libpath" | |
| # install_name_tool -change $libpath @executable_path/../Frameworks/$lib $exe | |
| # done | |
| #done | |
| - 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 -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 $KEYCHAIN_PATH | |
| # signing occurs via avogadroapp cpack instructions | |
| fi # certificate exists | |
| fi # password exists | |
| # remove any previous DMG in case they're still around | |
| rm -f avogadroapp/*.dmg | |
| - name: Create Mac and Windows Packages | |
| shell: bash | |
| run: | | |
| if [ -z "${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: ${{ secrets.CODESIGN_ID }} | |
| - name: Notarize Mac DMG | |
| if: runner.os == 'macOS' | |
| run: | | |
| # check if we have the password and the username | |
| if [ -n "${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 | |
| uses: actions/upload-artifact@v4 | |
| 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 ./ |