Add yml files back in

.github/workflows/build_cmake.yml

@@ -0,0 +1,307 @@
+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
+
+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",
+            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",
+            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: "",
+            build_flags: "-j 2",
+            cpack_flags: "-G NSIS",
+          }
+        - {
+            name: "Ubuntu Address Sanitizer", artifact: "",
+            os: ubuntu-latest,
+            cc: "gcc", cxx: "g++",
+            build_type: "asan",
+            cmake_flags: "-G Ninja -DENABLE_TESTING=ON -DTEST_QTGL=OFF",
+            cpack: "",
+          }
+        - {
+            name: "Ubuntu Leak Sanitizer", artifact: "",
+            os: ubuntu-latest,
+            cc: "gcc", cxx: "g++",
+            build_type: "lsan",
+            cmake_flags: "-G Ninja -DENABLE_TESTING=ON -DTEST_QTGL=OFF",
+            cpack: "",
+          }
+        - {
+            name: "Ubuntu Thread Sanitizer", artifact: "",
+            os: ubuntu-latest,
+            cc: "gcc", cxx: "g++",
+            build_type: "tsan",
+            cmake_flags: "-G Ninja -DENABLE_TESTING=ON -DTEST_QTGL=OFF",
+            cpack: "",
+          }
+        - {
+            name: "Ubuntu Undefined Behavior Sanitizer", artifact: "",
+            os: ubuntu-latest,
+            cc: "gcc", cxx: "g++",
+            build_type: "ubsan",
+            cmake_flags: "-G Ninja -DENABLE_TESTING=ON -DTEST_QTGL=OFF",
+            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
+    - 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@v3
+      with:
+        repository: openchemistry/openchemistry
+        submodules: recursive
+
+    - name: Checkout avogadroapp
+      uses: actions/checkout@v3
+      with:
+        repository: openchemistry/avogadroapp
+        path: avogadroapp
+
+    - name: Checkout avogadrolibs
+      uses: actions/checkout@v3
+      with:
+        path: avogadrolibs
+
+    - name: Install Qt
+      uses: jurplel/install-qt-action@v3
+      with:
+        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@v3
+      if: runner.os != 'Windows'
+      with:
+        path: |
+          ${{ runner.workspace }}/build/thirdparty
+          ${{ runner.workspace }}/build/Downloads
+        key: ${{ matrix.config.name }}-thirdparty
+
+    - name: Configure
+      run: |
+        if [ ! -d "${{ 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 ${{env.FEATURES}} -DCMAKE_BUILD_TYPE=${{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/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/
+
+    - name: Run tests
+      if: matrix.config.os == 'ubuntu-latest'
+      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 $KEYCHAIN_PATH
+
+            # signing occurs via avogadroapp cpack instructions
+          fi # certificate exists
+        fi # password exists
+
+    - name: Pack
+      if: matrix.config.artifact != 0
+      shell: bash
+      run: |
+        if [ -z "${P12_PASSWORD}" ]; then
+          unset CODESIGN_IDENTITY # to prevent cpack failing when trying to sign
+        fi
+        cpack ${{ matrix.config.cpack_flags }}
+      env:
+        P12_PASSWORD: ${{ secrets.P12_PASSWORD }}
+        CODESIGN_IDENTITY: ${{ secrets.CODESIGN_ID }}
+      working-directory: ${{ runner.workspace }}/build/avogadroapp
+
+    - name: AppImage
+      if: matrix.config.os == 'ubuntu-18.04'
+      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
+        # remove the cpack files
+        rm avogadroapp/Avogadro2*Linux.*
+      working-directory: ${{ runner.workspace }}/build
+
+    - name: Notarize Mac DMG
+      if: runner.os == 'macOS'
+      run: |
+        # check current directory (failing signing)
+        echo `pwd`
+        ls -ld
+        # check if we have the password and the username
+        if [ -n "${NOTARIZE_PASSWORD}" ] && [ -n "${NOTARIZE_USERNAME}" ]; then
+          codesign -s "$CODESIGN_IDENTITY" --timestamp Avogadro2*.dmg
+          npx notarize-cli --file Avogadro2*.dmg
+        fi
+      working-directory: ${{ runner.workspace }}/build/avogadroapp
+      env:
+        NOTARIZE_USERNAME: ${{ secrets.AC_USERNAME }}
+        NOTARIZE_PASSWORD: ${{ secrets.AC_PASSWORD }}
+        CODESIGN_IDENTITY: ${{ secrets.CODESIGN_ID }}
+        PRODUCT_BUNDLE_IDENTIFIER: cc.avogadro
+
+    - 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 ./
+