From c7b9b678c5efd27d3447b5000e4f16090d3c2311 Mon Sep 17 00:00:00 2001
From: "Matthew J. Milner" <matterhorn103@proton.me>
Date: Mon, 16 Dec 2024 03:20:16 +0100
Subject: [PATCH 1/7] Synchronize workflows

Signed-off-by: Matthew J. Milner <matterhorn103@proton.me>
---
 .github/workflows/build_cmake.yml             | 318 ------------------
 .../{flatpak.yml => build_flatpak.yml}        |   2 +-
 .github/workflows/build_linux.yml             | 155 +++++++++
 .github/workflows/build_mac.yml               | 247 ++++++++++++++
 .github/workflows/build_windows.yml           | 190 +++++++++++
 5 files changed, 593 insertions(+), 319 deletions(-)
 delete mode 100644 .github/workflows/build_cmake.yml
 rename .github/workflows/{flatpak.yml => build_flatpak.yml} (99%)
 create mode 100644 .github/workflows/build_linux.yml
 create mode 100644 .github/workflows/build_mac.yml
 create mode 100644 .github/workflows/build_windows.yml

diff --git a/.github/workflows/build_cmake.yml b/.github/workflows/build_cmake.yml
deleted file mode 100644
index 498ad472..00000000
--- a/.github/workflows/build_cmake.yml
+++ /dev/null
@@ -1,318 +0,0 @@
-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]
-
-env:
-  BUILD_TYPE: Release
-  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: -DUSE_VTK=ON -DBUILD_GPL_PLUGINS=ON -DWITH_COORDGEN=OFF
-
-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 -DCMAKE_BUILD_TYPE=Release",
-            cpack: "",
-          }
-        - {
-            name: "Ubuntu AppImage", artifact: "Avogadro2.AppImage",
-            os: ubuntu-20.04,
-            cc: "gcc", cxx: "g++",
-            build_type: "Release",
-            cmake_flags: "-G Ninja -DBUILD_MOLEQUEUE=OFF -DINSTALL_BUNDLE_FILES=ON -DCMAKE_BUILD_TYPE=Release",
-            cpack: "",
-          }
-        - {
-            name: "macOS Latest Clang", artifact: "macOS.dmg",
-            os: macos-latest,
-            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",
-            ssl_env: "D:\\a\\avogadroapp\\Qt\\Tools\\OpenSSLv3\\Win_x64",
-          }
-        - {
-            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",
-            cpack: "",
-          }
-        - {
-            name: "Ubuntu Leak Sanitizer", artifact: "",
-            os: ubuntu-20.04,
-            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-20.04,
-            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-20.04,
-            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: |
-        brew install ninja boost eigen glew open-babel
-    - 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:
-        path: avogadroapp
-
-    - name: Checkout avogadrolibs
-      uses: actions/checkout@v4
-      with:
-        repository: openchemistry/avogadrolibs
-        path: avogadrolibs
-
-    - name: Cache Qt
-      id: cache-qt
-      uses: actions/cache@v4
-      with:
-        path: ../Qt
-        key: ${{ runner.os }}-QtCache
-
-    - name: Install Qt
-      uses: jurplel/install-qt-action@v3
-      with:
-        aqtversion: '==3.1.*'
-        cache: true
-        version: ${{ env.QT_VERSION }}
-
-    - name: Install OpenSSL (Win64)
-      if: runner.os == 'Windows'
-      uses: jurplel/install-qt-action@v3
-      with:
-        aqtversion: '==3.1.*'
-        cache: true
-        host: 'windows'
-        target: 'desktop'
-        tools-only: 'true'
-        tools: 'tools_opensslv3_x64'
-
-    - name: Configure MSVC Command Prompt
-      if: runner.os == 'Windows'
-      uses: ilammy/msvc-dev-cmd@v1
-      with:
-        arch: x64
-
-    - name: Configure
-      run: |
-        if [ ! -d "${{ 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: Setup tmate session
-      if: failure()
-      uses: mxschmitt/action-tmate@v3
-
-    - 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-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 $KEYCHAIN_PATH
-
-            # signing occurs via avogadroapp cpack instructions
-          fi # certificate exists
-        fi # password exists
-
-    - name: Pack
-      if: matrix.config.artifact != 0
-      shell: bash
-      run: |
-        if [ -z "${P12_PASSWORD}" ]; then
-          unset CODESIGN_IDENTITY # to prevent cpack failing when trying to sign
-        fi
-        if [ -z "${OPENSSL_ROOT_DIR}" ]; then
-          unset OPENSSL_ROOT_DIR
-        fi
-        cpack ${{ matrix.config.cpack_flags }}
-      env:
-        P12_PASSWORD: ${{ secrets.P12_PASSWORD }}
-        CODESIGN_IDENTITY: ${{ secrets.CODESIGN_ID }}
-        OPENSSL_ROOT_DIR: ${{ matrix.config.ssl_env }}
-      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: 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 ./
diff --git a/.github/workflows/flatpak.yml b/.github/workflows/build_flatpak.yml
similarity index 99%
rename from .github/workflows/flatpak.yml
rename to .github/workflows/build_flatpak.yml
index bd8cb679..90266880 100644
--- a/.github/workflows/flatpak.yml
+++ b/.github/workflows/build_flatpak.yml
@@ -9,7 +9,7 @@ jobs:
 
     steps:
     - name: Install dependencies
-      run: sudo apt update -qq && sudo apt install -y -qq flatpak flatpak-builder
+      run: sudo apt update -qq && sudo apt install -y -qq flatpak
     
     - name: Configure flatpak
       run: flatpak remote-add --if-not-exists --user flathub https://dl.flathub.org/repo/flathub.flatpakrepo
diff --git a/.github/workflows/build_linux.yml b/.github/workflows/build_linux.yml
new file mode 100644
index 00000000..2d4eb883
--- /dev/null
+++ b/.github/workflows/build_linux.yml
@@ -0,0 +1,155 @@
+name: Linux 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]
+
+env:
+  QT_VERSION: 6.8.1
+  FEATURES: -DUSE_VTK=ON -DBUILD_GPL_PLUGINS=ON -DBUILD_MOLEQUEUE=OFF -DWITH_COORDGEN=OFF -DQT_VERSION=6
+
+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", artifact: "ubuntu-x86_64.tar.gz",
+            os: ubuntu-latest,
+            cc: "gcc", cxx: "g++",
+            build_type: "Release",
+            cmake_flags: "-G Ninja",
+          }
+        - {
+            name: "AppImage", artifact: "Avogadro2.AppImage",
+            os: ubuntu-22.04,
+            cc: "gcc", cxx: "g++",
+            build_type: "Release",
+            cmake_flags: "-G Ninja -DINSTALL_BUNDLE_FILES=ON",
+          }
+        - {
+            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 -USE_SYSTEM_ZLIB=ON",
+          }
+        - {
+            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 -USE_SYSTEM_ZLIB=ON",
+          }
+
+    steps:
+
+    - name: Install Dependencies
+      run: |
+        sudo apt-get -qq update
+        sudo apt-get -qq install ninja-build libeigen3-dev libboost-all-dev libglew-dev libxml2-dev
+
+    - name: Checkout openchemistry
+      uses: actions/checkout@v4
+      with:
+        repository: openchemistry/openchemistry
+        submodules: recursive
+        path: openchemistry
+          
+    - name: Checkout avogadroapp
+      uses: actions/checkout@v4
+      with:
+        path: openchemistry/avogadroapp
+        fetch-depth: 0
+        
+    - name: Checkout avogadrolibs
+      uses: actions/checkout@v4
+      with:
+        repository: openchemistry/avogadroapp
+        path: openchemistry/avogadrolibs
+        fetch-depth: 0
+
+    - name: Checkout i18n
+      uses: actions/checkout@v4
+      with:
+        repository: openchemistry/avogadro-i18n
+        path: openchemistry/avogadro-i18n
+    
+    - name: Checkout avogadrogenerators
+      uses: actions/checkout@v4
+      with:
+        repository: openchemistry/avogenerators
+        path: openchemistry/avogadrogenerators
+
+    - name: Checkout crystals
+      uses: actions/checkout@v4
+      with:
+        repository: openchemistry/crystals
+        path: openchemistry/crystals
+
+    - name: Checkout fragments
+      uses: actions/checkout@v4
+      with:
+        repository: openchemistry/fragments
+        path: openchemistry/fragments
+
+    - name: Checkout molecules
+      uses: actions/checkout@v4
+      with:
+        repository: openchemistry/molecules
+        path: openchemistry/molecules
+
+    - name: Install Qt
+      uses: jurplel/install-qt-action@v4
+      with:
+        version: ${{ env.QT_VERSION }}
+
+    - name: Configure
+      run: |
+        if [ ! -d "${{ runner.workspace }}/build" ]; then mkdir "${{ runner.workspace }}/build"; fi
+        cd "${{ runner.workspace }}/build"
+        # won't have any effect except on Mac
+        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: 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: Upload
+      if: matrix.config.artifact != 0
+      uses: actions/upload-artifact@v4
+      with:
+        path: ${{ runner.workspace }}/build/avogadroapp/Avogadro2*.*
+        name: ${{ matrix.config.artifact }}
+
+    - name: Setup tmate session
+      if: ${{ failure() }}
+      uses: mxschmitt/action-tmate@v3
diff --git a/.github/workflows/build_mac.yml b/.github/workflows/build_mac.yml
new file mode 100644
index 00000000..48d6bacf
--- /dev/null
+++ b/.github/workflows/build_mac.yml
@@ -0,0 +1,247 @@
+name: macOS Build Matrix
+
+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: 12
+  QT_VERSION: 5.15.2
+  FEATURES: -DUSE_VTK=ON -DBUILD_GPL_PLUGINS=ON -DBUILD_MOLEQUEUE=OFF -DWITH_COORDGEN=OFF
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build:
+    name: ${{ matrix.config.name }}
+    runs-on: ${{ matrix.config.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+        - {
+            name: "macOS Intel", artifact: "macOS-x86_64.dmg",
+            os: macos-latest,
+            cc: "clang", cxx: "clang++",
+            build_type: "Release",
+            cmake_flags: "-G Ninja -DCMAKE_OSX_ARCHITECTURES='x86_64'",
+            cpack_flags: "-G DragNDrop",
+          }
+        - {
+            name: "macOS Apple Silicon", artifact: "macOS-arm64.dmg",
+            os: [self-hosted, macOS],
+            cc: "clang", cxx: "clang++",
+            build_type: "Release",
+            cmake_flags: "-G Ninja -DCMAKE_PREFIX_PATH=/opt/homebrew/Cellar/qt@5/5.15.5_1/lib/cmake/Qt5",
+            cpack_flags: "-G DragNDrop",
+          }
+        - {
+            name: "macOS Qt6", artifact: "",
+            os: macos-latest,
+            cc: "clang", cxx: "clang++",
+            build_type: "Release",
+            cmake_flags: "-G Ninja -DCMAKE_OSX_ARCHITECTURES='arm64;x86_64'",
+            cpack_flags: "-G DragNDrop",
+            env: {
+              QT_VERSION: 6.8.1,
+            }
+          }
+
+    steps:
+
+    - name: Install Dependencies (macOS)
+      if: runner.os == 'macOS'
+      run: |
+        if uname -p | grep -q "arm" ; then
+           export PATH=/opt/homebrew/bin:$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
+        path: openchemistry
+      
+    - name: Checkout avogadroapp
+      uses: actions/checkout@v4
+      with:
+        repository: openchemistry/avogadroapp
+        path: openchemistry/avogadroapp
+        fetch-depth: 0
+        
+    - name: Checkout avogadrolibs
+      uses: actions/checkout@v4
+      with:
+        path: openchemistry/avogadrolibs
+        fetch-depth: 0
+
+    - name: Checkout i18n
+      uses: actions/checkout@v4
+      with:
+        repository: openchemistry/avogadro-i18n
+        path: openchemistry/avogadro-i18n
+    
+    - name: Checkout avogadrogenerators
+      uses: actions/checkout@v4
+      with:
+        repository: openchemistry/avogenerators
+        path: openchemistry/avogadrogenerators
+
+    - name: Checkout crystals
+      uses: actions/checkout@v4
+      with:
+        repository: openchemistry/crystals
+        path: openchemistry/crystals
+
+    - name: Checkout fragments
+      uses: actions/checkout@v4
+      with:
+        repository: openchemistry/fragments
+        path: openchemistry/fragments
+
+    - name: Checkout molecules
+      uses: actions/checkout@v4
+      with:
+        repository: openchemistry/molecules
+        path: openchemistry/molecules
+    
+    - name: Install Qt
+      # Only if not self-hosted
+      if: runner.name != 'macOS Apple Silicon'
+      uses: jurplel/install-qt-action@v4
+      with:
+        version: ${{ env.QT_VERSION }}
+
+    - name: Configure
+      run: |
+        if [ ! -d "${{ 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 ./
diff --git a/.github/workflows/build_windows.yml b/.github/workflows/build_windows.yml
new file mode 100644
index 00000000..6cd0dc85
--- /dev/null
+++ b/.github/workflows/build_windows.yml
@@ -0,0 +1,190 @@
+name: Windows 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/
+
+# This workflow will build and sign on Windows
+# .. since SignPath requires only a Windows build in the action
+# .. to successfully sign
+
+on: [push, pull_request, workflow_dispatch]
+
+env:
+  QT_VERSION: 5.15.2
+  FEATURES: -DUSE_VTK=ON -DBUILD_GPL_PLUGINS=ON -DBUILD_MOLEQUEUE=OFF -DWITH_COORDGEN=OFF
+
+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: "Windows", artifact: "windows-x86_64.exe",
+            os: windows-latest,
+            cc: "cl", cxx: "cl",
+            build_type: "Release",
+            cmake_flags: "",
+            build_flags: "",
+            cpack_flags: "-G NSIS",
+          }
+        - {
+            name: "Windows Qt6", artifact: "",
+            os: windows-latest,
+            cc: "cl", cxx: "cl",
+            build_type: "Release",
+            cmake_flags: "",
+            build_flags: "",
+            cpack_flags: "-G NSIS",
+            env: {
+              QT_VERSION: 6.8.1,
+            }
+          }
+
+    steps:
+
+    - 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
+        path: openchemistry
+          
+    - name: Checkout avogadroapp
+      uses: actions/checkout@v4
+      with:
+        repository: openchemistry/avogadroapp
+        path: openchemistry/avogadroapp
+        fetch-depth: 0
+        
+    - name: Checkout avogadrolibs
+      uses: actions/checkout@v4
+      with:
+        path: openchemistry/avogadrolibs
+        fetch-depth: 0
+
+    - name: Checkout i18n
+      uses: actions/checkout@v4
+      with:
+        repository: openchemistry/avogadro-i18n
+        path: openchemistry/avogadro-i18n
+    
+    - name: Checkout avogadrogenerators
+      uses: actions/checkout@v4
+      with:
+        repository: openchemistry/avogenerators
+        path: openchemistry/avogadrogenerators
+
+    - name: Checkout crystals
+      uses: actions/checkout@v4
+      with:
+        repository: openchemistry/crystals
+        path: openchemistry/crystals
+
+    - name: Checkout fragments
+      uses: actions/checkout@v4
+      with:
+        repository: openchemistry/fragments
+        path: openchemistry/fragments
+
+    - name: Checkout molecules
+      uses: actions/checkout@v4
+      with:
+        repository: openchemistry/molecules
+        path: openchemistry/molecules
+
+    - name: Install Qt
+      uses: jurplel/install-qt-action@v4
+      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: ${{ matrix.config.name }}-downloads
+
+    - name: Configure
+      run: |
+        if [ ! -d "${{ runner.workspace }}/build" ]; then mkdir "${{ runner.workspace }}/build"; fi
+        cd "${{ runner.workspace }}/build"
+        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: ${{ runner.workspace }}/build
+
+    - name: Create Windows Package
+      if: matrix.config.os == 'windows-latest'
+      shell: bash
+      run: |
+        [[ ! "${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:
+        OPENSSL_ROOT_DIR: ${{ matrix.config.ssl_env }}
+
+    - name: Upload
+      if: matrix.config.artifact != 0
+      id: upload-artifact
+      uses: actions/upload-artifact@v4
+      with:
+        path: ${{ runner.workspace }}/build/avogadroapp/Avogadro*.*
+        name: ${{ matrix.config.artifact }}
+
+    - name: Sign Windows release
+      if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags/')
+      uses: signpath/github-action-submit-signing-request@v1
+      with:
+        api-token: '${{ secrets.SIGNPATH_API_TOKEN }}'
+        organization-id: '${{ secrets.SIGNPATH_ORG_ID }}'
+        project-slug: 'avogadrolibs'
+        signing-policy-slug: 'release-signing'
+        github-artifact-id: '${{ steps.upload-artifact.outputs.artifact-id }}'
+        wait-for-completion: true
+        output-artifact-directory: '../build/'
+
+    - name: Upload
+      if: matrix.config.artifact != 0
+      id: upload-signed-artifact
+      uses: actions/upload-artifact@v4
+      with:
+        path: ${{ runner.workspace }}/build/Avogadro2*.*
+        name: 'Win64-signed.exe'
+
+    - 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 ./

From 7badb078515a22a792845ece16f34d7294618c1f Mon Sep 17 00:00:00 2001
From: "Matthew J. Milner" <matterhorn103@proton.me>
Date: Mon, 16 Dec 2024 03:32:28 +0100
Subject: [PATCH 2/7] Fix macOS checkouts, add cleanup step to Linux

Signed-off-by: Matthew J. Milner <matterhorn103@proton.me>
---
 .github/workflows/build_linux.yml | 9 +++++++++
 .github/workflows/build_mac.yml   | 2 +-
 2 files changed, 10 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/build_linux.yml b/.github/workflows/build_linux.yml
index 2d4eb883..f0da7434 100644
--- a/.github/workflows/build_linux.yml
+++ b/.github/workflows/build_linux.yml
@@ -153,3 +153,12 @@ jobs:
     - 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 ./
diff --git a/.github/workflows/build_mac.yml b/.github/workflows/build_mac.yml
index 48d6bacf..a2efc0a0 100644
--- a/.github/workflows/build_mac.yml
+++ b/.github/workflows/build_mac.yml
@@ -70,13 +70,13 @@ jobs:
     - name: Checkout avogadroapp
       uses: actions/checkout@v4
       with:
-        repository: openchemistry/avogadroapp
         path: openchemistry/avogadroapp
         fetch-depth: 0
         
     - name: Checkout avogadrolibs
       uses: actions/checkout@v4
       with:
+        repository: openchemistry/avogadrolibs
         path: openchemistry/avogadrolibs
         fetch-depth: 0
 

From c745425f82dc5701b0321bcc57b45c0b41df93eb Mon Sep 17 00:00:00 2001
From: "Matthew J. Milner" <matterhorn103@proton.me>
Date: Mon, 16 Dec 2024 03:37:53 +0100
Subject: [PATCH 3/7] Remove fetch depth limits

Signed-off-by: Matthew J. Milner <matterhorn103@proton.me>
---
 .github/workflows/build_linux.yml   | 2 --
 .github/workflows/build_mac.yml     | 2 --
 .github/workflows/build_windows.yml | 2 --
 3 files changed, 6 deletions(-)

diff --git a/.github/workflows/build_linux.yml b/.github/workflows/build_linux.yml
index f0da7434..7524297a 100644
--- a/.github/workflows/build_linux.yml
+++ b/.github/workflows/build_linux.yml
@@ -68,14 +68,12 @@ jobs:
       uses: actions/checkout@v4
       with:
         path: openchemistry/avogadroapp
-        fetch-depth: 0
         
     - name: Checkout avogadrolibs
       uses: actions/checkout@v4
       with:
         repository: openchemistry/avogadroapp
         path: openchemistry/avogadrolibs
-        fetch-depth: 0
 
     - name: Checkout i18n
       uses: actions/checkout@v4
diff --git a/.github/workflows/build_mac.yml b/.github/workflows/build_mac.yml
index a2efc0a0..c80b7144 100644
--- a/.github/workflows/build_mac.yml
+++ b/.github/workflows/build_mac.yml
@@ -71,14 +71,12 @@ jobs:
       uses: actions/checkout@v4
       with:
         path: openchemistry/avogadroapp
-        fetch-depth: 0
         
     - name: Checkout avogadrolibs
       uses: actions/checkout@v4
       with:
         repository: openchemistry/avogadrolibs
         path: openchemistry/avogadrolibs
-        fetch-depth: 0
 
     - name: Checkout i18n
       uses: actions/checkout@v4
diff --git a/.github/workflows/build_windows.yml b/.github/workflows/build_windows.yml
index 6cd0dc85..31e26656 100644
--- a/.github/workflows/build_windows.yml
+++ b/.github/workflows/build_windows.yml
@@ -65,13 +65,11 @@ jobs:
       with:
         repository: openchemistry/avogadroapp
         path: openchemistry/avogadroapp
-        fetch-depth: 0
         
     - name: Checkout avogadrolibs
       uses: actions/checkout@v4
       with:
         path: openchemistry/avogadrolibs
-        fetch-depth: 0
 
     - name: Checkout i18n
       uses: actions/checkout@v4

From 73baf50132bb49c735a46342ab954841d4670134 Mon Sep 17 00:00:00 2001
From: "Matthew J. Milner" <matterhorn103@proton.me>
Date: Mon, 16 Dec 2024 03:52:28 +0100
Subject: [PATCH 4/7] Use correct path for configure step

Signed-off-by: Matthew J. Milner <matterhorn103@proton.me>
---
 .github/workflows/build_linux.yml   | 2 +-
 .github/workflows/build_mac.yml     | 2 +-
 .github/workflows/build_windows.yml | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/build_linux.yml b/.github/workflows/build_linux.yml
index 7524297a..c3cc6d9c 100644
--- a/.github/workflows/build_linux.yml
+++ b/.github/workflows/build_linux.yml
@@ -115,7 +115,7 @@ jobs:
         if [ ! -d "${{ runner.workspace }}/build" ]; then mkdir "${{ runner.workspace }}/build"; fi
         cd "${{ runner.workspace }}/build"
         # won't have any effect except on Mac
-        CC=${{matrix.config.cc}} CXX=${{matrix.config.cxx}} cmake $GITHUB_WORKSPACE ${{env.FEATURES}} -DCMAKE_BUILD_TYPE=${{matrix.config.build_type}} ${{matrix.config.cmake_flags}}
+        CC=${{matrix.config.cc}} CXX=${{matrix.config.cxx}} cmake "${{ runner.workspace }}/openchemistry" ${{env.FEATURES}} -DCMAKE_BUILD_TYPE=${{matrix.config.build_type}} ${{matrix.config.cmake_flags}}
       shell: bash
 
     - name: Build
diff --git a/.github/workflows/build_mac.yml b/.github/workflows/build_mac.yml
index c80b7144..75ec1835 100644
--- a/.github/workflows/build_mac.yml
+++ b/.github/workflows/build_mac.yml
@@ -120,7 +120,7 @@ jobs:
         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}} ${{matrix.config.cmake_flags}}
+        CC=${{matrix.config.cc}} CXX=${{matrix.config.cxx}} cmake "${{ runner.workspace }}/openchemistry" ${{env.FEATURES}} -DCMAKE_BUILD_TYPE=${{matrix.config.build_type}} ${{matrix.config.cmake_flags}}
       shell: bash
 
     - name: Build
diff --git a/.github/workflows/build_windows.yml b/.github/workflows/build_windows.yml
index 31e26656..4cf7370a 100644
--- a/.github/workflows/build_windows.yml
+++ b/.github/workflows/build_windows.yml
@@ -126,7 +126,7 @@ jobs:
       run: |
         if [ ! -d "${{ runner.workspace }}/build" ]; then mkdir "${{ runner.workspace }}/build"; fi
         cd "${{ runner.workspace }}/build"
-        CC=${{matrix.config.cc}} CXX=${{matrix.config.cxx}} cmake $GITHUB_WORKSPACE ${{env.FEATURES}} -DCMAKE_BUILD_TYPE=${{matrix.config.build_type}} ${{matrix.config.cmake_flags}}
+        CC=${{matrix.config.cc}} CXX=${{matrix.config.cxx}} cmake "${{ runner.workspace }}/openchemistry" ${{env.FEATURES}} -DCMAKE_BUILD_TYPE=${{matrix.config.build_type}} ${{matrix.config.cmake_flags}}
       shell: bash
 
     - name: Build

From a901f8764901b38bb2d7a6ef7f3fdae995499e44 Mon Sep 17 00:00:00 2001
From: "Matthew J. Milner" <matterhorn103@proton.me>
Date: Mon, 16 Dec 2024 04:12:02 +0100
Subject: [PATCH 5/7] Try another path

Signed-off-by: Matthew J. Milner <matterhorn103@proton.me>
---
 .github/workflows/build_linux.yml   | 2 +-
 .github/workflows/build_mac.yml     | 2 +-
 .github/workflows/build_windows.yml | 2 +-
 3 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/build_linux.yml b/.github/workflows/build_linux.yml
index c3cc6d9c..35486a34 100644
--- a/.github/workflows/build_linux.yml
+++ b/.github/workflows/build_linux.yml
@@ -115,7 +115,7 @@ jobs:
         if [ ! -d "${{ runner.workspace }}/build" ]; then mkdir "${{ runner.workspace }}/build"; fi
         cd "${{ runner.workspace }}/build"
         # won't have any effect except on Mac
-        CC=${{matrix.config.cc}} CXX=${{matrix.config.cxx}} cmake "${{ runner.workspace }}/openchemistry" ${{env.FEATURES}} -DCMAKE_BUILD_TYPE=${{matrix.config.build_type}} ${{matrix.config.cmake_flags}}
+        CC=${{matrix.config.cc}} CXX=${{matrix.config.cxx}} cmake $GITHUB_WORKSPACE/openchemistry ${{env.FEATURES}} -DCMAKE_BUILD_TYPE=${{matrix.config.build_type}} ${{matrix.config.cmake_flags}}
       shell: bash
 
     - name: Build
diff --git a/.github/workflows/build_mac.yml b/.github/workflows/build_mac.yml
index 75ec1835..307475f5 100644
--- a/.github/workflows/build_mac.yml
+++ b/.github/workflows/build_mac.yml
@@ -120,7 +120,7 @@ jobs:
         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=${{matrix.config.cxx}} cmake "${{ runner.workspace }}/openchemistry" ${{env.FEATURES}} -DCMAKE_BUILD_TYPE=${{matrix.config.build_type}} ${{matrix.config.cmake_flags}}
+        CC=${{matrix.config.cc}} CXX=${{matrix.config.cxx}} cmake $GITHUB_WORKSPACE/openchemistry ${{env.FEATURES}} -DCMAKE_BUILD_TYPE=${{matrix.config.build_type}} ${{matrix.config.cmake_flags}}
       shell: bash
 
     - name: Build
diff --git a/.github/workflows/build_windows.yml b/.github/workflows/build_windows.yml
index 4cf7370a..cf5cb151 100644
--- a/.github/workflows/build_windows.yml
+++ b/.github/workflows/build_windows.yml
@@ -126,7 +126,7 @@ jobs:
       run: |
         if [ ! -d "${{ runner.workspace }}/build" ]; then mkdir "${{ runner.workspace }}/build"; fi
         cd "${{ runner.workspace }}/build"
-        CC=${{matrix.config.cc}} CXX=${{matrix.config.cxx}} cmake "${{ runner.workspace }}/openchemistry" ${{env.FEATURES}} -DCMAKE_BUILD_TYPE=${{matrix.config.build_type}} ${{matrix.config.cmake_flags}}
+        CC=${{matrix.config.cc}} CXX=${{matrix.config.cxx}} cmake $GITHUB_WORKSPACE/openchemistry ${{env.FEATURES}} -DCMAKE_BUILD_TYPE=${{matrix.config.build_type}} ${{matrix.config.cmake_flags}}
       shell: bash
 
     - name: Build

From 53c78fdb290415ac73f4f20c83cdf2b2ad881c33 Mon Sep 17 00:00:00 2001
From: "Matthew J. Milner" <matterhorn103@proton.me>
Date: Mon, 16 Dec 2024 14:41:20 +0100
Subject: [PATCH 6/7] Fix conditionals in mac workflow

Signed-off-by: Matthew J. Milner <matterhorn103@proton.me>
---
 .github/workflows/build_mac.yml | 20 ++++++++------------
 1 file changed, 8 insertions(+), 12 deletions(-)

diff --git a/.github/workflows/build_mac.yml b/.github/workflows/build_mac.yml
index 307475f5..fe6effb2 100644
--- a/.github/workflows/build_mac.yml
+++ b/.github/workflows/build_mac.yml
@@ -51,14 +51,13 @@ jobs:
 
     steps:
 
-    - name: Install Dependencies (macOS)
-      if: runner.os == 'macOS'
-      run: |
-        if uname -p | grep -q "arm" ; then
-           export PATH=/opt/homebrew/bin:$PATH
-        else # not self-hosted runner
-          brew install ninja eigen glew
-        fi
+    - name: Install Dependencies
+      if: matrix.config.name != 'macOS Apple Silicon'
+      run: brew install ninja eigen glew
+    
+    - name: Set PATH (self-hosted)
+      if: matrix.config.name == 'macOS Apple Silicon'
+      run: export PATH=/opt/homebrew/bin:$PATH
 
     - name: Checkout openchemistry
       uses: actions/checkout@v4
@@ -110,7 +109,7 @@ jobs:
     
     - name: Install Qt
       # Only if not self-hosted
-      if: runner.name != 'macOS Apple Silicon'
+      if: matrix.config.name != 'macOS Apple Silicon'
       uses: jurplel/install-qt-action@v4
       with:
         version: ${{ env.QT_VERSION }}
@@ -130,7 +129,6 @@ jobs:
       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
@@ -163,7 +161,6 @@ jobs:
 
     - 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 }}
@@ -212,7 +209,6 @@ jobs:
         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

From 1fa2c124f1ad93414352622339703cdb4ce57dc6 Mon Sep 17 00:00:00 2001
From: "Matthew J. Milner" <matterhorn103@proton.me>
Date: Mon, 16 Dec 2024 14:57:34 +0100
Subject: [PATCH 7/7] Switch to GitHub Apple Silicon runner

Signed-off-by: Matthew J. Milner <matterhorn103@proton.me>
---
 .github/workflows/build_mac.yml | 13 +++----------
 1 file changed, 3 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/build_mac.yml b/.github/workflows/build_mac.yml
index fe6effb2..4faa2008 100644
--- a/.github/workflows/build_mac.yml
+++ b/.github/workflows/build_mac.yml
@@ -23,7 +23,7 @@ jobs:
         config:
         - {
             name: "macOS Intel", artifact: "macOS-x86_64.dmg",
-            os: macos-latest,
+            os: macos-13,
             cc: "clang", cxx: "clang++",
             build_type: "Release",
             cmake_flags: "-G Ninja -DCMAKE_OSX_ARCHITECTURES='x86_64'",
@@ -31,10 +31,10 @@ jobs:
           }
         - {
             name: "macOS Apple Silicon", artifact: "macOS-arm64.dmg",
-            os: [self-hosted, macOS],
+            os: macos-latest,
             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",
+            cmake_flags: "-G Ninja -DCMAKE_OSX_ARCHITECTURES='arm64'",
             cpack_flags: "-G DragNDrop",
           }
         - {
@@ -52,12 +52,7 @@ jobs:
     steps:
 
     - name: Install Dependencies
-      if: matrix.config.name != 'macOS Apple Silicon'
       run: brew install ninja eigen glew
-    
-    - name: Set PATH (self-hosted)
-      if: matrix.config.name == 'macOS Apple Silicon'
-      run: export PATH=/opt/homebrew/bin:$PATH
 
     - name: Checkout openchemistry
       uses: actions/checkout@v4
@@ -108,8 +103,6 @@ jobs:
         path: openchemistry/molecules
     
     - name: Install Qt
-      # Only if not self-hosted
-      if: matrix.config.name != 'macOS Apple Silicon'
       uses: jurplel/install-qt-action@v4
       with:
         version: ${{ env.QT_VERSION }}