Merge branch 'master' into enh/code_cleanup

Signed-off-by: Nathan Young <[email protected]>

.github/workflows/build_qt6.yml

@@ -7,7 +7,7 @@ name: Qt6 Build Matrix
 on: [push, pull_request, workflow_dispatch]
 
 env:
-  QT_VERSION: 6.5.3
+  QT_VERSION: 6.8.0
   # this is different from MACOSX_DEPLOYMENT_TARGET to prevent build problems
   # we set MACOSX_DEPLOYMENT_TARGET later
   MACOS_TARGET: 10.15
@@ -39,10 +39,10 @@ jobs:
           }
         - {
             name: "macOS Qt6", artifact: "",
-            os: macos-13,
+            os: macos-latest,
             cc: "clang", cxx: "clang++",
             build_type: "Release",
-            cmake_flags: "-G Ninja",
+            cmake_flags: "-G Ninja -DCMAKE_OSX_ARCHITECTURES='arm64;x86_64'",
             cpack_flags: "-G DragNDrop",
           }
         - {
@@ -65,11 +65,7 @@ jobs:
     - 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
+        brew install ninja eigen glew
     - name: Install Dependencies (Windows)
       if: runner.os == 'Windows'
       run: choco install ninja
@@ -92,11 +88,20 @@ jobs:
         path: avogadrolibs
 
     - name: Install Qt
+      if: runner.os != 'Windows'
+      uses: jurplel/install-qt-action@v3
+      with:
+        version: ${{ env.QT_VERSION }}
+        aqtversion: '==3.1.*'
+
+    - name: Install Qt (Windows)
+      if: runner.os == 'Windows'
       uses: jurplel/install-qt-action@v3
       with:
         version: ${{ env.QT_VERSION }}
         aqtversion: '==3.1.*'
-        modules: 'qt5compat'
+        host: windows
+        arch: win64_msvc2022_64
 
     - name: Configure MSVC Command Prompt
       if: runner.os == 'Windows'
@@ -135,7 +140,7 @@ jobs:
         if (NOT result EQUAL 0)
           message(FATAL_ERROR "Running tests failed!")
         endif()
-    
+
     - name: Upload
       if: matrix.config.artifact != 0
       uses: actions/upload-artifact@v4

.github/workflows/flatpak.yml

@@ -0,0 +1,101 @@
+name: Build Flatpak
+
+on: [push, pull_request, workflow_dispatch]
+
+jobs:
+  flatpak:
+    name: "Flatpak"
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Install dependencies
+      run: sudo apt update -qq && sudo apt install -y -qq flatpak flatpak-builder
+
+    - name: Configure flatpak
+      run: flatpak remote-add --if-not-exists --user flathub https://dl.flathub.org/repo/flathub.flatpakrepo
+
+    - name: Configure git
+      run: git config --global protocol.file.allow always
+      # Have to do this because for a while git's handling of submodules was broken
+      # See https://github.com/flatpak/flatpak-builder/issues/495
+
+    - name: Checkout openchemistry
+      uses: actions/checkout@v4
+      with:
+        repository: openchemistry/openchemistry
+        submodules: false
+        path: openchemistry
+
+    - name: Checkout avogadroapp
+      uses: actions/checkout@v4
+      with:
+        repository: openchemistry/avogadroapp
+        path: openchemistry/avogadroapp
+
+    - name: Checkout avogadrolibs
+      uses: actions/checkout@v4
+      with:
+        path: openchemistry/avogadrolibs
+
+    - 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: Checkout Flathub shared-modules
+      uses: actions/checkout@v4
+      with:
+        repository: flathub/shared-modules
+        path: shared-modules
+
+    - name: Set up tmate session
+      if: failure()
+      uses: mxschmitt/action-tmate@v3
+
+    - name: Move manifest
+      run: mv openchemistry/avogadroapp/flatpak/org.openchemistry.Avogadro2.yaml ./
+
+    - name: Build with flatpak-builder
+      run: flatpak-builder --force-clean --user --install-deps-from=flathub --arch=x86_64 --default-branch=test --repo=repo builddir org.openchemistry.Avogadro2.yaml
+
+    - name: Create bundle
+      run: flatpak build-bundle repo Avogadro2.flatpak org.openchemistry.Avogadro2 test
+
+    - name: Upload bundle
+      uses: actions/upload-artifact@v4
+      with:
+        path: Avogadro2.flatpak
+
+    - 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 ./

avogadro/core/layermanager.h

@@ -39,6 +39,8 @@ struct LayerData
 
   virtual ~LayerData() = default;
 
+  virtual LayerData* clone() { return new LayerData(serialize()); };
+
   /** get the saved data */
   std::string getSave() const { return m_save; }
 

avogadro/core/utilities.h

@@ -6,6 +6,7 @@
 #ifndef AVOGADRO_CORE_UTILITIES_H
 #define AVOGADRO_CORE_UTILITIES_H
 
+#include <algorithm>
 #include <sstream>
 #include <string>
 #include <vector>
@@ -39,10 +40,20 @@ inline std::vector<std::string> split(const std::string& string, char delimiter,
  * @param search String that will be searched for.
  * @return True if the string contains search, false otherwise.
  */
-inline bool contains(const std::string& input, const std::string& search)
+inline bool contains(const std::string& input, const std::string& search,
+                     bool caseSensitive = true)
 {
-  size_t found = input.find(search);
-  return found != std::string::npos;
+  if (caseSensitive) {
+    return input.find(search) != std::string::npos;
+  } else {
+    std::string inputLower = input;
+    std::string searchLower = search;
+    std::transform(inputLower.begin(), inputLower.end(), inputLower.begin(),
+                   ::tolower);
+    std::transform(searchLower.begin(), searchLower.end(), searchLower.begin(),
+                   ::tolower);
+    return inputLower.find(searchLower) != std::string::npos;
+  }
 }
 
 /**

avogadro/qtgui/pluginlayermanager.h

@@ -10,6 +10,7 @@
 
 #include <avogadro/core/layermanager.h>
 #include <cassert>
+#include <iostream>
 
 namespace Avogadro {
 namespace QtGui {
@@ -79,22 +80,25 @@ class AVOGADROQTGUI_EXPORT PluginLayerManager : protected Core::LayerManager
   /** @return custom data T derived from LayerData. if @p layer is equal to
    * MaxIndex returns activeLayer */
   template <typename T>
-  T& getSetting(size_t layer = MaxIndex)
+  T* getSetting(size_t layer = MaxIndex)
   {
     auto info = m_molToInfo[m_activeMolecule];
+
     if (layer == MaxIndex) {
       layer = info->layer.activeLayer();
     }
+
     assert(layer <= info->layer.maxLayer());
     if (info->settings.find(m_name) == info->settings.end()) {
       info->settings[m_name] = Core::Array<Core::LayerData*>();
     }
 
+    // do we need to create new layers in the array?
     while (info->settings[m_name].size() < layer + 1) {
       info->settings[m_name].push_back(new T());
     }
-    auto result = static_cast<T*>(info->settings[m_name][layer]);
-    return *result;
+    auto* result = static_cast<T*>(info->settings[m_name][layer]);
+    return result;
   }
 
 private:

avogadro/qtgui/rwlayermanager.cpp

@@ -45,7 +45,6 @@ class AddLayerCommand : public QUndoCommand
       auto value = names.second[activeLayer];
       m_settings[names.first] = value;
     }
-
   }
 
   void redo() override
@@ -59,7 +58,9 @@ class AddLayerCommand : public QUndoCommand
       m_moleculeInfo->enable[enable.first].push_back(enable.second);
     }
     for (const auto& settings : m_settings) {
-      m_moleculeInfo->settings[settings.first].push_back(settings.second);
+      // create newSettings pointer with the same type as settings.second
+      auto* newSettings = settings.second->clone();
+      m_moleculeInfo->settings[settings.first].push_back(newSettings);
     }
 
     m_moleculeInfo->layer.addLayer();
@@ -130,7 +131,8 @@ class RemoveLayerCommand : public QUndoCommand
   RemoveLayerCommand(shared_ptr<MoleculeInfo> mol, size_t layer)
     : QUndoCommand(QObject::tr("Modify Layers")), m_moleculeInfo(mol),
       m_layer(layer)
-  {}
+  {
+  }
 
   void redo() override
   {
@@ -285,4 +287,4 @@ Array<std::pair<size_t, string>> RWLayerManager::activeMoleculeNames() const
   return result;
 }
 
-} // namespace Avogadro
+} // namespace Avogadro::QtGui