Merge branch 'master' of github.com:openchemistry/avogadrolibs into a…

…dd-bond-labels

Signed-off-by: Geoff Hutchison <[email protected]>

.github/workflows/build_cmake.yml

@@ -83,7 +83,7 @@ jobs:
       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 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
     - name: Install Dependencies (macOS)
@@ -178,34 +178,36 @@ jobs:
 
     - name: Fix Mac plugins
       if: runner.os == 'macOS'
-      working-directory: ${{ runner.workspace }}/build/prefix/lib/openbabel 
+      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 
+          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 
+        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
+        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'
@@ -314,7 +316,7 @@ jobs:
 
     - name: Upload
       if: matrix.config.artifact != 0
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       with:
         path: ${{ runner.workspace }}/build/avogadroapp/Avogadro2*.*
         name: ${{ matrix.config.artifact }}
@@ -327,4 +329,3 @@ jobs:
         rm -rf ./* || true
         rm -rf ./.??* || true
         ls -la ./
- 

.github/workflows/build_m1.yml

@@ -184,7 +184,7 @@ jobs:
 
     - name: Upload
       if: matrix.config.artifact != 0
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       with:
         path: ${{ runner.workspace }}/build/avogadroapp/Avogadro2*.*
         name: ${{ matrix.config.artifact }}

.github/workflows/build_wheels.yml

@@ -16,7 +16,7 @@ env:
   CIBW_BEFORE_ALL_LINUX: yum install -y git eigen3-devel
 
   # Specify eigen location for windows
-  CIBW_ENVIRONMENT_WINDOWS: "EXTRA_CMAKE_ARGS=-DEigen3_INCLUDE_DIR:PATH=/c/eigen"
+  CIBW_ENVIRONMENT_WINDOWS: "EXTRA_CMAKE_ARGS=-DEIGEN3_INCLUDE_DIR:PATH=/c/eigen"
 
   # On Mac build both x64 and arm64
   CIBW_ARCHS_MACOS: "x86_64 arm64"
@@ -52,22 +52,24 @@ jobs:
           # give it a correct version even on non-tag push.
           fetch-depth: 0
 
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         name: Install Python
         with:
-          python-version: '3.7'
+          python-version: '3.8'
+          cache: 'pip' # caching pip dependencies
 
       - name: Install cibuildwheel
-        run: pip install cibuildwheel==2.12.3
+        run: pip install cibuildwheel==2.16.2
 
       - name: Install dependencies
         run: . ./scripts/github-actions/install.sh
 
       - name: Build wheels
         run:  cibuildwheel --output-dir wheelhouse
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
+          name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
           path: ./wheelhouse/*.whl
 
   upload_pypi:
@@ -77,7 +79,7 @@ jobs:
     # upload to PyPI on every tag push
     if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags/')
     steps:
-      - uses: actions/download-artifact@v3
+      - uses: actions/download-artifact@v4
         with:
           name: artifact
           path: dist

.github/workflows/clang-format-check.yml

@@ -33,7 +33,7 @@ jobs:
 
     - name: Upload patch
       if: failure()
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       with:
         path: ${{ runner.workspace }}/clang-format.diff
         name: clang-format.diff

.github/workflows/clang-tidy.yml

@@ -103,7 +103,7 @@ jobs:
         echo ${{ github.event.pull_request.head.repo.full_name }} > ${{ runner.workspace }}/clang-tidy-result/pr-head-repo.txt
         echo ${{ github.event.pull_request.head.ref }} > ${{ runner.workspace }}/clang-tidy-result/pr-head-ref.txt
 
-    - uses: actions/upload-artifact@v3
+    - uses: actions/upload-artifact@v4
       with:
         name: clang-tidy-result
         path: ${{ runner.workspace }}/clang-tidy-result/

.github/workflows/codacy.yml

@@ -64,6 +64,6 @@ jobs:
 
       # Upload the SARIF file generated in the previous step
       - name: Upload SARIF results file
-        uses: github/codeql-action/upload-sarif@v2
+        uses: github/codeql-action/upload-sarif@v3
         with:
           sarif_file: filtered.sarif

.github/workflows/codeql.yml

@@ -92,7 +92,7 @@ jobs:
 
     # Initializes the CodeQL tools for scanning.
     - name: Initialize CodeQL
-      uses: github/codeql-action/init@v2
+      uses: github/codeql-action/init@v3
       with:
         languages: ${{ matrix.language }}
         source-root: ${{ github.workspace }}/avogadrolibs
@@ -105,7 +105,7 @@ jobs:
       shell: bash
 
     - name: Perform CodeQL Analysis
-      uses: github/codeql-action/analyze@v2
+      uses: github/codeql-action/analyze@v3
       with:
         category: "/language:${{matrix.language}}"
         checkout_path: ${{ github.workspace }}/avogadrolibs

avogadro/core/CMakeLists.txt

@@ -26,7 +26,7 @@ target_sources(Headers PUBLIC
     utilities.h
     vector.h
 )
-target_link_libraries(Headers INTERFACE Eigen3::Eigen3)
+target_link_libraries(Headers INTERFACE Eigen3::Eigen)
 install(TARGETS Headers
   EXPORT "AvogadroLibsTargets"
   FILE_SET HEADERS DESTINATION "${INSTALL_INCLUDE_DIR}")

avogadro/core/molecule.cpp

@@ -36,11 +36,11 @@ Molecule::Molecule()
 
 Molecule::Molecule(const Molecule& other)
   : m_data(other.m_data), m_partialCharges(other.m_partialCharges),
-    m_customElementMap(other.m_customElementMap), m_elements(other.m_elements),
-    m_positions2d(other.m_positions2d), m_positions3d(other.m_positions3d),
-    m_atomLabels(other.m_atomLabels), m_bondLabels(other.m_bondLabels),
-    m_coordinates3d(other.m_coordinates3d), m_timesteps(other.m_timesteps),
-    m_hybridizations(other.m_hybridizations),
+    m_spectra(other.m_spectra), m_customElementMap(other.m_customElementMap),
+    m_elements(other.m_elements), m_positions2d(other.m_positions2d),
+    m_positions3d(other.m_positions3d), m_atomLabels(other.m_atomLabels),
+    m_bondLabels(other.m_bondLabels), m_coordinates3d(other.m_coordinates3d),
+    m_timesteps(other.m_timesteps), m_hybridizations(other.m_hybridizations),
     m_formalCharges(other.m_formalCharges), m_colors(other.m_colors),
     m_vibrationFrequencies(other.m_vibrationFrequencies),
     m_vibrationIRIntensities(other.m_vibrationIRIntensities),
@@ -79,7 +79,8 @@ Molecule::Molecule(const Molecule& other)
 
 void Molecule::readProperties(const Molecule& other)
 {
-  m_label = other.m_label;
+  m_atomLabels = other.m_atomLabels;
+  m_bondLabels = other.m_bondLabels;
   m_colors = other.m_colors;
   // merge data maps by iterating through other's map
   for (auto it = other.m_data.constBegin(); it != other.m_data.constEnd();
@@ -93,6 +94,9 @@ void Molecule::readProperties(const Molecule& other)
     m_partialCharges[it->first] = it->second;
   }
 
+  // copy spectra
+  m_spectra = other.m_spectra;
+
   // copy orbital information
   SlaterSet* slaterSet = dynamic_cast<SlaterSet*>(other.m_basisSet);
   if (slaterSet != nullptr) {
@@ -128,6 +132,7 @@ void Molecule::readProperties(const Molecule& other)
 
 Molecule::Molecule(Molecule&& other) noexcept
   : m_data(other.m_data), m_partialCharges(std::move(other.m_partialCharges)),
+    m_spectra(other.m_spectra),
     m_customElementMap(std::move(other.m_customElementMap)),
     m_elements(other.m_elements), m_positions2d(other.m_positions2d),
     m_positions3d(other.m_positions3d), m_atomLabels(other.m_atomLabels),
@@ -167,6 +172,7 @@ Molecule& Molecule::operator=(const Molecule& other)
   if (this != &other) {
     m_data = other.m_data;
     m_partialCharges = other.m_partialCharges;
+    m_spectra = other.m_spectra;
     m_customElementMap = other.m_customElementMap;
     m_elements = other.m_elements;
     m_positions2d = other.m_positions2d;
@@ -229,6 +235,7 @@ Molecule& Molecule::operator=(Molecule&& other) noexcept
   if (this != &other) {
     m_data = other.m_data;
     m_partialCharges = std::move(other.m_partialCharges);
+    m_spectra = other.m_spectra;
     m_customElementMap = std::move(other.m_customElementMap);
     m_elements = other.m_elements;
     m_positions2d = other.m_positions2d;
@@ -325,6 +332,31 @@ std::set<std::string> Molecule::partialChargeTypes() const
   return types;
 }
 
+std::set<std::string> Molecule::spectraTypes() const
+{
+  std::set<std::string> types;
+  for (auto& it : m_spectra)
+    types.insert(it.first);
+  return types;
+}
+
+void Molecule::setSpectra(const std::string& type, const MatrixX& value)
+{
+  m_spectra[type] = value;
+}
+
+MatrixX Molecule::spectra(const std::string& type) const
+{
+  MatrixX value;
+
+  auto search = m_spectra.find(type);
+  if (search != m_spectra.end()) {
+    value = search->second; // value from the map
+  }
+
+  return value;
+}
+
 void Molecule::setFrozenAtom(Index atomId, bool frozen)
 {
   if (atomId >= m_atomicNumbers.size())

avogadro/core/molecule.h

@@ -100,6 +100,15 @@ class AVOGADROCORE_EXPORT Molecule
   /** \overload */
   VariantMap& dataMap();
 
+  /** @return a specific spectra entry */
+  MatrixX spectra(const std::string& name) const;
+
+  /** Sets the spectra value with @p name to @p value. */
+  void setSpectra(const std::string& name, const MatrixX& value);
+
+  /** @return the list of available spectra */
+  std::set<std::string> spectraTypes() const;
+
   /** Sets atomic partial charges with @p type to @p value. */
   void setPartialCharges(const std::string& type, const MatrixX& value);
 
@@ -804,6 +813,8 @@ class AVOGADROCORE_EXPORT Molecule
   VariantMap m_data;
   std::map<std::string, MatrixX>
     m_partialCharges; //!< Sets of atomic partial charges
+
+  std::map<std::string, MatrixX> m_spectra; //!< Sets of spectra
   CustomElementMap m_customElementMap;
   ElementMask m_elements; //!< Which elements this molecule contains (e.g., for
                           //!< force fields)