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

…mplement-g-angular-momentum

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_qt6.yml

@@ -0,0 +1,151 @@
+name: Qt6 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: 6.5.3
+  # this is different from MACOSX_DEPLOYMENT_TARGET to prevent build problems
+  # we set MACOSX_DEPLOYMENT_TARGET later
+  MACOS_TARGET: 10.15
+  FEATURES: -DBUILD_GPL_PLUGINS=ON -DWITH_COORDGEN=OFF -DUSE_VTK=ON -DQT_VERSION=6
+
+jobs:
+  build:
+    name: ${{ matrix.config.name }}
+    runs-on: ${{ matrix.config.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+        - {
+            name: "Ubuntu Qt6", artifact: "",
+            os: ubuntu-latest,
+            cc: "gcc", cxx: "g++",
+            build_type: "Release",
+            cmake_flags: "-G Ninja",
+            cpack: "",
+          }
+        - {
+            name: "Ubuntu Qt6 AppImage", artifact: "",
+            os: ubuntu-20.04,
+            cc: "gcc", cxx: "g++",
+            build_type: "Release",
+            cmake_flags: "-G Ninja -DINSTALL_BUNDLE_FILES=ON",
+            cpack: "",
+          }
+        - {
+            name: "macOS Qt6", artifact: "",
+            os: macos-latest,
+            cc: "clang", cxx: "clang++",
+            build_type: "Release",
+            cmake_flags: "-G Ninja",
+            cpack_flags: "-G DragNDrop",
+          }
+        - {
+            name: "Windows Qt6", artifact: "",
+            os: windows-latest,
+            cc: "cl", cxx: "cl",
+            build_type: "Release",
+            cmake_flags: "",
+            build_flags: "-j 2",
+            cpack_flags: "-G NSIS",
+          }
+
+    steps:
+
+    - name: Install Dependencies (Linux)
+      if: runner.os == 'Linux'
+      run: |
+        sudo apt-get -qq update
+        sudo apt-get -qq install ninja-build libeigen3-dev libboost-all-dev libglew-dev libxml2-dev
+    - name: Install Dependencies (macOS)
+      if: runner.os == 'macOS'
+      run: |
+        if uname -p | grep -q "arm" ; then
+           export PATH=/opt/homebrew/bin:$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@v4
+      with:
+        repository: openchemistry/openchemistry
+        submodules: recursive
+
+    - name: Checkout avogadroapp
+      uses: actions/checkout@v4
+      with:
+        repository: openchemistry/avogadroapp
+        path: avogadroapp
+
+    - name: Checkout avogadrolibs
+      uses: actions/checkout@v4
+      with:
+        path: avogadrolibs
+
+    - name: Install Qt
+      uses: jurplel/install-qt-action@v3
+      with:
+        cache: true
+        version: ${{ env.QT_VERSION }}
+        aqtversion: '==3.1.*'
+        modules: 'qt5compat'
+
+    - 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: 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: Setup tmate session
+      if: ${{ failure() }}
+      uses: mxschmitt/action-tmate@v3

.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/atom.h

@@ -380,13 +380,13 @@ Vector3 AtomTemplate<Molecule_T>::forceVector() const
 template <class Molecule_T>
 void AtomTemplate<Molecule_T>::setLabel(const std::string& label)
 {
-  m_molecule->setLabel(m_index, label);
+  m_molecule->setAtomLabel(m_index, label);
 }
 
 template <class Molecule_T>
 std::string AtomTemplate<Molecule_T>::label() const
 {
-  return m_molecule->label(m_index);
+  return m_molecule->atomLabel(m_index);
 }
 
 } // namespace Core

avogadro/core/atomutilities.h

@@ -8,8 +8,6 @@
 
 #include "avogadrocoreexport.h"
 
-#include "avogadrocoreexport.h"
-
 #include <avogadro/core/molecule.h>
 
 #include <vector>

avogadro/core/coordinateblockgenerator.h

@@ -6,7 +6,7 @@
 #ifndef AVOGADRO_CORE_COORDINATEBLOCKGENERATOR_H
 #define AVOGADRO_CORE_COORDINATEBLOCKGENERATOR_H
 
-#include <avogadrocoreexport.h>
+#include "avogadrocoreexport.h"
 
 #include <sstream>
 #include <string>