Merge branch 'master' of github.com:OpenChemistry/avogadrolibs into c…

…lang-tidy-fixes

Signed-off-by: Geoff Hutchison <geoff.hutchison@gmail.com>

.clang-tidy

@@ -1,35 +1,27 @@
-Checks: 'clang-analyzer*,
+Checks: 'bugprone*,
+        clang-analyzer*,
+        cppcoreguidelines*,
+        misc-uniqueptr-reset-release,
         misc-unused*,
         misc-redundant-expression,
-        modernize-avoid-bind,
-        modernize-concat-nested-namespaces,
-        modernize-loop-convert,
-        modernize-macro-to-enum,
-        modernize-pass-by-value
-        modernize-raw-string-literal,
-        modernize-use-auto,
-        modernize-use-bool-literals,
-        modernize-use-emplace,
-        modernize-use-nullptr,
-        modernize-use-override,
+        modernize-avoid-bind,modernize-concat-nested-namespaces,
+        modernize-loop-convert,modernize-macro-to-enum,modernize-use-bool-literals,
+        modernize-use-auto,modernize-use-nullptr,modernize-use-override,
+        modernize-raw-string-literal,modernize-use-emplace,modernize-pass-by-value,
+        modernize-use-using,
         performance-avoid-endl,
+        performance-faster*,
         performance-for-range-copy,
-        performance-inefficient*,
-        performance-move-const-arg,
-        performance-type-promotion*,
+        performance-inefficient*,performance-type-promotion*,
         performance-unnecessary-copy-initialization,
-        readability-container-data-pointer,
-        readability-container-size-empty,
+        performance-move-const-arg,
         readability-const-return-type,
-        readability-delete-null-pointer,
+        readability-container*,
         readability-duplicate-include,
+        readability-delete-null-pointer,
         readability-qualified-auto,
-        readability-redundant-access-specifiers,
-        readability-redundant-declaration,
-        readability-redundant-string-cstr,
-        readability-redundant-string-init,
-        readability-simplify*
-        -bugprone-easily-swappable-parameters,
+        readability-redundant*,
+        readability-simplify*,
         -cppcoreguidelines-avoid-magic-numbers,
         -cppcoreguidelines-owning-memory,
         -readability-else-after-return,

.github/workflows/build_cmake.yml

@@ -12,6 +12,8 @@ env:
   # we set MACOSX_DEPLOYMENT_TARGET later
   MACOS_TARGET: 10.12
   FEATURES: -DBUILD_GPL_PLUGINS=ON -DWITH_COORDGEN=OFF -DUSE_VTK=ON
+  CACHE: -DCMAKE_C_COMPILER_LAUNCHER=sccache -DCMAKE_CXX_COMPILER_LAUNCHER=sccache
+  SCCACHE_GHA_ENABLED: "true"
 
 jobs:
   build:
@@ -26,15 +28,15 @@ jobs:
             os: ubuntu-latest,
             cc: "gcc", cxx: "g++",
             build_type: "Release",
-            cmake_flags: "-G Ninja -DENABLE_TESTING=ON -DTEST_QTGL=OFF -DCMAKE_BUILD_TYPE=Release",
+            cmake_flags: "-G Ninja -DENABLE_TESTING=ON -DTEST_QTGL=OFF -USE_SYSTEM_ZLIB=ON",
             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 -DCMAKE_BUILD_TYPE=Release",
+            cmake_flags: "-G Ninja -DINSTALL_BUNDLE_FILES=ON -USE_SYSTEM_ZLIB=ON",
             cpack: "",
           }
         - {
@@ -50,7 +52,7 @@ jobs:
             os: windows-latest,
             cc: "cl", cxx: "cl",
             build_type: "Release",
-            cmake_flags: "",
+            cmake_flags: "-DOPENSSL_ROOT_DIR=D:\\a\\Tools\\OpenSSL\\Win_x64",
             build_flags: "-j 2",
             cpack_flags: "-G NSIS",
           }
@@ -59,31 +61,31 @@ jobs:
             os: ubuntu-20.04,
             cc: "gcc", cxx: "g++",
             build_type: "asan",
-            cmake_flags: "-G Ninja -DENABLE_TESTING=ON -DTEST_QTGL=OFF",
+            cmake_flags: "-G Ninja -DENABLE_TESTING=ON -DTEST_QTGL=OFF -USE_SYSTEM_ZLIB=ON",
             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",
+            cmake_flags: "-G Ninja -DENABLE_TESTING=ON -DTEST_QTGL=OFF -USE_SYSTEM_ZLIB=ON",
             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",
+            cmake_flags: "-G Ninja -DENABLE_TESTING=ON -DTEST_QTGL=OFF -USE_SYSTEM_ZLIB=ON",
             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",
+            cmake_flags: "-G Ninja -DENABLE_TESTING=ON -DTEST_QTGL=OFF -USE_SYSTEM_ZLIB=ON",
             cpack: "",
           }
 
@@ -124,18 +126,22 @@ jobs:
       with:
         path: avogadrolibs
 
-    - name: Cache Qt
-      id: cache-qt
-      uses: actions/cache@v3
+    - name: Install Qt
+      uses: jurplel/install-qt-action@v3
       with:
-        path: ../Qt
-        key: ${{ runner.os }}-QtCache
+        cache: True
+        version: ${{ env.QT_VERSION }}
 
-    - name: Install Qt
+    - name: Install OpenSSL (Win64)
+      if: runner.os == 'Windows'
       uses: jurplel/install-qt-action@v3
       with:
-        cached: ${{ steps.cache-qt.outputs.cache-hit }}
+        cache: True
+        tools: 'tools_openssl_x64'
         version: ${{ env.QT_VERSION }}
+        host: 'windows'
+        target: 'desktop'
+        arch: 'win64_msvc2019_64'
 
     - name: Configure MSVC Command Prompt
       if: runner.os == 'Windows'
@@ -148,22 +154,24 @@ jobs:
       if: runner.os != 'Windows'
       with:
         path: |
-          ${{ runner.workspace }}/build/thirdparty
           ${{ runner.workspace }}/build/Downloads
-        key: ${{ matrix.config.name }}-thirdparty
+        key: ${{ matrix.config.name }}-downloads
+
+    - name: Run sccache-cache
+      uses: mozilla-actions/sccache-action@main
 
     - 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}} ${{matrix.config.cmake_flags}}
+        CC=${{matrix.config.cc}} CXX=${{matrix.config.cxx}} cmake $GITHUB_WORKSPACE ${{env.FEATURES}} ${{env.CACHE}} -DCMAKE_BUILD_TYPE=${{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}} ${{matrix.config.build_flags}}
+        CC=${{matrix.config.cc}} CXX=${{matrix.config.cxx}} CMAKE_C_COMPILER_LAUNCHER=sccache CMAKE_CXX_COMPILER_LAUNCHER=sccache cmake --build . --config ${{matrix.config.build_type}} ${{matrix.config.build_flags}}
       shell: bash
       working-directory: ${{ runner.workspace }}/build
 

.github/workflows/clang-tidy.yml

@@ -1,11 +1,10 @@
-name: Static Analysis
+name: Clang-Tidy Static Analysis
 
 on: 
-  pull_request:
   workflow_dispatch:
 
 env:
-  FEATURES: -DUSE_VTK=OFF -DBUILD_GPL_PLUGINS=ON -DWITH_COORDGEN=OFF
+  FEATURES: -DUSE_VTK=ON -DBUILD_GPL_PLUGINS=ON -DWITH_COORDGEN=OFF -DUSE_YAEHMOP=ON
   BUILD_TYPE: RelWithDebInfo
   QT_VERSION: 5.15.2
 
@@ -59,6 +58,15 @@ jobs:
         path: avogadrolibs
         fetch-depth: 2
 
+    - 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
@@ -77,25 +85,28 @@ jobs:
 
     - name: Create results directory
       run: |
-        mkdir clang-tidy-result
+        mkdir ${{ runner.workspace }}/clang-tidy-result
     
     - name: Analyze
       run: |
-        git fetch
-        pip install pyyaml
-        git diff -U0 HEAD^ | clang-tidy-diff -p1 -path ../build -export-fixes ../clang-tidy-result/fixes.yml
+        # generate the fixes and we'll make a diff
+        run-clang-tidy -p ../build -fix
+        cd avogadrolibs
+        pwd
+        echo "Generating diff"
+        git diff >${{ runner.workspace }}/clang-tidy-result/tidy.patch
       working-directory: ${{ runner.workspace }}/avogadrolibs
 
     - name: Save PR metadata
       run: |
-        echo ${{ github.event.number }} > clang-tidy-result/pr-id.txt
-        echo ${{ github.event.pull_request.head.repo.full_name }} > clang-tidy-result/pr-head-repo.txt
-        echo ${{ github.event.pull_request.head.ref }} > clang-tidy-result/pr-head-ref.txt
-    
+        echo ${{ github.event.number }} > ${{ runner.workspace }}/clang-tidy-result/pr-id.txt
+        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
       with:
         name: clang-tidy-result
-        path: clang-tidy-result/
+        path: ${{ runner.workspace }}/clang-tidy-result/
 
     - name: Setup tmate session
       if: ${{ failure() }}

.github/workflows/codeql.yml

@@ -67,17 +67,10 @@ jobs:
         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: Cache Qt
-      id: cache-qt
-      uses: actions/cache@v3
-      with:
-        path: ../Qt
-        key: ${{ runner.os }}-QtCache
-
     - name: Install Qt
       uses: jurplel/install-qt-action@v3
       with:
-        cached: ${{ steps.cache-qt.outputs.cache-hit }}
+        cache: True
         version: ${{ env.QT_VERSION }}
 
     - name: Grab cache files

CMakeLists.txt

@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 3.23 FATAL_ERROR)
+cmake_minimum_required(VERSION 3.24 FATAL_ERROR)
 
 project(AvogadroLibs)
 
@@ -54,15 +54,18 @@ option(USE_LIBMSYM "Enable optional features using libmsym" ON)
 option(USE_SPGLIB "Enable optional features using spglib" ON)
 option(USE_MMTF "Enable optional features using mmtf" ON)
 option(USE_PYTHON "Use Python to wrap some of our API" OFF)
+option(USE_EXTERNAL_NLOHMANN "Use an externally-provided version of the nlohmann JSON library" OFF)
+option(USE_EXTERNAL_PUGIXML "Use an externally-provided version of pugixml" OFF)
+option(USE_EXTERNAL_STRUCT "Use an externally-provided version of the struct binary data formatting library" OFF)
 set(QT_VERSION "5" CACHE STRING "What major version of Qt")
 set(QT_VERSIONS_SUPPORTED 5 6)
 set_property(CACHE QT_VERSION PROPERTY STRINGS 5 6)
 if(NOT QT_VERSION IN_LIST QT_VERSIONS_SUPPORTED)
   message(FATAL_ERROR "Qt version must be one of ${QT_VERSIONS_SUPPORTED}")
 endif()
 
-add_subdirectory(utilities)
 add_subdirectory(thirdparty)
+add_subdirectory(utilities)
 add_subdirectory(avogadro)
 
 if(ENABLE_TESTING)
@@ -114,7 +117,6 @@ if (NOT SKBUILD)
     "${AvogadroLibs_BINARY_DIR}/AvogadroLibsConfig.cmake"
     "${AvogadroLibs_BINARY_DIR}/AvogadroLibsConfigVersion.cmake"
     "${CMAKE_CURRENT_SOURCE_DIR}/cmake/FindEigen3.cmake"
-    "${CMAKE_CURRENT_SOURCE_DIR}/cmake/FindLIBARCHIVE.cmake"
     "${CMAKE_CURRENT_SOURCE_DIR}/cmake/Findlibmsym.cmake"
     DESTINATION "${INSTALL_LIBRARY_DIR}/cmake/avogadrolibs")
   install(EXPORT "AvogadroLibsTargets"