Merge pull request #10 from 3dJan/3dJan/ExtendedVolumetricSpec

3d jan/extended volumetric spec

Author: 3dJan

.github/chatmodes/reviewer.chatmode.md

@@ -0,0 +1,20 @@
+---
+description: 'Reviews code, documents, or other materials, providing feedback and suggestions for improvement.'
+tools: ['edit', 'runNotebooks', 'search', 'new', 'runCommands', 'runTasks', 'usages', 'vscodeAPI', 'think', 'problems', 'changes', 'testFailure', 'openSimpleBrowser', 'fetch', 'githubRepo', 'extensions', 'todos', 'runTests', 'serena']
+---
+
+Start with using git log and git diff to understand the last 10 commits. Then create yourself a plan how to proceed.
+
+Your task is to ensure that the code is high-quality, efficient, and maintainable. 
+Check for adherence to coding standards, best practices, and overall functionality. If a spec is provided, ensure the code meets the requirements outlined in it.
+Check for 
+- Is the code reusable and modular?
+- Can the code be optimized for better performance?
+- Are there any security vulnerabilities?
+- Can the code be simplified for better readability?
+- Does the code follow the project's coding standards and conventions?
+- Does the code follow KISS (Keep It Simple, Stupid) and DRY (Don't Repeat Yourself) principles?
+- Are there any potential bugs or edge cases that have not been handled?
+- Is the code well-documented and easy to understand?
+- Is the code covered by tests? If not, suggest appropriate tests to add.
+

.github/codeql/codeql-config.yml

@@ -0,0 +1,43 @@
+name: "CodeQL Configuration"
+
+# Exclude vcpkg directories and third-party libraries from CodeQL scanning
+paths-ignore:
+  # vcpkg installation directories
+  - "vcpkg_installed/**"
+  - "**/vcpkg_installed/**"
+
+  - "vcpkg/**"
+  - "**/vcpkg/**"
+
+  # Ignore vcpkg buildtrees directory
+  - "vcpkg/buildtrees/**"
+  - "**/vcpkg/buildtrees/**"
+
+  # Common build artifact directories that may contain vcpkg dependencies
+  - "build/**"
+  - "**/build/**"
+  - "out/**"
+  - "**/out/**"
+
+  # vcpkg tool directory (if cloned locally)
+  - "vcpkg/**"
+  - "**/vcpkg/**"
+
+  # CMake build directories that might contain FetchContent or vcpkg deps
+  - "_deps/**"
+  - "**/_deps/**"
+
+  # Other common build artifact directories
+  - ".vs/**"
+  - "**/CMakeFiles/**"
+  - "**/.cmake/**"
+
+# Include only our project source directories
+paths:
+  - "gladius/src/**"
+  - "gladius/library/**"
+  - "gladius/components/**"
+  - "gladius/examples/**"
+  - "gladius/tests/**"
+  - "gladius/cmake/**"
+  - "scripts/**"

.github/workflows/build.yml

@@ -112,7 +112,6 @@ jobs:
     - name: Build
       # Build your program with the given configuration. Note that --config is needed because the default Windows generator is a multi-config generator (Visual Studio generator).
       run: cmake --build ${{ steps.strings.outputs.build-output-dir }} --config ${{ matrix.build_type }}
-    
     - name: Test
       # Run only unit tests, excluding integration tests
       working-directory: ${{ steps.strings.outputs.build-output-dir }}

.github/workflows/codeql.yml

@@ -0,0 +1,86 @@
+name: "CodeQL"
+
+on:
+  push:
+    branches: [ "main", "develop" ]
+  pull_request:
+    branches: [ "main" ]
+  schedule:
+    - cron: '42 5 * * 1'  # Weekly on Mondays
+
+jobs:
+  analyze:
+    name: Analyze (${{ matrix.language }})
+    runs-on: ubuntu-latest
+    timeout-minutes: 120
+    permissions:
+      # required for all workflows
+      security-events: write
+      # required to fetch internal or private CodeQL packs
+      packages: read
+      # only required for workflows in private repositories
+      actions: read
+      contents: read
+
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+        - language: c-cpp
+          build-mode: manual
+
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+      with:
+        submodules: true
+
+    - name: Install dependencies
+      run: sudo apt-get update && sudo apt-get install -y libxrandr-dev libxinerama-dev libxcursor-dev libxi-dev build-essential libglfw3-dev ninja-build
+
+    - name: Setup vcpkg environment
+      shell: bash
+      run: |
+        echo "CMAKE_GENERATOR=Ninja" >> $GITHUB_ENV
+
+    - name: Setup vcpkg
+      uses: lukka/run-vcpkg@v11
+      with:
+        vcpkgGitCommitId: 'f2bf7d935af722c0cd8219c1f6e30d5ae3d666f2'
+        vcpkgJsonGlob: '${{ github.workspace }}/gladius/vcpkg.json'
+      env:
+        VCPKG_OVERLAY_PORTS: '${{ github.workspace }}/gladius/vcpkg-overlay-ports'
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v3
+      with:
+        languages: ${{ matrix.language }}
+        build-mode: ${{ matrix.build-mode }}
+        config-file: .github/codeql/codeql-config.yml
+
+    - name: Set reusable strings
+      id: strings
+      shell: bash
+      run: |
+        echo "build-output-dir=${{ github.workspace }}/build" >> "$GITHUB_OUTPUT"
+
+    - name: Configure CMake
+      run: >
+        cmake -B ${{ steps.strings.outputs.build-output-dir }}
+        -DCMAKE_CXX_COMPILER=clang++
+        -DCMAKE_C_COMPILER=clang
+        -DCMAKE_BUILD_TYPE=Release
+        -DENABLE_OPENCL_TESTS=OFF
+        -G Ninja
+        -S ${{ github.workspace }}/gladius
+      env:
+        VCPKG_OVERLAY_PORTS: '${{ github.workspace }}/gladius/vcpkg-overlay-ports'
+
+    - name: Build
+      run: cmake --build ${{ steps.strings.outputs.build-output-dir }} --config Release
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v3
+      with:
+        category: "/language:${{matrix.language}}"

.gitignore

@@ -38,3 +38,8 @@ build/
 gladius/vcpkg_installed/*
 gladius/.serena/cache/
 gladius/compile_commands.json
+build/build_test/
+vcpkg/buildtrees/
+**/vcpkg_installed/
+_CPack_Packages/*
+*.deb

gladius/CMakeLists.txt

@@ -16,7 +16,7 @@ option(ENABLE_OPENCL_TESTS "Enable tests that require OpenCL" ON)
 
 set(CPACK_PACKAGE_VERSION_MAJOR "1")
 set(CPACK_PACKAGE_VERSION_MINOR "2")
-set(CPACK_PACKAGE_VERSION_PATCH "14")
+set(CPACK_PACKAGE_VERSION_PATCH "15")
 
 # Set the version of the package in src/version.h
 configure_file(
@@ -37,6 +37,8 @@ if(buildcache_program)
 else()
   message("buildcache not found")
 endif()
+else()
+  message("Not using build cache. You can enable it by setting USE_CACHE=ON")
 endif() # USE_CACHE
 message("CMAKE_TOOLCHAIN_FILE=${CMAKE_TOOLCHAIN_FILE}")
 message("VCPKG_ROOT=${VCPKG_ROOT}")
@@ -84,6 +86,10 @@ project(gladius)
 # Include coverage support after project declaration so compiler info is available
 include(cmake/Coverage.cmake)
 
+# Ensure the 'install' target depends on building all targets first
+# (so CPack does not try to install artifacts that were not built yet).
+set(CMAKE_SKIP_INSTALL_ALL_DEPENDENCY OFF)
+
 if (MSVC)
     add_compile_options(/bigobj /utf-8 /Zc:__cplusplus)
 
@@ -124,11 +130,15 @@ set(CMAKE_POSITION_INDEPENDENT_CODE ON)
 
 # Ensure installed binaries look for co-located shared libraries first
 if(UNIX)
-  # Use $ORIGIN so binaries in /opt/gladius/<version> can find bundled .so
+  # Install tree: Use $ORIGIN so installed binaries in /opt/gladius/<version> resolve
+  # bundled shared objects (e.g. our patched lib3mf) placed alongside them.
   set(CMAKE_INSTALL_RPATH "$ORIGIN")
-  # Build artifacts will already carry the final install RPATH, avoiding RPATH rewrite during install
-  set(CMAKE_BUILD_WITH_INSTALL_RPATH ON)
-  set(CMAKE_SKIP_BUILD_RPATH  OFF)
+  # Build tree: DO NOT force build RPATH to install RPATH. Tests run from the
+  # build tree (e.g. build/tests/unittests) and previously failed to locate
+  # lib3mf.so.2 when we set CMAKE_BUILD_WITH_INSTALL_RPATH ON (RPATH became
+  # just $ORIGIN which points to the test directory that does not contain lib3mf).
+  set(CMAKE_BUILD_WITH_INSTALL_RPATH OFF)
+  set(CMAKE_SKIP_BUILD_RPATH OFF)
   set(CMAKE_INSTALL_RPATH_USE_LINK_PATH ON)
 endif()
 
@@ -212,10 +222,17 @@ if(UNIX)
   if(_lib3mf_resolved)
     get_filename_component(_lib3mf_dir "${_lib3mf_resolved}" DIRECTORY)
     if(EXISTS "${_lib3mf_dir}")
+      # Bundle all versioned variants (lib3mf.so, lib3mf.so.2, etc.) into install prefix.
       file(GLOB _lib3mf_so_files "${_lib3mf_dir}/lib3mf.so*")
       if(_lib3mf_so_files)
         install(FILES ${_lib3mf_so_files} DESTINATION ${INSTALL_PREFIX})
       endif()
+      # Ensure build-tree executables (tests, tools) can locate lib3mf at runtime
+      # by appending its directory to the build RPATH. This fixes CI failures like:
+      #   error while loading shared libraries: lib3mf.so.2: cannot open shared object file
+      list(APPEND CMAKE_BUILD_RPATH "${_lib3mf_dir}")
+      list(REMOVE_DUPLICATES CMAKE_BUILD_RPATH)
+      set(CMAKE_BUILD_RPATH "${CMAKE_BUILD_RPATH}" CACHE STRING "RPATH for build tree executables" FORCE)
     endif()
   endif()
 endif()
@@ -274,8 +291,24 @@ install(DIRECTORY components/licenses DESTINATION ${INSTALL_PREFIX}/doc/licenses
 # Install imgui.ini
 install(FILES src/imgui.ini DESTINATION ${INSTALL_PREFIX})
 
-# Install icon
-install(FILES ${CMAKE_SOURCE_DIR}/documentation/img/gladius.ico DESTINATION ${INSTALL_PREFIX}/share/pixmaps/)
+# Icon installation and desktop integration assets (no build-time conversion)
+if(UNIX)
+  set(GLADIUS_ICON_NAME gladius)
+  # Install pre-generated PNG icon to hicolor so Icon=gladius works via theme
+  install(FILES ${CMAKE_SOURCE_DIR}/documentation/img/gladius.png DESTINATION /usr/share/icons/hicolor/256x256/apps/ RENAME ${GLADIUS_ICON_NAME}.png)
+  set(GLADIUS_ICON ${GLADIUS_ICON_NAME})
+endif()
+
+# Linux desktop integration (GNOME/KDE): install .desktop file and icon into system directories
+if(UNIX)
+  # Generate desktop launcher file
+  set(GLADIUS_DESKTOP_FILE "${PROJECT_BINARY_DIR}/gladius.desktop")
+  # Paths used inside the desktop file
+  set(GLADIUS_EXEC "/usr/bin/gladius")
+  configure_file(${CMAKE_SOURCE_DIR}/cmake/desktop/gladius.desktop.in ${GLADIUS_DESKTOP_FILE} @ONLY)
+  # Install desktop entry for all users
+  install(FILES ${GLADIUS_DESKTOP_FILE} DESTINATION /usr/share/applications)
+endif()
 
 # Install documentation - not yet available
 # install(DIRECTORY ${CMAKE_SOURCE_DIR}/documentation/ DESTINATION ${INSTALL_PREFIX}/share/doc/)
@@ -316,15 +349,15 @@ if(UNIX)
   file(WRITE "${GLADIUS_LAUNCHER}" "#!/bin/sh\n"
     "# Added by CMake: ensure Gladius' private libs (e.g., custom lib3mf) are found first.\n"
     "GLADIUS_DIR=\"${INSTALL_PREFIX}\"\n"
-    "if [ -z \"\\$LD_LIBRARY_PATH\" ]; then\n"
-    "  export LD_LIBRARY_PATH=\\"\\$GLADIUS_DIR\\"\n"
+    "if [ -z \"\$LD_LIBRARY_PATH\" ]; then\n"
+    "  export LD_LIBRARY_PATH=\"\$GLADIUS_DIR\"\n"
     "else\n"
-    "  case :\\$LD_LIBRARY_PATH: in\n"
-    "    *:\\$GLADIUS_DIR:*) ;;\n"
-    "    *) export LD_LIBRARY_PATH=\\"\\$GLADIUS_DIR:\\$LD_LIBRARY_PATH\\" ;;\n"
+    "  case :\$LD_LIBRARY_PATH: in\n"
+    "    *:\$GLADIUS_DIR:*) ;;\n"
+    "    *) export LD_LIBRARY_PATH=\"\$GLADIUS_DIR:\$LD_LIBRARY_PATH\" ;;\n"
     "  esac\n"
     "fi\n"
-    "exec \"\\$GLADIUS_DIR/gladius\" \"$@\"\n")
+    "exec \"\$GLADIUS_DIR/gladius\" \"$@\"\n")
   install(PROGRAMS "${GLADIUS_LAUNCHER}" DESTINATION ${SYMLINK_BIN_DIR} RENAME gladius)
 endif()
 
@@ -358,8 +391,12 @@ if (UNIX)
 endif()
 
 include(CPack)
-add_custom_target( Generate_Installer
-            COMMAND "${CMAKE_CPACK_COMMAND}"
-            WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
-            DEPENDS gladius gladiuslib
-            COMMENT "Running CPack. Please wait...")
+
+# Convenience target to generate installer and ensure required binaries are built first
+add_custom_target(Generate_Installer
+  COMMAND "${CMAKE_CPACK_COMMAND}"
+  WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
+  # Make sure both desktop app variants are built before packaging
+  DEPENDS gladius gladiusmcp gladius_lib
+  COMMENT "Running CPack. Please wait...")
+

gladius/CMakePresets.json

@@ -6,7 +6,7 @@
             "hidden": true,
             "generator": "Ninja",
             "binaryDir": "${sourceDir}/out/build/${presetName}",
-            "installDir": "$env{CML}/gladius/gladius-1.2.14",
+            "installDir": "$env{CML}/gladius/gladius-1.2.15",
             "condition": {
                 "type": "equals",
                 "lhs": "${hostSystemName}",

gladius/cmake/desktop/gladius.desktop.in

@@ -0,0 +1,15 @@
+[Desktop Entry]
+Version=@CPACK_PACKAGE_VERSION_MAJOR@.@CPACK_PACKAGE_VERSION_MINOR@.@CPACK_PACKAGE_VERSION_PATCH@
+Type=Application
+Name=Gladius
+GenericName=3MF Volumetric/Implicit Tool
+Comment=Work with 3MF Volumetric and Implicit extensions
+TryExec=@GLADIUS_EXEC@
+Exec=@GLADIUS_EXEC@ %F
+Icon=@GLADIUS_ICON@
+Terminal=false
+Categories=Graphics;3DGraphics;Engineering;
+Keywords=3MF;3D;Printing;Volumetric;Implicit;Gladius;
+StartupNotify=true
+# Uncomment when MIME is registered; left here for future integration
+# MimeType=application/3mf;

gladius/documentation/img/gladius.png

@@ -12,12 +12,12 @@ namespace gladius
                                              std::vector<BeamData> && beams,
                                              std::vector<BallData> && balls,
                                              BeamLatticeBallConfig ballConfig,
-                                             bool useVoxelAcceleration)
+                                             BeamLatticeAcceleration acceleration)
         : ResourceBase(std::move(key))
         , m_beams(std::move(beams))
         , m_balls(std::move(balls))
         , m_ballConfig(ballConfig)
-        , m_useVoxelAcceleration(useVoxelAcceleration)
+        , m_acceleration(acceleration)
     {
         // Validate ball configuration per 3MF specification
         if (!m_ballConfig.isValid())
@@ -55,7 +55,7 @@ namespace gladius
 
     void BeamLatticeResource::buildAccelerationStructure()
     {
-        if (m_useVoxelAcceleration)
+        if (m_acceleration == BeamLatticeAcceleration::Voxel)
         {
             buildVoxelAcceleration();
         }