Replace diff_engine_core submodule with subtree

diff_engine_core/.clang-format

@@ -0,0 +1,45 @@
+# .clang-format for C project with Allman style braces
+BasedOnStyle: LLVM
+
+# Indentation
+IndentWidth: 4
+UseTab: Never
+TabWidth: 4
+
+# Line length
+ColumnLimit: 85
+BinPackParameters: true
+BinPackArguments: true
+
+# Braces style
+BreakBeforeBraces: Allman   # Allman style: brace on next line
+BraceWrapping:
+  AfterFunction: true
+  AfterControlStatement: true
+  AfterStruct: true
+  AfterClass: true
+  AfterNamespace: false
+  IndentBraces: false
+
+# Pointers
+PointerAlignment: Right      
+
+# Spaces
+SpaceAfterCStyleCast: true
+SpaceAfterLogicalNot: false
+SpacesInParentheses: false
+SpacesInContainerLiterals: false
+SpaceBeforeParens: ControlStatements
+
+# Allow single-line short statements if simple
+AllowShortIfStatementsOnASingleLine: true
+AllowShortLoopsOnASingleLine: true
+AllowShortFunctionsOnASingleLine: Inline
+AllowAllParametersOfDeclarationOnNextLine: true
+
+
+# Other
+ReflowComments: true
+IndentCaseLabels: true
+AlignOperands: true
+InsertNewlineAtEOF: true              

diff_engine_core/.github/workflows/cmake.yml

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+name: CMake Build and Test
+
+on:
+  push:
+    branches: [main, development]
+  pull_request:
+    branches: [main, development]
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        build_type: [Release, Debug]
+
+    steps:
+    - uses: actions/checkout@v3
+
+    - name: Configure CMake
+      run: cmake -B build -S . -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} -DCMAKE_VERBOSE_MAKEFILE=ON
+
+    - name: Build
+      run: cmake --build build --config ${{ matrix.build_type }}
+
+    - name: Run tests
+      run: cd build && ctest -C ${{ matrix.build_type }} --verbose

diff_engine_core/.github/workflows/formatting.yml

@@ -0,0 +1,38 @@
+name: Code Formatting
+
+on:
+  push:
+    branches: [main, development]
+  pull_request:
+    branches: [main, development]
+
+jobs:
+  format:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+
+    steps:
+      - uses: actions/checkout@v5
+
+      # Install clang-format if needed
+      - name: Install clang-format (Linux)
+        if: matrix.os == 'ubuntu-latest'
+        run: sudo apt-get update && sudo apt-get install -y clang-format
+
+      - name: Install clang-format (macOS)
+        if: matrix.os == 'macos-latest'
+        run: brew install clang-format || true
+
+      # Check formatting
+      - name: Check C/C++ formatting
+        run: |
+          misformatted=$(find . -name '*.c' -o -name '*.h' -print0 | xargs -0 clang-format -style=file -output-replacements-xml | grep "<replacement " || true)
+          if [ -n "$misformatted" ]; then
+            echo "ERROR: Some files are not properly formatted. Run clang-format -i."
+            exit 1
+          else
+            echo "All files are properly formatted."
+            exit 0
+          fi

diff_engine_core/.github/workflows/release.yml

@@ -0,0 +1,39 @@
+name: Release
+
+on:
+  push:
+    tags:
+      - 'v*'
+
+jobs:
+  # Run tests before creating release
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Configure CMake
+        run: cmake -B build -S . -DCMAKE_BUILD_TYPE=Release
+
+      - name: Build
+        run: cmake --build build --config Release
+
+      - name: Run tests
+        run: ./build/all_tests
+
+  # Create GitHub release after tests pass
+  release:
+    needs: test
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Create Release
+        uses: softprops/action-gh-release@v2
+        with:
+          generate_release_notes: true

diff_engine_core/.github/workflows/sanitizer.yml

@@ -0,0 +1,32 @@
+name: ASan+UBSan
+
+on:
+  push:
+    branches: [main, development]
+  pull_request:
+    branches: [main, development]
+
+jobs:
+  build:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+
+    steps:
+      - uses: actions/checkout@v5
+
+      # Configure CMake with ASan + UBSan
+      - name: Configure with sanitizers
+        run: cmake -B build -S . \
+          -DCMAKE_BUILD_TYPE=Debug \
+          -DCMAKE_C_FLAGS="-fsanitize=address,undefined -fno-omit-frame-pointer -g" \
+          -DCMAKE_CXX_FLAGS="-fsanitize=address,undefined -fno-omit-frame-pointer -g"
+
+      # Build
+      - name: Build
+        run: cmake --build build --config Debug
+
+      # Run tests
+      - name: Run tests under ASan+UBSan
+        run: ./build/all_tests

diff_engine_core/.github/workflows/valgrind.yml

@@ -0,0 +1,27 @@
+name: Valgrind
+
+on: [push, pull_request]
+
+jobs:
+  linux:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Install dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y valgrind
+
+      - name: Configure Debug build
+        run: cmake -B build -S . -DCMAKE_BUILD_TYPE=Debug
+
+      - name: Build
+        run: cmake --build build --config Debug
+
+      - name: Run tests under Valgrind
+        run: |
+          valgrind --leak-check=full --show-leak-kinds=all \
+                   --track-origins=yes -s --show-reachable=yes \
+                   --error-exitcode=1 build/all_tests
+

diff_engine_core/.gitignore

@@ -0,0 +1,79 @@
+# Prerequisites
+*.d
+
+# Object files
+*.o
+*.ko
+*.obj
+*.elf
+
+# Linker output
+*.ilk
+*.map
+*.exp
+
+# Precompiled Headers
+*.gch
+*.pch
+
+# Libraries
+*.lib
+*.a
+*.la
+*.lo
+
+# Shared objects (inc. Windows DLLs)
+*.dll
+*.so
+*.so.*
+*.dylib
+
+# Executables
+*.exe
+*.out
+*.app
+*.i*86
+*.x86_64
+*.hex
+
+# Debug files
+*.dSYM/
+*.su
+*.idb
+*.pdb
+
+# Kernel Module Compile Results
+*.mod*
+*.cmd
+.tmp_versions/
+modules.order
+Module.symvers
+Mkfile.old
+dkms.conf
+
+# CMake
+CMakeCache.txt
+CMakeFiles/
+CMakeScripts/
+Testing/
+Makefile
+cmake_install.cmake
+install_manifest.txt
+compile_commands.json
+CTestTestfile.cmake
+_deps
+build/
+Build/
+out/
+
+# IDEs
+.vscode/
+.idea/
+*.swp
+*.swo
+*~
+.DS_Store
+
+.venv/
+__pycache__/
+uv.lock

diff_engine_core/CMakeLists.txt

@@ -0,0 +1,94 @@
+cmake_minimum_required(VERSION 3.15)
+project(DNLP_Diff_Engine C)
+set(CMAKE_C_STANDARD 99)
+
+set(DIFF_ENGINE_VERSION_MAJOR 0)
+set(DIFF_ENGINE_VERSION_MINOR 1)
+set(DIFF_ENGINE_VERSION_PATCH 1)
+set(DIFF_ENGINE_VERSION "${DIFF_ENGINE_VERSION_MAJOR}.${DIFF_ENGINE_VERSION_MINOR}.${DIFF_ENGINE_VERSION_PATCH}")
+add_compile_definitions(DIFF_ENGINE_VERSION="${DIFF_ENGINE_VERSION}")
+
+message(STATUS "Configuring DNLP Differentiation Engine (version ${DIFF_ENGINE_VERSION})")
+
+
+#Set default build type to Release if not specified
+if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES)
+  message(STATUS "Setting build type to 'Release' as none was specified.")
+  set(CMAKE_BUILD_TYPE Release CACHE STRING "Choose the type of build." FORCE)
+  set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS "Debug" "Release" "MinSizeRel" "RelWithDebInfo")
+else()
+  message(STATUS "Build type: ${CMAKE_BUILD_TYPE}")
+endif()
+
+# Warning flags (compiler-specific)
+if(MSVC)
+    add_compile_options(/W4 /WX)
+else()
+    add_compile_options(
+        -Wall                  # Enable most warnings
+        -Wextra                # Extra warnings
+        -Wpedantic             # Strict ISO C compliance
+        -Wshadow               # Warn about variable shadowing
+        -Wformat=2             # Extra format string checks
+        -Wcast-qual            # Warn about cast that removes qualifiers
+        -Wcast-align           # Warn about pointer cast alignment issues
+        -Wunused               # Warn about unused variables/functions
+        -Wdouble-promotion     # Warn about float to double promotion
+        -Wnull-dereference     # Warn about null pointer dereference
+    )
+endif()
+
+# Include directories
+include_directories(${PROJECT_SOURCE_DIR}/include)
+
+# Source files - automatically gather all .c files from src/
+file(GLOB_RECURSE SOURCES "src/*.c")
+
+
+# Create core library
+add_library(dnlp_diff ${SOURCES})
+
+# Link math library (Unix/Linux only)
+if(NOT MSVC)
+    target_link_libraries(dnlp_diff m)
+endif()
+
+# Config-specific compile options (compiler-specific)
+if(MSVC)
+    target_compile_options(dnlp_diff PRIVATE
+        $<$<CONFIG:Debug>:/Od /Zi>
+        $<$<CONFIG:Release>:/O2 /DNDEBUG>
+        $<$<CONFIG:RelWithDebInfo>:/O2 /Zi /DNDEBUG>
+        $<$<CONFIG:MinSizeRel>:/Os /DNDEBUG>
+    )
+else()
+    target_compile_options(dnlp_diff PRIVATE
+        $<$<CONFIG:Debug>:-g -O0>
+        $<$<CONFIG:Release>:-O3 -DNDEBUG>
+        $<$<CONFIG:RelWithDebInfo>:-O2 -g -DNDEBUG>
+        $<$<CONFIG:MinSizeRel>:-Os -DNDEBUG>
+    )
+endif()
+
+# This is needed for clock_gettime on Linux without compiler extensions
+if(CMAKE_SYSTEM_NAME STREQUAL "Linux")
+    add_compile_definitions(_POSIX_C_SOURCE=200809L)
+endif()
+
+# Enable position-independent code for shared library compatibility
+set_property(TARGET dnlp_diff PROPERTY POSITION_INDEPENDENT_CODE ON)
+
+# =============================================================================
+# C tests (only for standalone builds)
+# =============================================================================
+if(NOT SKBUILD)
+    include_directories(${PROJECT_SOURCE_DIR}/tests)
+    enable_testing()
+
+    add_executable(all_tests
+        tests/all_tests.c
+        tests/test_helpers.c
+    )
+    target_link_libraries(all_tests dnlp_diff)
+    add_test(NAME AllTests COMMAND all_tests)
+endif()