feat: refactor

.clang-format

@@ -0,0 +1,19 @@
+---
+BasedOnStyle: LLVM
+Standard: Latest
+IndentWidth: 2
+TabWidth: 2
+UseTab: Never
+ColumnLimit: 100
+ContinuationIndentWidth: 4
+PointerAlignment: Left
+ReferenceAlignment: Left
+BreakBeforeBraces: Attach
+AllowShortFunctionsOnASingleLine: Empty
+AllowShortIfStatementsOnASingleLine: Never
+AllowShortLoopsOnASingleLine: false
+NamespaceIndentation: None
+SortIncludes: true
+IncludeBlocks: Preserve
+ReflowComments: false
+...

.clang-tidy

@@ -0,0 +1,44 @@
+---
+Checks: >
+  -*,
+  bugprone-branch-clone,
+  bugprone-copy-constructor-init,
+  bugprone-dangling-handle,
+  bugprone-fold-init-type,
+  bugprone-forward-declaration-namespace,
+  bugprone-inaccurate-erase,
+  bugprone-infinite-loop,
+  bugprone-macro-parentheses,
+  bugprone-misplaced-operator-in-strlen-in-alloc,
+  bugprone-move-forwarding-reference,
+  bugprone-multiple-statement-macro,
+  bugprone-sizeof-container,
+  bugprone-sizeof-expression,
+  bugprone-string-constructor,
+  bugprone-string-integer-assignment,
+  bugprone-suspicious-enum-usage,
+  bugprone-suspicious-include,
+  bugprone-suspicious-memory-comparison,
+  bugprone-suspicious-memset-usage,
+  bugprone-unchecked-optional-access,
+  bugprone-undefined-memory-manipulation,
+  bugprone-use-after-move,
+  performance-for-range-copy,
+  performance-inefficient-string-concatenation,
+  performance-inefficient-vector-operation,
+  performance-move-const-arg,
+  performance-no-automatic-move,
+  modernize-use-nullptr,
+  modernize-use-override,
+  modernize-use-using,
+  readability-const-return-type,
+  readability-duplicate-include,
+  readability-redundant-control-flow,
+  readability-simplify-boolean-expr
+WarningsAsErrors: ""
+HeaderFilterRegex: "^(.*(/include/igneous/|/src/).*)$"
+FormatStyle: file
+CheckOptions:
+  - key: modernize-use-nullptr.NullMacros
+    value: "NULL"
+...

.github/workflows/ci.yml

@@ -171,3 +171,119 @@ jobs:
         with:
           name: compile-commands
           path: build-debug/compile_commands.json
+
+  lint:
+    name: Lint (clang-tidy)
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout source
+        uses: actions/checkout@v4
+
+      - name: Install lint tools
+        shell: bash
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y clang-tidy ripgrep
+
+      - name: Checkout vcpkg
+        uses: actions/checkout@v4
+        with:
+          repository: microsoft/vcpkg
+          path: vcpkg
+
+      - name: Restore vcpkg cache
+        uses: actions/cache@v4
+        with:
+          path: |
+            ~/.cache/vcpkg/archives
+            ${{ github.workspace }}/vcpkg/downloads
+          key: vcpkg-${{ runner.os }}-x64-linux-${{ hashFiles('vcpkg.json', 'CMakeLists.txt') }}
+
+      - name: Bootstrap vcpkg
+        shell: bash
+        run: ./vcpkg/bootstrap-vcpkg.sh
+
+      - name: Configure (Lint)
+        shell: bash
+        run: >-
+          cmake -S . -B build-lint -G Ninja
+          -DCMAKE_BUILD_TYPE=Debug
+          -DCMAKE_TOOLCHAIN_FILE=${{ github.workspace }}/vcpkg/scripts/buildsystems/vcpkg.cmake
+          -DVCPKG_TARGET_TRIPLET=x64-linux
+          -DCMAKE_EXPORT_COMPILE_COMMANDS=ON
+
+      - name: Run clang-tidy (all)
+        shell: bash
+        run: IGNEOUS_LINT_SCOPE=all IGNEOUS_LINT_HEADERS=1 IGNEOUS_LINT_JOBS=4 ./scripts/dev/lint.sh build-lint
+
+  format-check:
+    name: Format Check (clang-format)
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout source
+        uses: actions/checkout@v4
+
+      - name: Install format tools
+        shell: bash
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y python3-pip ripgrep
+          python3 -m pip install --user clang-format==20.1.3
+
+      - name: Run clang-format check
+        shell: bash
+        run: |
+          export IGNEOUS_CLANG_FORMAT_BIN="$HOME/.local/bin/clang-format"
+          "$IGNEOUS_CLANG_FORMAT_BIN" --version
+          ./scripts/dev/format.sh --check
+
+  docs:
+    name: API Docs (doxygen)
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout source
+        uses: actions/checkout@v4
+
+      - name: Install docs tools
+        shell: bash
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y doxygen graphviz
+
+      - name: Checkout vcpkg
+        uses: actions/checkout@v4
+        with:
+          repository: microsoft/vcpkg
+          path: vcpkg
+
+      - name: Restore vcpkg cache
+        uses: actions/cache@v4
+        with:
+          path: |
+            ~/.cache/vcpkg/archives
+            ${{ github.workspace }}/vcpkg/downloads
+          key: vcpkg-${{ runner.os }}-x64-linux-${{ hashFiles('vcpkg.json', 'CMakeLists.txt') }}
+
+      - name: Bootstrap vcpkg
+        shell: bash
+        run: ./vcpkg/bootstrap-vcpkg.sh
+
+      - name: Configure (Docs)
+        shell: bash
+        run: >-
+          cmake -S . -B build-docs -G Ninja
+          -DCMAKE_BUILD_TYPE=Release
+          -DCMAKE_TOOLCHAIN_FILE=${{ github.workspace }}/vcpkg/scripts/buildsystems/vcpkg.cmake
+          -DVCPKG_TARGET_TRIPLET=x64-linux
+          -DIGNEOUS_BUILD_DOCS=ON
+
+      - name: Build docs
+        shell: bash
+        run: cmake --build build-docs --target docs
+
+      - name: Verify docs output
+        shell: bash
+        run: test -f build-docs/docs/html/index.html

.github/workflows/docs.yml

@@ -0,0 +1,80 @@
+name: Docs
+
+on:
+  push:
+    branches:
+      - main
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+concurrency:
+  group: docs-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build-docs:
+    name: Build API Docs
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout source
+        uses: actions/checkout@v4
+
+      - name: Install docs tools
+        shell: bash
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y doxygen graphviz
+
+      - name: Checkout vcpkg
+        uses: actions/checkout@v4
+        with:
+          repository: microsoft/vcpkg
+          path: vcpkg
+
+      - name: Restore vcpkg cache
+        uses: actions/cache@v4
+        with:
+          path: |
+            ~/.cache/vcpkg/archives
+            ${{ github.workspace }}/vcpkg/downloads
+          key: vcpkg-${{ runner.os }}-x64-linux-${{ hashFiles('vcpkg.json', 'CMakeLists.txt') }}
+
+      - name: Bootstrap vcpkg
+        shell: bash
+        run: ./vcpkg/bootstrap-vcpkg.sh
+
+      - name: Configure (Docs)
+        shell: bash
+        run: >-
+          cmake -S . -B build-docs -G Ninja
+          -DCMAKE_BUILD_TYPE=Release
+          -DCMAKE_TOOLCHAIN_FILE=${{ github.workspace }}/vcpkg/scripts/buildsystems/vcpkg.cmake
+          -DVCPKG_TARGET_TRIPLET=x64-linux
+          -DIGNEOUS_BUILD_DOCS=ON
+
+      - name: Build docs
+        shell: bash
+        run: cmake --build build-docs --target docs
+
+      - name: Upload Pages artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: build-docs/docs/html
+
+  deploy:
+    name: Deploy to GitHub Pages
+    needs: build-docs
+    runs-on: ubuntu-latest
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+
+    steps:
+      - name: Deploy
+        id: deployment
+        uses: actions/deploy-pages@v4

CMakeLists.txt

@@ -5,6 +5,7 @@ set(CMAKE_CXX_STANDARD 23)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 set(CMAKE_CXX_EXTENSIONS OFF)
 add_compile_options(-Wall -Wextra -Wpedantic)
+option(IGNEOUS_BUILD_DOCS "Build Doxygen API documentation target" ON)
 
 if(APPLE)
   enable_language(OBJCXX)
@@ -43,6 +44,28 @@ target_link_libraries(
             Spectra::Spectra
             igneous_runtime)
 
+if(IGNEOUS_BUILD_DOCS)
+  find_package(Doxygen QUIET)
+  if(DOXYGEN_FOUND)
+    set(IGNEOUS_DOXYFILE_IN ${CMAKE_SOURCE_DIR}/docs/Doxyfile.in)
+    set(IGNEOUS_DOXYFILE_OUT ${CMAKE_BINARY_DIR}/Doxyfile)
+    configure_file(${IGNEOUS_DOXYFILE_IN} ${IGNEOUS_DOXYFILE_OUT} @ONLY)
+    add_custom_target(
+      docs
+      COMMAND ${DOXYGEN_EXECUTABLE} ${IGNEOUS_DOXYFILE_OUT}
+      WORKING_DIRECTORY ${CMAKE_BINARY_DIR}
+      COMMENT "Generating API documentation with Doxygen"
+      VERBATIM)
+  else()
+    message(STATUS "Doxygen not found; 'docs' target will print install guidance")
+    add_custom_target(
+      docs
+      COMMAND ${CMAKE_COMMAND} -E echo "Doxygen not found. Install doxygen (and graphviz optionally), then re-run CMake configure."
+      COMMENT "API docs unavailable: Doxygen not installed"
+      VERBATIM)
+  endif()
+endif()
+
 enable_testing()
 
 function(add_igneous_test name source)
@@ -52,8 +75,9 @@ function(add_igneous_test name source)
 endfunction()
 
 add_igneous_test(test_algebra tests/test_algebra.cpp)
-add_igneous_test(test_topology_triangle tests/test_topology_triangle.cpp)
-add_igneous_test(test_topology_diffusion tests/test_topology_diffusion.cpp)
+add_igneous_test(test_structure_dec tests/test_structure_dec.cpp)
+add_igneous_test(test_structure_diffusion_geometry
+                 tests/test_structure_diffusion_geometry.cpp)
 add_igneous_test(test_ops_curvature_flow tests/test_ops_curvature_flow.cpp)
 add_igneous_test(test_ops_spectral_geometry tests/test_ops_spectral_geometry.cpp)
 add_igneous_test(test_ops_hodge tests/test_ops_hodge.cpp)
@@ -89,8 +113,8 @@ target_link_libraries(igneous-spectral PRIVATE igneous fmt::fmt)
 add_executable(igneous-hodge src/main_hodge.cpp)
 target_link_libraries(igneous-hodge PRIVATE igneous fmt::fmt)
 
-add_executable(igneous-diffusion-topology src/main_diffusion_topology.cpp)
-target_link_libraries(igneous-diffusion-topology PRIVATE igneous fmt::fmt)
+add_executable(igneous-diffusion-geometry src/main_diffusion_geometry.cpp)
+target_link_libraries(igneous-diffusion-geometry PRIVATE igneous fmt::fmt)
 
 add_test(
   NAME test_hodge_cli_outputs
@@ -106,7 +130,7 @@ set_tests_properties(test_hodge_parity_optional PROPERTIES LABELS "hodge;parity"
 add_test(
   NAME test_diffgeo_cli_outputs
   COMMAND bash ${CMAKE_SOURCE_DIR}/tests/test_diffgeo_cli_outputs.sh
-          $<TARGET_FILE:igneous-diffusion-topology>)
+          $<TARGET_FILE:igneous-diffusion-geometry>)
 set_tests_properties(test_diffgeo_cli_outputs PROPERTIES LABELS "diffgeo;cli")
 
 add_test(