Refactor code

.clang-format

@@ -0,0 +1,19 @@
+---
+Language:                 Cpp
+BasedOnStyle:             Google
+
+ColumnLimit:              100
+
+BreakBeforeBraces:        Custom
+BraceWrapping:
+  AfterClass:             true
+  AfterControlStatement:  false
+  AfterEnum:              true
+  AfterFunction:          true
+  AfterNamespace:         false
+  AfterObjCDeclaration:   true
+  AfterStruct:            true
+  AfterUnion:             true
+  BeforeCatch:            false
+  BeforeElse:             false
+  IndentBraces:           false

.editorconfig

@@ -0,0 +1,22 @@
+root = true
+
+[*]
+indent_style = space
+indent_size = 2
+end_of_line = lf
+charset = utf-8
+trim_trailing_whitespace = true
+insert_final_newline = false
+max_line_length = 100
+
+[*.py]
+indent_size = 4
+
+[Makefile]
+indent_style = tab
+
+[CMakeLists.txt]
+indent_size = 2
+
+[*.{json,yml,yaml}]
+indent_size = 2

.github/workflows/default.yml

@@ -15,38 +15,37 @@ jobs:
 
     steps:
 
-    - name: Checkout repository
-      uses: actions/checkout@v4
-
-    - name: Install dependencies
-      run: |
-        sudo apt-get install -y build-essential python-dev-is-python3 python3-numpy python3-pytest
-
-    - name: Build library
-      run: make PYTHON=python
-
-    - name: Run library tests
-      run: make test PYTHON=python
-
-    - name: Copy library to docs/ directory
-      run: cp -r permanent/ docs/permanent/
-
-    - name: Build documentation
-      uses: ammaraskar/sphinx-action@master
-      with:
-        build-command: "make html"
-        docs-folder: "docs/"
-
-    - name: Fix documentation permissions
-      run: |
-        chmod -c -R +rX "docs/build/html/" | while read line; do
-          echo "::warning title=Invalid file permissions automatically fixed::$line"
-        done
-
-    - name: Upload Pages artifact
-      uses: actions/upload-pages-artifact@v3
-      with:
-        path: docs/build/html/
+      - uses: actions/checkout@v4
+
+      - name: Install dependencies
+        run: sudo apt-get install -y build-essential cmake
+
+      - name: Install Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+      - run: pip install .
+
+      - name: PyTest
+        run: |
+          pip install pytest
+          pytest -v tests
+
+      - name: Build documentation
+        run: |
+          pip install sphinx sphinx_rtd_theme sphinx_copybutton
+          cd docs && make html
+
+      - name: Fix documentation permissions
+        run: |
+          chmod -c -R +rX "docs/build/html/" | while read line; do
+            echo "::warning title=Invalid file permissions automatically fixed::$line"
+          done
+
+      - name: Upload Pages artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: docs/build/html/
 
   deploy:
 

.github/workflows/pull_request.yml

@@ -10,35 +10,34 @@ jobs:
 
     steps:
 
-    - name: Checkout repository
-      uses: actions/checkout@v4
-
-    - name: Install dependencies
-      run: |
-        sudo apt-get install -y build-essential python-dev-is-python3 python3-numpy python3-pytest
-
-    - name: Build library
-      run: make PYTHON=python
-
-    - name: Run library tests
-      run: make test PYTHON=python
-
-    - name: Copy library to docs/ directory
-      run: cp -r permanent/ docs/permanent/
-
-    - name: Build documentation
-      uses: ammaraskar/sphinx-action@master
-      with:
-        build-command: "make html"
-        docs-folder: "docs/"
-
-    - name: Fix documentation permissions
-      run: |
-        chmod -c -R +rX "docs/build/html/" | while read line; do
-          echo "::warning title=Invalid file permissions automatically fixed::$line"
-        done
-
-    - name: Upload Pages artifact
-      uses: actions/upload-pages-artifact@v3
-      with:
-        path: docs/build/html/
+      - uses: actions/checkout@v4
+
+      - name: Install dependencies
+        run: sudo apt-get install -y build-essential cmake
+
+      - name: Install Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+      - run: pip install .
+
+      - name: PyTest
+        run: |
+          pip install pytest
+          pytest -v tests
+
+      - name: Build documentation
+        run: |
+          pip install sphinx sphinx_rtd_theme sphinx_copybutton
+          cd docs && make html
+
+      - name: Fix documentation permissions
+        run: |
+          chmod -c -R +rX "docs/build/html/" | while read line; do
+            echo "::warning title=Invalid file permissions automatically fixed::$line"
+          done
+
+      - name: Upload Pages artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: docs/build/html/

.gitignore

@@ -84,7 +84,8 @@ tags
 .vscode/
 
 # Project files
-compile_flags.txt
-src/tuning
-src/tuning.h
-src/tuning.csv
+/include/permanent/tuning.h
+
+# Language server files
+compile_commands.json
+.ccls-cache

.pre-commit-config.yaml

@@ -52,8 +52,8 @@ repos:
     hooks:
       - id: cppcheck
         args: ["--inline-suppr", "--suppress=missingIncludeSystem",
-          "--suppress=*:src/swap.h", "--suppress=*:src/perm-mv0.h", "--suppress=*:src/kperm-gray.h"]
+          "--suppress=*:include/permanent/swap.h", "--suppress=*:include/permanent/perm-mv0.h", "--suppress=*:include/permanent/kperm-gray.h"]
       - id: cpplint
         args: ["--root=src", "--filter=-build/include_subdir"]
       - id: clang-format
-        args: ["-i", "-style={BasedOnStyle: google, IndentWidth: 4}"]
+        args: ["-i", "-style=file"]

CMakeLists.txt

@@ -0,0 +1,186 @@
+# Supported CMake versions
+
+cmake_minimum_required(VERSION 3.23 FATAL_ERROR)
+
+# Project configuration
+
+set(CMAKE_CXX_STANDARD 20)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+
+project(MatrixPermanent VERSION 0.0.1 LANGUAGES CXX)
+
+if(PROJECT_SOURCE_DIR STREQUAL PROJECT_BINARY_DIR)
+  message(
+    FATAL_ERROR
+      "In-source builds not allowed; make a build directory and run CMake from it\n")
+endif()
+
+if(ENV{PERMANENT_TUNE})
+  set(PERMANENT_TUNE ON)
+endif()
+
+if(SKBUILD OR ENV{PERMANENT_PYTHON})
+  set(PERMANENT_PYTHON ON)
+endif()
+
+# Dependencies
+
+if(PROJECT_IS_TOP_LEVEL AND PERMANENT_PYTHON)
+  find_package(Python REQUIRED COMPONENTS Interpreter Development.Module)
+elseif(PERMANENT_TUNE)
+  find_package(Python REQUIRED COMPONENTS Interpreter)
+endif()
+
+# Tuning header target
+
+set(PERMANENT_TUNING_HEADER "${CMAKE_CURRENT_SOURCE_DIR}/include/permanent/tuning.h")
+set(PERMANENT_TUNING_DATA "${CMAKE_BINARY_DIR}/tuning.csv")
+
+if(PERMANENT_TUNE)
+  add_executable(PermanentTune src/tuning.cc)
+  target_include_directories(PermanentTune PRIVATE include)
+
+  add_custom_target(TuningData ALL
+    COMMAND
+      PermanentTune "${PERMANENT_TUNING_DATA}"
+    BYPRODUCTS
+      "${PERMANENT_TUNING_DATA}")
+
+  add_custom_target(TuningHeader ALL
+    COMMAND
+    ${Python_EXECUTABLE}
+        "${CMAKE_CURRENT_SOURCE_DIR}/tools/generate_tuning_header.py"
+        "${PERMANENT_TUNING_DATA}"
+        "${PERMANENT_TUNING_HEADER}"
+    BYPRODUCTS
+      "${PERMANENT_TUNING_HEADER}")
+  add_dependencies(TuningHeader TuningData)
+else()
+  add_custom_target(TuningHeader ALL
+    COMMAND
+      cp "-f"
+        "${CMAKE_CURRENT_SOURCE_DIR}/include/permanent/tuning.default.h"
+        "${PERMANENT_TUNING_HEADER}"
+    BYPRODUCTS
+      "${PERMANENT_TUNING_HEADER}")
+endif()
+
+# Header library target
+
+add_library(permanent_headers INTERFACE)
+add_library(MatrixPermanent::headers ALIAS permanent_headers)
+add_dependencies(permanent_headers TuningHeader)
+target_include_directories(permanent_headers
+  INTERFACE
+    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>
+    $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>)
+
+if(PROJECT_IS_TOP_LEVEL)
+  set(CPACK_RESOURCE_FILE_LICENSE "${PROJECT_SOURCE_DIR}/LICENSE")
+  include(GNUInstallDirs)
+  include(CMakePackageConfigHelpers)
+  include(CPack)
+  write_basic_package_version_file(
+    "${PROJECT_NAME}ConfigVersion.cmake"
+    VERSION
+        ${PROJECT_VERSION}
+    COMPATIBILITY
+        SameMajorVersion)
+  configure_package_config_file(
+    "${PROJECT_SOURCE_DIR}/cmake/${PROJECT_NAME}Config.cmake.in"
+    "${PROJECT_BINARY_DIR}/${PROJECT_NAME}Config.cmake"
+    INSTALL_DESTINATION
+      ${CMAKE_INSTALL_DATAROOTDIR}/${PROJECT_NAME}/cmake)
+
+  install(TARGETS permanent_headers
+    EXPORT ${PROJECT_NAME}_Targets
+    ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
+    LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
+    RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR})
+
+  install(
+    EXPORT
+      ${PROJECT_NAME}_Targets
+    FILE
+      ${PROJECT_NAME}Targets.cmake
+    NAMESPACE
+      ${PROJECT_NAME}::
+    DESTINATION
+      ${CMAKE_INSTALL_DATAROOTDIR}/${PROJECT_NAME}/cmake)
+
+  install(
+    FILES
+      "${PROJECT_BINARY_DIR}/${PROJECT_NAME}Config.cmake"
+      "${PROJECT_BINARY_DIR}/${PROJECT_NAME}ConfigVersion.cmake"
+    DESTINATION
+      ${CMAKE_INSTALL_DATAROOTDIR}/${PROJECT_NAME}/cmake)
+
+  install(
+    DIRECTORY
+      ${PROJECT_SOURCE_DIR}/include/permanent
+    DESTINATION
+      include)
+endif()
+
+# Python library target
+
+if(PROJECT_IS_TOP_LEVEL AND PERMANENT_PYTHON)
+  execute_process(
+    COMMAND
+      sh -c "${CMAKE_CXX_COMPILER} --version | head -n 1"
+    WORKING_DIRECTORY
+      ${PROJECT_SOURCE_DIR}
+    OUTPUT_VARIABLE
+      _PERMANENT_COMPILER_VERSION
+    OUTPUT_STRIP_TRAILING_WHITESPACE)
+
+  execute_process(
+    COMMAND
+      git rev-parse --abbrev-ref HEAD
+    WORKING_DIRECTORY
+      ${PROJECT_SOURCE_DIR}
+    OUTPUT_VARIABLE
+      _PERMANENT_GIT_BRANCH
+    OUTPUT_STRIP_TRAILING_WHITESPACE)
+
+  execute_process(
+    COMMAND
+      git log -1 --format=%h
+    WORKING_DIRECTORY
+      ${PROJECT_SOURCE_DIR}
+    OUTPUT_VARIABLE
+      _PERMANENT_GIT_COMMIT_HASH
+    OUTPUT_STRIP_TRAILING_WHITESPACE)
+
+  execute_process(
+    COMMAND
+    ${Python_EXECUTABLE} "-c" "import numpy; print(numpy.get_include())"
+    OUTPUT_VARIABLE
+      NumPy_INCLUDE_DIRS
+    OUTPUT_STRIP_TRAILING_WHITESPACE)
+
+  python_add_library(permanent MODULE src/main.cc WITH_SOABI)
+  target_include_directories(permanent
+    PRIVATE
+      include
+      ${NumPy_INCLUDE_DIRS})
+  target_compile_definitions(permanent
+    PRIVATE
+      "_PERMANENT_VERSION=${PROJECT_VERSION}"
+      "_PERMANENT_COMPILER_VERSION=${_PERMANENT_COMPILER_VERSION}"
+      "_PERMANENT_GIT_BRANCH=${_PERMANENT_GIT_BRANCH}"
+      "_PERMANENT_GIT_COMMIT_HASH=${_PERMANENT_GIT_COMMIT_HASH}"
+  )
+  if (UNIX)
+    if (APPLE)
+      set_target_properties(permanent
+        PROPERTIES
+          LINK_FLAGS "-Wl,-dylib,-undefined,dynamic_lookup")
+    else()
+      set_target_properties(permanent
+        PROPERTIES
+          LINK_FLAGS "-Wl,--allow-shlib-undefined")
+    endif()
+  endif()
+  install(TARGETS permanent DESTINATION .)
+endif()