Upgrade VMD_cpp into a reusable library and CLI

.github/workflows/ci.yml

@@ -0,0 +1,109 @@
+name: CI
+
+on:
+  push:
+  pull_request:
+
+permissions:
+  contents: read
+
+jobs:
+  build-and-test:
+    name: ${{ matrix.name }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - name: MSVC
+            os: windows-latest
+          - name: GCC
+            os: ubuntu-latest
+            cc: gcc
+            cxx: g++
+          - name: Clang
+            os: ubuntu-latest
+            cc: clang
+            cxx: clang++
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Install Linux dependencies
+        if: runner.os == 'Linux'
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y libeigen3-dev ninja-build
+
+      - name: Configure (MSVC)
+        if: runner.os == 'Windows'
+        run: >-
+          cmake -S . -B build-ci
+          -DVMD_USE_VENDORED_EIGEN=ON
+          -DVMD_BUILD_DOCS=OFF
+          -DVMD_ENABLE_WARNINGS=ON
+
+      - name: Configure (GCC or Clang)
+        if: runner.os == 'Linux'
+        env:
+          CC: ${{ matrix.cc }}
+          CXX: ${{ matrix.cxx }}
+        run: >-
+          cmake -S . -B build-ci -G Ninja
+          -DCMAKE_BUILD_TYPE=Release
+          -DVMD_BUILD_DOCS=OFF
+          -DVMD_ENABLE_WARNINGS=ON
+
+      - name: Build
+        run: cmake --build build-ci --config Release --parallel 2
+
+      - name: Test
+        run: ctest --test-dir build-ci -C Release --output-on-failure
+
+  install-package:
+    name: Installed package consumer
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y libeigen3-dev ninja-build
+      - name: Build and install VMD_cpp
+        run: |
+          cmake -S . -B build-install -G Ninja -DCMAKE_BUILD_TYPE=Release -DVMD_BUILD_DOCS=OFF
+          cmake --build build-install --parallel 2
+          cmake --install build-install --prefix "$PWD/install"
+      - name: Build downstream consumer
+        run: |
+          cmake -S tests/package_consumer -B build-consumer -G Ninja -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH="$PWD/install"
+          cmake --build build-consumer --parallel 2
+          ./build-consumer/vmd_package_consumer
+
+  sanitizers:
+    name: Clang ASan and UBSan
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y clang libeigen3-dev ninja-build
+      - name: Configure
+        env:
+          CC: clang
+          CXX: clang++
+        run: >-
+          cmake -S . -B build-sanitizers -G Ninja
+          -DCMAKE_BUILD_TYPE=Debug
+          -DVMD_BUILD_DOCS=OFF
+          -DVMD_BUILD_BENCHMARKS=OFF
+          -DVMD_ENABLE_SANITIZERS=ON
+          -DVMD_ENABLE_WARNINGS=ON
+      - name: Build
+        run: cmake --build build-sanitizers --parallel 2
+      - name: Test
+        env:
+          ASAN_OPTIONS: detect_leaks=1:halt_on_error=1
+          UBSAN_OPTIONS: print_stacktrace=1:halt_on_error=1
+        run: ctest --test-dir build-sanitizers --output-on-failure

.gitignore

@@ -1974,3 +1974,7 @@ eigen-3.4.0/unsupported/test/special_functions.cpp
 eigen-3.4.0/unsupported/test/special_packetmath.cpp
 eigen-3.4.0/unsupported/test/splines.cpp
 eigen-3.4.0/ci/build.gitlab-ci.yml
+# Local CMake and Codex build trees
+/.codex-build/
+/build-*/
+/vmd-output/

CMakeLists.txt

@@ -1,15 +1,192 @@
-cmake_minimum_required (VERSION 3.8)
+cmake_minimum_required(VERSION 3.20)
 
-project ("VMD_CPP")
+project(VMD_cpp VERSION 2.0.0 LANGUAGES CXX)
 
-find_package(Eigen3)
+include(CMakePackageConfigHelpers)
+include(CTest)
+include(FetchContent)
+include(GNUInstallDirs)
 
-include_directories($SYSTEM ${CMAKE_CURRENT_SOURCE_DIR}/Eigen)
-include_directories($SYSTEM ${CMAKE_CURRENT_SOURCE_DIR}/Eigen/unsupported )
-add_executable (VMD_CPP "VMD.cpp" "VMD.h" "VMD_Utils.cpp")
+option(VMD_BUILD_CLI "Build the vmd_cli executable" ON)
+option(VMD_BUILD_EXAMPLES "Build examples" ON)
+option(VMD_BUILD_TESTS "Build tests" ${BUILD_TESTING})
+option(VMD_BUILD_BENCHMARKS "Build benchmarks" ON)
+option(VMD_BUILD_DOCS "Add the optional Doxygen docs target" ON)
+option(VMD_ENABLE_WARNINGS "Enable high compiler warnings" ON)
+option(VMD_ENABLE_SANITIZERS "Enable AddressSanitizer and UndefinedBehaviorSanitizer" OFF)
+option(VMD_USE_VENDORED_EIGEN "Use the repository's Eigen checkout before downloading Eigen" OFF)
 
-add_custom_target(build_all_configs
-    COMMAND ${CMAKE_COMMAND} --build ${CMAKE_BINARY_DIR} --target ALL_BUILD --config Debug
-    COMMAND ${CMAKE_COMMAND} --build ${CMAKE_BINARY_DIR} --target ALL_BUILD --config RelWithDebInfo
-    COMMAND ${CMAKE_COMMAND} --build ${CMAKE_BINARY_DIR} --target ALL_BUILD --config Release
-)
+set(VMD_FFT_BACKEND "Eigen" CACHE STRING "FFT backend: Eigen, FFTW, or MKL")
+set_property(CACHE VMD_FFT_BACKEND PROPERTY STRINGS Eigen FFTW MKL)
+
+find_package(Eigen3 3.3 CONFIG QUIET)
+if(NOT TARGET Eigen3::Eigen AND VMD_USE_VENDORED_EIGEN AND EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/Eigen/Eigen/Core")
+    add_library(Eigen3::Eigen INTERFACE IMPORTED)
+    set_target_properties(Eigen3::Eigen PROPERTIES
+        INTERFACE_SYSTEM_INCLUDE_DIRECTORIES "${CMAKE_CURRENT_SOURCE_DIR}/Eigen"
+        INTERFACE_INCLUDE_DIRECTORIES "${CMAKE_CURRENT_SOURCE_DIR}/Eigen")
+endif()
+
+if(NOT TARGET Eigen3::Eigen)
+    FetchContent_Declare(
+        eigen
+        URL https://gitlab.com/libeigen/eigen/-/archive/3.4.0/eigen-3.4.0.tar.gz
+        URL_HASH SHA256=8586084f71f9bde545ee7fa6d00288b264a2b7ac3607b974e54d13e7162c1c72
+        DOWNLOAD_EXTRACT_TIMESTAMP TRUE
+    )
+    if(POLICY CMP0169)
+        cmake_policy(SET CMP0169 OLD)
+    endif()
+    FetchContent_GetProperties(eigen)
+    if(NOT eigen_POPULATED)
+        FetchContent_Populate(eigen)
+    endif()
+    add_library(Eigen3::Eigen INTERFACE IMPORTED)
+    set_target_properties(Eigen3::Eigen PROPERTIES
+        INTERFACE_SYSTEM_INCLUDE_DIRECTORIES "${eigen_SOURCE_DIR}"
+        INTERFACE_INCLUDE_DIRECTORIES "${eigen_SOURCE_DIR}")
+endif()
+
+add_library(vmd
+    src/fft_backend.cpp
+    src/vmd.cpp
+    VMD_Utils.cpp
+)
+add_library(VMD_cpp::vmd ALIAS vmd)
+
+target_compile_features(vmd PUBLIC cxx_std_17)
+target_include_directories(vmd
+    PUBLIC
+        $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>
+        $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}>
+        $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
+    PRIVATE src
+)
+target_link_libraries(vmd PUBLIC
+    $<BUILD_INTERFACE:Eigen3::Eigen>
+    $<INSTALL_INTERFACE:Eigen3::Eigen>
+)
+
+string(TOUPPER "${VMD_FFT_BACKEND}" VMD_FFT_BACKEND_UPPER)
+if(VMD_FFT_BACKEND_UPPER STREQUAL "EIGEN")
+    target_compile_definitions(vmd PRIVATE VMD_FFT_BACKEND_EIGEN=1)
+elseif(VMD_FFT_BACKEND_UPPER STREQUAL "FFTW")
+    find_path(FFTW3_INCLUDE_DIR fftw3.h REQUIRED)
+    find_library(FFTW3_LIBRARY NAMES fftw3 libfftw3-3 REQUIRED)
+    if(NOT TARGET FFTW3::fftw3)
+        add_library(FFTW3::fftw3 UNKNOWN IMPORTED)
+        set_target_properties(FFTW3::fftw3 PROPERTIES
+            IMPORTED_LOCATION "${FFTW3_LIBRARY}"
+            INTERFACE_INCLUDE_DIRECTORIES "${FFTW3_INCLUDE_DIR}"
+        )
+    endif()
+    target_link_libraries(vmd PRIVATE FFTW3::fftw3)
+    target_compile_definitions(vmd PRIVATE VMD_FFT_BACKEND_FFTW=1)
+elseif(VMD_FFT_BACKEND_UPPER STREQUAL "MKL")
+    find_package(MKL CONFIG REQUIRED)
+    target_link_libraries(vmd PRIVATE MKL::MKL)
+    target_compile_definitions(vmd PRIVATE VMD_FFT_BACKEND_MKL=1)
+else()
+    message(FATAL_ERROR "VMD_FFT_BACKEND must be Eigen, FFTW, or MKL")
+endif()
+
+function(vmd_enable_warnings target)
+    if(MSVC)
+        target_compile_options(${target} PRIVATE /utf-8)
+    endif()
+    if(NOT VMD_ENABLE_WARNINGS)
+        return()
+    endif()
+    if(MSVC)
+        target_compile_options(${target} PRIVATE /W4 /permissive-)
+    else()
+        target_compile_options(${target} PRIVATE -Wall -Wextra -Wpedantic -Wconversion -Wshadow)
+    endif()
+endfunction()
+vmd_enable_warnings(vmd)
+
+if(VMD_ENABLE_SANITIZERS AND NOT MSVC)
+    target_compile_options(vmd PUBLIC -fsanitize=address,undefined -fno-omit-frame-pointer)
+    target_link_options(vmd PUBLIC -fsanitize=address,undefined)
+endif()
+
+if(VMD_BUILD_CLI)
+    add_library(vmd_cli_support STATIC app/cli_io.cpp app/report.cpp)
+    target_compile_features(vmd_cli_support PUBLIC cxx_std_17)
+    target_include_directories(vmd_cli_support PUBLIC app)
+    target_link_libraries(vmd_cli_support PUBLIC vmd)
+    vmd_enable_warnings(vmd_cli_support)
+
+    add_executable(vmd_cli app/vmd_cli.cpp)
+    target_link_libraries(vmd_cli PRIVATE vmd_cli_support)
+    vmd_enable_warnings(vmd_cli)
+endif()
+
+if(VMD_BUILD_EXAMPLES)
+    add_executable(vmd_example examples/vmd_example.cpp)
+    target_link_libraries(vmd_example PRIVATE vmd)
+    vmd_enable_warnings(vmd_example)
+endif()
+
+if(VMD_BUILD_TESTS AND BUILD_TESTING)
+    add_executable(vmd_tests tests/vmd_tests.cpp)
+    target_link_libraries(vmd_tests PRIVATE vmd)
+    vmd_enable_warnings(vmd_tests)
+    add_test(NAME vmd.unit COMMAND vmd_tests)
+
+    if(VMD_BUILD_CLI)
+        add_test(
+            NAME vmd.cli.e2e
+            COMMAND ${CMAKE_COMMAND}
+                -DCLI=$<TARGET_FILE:vmd_cli>
+                -DOUTPUT_DIR=${CMAKE_CURRENT_BINARY_DIR}/cli-e2e-output
+                -P ${CMAKE_CURRENT_SOURCE_DIR}/tests/cli_e2e.cmake
+        )
+    endif()
+endif()
+
+if(VMD_BUILD_BENCHMARKS)
+    add_executable(vmd_benchmark benchmarks/vmd_benchmark.cpp)
+    target_link_libraries(vmd_benchmark PRIVATE vmd)
+    vmd_enable_warnings(vmd_benchmark)
+endif()
+
+if(VMD_BUILD_DOCS)
+    find_package(Doxygen QUIET)
+    if(Doxygen_FOUND)
+        set(DOXYGEN_USE_MDFILE_AS_MAINPAGE README.md)
+        doxygen_add_docs(docs README.md include/vmd docs COMMENT "Generate VMD_cpp API documentation")
+    else()
+        message(STATUS "Doxygen not found; the optional docs target will not be generated")
+    endif()
+endif()
+
+install(TARGETS vmd EXPORT VMD_cppTargets
+    ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}
+    LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}
+    RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
+    INCLUDES DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}
+)
+install(DIRECTORY include/ DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
+install(FILES VMD.h DESTINATION ${CMAKE_INSTALL_INCLUDEDIR})
+
+configure_package_config_file(
+    cmake/VMD_cppConfig.cmake.in
+    ${CMAKE_CURRENT_BINARY_DIR}/VMD_cppConfig.cmake
+    INSTALL_DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/VMD_cpp
+)
+write_basic_package_version_file(
+    ${CMAKE_CURRENT_BINARY_DIR}/VMD_cppConfigVersion.cmake
+    VERSION ${PROJECT_VERSION}
+    COMPATIBILITY SameMajorVersion
+)
+install(EXPORT VMD_cppTargets
+    FILE VMD_cppTargets.cmake
+    NAMESPACE VMD_cpp::
+    DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/VMD_cpp
+)
+install(FILES
+    ${CMAKE_CURRENT_BINARY_DIR}/VMD_cppConfig.cmake
+    ${CMAKE_CURRENT_BINARY_DIR}/VMD_cppConfigVersion.cmake
+    DESTINATION ${CMAKE_INSTALL_LIBDIR}/cmake/VMD_cpp
+)

Eigen/.gitignore

@@ -8,8 +8,8 @@ save
 *.old
 *.gmo
 *.qm
-core
-core.*
+/core
+/core.*
 *.bak
 *~
 *build*