CMakeLists.txt

cmake_minimum_required(VERSION 3.9)
project(ReDyMo)

#######
# Make sure libs are available locally
#######
execute_process(COMMAND git submodule update --init)
# We have to run these commands twice because of submodules that have
# submodules. They will be accounted for only after the first command.
execute_process(COMMAND git submodule foreach --recursive git submodule update --init)
execute_process(COMMAND git submodule foreach --recursive git submodule update --init)

#######
# Declare our custom options
#######
OPTION(BUILD_GPGPU "Wether to build the OpenCL dependant GPU code." OFF)
OPTION(BUILD_TESTING "Wether to build the tests." ON)
OPTION(COVERAGE "Wether to configure test coverage report." OFF)

#######
# Set flags for our custom build types
#######
set(CMAKE_CXX_FLAGS_DEBUG "-Wall -O0 -g -pg" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_COVERAGE "-Wall -O0 -g -pg" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_PERFORMANCE "-Wall -Ofast -march=native" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_RELEASE "-w -O3" CACHE STRING "" FORCE)

mark_as_advanced(
    CMAKE_CXX_FLAGS_DEBUG
    CMAKE_CXX_FLAGS_COVERAGE
    CMAKE_CXX_FLAGS_PERFORMANCE
    CMAKE_CXX_FLAGS_RELEASE
)

if(NOT CMAKE_BUILD_TYPE)
   set(CMAKE_BUILD_TYPE Debug
       CACHE STRING "Choose the type of build : None Debug Coverage Release Performace."
       FORCE)
endif(NOT CMAKE_BUILD_TYPE)
message("* Current build type is : ${CMAKE_BUILD_TYPE}")

if (CMAKE_BUILD_TYPE STREQUAL "Performance")
    set(COVERAGE OFF)
    message("* Performance BUILD TYPE -> COVERAGE SET TO OFF")
elseif(CMAKE_BUILD_TYPE STREQUAL "Coverage")
    set(COVERAGE ON)
    message("* Coverage BUILD TYPE -> COVERAGE SET TO ON")
endif()


#######
# OpenMP
#######
find_package(OpenMP)

#######
# OpenCL
#######
if (BUILD_GPGPU)
    find_package(OpenCL REQUIRED)
    include_directories(${OpenCL_INCLUDE_DIRS})
    link_directories(${OpenCL_LIBRARY})
endif()

#######
# Rapid YAML
#######
add_subdirectory(${CMAKE_CURRENT_LIST_DIR}/thirdparty/rapidyaml ryml)
include_directories(${CMAKE_CURRENT_LIST_DIR}/thirdparty/rapidyaml/ext/c4core/src)
include_directories(${CMAKE_CURRENT_LIST_DIR}/thirdparty/rapidyaml/src)

#######
# SQLite Cpp
#######
add_subdirectory(${CMAKE_CURRENT_LIST_DIR}/thirdparty/SQLiteCpp)
include_directories(
  ${CMAKE_CURRENT_LIST_DIR}/thirdparty/SQLiteCpp/include
)

#######
# Zstd
#######
add_subdirectory(${CMAKE_CURRENT_LIST_DIR}/thirdparty/zstd/build/cmake)
include_directories(${CMAKE_CURRENT_LIST_DIR}/thirdparty/zstd/lib)

#######
# Add the ReDyMo include folder
#######
include_directories(include)

#######
# Compile componenets in libraries
#######
add_library(
    deps
    src/chromosome.cpp
    src/data_manager.cpp
    src/fork_manager.cpp
    src/genome.cpp
    src/genomic_location.cpp
    src/replication_fork.cpp
    src/util.cpp
    src/s_phase.cpp

    src/configuration.cpp
    src/evolution_data_provider.cpp
    src/evolution.cpp
)

if (BUILD_GPGPU)
    add_library(
        gpudeps
        src/gpu_s_phase.cpp
        src/gpu_chromosome.cpp
    )
endif()

add_executable(simulator src/main.cpp)
target_link_libraries(simulator deps SQLiteCpp libzstd_static sqlite3 pthread dl ryml OpenMP::OpenMP_CXX)

if (BUILD_GPGPU)
    target_link_libraries(simulator gpudeps ${OpenCL_LIBRARY})
endif()

#######
# Testing
#######
if(BUILD_TESTING)
    include(CTest)
    include(GoogleTest)

    #######
    # Google Test
    #######
    add_subdirectory(${CMAKE_CURRENT_LIST_DIR}/thirdparty/googletest)
    include_directories(${gtest_SOURCE_DIR}/include)
    include_directories(${gmock_SOURCE_DIR}/include)

    enable_testing()

    add_executable(test_chromosome test/test_chromosome.cpp)
    add_executable(test_genome test/test_genome.cpp)
    add_executable(test_genomic_location test/test_genomic_location.cpp)
    add_executable(test_replication_fork test/test_replication_fork.cpp)
    add_executable(test_fork_manager test/test_fork_manager.cpp)
    add_executable(test_data_manager test/test_data_manager.cpp)
    add_executable(test_configuration test/test_configuration.cpp)
    add_executable(test_evolution test/test_evolution.cpp)
    add_executable(test_s_phase test/test_s_phase.cpp)

    target_link_libraries(simulator deps gtest)

    target_link_libraries(test_chromosome deps gtest gmock gcov)
    target_link_libraries(test_genome deps libzstd_static gtest gcov)
    target_link_libraries(test_genomic_location deps libzstd_static gtest gcov)
    target_link_libraries(test_replication_fork deps libzstd_static gtest gcov)
    target_link_libraries(test_fork_manager deps libzstd_static gtest gcov)
    target_link_libraries(test_data_manager deps gtest SQLiteCpp libzstd_static sqlite3 pthread dl gcov)
    target_link_libraries(test_configuration deps ryml gtest gcov)
    target_link_libraries(test_evolution deps SQLiteCpp sqlite3 dl ryml gtest gmock gcov OpenMP::OpenMP_CXX)
    target_link_libraries(test_s_phase deps SQLiteCpp sqlite3 gtest gmock gcov dl ryml)


    gtest_discover_tests(test_chromosome)
    gtest_discover_tests(test_genome)
    gtest_discover_tests(test_genomic_location)
    gtest_discover_tests(test_replication_fork)
    gtest_discover_tests(test_fork_manager)
    gtest_discover_tests(test_data_manager)
    gtest_discover_tests(test_configuration)
    gtest_discover_tests(test_evolution)


    #######
    # Coverage report
    #######
    if(COVERAGE AND CMAKE_COMPILER_IS_GNUCXX)
        LIST(APPEND CMAKE_MODULE_PATH "${PROJECT_SOURCE_DIR}/thirdparty/CMakeModules")

        include(CodeCoverage)
        APPEND_COVERAGE_COMPILER_FLAGS()

        # The ctest_no_fail.sh is used because the coverage tests won't
        # continue if the ctest returns non zero. Ctest will returns 0 only if
        # all tests pass.
        setup_target_for_coverage_lcov(
            NAME coverage
            EXECUTABLE ${CMAKE_CURRENT_LIST_DIR}/script/ctest_no_fail.sh
            EXCLUDE "thirdparty/*" "include/*" "test/*"
            DEPENDENCIES test_chromosome test_genome test_genomic_location test_replication_fork test_fork_manager test_data_manager test_configuration test_evolution test_s_phase
        )
        setup_target_for_coverage_lcov(
            NAME coverage_integrated_tests
            EXECUTABLE ${CMAKE_CURRENT_LIST_DIR}/build/test_s_phase
            EXCLUDE "thirdparty/*" "include/*" "test/*"
            DEPENDENCIES test_s_phase
        )
    endif()
endif()