CMakeLists.txt

cmake_minimum_required(VERSION 3.20)
project(baysor VERSION 0.8.3 LANGUAGES C CXX)

set(CMAKE_CXX_STANDARD 17)
set(CMAKE_CXX_STANDARD_REQUIRED ON)

# Keep default installs user-owned. Presets and explicit command-line values can
# still override this with CMAKE_INSTALL_PREFIX or cmake --install --prefix.
if(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT)
    set(CMAKE_INSTALL_PREFIX "${CMAKE_CURRENT_SOURCE_DIR}/install" CACHE PATH "Default Baysor install prefix." FORCE)
endif()

option(BAYSOR_EXPORT_COMPILE_COMMANDS "Export compile_commands.json for developer tooling" OFF)
if(BAYSOR_EXPORT_COMPILE_COMMANDS)
    set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
endif()
include(GNUInstallDirs)

if(APPLE)
    foreach(_homebrew_prefix /opt/homebrew /usr/local)
        if(EXISTS "${_homebrew_prefix}")
            list(APPEND CMAKE_PREFIX_PATH "${_homebrew_prefix}")
        endif()
    endforeach()

    if(NOT DEFINED OpenMP_ROOT)
        foreach(_libomp_prefix /opt/homebrew/opt/libomp /usr/local/opt/libomp)
            if(EXISTS "${_libomp_prefix}")
                set(OpenMP_ROOT "${_libomp_prefix}" CACHE PATH "Homebrew libomp prefix")
                break()
            endif()
        endforeach()
    endif()
endif()

list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cmake")
include(BaysorDependencies)

# Prefer optimized single-config builds unless the user explicitly chose
# something else. This does not affect multi-config generators.
if(NOT CMAKE_CONFIGURATION_TYPES AND NOT CMAKE_BUILD_TYPE)
    set(CMAKE_BUILD_TYPE Release CACHE STRING "Build type" FORCE)
endif()

# Options
option(BAYSOR_WITH_CUDA "Enable CUDA/GPU support" OFF)
option(BAYSOR_WITH_TESTS "Build tests" OFF)
option(BAYSOR_WITH_REPORTING "Build reporting/visualization support" ON)

# Dependencies managed by vcpkg or find_package
# Core (always required)
baysor_find_package(Eigen3
    VERSION 3.3
    TARGET Eigen3::Eigen
    INSTALL_HINT "Ubuntu: sudo apt-get install libeigen3-dev\nmacOS: brew install eigen\nvcpkg: vcpkg install eigen3"
)
baysor_find_package(OpenMP
    COMPONENTS CXX
    TARGET OpenMP::OpenMP_CXX
    INSTALL_HINT "Ubuntu/GCC: OpenMP is provided by the compiler runtime; install libomp-dev for Clang.\nmacOS: brew install libomp\nWindows/MSVC: OpenMP is provided by Visual Studio."
)
baysor_find_package(spdlog
    TARGET spdlog::spdlog
    INSTALL_HINT "Ubuntu: sudo apt-get install libspdlog-dev\nmacOS: brew install spdlog\nvcpkg: vcpkg install spdlog"
)

# UMAP and dependencies (all header-only, fetched via FetchContent).
# We only need the headers, so avoid adding upstream CMake projects here.
# Some upstream CMakeLists require newer CMake versions than Baysor itself.
include(FetchContent)
if(POLICY CMP0169)
    cmake_policy(SET CMP0169 OLD)
endif()
FetchContent_Declare(aarand
    GIT_REPOSITORY https://github.com/LTLA/aarand
    GIT_TAG v1.0.2
)
# knncolle v2.3.0 transitively depends on kmeans v3.x and subpar v0.2.1
FetchContent_Declare(kmeans
    GIT_REPOSITORY https://github.com/LTLA/CppKmeans
    GIT_TAG v3.1.1
)
FetchContent_Declare(subpar
    GIT_REPOSITORY https://github.com/LTLA/subpar
    GIT_TAG v0.3.1
)
FetchContent_Declare(knncolle
    GIT_REPOSITORY https://github.com/knncolle/knncolle
    GIT_TAG v2.3.0
)
FetchContent_Declare(irlba
    GIT_REPOSITORY https://github.com/LTLA/CppIrlba
    GIT_TAG v2.0.2
)
FetchContent_Declare(umappp
    GIT_REPOSITORY https://github.com/LTLA/umappp
    GIT_TAG v2.0.1
)

function(baysor_fetch_header_only_dependency dependency target alias)
    FetchContent_GetProperties(${dependency})
    if(NOT ${dependency}_POPULATED)
        FetchContent_Populate(${dependency})
    endif()

    if(NOT TARGET ${target})
        add_library(${target} INTERFACE)
        target_include_directories(${target} INTERFACE "${${dependency}_SOURCE_DIR}/include")
        target_compile_features(${target} INTERFACE cxx_std_17)
    endif()
    if(alias AND NOT TARGET ${alias})
        add_library(${alias} ALIAS ${target})
    endif()
endfunction()

baysor_fetch_header_only_dependency(aarand aarand ltla::aarand)
baysor_fetch_header_only_dependency(subpar subpar ltla::subpar)
baysor_fetch_header_only_dependency(kmeans kmeans ltla::kmeans)
baysor_fetch_header_only_dependency(knncolle knncolle knncolle::knncolle)
baysor_fetch_header_only_dependency(irlba irlba ltla::irlba)
baysor_fetch_header_only_dependency(umappp umappp libscran::umappp)

target_link_libraries(kmeans INTERFACE ltla::aarand ltla::subpar)
target_link_libraries(knncolle INTERFACE ltla::kmeans ltla::subpar)
target_link_libraries(irlba INTERFACE Eigen3::Eigen ltla::aarand ltla::subpar)
target_link_libraries(umappp INTERFACE ltla::aarand ltla::irlba knncolle::knncolle)

# Patch irlba v2.0.2 bug: Eigen::VectorXd has no begin()/end().
# Replace std::max_element(BS.begin(), BS.end()) with BS.maxCoeff().
FetchContent_GetProperties(irlba)
set(_irlba_compute "${irlba_SOURCE_DIR}/include/irlba/compute.hpp")
if(EXISTS "${_irlba_compute}")
    file(READ "${_irlba_compute}" _irlba_content)
    string(REPLACE
        "*std::max_element(BS.begin(), BS.end())"
        "BS.maxCoeff()"
        _irlba_content "${_irlba_content}")
    file(WRITE "${_irlba_compute}" "${_irlba_content}")
endif()

# Spatial
baysor_find_package(CGAL
    TARGET CGAL::CGAL
    INSTALL_HINT "Ubuntu: sudo apt-get install libcgal-dev\nmacOS: brew install cgal\nvcpkg: vcpkg install cgal"
)
# nanoflann is header-only, vendored in third_party/ or found via find_package
# find_package(nanoflann REQUIRED)

# I/O
baysor_find_package(Parquet
    INSTALL_HINT "Ubuntu: install libparquet-dev from the Apache Arrow apt repository\nmacOS: brew install apache-arrow\nvcpkg: vcpkg install 'arrow[parquet]'"
)
if(NOT TARGET Arrow::arrow_shared AND NOT TARGET Arrow::arrow_static)
    baysor_find_package(Arrow
        INSTALL_HINT "Ubuntu: install libarrow-dev from the Apache Arrow apt repository\nmacOS: brew install apache-arrow\nvcpkg: vcpkg install 'arrow[compute,csv,parquet]'"
    )
endif()
baysor_find_package(HDF5
    COMPONENTS C
    INSTALL_HINT "Ubuntu: sudo apt-get install libhdf5-dev\nmacOS: brew install hdf5\nvcpkg: vcpkg install 'hdf5[zlib]'"
)
baysor_find_package(nlohmann_json
    TARGET nlohmann_json::nlohmann_json
    INSTALL_HINT "Ubuntu: sudo apt-get install nlohmann-json3-dev\nmacOS: brew install nlohmann-json\nvcpkg: vcpkg install nlohmann-json"
)
baysor_find_package(TIFF
    TARGET TIFF::TIFF
    INSTALL_HINT "Ubuntu: sudo apt-get install libtiff-dev\nmacOS: brew install libtiff\nvcpkg: vcpkg install tiff"
)
baysor_select_target(BAYSOR_ARROW_TARGET Arrow::arrow_shared Arrow::arrow_static)
baysor_select_target(BAYSOR_PARQUET_TARGET Parquet::parquet_shared Parquet::parquet_static)
message(STATUS "Using Arrow target: ${BAYSOR_ARROW_TARGET}")
message(STATUS "Using Parquet target: ${BAYSOR_PARQUET_TARGET}")
if(TARGET hdf5::hdf5)
    set(BAYSOR_HDF5_LIBRARIES hdf5::hdf5)
elseif(TARGET HDF5::HDF5)
    set(BAYSOR_HDF5_LIBRARIES HDF5::HDF5)
else()
    set(BAYSOR_HDF5_LIBRARIES ${HDF5_C_LIBRARIES})
    set(BAYSOR_HDF5_INCLUDE_DIRS ${HDF5_INCLUDE_DIRS})
endif()

# CLI
# CLI11 and toml++ are header-only
# find_package(CLI11 REQUIRED)
# find_package(tomlplusplus REQUIRED)

if(BAYSOR_WITH_CUDA)
    enable_language(CUDA)
    baysor_find_package(CUDAToolkit
        TARGET CUDA::cudart
        INSTALL_HINT "Install the NVIDIA CUDA Toolkit and reconfigure with -DBAYSOR_WITH_CUDA=ON only on CUDA-capable systems."
    )
    # find_package(faiss REQUIRED)
    add_compile_definitions(BAYSOR_CUDA_ENABLED)
endif()

# --- Library target ---
add_library(baysor_lib
    # Utils
    src/utils/general.cpp
    src/utils/options.cpp
    src/utils/xenium.cpp

    # Data loading
    src/data_loading/data.cpp
    src/data_loading/prior_segmentation.cpp

    # Processing - distributions
    src/processing/distributions/mv_normal.cpp
    src/processing/distributions/categorical_smoothed.cpp

    # Processing - models
    src/processing/models/adj_list.cpp
    src/processing/models/component.cpp
    src/processing/models/bmm_data.cpp

    # Processing - data_processing
    src/processing/data_processing/triangulation.cpp
    src/processing/data_processing/initialization.cpp
    src/processing/data_processing/neighborhood_composition.cpp
    src/processing/data_processing/noise_estimation.cpp
    src/processing/data_processing/boundary_estimation.cpp
    # Processing - bmm_algorithm
    src/processing/bmm_algorithm/bmm_algorithm.cpp
    src/processing/bmm_algorithm/molecule_clustering.cpp
    src/processing/bmm_algorithm/molecule_clustering_louvain.cpp
    src/processing/bmm_algorithm/compartment_segmentation.cpp
    src/processing/bmm_algorithm/tracing.cpp
    src/processing/bmm_algorithm/history_analysis.cpp

    # Processing - utils
    src/processing/utils/utils.cpp
    src/processing/utils/convex_hull.cpp

    # Reporting
    src/reporting/color_utils.cpp
    src/reporting/gene_structure.cpp
    src/reporting/output.cpp
    src/reporting/preview_report.cpp
    src/reporting/run_report.cpp
)

add_library(baysor_umap_wrappers STATIC
    src/processing/data_processing/umap_wrappers.cpp
)

target_include_directories(baysor_umap_wrappers PUBLIC
    ${CMAKE_CURRENT_SOURCE_DIR}/include
)

target_link_libraries(baysor_umap_wrappers PUBLIC
    Eigen3::Eigen
    umappp
    knncolle::knncolle
)

target_include_directories(baysor_lib PUBLIC
    ${CMAKE_CURRENT_SOURCE_DIR}/include
    ${BAYSOR_HDF5_INCLUDE_DIRS}
)

target_link_libraries(baysor_lib PUBLIC
    Eigen3::Eigen
    OpenMP::OpenMP_CXX
    spdlog::spdlog
    CGAL::CGAL
    ${BAYSOR_ARROW_TARGET}
    ${BAYSOR_PARQUET_TARGET}
    ${BAYSOR_HDF5_LIBRARIES}
    nlohmann_json::nlohmann_json
    TIFF::TIFF
    baysor_umap_wrappers
)

if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
    target_compile_options(baysor_lib PRIVATE -Wno-stringop-overflow)
endif()

if(BAYSOR_WITH_CUDA)
    target_link_libraries(baysor_lib PUBLIC
        CUDA::cudart
        CUDA::cusparse
    )
endif()

# --- Executable ---
add_executable(baysor
    src/cli/main.cpp
)

target_link_libraries(baysor PRIVATE baysor_lib)
install(TARGETS baysor RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR})

if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
    target_compile_options(baysor PRIVATE -Wno-stringop-overflow)
endif()

# --- Tests ---
if(BAYSOR_WITH_TESTS)
    enable_testing()
    baysor_find_package(GTest
        TARGET GTest::gtest_main
        INSTALL_HINT "Ubuntu: sudo apt-get install libgtest-dev\nmacOS: brew install googletest\nvcpkg: enable the 'tests' manifest feature or install gtest"
    )

    add_executable(baysor_tests
        tests/test_main.cpp
    )
    target_link_libraries(baysor_tests PRIVATE baysor_lib GTest::gtest_main)
    if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
        target_compile_options(baysor_tests PRIVATE -Wno-stringop-overflow)
    endif()
    add_test(NAME baysor_tests COMMAND baysor_tests)
endif()