cmake updates

Author: Kharchenko

CMakeLists.txt

@@ -221,8 +221,6 @@ add_library(baysor_lib
     src/processing/data_processing/neighborhood_composition.cpp
     src/processing/data_processing/noise_estimation.cpp
     src/processing/data_processing/boundary_estimation.cpp
-    src/processing/data_processing/umap_wrappers.cpp
-
     # Processing - bmm_algorithm
     src/processing/bmm_algorithm/bmm_algorithm.cpp
     src/processing/bmm_algorithm/molecule_clustering.cpp
@@ -242,6 +240,20 @@ add_library(baysor_lib
     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}
@@ -257,8 +269,7 @@ target_link_libraries(baysor_lib PUBLIC
     ${BAYSOR_HDF5_LIBRARIES}
     nlohmann_json::nlohmann_json
     TIFF::TIFF
-    umappp
-    knncolle::knncolle
+    baysor_umap_wrappers
 )
 
 if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU")

cmake/build_and_install.cmake

@@ -53,6 +53,50 @@ function(_baysor_run)
     endif()
 endfunction()
 
+find_program(_baysor_ninja NAMES ninja ninja-build)
+if(NOT _baysor_ninja)
+    if(APPLE)
+        set(_baysor_ninja_install_hint [=[
+On macOS, install Ninja with Homebrew:
+  brew install ninja
+
+Then rerun:
+  cmake -P cmake/build_and_install.cmake
+
+If you do not use Homebrew, install Ninja with your package manager and make sure the 'ninja' executable is on PATH.]=])
+    elseif(UNIX)
+        set(_baysor_ninja_install_hint [=[
+Install Ninja with your system package manager, for example:
+  sudo apt-get install ninja-build    # Debian/Ubuntu
+  sudo dnf install ninja-build        # Fedora
+  sudo pacman -S ninja                # Arch
+
+Then rerun:
+  cmake -P cmake/build_and_install.cmake]=])
+    elseif(WIN32)
+        set(_baysor_ninja_install_hint [=[
+Install Ninja with your package manager, for example:
+  winget install Ninja-build.Ninja
+  choco install ninja
+
+Then rerun:
+  cmake -P cmake/build_and_install.cmake
+
+Make sure the 'ninja' executable is on PATH.]=])
+    else()
+        set(_baysor_ninja_install_hint [=[
+Install Ninja from https://ninja-build.org/ and make sure the 'ninja'
+executable is on PATH. Then rerun:
+  cmake -P cmake/build_and_install.cmake]=])
+    endif()
+
+    message(FATAL_ERROR
+        "Baysor's build helper uses the Ninja CMake generator, but Ninja was "
+        "not found on PATH.\n\n"
+        "${_baysor_ninja_install_hint}"
+    )
+endif()
+
 set(_configure_args
     -S "${_source_dir}"
     -B "${_build_dir}"