Define and link targets separately

cmake/SetupHDF5.cmake

@@ -1,9 +1,18 @@
 include(${CMAKE_CURRENT_LIST_DIR}/Util.cmake)
 
-function(setup_hdf5 TARGET_NAME)
+function(add_hdf5_to_target TARGET_NAME)
     if(NOHDF5)
         target_compile_definitions(${TARGET_NAME} PRIVATE NHDF5RH=1)
     else()
+        if(HDF5_COMPILE)
+            add_dependencies(${TARGET_NAME} hdf5_build)
+        endif()
+        link_imported_library(${TARGET_NAME} hdf5 ${HDF5_DIR})
+    endif()
+endfunction()
+
+function(setup_hdf5)
+    if(NOT NOHDF5)
         # print HDF5_DIR
         message(STATUS "EXTERNAL_PROJECTS_BUILD_DIR: ${EXTERNAL_PROJECTS_BUILD_DIR}")
         message(STATUS "HDF5_DIR: ${HDF5_DIR}")
@@ -21,12 +30,11 @@ function(setup_hdf5 TARGET_NAME)
                 # INSTALL_DIR and DCMAKE_INSTALL_PREFIX are ignored by hdf5
                 INSTALL_COMMAND make install prefix=${HDF5_DIR}
             )
-            add_dependencies(${TARGET_NAME} hdf5_build)
         else()
             if(NOT HDF5_DIR)
                 message(FATAL_ERROR "HDF5_COMPILE is OFF, but no dir provided")
             endif()
         endif()
-        link_imported_library(${TARGET_NAME} hdf5 ${HDF5_DIR})
+        define_imported_library(hdf5 ${HDF5_DIR})
     endif()
 endfunction()

cmake/SetupPOD5.cmake

@@ -1,22 +1,44 @@
 include(${CMAKE_CURRENT_LIST_DIR}/Util.cmake)
 
-function(setup_zstd TARGET_NAME)
-set(ZSTD_DIR ${EXTERNAL_PROJECTS_BUILD_DIR}/zstd)
+function(add_zstd_to_target TARGET_NAME)
+    set(ZSTD_DIR ${EXTERNAL_PROJECTS_BUILD_DIR}/zstd)
+    add_dependencies(${TARGET_NAME} zstd_build)
+    link_imported_library(${TARGET_NAME} zstd ${ZSTD_DIR})
+endfunction()
+
+function(setup_zstd)
+    set(ZSTD_DIR ${EXTERNAL_PROJECTS_BUILD_DIR}/zstd)
     ExternalProject_Add(
         zstd_build
         SOURCE_DIR ${CMAKE_SOURCE_DIR}/extern/zstd/build/cmake
         BINARY_DIR ${ZSTD_DIR}/build
         CMAKE_ARGS -DCMAKE_INSTALL_PREFIX=${ZSTD_DIR}
     )
-    add_dependencies(${TARGET_NAME} zstd_build)
-    link_imported_library(${TARGET_NAME} zstd ${ZSTD_DIR})
+    define_imported_library(zstd ${ZSTD_DIR})
 endfunction()
 
-function(setup_pod5 TARGET_NAME)
+function(add_pod5_to_target TARGET_NAME)
     if(NOPOD5)
         target_compile_definitions(${TARGET_NAME} PRIVATE NPOD5RH=1)
     else()
-        setup_zstd(${TARGET_NAME})
+        add_zstd_to_target(${TAARGET_NAME})
+
+        set(POD5_VERSION "0.2.2")
+        set(POD5_URLDIR "pod5-${POD5_VERSION}-${CMAKE_SYSTEM_NAME}")
+        set(POD5_REPO "https://github.com/nanoporetech/pod5-file-format")
+
+        resolve_pod5_url()
+
+        if(POD5_DOWNLOAD)
+            add_dependencies(${TARGET_NAME} pod5_download)
+        endif()
+        target_link_libraries(${TARGET_NAME} PRIVATE ${POD5_LIBRARIES} zstd)
+    endif()
+endfunction()
+
+function(setup_pod5)
+    if(NOT NOPOD5)
+        setup_zstd()
 
         set(POD5_VERSION "0.2.2")
         set(POD5_URLDIR "pod5-${POD5_VERSION}-${CMAKE_SYSTEM_NAME}")
@@ -45,7 +67,6 @@ function(setup_pod5 TARGET_NAME)
             endif()
         endif()
         include_directories(${POD5_DIR}/include)
-        target_link_libraries(${TARGET_NAME} PRIVATE ${POD5_LIBRARIES} zstd)
     endif()
 endfunction()
 

cmake/SetupRUClient.cmake

@@ -1,10 +1,16 @@
 include(${CMAKE_CURRENT_LIST_DIR}/Util.cmake)
 
-function(setup_ruclient TARGET_NAME)
+function(add_ruclient_to_target TARGET_NAME)
+    if(RUCLIENT_ENABLED)
+        set_target_properties(${TARGET_NAME} PROPERTIES CXX_STANDARD 20)
+        target_compile_definitions(${TARGET_NAME} PRIVATE RUCLIENT_ENABLED)
+        target_sources(${TARGET_NAME} PRIVATE rawhash_ruclient.cpp)
+        add_dependencies(${TARGET_NAME} ruclient_build)
+    endif()
+endfunction()
+
+function(setup_ruclient)
     if(RUCLIENT_ENABLED)
-    set_target_properties(${TARGET_NAME} PROPERTIES CXX_STANDARD 20)
-    target_compile_definitions(${TARGET_NAME} PRIVATE RUCLIENT_ENABLED)
-    target_sources(${TARGET_NAME} PRIVATE rawhash_ruclient.cpp)
         if(NOT RUCLIENT_DIR)
             override_cached(RUCLIENT_DIR ${EXTERNAL_PROJECTS_BUILD_DIR}/ruclient)
         endif()
@@ -15,7 +21,6 @@ function(setup_ruclient TARGET_NAME)
             CMAKE_ARGS
                 -DCMAKE_INSTALL_PREFIX=${RUCLIENT_DIR}
         )
-        add_dependencies(${TARGET_NAME} ruclient_build)
         include_directories(${RUCLIENT_DIR}/include)
         message(STATUS "ruclient enabled")
     else()

cmake/SetupRawHashLikeTarget.cmake

@@ -1,3 +1,15 @@
+include(${CMAKE_CURRENT_LIST_DIR}/SetupRUClient.cmake)
+include(${CMAKE_CURRENT_LIST_DIR}/SetupPOD5.cmake)
+include(${CMAKE_CURRENT_LIST_DIR}/SetupHDF5.cmake)
+include(${CMAKE_CURRENT_LIST_DIR}/SetupSLOW5.cmake)
+include(${CMAKE_CURRENT_LIST_DIR}/SetupTFLite.cmake)
+
+setup_pod5()
+setup_ruclient()
+setup_hdf5()
+setup_slow5()
+setup_tflite()
+
 function(setup_rawhashlike_target TARGET_NAME)
     # if(PYBINDING)
     #     message(FATAL_ERROR "Building with Python binding support is not implemented")
@@ -77,4 +89,10 @@ function(setup_rawhashlike_target TARGET_NAME)
             PROFILERH=1
         )
     endif()
+
+    add_pod5_to_target(${TARGET_NAME})
+    add_hdf5_to_target(${TARGET_NAME})
+    add_slow5_to_target(${TARGET_NAME})
+    add_tflite_to_target(${TARGET_NAME})
+    add_ruclient_to_target(${TARGET_NAME})
 endfunction()

cmake/SetupSLOW5.cmake

@@ -1,9 +1,18 @@
 include(${CMAKE_CURRENT_LIST_DIR}/Util.cmake)
 
-function(setup_slow5 TARGET_NAME)
+function(add_slow5_to_target TARGET_NAME)
     if(NOSLOW5)
         target_compile_definitions(${TARGET_NAME} PRIVATE NSLOW5RH=1)
     else()
+        if(SLOW5_COMPILE)
+            add_dependencies(${TARGET_NAME} slow5_build)
+        endif()
+        link_imported_library(${TARGET_NAME} slow5 ${SLOW5_DIR})
+    endif()
+endfunction()
+
+function(setup_slow5)
+    if(NOT NOSLOW5)
         set(SLOW5_SOURCE_DIR ${CMAKE_SOURCE_DIR}/extern/slow5lib)
         if(SLOW5_COMPILE)
             if(NOT SLOW5_DIR)
@@ -19,13 +28,12 @@ function(setup_slow5 TARGET_NAME)
                              && ${CMAKE_COMMAND} -E rename ${SLOW5_DIR}/libslow5.so ${SLOW5_DIR}/lib/libslow5.so
             )
             message(STATUS "Current dir: ${CMAKE_CURRENT_BINARY_DIR}")
-            add_dependencies(${TARGET_NAME} slow5_build)
         else()
             if(NOT SLOW5_DIR)
                 message(FATAL_ERROR "SLOW5_COMPILE is OFF, but no dir provided")
             endif()
         endif()
         message(STATUS "Using slow5 from ${SLOW5_DIR}")
-        link_imported_library(${TARGET_NAME} slow5 ${SLOW5_DIR})
+        define_imported_library(slow5 ${SLOW5_DIR})
     endif()
 endfunction()

cmake/SetupTFLite.cmake

@@ -1,8 +1,11 @@
 include(${CMAKE_CURRENT_LIST_DIR}/Util.cmake)
 
-function(setup_tflite TARGET_NAME)
+function(add_tflite_to_target TARGET_NAME)
+    target_link_libraries(${TARGET_NAME} PRIVATE tensorflow-lite)
+endfunction()
+
+function(setup_tflite)
     set(TF_SOURCE_DIR ${CMAKE_SOURCE_DIR}/extern/tensorflow)
     add_subdirectory(${TF_SOURCE_DIR}/tensorflow/lite ${EXTERNAL_PROJECTS_BUILD_DIR}/tflite EXCLUDE_FROM_ALL)
     include_directories(${TF_SOURCE_DIR})
-    target_link_libraries(${TARGET_NAME} PRIVATE tensorflow-lite)
 endfunction()

cmake/Util.cmake

@@ -7,16 +7,22 @@ function(override_cached name value)
     set(${name} ${value} CACHE ${type} ${doc_string} FORCE)
 endfunction()
 
+
 function(link_imported_library TARGET_NAME LIB_NAME LIB_DIR)
-    add_library(${LIB_NAME} SHARED IMPORTED)
-    file(MAKE_DIRECTORY ${LIB_DIR}/include)
     set_target_properties(${LIB_NAME} PROPERTIES
         IMPORTED_LOCATION ${LIB_DIR}/lib/lib${LIB_NAME}.so
         INTERFACE_INCLUDE_DIRECTORIES ${LIB_DIR}/include
     )
     target_link_libraries(${TARGET_NAME} PRIVATE ${LIB_NAME})
 endfunction()
 
+
+function(define_imported_library LIB_NAME LIB_DIR)
+    add_library(${LIB_NAME} SHARED IMPORTED)
+    file(MAKE_DIRECTORY ${LIB_DIR}/include)
+endfunction()
+
+
 function(check_directory_exists_and_non_empty DIR)
     if(NOT EXISTS ${DIR})
         message(FATAL_ERROR "Directory ${DIR} does not exist.")

src/CMakeLists.txt

@@ -34,62 +34,19 @@ set(EXTERNAL_PROJECTS_BUILD_DIR ${CMAKE_BINARY_DIR}/extern) # default build dire
 file(MAKE_DIRECTORY ${EXTERNAL_PROJECTS_BUILD_DIR})
 message(STATUS "External projects build directory: ${EXTERNAL_PROJECTS_BUILD_DIR}")
 
-include(../cmake/SetupCCacheMold.cmake)
-include(../cmake/SetupRawHashLikeTarget.cmake)
-include(../cmake/SetupRUClient.cmake)
-include(../cmake/SetupPOD5.cmake)
-include(../cmake/SetupHDF5.cmake)
-include(../cmake/SetupSLOW5.cmake)
-include(../cmake/SetupTFLite.cmake)
+include(${CMAKE_SOURCE_DIR}/cmake/SetupCCacheMold.cmake)
+include(${CMAKE_SOURCE_DIR}/cmake/SetupRawHashLikeTarget.cmake)
 
 set(CMAKE_VERBOSE_MAKEFILE TRUE CACHE BOOL "verbose makefile" FORCE) # print compilation commands
 
 enable_ccache()
 set_alternate_linker(mold)
 
-# todo: currently can only compile rawhash2 or the below, not both
-# this happens because functions like setup_hdf5 define the hdf5 target and the relationship to the target name
-# rather than doing it separately
-set(build_cli ON)
+add_executable(rawhash2 main.cpp)
+setup_rawhashlike_target(rawhash2)
 
-if (build_cli)
-    message(STATUS "Building CLI")
-
-    set(TARGET_NAME rawhash2)
-    add_executable(${TARGET_NAME} main.cpp)
-    setup_rawhashlike_target(${TARGET_NAME})
-    setup_pod5(${TARGET_NAME})
-    setup_ruclient(${TARGET_NAME})
-    setup_hdf5(${TARGET_NAME})
-    setup_slow5(${TARGET_NAME})
-    setup_tflite(${TARGET_NAME})
+add_library(rawhash2_wrapper SHARED rawhash_wrapper.cpp rawhash_wrapper.hpp)
+setup_rawhashlike_target(rawhash2_wrapper)
 
-else()
-    message(STATUS "Building shared library")
-
-    # set(TARGET_NAME rawhash2_wrapper_example)
-    # add_executable(${TARGET_NAME} wrapper_example.cpp rawhash_wrapper.cpp rawhash_wrapper.hpp)
-    set(TARGET_NAME rawhash2_wrapper)
-    add_library(${TARGET_NAME} SHARED rawhash_wrapper.cpp rawhash_wrapper.hpp)
-    setup_rawhashlike_target(${TARGET_NAME})
-    setup_pod5(${TARGET_NAME})
-    setup_ruclient(${TARGET_NAME})
-    setup_hdf5(${TARGET_NAME})
-    setup_slow5(${TARGET_NAME})
-    setup_tflite(${TARGET_NAME})
-
-    set(TARGET_NAME rawhash2_usinglib)
-    add_executable(${TARGET_NAME} wrapper_example.cpp)
-    target_link_libraries(${TARGET_NAME} PRIVATE rawhash2_wrapper)
-    # setup_rawhashlike_target(${TARGET_NAME})
-    # # setup_pod5(${TARGET_NAME})
-    # target_compile_definitions(${TARGET_NAME} PRIVATE NPOD5RH=1) # todo: workaround
-    # setup_ruclient(${TARGET_NAME})
-    # setup_hdf5(${TARGET_NAME})
-    # setup_slow5(${TARGET_NAME})
-    # setup_tflite(${TARGET_NAME})
-endif()
-
-
-# setup_pod5()
-# add_pod5_to_target(${TARGET_NAME})
+add_executable(rawhash2_usinglib wrapper_example.cpp)
+target_link_libraries(rawhash2_usinglib PRIVATE rawhash2_wrapper)