Improve CMake

.github/workflows/docker-build.yml

@@ -5,6 +5,12 @@ on:
     branches:
       - main
   pull_request:
+  workflow_dispatch:
+    inputs:
+      use_cache:
+        description: 'Use cache for this run'
+        required: true
+        default: 'true'
 
 jobs:
   build:
@@ -30,6 +36,7 @@ jobs:
           password: ${{ secrets.GITHUB_TOKEN }}
 
       - name: Cache build directory
+        if: github.event_name != 'workflow_dispatch' || github.event.inputs.use_cache == 'true'
         uses: actions/cache@v3
         with:
           path: build

CMakeLists.txt

@@ -1,4 +1,4 @@
 cmake_minimum_required(VERSION 3.10)
-project(RawHash2)
+project(RawHash2Root)
 
 add_subdirectory(src)

Dockerfile

@@ -9,7 +9,7 @@ COPY . /rawhash2
 
 RUN mkdir -p build && cd build \
     && cmake .. \
-    && make -j 3
+    && make -j 2
 
 ENTRYPOINT ["./build/bin/rawhash2"]
 

README.md

@@ -45,7 +45,7 @@ cd rawhash2 && git submodule update --init --recursive
 # if not doing a fresh clone, make sure that the submodules don't have anything built from previous makefile-based 
 # setup , i.e. delete extern directory, then initialize submodules as above
 (mkdir -p build && cd build && cmake .. && make -j)
-build/bin/rawhash2
+build/bin/rawhash2 -h
 ```
 
 Troubleshooting:
@@ -54,6 +54,26 @@ Troubleshooting:
 
 If the compilation is successful, the default path to the binary will be `build/bin/rawhash2`.
 
+* Installation
+
+You can install RawHash2 into the CMake-provided platform-specific destination (e.g. `/usr/local/` on UNIX) with `make install`:
+
+```bash
+make install
+rawhash2 -h
+```
+
+Installation directory can be overridden by providing `-DCMAKE_INSTALL_PREFIX=...` argument to the `cmake ..` command, e.g.
+
+```bash
+cmake -DCMAKE_INSTALL_PREFIX=./install ..
+make -j
+make install
+./install/bin/rawhash2 -h
+```
+
+Note that `CMAKE_INSTALL_PREFIX` is a cached variable in CMake.
+
 ## Compiling with HDF5, SLOW5, and POD5
 
 We are aware that some of the pre-compiled libraries (e.g., POD5) may not work in your system and you may need to compile these libraries from scratch. Additionally, it may be possible that you may not want to compile any of the HDF5, SLOW5, or POD5 libraries if you are not going to use them. RawHash2 provides several CMake options to enable custom compilation of these libraries.

cmake/SetupHDF5.cmake

@@ -1,9 +1,18 @@
-include(${CMAKE_CURRENT_LIST_DIR}/Util.cmake)
+include(${CMAKE_CURRENT_LIST_DIR}/Utils.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()
+        target_link_libraries(${TARGET_NAME} PRIVATE hdf5)
+    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(${CMAKE_CURRENT_LIST_DIR}/Util.cmake)
+include(${CMAKE_CURRENT_LIST_DIR}/Utils.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)
+    target_link_libraries(${TARGET_NAME} PRIVATE zstd)
+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()
 
@@ -79,7 +100,7 @@ endfunction()
 
 
 # not working because of improper design, PARENT_SCOPE should not be used, rather define targets properly
-# include(${CMAKE_CURRENT_LIST_DIR}/Util.cmake)
+# include(${CMAKE_CURRENT_LIST_DIR}/Utils.cmake)
 
 # set(ZSTD_DIR ${EXTERNAL_PROJECTS_BUILD_DIR}/zstd)
 

cmake/SetupRUClient.cmake

@@ -1,10 +1,16 @@
-include(${CMAKE_CURRENT_LIST_DIR}/Util.cmake)
+include(${CMAKE_CURRENT_LIST_DIR}/Utils.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(${CMAKE_CURRENT_LIST_DIR}/Util.cmake)
+include(${CMAKE_CURRENT_LIST_DIR}/Utils.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()
+        target_link_libraries(${TARGET_NAME} PRIVATE slow5)
+    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(${CMAKE_CURRENT_LIST_DIR}/Util.cmake)
+include(${CMAKE_CURRENT_LIST_DIR}/Utils.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 → cmake/Utils.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)
+
+function(define_imported_library 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})
+        INTERFACE_INCLUDE_DIRECTORIES ${LIB_DIR}/include)
+    file(MAKE_DIRECTORY ${LIB_DIR}/include)
+    # Can't install(TARGETS ...) for external projects
+    # Also some .so are symlinks, so install all
+    install(DIRECTORY ${LIB_DIR}/lib/ DESTINATION lib
+            FILES_MATCHING PATTERN "*.so*")
+    install(DIRECTORY ${LIB_DIR}/include/
+            DESTINATION include/${PROJECT_NAME})
 endfunction()
 
+
 function(check_directory_exists_and_non_empty DIR)
     if(NOT EXISTS ${DIR})
         message(FATAL_ERROR "Directory ${DIR} does not exist.")

src/CMakeLists.txt

@@ -1,5 +1,5 @@
 cmake_minimum_required(VERSION 3.10)
-project(RawHash2Src)
+project(RawHash2)
 
 # option(USE_CCACHE "Use ccache to speed up rebuilds" ON)
 # option(USE_MOLD "Use mold linker for faster linking" ON)
@@ -34,62 +34,28 @@ 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_builtin main.cpp)
+setup_rawhashlike_target(rawhash2_builtin)
 
-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_lib SHARED rawhash_wrapper.cpp rawhash_wrapper.hpp)
+setup_rawhashlike_target(rawhash2_lib)
 
-else()
-    message(STATUS "Building shared library")
+file(GLOB_RECURSE HEADER_FILES ${CMAKE_SOURCE_DIR}/src/*.h ${CMAKE_SOURCE_DIR}/src/*.hpp)
+set_property(TARGET rawhash2_lib PROPERTY PUBLIC_HEADER ${HEADER_FILES})
+set_target_properties(rawhash2_lib PROPERTIES INSTALL_RPATH $ORIGIN OUTPUT_NAME rawhash2)
+install(TARGETS rawhash2_lib
+        LIBRARY DESTINATION lib
+        PUBLIC_HEADER DESTINATION include/${PROJECT_NAME})
 
-    # 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 wrapper_example.cpp)
+target_link_libraries(rawhash2 PRIVATE rawhash2_lib)
+set_target_properties(rawhash2 PROPERTIES INSTALL_RPATH $ORIGIN/../lib)
+install(TARGETS rawhash2 RUNTIME DESTINATION bin)