Improve CMake

.github/workflows/docker-build.yml

@@ -5,6 +5,16 @@ on:
     branches:
       - main
   pull_request:
+  workflow_dispatch:
+    inputs:
+      use_cache:
+        description: 'Use cache for this run'
+        required: true
+        default: 'true'
+      num_build_jobs:
+        description: 'Number of build jobs'
+        required: true
+        default: '2'
 
 jobs:
   build:
@@ -30,6 +40,7 @@ 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
@@ -51,6 +62,7 @@ jobs:
           cache-to: type=gha,mode=max
           build-args: |
             BUILDKIT_INLINE_CACHE=1
+            RAWHASH_NUM_BUILD_JOBS=${{ github.event.inputs.num_build_jobs || '2' }}
 
       - name: Extract build directory from Docker image
         run: |

CMakeLists.txt

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

Dockerfile

@@ -7,9 +7,10 @@ RUN apt-get update && apt-get install -y \
 WORKDIR /rawhash2
 COPY . /rawhash2
 
+ARG RAWHASH_NUM_BUILD_JOBS
 RUN mkdir -p build && cd build \
     && cmake .. \
-    && make -j 3
+    && make -j $RAWHASH_NUM_BUILD_JOBS
 
 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()
+        add_imported_library(${TARGET_NAME} 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}")
@@ -15,18 +24,18 @@ function(setup_hdf5 TARGET_NAME)
             set(HDF5_BUILD_DIR ${HDF5_DIR}/build)
             ExternalProject_Add(
                 hdf5_build
+                BUILD_ALWAYS 1 # Rebuild if local checkout is updated
                 SOURCE_DIR ${HDF5_SOURCE_DIR}
                 BINARY_DIR ${HDF5_BUILD_DIR}
                 CONFIGURE_COMMAND ${HDF5_SOURCE_DIR}/configure --enable-threadsafe --disable-hl --prefix=${HDF5_BUILD_DIR}
                 # 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} SHARED)
     endif()
 endfunction()

cmake/SetupPOD5.cmake

@@ -1,22 +1,45 @@
-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)
+    add_imported_library(${TARGET_NAME} zstd)
+endfunction()
+
+function(setup_zstd)
+    set(ZSTD_DIR ${EXTERNAL_PROJECTS_BUILD_DIR}/zstd)
     ExternalProject_Add(
         zstd_build
+        BUILD_ALWAYS 1 # Rebuild if local checkout is updated
         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} SHARED)
 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(${TARGET_NAME})
+
+        set(POD5_VERSION "0.2.2")
+        set(POD5_URLDIR "pod5-${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})
+    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 +68,6 @@ 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 +101,7 @@ 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

@@ -1,23 +1,22 @@
-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(${TARGET_NAME} PRIVATE rawhash_ruclient.cpp)
+        target_link_libraries(${TARGET_NAME} PRIVATE ont_device_client_LIB ru_method_LIB)
+    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()
-        ExternalProject_Add(
-            ruclient_build
-            SOURCE_DIR ${CMAKE_SOURCE_DIR}/extern/readuntil_fake
-            BINARY_DIR ${RUCLIENT_DIR}/build
-            CMAKE_ARGS
-                -DCMAKE_INSTALL_PREFIX=${RUCLIENT_DIR}
-        )
-        add_dependencies(${TARGET_NAME} ruclient_build)
-        include_directories(${RUCLIENT_DIR}/include)
-        message(STATUS "ruclient enabled")
+        set(RUCLIENT_SOURCE_DIR ${CMAKE_SOURCE_DIR}/extern/readuntil_fake)
+        add_subdirectory(${RUCLIENT_SOURCE_DIR} ${RUCLIENT_DIR})
+        include_directories(${RUCLIENT_SOURCE_DIR}/include)
     else()
         message(STATUS "ruclient disabled")
     endif()

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()
+        add_imported_library(${TARGET_NAME} 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)
@@ -12,20 +21,20 @@ function(setup_slow5 TARGET_NAME)
             message(STATUS "Compiling slow5 to ${SLOW5_DIR}")
             ExternalProject_Add(
                 slow5_build
+                BUILD_ALWAYS 1 # Rebuild if local checkout is updated
                 BINARY_DIR ${SLOW5_DIR}
                 SOURCE_DIR ${SLOW5_SOURCE_DIR}
                 INSTALL_COMMAND ${CMAKE_COMMAND} -E copy_directory ${SLOW5_SOURCE_DIR}/include ${SLOW5_DIR}/include
                              && ${CMAKE_COMMAND} -E make_directory ${SLOW5_DIR}/lib
                              && ${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} SHARED)
     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()