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.github/workflows/testmac.yml

@@ -26,7 +26,7 @@ jobs:
       - name: Run build and test
         run: |
           set -e
-          brew install libomp doxygen jansson
+          brew install libomp doxygen jansson boost
           mkdir -p build
           cd build
           cmake .. -DRUN_DOXYGEN=ON -DPYTHON_EXECUTABLE="$(which python3)"

CMakeLists.txt

@@ -18,8 +18,8 @@ OPTION(USE_INSTALLED_LIBHANDLEGRAPH "Use the version of libhandlegraph installed
 # TODO: We can only do out-of-source builds!
 # TODO: How do we error out meaningfully on in-source builds?
 
-# We build using c++14
-set(CMAKE_CXX_STANDARD 14)
+# We build using c++20
+set(CMAKE_CXX_STANDARD 20)
 # We need library paths to be relative in the build directories so we can let
 # the libraries in our Python module find each other when we package them into
 # a wheel. This only works on CMake 3.14+; older CMake we have to bully with
@@ -143,6 +143,8 @@ endif()
 # Find other system dependencies
 pkg_check_modules(Jansson REQUIRED IMPORTED_TARGET jansson)
 
+find_package(Boost REQUIRED)
+
 # Find our bdsg package directory where input sources and dependencies are
 set(bdsg_DIR "${CMAKE_CURRENT_SOURCE_DIR}/bdsg")
 
@@ -158,15 +160,19 @@ include(ExternalProject)
 
 # sdsl-lite (gives an "sdsl" target)
 set(BUILD_SHARED_LIBS ON CACHE BOOL "Build sdsl-lite shared libraries")
-add_subdirectory("${bdsg_DIR}/deps/sdsl-lite")
+if (NOT TARGET sdsl)
+    add_subdirectory("${bdsg_DIR}/deps/sdsl-lite")
+endif()
 if (${CMAKE_SYSTEM_NAME} MATCHES "Darwin")
     # It produces divsufsort and divsufsort64 targets that don't know they need OMP on Mac.
     set_target_properties(divsufsort PROPERTIES LINK_FLAGS "-lomp")
     set_target_properties(divsufsort64 PROPERTIES LINK_FLAGS "-lomp")
 endif()
 
 # hopscotch_map (required by DYNAMIC, gives a "tsl::hopscotch_map" target)
-add_subdirectory("${bdsg_DIR}/deps/hopscotch-map")
+if (NOT TARGET tsl::hopscotch_map)
+    add_subdirectory("${bdsg_DIR}/deps/hopscotch-map")
+endif()
 
 # DYNAMIC (header only)
 # Does not ship its own install step or define a target, so we make our own target
@@ -185,7 +191,9 @@ elseif (TARGET handlegraph_objs)
     message("Using libhandlegraph built by another CMake")
 else ()
     message("Using bundled libhandlegraph")
-    add_subdirectory("${bdsg_DIR}/deps/libhandlegraph")
+    if (NOT TARGET handlegraph_shared AND NOT TARGET handlegraph)
+        add_subdirectory("${bdsg_DIR}/deps/libhandlegraph")
+    endif()
 endif()
 
 
@@ -201,7 +209,9 @@ add_library(sparsepp INTERFACE)
 target_include_directories(sparsepp INTERFACE "${bdsg_DIR}/deps/sparsepp/")
 
 # mio (header only)
-add_subdirectory("${bdsg_DIR}/deps/mio")
+if (NOT TARGET mio::mio)
+    add_subdirectory("${bdsg_DIR}/deps/mio")
+endif()
 
 if (BUILD_PYTHON_BINDINGS)
 
@@ -306,6 +316,7 @@ add_library(bdsg_objs OBJECT
   ${bdsg_DIR}/src/strand_split_overlay.cpp
   ${bdsg_DIR}/src/utility.cpp
   ${bdsg_DIR}/src/vectorizable_overlays.cpp
+  ${bdsg_DIR}/src/ch.cpp
   ${bdsg_DIR}/src/snarl_distance_index.cpp
   )
 
@@ -324,7 +335,8 @@ set(bdsg_TARGET_DEPS
   bbhash
   sparsepp
   mio::mio
-  PkgConfig::Jansson)
+  PkgConfig::Jansson
+  Boost::boost)
 
 set(bdsg_LIBS
   ${bdsg_TARGET_DEPS}
@@ -338,7 +350,7 @@ target_include_directories(bdsg_objs PUBLIC ${bdsg_INCLUDES})
 set_target_properties(bdsg_objs PROPERTIES POSITION_INDEPENDENT_CODE TRUE)
 
 if (CMAKE_MAJOR_VERSION EQUAL "3" AND (CMAKE_MINOR_VERSION EQUAL "10" OR CMAKE_MINOR_VERSION EQUAL "11"))
-    # Before CMake 3.12 we can't ise target_link_libraries on an object library to convey the need to use depencies' include directories
+    # Before CMake 3.12 we can't use target_link_libraries on an object library to convey the need to use depencies' include directories
     get_target_property(sdsl_INCLUDE sdsl INTERFACE_INCLUDE_DIRECTORIES)
     target_include_directories(bdsg_objs PUBLIC ${sdsl_INCLUDE})
     get_target_property(hopscotch_map_INCLUDE tsl::hopscotch_map INTERFACE_INCLUDE_DIRECTORIES)

Makefile

@@ -24,6 +24,7 @@ OBJS += $(OBJ_DIR)/path_subgraph_overlay.o
 OBJS += $(OBJ_DIR)/subgraph_overlay.o
 OBJS += $(OBJ_DIR)/vectorizable_overlays.o 
 OBJS += $(OBJ_DIR)/packed_subgraph_overlay.o 
+OBJS += $(OBJ_DIR)/ch.o
 OBJS += $(OBJ_DIR)/snarl_distance_index.o
 OBJS += $(OBJ_DIR)/strand_split_overlay.o 
 OBJS += $(OBJ_DIR)/utility.o

README.md

@@ -93,6 +93,7 @@ The documentation can then be found at `docs/_build/html/index.html`.
 - [`DYNAMIC`](https://github.com/xxsds/DYNAMIC)
 - [`BBHash/alltypes`](https://github.com/rizkg/BBHash/tree/alltypes) 
 - [`jansson`](https://github.com/akheron/jansson)
+- [`Boost`](https://www.boost.org/).
 
 The build process with `make` assumes that these libraries and their headers have been installed in a place on the system where the compiler can find them (e.g. in `CPLUS_INCLUDE_PATH`).