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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

@@ -18,10 +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++17
-# See also: standard in make_and_run_binder.py
-# See also: standard in Makefile
-set(CMAKE_CXX_STANDARD 17)
+# 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
@@ -145,6 +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")
 
@@ -160,15 +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
@@ -187,7 +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()
 
 
@@ -203,7 +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)
 
@@ -308,6 +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
   )
 
@@ -326,7 +335,8 @@ set(bdsg_TARGET_DEPS
   bbhash
   sparsepp
   mio::mio
-  PkgConfig::Jansson)
+  PkgConfig::Jansson
+  Boost::boost)
 
 set(bdsg_LIBS
   ${bdsg_TARGET_DEPS}
@@ -340,7 +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`).
 

bdsg/cmake_bindings/bdsg/internal/mapped_structs.cpp

@@ -20,15 +20,15 @@
 
 void bind_bdsg_internal_mapped_structs(std::function< pybind11::module &(std::string const &namespace_) > &M)
 {
-	{ // bdsg::STLBackend file:bdsg/internal/mapped_structs.hpp line:44
+	{ // bdsg::STLBackend file:bdsg/internal/mapped_structs.hpp line:45
 		pybind11::class_<bdsg::STLBackend, std::shared_ptr<bdsg::STLBackend>> cl(M("bdsg"), "STLBackend", "Type enum value for selecting data structures that use the STL and SDSL.");
 		cl.def( pybind11::init( [](){ return new bdsg::STLBackend(); } ) );
 	}
-	{ // bdsg::VectorFor file:bdsg/internal/mapped_structs.hpp line:66
+	{ // bdsg::VectorFor file:bdsg/internal/mapped_structs.hpp line:67
 		pybind11::class_<bdsg::VectorFor<bdsg::STLBackend>, std::shared_ptr<bdsg::VectorFor<bdsg::STLBackend>>> cl(M("bdsg"), "VectorFor_bdsg_STLBackend_t", "");
 		cl.def( pybind11::init( [](){ return new bdsg::VectorFor<bdsg::STLBackend>(); } ) );
 	}
-	{ // bdsg::IntVectorFor file:bdsg/internal/mapped_structs.hpp line:72
+	{ // bdsg::IntVectorFor file:bdsg/internal/mapped_structs.hpp line:73
 		pybind11::class_<bdsg::IntVectorFor<bdsg::STLBackend>, std::shared_ptr<bdsg::IntVectorFor<bdsg::STLBackend>>> cl(M("bdsg"), "IntVectorFor_bdsg_STLBackend_t", "");
 		cl.def( pybind11::init( [](){ return new bdsg::IntVectorFor<bdsg::STLBackend>(); } ) );
 	}

bdsg/cmake_bindings/bdsg/internal/mapped_structs_1.cpp

@@ -26,37 +26,38 @@
 
 void bind_bdsg_internal_mapped_structs_1(std::function< pybind11::module &(std::string const &namespace_) > &M)
 {
-	{ // bdsg::CompatBackend file:bdsg/internal/mapped_structs.hpp line:1144
+	{ // bdsg::CompatBackend file:bdsg/internal/mapped_structs.hpp line:1150
 		pybind11::class_<bdsg::CompatBackend, std::shared_ptr<bdsg::CompatBackend>> cl(M("bdsg"), "CompatBackend", "Type enum value for selecting data structures that use memory-mappable data\n structures but with the standard allocator.");
 		cl.def( pybind11::init( [](){ return new bdsg::CompatBackend(); } ) );
 	}
-	{ // bdsg::MappedBackend file:bdsg/internal/mapped_structs.hpp line:1155
+	{ // bdsg::MappedBackend file:bdsg/internal/mapped_structs.hpp line:1161
 		pybind11::class_<bdsg::MappedBackend, std::shared_ptr<bdsg::MappedBackend>> cl(M("bdsg"), "MappedBackend", "Type enum value for selecting data structures that use YOMO memory mapping\n and the YOMO allocator.\n\n They can safely exist outside of mapped memory, but are probably slower\n there since YOMO's internal tables still need to be consulted when following\n pointers.");
 		cl.def( pybind11::init( [](){ return new bdsg::MappedBackend(); } ) );
 	}
-	{ // bdsg::VectorFor file:bdsg/internal/mapped_structs.hpp line:1161
+	{ // bdsg::VectorFor file:bdsg/internal/mapped_structs.hpp line:1167
 		pybind11::class_<bdsg::VectorFor<bdsg::MappedBackend>, std::shared_ptr<bdsg::VectorFor<bdsg::MappedBackend>>> cl(M("bdsg"), "VectorFor_bdsg_MappedBackend_t", "");
 		cl.def( pybind11::init( [](){ return new bdsg::VectorFor<bdsg::MappedBackend>(); } ) );
 	}
-	{ // bdsg::IntVectorFor file:bdsg/internal/mapped_structs.hpp line:1167
+	{ // bdsg::IntVectorFor file:bdsg/internal/mapped_structs.hpp line:1173
 		pybind11::class_<bdsg::IntVectorFor<bdsg::MappedBackend>, std::shared_ptr<bdsg::IntVectorFor<bdsg::MappedBackend>>> cl(M("bdsg"), "IntVectorFor_bdsg_MappedBackend_t", "");
 		cl.def( pybind11::init( [](){ return new bdsg::IntVectorFor<bdsg::MappedBackend>(); } ) );
 	}
-	{ // bdsg::VectorFor file:bdsg/internal/mapped_structs.hpp line:1177
+	{ // bdsg::VectorFor file:bdsg/internal/mapped_structs.hpp line:1183
 		pybind11::class_<bdsg::VectorFor<bdsg::CompatBackend>, std::shared_ptr<bdsg::VectorFor<bdsg::CompatBackend>>> cl(M("bdsg"), "VectorFor_bdsg_CompatBackend_t", "");
 		cl.def( pybind11::init( [](){ return new bdsg::VectorFor<bdsg::CompatBackend>(); } ) );
 	}
-	{ // bdsg::IntVectorFor file:bdsg/internal/mapped_structs.hpp line:1183
+	{ // bdsg::IntVectorFor file:bdsg/internal/mapped_structs.hpp line:1189
 		pybind11::class_<bdsg::IntVectorFor<bdsg::CompatBackend>, std::shared_ptr<bdsg::IntVectorFor<bdsg::CompatBackend>>> cl(M("bdsg"), "IntVectorFor_bdsg_CompatBackend_t", "");
 		cl.def( pybind11::init( [](){ return new bdsg::IntVectorFor<bdsg::CompatBackend>(); } ) );
 	}
-	{ // bdsg::PackedDeque file:bdsg/internal/packed_structs.hpp line:491
+	{ // bdsg::PackedDeque file:bdsg/internal/packed_structs.hpp line:404
 		pybind11::class_<bdsg::PackedDeque<bdsg::STLBackend>, std::shared_ptr<bdsg::PackedDeque<bdsg::STLBackend>>> cl(M("bdsg"), "PackedDeque_bdsg_STLBackend_t", "");
 		cl.def( pybind11::init( [](){ return new bdsg::PackedDeque<bdsg::STLBackend>(); } ) );
 		cl.def( pybind11::init( [](bdsg::PackedDeque<bdsg::STLBackend> const &o){ return new bdsg::PackedDeque<bdsg::STLBackend>(o); } ) );
 		cl.def("assign", (class bdsg::PackedDeque<> & (bdsg::PackedDeque<bdsg::STLBackend>::*)(const class bdsg::PackedDeque<> &)) &bdsg::PackedDeque<>::operator=, "C++: bdsg::PackedDeque<>::operator=(const class bdsg::PackedDeque<> &) --> class bdsg::PackedDeque<> &", pybind11::return_value_policy::automatic, pybind11::arg("other"));
 		cl.def("set", (void (bdsg::PackedDeque<bdsg::STLBackend>::*)(const unsigned long &, const unsigned long long &)) &bdsg::PackedDeque<>::set, "C++: bdsg::PackedDeque<>::set(const unsigned long &, const unsigned long long &) --> void", pybind11::arg("i"), pybind11::arg("value"));
 		cl.def("get", (unsigned long long (bdsg::PackedDeque<bdsg::STLBackend>::*)(const unsigned long &) const) &bdsg::PackedDeque<>::get, "C++: bdsg::PackedDeque<>::get(const unsigned long &) const --> unsigned long long", pybind11::arg("i"));
+		cl.def("__getitem__", (unsigned long long (bdsg::PackedDeque<bdsg::STLBackend>::*)(unsigned long) const) &bdsg::PackedDeque<>::operator[], "C++: bdsg::PackedDeque<>::operator[](unsigned long) const --> unsigned long long", pybind11::arg("i"));
 		cl.def("push_front", (void (bdsg::PackedDeque<bdsg::STLBackend>::*)(const unsigned long long &)) &bdsg::PackedDeque<>::push_front, "C++: bdsg::PackedDeque<>::push_front(const unsigned long long &) --> void", pybind11::arg("value"));
 		cl.def("append_front", (void (bdsg::PackedDeque<bdsg::STLBackend>::*)(const unsigned long long &)) &bdsg::PackedDeque<>::append_front, "C++: bdsg::PackedDeque<>::append_front(const unsigned long long &) --> void", pybind11::arg("value"));
 		cl.def("push_back", (void (bdsg::PackedDeque<bdsg::STLBackend>::*)(const unsigned long long &)) &bdsg::PackedDeque<>::push_back, "C++: bdsg::PackedDeque<>::push_back(const unsigned long long &) --> void", pybind11::arg("value"));
@@ -69,7 +70,7 @@ void bind_bdsg_internal_mapped_structs_1(std::function< pybind11::module &(std::
 		cl.def("clear", (void (bdsg::PackedDeque<bdsg::STLBackend>::*)()) &bdsg::PackedDeque<>::clear, "C++: bdsg::PackedDeque<>::clear() --> void");
 		cl.def("memory_usage", (unsigned long (bdsg::PackedDeque<bdsg::STLBackend>::*)() const) &bdsg::PackedDeque<>::memory_usage, "C++: bdsg::PackedDeque<>::memory_usage() const --> unsigned long");
 	}
-	{ // bdsg::PackedSet file:bdsg/internal/packed_structs.hpp line:597
+	{ // bdsg::PackedSet file:bdsg/internal/packed_structs.hpp line:513
 		pybind11::class_<bdsg::PackedSet<bdsg::STLBackend>, std::shared_ptr<bdsg::PackedSet<bdsg::STLBackend>>> cl(M("bdsg"), "PackedSet_bdsg_STLBackend_t", "");
 		cl.def( pybind11::init( [](){ return new bdsg::PackedSet<bdsg::STLBackend>(); } ) );
 		cl.def( pybind11::init( [](bdsg::PackedSet<bdsg::STLBackend> const &o){ return new bdsg::PackedSet<bdsg::STLBackend>(o); } ) );

bdsg/cmake_bindings/bdsg/overlays/vectorizable_overlays.cpp

@@ -29,7 +29,7 @@
 	PYBIND11_MAKE_OPAQUE(std::shared_ptr<void>)
 #endif
 
-// bdsg::PathVectorizableOverlay file:bdsg/overlays/vectorizable_overlays.hpp line:197
+// bdsg::PathVectorizableOverlay file:bdsg/overlays/vectorizable_overlays.hpp line:201
 struct PyCallBack_bdsg_PathVectorizableOverlay : public bdsg::PathVectorizableOverlay {
 	using bdsg::PathVectorizableOverlay::PathVectorizableOverlay;
 
@@ -751,7 +751,7 @@ struct PyCallBack_bdsg_PathVectorizableOverlay : public bdsg::PathVectorizableOv
 	}
 };
 
-// bdsg::PathPositionVectorizableOverlay file:bdsg/overlays/vectorizable_overlays.hpp line:292
+// bdsg::PathPositionVectorizableOverlay file:bdsg/overlays/vectorizable_overlays.hpp line:296
 struct PyCallBack_bdsg_PathPositionVectorizableOverlay : public bdsg::PathPositionVectorizableOverlay {
 	using bdsg::PathPositionVectorizableOverlay::PathPositionVectorizableOverlay;
 
@@ -1527,7 +1527,7 @@ struct PyCallBack_bdsg_PathPositionVectorizableOverlay : public bdsg::PathPositi
 
 void bind_bdsg_overlays_vectorizable_overlays(std::function< pybind11::module &(std::string const &namespace_) > &M)
 {
-	{ // bdsg::PathVectorizableOverlay file:bdsg/overlays/vectorizable_overlays.hpp line:197
+	{ // bdsg::PathVectorizableOverlay file:bdsg/overlays/vectorizable_overlays.hpp line:201
 		pybind11::class_<bdsg::PathVectorizableOverlay, std::shared_ptr<bdsg::PathVectorizableOverlay>, PyCallBack_bdsg_PathVectorizableOverlay, bdsg::VectorizableOverlay, handlegraph::PathHandleGraph> cl(M("bdsg"), "PathVectorizableOverlay", "");
 		cl.def( pybind11::init<const class handlegraph::PathHandleGraph *>(), pybind11::arg("path_graph") );
 
@@ -1549,7 +1549,7 @@ void bind_bdsg_overlays_vectorizable_overlays(std::function< pybind11::module &(
 		cl.def("get_next_step", (struct handlegraph::step_handle_t (bdsg::PathVectorizableOverlay::*)(const struct handlegraph::step_handle_t &) const) &bdsg::PathVectorizableOverlay::get_next_step, "Returns a handle to the next step on the path. If the given step is the final step\n of a non-circular path, this method has undefined behavior. In a circular path,\n the \"last\" step will loop around to the \"first\" step.\n\nC++: bdsg::PathVectorizableOverlay::get_next_step(const struct handlegraph::step_handle_t &) const --> struct handlegraph::step_handle_t", pybind11::arg("step_handle"));
 		cl.def("get_previous_step", (struct handlegraph::step_handle_t (bdsg::PathVectorizableOverlay::*)(const struct handlegraph::step_handle_t &) const) &bdsg::PathVectorizableOverlay::get_previous_step, "Returns a handle to the previous step on the path. If the given step is the first\n step of a non-circular path, this method has undefined behavior. In a circular path,\n it will loop around from the \"first\" step (i.e. the one returned by path_begin) to\n the \"last\" step.\n\nC++: bdsg::PathVectorizableOverlay::get_previous_step(const struct handlegraph::step_handle_t &) const --> struct handlegraph::step_handle_t", pybind11::arg("step_handle"));
 	}
-	{ // bdsg::PathPositionVectorizableOverlay file:bdsg/overlays/vectorizable_overlays.hpp line:292
+	{ // bdsg::PathPositionVectorizableOverlay file:bdsg/overlays/vectorizable_overlays.hpp line:296
 		pybind11::class_<bdsg::PathPositionVectorizableOverlay, std::shared_ptr<bdsg::PathPositionVectorizableOverlay>, PyCallBack_bdsg_PathPositionVectorizableOverlay, bdsg::PathVectorizableOverlay, handlegraph::PathPositionHandleGraph> cl(M("bdsg"), "PathPositionVectorizableOverlay", "");
 		cl.def( pybind11::init<const class handlegraph::PathPositionHandleGraph *>(), pybind11::arg("path_position_graph") );