feat: integrating geography spatial graph with C++23

.devcontainer/Dockerfile-ubuntu

@@ -6,8 +6,8 @@ RUN apt-get update -y
 RUN apt-get install -y --no-install-recommends\
                     vim \
                     git \
-                    gcc-12 \
-                    g++-12 \
+                    gcc-13 \
+                    g++-13 \
                     build-essential \
                     libboost-all-dev \
                     cmake \

docs/4-tutorials.md

@@ -853,11 +853,11 @@ Quetzal incorporates various kernel types available in the `quetzal::demography:
 
 **Input**
 
-@include{lineno} dispersal_kernel.cpp
+@include{lineno} demography_dispersal_kernel.cpp
 
 **Output**
 
-@include{lineno} dispersal_kernel.txt
+@include{lineno} demography_dispersal_kernel.txt
 
 ---
 

example/CMakeLists.txt

@@ -32,7 +32,7 @@ foreach(testSrc ${SRCS})
   # Add compile target
   add_executable(${testName} ${testSrc})
   # Require the standard
-  target_compile_features(${testName} PUBLIC cxx_std_20)
+  target_compile_features(${testName} PUBLIC cxx_std_23)
   # Ignore warnings about subtle ABI change
   target_compile_options(${testName} PUBLIC "-Wno-psabi")
   # Link to Boost libraries AND other targets and dependencies

example/spatial_graph.cpp → example/geography_graph_complete.cpp

@@ -1,8 +1,7 @@
 #include "quetzal/quetzal.hpp"
 #include <filesystem>
 #include <cassert>
-
-using namespace quetzal;
+//#include <print>
 
 int main()
 {
@@ -18,15 +17,17 @@ int main()
 	auto env = quetzal::geography::landscape<>::from_files( { {"bio1", file1}, {"bio12", file2} }, times );
 	std::cout << env << std::endl;
 
-	// // Embed default demographic quantities along vertices (N_{xt}) and edges (Phi_{xyt})
-	// auto graph1 = env.to_4_neighborhood_graph<>();
-	// auto graph2 = env.to_8_neighborhood_graph<>();
-	// auto graph3 = env.to_complete_graph<>();
+	// We convert the grid to a fully connected graph
+	auto graph = env.to_complete_graph<>();
+
+	// A little helper function
+	auto constexpr sphere_distance = [&]( auto const& p1, auto const& p2 ){ 
+		return env.to_latlon( p1 ).great_circle_distance( env.to_latlon( p2 ) );}
+
+	auto v = graph.edges()
+		| std::transform( [&](auto const& e){ sphere_distance( graph.source( e ), graph.target( e ) );} )
+		| std::transform( [&](auto const& d){ return quetzal::demography::dispersal_kernel::exponential_power( d, {.a=1., .b=5.5} ) ;} )
+		| std::ranges::to<std::vector>();
 
-	// auto weights graph.edges()
-	// 	| [](const & e){ return { graph.source(e), graph.target(e)};  }
-	// 	| [](const & p){ return { env.to_latlon(s), graph.to_latlon(t)};  }
-	// 	| [](const & p){ return x.great_circle_distance_to(y);}
-	// 	| [](const & d){ return quetzal::demography::dispersal_kernel::ExponentialPower(d, {.a=1., .b=5.5});}
-	// 	| []()
+    //std::println("{}", v);
 }

src/CMakeLists.txt

@@ -26,7 +26,7 @@ target_include_directories(${PROJECT_NAME}
   $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>)
 
 # If we have compiler requirements for this library, list them here
-target_compile_features(${PROJECT_NAME} INTERFACE cxx_std_20)
+target_compile_features(${PROJECT_NAME} INTERFACE cxx_std_23)
 
 ###########################
 # INSTALLATION

src/include/quetzal/geography.hpp

@@ -11,6 +11,7 @@
 
 #include "geography/landscape.hpp"
 #include "geography/coordinates.hpp"
+#include "geography/graph/graph.hpp"
 ///
 /// @brief Geospatial data formatting and processing
 ///

src/include/quetzal/geography/graph/detail/adl_resolution.hpp

@@ -0,0 +1,33 @@
+// Copyright 2021 Arnaud Becheler    <abechele@umich.edu>
+
+///////////////////////////////////////////////////////////////////////////                                                                       *
+/// This program is free software; you can redistribute it and/or modify ///
+/// it under the terms of the GNU General Public License as published by ///
+/// the Free Software Foundation; either version 2 of the License, or    ///
+/// (at your option) any later version.                                  ///
+///                                                                     ///
+///////////////////////////////////////////////////////////////////////////
+
+#pragma once
+
+namespace quetzal::geography::detail
+{
+    namespace adl_resolution
+    {
+      void add_edge() = delete;
+      void add_left_edge() = delete;
+      void add_right_edge() = delete;
+      void add_vertex() = delete;
+      void out_degree() = delete;
+      void root() = delete;
+      void is_left_successor() = delete;
+      void is_right_successor() = delete;
+      void has_predecessor() = delete;
+      void predecessor() = delete;
+      void depth_first_search() = delete;
+      void isomorphism() = delete;
+      void in_edges() = delete;
+      void degree() = delete;
+      void edge() = delete;
+    }
+}

src/include/quetzal/geography/graph/detail/graph_traits.hpp

@@ -0,0 +1,55 @@
+// Copyright 2021 Arnaud Becheler    <abechele@umich.edu>
+
+///////////////////////////////////////////////////////////////////////////                                                                       *
+/// This program is free software; you can redistribute it and/or modify ///
+/// it under the terms of the GNU General Public License as published by ///
+/// the Free Software Foundation; either version 2 of the License, or    ///
+/// (at your option) any later version.                                  ///
+///                                                                     ///
+///////////////////////////////////////////////////////////////////////////
+
+#pragma once
+
+#include <boost/graph/adjacency_list.hpp>
+#include <boost/graph/adjacency_matrix.hpp>
+
+namespace quetzal::geography::detail
+{
+    ///
+    /// @brief Defines the common desired graph properties and constraints for a complete and sparse spatial graph
+    ///
+    struct common_graph_traits
+    {
+        /// @brief We want to enforce avoiding multi-graphs (edges with same end nodes)
+        using out_edge_list_type = boost::setS;
+
+        /// @brief We don't allow for inserting vertices except at the end and we don't remove vertices.
+        ///        This means that neither reallocation cost nor stability are reasons for preferring listS to vecS.
+        using vertex_list_type = boost::vecS;
+
+        /// @brief We need bidirectionality for in-edges access
+        /// @remark Bidirectionality trades off storage/insertion overhead for the ability to get in-edges
+        ///         and in-degree without having to enumerate all vertices or edges
+        using directed_type = boost::bidirectionalS;
+    };
+
+    ///
+    /// @brief Defines the desired graph properties and constraints for a complete spatial graph
+    ///
+    struct dense_graph_traits : public common_graph_traits
+    {
+        /// @brief Better to use the adjacency_matrix for dense graphs (E is close to V^2) rather than adjacency_list
+        template <class... Types>
+        using model = boost::adjacency_matrix<Types...>;
+    };
+
+    ///
+    /// @brief Defines the desired graph properties and constraints for a 8 or 4 neighbors spatial graph
+    ///
+    struct sparse_graph_traits : public common_graph_traits
+    {
+        /// @brief Better to use the adjacency_list for sparse graphs (E is closer to 4*V or 8*V than V^2)
+        template <class... Types>
+        using model = boost::adjacency_matrix<Types...>;
+    };
+}