Merge pull request #13 from Becheler/develop

docs: test code for tutorial 4 on splittable populations

test/CMakeLists.txt

@@ -63,10 +63,41 @@ target_include_directories(model_3
 add_test(SpatialExpansionMassBasedSerialized model_3 ${CMAKE_CURRENT_SOURCE_DIR}/data/europe_temp.tif)
 
 ### TUTORIAL TESTS
+#
+# add_executable(tuto_1 tutorials_test/tuto_1.cpp)
+# target_link_libraries(tuto_1 LINK_PUBLIC ${GDAL_LIBRARY} )
+# target_include_directories(tuto_1
+#   PRIVATE $<BUILD_INTERFACE:${PROJECT_SOURCE_DIR}/include>
+#   $<BUILD_INTERFACE:${CMAKE_CURRENT_LIST_DIR}/include>)
+# add_test(TwoDemesIndividualBased tuto_1)
 
-add_executable(tuto_1 tutorials_test/tuto_1.cpp)
-target_link_libraries(tuto_1 LINK_PUBLIC ${GDAL_LIBRARY} )
-target_include_directories(tuto_1
-  PRIVATE $<BUILD_INTERFACE:${PROJECT_SOURCE_DIR}/include>
-  $<BUILD_INTERFACE:${CMAKE_CURRENT_LIST_DIR}/include>)
-add_test(TwoDemesIndividualBased tuto_1)
+
+# Keep test files in a separate source directory called test
+file(GLOB TUTO_SRCS RELATIVE ${CMAKE_CURRENT_SOURCE_DIR} tutorials_test/*.cpp)
+
+# Run through each source
+foreach(testSrc ${TUTO_SRCS})
+        # Extract the filename without an extension (NAME_WE)
+        get_filename_component(testName ${testSrc} NAME_WE)
+        # Add compile target
+        add_executable(${testName} ${testSrc})
+        # Link to Boost libraries AND other targets and dependencies
+        target_link_libraries(${testName}
+                                ${Boost_LIBRARIES}
+                                ${Boost_FILESYSTEM_LIBRARY}
+                                ${Boost_SYSTEM_LIBRARY}
+                                ${Boost_SERIALIZATION_LIBRARY}
+                                ${GDAL_LIBRARY}
+                                Boost::headers)
+        # I like to move testing binaries into a testBin directory
+        set_target_properties(${testName} PROPERTIES
+            RUNTIME_OUTPUT_DIRECTORY  ${CMAKE_CURRENT_SOURCE_DIR}/build/testBin)
+        # Specifies include directories to use when compiling a given target
+        target_include_directories(
+          ${testName} PRIVATE $<BUILD_INTERFACE:${PROJECT_SOURCE_DIR}/include>
+                              $<BUILD_INTERFACE:${CMAKE_CURRENT_LIST_DIR}/include>)
+        #Finally add it to test execution: notice the WORKING_DIRECTORY and COMMAND
+        add_test(NAME ${testName}
+                 WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/build/testBin
+                 COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/build/testBin/${testName})
+endforeach(testSrc)

test/tutorials_test/tuto_1.cpp → test/tutorials_test/tuto_3.cpp

@@ -43,4 +43,5 @@ int main(){
   {
     std::cout << "N(" << x << "," << nb_generations -1 << ") = " << N(x,t) << std::endl;
   }
+  return 0;
 } // end main

test/tutorials_test/tuto_4.cpp

@@ -0,0 +1,45 @@
+#include "quetzal/demography.h"
+#include <iostream>
+#include <random>
+#include <map>
+// Define a customized transition matrix
+struct transition_matrix
+{
+	// Two demes, but identified by string
+	using coord_type = std::string;
+	using time_type = int;
+	// Mandatory interface with the quetzal algorithms:
+	// Take a the coordinate of start
+	// Returns the vector of possible arrival coordinates
+	std::vector<coord_type> arrival_space(coord_type x)
+	{
+		// Whatever the coordinate to start from, redirect them either in Paris or A.A
+		return {"Paris", "Ann Arbor"};
+	}
+	// Second mandatory interface: what is the probability to move from x to y?
+	double operator()(coord_type x, coord_type y)
+	{
+		return 0.5; // 1/2 probability to change of location
+	}
+};
+int main(){
+	using coord_type = std::string;
+	using time_type = int;
+	using generator_type = std::mt19937;
+	using quetzal::demography::demographic_policy::mass_based;
+  using quetzal::demography::memory_policy::on_RAM;
+	int N0 = 100;
+	// Number of non-overlapping generations for the demographic simulation
+	int nb_generations = 10;
+	quetzal::demography::History<coord_type, mass_based, on_RAM> history("Paris", N0, nb_generations);
+	// Growth function
+	auto N = history.get_functor_N();
+	auto growth = [N](auto& gen, coord_type x, time_type t){ return 2*N(x,t) ; };
+	// Random number generation
+	generator_type gen;
+	// Define the transition probabilities
+	transition_matrix M;
+	// Pass everything to the simulation
+	history.simulate_forward(growth, M, gen);
+	return 0;
+}