Merge pull request #194 from K-Johnson-Horrigan/refactor

Intergration tests, not sure why codecov thinks coverage is going down, but it's clearly wrong, oh well!

source/catch/main.cc

@@ -33,6 +33,7 @@
 #include "../test/integration_test/lysogeny/plr.test.cc"
 #include "../test/integration_test/endosymbiosis/res_distribute.test.cc"
 #include "../test/integration_test/dirty_transmission/hz_mut_rate.test.cc"
+#include "../test/integration_test/multi_infection/pgg.test.cc"
 
 //#include "../PGGendtoend.test.cc"
 //#include "../test/end_to_end.test.cc"

source/test/efficient_mode_test/EfficientDataNodes.test.cc

@@ -1,7 +1,6 @@
 #include "../../efficient_mode/EfficientHost.h"
 #include "../../efficient_mode/EfficientSymbiont.h"
 #include "../../efficient_mode/EfficientWorld.h"
-#include "../../efficient_mode/EfficientWorldSetup.cc"
 
 TEST_CASE("GetEfficiencyDataNode", "[efficient]"){
   GIVEN("a world"){

source/test/integration_test/dirty_transmission/hz_mut_rate.test.cc

@@ -1,3 +1,118 @@
+#include "../../../efficient_mode/EfficientWorldSetup.cc"
+
 TEST_CASE("Horizontal Mutation Rate Results", "[integration]"){
-
-}
+  emp::Random random(14);
+  SymConfigBase config;
+  EfficientWorld world(random, &config);
+
+  config.HOST_INT(-2);
+  config.SYM_INT(-2);
+  config.EFFICIENT_SYM(1);
+  config.SYNERGY(2);
+  config.MUTATION_RATE(0.1);
+  config.HOST_AGE_MAX(100);
+  config.SYM_AGE_MAX(50);
+  config.UPDATES(2001);
+
+  config.GRID_X(10);
+  config.GRID_Y(10);
+
+  emp::DataMonitor<double, emp::data::Histogram>& sym_val_node = world.GetHostedSymIntValDataNode();
+  emp::DataMonitor<double>& sym_eff_node = world.GetEfficiencyDataNode();
+
+  WHEN("Vertical transmission rate is low"){
+	config.VERTICAL_TRANSMISSION(0.1);
+	world.Setup();
+	WHEN("Horizontal transmission mutation rate is low") {
+	  config.HORIZ_MUTATION_RATE(0.1);
+	  world.RunExperiment(false);
+	  THEN("Symbionts evolve to be parasitic and efficient") {
+		REQUIRE(sym_val_node.GetMean() < -0.7);
+		REQUIRE(sym_eff_node.GetMean() > 0.94);
+	  }
+	}
+	WHEN("Horizontal transmission mutation rate is intermediate") {
+	  config.HORIZ_MUTATION_RATE(0.5);
+	  world.RunExperiment(false);
+	  THEN("Symbionts evolve to be parasitic and efficient") {
+		REQUIRE(sym_val_node.GetMean() < -0.6);
+		REQUIRE(sym_eff_node.GetMean() > 0.94);
+	  }
+	}
+	WHEN("Horizontal transmission mutation rate is high") {
+	  config.HORIZ_MUTATION_RATE(1);
+	  world.RunExperiment(false);
+	  THEN("Symbionts evolve to be parasitic and efficient") {
+		REQUIRE(sym_val_node.GetMean() < -0.7);
+		REQUIRE(sym_eff_node.GetMean() > 0.95);
+	  }
+	}
+  }
+  WHEN("Vertical transmission rate is intermediate") {
+	//other tests work fine with both constrained and paper-replicating world conditions 
+	// (large to reduce drift vs. small for speed 
+	//but in intermediate case need larger world to replicate paper results
+	config.GRID_X(100);
+	config.GRID_Y(100);
+	config.VERTICAL_TRANSMISSION(0.3);
+	world.Setup();
+	WHEN("Horizontal transmission mutation rate is low") {
+	  config.HORIZ_MUTATION_RATE(0.1);
+	  world.RunExperiment(false);
+	  THEN("Symbionts evolve to be slightly parasitic and efficient") {
+		double sym_val_mean = sym_val_node.GetMean();
+		REQUIRE(sym_val_mean < 0);
+		REQUIRE(sym_val_mean > -0.7);
+		REQUIRE(sym_eff_node.GetMean() > 0.94);
+	  }
+	}
+	WHEN("Horizontal transmission mutation rate is intermediate") {
+	  config.HORIZ_MUTATION_RATE(0.5);
+	  world.RunExperiment(false);
+	  THEN("Symbionts are evolve between slight parasitism and slight mutualism and evolve to be efficient") {
+		double sym_val_mean = sym_val_node.GetMean();
+		REQUIRE(sym_val_mean < 0.5);
+		REQUIRE(sym_val_mean > -0.5);
+		REQUIRE(sym_eff_node.GetMean() > 0.94);
+	  }
+	}
+	WHEN("Horizontal transmission mutation rate is high") {
+	  config.HORIZ_MUTATION_RATE(1);
+	  world.RunExperiment(false);
+	  THEN("Symbionts evolve to be slightly mutualistic and efficient") {
+		double sym_val_mean = sym_val_node.GetMean();
+		REQUIRE(sym_val_mean > 0);
+		REQUIRE(sym_val_mean < 0.7);
+		REQUIRE(sym_eff_node.GetMean() > 0.94);
+	  }
+	}
+  }
+  WHEN("Vertical transmission rate is high") {
+	config.VERTICAL_TRANSMISSION(0.9);
+	world.Setup();
+	WHEN("Horizontal transmission mutation rate is low") {
+	  config.HORIZ_MUTATION_RATE(0.1);
+	  world.RunExperiment(false);
+	  THEN("Symbionts evolve to be mutualistic and efficient") {
+		REQUIRE(sym_val_node.GetMean() > 0.7);
+		REQUIRE(sym_eff_node.GetMean() > 0.94);
+	  }
+	}
+	WHEN("Horizontal transmission mutation rate is intermediate") {
+	  config.HORIZ_MUTATION_RATE(0.5);
+	  world.RunExperiment(false);
+	  THEN("Symbionts evolve to be mutualistic and efficient") {
+		REQUIRE(sym_val_node.GetMean() > 0.7);
+		REQUIRE(sym_eff_node.GetMean() > 0.94);
+	  }
+	}
+	WHEN("Horizontal transmission mutation rate is high") {
+	  config.HORIZ_MUTATION_RATE(1);
+	  world.RunExperiment(false);
+	  THEN("Symbionts evolve to be mutualistic and efficient") {
+		REQUIRE(sym_val_node.GetMean() > 0.7);
+		REQUIRE(sym_eff_node.GetMean() > 0.94);
+	  }
+	}
+  }
+}

source/test/integration_test/lysogeny/plr.test.cc

@@ -1,7 +1,3 @@
-#include "../../../lysis_mode/Bacterium.h"
-#include "../../../lysis_mode/Phage.h"
-#include "../../../lysis_mode/LysisWorld.h"
-#include "../../../default_mode/WorldSetup.cc"
 #include "../../../lysis_mode/LysisWorldSetup.cc"
 
 TEST_CASE("Prophage Loss Rate Results", "[integration]"){

source/test/integration_test/multi_infection/pgg.test.cc

@@ -0,0 +1,60 @@
+#include "../../../pgg_mode/PGGWorldSetup.cc"
+
+
+TEST_CASE("Multi-infection results", "[integration]") {
+  emp::Random random(29);
+  SymConfigBase config;
+  PGGWorld world(random, &config);
+  config.HOST_INT(0);
+  config.SYM_INT(0);
+  config.PGG(1);
+  config.MUTATION_SIZE(0.05);
+  config.UPDATES(2000);
+  world.Setup();
+
+  config.GRID_X(5);
+  config.GRID_Y(5);
+
+  emp::DataMonitor<double, emp::data::Histogram>& sym_val_node = world.GetHostedSymIntValDataNode();
+  emp::DataMonitor<double, emp::data::Histogram>& host_val_node = world.GetHostIntValDataNode();
+
+
+  WHEN("There are few symbionts per host") {
+	config.SYM_LIMIT(1);
+	WHEN("Vertical transmission rate is intermediate") {
+	  config.VERTICAL_TRANSMISSION(0.7);
+	  world.RunExperiment(false);
+	  THEN("Mutualism evolves"){
+		REQUIRE(sym_val_node.GetMean() > 0.1);
+		REQUIRE(host_val_node.GetMean() > 0.1);
+	  }
+	}
+	WHEN("Vertical transmission rate is high") {
+	  config.VERTICAL_TRANSMISSION(1);
+	  world.RunExperiment(false);
+	  THEN("Mutualism evolves"){
+		REQUIRE(sym_val_node.GetMean() > 0.1);
+		REQUIRE(host_val_node.GetMean() > 0.1);
+	  }
+	}
+  }
+  WHEN("There can be many symbionts per host") {
+	config.SYM_LIMIT(10);
+	WHEN("Vertical transmission rate is intermediate") {
+	  config.VERTICAL_TRANSMISSION(0.7);
+	  world.RunExperiment(false);
+	  THEN("Mutualism does not evolve") {
+		REQUIRE(sym_val_node.GetMean() < -0.1);
+		REQUIRE(host_val_node.GetMean() < -0.1);
+	  }
+	}
+	WHEN("Vertical transmission rate is high") {
+	  config.VERTICAL_TRANSMISSION(1);
+	  world.RunExperiment(false);
+	  THEN("Mutualism evolves") {
+		REQUIRE(sym_val_node.GetMean() > 0.1);
+		REQUIRE(host_val_node.GetMean() > 0.1);
+	  }
+	}
+  }
+}

source/test/integration_test/spatial_structure/vt.test.cc

@@ -1,3 +1,183 @@
+#include "../../../default_mode/WorldSetup.cc"
+
+
 TEST_CASE("Vertical Transmission Results", "[integration]"){
-
+  //based on paper: Vostinar and Ofria, 2018, "Spatial Structure Can Decrease Symbiotic Cooperation."
+
+  emp::Random random(29);
+  SymConfigBase config;
+  SymWorld world(random, &config);
+
+  config.MUTATION_SIZE(0.05);
+
+  emp::DataMonitor<double, emp::data::Histogram>& sym_val_node = world.GetHostedSymIntValDataNode();
+  emp::DataMonitor<int>& sym_count_node = world.GetCountHostedSymsDataNode();
+
+  WHEN("Mutualists are already present in the population (mixed population)") {
+    config.HOST_INT(-2);
+    config.SYM_INT(-2);
+    world.Setup();
+
+    WHEN("Vertical transmission rate is 0") {
+      config.VERTICAL_TRANSMISSION(0);
+      world.RunExperiment(false);
+      THEN("Clear parasitism evolves") {
+        REQUIRE(sym_val_node.GetMean() < -0.5);
+      }
+    }
+    WHEN("Vertical transmission rate is 1") {
+      config.VERTICAL_TRANSMISSION(1);
+      world.RunExperiment(false);
+      THEN("Clear mutualism evolves") {
+        REQUIRE(sym_val_node.GetMean() > 0.5);
+      }
+    }
+    WHEN("Vertical transmission rate  is low (0.09)") {
+      config.VERTICAL_TRANSMISSION(0.09);
+      int parasite_count = 0;
+      int mutualist_count = 0;
+      world.RunExperiment(false);
+      THEN("A cooexistence between parasitic and mutualistic symbionts may develop") {
+        for (int i = 0; i < 6; i++) {
+          parasite_count += sym_val_node.GetHistCounts()[i];
+          mutualist_count += sym_val_node.GetHistCounts()[19-i];
+        }
+        REQUIRE(mutualist_count > 0);
+        REQUIRE(parasite_count > 0);
+        REQUIRE(parasite_count / mutualist_count > 0.1);
+      }
+    }
+  }
+  WHEN("Organisms begin the experiment with an interaction value of 0 (all-neutral population)") {
+    config.HOST_INT(0);
+    config.SYM_INT(0);
+
+
+    WHEN("Vertical transmission rate is 1") {
+      config.VERTICAL_TRANSMISSION(1);
+      world.Setup();
+      world.RunExperiment(false);
+      THEN("Mutualists evolve"){
+        REQUIRE(sym_val_node.GetMean() > 0.5);
+      }
+    }
+    WHEN("Vertical transmission rate is less than 1") {
+      config.VERTICAL_TRANSMISSION(0.2);
+      config.MUTATION_SIZE(0.01);
+      config.START_MOI(0.5);
+      world.Setup();
+      world.RunExperiment(false);
+      THEN("Symbionts go extinct"){
+        REQUIRE(sym_count_node.GetTotal() == 0);
+      }
+    }
+  }
+  WHEN("Symbionts begin the experiment with parasitic phenotypes"){
+    config.HOST_INT(0);
+    // not using random parasite values, which the paper used
+    config.SYM_INT(-0.5); 
+    world.Setup();
+
+    WHEN("Vertical transmission rate is 0") {
+      config.VERTICAL_TRANSMISSION(0);
+      world.RunExperiment(false);
+      THEN("Symbionts become very parasitic"){
+        REQUIRE(sym_val_node.GetMean() < -0.5);
+      }
+    }
+    WHEN("Vertical transmission rate is intermediate (0.5)"){
+      config.VERTICAL_TRANSMISSION(0.5);
+      world.RunExperiment(false);
+      THEN("Symbionts become slightly parasitic"){
+        REQUIRE(sym_val_node.GetMean() < -0.2);
+
+      }
+    }
+    WHEN("Vertical transmission rate is high"){
+      config.VERTICAL_TRANSMISSION(0.7);
+      config.MUTATION_RATE(0.95);
+      config.MUTATION_SIZE(0.04);
+      world.RunExperiment(false);
+      THEN("Symbionts become neutral"){
+        double mean_sym_val = sym_val_node.GetMean();
+        REQUIRE(mean_sym_val > -0.2);
+        REQUIRE(mean_sym_val < 0.2);
+      }
+    }
+  }
+  WHEN("Symbionts begin the experiment with mutualistic phenotypes"){
+    config.HOST_INT(0);
+    // not using random parasite values, which the paper used
+    config.SYM_INT(0.5);
+    world.Setup();
+
+    WHEN("Vertical transmission rate is 0") {
+      config.VERTICAL_TRANSMISSION(0);
+      world.RunExperiment(false);
+      THEN("Symbionts become extinct") {
+        REQUIRE(sym_count_node.GetTotal() == 0);
+      }
+    }
+    WHEN("Vertical transmission rate is intermediate (0.5)") {
+      config.VERTICAL_TRANSMISSION(0.5);
+      world.RunExperiment(false);
+      THEN("Symbionts become mutualistic") {
+        REQUIRE(sym_val_node.GetMean() > 0.3);
+      }
+    }
+    WHEN("Vertical transmission rate is high") {
+      config.VERTICAL_TRANSMISSION(1);
+      world.RunExperiment(false);
+      THEN("Symbionts become very mutualistic") {
+        REQUIRE(sym_val_node.GetMean() > 0.7);
+      }
+    }
+  }
+
+  WHEN("Spatial structure is on") {
+    SymWorld off_world(random, &config);
+    emp::DataMonitor<double, emp::data::Histogram>& off_sym_val_node = off_world.GetHostedSymIntValDataNode();
+    emp::DataMonitor<int>& off_sym_count_node = off_world.GetCountHostedSymsDataNode();
+
+    config.HOST_INT(0);
+    config.SYM_INT(0);
+    config.GRID(1);
+    world.Setup();
+
+    WHEN("Vertical transmission rate is high-intermediate (0.7)"){
+      config.VERTICAL_TRANSMISSION(0.7);
+      world.RunExperiment(false);
+
+      config.GRID(0);
+      off_world.Setup(); 
+      off_world.RunExperiment(false);
+
+      double grid_on_sym_val = sym_val_node.GetMean();
+      double grid_off_sym_val = off_sym_val_node.GetMean();
+
+      THEN("Symbionts evolve to be more parasitic compared to when spatial structure is off"){
+        REQUIRE(off_sym_count_node.GetTotal() > 0);
+        REQUIRE(sym_count_node.GetTotal() > 0);
+        REQUIRE(grid_on_sym_val < grid_off_sym_val);
+      }
+    }
+
+    WHEN("Vertical transmission rate is low-intermediate (0.3)") {
+      config.VERTICAL_TRANSMISSION(0.3);
+      world.RunExperiment(false);
+
+      config.GRID(0);
+      off_world.Setup();
+      off_world.RunExperiment(false);
+
+      double grid_on_sym_val = sym_val_node.GetMean();
+      double grid_off_sym_val = off_sym_val_node.GetMean();
+
+      THEN("Symbionts evolve to be less parasitic compared to when spatial structure is off") {
+        REQUIRE(off_sym_count_node.GetTotal() > 0);
+        REQUIRE(sym_count_node.GetTotal() > 0);
+        REQUIRE(grid_on_sym_val > grid_off_sym_val);
+      }
+    }
+  }
 }