little comment tweaks and such

Author: bhaller

core/individual.cpp

@@ -1989,6 +1989,7 @@ EidosValue *Individual::GetProperty_Accelerated_cachedFitness(EidosGlobalStringI
 EidosValue *Individual::GetProperty_Accelerated_reproductiveOutput(EidosGlobalStringID p_property_id, EidosObject **p_values, size_t p_values_size)
 {
 #pragma unused (p_property_id)
+	// FIXME: This could be called for a vector of individuals of mixed species, so this check is inadequate, right?
 	if ((p_values_size > 0) && !((Individual *)(p_values[0]))->subpopulation_->species_.PedigreesEnabledByUser())
 		EIDOS_TERMINATION << "ERROR (Individual::GetProperty): property reproductiveOutput is not available because pedigree recording has not been enabled." << EidosTerminate();
 

core/species.cpp

@@ -8345,7 +8345,7 @@ void Species::SetCurrentNewIndividual(__attribute__((unused))Individual *p_indiv
 		EIDOS_TERMINATION << "ERROR (Species::SetCurrentNewIndividual): (internal error) tree sequence recording method called with recording off." << EidosTerminate();
 #endif
 
-	// This is called by code where new individuals are created
+	// This is called by code where new individuals are created, when treeseq recording is enabled
 
 	// Remember the new individual being defined; we don't need this right now,
 	// but it seems to keep coming back, so I've kept the code for it...
@@ -8375,7 +8375,8 @@ void Species::SetCurrentNewIndividual(__attribute__((unused))Individual *p_indiv
 	// this code is not thread-safe!  The design is this way because the size of HaplosomeMetadataRec
 	// is determined dynamically at runtime, depending on the number of chromosomes in the model.
 	// (If we want this to run in parallel across chromosomes eventually, we could keep separate
-	// copies of the default haplosome metadata for each chromosome, to make this thread-safe...)
+	// copies of the default haplosome metadata for each chromosome, to make this thread-safe...
+	// but this code adds entries to the shared node table, so that would also need locking, etc.)
 	THREAD_SAFETY_IN_ACTIVE_PARALLEL();
 	static_assert(sizeof(HaplosomeMetadataRec) == 9, "HaplosomeMetadataRec has changed size; this code probably needs to be updated");
 	HaplosomeMetadataRec *metadata1, *metadata2;
@@ -8410,8 +8411,6 @@ void Species::SetCurrentNewIndividual(__attribute__((unused))Individual *p_indiv
 	// The individual remembers the tskid of the first node (which is the same across all haplosomes
 	// in 1st position).  For haplosomes in 2nd position, it is first_tsk_node_id + 1.
 	p_individual->SetTskitNodeIdBase(nodeTSKID1);
-	
-	// The haplosome metadata is presently all zero.  FinalizeCurrentNewIndividual() will clean it up.
 }
 
 void Species::RetractNewIndividual()

core/species.h

@@ -40,8 +40,7 @@
 #include "mutation_run.h"
 #include "mutation_block.h"
 
-//TREE SEQUENCE
-//INCLUDE JEROME's TABLES API
+// TREE SEQUENCE RECORDING
 #ifdef __cplusplus
 extern "C" {
 #endif

core/subpopulation.cpp

@@ -414,6 +414,7 @@ void Subpopulation::GenerateParentsToFit(slim_age_t p_initial_age, double p_sex_
 	}
 }
 
+#if DEBUG
 void Subpopulation::CheckIndividualIntegrity(void) const
 {
 	ClearErrorPosition();
@@ -1120,6 +1121,7 @@ void Subpopulation::CheckIndividualIntegrity(void) const
 		}
 	}
 }
+#endif
 
 Subpopulation::Subpopulation(Population &p_population, slim_objectid_t p_subpopulation_id, slim_popsize_t p_subpop_size, bool p_record_in_treeseq, bool p_haploid) :
 	self_symbol_(EidosStringRegistry::GlobalStringIDForString(SLiMEidosScript::IDStringWithPrefix('p', p_subpopulation_id)), EidosValue_SP(new (gEidosValuePool->AllocateChunk()) EidosValue_Object(this, gSLiM_Subpopulation_Class))), 

core/subpopulation.h

@@ -377,7 +377,10 @@ class Subpopulation : public EidosDictionaryUnretained
 	}
 
 	void GenerateParentsToFit(slim_age_t p_initial_age, double p_sex_ratio, bool p_allow_zero_size, bool p_require_both_sexes, bool p_record_in_treeseq, bool p_haploid, float p_mean_parent_age);	// given the set subpop size and requested sex ratio, make new haplosomes and individuals to fit
+	
+#if DEBUG
 	void CheckIndividualIntegrity(void) const;
+#endif
 
 	// this is called by Population::RecalculateFitness(); first it expresses demand for traits that have direct fitness effects, then it recalculates fitness values
 	void UpdateFitness(const std::vector<SLiMEidosBlock*> &p_subpop_mutationEffect_callbacks, const std::vector<SLiMEidosBlock*> &p_subpop_fitnessEffect_callbacks, const std::vector<slim_trait_index_t> &p_direct_effect_trait_indices, bool p_force_trait_recalculation);