fix CI build problems

core/chromosome.cpp

@@ -59,13 +59,14 @@ inline __attribute__((always_inline)) GESubrange::GESubrange(GenomicElement *p_g
 #pragma mark Chromosome
 #pragma mark -
 
-Chromosome::Chromosome(Species &p_species, ChromosomeType p_type, int64_t p_id, std::string p_symbol, slim_chromosome_index_t p_index) :
+Chromosome::Chromosome(Species &p_species, ChromosomeType p_type, int64_t p_id, std::string p_symbol, slim_chromosome_index_t p_index, int p_preferred_mutcount) :
 	id_(p_id),
 	symbol_(p_symbol),
 	name_(),
 	index_(p_index),
 	type_(p_type),
-
+	preferred_mutrun_count_(p_preferred_mutcount),
+
 	exp_neg_overall_mutation_rate_H_(0.0), exp_neg_overall_mutation_rate_M_(0.0), exp_neg_overall_mutation_rate_F_(0.0),
 	exp_neg_overall_recombination_rate_H_(0.0), exp_neg_overall_recombination_rate_M_(0.0), exp_neg_overall_recombination_rate_F_(0.0), 
 

core/chromosome.h

@@ -244,13 +244,15 @@ class Chromosome : public EidosDictionaryRetained
 	Chromosome& operator=(const Chromosome&) = delete;						// no copying
 	Chromosome(void) = delete;												// no null constructor
 
-	explicit Chromosome(Species &p_species, ChromosomeType p_type, int64_t p_id, std::string p_symbol, slim_chromosome_index_t p_index);
+	explicit Chromosome(Species &p_species, ChromosomeType p_type, int64_t p_id, std::string p_symbol, slim_chromosome_index_t p_index, int p_preferred_mutcount);
 	~Chromosome(void);
 
 	inline __attribute__((always_inline)) int64_t ID(void)	{ return id_; }
 	inline __attribute__((always_inline)) const std::string &Symbol(void)	{ return symbol_; }
 	inline __attribute__((always_inline)) slim_chromosome_index_t Index(void) { return index_; }
 	inline __attribute__((always_inline)) ChromosomeType Type(void) { return type_; }
+	inline __attribute__((always_inline)) const std::string &Name(void) { return name_; }
+	inline __attribute__((always_inline)) void SetName(const std::string &p_name) { name_ = p_name; }
 
 	inline __attribute__((always_inline)) std::vector<GenomicElement *> &GenomicElements(void)			{ return genomic_elements_; }
 	inline __attribute__((always_inline)) NucleotideArray *AncestralSequence(void)						{ return ancestral_seq_buffer_; }

core/population.cpp

@@ -2597,7 +2597,7 @@ void Population::DoCrossoverMutation(Subpopulation *p_source_subpop, Haplosome &
 	{
 		// If we're modeling autosomes, we can disregard p_child_sex entirely; we don't care whether we're modeling sexual or hermaphrodite individuals
 #if DEBUG
-		if (species_.has_genetics_)
+		if (species_.HasGenetics())
 		{
 			if (child_haplosome_null)
 				EIDOS_TERMINATION << "ERROR (Population::DoCrossoverMutation): A null child haplosome was requested in the autosomal case." << EidosTerminate();

core/species.cpp

@@ -156,7 +156,7 @@ void Species::MakeImplicitChromosome(ChromosomeType p_type)
 		EIDOS_TERMINATION << "ERROR (Species::MakeImplicitChromosome): (internal error) explicit chromosome already exists." << EidosTerminate();
 
 	// Create an implicit Chromosome object with a retain on it from EidosDictionaryRetained::EidosDictionaryRetained()
-	Chromosome *chromosome = new Chromosome(*this, p_type, 1, "1", 0);
+	Chromosome *chromosome = new Chromosome(*this, p_type, 1, "1", /* p_index */ 0, /* p_preferred_mutcount */ 0);
 	int64_t id = chromosome->ID();
 	std::string symbol = chromosome->Symbol();
 
@@ -1875,7 +1875,7 @@ void Species::RunInitializeCallbacks(void)
 		has_genetics_ = false;
 
 		// Make a dummy chromosome of length zero, id 0, symbol "0"
-		Chromosome *dummy_chromosome = new Chromosome(*this, ChromosomeType::kA_DiploidAutosome, 0, "0", 0);
+		Chromosome *dummy_chromosome = new Chromosome(*this, ChromosomeType::kA_DiploidAutosome, 0, "0", /* p_index */ 0, /* p_preferred_mutcount */ 0);
 		int64_t id = dummy_chromosome->ID();
 		std::string symbol = dummy_chromosome->Symbol();
 

core/species_eidos.cpp

@@ -296,15 +296,13 @@ EidosValue_SP Species::ExecuteContextFunction_initializeChromosome(const std::st
 	}
 
 	// Set up the new chromosome object
-	Chromosome *chromosome = new Chromosome(*this, chromosome_type, id, symbol, 0);
+	Chromosome *chromosome = new Chromosome(*this, chromosome_type, id, symbol, /* p_index */ 0, (int)mutrun_count);
+	chromosome->SetName(name);
 
 	chromosomes_.push_back(chromosome);
 	chromosome_from_id_.emplace(id, chromosome);
 	chromosome_from_symbol_.emplace(symbol, chromosome);
 
-	chromosome->name_ = name;
-	chromosome->preferred_mutrun_count_ = (int)mutrun_count;
-
 	num_chromosome_inits_++;
 	has_currently_initializing_chromosome_ = true;