step one, no chromosome for no genetics

SLiMgui/ChromosomeView.mm

@@ -222,10 +222,18 @@ - (NSRange)selectedRange
 	{
 		SLiMWindowController *controller = (SLiMWindowController *)[[self window] windowController];
 		Species *displaySpecies = [controller focalDisplaySpecies];
-		Chromosome &chromosome = displaySpecies->TheChromosome();
-		slim_position_t chromosomeLastPosition = chromosome.last_position_;
 
-		return NSMakeRange(0, chromosomeLastPosition + 1);	// chromosomeLastPosition + 1 bases are encompassed
+		if (displaySpecies->chromosomes_.size())
+		{
+			Chromosome &chromosome = displaySpecies->TheChromosome();
+			slim_position_t chromosomeLastPosition = chromosome.last_position_;
+
+			return NSMakeRange(0, chromosomeLastPosition + 1);	// chromosomeLastPosition + 1 bases are encompassed
+		}
+		else
+		{
+			return NSMakeRange(0, 0);
+		}
 	}
 }
 

core/haplosome.h

@@ -109,7 +109,6 @@ class Haplosome : public EidosObject
 private:
 #endif
 
-	// FIXME MULTICHROM chromosome_index_ needs to get set up properly
 	slim_chromosome_index_t /* uint8_t */ chromosome_index_ = 0;	// the index of this haplosome's chromosome
 	int8_t scratch_;												// temporary scratch space that can be used locally in algorithms
 

core/species.cpp

@@ -250,10 +250,6 @@ void Species::AddChromosome(Chromosome *p_chromosome)
 		case ChromosomeType::kML_HaploidMaleLine:
 		case ChromosomeType::kHNull_HaploidAutosomeWithNull:
 		case ChromosomeType::kNullY_YSexChromosomeWithNull:
-			// FIXME MULTICHROM we need to keep an overall flag at the species level, based on
-			// the chromosome types in play, and then copy that (and modify it as needed) at
-			// the subpopulation level so each subpop can potentially differ; or maybe that is
-			// excessively complex and we should just keep a single species flag; yeah, probably
 			chromosomes_use_null_haplosomes_ = true;
 			break;
 	}
@@ -1918,50 +1914,25 @@ void Species::RunInitializeCallbacks(void)
 		// They always use null haplosomes, so any attempt to access their genetics is illegal.  They have no mutruns.
 		// BCH 18 September 2024: They also cannot have any declared chromosomes, or do anything that would cause an
 		// implicit chromosome to be defined.
-		// FIXME MULTICHROM eventually no-genetics models should have no chromosome object at all
+		// BCH 10 October 2024: No-genetics models now have no Chromosome object at all
 		if (recording_tree_)
 			EIDOS_TERMINATION << "ERROR (Species::RunInitializeCallbacks): no-genetics species cannot use tree-sequence recording; either add genetic initialization calls, or disable tree-sequence recording." << EidosTerminate();
 		if (nucleotide_based_)
 			EIDOS_TERMINATION << "ERROR (Species::RunInitializeCallbacks): no-genetics species cannot be nucleotide-based; either add genetic initialization calls, or turn off nucleotides." << EidosTerminate();
 
 		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", /* p_index */ 0, /* p_preferred_mutcount */ 0);
-		AddChromosome(dummy_chromosome);
-		has_implicit_chromosome_ = true;
-		has_currently_initializing_chromosome_ = true;
-
-		// initializeMutationRate(): initialize to zero
-		{
-			std::vector<slim_position_t> &positions = dummy_chromosome->mutation_end_positions_H_;
-			std::vector<double> &rates = dummy_chromosome->mutation_rates_H_;
-			rates.clear();
-			positions.clear();
-			rates.emplace_back(0.0);
-			num_mutrate_inits_++;
-		}
-
-		// initializeRecombinationRate(): initialize to zero
-		{
-			std::vector<slim_position_t> &positions = dummy_chromosome->recombination_end_positions_H_;
-			std::vector<double> &rates = dummy_chromosome->recombination_rates_H_;
-			rates.clear();
-			positions.clear();
-			rates.emplace_back(0.0);
-			num_recrate_inits_++;
-		}
-
-		community_.chromosome_changed_ = true;
 	}
 
 	if (has_genetics_ && (!has_implicit_chromosome_) && (num_chromosome_inits_ == 0))
 		EIDOS_TERMINATION << "ERROR (Species::RunInitializeCallbacks): (internal error) a chromosome has not been set up properly." << EidosTerminate();
+	if (!has_genetics_ && (has_implicit_chromosome_ || (num_chromosome_inits_ > 0)))
+		EIDOS_TERMINATION << "ERROR (Species::RunInitializeCallbacks): (internal error) a chromosome was set up in a no-genetics model." << EidosTerminate();
 
 	// From the initialization that has occurred, there should now be a currently initializing chromosome,
 	// whether implicitly or explicitly defined.  We now close out its definition and check it for
 	// correctness.  If this is a multichromosome model, this has already been done for the previous ones.
-	EndCurrentChromosome(/* starting_new_chromosome */ false);
+	if (has_genetics_)
+		EndCurrentChromosome(/* starting_new_chromosome */ false);
 
 	// set a default avatar string if one was not provided; these will be A, B, etc.
 	if (avatar_.length() == 0)
@@ -2203,11 +2174,13 @@ void Species::MaintainMutationRegistry(void)
 
 void Species::RecalculateFitness(void)
 {
-	TheChromosome().StartMutationRunExperimentClock();
+	if (has_genetics_)
+		TheChromosome().StartMutationRunExperimentClock();
 
 	population_.RecalculateFitness(cycle_);	// used to be cycle_ + 1 in the WF cycle; removing that 18 Feb 2016 BCH
 
-	TheChromosome().StopMutationRunExperimentClock();
+	if (has_genetics_)
+		TheChromosome().StopMutationRunExperimentClock();
 }
 
 void Species::MaintainTreeSequence(void)
@@ -2307,12 +2280,14 @@ void Species::WF_GenerateOffspring(void)
 
 	if (no_active_callbacks)
 	{
-		TheChromosome().StartMutationRunExperimentClock();
+		if (has_genetics_)
+			TheChromosome().StartMutationRunExperimentClock();
 
 		for (std::pair<const slim_objectid_t,Subpopulation*> &subpop_pair : population_.subpops_)
 			population_.EvolveSubpopulation(*subpop_pair.second, false, false, false, false, false);
 
-		TheChromosome().StopMutationRunExperimentClock();
+		if (has_genetics_)
+			TheChromosome().StopMutationRunExperimentClock();
 	}
 	else
 	{
@@ -2368,12 +2343,14 @@ void Species::WF_GenerateOffspring(void)
 		}
 
 		// then evolve each subpop
-		TheChromosome().StartMutationRunExperimentClock();
+		if (has_genetics_)
+			TheChromosome().StartMutationRunExperimentClock();
 
 		for (std::pair<const slim_objectid_t,Subpopulation*> &subpop_pair : population_.subpops_)
 			population_.EvolveSubpopulation(*subpop_pair.second, mate_choice_callbacks_present, modify_child_callbacks_present, recombination_callbacks_present, mutation_callbacks_present, type_s_dfes_present_);
 
-		TheChromosome().StopMutationRunExperimentClock();
+		if (has_genetics_)
+			TheChromosome().StopMutationRunExperimentClock();
 	}
 }
 
@@ -2387,11 +2364,13 @@ void Species::WF_SwitchToChildGeneration(void)
 	// population is in a standard state for CheckIndividualIntegrity() at the end of this stage
 	// BCH 4/22/2023: this is no longer relevant in terms of accurate MutationRun refcounts, since
 	// we no longer refcount those, but they still need to be zeroed out so they're ready for reuse
-	TheChromosome().StartMutationRunExperimentClock();
+	if (has_genetics_)
+		TheChromosome().StartMutationRunExperimentClock();
 
 	population_.ClearParentalHaplosomes();
 
-	TheChromosome().StopMutationRunExperimentClock();
+	if (has_genetics_)
+		TheChromosome().StopMutationRunExperimentClock();
 }
 
 void Species::WF_SwapGenerations(void)

core/species.h

@@ -400,7 +400,12 @@ class Species : public EidosDictionaryUnretained
 
 	// Chromosome configuration and access
 #warning remove TheChromosome() step by step
-	inline __attribute__((always_inline)) Chromosome &TheChromosome(void)						{ return *(chromosomes_[0]); }
+	inline __attribute__((always_inline)) Chromosome &TheChromosome(void)
+	{
+		if (chromosomes_.size() == 0)
+			EIDOS_TERMINATION << "ERROR (Species::TheChromosome): (internal error) there is no chromosome; check for no genetics first." << EidosTerminate();
+		return *(chromosomes_[0]);
+	}
 	inline __attribute__((always_inline)) const std::vector<Chromosome *> &Chromosomes(void)	{ return chromosomes_; }
 	Chromosome *ChromosomeFromID(int64_t p_id);
 	Chromosome *ChromosomeFromSymbol(const std::string &p_symbol);