improve SLiM unit test coverage, minor cleanup

SLiMgui/SLiMHelpClasses.rtf

@@ -3025,18 +3025,16 @@ See the description of the
 \f4   This method is provided primarily for speed; it executes much faster than the Eidos equivalent above.  Indeed, it is faster than just 
 \f3\fs18 individual.genomes.mutations
 \f4\fs20 , and gives uniquing and sorting on top of that, so it is advantageous unless duplicate entries for homozygous mutations are actually needed.\
-\pard\pardeftab720\li720\fi-446\ri720\sb180\sa60\partightenfactor0
+\pard\pardeftab397\li720\fi-446\ri720\sb180\sa60\partightenfactor0
 
-\f3\fs18 \cf0 x <\'96> (float$)\
-\pard\pardeftab720\li547\ri720\sb60\sa60\partightenfactor0
+\f3\fs18 \cf2 x <\'96> (float$)\
+\pard\pardeftab397\li547\ri720\sb60\sa60\partightenfactor0
 
-\f4\fs20 \cf0 A user-defined 
+\f4\fs20 \cf2 A user-defined 
 \f3\fs18 float
 \f4\fs20  value.  The value of 
 \f3\fs18 x
-\f4\fs20  is initially undefined (i.e., has an effectively random value that could be different every time you run your model); if you wish it to have a defined value, you must arrange that yourself by explicitly setting its value prior to using it elsewhere in your code, typically in a 
-\f3\fs18 modifyChild()
-\f4\fs20  callback.  The value of 
+\f4\fs20  is initially undefined (i.e., has an effectively random value that could be different every time you run your model); if you wish it to have a defined value, you must arrange that yourself by explicitly setting its value prior to using it elsewhere in your code.  The value of 
 \f3\fs18 x
 \f4\fs20  is not used by SLiM unless the optional \'93continuous space\'94 facility is enabled with the 
 \f3\fs18 dimensionality
@@ -3050,19 +3048,69 @@ See the description of the
 \f3\fs18 x
 \f4\fs20  as an additional tag value of type 
 \f3\fs18 float
-\f5\fs20 .\
-\pard\pardeftab720\li720\fi-446\ri720\sb180\sa60\partightenfactor0
+\f4\fs20 .\
+\pard\pardeftab397\li720\fi-446\ri720\sb180\sa60\partightenfactor0
 
-\f3\fs18 \cf0 y <\'96> (float$)\
-\pard\pardeftab720\li547\ri720\sb60\sa60\partightenfactor0
+\f3\fs18 \cf2 xy => (float)\
+\pard\pardeftab397\li547\ri720\sb60\sa60\partightenfactor0
 
-\f4\fs20 \cf0 A user-defined 
+\f4\fs20 \cf2 This property provides joint read-only access to the 
+\f3\fs18 x
+\f4\fs20  and 
+\f3\fs18 y
+\f4\fs20  properties; they are returned as a two-element 
+\f3\fs18 float
+\f4\fs20  vector.  This can be useful in complex spatial models in which the spatiality of interactions/maps differs from the overall dimensionality of the model.  See the documentation for the separate properties 
+\f3\fs18 x
+\f4\fs20  and 
+\f3\fs18 y
+\f4\fs20  for further comments.\
+\pard\pardeftab397\li720\fi-446\ri720\sb180\sa60\partightenfactor0
+
+\f3\fs18 \cf2 xyz => (float)\
+\pard\pardeftab397\li547\ri720\sb60\sa60\partightenfactor0
+
+\f4\fs20 \cf2 This property provides joint read-only access to the 
+\f3\fs18 x
+\f4\fs20 , 
+\f3\fs18 y
+\f4\fs20 , and 
+\f3\fs18 z
+\f4\fs20  properties; they are returned as a three-element 
+\f3\fs18 float
+\f4\fs20  vector.  This can be useful in complex spatial models in which the spatiality of interactions/maps differs from the overall dimensionality of the model.  See the documentation for the separate properties 
+\f3\fs18 x
+\f4\fs20 , 
+\f3\fs18 y
+\f4\fs20 , and 
+\f3\fs18 z
+\f4\fs20  for further comments.\
+\pard\pardeftab397\li720\fi-446\ri720\sb180\sa60\partightenfactor0
+
+\f3\fs18 \cf2 xz => (float)\
+\pard\pardeftab397\li547\ri720\sb60\sa60\partightenfactor0
+
+\f4\fs20 \cf2 This property provides joint read-only access to the 
+\f3\fs18 x
+\f4\fs20  and 
+\f3\fs18 z
+\f4\fs20  properties; they are returned as a two-element 
+\f3\fs18 float
+\f4\fs20  vector.  This can be useful in complex spatial models in which the spatiality of interactions/maps differs from the overall dimensionality of the model.  See the documentation for the separate properties 
+\f3\fs18 x
+\f4\fs20  and 
+\f3\fs18 z
+\f4\fs20  for further comments.\
+\pard\pardeftab397\li720\fi-446\ri720\sb180\sa60\partightenfactor0
+
+\f3\fs18 \cf2 y <\'96> (float$)\
+\pard\pardeftab397\li547\ri720\sb60\sa60\partightenfactor0
+
+\f4\fs20 \cf2 A user-defined 
 \f3\fs18 float
 \f4\fs20  value.  The value of 
 \f3\fs18 y
-\f4\fs20  is initially undefined (i.e., has an effectively random value that could be different every time you run your model); if you wish it to have a defined value, you must arrange that yourself by explicitly setting its value prior to using it elsewhere in your code, typically in a 
-\f3\fs18 modifyChild()
-\f4\fs20  callback.  The value of 
+\f4\fs20  is initially undefined (i.e., has an effectively random value that could be different every time you run your model); if you wish it to have a defined value, you must arrange that yourself by explicitly setting its value prior to using it elsewhere in your code.  The value of 
 \f3\fs18 y
 \f4\fs20  is not used by SLiM unless the optional \'93continuous space\'94 facility is enabled with the 
 \f3\fs18 dimensionality
@@ -3084,19 +3132,33 @@ See the description of the
 \f3\fs18 y
 \f4\fs20  as an additional tag value of type 
 \f3\fs18 float
-\f5\fs20 .\
-\pard\pardeftab720\li720\fi-446\ri720\sb180\sa60\partightenfactor0
+\f4\fs20 .\
+\pard\pardeftab397\li720\fi-446\ri720\sb180\sa60\partightenfactor0
 
-\f3\fs18 \cf0 z <\'96> (float$)\
-\pard\pardeftab720\li547\ri720\sb60\sa60\partightenfactor0
+\f3\fs18 \cf2 yz => (float)\
+\pard\pardeftab397\li547\ri720\sb60\sa60\partightenfactor0
 
-\f4\fs20 \cf0 A user-defined 
+\f4\fs20 \cf2 This property provides joint read-only access to the 
+\f3\fs18 y
+\f4\fs20  and 
+\f3\fs18 z
+\f4\fs20  properties; they are returned as a two-element 
+\f3\fs18 float
+\f4\fs20  vector.  This can be useful in complex spatial models in which the spatiality of interactions/maps differs from the overall dimensionality of the model.  See the documentation for the separate properties 
+\f3\fs18 y
+\f4\fs20  and 
+\f3\fs18 z
+\f4\fs20  for further comments.\
+\pard\pardeftab397\li720\fi-446\ri720\sb180\sa60\partightenfactor0
+
+\f3\fs18 \cf2 z <\'96> (float$)\
+\pard\pardeftab397\li547\ri720\sb60\sa60\partightenfactor0
+
+\f4\fs20 \cf2 A user-defined 
 \f3\fs18 float
 \f4\fs20  value.  The value of 
 \f3\fs18 z
-\f4\fs20  is initially undefined (i.e., has an effectively random value that could be different every time you run your model); if you wish it to have a defined value, you must arrange that yourself by explicitly setting its value prior to using it elsewhere in your code, typically in a 
-\f3\fs18 modifyChild()
-\f4\fs20  callback.  The value of 
+\f4\fs20  is initially undefined (i.e., has an effectively random value that could be different every time you run your model); if you wish it to have a defined value, you must arrange that yourself by explicitly setting its value prior to using it elsewhere in your code.  The value of 
 \f3\fs18 z
 \f4\fs20  is not used by SLiM unless the optional \'93continuous space\'94 facility is enabled with the 
 \f3\fs18 dimensionality
@@ -3114,7 +3176,7 @@ See the description of the
 \f3\fs18 z
 \f4\fs20  as an additional tag value of type 
 \f3\fs18 float
-\f5\fs20 .\
+\f4\fs20 .\
 \pard\pardeftab397\ri720\sb120\sa60\partightenfactor0
 
 \f1\i\fs22 \cf0 5.7.2  

VERSIONS

@@ -172,6 +172,7 @@ development head (in the master branch):
 	modify recipes that use addRecombinant() to use randomizeStrands=T where appropriate: 16.17, 16.25
 	add lowerTri(), upperTri(), and diag(); thanks to Nick O'Brien (@nobrien97) for this contribution
 	modify recipes to use count= parameter to addCrossed() etc., where appropriate: 16.3, 16.23
+	add xy, xz, yz, and xyz properties to Individual that allow joint access to the x/y/z properties, for easier spatiality operations in complex spatial models (and to support some unit testing additions)
 
 
 version 4.0.1 (Eidos version 3.0.1):

core/individual.cpp

@@ -608,36 +608,6 @@ EidosValue_SP Individual::GetProperty(EidosGlobalStringID p_property_id)
 			}
 
 			return result_SP;
-			/*
-			 The code above for uniqueMutations can be tested with the simple SLiM script below.  Positions are tested with
-			 identical() instead of the mutation vectors themselves, only because the sorted order of mutations at exactly
-			 the same position may differ; identical(um1, um2) will occasionally flag these as false positives.
-			 
-			 initialize() {
-				 initializeMutationRate(1e-5);
-				 initializeMutationType("m1", 0.5, "f", 0.0);
-				 initializeGenomicElementType("g1", m1, 1.0);
-				 initializeGenomicElement(g1, 0, 99999);
-				 initializeRecombinationRate(1e-8);
-			 }
-			 1 early() {
-				sim.addSubpop("p1", 500);
-			 }
-			 1:20000 late() {
-				 for (i in p1.individuals)
-				 {
-					 um1 = i.uniqueMutations;
-					 um2 = sortBy(unique(i.genomes.mutations), "position");
-					 
-					 if (!identical(um1.position, um2.position))
-					 {
-						 print("Mismatch!");
-						 print(um1.position);
-						 print(um2.position);
-					 }
-				 }
-			 }
-			 */
 		}
 
 			// variables
@@ -723,6 +693,25 @@ EidosValue_SP Individual::GetProperty(EidosGlobalStringID p_property_id)
 			return EidosValue_SP(new (gEidosValuePool->AllocateChunk()) EidosValue_Float_singleton(spatial_z_));
 		}
 
+			// These properties are presently undocumented, used for testing purposes, but maybe they are useful to others?
+			// They provide x/y/z as pairs or a triplet, whether the model is spatial or not, regardless of dimensionality
+		case gEidosID_xy:
+		{
+			return EidosValue_SP(new (gEidosValuePool->AllocateChunk()) EidosValue_Float_vector({spatial_x_, spatial_y_}));
+		}
+		case gEidosID_xz:
+		{
+			return EidosValue_SP(new (gEidosValuePool->AllocateChunk()) EidosValue_Float_vector({spatial_x_, spatial_z_}));
+		}
+		case gEidosID_yz:
+		{
+			return EidosValue_SP(new (gEidosValuePool->AllocateChunk()) EidosValue_Float_vector({spatial_y_, spatial_z_}));
+		}
+		case gEidosID_xyz:
+		{
+			return EidosValue_SP(new (gEidosValuePool->AllocateChunk()) EidosValue_Float_vector({spatial_x_, spatial_y_, spatial_z_}));
+		}
+
 			// all others, including gID_none
 		default:
 			return super::GetProperty(p_property_id);
@@ -1045,6 +1034,7 @@ EidosValue *Individual::GetProperty_Accelerated_spatialPosition(EidosObject **p_
 	else
 	{
 		// Mixed-species group, so we have to figure out the dimensionality for each individual separately
+		// FIXME: Do we really want to allow this?  seems crazy - how would the user actually use this?
 		float_result = (new (gEidosValuePool->AllocateChunk()) EidosValue_Float_vector());
 
 		for (size_t value_index = 0; value_index < p_values_size; ++value_index)
@@ -2220,6 +2210,10 @@ const std::vector<EidosPropertySignature_CSP> *Individual_Class::Properties(void
 		properties->emplace_back((EidosPropertySignature *)(new EidosPropertySignature(gEidosStr_x,					false,	kEidosValueMaskFloat | kEidosValueMaskSingleton))->DeclareAcceleratedGet(Individual::GetProperty_Accelerated_x)->DeclareAcceleratedSet(Individual::SetProperty_Accelerated_x));
 		properties->emplace_back((EidosPropertySignature *)(new EidosPropertySignature(gEidosStr_y,					false,	kEidosValueMaskFloat | kEidosValueMaskSingleton))->DeclareAcceleratedGet(Individual::GetProperty_Accelerated_y)->DeclareAcceleratedSet(Individual::SetProperty_Accelerated_y));
 		properties->emplace_back((EidosPropertySignature *)(new EidosPropertySignature(gEidosStr_z,					false,	kEidosValueMaskFloat | kEidosValueMaskSingleton))->DeclareAcceleratedGet(Individual::GetProperty_Accelerated_z)->DeclareAcceleratedSet(Individual::SetProperty_Accelerated_z));
+		properties->emplace_back((EidosPropertySignature *)(new EidosPropertySignature(gEidosStr_xy,				true,	kEidosValueMaskFloat)));
+		properties->emplace_back((EidosPropertySignature *)(new EidosPropertySignature(gEidosStr_xz,				true,	kEidosValueMaskFloat)));
+		properties->emplace_back((EidosPropertySignature *)(new EidosPropertySignature(gEidosStr_yz,				true,	kEidosValueMaskFloat)));
+		properties->emplace_back((EidosPropertySignature *)(new EidosPropertySignature(gEidosStr_xyz,				true,	kEidosValueMaskFloat)));
 		properties->emplace_back((EidosPropertySignature *)(new EidosPropertySignature(gStr_age,					false,	kEidosValueMaskInt | kEidosValueMaskSingleton))->DeclareAcceleratedGet(Individual::GetProperty_Accelerated_age)->DeclareAcceleratedSet(Individual::SetProperty_Accelerated_age));
 		properties->emplace_back((EidosPropertySignature *)(new EidosPropertySignature(gStr_meanParentAge,			true,	kEidosValueMaskFloat | kEidosValueMaskSingleton)));
 		properties->emplace_back((EidosPropertySignature *)(new EidosPropertySignature(gStr_pedigreeID,				true,	kEidosValueMaskInt | kEidosValueMaskSingleton))->DeclareAcceleratedGet(Individual::GetProperty_Accelerated_pedigreeID));

core/interaction_type.cpp

@@ -5703,8 +5703,8 @@ EidosValue_SP InteractionType::ExecuteMethod_neighborCountOfPoint(EidosGlobalStr
 	return EidosValue_SP(new (gEidosValuePool->AllocateChunk()) EidosValue_Int_singleton(neighborCount));
 }
 
-//	*********************	- (void)setConstraints(string$ who, [Ns$ sex = NULL], [Ni$ tag = NULL], [Ni$ minAge = NULL], [Ni$ maxAge = NULL], [Nl$ migrant = NULL],
-//													[Nl$ tagL0 = NULL], [Nl$ tagL1 = NULL], [Nl$ tagL2 = NULL], [Nl$ tagL3 = NULL], [Nl$ tagL4 = NULL])
+//	*********************	- (void)setConstraints(string$ who, [Ns$ sex = NULL], [Ni$ tag = NULL], [Ni$ minAge = NULL], [Ni$ maxAge = NULL], [Nl$ migrant = NULL],
+//													[Nl$ tagL0 = NULL], [Nl$ tagL1 = NULL], [Nl$ tagL2 = NULL], [Nl$ tagL3 = NULL], [Nl$ tagL4 = NULL])
 //
 EidosValue_SP InteractionType::ExecuteMethod_setConstraints(EidosGlobalStringID p_method_id, const std::vector<EidosValue_SP> &p_arguments, EidosInterpreter &p_interpreter)
 {