Fixed the (hopefully) remaining bugs in the species macros

This seems to work as intended now! :D

src/core/simulation.jl

@@ -48,14 +48,12 @@ Execute one update of the model.
 function stepsimulation!(model::AgentBasedModel)
     @info "Simulating day $(model.date)."
     for a in Schedulers.ByType((Farmer,FarmPlot,Animal), true)(model)
-        #The animal may have been killed, so we need a try/catch 
-        # try
-        #     stepagent!(model[a], model)
-        # catch exc
-        #     #FIXME check if the KeyError comes from the model[a] or the function call
-        #     isa(exc, KeyError) ? continue : throw(exc)
-        # end
-        stepagent!(model[a], model)
+        try #The animal may have been killed
+            stepagent!(model[a], model)
+        catch exc
+            # check if the KeyError comes from the `model[a]` or the function call
+            isa(exc, KeyError) && isa(exc.key, Int) ? continue : throw(exc)
+        end
     end
     updateevents!(model)
     outputdata(model)

src/nature/nature.jl

@@ -62,6 +62,11 @@ end
 
 ### MACROS IMPLEMENTING THE DOMAIN-SPECIFIC LANGUAGE FOR DEFINING SPECIES
 
+## Note that this DSL consists of lots of deeply nested macro calls, which is a
+## known tricky issue in Julia (https://github.com/JuliaLang/julia/issues/23221,
+## https://github.com/p-i-/MetaGuideJulia/wiki#example-swap-macro-to-illustrate-esc).
+## Hence all the `esc`apes in the following code - be careful when modifying!
+
 """
     @species(name, body)
 
@@ -125,8 +130,7 @@ Note: if this macro is not used, the variable `initialise!` must be set manually
 species definition.
 """
 macro initialise(habitatdescriptor, kwargs...)
-    #FIXME does the habitatdescriptor need to be `esc`aped due to scoping issues?
-    :($(esc(:initialise!)) = initpopulation($habitatdescriptor, $(kwargs...)))
+    :($(esc(:initialise!)) = initpopulation($(esc(habitatdescriptor)); $(map(esc, kwargs)...)))
 end
 
 """
@@ -159,6 +163,7 @@ the phase that animals are assigned at birth, unless the variable `phase` is
 explicitly defined by the user in the species definition block.
 """
 macro phase(name, body)
+    #TODO the docstrings give a lot of warnings in the log - can I fix that?
     quote
         Core.@__doc__ function $(esc(name))($(esc(:animal))::Animal, $(esc(:model))::AgentBasedModel)
             $(esc(:pos)) = $(esc(:animal)).pos
@@ -251,7 +256,7 @@ This can only be used nested within `@phase`.
 """
 macro neighbours(radius)
     #TODO enable filtering by species
-    :(nearby_animals($(esc(:animal)), $(esc(:model)), $radius))
+    :(nearby_animals($(esc(:animal)), $(esc(:model)), $(esc(radius))))
 end
 
 """
@@ -336,7 +341,7 @@ Calculate the distance to the closest habitat of the specified type or descripto
 This is a utility wrapper that can only be used nested within `@phase` or `@habitat`.
 """
 macro distanceto(habitat)
-    :(distanceto($(esc(:pos)), $(esc(:model)), $habitat))
+    :(distanceto($(esc(:pos)), $(esc(:model)), $(esc(habitat))))
 end
 
 """

src/nature/species/wyvern.jl

@@ -18,7 +18,7 @@ legs, but that doesn't make it any less dangerous...
     aggression = 0.2
     huntsuccess = 0.8
 
-    initialise! = initrandompopulation(popsize)
+    @initialise(@habitat(@landcover() in (grass, soil, agriculture, builtup)), popsize=popsize)
     phase = "winter"
 
     """
@@ -26,7 +26,7 @@ legs, but that doesn't make it any less dangerous...
     prey: wolpertingers...
     """
     @phase summer begin
-        for a in nearby_agents(animal, model, @trait(speed))
+        for a in @neighbours(@trait(speed))
             # check if a wolpertinger is in pouncing distance
             if a.traits["name"] == "Wolpertinger"
                 move_agent!(animal, a.pos, model)
@@ -50,7 +50,7 @@ legs, but that doesn't make it any less dangerous...
         end
         # check if a wolpertinger is in seeing distance, or walk in a random direction
         direction = Tuple(rand([-1,1], 2))
-        for a in nearby_agents(animal, model, @trait(vision))
+        for a in @neighbours(@trait(vision))
             if a.traits["name"] == "Wolpertinger"
                 direction = get_direction(animal.pos, a.pos, model)
                 break

src/parameters.toml

@@ -16,8 +16,8 @@ loglevel = "debug" # verbosity level: "debug", "info", "quiet"
 seed = 0 # seed value for the RNG (0 -> random value)
 # dates to start and end the simulation
 startdate = 2022-01-01
-enddate = 2022-01-02
-#enddate = 2022-12-31
+#enddate = 2022-01-02
+enddate = 2022-12-31
 
 [farm]
 farmmodel = "FieldManager" # which version of the farm model to use (not yet implemented)

test/nature_tests.jl

@@ -15,7 +15,7 @@
     h1 = @habitat(@landcover() == Ps.water)
     h2 = @habitat(@croptype() == Ps.wheat &&
                   @cropheight() < 2)
-    h3 = @habitat(@distanceto(water) > 2 &&
+    h3 = @habitat(@distanceto(Ps.water) > 2 &&
                   @distancetoedge() <= 2)
     h4 = @habitat(@countanimals(species="test_animal", radius=1) == 1)
     # test the descriptors
@@ -67,18 +67,13 @@ end
 end
 
 @testset "Species macros" begin
-    #FIXME I am having tons of trouble here with module scoping and macro expansion,
-    # a known tricky issue in Julia (https://github.com/JuliaLang/julia/issues/23221,
-    # https://github.com/p-i-/MetaGuideJulia/wiki#example-swap-macro-to-illustrate-esc).
-    # Basically, one needs to avoid nesting modules too deeply (i.e. more than one nesting level)
-    # -- is that so?? --
+    # create a model landscape and a test species
     model = smalltestlandscape(Union{Animal,Farmer,FarmPlot})
 
     @species Mermaid begin
         ageofmaturity = 2
         pesticidemortality = 1.0
-        #@initialise!(@habitat(@landcover() == Persephone.water), pairs=true) #FIXME
-        initialise! = Persephone.initpopulation(@habitat(@landcover() == Persephone.water), pairs=true)
+        @initialise(@habitat(@landcover() == Persephone.water), pairs=true)
         @phase life begin
             @debug "$(Persephone.animalid(animal)) is swimming happily in its pond."
             @respond Persephone.pesticide @kill(@trait(pesticidemortality))