From f7d339d578ab048e7298396464621efd18f0e40d Mon Sep 17 00:00:00 2001
From: Daniel Vedder <daniel.vedder@idiv.de>
Date: Fri, 20 Jan 2023 10:49:17 +0100
Subject: [PATCH] Bugfixes in the species macros
---
src/nature/nature.jl | 34 ++++++++++++++++++++--------------
src/nature/populations.jl | 7 ++-----
test/nature_tests.jl | 15 ++++++---------
3 files changed, 28 insertions(+), 28 deletions(-)
diff --git a/src/nature/nature.jl b/src/nature/nature.jl
index 27dc09b..c8696da 100644
--- a/src/nature/nature.jl
+++ b/src/nature/nature.jl
@@ -40,7 +40,6 @@ end
Update an animal by one day, executing it's currently active phase function.
"""
function stepagent!(animal::Animal, model::AgentBasedModel)
- @debug "Updating $(animalid(animal))."
animal.age += 1
animal.traits[animal.traits["phase"]](animal,model)
end
@@ -73,7 +72,7 @@ custom syntax to describe species' biology:
```julia
@species name begin
- @initialise!(@habitat(...))
+ @initialise(@habitat(...))
speciesvar1 = 3.14
...
@@ -96,22 +95,28 @@ the `model` variable (an object of type `AgentBasedModel`).
macro species(name, body)
quote
Core.@__doc__ function $(esc(name))($(esc(:model))::AgentBasedModel)
+ # create internal variables and execute the definition body
$(esc(:name)) = string($(QuoteNode(name)))
$(esc(:phase)) = ""
$(esc(body))
+ # extract and process the local variables into a species dict
vardict = Base.@locals
speciesdict = Dict{String,Any}()
- #delete!(speciesdict, $name) #FIXME remove circular reference from speciesdict
for k in keys(vardict)
speciesdict[string(k)] = vardict[k]
end
+ delete!(speciesdict, "model")
+ delete!(speciesdict, $(string(name)))
return speciesdict
end
+ # allow species to be defined outside of the Persephone module, but still available
+ # inside it (needed by `initnature!()` and `reproduce!()`)
+ (@__MODULE__() != $(esc(:Persephone))) && ($(esc(:Persephone)).$name = $(esc(name)))
end
end
"""
- @initialise!(habitatdescriptor; kwargs...)
+ @initialise(habitatdescriptor; kwargs...)
Call this macro within the body of `@species`. It passes the given habitat descriptor
function and keyword arguments on to `initpopulation()` when setting up the simulation.
@@ -119,7 +124,7 @@ function and keyword arguments on to `initpopulation()` when setting up the simu
Note: if this macro is not used, the variable `initialise!` must be set manually in the
species definition.
"""
-macro initialise!(habitatdescriptor, kwargs...)
+macro initialise(habitatdescriptor, kwargs...)
#FIXME does the habitatdescriptor need to be `esc`aped due to scoping issues?
:($(esc(:initialise!)) = initpopulation($habitatdescriptor, $(kwargs...)))
end
@@ -154,10 +159,8 @@ 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)
- #XXX make this documentable?
- #FIXME Somehow, errors in the phase body are not shown?
quote
- Core.@__doc__ $(esc(name)) = function($(esc(:animal))::Animal, $(esc(:model))::AgentBasedModel)
+ Core.@__doc__ function $(esc(name))($(esc(:animal))::Animal, $(esc(:model))::AgentBasedModel)
$(esc(:pos)) = $(esc(:animal)).pos
$(esc(body))
end
@@ -209,22 +212,23 @@ end
"""
@here(property)
-A utility macro to quickly access a property of the animal's current position.
+A utility macro to quickly access a property of the animal's current position
+(i.e. `landcover`, `fieldid`, or `events` - see the `Pixel` struct).
This can only be used nested within `@phase`.
"""
macro here(property)
- :(model.landscape[animal.pos...].$(property))
+ :($(esc(:model)).landscape[$(esc(:animal)).pos...].$(property))
end
"""
@kill
-Kill this animal. This is a thin wrapper around `kill!()`, and passes on any arguments.
-This can only be used nested within `@phase`.
+Kill this animal (and immediately abort its current update). This is a thin wrapper
+around `kill!()`, and passes on any arguments. This can only be used nested within `@phase`.
"""
macro kill(args...)
quote
- kill!($(esc(:animal)), $(esc(:model)), $(args...))
+ kill!($(esc(:animal)), $(esc(:model)), $(map(esc, args)...))
return
end
end
@@ -236,7 +240,7 @@ Let this animal reproduce. This is a thin wrapper around `reproduce!()`, and pas
any arguments. This can only be used nested within `@phase`.
"""
macro reproduce(args...)
- :(reproduce!($(esc(:animal)), $(esc(:model)), $(args...)))
+ :(reproduce!($(esc(:animal)), $(esc(:model)), $(map(esc, args)...)))
end
"""
@@ -279,6 +283,8 @@ For more complex habitat suitability checks, the use of this macro can be
circumvented by directly creating an equivalent function.
"""
macro habitat(body)
+ #XXX I suspect that I may have less problems with macro expansion and module
+ # scoping if @habitat did not create a new function. But is there a different way?
quote
function($(esc(:pos)), $(esc(:model)))
if $(esc(body))
diff --git a/src/nature/populations.jl b/src/nature/populations.jl
index f4e05f7..dbe6924 100644
--- a/src/nature/populations.jl
+++ b/src/nature/populations.jl
@@ -43,10 +43,6 @@ function initpopulation(habitatdescriptor::Function; phase::Union{String,Nothing
for x in shuffle!(Vector(1:width))
for y in shuffle!(Vector(1:height))
if habitatdescriptor((x,y), model)
- #FIXME we probably have to do a deepcopy here, to prevent all conspecifics
- # sharing the same speciesdict object. However, this is (a) expensive
- # and (b) we seem to have a self-reference in the speciesdict, leading to
- # an infinity loop on deepcopying...
if pairs
add_agent!((x,y), Animal, model, deepcopy(species), female, 0)
add_agent!((x,y), Animal, model, deepcopy(species), male, 0)
@@ -93,7 +89,8 @@ Produce one or more offspring for the given animal at its current location.
function reproduce!(animal::Animal, model::AgentBasedModel, n::Int64=1)
for i in 1:n
sex = (animal.sex == hermaphrodite) ? hermaphrodite : rand([male, female])
- species = animal.traits # @eval $(Symbol(animal.traits["name"]))($model) #FIXME
+ # We need to generate a fresh species dict here
+ species = @eval $(Symbol(animal.traits["name"]))($model)
add_agent!(animal.pos, Animal, model, species, sex, 0)
end
@debug "$(animalid(animal)) has reproduced."
diff --git a/test/nature_tests.jl b/test/nature_tests.jl
index 74b9c15..e44fbc0 100644
--- a/test/nature_tests.jl
+++ b/test/nature_tests.jl
@@ -67,37 +67,34 @@ end
end
@testset "Species macros" begin
- # set up an example landscape and species
- # (note: have to use `Persephone` instead of `Ps` due to macro expansion issues)
#FIXME I am having tons of trouble here with module scoping and macro expansion,
# a known tricky issue in Julia (https://github.com/JuliaLang/julia/issues/23221,
# https://github.com/p-i-/MetaGuideJulia/wiki#example-swap-macro-to-illustrate-esc).
# Basically, one needs to avoid nesting modules too deeply (i.e. more than one nesting level)
+ # -- is that so?? --
model = smalltestlandscape(Union{Animal,Farmer,FarmPlot})
-
+
@species Mermaid begin
ageofmaturity = 2
+ pesticidemortality = 1.0
#@initialise!(@habitat(@landcover() == Persephone.water), pairs=true) #FIXME
initialise! = Persephone.initpopulation(@habitat(@landcover() == Persephone.water), pairs=true)
-
@phase life begin
@debug "$(Persephone.animalid(animal)) is swimming happily in its pond."
- @respond Persephone.pesticide @kill()
+ @respond Persephone.pesticide @kill(@trait(pesticidemortality))
@respond Persephone.harvest @setphase(drought)
@debug "Animal: $animal"
if @trait(sex) == Persephone.female && @countanimals() < 3 &&
- @trait(age) >= @trait(ageofmaturity)
- @debug "$(Persephone.animalid(animal)) is reproducing."
+ @trait(age) >= @trait(ageofmaturity) && @here(landcover) == Persephone.water
@reproduce()
end
end
-
@phase drought begin
@debug "$(Persephone.animalid(animal)) is trying to survive a drought."
@respond Persephone.sowing @setphase(life)
end
end
-
+
# test a complete mermaid life cycle
pond = (6,4)
mermaid = Mermaid(model)
--
GitLab