From bf5024876b440bbd1eecccc4179c10e23cec2bd4 Mon Sep 17 00:00:00 2001
From: Daniel Vedder <daniel.vedder@idiv.de>
Date: Fri, 24 May 2024 10:33:45 +0200
Subject: [PATCH] Started upgrading nature tests
---
src/core/simulation.jl | 2 +-
src/nature/macros.jl | 7 +-
test/nature_tests.jl | 306 ++++++++++++++++++++++-------------------
3 files changed, 168 insertions(+), 147 deletions(-)
diff --git a/src/core/simulation.jl b/src/core/simulation.jl
index b4a0228..dd454c7 100644
--- a/src/core/simulation.jl
+++ b/src/core/simulation.jl
@@ -35,7 +35,7 @@ end
Return the total number of agents in a model object.
"""
function nagents(model::AgricultureModel)
- length(model.animals)+length(model.farmers)+length(model.farmplots)
+ length(model.animals)+length(model.migrants)+length(model.farmers)+length(model.farmplots)
end
"""
diff --git a/src/nature/macros.jl b/src/nature/macros.jl
index fb2f107..e0df561 100644
--- a/src/nature/macros.jl
+++ b/src/nature/macros.jl
@@ -47,13 +47,12 @@ the `model` variable (an object of type `SimulationModel`).
"""
macro species(name, body)
quote
- #XXX species are created/referenced as Persefone.<speciesname>, is this relevant?
@kwdef mutable struct $(name) <: Animal
const id::Int64
const sex::Sex = hermaphrodite
const parents::Tuple{Int64,Int64} = (-1, -1) #XXX assumes sexual reprod.
pos::Tuple{Int64,Int64}
- phase::Function = ()->0
+ phase::Function = (self,model)->nothing
age::Int = 0
energy::Union{EnergyBudget,Nothing} = nothing # DEB is optional
offspring::Vector{Int64} = Vector{Int64}()
@@ -62,8 +61,8 @@ macro species(name, body)
# define a constructor giving the minimum necessary arguments as positional arguments
$(esc(name))(id, sex, parents, pos, phase) =
$(esc(name))(id=id, sex=sex, parents=parents, pos=pos, phase=phase)
- # define a zero-argument constructor to access default field values #XXX probably not needed
- #$(esc(name))(id) = $(esc(name))(id=id, parents=(-1, -1), pos=(-1, -1))
+ # define a single-argument constructor for utility purposes (especially testing)
+ $(esc(name))(id) = $(esc(name))(id=id, parents=(-1, -1), pos=(-1, -1))
# allow species to be defined outside of the Persefone module, but still
# available inside it (needed by `initnature!()` and `reproduce!()`)
(@__MODULE__() != $(esc(:Persefone))) && ($(esc(:Persefone)).$name = $(name))
diff --git a/test/nature_tests.jl b/test/nature_tests.jl
index ef945ff..b552dfa 100644
--- a/test/nature_tests.jl
+++ b/test/nature_tests.jl
@@ -3,23 +3,61 @@
### These are the tests for the nature model (excluding individual species).
###
+## Test species definition
+
+@species Mermaid begin
+ ageofmaturity = 2
+ pesticidemortality = 1.0
+end
+
+@create Mermaid begin
+ @debug "Created $(animalid(self))."
+end
+
+@phase Mermaid life begin
+ @debug "$(Persefone.animalid(self)) is swimming happily in its pond."
+ @respond Persefone.pesticide @kill(self.pesticidemortality, "poisoning")
+ @respond Persefone.harvesting @setphase(drought)
+ @debug "Animal: $self"
+ if self.sex == Persefone.female && length(@neighbours()) < 3 &&
+ self.age >= self.ageofmaturity && @landcover() == Persefone.water
+ @reproduce()
+ end
+end
+
+@phase Mermaid drought begin
+ n = sum(1 for a in @neighbours())
+ @debug "$(Persefone.animalid(self)) is experiencing drought with $n neighbour(s)."
+ @respond Persefone.sowing @setphase(life)
+end
+
+@populate Mermaid begin
+ birthphase = life
+ initphase = life
+ habitat = @habitat(@landcover() == Persefone.water)
+ pairs=true
+end
+
+## Test sets
+
+#FIXME
@testset "Habitat macros" begin
# set up the testing landscape
model = inittestmodel()
- model.landscape[6,6] = Pixel(Ps.agriculture, 1, [])
- species::Dict{String,Any} = Dict("name"=>"test_animal")
- add_agent!((6,6), FarmPlot, model,
- [(6,6)], model.crops["winter wheat"], Ps.janfirst,
- 0.0, 0.0, 0.0, 0.0, Vector{Ps.EventType}())
- add_agent!((3,3), Animal, model, species, Ps.male, 1)
- add_agent!((4,4), Animal, model, species, Ps.female, 1)
+ model.landscape[6,6] = Pixel(Ps.agriculture, 1, [], [])
+ push!(model.farmplots,
+ FarmPlot(1, [(6,6)], model.crops["winter wheat"], Ps.janfirst,
+ 0.0, 0.0, 0.0, 0.0, Vector{Ps.EventType}()))
+ push!(model.animals,
+ Mermaid(1, Ps.male, (-1,-1), (3,3), life), #FIXME unsupported keyword arguments?
+ Mermaid(2, Ps.female, (-1,-1), (4,4), life))
# create a set of habitat descriptors
h1 = @habitat(@landcover() == Ps.water)
h2 = @habitat(@cropname() == "winter wheat" &&
@cropheight() < 2)
h3 = @habitat(@distanceto(Ps.water) > 2 &&
@distancetoedge() <= 2)
- h4 = @habitat(@countanimals(species="test_animal", radius=1) == 1)
+ h4 = @habitat(length(@neighbours(1)) == 1)
# test the descriptors
@test h1((6,4), model) == true
@test h1((5,4), model) == false
@@ -33,111 +71,93 @@
@test h4((1,1), model) == false
end
-@testset "Species initialisation" begin
- model = inittestmodel()
- spec = "test_animal"
- species::Dict{String,Any} = Dict("name"=>spec)
- # create a set of initialisation functions
- initfun1 = Ps.initrandompopulation(10)
- initfun2 = Ps.initrandompopulation(8*8*3, asexual=true)
- initfun3 = Ps.initpopulation(@habitat(@landcover() == Ps.grass), pairs=true)
- initfun4 = Ps.initpopulation(@habitat(@landcover() == Ps.water &&
- @countanimals(species="test_animal", radius=0) < 5),
- popsize=10)
- # apply and test the initialisation functions
- @test_logs (:info, "Initialised 10 $(spec)s.") initfun1(species, model)
- @test all(a -> a.sex in (Ps.male, Ps.female), allagents(model))
- genocide!(model)
- @test_logs (:info, "Initialised 192 $(spec)s.") initfun2(species, model)
- @test Ps.countanimals((1,1), model, species=spec, radius=0) ==
- Ps.countanimals((6,6), model, species=spec, radius=0) == 3
- @test all(a -> a.sex == Ps.hermaphrodite, allagents(model))
- genocide!(model)
- @test_logs (:info, "Initialised 36 $(spec)s.") initfun3(species, model)
- @test Ps.countanimals((2,2), model, species=spec, radius=2) ==
- Ps.countanimals((5,3), model, species=spec, radius=1) == 0
- @test Ps.countanimals((5,5), model, species=spec, radius=0) ==
- Ps.countanimals((6,6), model, species=spec, radius=0) == 2
- a1, a2 = Ps.nearby_animals((6,6), model, 0)
- @test a1.sex != a2.sex
- genocide!(model)
- @test_logs((:warn, "There are not enough suitable locations for $(spec) in the landscape."),
- (:info, "Initialised 5 $(spec)s."),
- initfun4(species, model))
- @test Ps.countanimals((1,1), model, species=spec, radius=4) == 0
- @test Ps.countanimals((6,4), model, species=spec, radius=0) == 5
-end
+#FIXME the way initialisation works has completely changed...
+# @testset "Species initialisation" begin
+# model = inittestmodel()
+# spec = "test_animal"
+# species::Dict{String,Any} = Dict("name"=>spec)
+# # create a set of initialisation functions
+# initfun1 = Ps.initrandompopulation(10)
+# initfun2 = Ps.initrandompopulation(8*8*3, asexual=true)
+# initfun3 = Ps.initpopulation(@habitat(@landcover() == Ps.grass), pairs=true)
+# initfun4 = Ps.initpopulation(@habitat(@landcover() == Ps.water &&
+# length(@neighbours(species="test_animal", radius=0)) < 5),
+# popsize=10)
+# # apply and test the initialisation functions
+# @test_logs (:info, "Initialised 10 $(spec)s.") initfun1(species, model)
+# @test all(a -> a.sex in (Ps.male, Ps.female), allagents(model))
+# genocide!(model)
+# @test_logs (:info, "Initialised 192 $(spec)s.") initfun2(species, model)
+# @test Ps.countanimals((1,1), model, species=spec, radius=0) ==
+# Ps.countanimals((6,6), model, species=spec, radius=0) == 3
+# @test all(a -> a.sex == Ps.hermaphrodite, allagents(model))
+# genocide!(model)
+# @test_logs (:info, "Initialised 36 $(spec)s.") initfun3(species, model)
+# @test Ps.countanimals((2,2), model, species=spec, radius=2) ==
+# Ps.countanimals((5,3), model, species=spec, radius=1) == 0
+# @test Ps.countanimals((5,5), model, species=spec, radius=0) ==
+# Ps.countanimals((6,6), model, species=spec, radius=0) == 2
+# a1, a2 = Ps.nearby_animals((6,6), model, 0)
+# @test a1.sex != a2.sex
+# genocide!(model)
+# @test_logs((:warn, "There are not enough suitable locations for $(spec) in the landscape."),
+# (:info, "Initialised 5 $(spec)s."),
+# initfun4(species, model))
+# @test Ps.countanimals((1,1), model, species=spec, radius=4) == 0
+# @test Ps.countanimals((6,4), model, species=spec, radius=0) == 5
+# end
-@testset "Species macros" begin
- # create a model landscape and a test species
- model = inittestmodel()
-
- @species Mermaid begin
- ageofmaturity = 2
- pesticidemortality = 1.0
- @initialise(@habitat(@landcover() == Persefone.water), pairs=true)
- @phase life begin
- @debug "$(Persefone.animalid(animal)) is swimming happily in its pond."
- @respond Persefone.pesticide @kill(@trait(pesticidemortality), "poisoning")
- @respond Persefone.harvesting @setphase(drought)
- @debug "Animal: $animal"
- if @trait(sex) == Persefone.female && @countanimals() < 3 &&
- @trait(age) >= @trait(ageofmaturity) && @landcover() == Persefone.water
- @reproduce(-1)
- end
- end
- @phase drought begin
- n = sum(1 for a in @neighbours(0))
- @debug "$(Persefone.animalid(animal)) is experiencing drought with $n neighbour(s)."
- @respond Persefone.sowing @setphase(life)
- end
- end
+#FIXME the way species work has completely changed...
+# @testset "Species macros" begin
+# # create a model landscape and a test species
+# model = inittestmodel()
+# # test a complete mermaid life cycle
+# pond = (6,4)
+# mermaid = Mermaid(1)
+# @test typeof(mermaid) <: Animal
+# @test typeof(life) <: Function
+# @test typeof(mermaid["initialise!"]) <: Function
+# @test typeof(mermaid[mermaid["phase"]]) <: Function
+# @test mermaid["phase"] == "life"
+# @test_logs (:info, "Initialised 2 Mermaids.") mermaid["initialise!"](mermaid, model)
+# @test Ps.countanimals((1,1), model, radius=4) == 0
+# @test Ps.countanimals(pond, model) == 2
+# @test model[1].age == 0
+# createevent!(model, [pond], Ps.harvesting)
+# @test_logs((:debug, "Mermaid 1 is swimming happily in its pond."),
+# (:debug, "Mermaid 2 is swimming happily in its pond."),
+# min_level=Logging.Debug, match_mode=:any,
+# stepsimulation!(Ps.withtestlogger(model)))
+# @test model[1].age == 1
+# @test model[2].traits["phase"] == "drought"
+# createevent!(model, [pond], Ps.sowing)
+# @test_logs((:debug, "Mermaid 1 is experiencing drought with 1 neighbour(s)."),
+# (:debug, "Mermaid 2 is experiencing drought with 1 neighbour(s)."),
+# min_level=Logging.Debug, match_mode=:any,
+# stepsimulation!(Ps.withtestlogger(model)))
+# @test_logs((:debug, "Mermaid 1 is swimming happily in its pond."),
+# (:debug, "Mermaid 1 has reproduced."),
+# (:debug, "Mermaid 2 is swimming happily in its pond."),
+# min_level=Logging.Debug, match_mode=:any,
+# stepsimulation!(Ps.withtestlogger(model)))
+# @test Ps.countanimals(pond, model) == 3
+# createevent!(model, [pond], Ps.pesticide)
+# @test_logs((:debug, "Mermaid 1 is swimming happily in its pond."),
+# (:debug, "Mermaid 1 has died from poisoning."),
+# (:debug, "Mermaid 2 is swimming happily in its pond."),
+# (:debug, "Mermaid 2 has died from poisoning."),
+# (:debug, "Mermaid 3 is swimming happily in its pond."),
+# (:debug, "Mermaid 3 has died from poisoning."),
+# min_level=Logging.Debug, match_mode=:any,
+# stepsimulation!(Ps.withtestlogger(model)))
+# @test Ps.countanimals(pond, model) == 0
- # test a complete mermaid life cycle
- pond = (6,4)
- mermaid = Mermaid(model)
- @test typeof(Mermaid) <: Function
- @test typeof(mermaid["life"]) <: Function
- @test typeof(mermaid["initialise!"]) <: Function
- @test typeof(mermaid[mermaid["phase"]]) <: Function
- @test mermaid["phase"] == "life"
- @test_logs (:info, "Initialised 2 Mermaids.") mermaid["initialise!"](mermaid, model)
- @test Ps.countanimals((1,1), model, radius=4) == 0
- @test Ps.countanimals(pond, model) == 2
- @test model[1].age == 0
- createevent!(model, [pond], Ps.harvesting)
- @test_logs((:debug, "Mermaid 1 is swimming happily in its pond."),
- (:debug, "Mermaid 2 is swimming happily in its pond."),
- min_level=Logging.Debug, match_mode=:any,
- stepsimulation!(Ps.withtestlogger(model)))
- @test model[1].age == 1
- @test model[2].traits["phase"] == "drought"
- createevent!(model, [pond], Ps.sowing)
- @test_logs((:debug, "Mermaid 1 is experiencing drought with 1 neighbour(s)."),
- (:debug, "Mermaid 2 is experiencing drought with 1 neighbour(s)."),
- min_level=Logging.Debug, match_mode=:any,
- stepsimulation!(Ps.withtestlogger(model)))
- @test_logs((:debug, "Mermaid 1 is swimming happily in its pond."),
- (:debug, "Mermaid 1 has reproduced."),
- (:debug, "Mermaid 2 is swimming happily in its pond."),
- min_level=Logging.Debug, match_mode=:any,
- stepsimulation!(Ps.withtestlogger(model)))
- @test Ps.countanimals(pond, model) == 3
- createevent!(model, [pond], Ps.pesticide)
- @test_logs((:debug, "Mermaid 1 is swimming happily in its pond."),
- (:debug, "Mermaid 1 has died from poisoning."),
- (:debug, "Mermaid 2 is swimming happily in its pond."),
- (:debug, "Mermaid 2 has died from poisoning."),
- (:debug, "Mermaid 3 is swimming happily in its pond."),
- (:debug, "Mermaid 3 has died from poisoning."),
- min_level=Logging.Debug, match_mode=:any,
- stepsimulation!(Ps.withtestlogger(model)))
- @test Ps.countanimals(pond, model) == 0
+# # test @rand (this is done more easily outside of @species)
+# @test typeof(@rand()) == Float64
+# @test @rand([true, true])
- # test @rand (this is done more easily outside of @species)
- @test typeof(@rand()) == Float64
- @test @rand([true, true])
-end
+# #TODO test movement macros
+# end
@testset "Insect submodel" begin
# create a set of pixels and dates for testing
@@ -145,12 +165,12 @@ end
date1 = Date("2023-05-08") # day 128 (season begin)
date2 = Date("2023-07-06") # day 187 (insect max)
date3 = Date("2023-09-27") # day 270 (season end)
- p1 = Pixel(Ps.agriculture, 1, [])
- p2 = Pixel(Ps.agriculture, 1, [Ps.pesticide])
- p3 = Pixel(Ps.grass, 1, [])
- p4 = Pixel(Ps.soil, 1, [Ps.fertiliser, Ps.pesticide])
- p5 = Pixel(Ps.forest, 1, [])
- p6 = Pixel(Ps.water, 1, [])
+ p1 = Pixel(Ps.agriculture, 1, [], [])
+ p2 = Pixel(Ps.agriculture, 1, [Ps.pesticide], [])
+ p3 = Pixel(Ps.grass, 1, [], [])
+ p4 = Pixel(Ps.soil, 1, [Ps.fertiliser, Ps.pesticide], [])
+ p5 = Pixel(Ps.forest, 1, [], [])
+ p6 = Pixel(Ps.water, 1, [], [])
# check whether the model calculates the same numbers I did by hand
model.date = date1
@test Ps.insectbiomass(p1, model) ≈ 0.00411 atol=0.0001
@@ -193,29 +213,31 @@ end
end
-@testset "Skylark submodel" begin
- # set up a modified test landscape
- model = inittestmodel()
- model.landscape[3,7] = Pixel(Ps.forest, missing, [])
- species = Ps.Skylark(model)
- # test migration
- @test_logs((:info, "Initialised 2 Skylarks."),
- (:debug, "Skylark 1 has migrated."),
- (:debug, "Skylark 2 has migrated."),
- min_level=Logging.Debug, match_mode=:any,
- species["initialise!"](species, Ps.withtestlogger(model)))
- @test nagents(model) == 0
- @test length(model.migrants) == 2
- @test model.migrants[1].first.sex != model.migrants[2].first.sex
- for a in model.migrants
- leave, arrive = a.first.migrationdates
- @test leave[1] in (9, 10) || (leave[1] == 11 && leave[2] <= 15)
- @test (arrive[1] == 2 && arrive[2] >= 15) || (arrive[1] == 3 && arrive[2] <= 15)
- end
- model.date = Date(year(model.date), 3, 17)
- @test_logs((:debug, "Skylark 1 has returned."),
- (:debug, "Skylark 2 has returned."),
- min_level=Logging.Debug, match_mode=:any,
- Ps.updatenature!(Ps.withtestlogger(model)))
- #TODO
-end
+# @testset "Skylark submodel" begin
+# # set up a modified test landscape
+# model = inittestmodel()
+# for x in 1:4
+# model.landscape[x,4] = Pixel(Ps.agriculture, missing, [], [])
+# end
+# # test migration
+# @test_logs((:info, "Initialised 2 Skylarks."),
+# (:debug, "Skylark 1 has migrated."),
+# (:debug, "Skylark 2 has migrated."),
+# min_level=Logging.Debug, match_mode=:any,
+# Ps.initpopulation!("Skylark", Ps.withtestlogger(model)))
+# @test length(model.animals) == 2
+# @test all(isnothing, model.animals)
+# @test length(model.migrants) == 2
+# @test model.migrants[1].first.sex != model.migrants[2].first.sex
+# for a in model.migrants
+# leave, arrive = a.first.migrationdates
+# @test leave[1] in (9, 10) || (leave[1] == 11 && leave[2] <= 15)
+# @test (arrive[1] == 2 && arrive[2] >= 15) || (arrive[1] == 3 && arrive[2] <= 15)
+# end
+# model.date = Date(year(model.date), 3, 17)
+# @test_logs((:debug, "Skylark 1 has returned."),
+# (:debug, "Skylark 2 has returned."),
+# min_level=Logging.Debug, match_mode=:any,
+# Ps.updatenature!(Ps.withtestlogger(model)))
+# #TODO
+# end
--
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