From 1e389e15765fabf88cfe5b3694d9c17d7b3de17e Mon Sep 17 00:00:00 2001
From: Daniel Vedder <daniel.vedder@idiv.de>
Date: Sat, 28 Oct 2023 19:01:52 +0200
Subject: [PATCH] Wrote tests for skylark migration
---
Project.toml | 2 +-
src/Persefone.jl | 2 +-
src/nature/nature.jl | 2 +-
src/nature/species/skylark.jl | 13 +++++++++----
test/io_tests.jl | 7 +++++--
test/landscape_tests.jl | 3 ++-
test/nature_tests.jl | 33 ++++++++++++++++++++++++++++++---
test/runtests.jl | 27 ++++++++++++++++-----------
8 files changed, 65 insertions(+), 24 deletions(-)
diff --git a/Project.toml b/Project.toml
index 10e11cc..7ed919c 100644
--- a/Project.toml
+++ b/Project.toml
@@ -1,7 +1,7 @@
name = "Persefone"
uuid = "039acd1d-2a07-4b33-b082-83a1ff0fd136"
authors = ["Daniel Vedder <daniel.vedder@idiv.de>"]
-version = "0.3.6"
+version = "0.4.0"
[deps]
Agents = "46ada45e-f475-11e8-01d0-f70cc89e6671"
diff --git a/src/Persefone.jl b/src/Persefone.jl
index e02955f..cc6fef7 100644
--- a/src/Persefone.jl
+++ b/src/Persefone.jl
@@ -110,7 +110,7 @@ include("nature/ecologicaldata.jl")
# for f in readdir("nature/species", join=true)
# endswith(f, ".jl") && include(f)
# end
-#include("nature/species/skylark.jl")
+include("nature/species/skylark.jl")
include("nature/species/wolpertinger.jl")
include("nature/species/wyvern.jl")
diff --git a/src/nature/nature.jl b/src/nature/nature.jl
index b9e96ee..4fca51f 100644
--- a/src/nature/nature.jl
+++ b/src/nature/nature.jl
@@ -95,7 +95,7 @@ Run processes that affect all animals.
function updatenature!(model::AgentBasedModel)
# The migrant pool is sorted by date of return, so we can simply look at the top
# of the stack to check whether any animals are returning today.
- while !isempty(model.migrants) && model.migrants[1].second == model.date
+ while !isempty(model.migrants) && model.migrants[1].second <= model.date
add_agent_pos!(model.migrants[1].first, model)
@debug "$(animalid(model.migrants[1].first)) has returned."
deleteat!(model.migrants, 1)
diff --git a/src/nature/species/skylark.jl b/src/nature/species/skylark.jl
index 98d7193..5b0a2e8 100644
--- a/src/nature/species/skylark.jl
+++ b/src/nature/species/skylark.jl
@@ -25,7 +25,7 @@ At the moment, this implementation is still in development.
migrationdates = ()
habitats = @habitat((@landcover() == grass ||
- (@landcover() == agriculture && @croptype() != maize)) &&
+ (@landcover() == agriculture && @cropname() != "maize")) &&
@distanceto(forest) > 5)
@initialise(habitats, pairs=true, initfunction=initskylark)
@@ -69,13 +69,18 @@ Initialise a skylark individual. Selects migration dates and checks if the
bird should currently be on migration.
"""
function initskylark(animal::Animal, model::AgentBasedModel)
+ @debug "Added $(animalid(animal)) at $(animal.pos)"
animal.migrationdates = migrationdates(animal, model)
leave = animal.migrationdates[1]
arrive = animal.migrationdates[2]
m, d = monthday(model.date)
migrate = (((m < arrive[1]) || (m == arrive[1] && d < arrive[2])) ||
((m > leave[1]) || (m == leave[1] && d >= leave[2])))
- migrate && @migrate(Date(year(model.date)+year(1), arrive[1], arrive[2]))
+ if migrate
+ returndate = Date(year(model.date), arrive[1], arrive[2])
+ model.date != @param(core.startdate) && (returndate += Year(1))
+ @migrate(returndate)
+ end
#TODO other stuff?
end
@@ -90,7 +95,7 @@ function migrationdates(skylark::Animal, model::AgentBasedModel)
minarrive = skylark.sex == male ? (2, 15) : (3, 1)
deltaleave = @rand(0:45) #XXX ought to be normally distributed
deltaarrive = @rand(0:15) #XXX ought to be normally distributed
- leave = monthday(Date(2000, minleave[1], minleave[2]) + Day(deltaleave))
- arrive = monthday(Date(2000, minarrive[1], minarrive[2]) + Day(deltaarrive))
+ leave = monthday(Date(2001, minleave[1], minleave[2]) + Day(deltaleave))
+ arrive = monthday(Date(2001, minarrive[1], minarrive[2]) + Day(deltaarrive))
(leave, arrive)
end
diff --git a/test/io_tests.jl b/test/io_tests.jl
index aa45dd2..734ee78 100644
--- a/test/io_tests.jl
+++ b/test/io_tests.jl
@@ -67,6 +67,8 @@ end
@testset "Model object serialization" begin
model = inittestmodel()
Ps.createdatadir(@param(core.outdir), true)
+ originalenddate = @param(core.enddate)
+ @param(core.enddate) = Date(year(model.date), 2, 5)
@test_logs((:debug, "Saved model object to results_testsuite/test.dat."),
min_level=Logging.Debug, match_mode=:any,
savemodelobject(model, "test"))
@@ -75,11 +77,12 @@ end
@test model.date == model2.date
@test model.settings == model2.settings
@test length(model.agents) == length(model2.agents)
- simulate!(model)
- simulate!(model2)
+ simulate!(Ps.withtestlogger(model))
+ simulate!(Ps.withtestlogger(model2))
@test model.date == model2.date
@test length(model.agents) == length(model2.agents)
rm(@param(core.outdir), force=true, recursive=true)
+ @param(core.enddate) = originalenddate
end
@testset "Output visualisation" begin
diff --git a/test/landscape_tests.jl b/test/landscape_tests.jl
index aaf1f8e..3a29f87 100644
--- a/test/landscape_tests.jl
+++ b/test/landscape_tests.jl
@@ -42,7 +42,8 @@ end
@testset "Landscape functions" begin
model = inittestmodel()
- @test Ps.distanceto((2,3), model, Ps.forest) == 0
+ @test Ps.distanceto((2,3), model, Ps.agriculture) == 0
+ @test Ps.distanceto((2,3), model, Ps.forest) == 2
@test Ps.distanceto((2,3), model, Ps.grass) == 2
@test Ps.distanceto((2,3), model, Ps.water) == 4
@test Ps.distanceto((2,3), model, Ps.soil) == Inf
diff --git a/test/nature_tests.jl b/test/nature_tests.jl
index 1d6276b..dddbb64 100644
--- a/test/nature_tests.jl
+++ b/test/nature_tests.jl
@@ -39,7 +39,7 @@ end
species::Dict{String,Any} = Dict("name"=>spec)
# create a set of initialisation functions
initfun1 = Ps.initrandompopulation(10)
- initfun2 = Ps.initrandompopulation(6*6*3, asexual=true)
+ 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),
@@ -48,12 +48,12 @@ end
@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 108 $(spec)s.") initfun2(species, 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 16 $(spec)s.") initfun3(species, 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) ==
@@ -192,3 +192,30 @@ end
#TODO
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
diff --git a/test/runtests.jl b/test/runtests.jl
index 78d3293..4636903 100644
--- a/test/runtests.jl
+++ b/test/runtests.jl
@@ -58,20 +58,25 @@ end
"""
smalltestlandscape()
-Create a 6x6 landscape with three land cover types for testing:
+Create a 8x8 landscape with five land cover types for testing:
- F F F F F F
- F F F F F F
- F F F F F F
- F F F F F W
- F F G G G G
- F F G G G G
+ A A A A A A A A
+ A A A A A A A A
+ A A A A A A A A
+ A A A A A W A A
+ F F G G G G G G
+ F F G G G G G G
+ F F G G G G G G
+ B B B B B B B B
"""
function smalltestlandscape()
- landscape = Matrix{Pixel}(undef, 6, 6)
- for x in 1:6
- for y in 1:6
- (x in (1:2) || y in (1:4)) ? lc = Ps.forest : lc = Ps.grass
+ landscape = Matrix{Pixel}(undef, 8, 8)
+ for x in 1:8
+ for y in 1:8
+ (y in (1:4)) ? lc = Ps.agriculture :
+ (x in (1:2)) ? lc = Ps.forest :
+ (y == 8) ? lc = Ps.builtup :
+ lc = Ps.grass
landscape[x,y] = Pixel(lc, missing, [])
end
end
--
GitLab