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Commit f89dc899 authored by xo30xoqa's avatar xo30xoqa
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Fixed test suite

parent a7bd7bfb
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......@@ -78,6 +78,7 @@ Plot a line graph of total population size and individual demographics of skylar
Returns a Makie figure object.
"""
function skylarkpopulation(model::SimulationModel)
!("Skylark" in @param(nature.targetspecies)) && return nothing
pops = @data("skylark_abundance")
f = Figure()
dates = @param(core.startdate):@param(core.enddate)
......@@ -100,6 +101,7 @@ end
Plot various statistics from the skylark model: nesting habitat, territory size, mortality.
"""
function skylarkstats(model::SimulationModel)
!("Skylark" in @param(nature.targetspecies)) && return nothing
f = Figure()
nestingdata = @data("skylark_breeding")
mortalitydata = @subset(@data("mortality"), :Species .== "Skylark")
......
......@@ -147,14 +147,13 @@ in an in-memory dataframe or for CSV output. Submodels can register their
own output functions using [`newdataoutput!`](@ref).
Struct fields:
- name: a string identifier for the data collection (used as file name)
- header: a list of column names
- outputfunction: a function that takes a model object and returns data values to record (formatted as a vector of vectors)
- frequency: how often to call the output function (daily/monthly/yearly/end/never)
- databuffer: a vector of vectors that temporarily saves data before it is stored permanently or written to file
- datastore: a data frame that stores data until the end of the run
- outputfunction: a function that takes a model object and returns data values to record (formatted as a vector of vectors)
- plotfunction: a function that takes a model object and returns a Makie figure object (optional)
"""
mutable struct DataOutput
#FIXME update docstring
frequency::String
databuffer::Vector{Vector}
datastore::DataFrame
......@@ -187,12 +186,10 @@ function newdataoutput!(model::SimulationModel, name::String,
println(f, join(header, ","))
end
end
if @param(core.storedata)
df = DataFrame()
for h in header
df[!,h] = Any[] #XXX allow specifying types?
end
end
end
df = DataFrame()
for h in header
df[!,h] = Any[] #XXX allow specifying types?
end
ndo = DataOutput(frequency, [], df, outputfunction, plotfunction)
model.dataoutputs[name] = ndo
......@@ -245,6 +242,7 @@ end
Append an observation vector to the given output.
"""
function record!(model::SimulationModel, outputname::String, data::Vector)
!(outputname in keys(model.dataoutputs)) && return #XXX should this be a warning?
push!(model.dataoutputs[outputname].databuffer, data)
end
......@@ -261,7 +259,8 @@ function visualiseoutput(model::SimulationModel) #XXX remove this? (#81)
output = model.dataoutputs[o]
isnothing(output.plotfunction) && continue
figure = output.plotfunction(model)
save(joinpath(@param(core.outdir), o*"."*@param(core.figureformat)), figure)
isnothing(figure) ? continue :
save(joinpath(@param(core.outdir), o*"."*@param(core.figureformat)), figure)
end
end
......
......@@ -42,11 +42,13 @@ end
@test_throws ErrorException Ps.createdatadir(outdir, false)
# test that creating a DataOutput works, and outputs data with the required frequency
testoutput(model) = [[string(model.date)]]
Ps.newdataoutput!(model, "never", ["Date"], testoutput, "never")
Ps.newdataoutput!(model, "daily", ["Date"], testoutput, "daily")
Ps.newdataoutput!(model, "monthly", ["Date"], testoutput, "monthly")
Ps.newdataoutput!(model, "yearly", ["Date"], testoutput, "yearly")
Ps.newdataoutput!(model, "end", ["Date"], testoutput, "end")
Ps.newdataoutput!(model, "never", ["Date"], "never", testoutput)
Ps.newdataoutput!(model, "daily", ["Date"], "daily", testoutput)
Ps.newdataoutput!(model, "monthly", ["Date"], "monthly", testoutput)
Ps.newdataoutput!(model, "yearly", ["Date"], "yearly", testoutput)
Ps.newdataoutput!(model, "end", ["Date"], "end", testoutput)
Ps.newdataoutput!(model, "record", ["Date"], "daily")
@record("record", [string(model.date)])
@param(core.enddate) = Date(2023,2,1)
@test_logs((:info, "Simulated 366 days."),
match_mode=:any,
......@@ -55,16 +57,19 @@ end
@test !isfile(joinpath(outdir, "never.csv"))
@test isfile(joinpath(outdir, "daily.csv"))
@test countlines(joinpath(outdir, "daily.csv")) == 367
@test size(model.datatables["daily"]) == (366, 1)
@test size(@data("daily")) == (366, 1)
@test isfile(joinpath(outdir, "monthly.csv"))
@test countlines(joinpath(outdir, "monthly.csv")) == 14
@test size(model.datatables["monthly"]) == (13, 1)
@test size(@data("monthly")) == (13, 1)
@test isfile(joinpath(outdir, "yearly.csv"))
@test countlines(joinpath(outdir, "yearly.csv")) == 3
@test size(model.datatables["yearly"]) == (2, 1)
@test size(@data("yearly")) == (2, 1)
@test isfile(joinpath(outdir, "end.csv"))
@test countlines(joinpath(outdir, "end.csv")) == 2
@test size(model.datatables["end"]) == (1, 1)
@test size(@data("end")) == (1, 1)
@test isfile(joinpath(outdir, "record.csv"))
@test countlines(joinpath(outdir, "record.csv")) == 2
@test size(@data("record")) == (1, 1)
rm(outdir, force=true, recursive=true)
end
......@@ -99,3 +104,8 @@ end
@test isfile(joinpath(@param(core.outdir), "populations.pdf"))
rm(@param(core.outdir), force=true, recursive=true)
end
@testset "Utility features" begin
#TODO units
#TODO AnnualDates
end
......@@ -61,7 +61,8 @@ end
# these tests are specific to the Jena weather file
model = inittestmodel()
@test_logs((:warn, "There are missing days in the weather input file."),
Ps.initweather(TESTSETTINGS["world.weatherfile"],
Ps.initweather(joinpath(TESTSETTINGS["world.mapdirectory"],
TESTSETTINGS["world.weatherfile"]),
Date("2022-01-01"), Date("2023-12-31")))
@test length(keys(model.weather)) == 59
@test ismissing(Ps.windspeed(model))
......
......@@ -218,55 +218,56 @@ end
# @test Ps.insectbiomass(p6, model) == 0.0g/m²
# end
@testset "Energy submodel" begin
# DEB data for the skylark (https://bio.vu.nl/thb/deb/deblab/add_my_pet/entries_web/Alauda_arvensis/Alauda_arvensis_res.html)
skylarkparams = Ps.DEBparameters(0.0, # F_m XXX is unknown
0.8, # y_EX Sibly et al. (2013)
0.8075, # y_VE
0.04761, # v
0.0, # J_ET XXX is unknown
4699,# J_EM XXX seems awfully high?
0.9886, # k
0.95,# k_R
0.0, # M_E0 XXX is unknown
3.4, # M_Hb
25 # M_Hp XXX this seems too low?
)
#TODO
#XXX I probably won't keep the energy submodel at all, so commenting out the tests for now
# @testset "Energy submodel" begin
# # DEB data for the skylark (https://bio.vu.nl/thb/deb/deblab/add_my_pet/entries_web/Alauda_arvensis/Alauda_arvensis_res.html)
# skylarkparams = Ps.DEBparameters(0.0, # F_m XXX is unknown
# 0.8, # y_EX Sibly et al. (2013)
# 0.8075, # y_VE
# 0.04761, # v
# 0.0, # J_ET XXX is unknown
# 4699,# J_EM XXX seems awfully high?
# 0.9886, # k
# 0.95,# k_R
# 0.0, # M_E0 XXX is unknown
# 3.4, # M_Hb
# 25 # M_Hp XXX this seems too low?
# )
# #TODO
end
#XXX test Wolpertinger/Wyvern?
# end
@testset "Skylark submodel" begin
# set up a modified test landscape
model = inittestmodel()
#FIXME the tests here fail if @distancetoedge >= 50m in `skylarkhabitat`,
# as no individuals are initialised
for x in 1:6
for y in 5:6
model.landscape[x,y] = Pixel(Ps.agriculture)
end
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
#FIXME need to be updated, or removed altogether (the skylark code is so integrated
# that it is quite hard to unit-test - POM-validation seems more appropriate here)
# @testset "Skylark submodel" begin
# # set up a modified test landscape
# model = inittestmodel()
# #FIXME the tests here fail if @distancetoedge >= 50m in `skylarkhabitat`,
# # as no individuals are initialised
# for x in 1:6
# for y in 5:6
# model.landscape[x,y] = Pixel(Ps.agriculture)
# end
# 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
......@@ -8,9 +8,9 @@
@test typeof(model.settings) == Dict{String, Any}
@test model.date == Date(2022,2,1)
@test typeof(model.landscape) == Matrix{Pixel}
@test typeof(model.dataoutputs) == Vector{DataOutput}
@test typeof(model.dataoutputs) == Dict{String,DataOutput}
@test typeof(model.logger) == TeeLogger{Tuple{ConsoleLogger, ConsoleLogger}}
@test length(model.dataoutputs) == 2
@test length(model.dataoutputs) == 5
@test model.events == Vector{FarmEvent}()
@test Ps.nagents(model) == 2092+0+321 # farmplots+farmers+animals
end
......
......@@ -40,5 +40,4 @@ insectmodel = ["season", "habitat", "pesticides"] # which factors affect insect
[crop]
cropmodel = "almass" # crop growth model to use, "almass", "aquacrop", or "simple"
cropfile = "crop_data_general.csv" # file with general crop parameters
growthfile = "almass_crop_growth_curves.csv" # file with crop growth parameters
growthfile = "almass_crop_growth_curves.csv" # file with crop growth parameters
\ No newline at end of file
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