Added tests for visualisation, changed colour scheme

Makefile

@@ -5,7 +5,7 @@ run:
 	# run an example simulation
 	if [ -d "example_results" ]; then rm -r example_results; fi
 	./run.jl -o example_results
-	src/analysis/analyse_nature.R example_results
+	#src/analysis/analyse_nature.R example_results
 
 test:
 	# running test suite

Project.toml

 name = "Persefone"
 uuid = "039acd1d-2a07-4b33-b082-83a1ff0fd136"
 authors = ["Daniel Vedder <daniel.vedder@idiv.de>"]
-version = "0.3.4"
+version = "0.3.5"
 
 [deps]
 Agents = "46ada45e-f475-11e8-01d0-f70cc89e6671"

src/analysis/makieplots.jl

@@ -28,6 +28,8 @@ function visualisemap(model::AgentBasedModel,date=nothing,landcover=nothing)
         return f
     end
     isnothing(date) && (date = inds.Date[end])
+    update_theme!(palette=(color=cgrad(:seaborn_bright, length(unique(inds.Species))),),
+                  cycle=[:color])
     for s in unique(inds.Species)
         points = @select!(@subset(inds, :Species .== s, :Date .== date),
                           :X, :Y)
@@ -60,7 +62,8 @@ function populationtrends(model::AgentBasedModel)
         deleteat!(ticks[1], 2:2:length(ticks[1]))
         deleteat!(ticks[2], 2:2:length(ticks[2]))            
     end
-        
+    update_theme!(palette=(color=cgrad(:seaborn_bright, length(unique(pops.Species))),),
+                  cycle=[:color])
     f = Figure()
     ax = Axis(f[1,1], xlabel="Date", ylabel="Population size",
               limits=((1, length(dates)), nothing), xticks = ticks)

src/core/output.jl

@@ -215,13 +215,13 @@ end
 Cycle through all data outputs and call their respective plot functions,
 saving each figure as a PDF.
 """
-function visualiseoutput(model::AgentBasedModel)
-    #TODO write tests
+function visualiseoutput(model::AgentBasedModel, format::String="pdf")
     @debug "Visualising output."
+    CairoMakie.activate!()
     for output in model.dataoutputs
         isnothing(output.plotfunction) && continue
         figure = output.plotfunction(model)
-        save(joinpath(@param(core.outdir), output.name*".pdf"), figure)
+        save(joinpath(@param(core.outdir), output.name*"."*format), figure)
     end
 end
 

src/nature/ecologicaldata.jl

@@ -3,10 +3,6 @@
 ### This file includes the functions for collecting and saving ecological output data.
 ###
 
-#XXX NOP functions while I try and get Makie to work
-visualisemap(model) = nothing
-populationtrends(model) = nothing
-
 """
     initecologicaldata()
 

test/io_tests.jl

@@ -66,7 +66,7 @@ end
 
 @testset "Model object serialization" begin
     model = inittestmodel()
-    Ps.createdatadir(@param(core.outdir), @param(core.overwrite))
+    Ps.createdatadir(@param(core.outdir), true)
     @test_logs((:debug, "Saved model object to results_testsuite/test.dat."),
                min_level=Logging.Debug, match_mode=:any,
                savemodelobject(model, "test"))
@@ -81,3 +81,14 @@ end
     @test length(model.agents) == length(model2.agents)
     rm(@param(core.outdir), force=true, recursive=true)
 end
+
+@testset "Output visualisation" begin
+    model = initialise(TESTPARAMETERS)
+    stepsimulation!(model)
+    @test_logs((:debug, "Visualising output."),
+               min_level=Logging.Debug, match_mode=:any,
+               visualiseoutput(model))
+    @test isfile(joinpath(@param(core.outdir), "individuals.pdf"))
+    @test isfile(joinpath(@param(core.outdir), "populations.pdf"))
+    rm(@param(core.outdir), force=true, recursive=true)
+end

test/test_parameters.toml

@@ -10,6 +10,7 @@ configfile = "test_parameters.toml" # location of the configuration file
 outdir = "results_testsuite" # location and name of the output folder
 overwrite = true # overwrite the output directory? (true/false/"ask")
 csvoutput = true # save collected data in CSV files
+visualise = true # generate result graphs
 storedata = true # keep collected data in memory
 loglevel = "warn" # verbosity level: "debug", "info", "warn"
 processors = 6 # number of processors to use on parallel runs
@@ -29,7 +30,7 @@ farmmodel = "FieldManager" # which version of the farm model to use (not yet imp
 [nature]
 targetspecies = ["Wolpertinger", "Wyvern"] # list of target species to simulate
 popoutfreq = "daily" # output frequency population-level data, daily/monthly/yearly/end/never
-indoutfreq = "end" # output frequency individual-level data, daily/monthly/yearly/end/never
+indoutfreq = "daily" # output frequency individual-level data, daily/monthly/yearly/end/never
 insectmodel = ["season", "habitat", "pesticides"] # which factors affect insect growth ("weather" is not yet implemented)
 	
 [crop]