Small bug fixes.

This closes #47

src/Persefone.jl

@@ -22,10 +22,11 @@ using
     DataFramesMeta,
     Distributed,
     FileIO,
+    #FIXME an upstream update broke GeoArrays for TableTransforms > 1.15.0
     GeoArrays, #XXX this is a big dependency - can we get rid of it?
     Logging,
     LoggingExtras,
-    CairoMakie,
+    CairoMakie, #XXX this is a very big dependency :-(
     Random,
     Serialization,
     StableRNGs,
@@ -34,13 +35,11 @@ using
 ## Packages that may be useful later on:
 # MacroTools, http://fluxml.ai/MacroTools.jl/stable/utilities/
 # Debugger, https://github.com/JuliaDebug/Debugger.jl
-# Makie, https://docs.makie.org/stable/
 # PackageCompiler, https://julialang.github.io/PackageCompiler.jl/stable/
 # SpatialEcology, https://github.com/EcoJulia/SpatialEcology.jl
 # OmniScape, https://circuitscape.org/
 # PlantSimEngine, https://virtualplantlab.github.io/PlantSimEngine.jl/stable/
 # Overseer, https://juliapackages.com/p/overseer -> ECS
-# QML, https://juliapackages.com/p/qml
 
 ## define exported functions and variables
 export

src/analysis/makieplots.jl

@@ -22,10 +22,11 @@ function visualisemap(model::AgentBasedModel, date::Union{Date,Nothing}=nothing)
     image!(f[1,1], rotr90(landcover))
     ax.aspect = DataAspect()
     # plot individuals
-    #FIXME this function displays the individuals in a different location than the
-    # R script does - somewhere, I'm confusing coordinates...
     for s in unique(inds.Species)
         points = @select!(@subset(inds, :Species .== s, :Date .== date), :X, :Y)
+        # The origin in Makie is in the bottom-left rather than in the top-left as
+        # on the model map, so we have to invert the Y coordinates
+        @transform!(points, :Y = size(model.landscape)[2] .- :Y)
         scatter!(f[1,1], Matrix{Float32}(points), markersize=10)
     end
     f

src/core/input.jl

@@ -13,6 +13,9 @@ const PARAMFILE = joinpath(pkgdir(Persefone), "src/parameters.toml")
 ## (DO NOT CHANGE THIS VALUE! Instead, specify simulation-specific configuration files
 ## by using the "--configfile" commandline argument, or when invoking simulate().) 
 
+#XXX do I need to use absolute paths for all input files in case working dir is changed?
+# (can be done with `joinpath(dirname(@__FILE__), <filename>)` )
+
 """
     @param(domainparam)
 
@@ -174,12 +177,11 @@ end
 """
     loadmodelobject(fullfilename)
 
-Serialise a model object and save it to file for later reference.
-Includes the current model and Julia versions for compatibility checking.
+Deserialise a model object that was previously saved with `[savemodelobject](@ref)`.
 """
 function loadmodelobject(fullfilename::String)
     object = deserialize(fullfilename)
-
+    # Do basic integrity checks
     if !(typeof(object) <: Dict && typeof(object["model"]) <: AgentBasedModel)
         @warn "This file does not contain a model object. Loading failed."
         return
@@ -189,6 +191,8 @@ function loadmodelobject(fullfilename::String)
         @warn "This model object was saved with a different version of Persefone or Julia. It may be incompatible."
     end
     model = object["model"]
-    model.logger = modellogger(@param(core.loglevel), @param(core.outdir)) #reset logger
+    # Reset the logger
+    !isdir(@param(core.outdir)) && mkpath(@param(core.outdir))
+    model.logger = modellogger(@param(core.loglevel), @param(core.outdir))
     model
 end