From 4ad42b9213658ecf30bc8a3e63a8f1ca2659b23a Mon Sep 17 00:00:00 2001
From: Daniel Vedder <daniel.vedder@idiv.de>
Date: Thu, 15 Dec 2022 22:46:57 +0100
Subject: [PATCH] Big rearrange in the nature model to accommodate the @species
syntax
Not yet functional!
---
src/Persephone.jl | 9 ++-
src/core/landscape.jl | 1 +
src/nature/ecologicaldata.jl | 12 +++
src/nature/lifehistory.jl | 12 +++
src/nature/nature.jl | 93 +++++++-----------------
src/nature/species.jl | 35 ---------
src/nature/{ => species}/wolpertinger.jl | 2 +
src/nature/{ => species}/wyvern.jl | 2 +
8 files changed, 63 insertions(+), 103 deletions(-)
create mode 100644 src/nature/lifehistory.jl
delete mode 100644 src/nature/species.jl
rename src/nature/{ => species}/wolpertinger.jl (98%)
rename src/nature/{ => species}/wyvern.jl (98%)
diff --git a/src/Persephone.jl b/src/Persephone.jl
index a8becf9..96bfece 100644
--- a/src/Persephone.jl
+++ b/src/Persephone.jl
@@ -16,7 +16,7 @@ using
Agents,
ArgParse,
Dates,
- GeoArrays,
+ GeoArrays, #XXX this is a big dependency - can we get rid of it?
Logging,
LoggingExtras,
Random,
@@ -24,6 +24,7 @@ using
## define exported functions and variables
export
+ param,
simulate,
initialise,
stepsimulation!,
@@ -42,9 +43,11 @@ include("core/landscape.jl")
include("farm/farm.jl")
include("crop/crops.jl")
include("nature/nature.jl")
+include("nature/lifehistory.jl")
include("nature/ecologicaldata.jl")
-include("nature/wolpertinger.jl")
-include("nature/wyvern.jl")
+#include("nature/species/skylark.jl")
+#include("nature/species/wolpertinger.jl")
+#include("nature/species/wyvern.jl")
include("core/simulation.jl")
end
diff --git a/src/core/landscape.jl b/src/core/landscape.jl
index f8f8fd8..573c951 100644
--- a/src/core/landscape.jl
+++ b/src/core/landscape.jl
@@ -17,6 +17,7 @@ in a single object. The model landscape consists of a matrix of pixels.
struct Pixel
landcover::LandCover
fieldid::Union{Missing, UInt32}
+ events::Vector{Symbol} #TODO implement the rest of the events system
#FIXME actually this is stupid - I don't want a field ID, I want a field object
end
diff --git a/src/nature/ecologicaldata.jl b/src/nature/ecologicaldata.jl
index f01ead1..c387eb2 100644
--- a/src/nature/ecologicaldata.jl
+++ b/src/nature/ecologicaldata.jl
@@ -6,6 +6,18 @@
const POPFILE = "populations.csv"
const INDFILE = "individuals.csv"
+"""
+ initecologicaldata()
+
+Create output files for each data group collected by the nature model.
+"""
+function initecologicaldata()
+ newdataoutput(POPFILE, "Date;Species;Abundance", savepopulationdata,
+ param("nature.popoutfreq"))
+ newdataoutput(INDFILE, "Date;ID;X;Y;Species;Sex;Age;Energy",
+ saveindividualdata, param("nature.indoutfreq"))
+end
+
"""
savepopulationdata(model)
diff --git a/src/nature/lifehistory.jl b/src/nature/lifehistory.jl
new file mode 100644
index 0000000..a8e70c0
--- /dev/null
+++ b/src/nature/lifehistory.jl
@@ -0,0 +1,12 @@
+### Persephone - a socio-economic-ecological model of European agricultural landscapes.
+###
+### This file contains a set of utility functions needed by species.
+###
+
+#TODO initrandompopulation
+
+#TODO killanimal!
+
+#TODO reproduce!
+
+#TODO parentsalive?
diff --git a/src/nature/nature.jl b/src/nature/nature.jl
index 6610e62..b39fb82 100644
--- a/src/nature/nature.jl
+++ b/src/nature/nature.jl
@@ -6,78 +6,46 @@
## An enum used to assign a sex to each animal
@enum Sex hermaphrodite male female
-"""
- Species
-
-Species are differentiated by their name, and the functions used to
-initialise their population and update each individual.
-"""
-struct Species
- name::String
- initpop!::Function # takes one argument: model
- update!::Function # takes two arguments: animal, model
- traits::Dict{String,Any} # a collection of species-specific traits
-end
-#TODO convert species into dicts
-
"""
Animal
This is the generic agent type for all animals. Species are differentiated
-by the `species` struct passed by them during initialisation.
+by trait dictionaries passed by them during initialisation.
"""
-
+#XXX fix the @agent docstring issue (https://github.com/JuliaDynamics/Agents.jl/issues/715)
@agent Animal GridAgent{2} begin
- species::Species
+ #XXX is it (performance-)wise to use a dict for the traits?
+ # Doesn't this rather obviate the point of having an agent struct?
+ traits::Dict{String,Any}
sex::Sex
age::Int32
- energy::Int32
end
-# This dict stores the definitions for all species that can be simulated.
-# (The definitions are created in separate files and registered here.)
-##TODO this needs to be rewritten to deal with the new @species macro
-let specieslist = Dict{String, Species}()
- """
- registerspecies(species)
-
- This function has to be called by every species definition file
- in order for the species to be used.
- """
- global function registerspecies(s::Species)
- specieslist[s.name] = s
- end
-
- """
- getspecies(name)
- Returns the definition struct for the named species.
- """
- global function getspecies(name::String)
- specieslist[name]
+### MACROS IMPLEMENTING THE DOMAIN-SPECIFIC LANGUAGE FOR DEFINING SPECIES
+
+macro species(name, body)
+ funcname = "speciesfunction_"*name
+ quote
+ Core.@__doc__ function $(esc(funcname))()
+ $(esc(:name)) = string($(QuoteNode(name)))
+ $(esc(body))
+ vardict = Base.@locals
+ speciesdict = Dict{String,Any}()
+ for k in keys(vardict)
+ speciesdict[string(k)] = vardict[k]
+ end
+ return speciesdict
+ end
end
end
-"""
- newspecies(properties...)
-
-A utility function to create and register a new species.
-All function arguments are passed on to Species().
-"""
-function newspecies(properties...)
- registerspecies(Species(properties...))
+macro phase(name, body)
+ :($(esc(name)) = function(animal::Animal, model::AgentBasedModel) $body end)
end
-"""
- trait(animal, trait)
-A utility function to return a trait value for this animal's species.
-Returns nothing if the trait is not defined.
-"""
-function trait(animal::Animal, trait::String)
- !(trait in keys(animal.species.traits)) && (return nothing)
- return animal.species.traits[trait]
-end
+### FUNCTIONS INTEGRATING THE NATURE MODEL WITH THE REST OF PERSEPHONE
"""
stepagent!(animal, model)
@@ -86,11 +54,7 @@ Update an animal by one day.
"""
function stepagent!(animal::Animal, model::AgentBasedModel)
animal.age += 1
- animal.species.update!(animal,model)
- if animal.energy <= 0
- @debug "$(animal.species.name) $(animal.id) has died."
- kill_agent!(animal, model)
- end
+ animal.traits[animal.traits["phase"]](animal,model)
end
"""
@@ -101,11 +65,10 @@ Initialise the model with all simulated animal populations.
function initnature!(model::AgentBasedModel)
# The config file determines which species are simulated in this run
for s in param("nature.targetspecies")
- getspecies(s).initpop!(model)
+ funcname = Symbol("speciesfunction_"*s)
+ species = @eval $funcname()
+ species["initialise!"](model)
end
# Initialise the data output
- newdataoutput(POPFILE, "Date;Species;Abundance", savepopulationdata,
- param("nature.popoutfreq"))
- newdataoutput(INDFILE, "Date;ID;X;Y;Species;Sex;Age;Energy",
- saveindividualdata, param("nature.indoutfreq"))
+ initecologicaldata()
end
diff --git a/src/nature/species.jl b/src/nature/species.jl
deleted file mode 100644
index 9cef463..0000000
--- a/src/nature/species.jl
+++ /dev/null
@@ -1,35 +0,0 @@
-### Persephone - a socio-economic-ecological model of European agricultural landscapes.
-###
-### This file implements the macros needed for the species DSL.
-###
-
-#XXX configure species traits via a separate TOML file?
-
-##TODO replace the current registerspecies()
-function registerspecies(speciesdict)
- println(speciesdict)
- processeddict = Dict{String,Any}()
- for k in keys(speciesdict)
- processeddict[string(k)] = speciesdict[k]
- end
- processeddict["testphase"]()
-end
-
-##TODO docstring
-macro species(name, body)
- speciesfun = gensym()
- quote
- Core.@__doc__ $speciesfun = function()
- $(esc(:name)) = string($(QuoteNode(name)))
- $(esc(body))
- return Base.@locals
- end
- registerspecies($speciesfun())
- end
-end
-
-##TODO docstring
-macro phase(name, body)
- :($(esc(name)) = function(animal::Animal, model::AgentBasedModel) $body end)
- #:($(esc(name)) = function() $body end) #for testing
-end
diff --git a/src/nature/wolpertinger.jl b/src/nature/species/wolpertinger.jl
similarity index 98%
rename from src/nature/wolpertinger.jl
rename to src/nature/species/wolpertinger.jl
index f22abc6..33a73e3 100644
--- a/src/nature/wolpertinger.jl
+++ b/src/nature/species/wolpertinger.jl
@@ -5,6 +5,8 @@
### Although I dare say the Wolpertinger is probably rather endangered...
###
+##TODO convert to @species syntax
+
"""
initwolpertinger!(model)
diff --git a/src/nature/wyvern.jl b/src/nature/species/wyvern.jl
similarity index 98%
rename from src/nature/wyvern.jl
rename to src/nature/species/wyvern.jl
index 13a364d..2c96df9 100644
--- a/src/nature/wyvern.jl
+++ b/src/nature/species/wyvern.jl
@@ -5,6 +5,8 @@
### Thankfully, wyverns are not a species we have to manage for...
###
+##TODO convert to @species syntax
+
"""
initwyvern!(model)
--
GitLab