From 6078618e7d19b2c26e2fe9e04e5aec2292d02541 Mon Sep 17 00:00:00 2001
From: Daniel Vedder <daniel.vedder@idiv.de>
Date: Tue, 10 Jan 2023 11:37:05 +0100
Subject: [PATCH] Finished rewriting parameter system.
This is a major change to the codebase. I'm not entirely convinced yet
that it actually makes sense, but overall I think the benefits
outweigh the problems. Closes issue #37.
---
src/Persephone.jl | 7 +-----
src/core/input.jl | 3 +--
src/core/landscape.jl | 8 +++----
src/core/output.jl | 46 ++++++++++++++++++------------------
src/core/simulation.jl | 42 +++++++++++++++++---------------
src/nature/ecologicaldata.jl | 12 +++++-----
src/nature/nature.jl | 4 ++--
test/io_tests.jl | 31 ++++++++++++++----------
test/landscape_tests.jl | 22 +++++++++--------
test/runtests.jl | 4 ++--
10 files changed, 92 insertions(+), 87 deletions(-)
diff --git a/src/Persephone.jl b/src/Persephone.jl
index eb7fd2b..43ef2f1 100644
--- a/src/Persephone.jl
+++ b/src/Persephone.jl
@@ -31,22 +31,17 @@ export
Animal,
Farmer,
#macros
+ @param,
@species,
@phase,
@habitat,
#functions
- param,
simulate,
initialise,
stepsimulation!,
createevent!,
finalise
-## The file that stores all default parameters
-const PARAMFILE = "src/parameters.toml"
-## (DO NOT CHANGE THIS VALUE! Instead, specify simulation-specific configuration files
-## by using the "--configfile" commandline argument, or when invoking simulate().)
-
## include all module files (note that the order matters - if file
## b references something from file a, it must be included later)
include("core/input.jl")
diff --git a/src/core/input.jl b/src/core/input.jl
index ada3f58..7009844 100644
--- a/src/core/input.jl
+++ b/src/core/input.jl
@@ -21,7 +21,6 @@ object is available.
macro param(domainparam)
domain = String(domainparam.args[1])
paramname = String(domainparam.args[2].value)
- #domain, paramname = split(domainparam, ".")
:($(esc(:model)).settings[$domain][$paramname])
end
@@ -31,7 +30,7 @@ end
Combines all configuration options to produce a single settings dict.
Precedence: commandline parameters - user config file - default values
"""
-function getsettings(configfile::String, seed::Union{Int64,Nothing)=nothing)
+function getsettings(configfile::String, seed::Union{Int64,Nothing}=nothing)
# read in and merge configurations from the commandline, the default config file
# and a user-supplied config file
defaults = TOML.parsefile(configfile)
diff --git a/src/core/landscape.jl b/src/core/landscape.jl
index 3ea00c3..a7f1085 100644
--- a/src/core/landscape.jl
+++ b/src/core/landscape.jl
@@ -36,15 +36,15 @@ mutable struct FarmEvent
end
"""
- initlandscape()
+ initlandscape(landcovermap, farmfieldsmap)
Initialise the model landscape based on the map files specified in the
configuration. Returns a matrix of pixels.
"""
-function initlandscape()
+function initlandscape(landcovermap::String, farmfieldsmap::String)
@debug "Initialising landscape"
- landcover = GeoArrays.read(param("core.landcovermap"))
- farmfields = GeoArrays.read(param("core.farmfieldsmap"))
+ landcover = GeoArrays.read(landcovermap)
+ farmfields = GeoArrays.read(farmfieldsmap)
(size(landcover) != size(farmfields)) && Base.error("Input map sizes don't match.")
width, height = size(landcover)[1:2]
landscape = Matrix{Pixel}(undef, width, height)
diff --git a/src/core/output.jl b/src/core/output.jl
index e34feb2..a75c347 100644
--- a/src/core/output.jl
+++ b/src/core/output.jl
@@ -13,12 +13,12 @@ const LOGFILE = "simulation.log"
Creates the output directory and copies relevant files into it.
"""
-function setupdatadir()
+function setupdatadir(model::AgentBasedModel)
# Check whether the output directory already exists and handle conflicts
- if isdir(param("core.outdir"))
- overwrite = param("core.overwrite")
- if param("core.overwrite") == "ask"
- println("The chosen output directory $(param("core.outdir")) already exists.")
+ if isdir(@param(core.outdir))
+ overwrite = @param(core.overwrite)
+ if @param(core.overwrite) == "ask"
+ println("The chosen output directory $(@param(core.outdir)) already exists.")
println("Type 'yes' to overwrite this directory. Otherwise, the simulation will abort.")
print("Overwrite? ")
answer = readline()
@@ -27,39 +27,39 @@ function setupdatadir()
if !overwrite
Base.error("Output directory exists, will not overwrite. Aborting.")
else
- @warn "Overwriting existing output directory $(param("core.outdir"))."
+ @warn "Overwriting existing output directory $(@param(core.outdir))."
end
end
- mkpath(param("core.outdir"))
+ mkpath(@param(core.outdir))
# Setup the logging system and logfile
loglevel = Logging.Info
- if param("core.loglevel") == "debug"
+ if @param(core.loglevel) == "debug"
loglevel = Logging.Debug
- elseif param("core.loglevel") == "quiet"
+ elseif @param(core.loglevel) == "quiet"
loglevel = Logging.Warn
end
- logfile = open(joinpath(param("core.outdir"), LOGFILE), "w+")
+ logfile = open(joinpath(@param(core.outdir), LOGFILE), "w+")
simulationlogger = TeeLogger(ConsoleLogger(logfile, loglevel),
ConsoleLogger(stdout, loglevel))
global_logger(simulationlogger)
- @debug "Setting up output directory $(param("core.outdir"))"
+ @debug "Setting up output directory $(@param(core.outdir))"
# Export a copy of the current parameter settings to the output folder.
# This can be used to replicate this exact run in future, and also
# records the current time and git commit.
- open(joinpath(param("core.outdir"), basename(param("core.configfile"))), "w") do f
+ open(joinpath(@param(core.outdir), basename(@param(core.configfile))), "w") do f
println(f, "#\n# --- Persephone configuration parameters ---")
println(f, "# This file was generated automatically.")
println(f, "# Simulation run on $(string(Dates.format(Dates.now(), "d u Y HH:MM:SS"))),")
println(f, "# with git commit $(read(`git rev-parse HEAD`, String))#\n")
- TOML.print(f, settings)
+ TOML.print(f, model.settings)
end
# Copy the map files to the output folder
- lcmap = param("core.landcovermap")
- ffmap = param("core.farmfieldsmap")
+ lcmap = @param(core.landcovermap)
+ ffmap = @param(core.farmfieldsmap)
!(isfile(lcmap)) && Base.error("The map file $(lcmap) doesn't exist.")
!(isfile(ffmap)) && Base.error("The map file $(ffmap) doesn't exist.")
- cp(lcmap, joinpath(param("core.outdir"), basename(lcmap)), force = true)
- cp(ffmap, joinpath(param("core.outdir"), basename(ffmap)), force = true)
+ cp(lcmap, joinpath(@param(core.outdir), basename(lcmap)), force = true)
+ cp(ffmap, joinpath(@param(core.outdir), basename(ffmap)), force = true)
end
"""
@@ -87,12 +87,12 @@ let outputregistry = Vector{DataOutput}(),
nextyearlyoutput = today()
"""
- newdataoutput(filename, header, outputfunction, frequency)
+ newdataoutput(model, filename, header, outputfunction, frequency)
Create and register a new data output. This function must be called by all submodels
that want to have their output functions called regularly.
"""
- global function newdataoutput(filename::String, header::String,
+ global function newdataoutput(model::AgentBasedModel, filename::String, header::String,
outputfunction::Function, frequency::String)
if !(frequency in ("daily", "monthly", "yearly", "end", "never"))
Base.error("Invalid frequency '$frequency' for $filename.")
@@ -100,7 +100,7 @@ let outputregistry = Vector{DataOutput}(),
ndo = DataOutput(filename, header, outputfunction, frequency)
append!(outputregistry, [ndo])
if frequency != "never"
- open(joinpath(param("core.outdir"), filename), "w") do f
+ open(joinpath(@param(core.outdir), filename), "w") do f
println(f, header)
end
end
@@ -115,7 +115,7 @@ let outputregistry = Vector{DataOutput}(),
global function outputdata(model::AgentBasedModel)
#XXX all output functions are run on the first update (regardless of frequency)
# -> should they all be run on the last update, too?
- if model.date == param("core.startdate")
+ if model.date == @param(core.startdate)
nextmonthlyoutput = model.date
nextyearlyoutput = model.date
end
@@ -125,8 +125,8 @@ let outputregistry = Vector{DataOutput}(),
if (output.frequency == "daily") ||
(output.frequency == "monthly" && model.date == nextmonthlyoutput) ||
(output.frequency == "yearly" && model.date == nextyearlyoutput) ||
- (output.frequency == "end" && model.date == param("core.enddate"))
- open(joinpath(param("core.outdir"), output.filename), "a") do f
+ (output.frequency == "end" && model.date == @param(core.enddate))
+ open(joinpath(@param(core.outdir), output.filename), "a") do f
outstring = output.outputfunction(model)
(outstring[end] != '\n') && (outstring *= '\n')
print(f, outstring)
diff --git a/src/core/simulation.jl b/src/core/simulation.jl
index d36aefa..11244c8 100644
--- a/src/core/simulation.jl
+++ b/src/core/simulation.jl
@@ -4,22 +4,25 @@
###
"""
- initialise(config, seed=nothing)
+The file that stores all default parameters.
+"""
+const PARAMFILE = "src/parameters.toml"
+## (DO NOT CHANGE THIS VALUE! Instead, specify simulation-specific configuration files
+## by using the "--configfile" commandline argument, or when invoking simulate().)
+
+"""
+ initialise(config=PARAMFILE, seed=nothing)
Initialise the model: read in parameters, create the output data directory,
-and instantiate the AgentBasedModel object. Optionally allows overriding the
-`seed` parameter.
+and instantiate the AgentBasedModel object. Optionally allows specifying the
+configuration file and overriding the `seed` parameter.
"""
-function initialise(config::String=PARAMFILE, seed::Union{Int64,Nothing)=nothing)
+function initialise(config::String=PARAMFILE, seed::Union{Int64,Nothing}=nothing)
@info "Simulation run started at $(Dates.now())."
- #TODO add a seed parameter - requires mutable parameters
- # do some housekeeping
- settings = initsettings(config, seed)
+ settings = getsettings(config, seed)
Random.seed!(settings["core"]["seed"])
- setupdatadir()
- # initialise world-level properties
- landscape = initlandscape()
events = Vector{FarmEvent}()
+ landscape = initlandscape(settings["core"]["landcovermap"], settings["core"]["farmfieldsmap"])
space = GridSpace(size(landscape), periodic=false)
properties = Dict{Symbol,Any}(:settings=>settings,
:date=>settings["core"]["startdate"],
@@ -27,8 +30,8 @@ function initialise(config::String=PARAMFILE, seed::Union{Int64,Nothing)=nothing
:events=>events)
@debug "Setting up model."
model = AgentBasedModel(Union{Farmer,Animal,FarmPlot}, space, properties=properties,
- rng=Random.Xoshiro(param("core.seed")), warn=false)
- # initialise submodels
+ rng=Random.Xoshiro(settings["core"]["seed"]), warn=false)
+ setupdatadir(model)
initfarms!(model)
initfields!(model)
initnature!(model)
@@ -57,20 +60,21 @@ end
Wrap up the simulation. Currently doesn't do anything except print some information.
"""
function finalise(model::AgentBasedModel)
- @info "Simulated $(model.date-param("core.startdate"))."
- @info "Simulation run completed at $(Dates.now()),\nwrote output to $(param("core.outdir"))."
+ @info "Simulated $(model.date-@param(core.startdate))."
+ @info "Simulation run completed at $(Dates.now()),\nwrote output to $(@param(core.outdir))."
#XXX is there anything to do here?
#genocide!(model)
end
"""
- simulate(config)
+ simulate(config=PARAMFILE, seed=nothing)
-Carry out a complete simulation run.
+Carry out a complete simulation run, optionally specifying a configuration file
+and a seed for the RNG.
"""
-function simulate(config::String=PARAMFILE)
- model = initialise(config) #TODO add seed value
- runtime = Dates.value(param("core.enddate")-param("core.startdate"))+1
+function simulate(config::String=PARAMFILE, seed::Union{Int64,Nothing}=nothing)
+ model = initialise(config, seed)
+ runtime = Dates.value(@param(core.enddate)-@param(core.startdate))+1
step!(model, dummystep, stepsimulation!, runtime)
finalise(model)
end
diff --git a/src/nature/ecologicaldata.jl b/src/nature/ecologicaldata.jl
index e57b15e..507ad17 100644
--- a/src/nature/ecologicaldata.jl
+++ b/src/nature/ecologicaldata.jl
@@ -11,11 +11,11 @@ const INDFILE = "individuals.csv"
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",
- saveindividualdata, param("nature.indoutfreq"))
+function initecologicaldata(model::AgentBasedModel)
+ newdataoutput(model, POPFILE, "Date;Species;Abundance", savepopulationdata,
+ @param(nature.popoutfreq))
+ newdataoutput(model, INDFILE, "Date;ID;X;Y;Species;Sex;Age",
+ saveindividualdata, @param(nature.indoutfreq))
end
"""
@@ -26,7 +26,7 @@ and population size for each animal species. May be called never, daily, monthly
yearly, or at the end of a simulation, depending on the parameter `nature.popoutfreq`.
"""
function savepopulationdata(model::AgentBasedModel)
- pops = Dict{String,Int}(s=>0 for s = param("nature.targetspecies"))
+ pops = Dict{String,Int}(s=>0 for s = @param(nature.targetspecies))
for a in allagents(model)
(typeof(a) != Animal) && continue
pops[a.traits["name"]] += 1
diff --git a/src/nature/nature.jl b/src/nature/nature.jl
index e15e65b..726d6f7 100644
--- a/src/nature/nature.jl
+++ b/src/nature/nature.jl
@@ -50,12 +50,12 @@ Initialise the model with all simulated animal populations.
"""
function initnature!(model::AgentBasedModel)
# The config file determines which species are simulated in this run
- for speciesname in param("nature.targetspecies")
+ for speciesname in @param(nature.targetspecies)
species = @eval $(Symbol(speciesname))($model)
species["initialise!"](species, model)
end
# Initialise the data output
- initecologicaldata()
+ initecologicaldata(model)
end
diff --git a/test/io_tests.jl b/test/io_tests.jl
index cb06bed..8534fbe 100644
--- a/test/io_tests.jl
+++ b/test/io_tests.jl
@@ -4,26 +4,31 @@
###
@testset "Model configuration" begin
- # `test_parameters.toml` is read in in `runtests.jl`
- @test param("core.configfile") == TESTPARAMETERS
- @test param("core.startdate") == Date(2020, 1, 1)
- @test param("nature.targetspecies") == ["Wolpertinger", "Wyvern"]
+ properties = Dict{Symbol,Any}(:settings=>TESTSETTINGS)
+ space = GridSpace((10,10), periodic=false)
+ model = AgentBasedModel(Animal, space, properties=properties, warn=false)
+ @test @param(core.configfile) == TESTPARAMETERS
+ @test @param(core.startdate) == Date(2020, 1, 1)
+ @test @param(nature.targetspecies) == ["Wolpertinger", "Wyvern"]
#TODO test commandline parameters
end
@testset "Output functions" begin
+ properties = Dict{Symbol,Any}(:settings=>TESTSETTINGS)
+ space = GridSpace((10,10), periodic=false)
+ model = AgentBasedModel(Animal, space, properties=properties, warn=false)
# test that the output directory is created with all files
logstring = "Setting up output directory results_testsuite_$(Dates.today())_s1"
- @test_logs (:debug, logstring) min_level=Logging.Debug Ps.setupdatadir()
- @test isdir(param("core.outdir"))
- @test isfile(joinpath(param("core.outdir"), param("core.landcovermap")))
- @test isfile(joinpath(param("core.outdir"), param("core.farmfieldsmap")))
- @test isfile(joinpath(param("core.outdir"), param("core.configfile")))
- @test isfile(joinpath(param("core.outdir"), Ps.LOGFILE))
+ @test_logs (:debug, logstring) min_level=Logging.Debug Ps.setupdatadir(model)
+ @test isdir(@param(core.outdir))
+ @test isfile(joinpath(@param(core.outdir), @param(core.landcovermap)))
+ @test isfile(joinpath(@param(core.outdir), @param(core.farmfieldsmap)))
+ @test isfile(joinpath(@param(core.outdir), @param(core.configfile)))
+ @test isfile(joinpath(@param(core.outdir), Ps.LOGFILE))
# check whether the overwrite warning/protection works
- logstring = "Overwriting existing output directory $(param("core.outdir"))."
- @test_logs (:warn, logstring) match_mode=:any Ps.setupdatadir()
+ logstring = "Overwriting existing output directory $(@param(core.outdir))."
+ @test_logs (:warn, logstring) match_mode=:any Ps.setupdatadir(model)
#TODO test overwrite protection (requires parameter mutability)
- rm(param("core.outdir"), force=true, recursive=true)
+ rm(@param(core.outdir), force=true, recursive=true)
#TODO test that creating a DataOutput works, and outputs data with the required frequency
end
diff --git a/test/landscape_tests.jl b/test/landscape_tests.jl
index ae6b3b1..78ea08e 100644
--- a/test/landscape_tests.jl
+++ b/test/landscape_tests.jl
@@ -25,17 +25,17 @@ function smalltestlandscape(agenttype::Type=Animal)
end
landscape[6,4] = Pixel(Ps.water, 0, [])
space = GridSpace(size(landscape), periodic=false)
- properties = Dict{Symbol,Any}(:landscape=>landscape)
+ properties = Dict{Symbol,Any}(:landscape=>landscape, :settings=>TESTSETTINGS)
return AgentBasedModel(agenttype, space, properties=properties, warn=false)
end
@testset "Landscape initialisation" begin
# initialise the landscape part of the model
- landscape = Ps.initlandscape()
+ landscape = Ps.initlandscape(TESTSETTINGS["core"]["landcovermap"],
+ TESTSETTINGS["core"]["farmfieldsmap"])
space = GridSpace(size(landscape), periodic=false)
- properties = Dict{Symbol,Any}(:landscape=>landscape)
- model = AgentBasedModel(FarmPlot, space, properties=properties,
- rng=Random.Xoshiro(param("core.seed")), warn=false)
+ properties = Dict{Symbol,Any}(:landscape=>landscape, :settings=>TESTSETTINGS)
+ model = AgentBasedModel(FarmPlot, space, properties=properties, warn=false)
Ps.initfields!(model)
# these tests are specific to the Jena maps
@test size(model.landscape) == (1754, 1602)
@@ -53,13 +53,15 @@ end
@testset "Event system" begin
# initialise a basic model landscape
- landscape = Ps.initlandscape()
+ landscape = Ps.initlandscape(TESTSETTINGS["core"]["landcovermap"],
+ TESTSETTINGS["core"]["farmfieldsmap"])
space = GridSpace(size(landscape), periodic=false)
- properties = Dict{Symbol,Any}(:date=>param("core.startdate"),
+ properties = Dict{Symbol,Any}(:date=>Date(2022, 1, 1),
:landscape=>landscape,
- :events=>Vector{FarmEvent}())
- model = AgentBasedModel(Union{Farmer,Animal,FarmPlot}, space, properties=properties,
- rng=Random.Xoshiro(param("core.seed")), warn=false)
+ :events=>Vector{FarmEvent}(),
+ :settings=>TESTSETTINGS)
+ model = AgentBasedModel(Union{Farmer,Animal,FarmPlot}, space,
+ properties=properties, warn=false)
# create some events and see whether they show up on the map and disappear as they should
createevent!(model, [(1,1), (1,2), (1,3), (2,1), (2,3)], Ps.tillage)
createevent!(model, [(1,1), (1,2), (1,3), (2,2)], Ps.sowing, 2)
diff --git a/test/runtests.jl b/test/runtests.jl
index 8ea5976..5d46318 100644
--- a/test/runtests.jl
+++ b/test/runtests.jl
@@ -16,9 +16,9 @@ using Agents
const Ps = Persephone
const TESTPARAMETERS = "test_parameters.toml"
+const TESTSETTINGS = Ps.getsettings(TESTPARAMETERS)
@testset "Persephone Tests" begin
- Ps.initsettings(TESTPARAMETERS)
@testset "Core model" begin
include("io_tests.jl")
include("landscape_tests.jl")
@@ -33,5 +33,5 @@ const TESTPARAMETERS = "test_parameters.toml"
@testset "Farm model" begin
include("farm_tests.jl")
end
- rm(param("core.outdir"), force=true, recursive=true)
+ rm(TESTSETTINGS["core"]["outdir"], force=true, recursive=true)
end
--
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