From 18f31e95dd48fac3fb3bbd7736b0cbc1f469913c Mon Sep 17 00:00:00 2001
From: Daniel Vedder <daniel.vedder@idiv.de>
Date: Sat, 21 Jan 2023 20:37:43 +0100
Subject: [PATCH] Made sure that the model RNG is used throughout
Using the GLOBAL_RNG introduces global state, which must be avoided
to preserve reproducibility. Therefore, all Persephone code must use
`model.rng` whenever calling `rand()`/`shuffle!()`/etc.
---
Project.toml | 4 ++++
src/Persephone.jl | 2 ++
src/core/input.jl | 6 ++++--
src/core/simulation.jl | 19 ++++++++++++++-----
src/crop/crops.jl | 2 +-
src/nature/nature.jl | 4 +++-
src/nature/species/wolpertinger.jl | 2 +-
test/io_tests.jl | 4 +++-
test/landscape_tests.jl | 3 ++-
test/nature_tests.jl | 14 +++++++++-----
test/runtests.jl | 9 +++++----
test/simulation_tests.jl | 27 ++++++++++++++++-----------
12 files changed, 64 insertions(+), 32 deletions(-)
diff --git a/Project.toml b/Project.toml
index 19374e6..9add9d6 100644
--- a/Project.toml
+++ b/Project.toml
@@ -14,3 +14,7 @@ Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
StableRNGs = "860ef19b-820b-49d6-a774-d7a799459cd3"
StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
TOML = "fa267f1f-6049-4f14-aa54-33bafae1ed76"
+
+[compat]
+julia = ">= 1.9"
+Agents = ">= 5.6"
\ No newline at end of file
diff --git a/src/Persephone.jl b/src/Persephone.jl
index 3d86d2d..8b56527 100644
--- a/src/Persephone.jl
+++ b/src/Persephone.jl
@@ -52,8 +52,10 @@ export
@distanceto,
@distancetoedge,
@countanimals,
+ @rand,
#functions
simulate,
+ simulate!,
initialise,
stepsimulation!,
createevent!,
diff --git a/src/core/input.jl b/src/core/input.jl
index 814d72d..2f5687e 100644
--- a/src/core/input.jl
+++ b/src/core/input.jl
@@ -53,7 +53,8 @@ function getsettings(configfile::String, seed::Union{Int64,Nothing}=nothing)
# pre-process certain parameters
if !isnothing(seed)
settings["core"]["seed"] = seed
- elseif settings["core"]["seed"] == 0
+ end
+ if settings["core"]["seed"] == 0
settings["core"]["seed"] = abs(rand(RandomDevice(), Int32))
end
defaultoutdir = defaults["core"]["outdir"]
@@ -74,7 +75,7 @@ Certain software parameters can be set via the commandline.
"""
function parsecommandline()
versionstring = """
- Persephone $(@project_version), commit $(read(`git rev-parse HEAD`, String)[1:8])
+ Persephone $(pkgversion(Persephone))
© 2022-2023 Daniel Vedder, Lea Kolb (MIT license)
https://git.idiv.de/xo30xoqa/persephone
"""
@@ -96,6 +97,7 @@ function parsecommandline()
arg_type = String
required = false
end
+ #XXX this changes the global RNG?! (https://github.com/carlobaldassi/ArgParse.jl/issues/121)
args = parse_args(s)
for a in keys(args)
(args[a] == nothing) && delete!(args, a)
diff --git a/src/core/simulation.jl b/src/core/simulation.jl
index d47c372..ca13ff2 100644
--- a/src/core/simulation.jl
+++ b/src/core/simulation.jl
@@ -72,14 +72,23 @@ function finalise!(model::AgentBasedModel)
end
"""
- simulate(config=PARAMFILE, seed=nothing)
+ simulate!(model)
-Carry out a complete simulation run, optionally specifying a configuration file
-and a seed for the RNG.
+Carry out a complete simulation run using a pre-initialised model object.
"""
-function simulate(config::String=PARAMFILE, seed::Union{Int64,Nothing}=nothing)
- model = initialise(config, seed)
+function simulate!(model::AgentBasedModel)
runtime = Dates.value(@param(core.enddate)-@param(core.startdate))+1
step!(model, dummystep, stepsimulation!, runtime)
finalise!(model)
end
+
+"""
+ simulate(config=PARAMFILE, seed=nothing)
+
+Initialise a model object and carry out a complete simulation run, optionally
+specifying a configuration file and a seed for the RNG.
+"""
+function simulate(config::String=PARAMFILE, seed::Union{Int64,Nothing}=nothing)
+ model = initialise(config, seed)
+ simulate!(model)
+end
diff --git a/src/crop/crops.jl b/src/crop/crops.jl
index 84a78f5..a16dae3 100644
--- a/src/crop/crops.jl
+++ b/src/crop/crops.jl
@@ -52,7 +52,7 @@ function initfields!(model::AgentBasedModel)
model.landscape[x,y].fieldid = objectid
push!(model[objectid].pixels, (x,y))
else
- fp = add_agent!(FarmPlot, model, [(x,y)], fallow, 0.0, 0.0)
+ fp = add_agent!((x,y), FarmPlot, model, [(x,y)], fallow, 0.0, 0.0)
model.landscape[x,y].fieldid = fp.id
convertid[rawid] = fp.id
n += 1
diff --git a/src/nature/nature.jl b/src/nature/nature.jl
index 8010f13..ffee8c2 100644
--- a/src/nature/nature.jl
+++ b/src/nature/nature.jl
@@ -372,7 +372,9 @@ Return a random number or element from the sample, using the model RNG.
This is a utility wrapper that can only be used nested within `@phase` or `@habitat`.
"""
macro rand(args...)
- :(rand($(esc(:model)).rng, $(map(esc, args)...)))
+ :($(esc(:rand))($(esc(:model)).rng, $(map(esc, args)...)))
end
+##TODO @chance macro: @chance(0.5) => rand(model.rng) < 0.5
+
##TODO add movement macros
diff --git a/src/nature/species/wolpertinger.jl b/src/nature/species/wolpertinger.jl
index af1f1b6..e51a475 100644
--- a/src/nature/species/wolpertinger.jl
+++ b/src/nature/species/wolpertinger.jl
@@ -24,7 +24,7 @@ of a deer.
and occasionally reproduce by spontaneous parthogenesis...
"""
@phase lifephase begin
- direction = Tuple(rand([-1,1], 2))
+ direction = Tuple(@rand([-1,1], 2))
for i in 1:@rand(1:@trait(maxspeed))
walk!(animal, direction, model; ifempty=false)
end
diff --git a/test/io_tests.jl b/test/io_tests.jl
index a9dd780..5884d9d 100644
--- a/test/io_tests.jl
+++ b/test/io_tests.jl
@@ -4,9 +4,11 @@
###
@testset "Model configuration" begin
- properties = Dict{Symbol,Any}(:settings=>TESTSETTINGS)
+ settings = Ps.getsettings(TESTPARAMETERS)
+ properties = Dict{Symbol,Any}(:settings=>settings)
space = GridSpace((10,10), periodic=false)
model = AgentBasedModel(Animal, space, properties=properties, warn=false)
+
@test @param(core.configfile) == TESTPARAMETERS
@test @param(core.startdate) == Date(2022, 2, 1)
@test @param(nature.targetspecies) == ["Wolpertinger", "Wyvern"]
diff --git a/test/landscape_tests.jl b/test/landscape_tests.jl
index b02ee20..ab8dac4 100644
--- a/test/landscape_tests.jl
+++ b/test/landscape_tests.jl
@@ -30,7 +30,8 @@ function smalltestlandscape(agenttype::Type=Animal)
:events=>Vector{FarmEvent}(),
:dataoutputs=>Vector{DataOutput}(),
:settings=>TESTSETTINGS)
- return AgentBasedModel(agenttype, space, properties=properties, warn=false)
+ return AgentBasedModel(agenttype, space, properties=properties,
+ rng=StableRNG(TESTSETTINGS["core"]["seed"]), warn=false)
end
@testset "Landscape initialisation" begin
diff --git a/test/nature_tests.jl b/test/nature_tests.jl
index 661ea57..c0e4158 100644
--- a/test/nature_tests.jl
+++ b/test/nature_tests.jl
@@ -68,15 +68,15 @@ end
@testset "Species macros" begin
# create a model landscape and a test species
- #TODO test @rand
model = smalltestlandscape(Union{Animal,Farmer,FarmPlot})
+
@species Mermaid begin
ageofmaturity = 2
pesticidemortality = 1.0
@initialise(@habitat(@landcover() == Persephone.water), pairs=true)
@phase life begin
@debug "$(Persephone.animalid(animal)) is swimming happily in its pond."
- @respond Persephone.pesticide @kill(@trait(pesticidemortality))
+ @respond Persephone.pesticide @kill(@trait(pesticidemortality), "poisoning")
@respond Persephone.harvest @setphase(drought)
@debug "Animal: $animal"
if @trait(sex) == Persephone.female && @countanimals() < 3 &&
@@ -123,12 +123,16 @@ end
@test Ps.countanimals(pond, model) == 3
createevent!(model, [pond], Ps.pesticide)
@test_logs((:debug, "Mermaid 1 is swimming happily in its pond."),
- (:debug, "Mermaid 1 has died."),
+ (:debug, "Mermaid 1 has died from poisoning."),
(:debug, "Mermaid 2 is swimming happily in its pond."),
- (:debug, "Mermaid 2 has died."),
+ (:debug, "Mermaid 2 has died from poisoning."),
(:debug, "Mermaid 3 is swimming happily in its pond."),
- (:debug, "Mermaid 3 has died."),
+ (:debug, "Mermaid 3 has died from poisoning."),
min_level=Logging.Debug, match_mode=:any,
stepsimulation!(model))
@test Ps.countanimals(pond, model) == 0
+
+ # test @rand (this is done more easily outside of @species)
+ @test typeof(@rand()) == Float64
+ @test @rand([true, true])
end
diff --git a/test/runtests.jl b/test/runtests.jl
index 5d46318..69bd24d 100644
--- a/test/runtests.jl
+++ b/test/runtests.jl
@@ -6,12 +6,13 @@
using Pkg
Pkg.activate("..")
+using Agents
+using Dates
+using Logging
using Persephone
-using Test
using Random
-using Logging
-using Dates
-using Agents
+using StableRNGs
+using Test
const Ps = Persephone
diff --git a/test/simulation_tests.jl b/test/simulation_tests.jl
index d4a2d0b..1be977a 100644
--- a/test/simulation_tests.jl
+++ b/test/simulation_tests.jl
@@ -15,19 +15,24 @@
end
@testset "Model simulation" begin
+ # The primary reason for this testset is to make sure that a complete
+ # simulation will run through without errors. Thus, there are few tests.
+ # Additionally, it makes sure that no part of the code uses the global
+ # RNG, as this would compromise reproducibility. If one of the `rand()`
+ # tests fail, that requirement has been violated somewhere.
+ Random.seed!(1)
+ rand1 = rand()
+ Random.seed!(1)
+ model = initialise(TESTPARAMETERS, 218)
+ #XXX upstream problem with ArgParse (https://github.com/carlobaldassi/ArgParse.jl/issues/121)
+ @test_broken rand() == rand1
Random.seed!(1)
- @test isapprox(rand(), 0.07337, atol=0.0001)
- model = simulate(TESTPARAMETERS, 218)
@test @param(core.seed) == 218
+ @test_logs((:info, "Simulating day 2022-02-01."),
+ (:info, "Simulated 59 days."),
+ min_level=Logging.Debug, match_mode=:any,
+ simulate!(model))
@test model.date == Date(2022,4,1)
- nwol = sum((typeof(a)==Animal && a.traits["name"]=="Wolpertinger") for a in allagents(model))
- nwyv = sum((typeof(a)==Animal && a.traits["name"]=="Wyvern") for a in allagents(model))
- #FIXME these still fail - although it might not be that clever to rely on random model outcomes
- @test nwol == 32
- @test nwyv == 9
- # To retain reproducibility, the model code must never use the global RNG.
- # If this next test fails, that requirement has probably been violated somewhere.
- #FIXME it does fail... Might it be called by some dependency?
- @test isapprox(rand(), 0.34924, atol=0.0001)
+ @test rand() == rand1
end
--
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