From a1e8f923bf0c52812939864288b1f8cddfc5221c Mon Sep 17 00:00:00 2001
From: Daniel Vedder <daniel.vedder@idiv.de>
Date: Wed, 12 Jun 2024 10:31:31 +0200
Subject: [PATCH] Added world.mapdirectory parameter
Also updated CONTRIBUTORS.md, added a "none" option for
`core.logoutput`, and added type annotations to the Skylark struct
---
CHANGELOG.md | 22 ++++++++++++++++++----
CONTRIBUTORS.md | 22 +++++++++-------------
LICENSE | 2 +-
README.md | 2 +-
src/analysis/makieplots.jl | 7 +++++--
src/core/output.jl | 8 +++++---
src/core/simulation.jl | 6 ++++--
src/nature/species/skylark.jl | 34 +++++++++++++++-------------------
src/parameters.toml | 13 +++++++------
src/world/landscape.jl | 6 ++++--
test/runtests.jl | 6 ++++--
test/test_parameters.toml | 1 +
12 files changed, 74 insertions(+), 55 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 9d58db8..3bf09dd 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -6,6 +6,24 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/),
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
+## [v0.5.1] - unreleased
+
+### Added
+
+- `core.logoutput` parameter to define whether logs are printed to screen, file, none, or both
+
+- `world.mapdirectory` parameter specifies the path to the directory in which
+ `landcovermap`, `farmfieldsmap`, and `weatherfile` are located
+
+### Changed
+
+### Deprecated
+
+### Removed
+
+### Fixed
+
+
## [v0.5.0] - 07-06-2024
This release doesn't add much new functionality, but represents a major restructuring
@@ -45,14 +63,10 @@ way the species definition macros work and are used.
- requires Julia 1.10
-### Deprecated
-
### Removed
- Agents.jl dependency (including `AgentBasedModel` and functions for adding/moving/removing agents)
-### Fixed
-
## [v0.4.1] - 2023-11-14
diff --git a/CONTRIBUTORS.md b/CONTRIBUTORS.md
index ce1b330..70d6208 100644
--- a/CONTRIBUTORS.md
+++ b/CONTRIBUTORS.md
@@ -2,28 +2,24 @@
### Lead developer
-- Daniel Vedder
+- Daniel Vedder (daniel.vedder@idiv.de)
+### Supervisor
-### Supporting developer(s)
-
-- Lea Kolb
+- Guy Pe'er (guy.peer@idiv.de)
+### Supporting developers
-### Code reviewer
+- Marco Matthies
+- Gabriel DÃaz Iturry
-- Ludmilla Figueiredo
+### Code reviewers
-### Supervisor
-
-- Guy Pe'er
-
+- Ludmilla Figueiredo
+- Marco Matthies
### Advisors
- Aletta Bonn
-
- Kerstin Wiegand
-
-- Birgit Müller
diff --git a/LICENSE b/LICENSE
index 16d4824..03fa7d5 100644
--- a/LICENSE
+++ b/LICENSE
@@ -1,6 +1,6 @@
MIT LICENSE
-Copyright (c) 2022-2023 Daniel Vedder, Lea Kolb
+Copyright (c) 2022-2024 Persefone.jl developers
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
diff --git a/README.md b/README.md
index 2b394d7..8281283 100644
--- a/README.md
+++ b/README.md
@@ -86,4 +86,4 @@ You can then access all Persefone functions, such as `simulate()`. (See
---
-© 2022-2023 the contributors (MIT license)
+© 2022-2024 the contributors (MIT license)
diff --git a/src/analysis/makieplots.jl b/src/analysis/makieplots.jl
index 739544a..7b1b901 100644
--- a/src/analysis/makieplots.jl
+++ b/src/analysis/makieplots.jl
@@ -4,7 +4,7 @@
###
"""
- visualisemap(model, date, landcovermap)
+ visualisemap(model, date, landcover)
Draw the model's land cover map and plot all individuals as points on it at
the specified date. If no date is passed, use the last date for which data
@@ -15,7 +15,10 @@ Returns a Makie figure object.
function visualisemap(model::SimulationModel,date=nothing,landcover=nothing)
# load and plot the map
# Note: if the landcover map is supplied, it needs to be rotr90'ed
- isnothing(landcover) && (landcover = rotr90(load(@param(world.landcovermap))))
+ if isnothing(landcover)
+ lcm = joinpath(@param(world.mapdirectory), @param(world.landcovermap))
+ landcover = rotr90(load(lcm))
+ end
f = Figure()
ax = Axis(f[1,1])
hidedecorations!(ax)
diff --git a/src/core/output.jl b/src/core/output.jl
index 9a3eefe..9842fef 100644
--- a/src/core/output.jl
+++ b/src/core/output.jl
@@ -32,7 +32,7 @@ end
"""
modellogger(loglevel, outdir, output="both")
-Create a logger object that writes output both to screen and to a logfile.
+Create a logger object that writes output to screen and/or a logfile.
This object is stored as `model.logger` and can then be used with `with_logger()`.
Note: requires [`createdatadir`](@ref) to be run first.
"""
@@ -51,6 +51,8 @@ function modellogger(loglevel::String, outdir::String, output::String="both")
return ConsoleLogger(logfile, loglevel)
elseif output == "screen"
return ConsoleLogger(stdout, loglevel)
+ elseif output == "none"
+ return NullLogger()
else
Base.error("Invalid log output target $output, should be file/screen/both.")
end
@@ -95,8 +97,8 @@ function saveinputfiles(model::SimulationModel)
TOML.print(f, prepareTOML(model.settings))
end
# Copy the map files to the output folder
- lcmap = @param(world.landcovermap)
- ffmap = @param(world.farmfieldsmap)
+ lcmap = joinpath(@param(world.mapdirectory), @param(world.landcovermap))
+ ffmap = joinpath(@param(world.mapdirectory), @param(world.farmfieldsmap))
#TODO replace errors with exceptions
!(isfile(lcmap)) && Base.error("The map file $(lcmap) doesn't exist.")
!(isfile(ffmap)) && Base.error("The map file $(ffmap) doesn't exist.")
diff --git a/src/core/simulation.jl b/src/core/simulation.jl
index fbc4235..05158aa 100644
--- a/src/core/simulation.jl
+++ b/src/core/simulation.jl
@@ -110,9 +110,11 @@ function initmodel(settings::Dict{String, Any})
settings["core.outdir"],
settings["core.logoutput"])
with_logger(logger) do
- landscape = initlandscape(settings["world.landcovermap"],
+ landscape = initlandscape(settings["world.mapdirectory"],
+ settings["world.landcovermap"],
settings["world.farmfieldsmap"])
- weather = initweather(settings["world.weatherfile"],
+ weather = initweather(joinpath(settings["world.mapdirectory"],
+ settings["world.weatherfile"]),
settings["core.startdate"],
settings["core.enddate"])
crops = readcropparameters(settings["crop.cropfile"],
diff --git a/src/nature/species/skylark.jl b/src/nature/species/skylark.jl
index 848858a..c9ecca8 100644
--- a/src/nature/species/skylark.jl
+++ b/src/nature/species/skylark.jl
@@ -4,13 +4,13 @@
###
skylarkhabitat = @habitat((@landcover() == grass ||
- # settle on grass or arable land (but not maize)
- (@landcover() == agriculture && @cropname() != "maize")) &&
- @distancetoedge() >= 5) # at least 50m from other habitats
- #XXX this ought to check for distance to forest and builtup,
- # but that's very expensive (see below)
- # @distanceto(forest) > 5 && # at least 50m from forest edges
- # @distanceto(builtup) > 5) # and from anthropogenic structures
+ # settle on grass or arable land (but not maize)
+ (@landcover() == agriculture && @cropname() != "maize")) &&
+ @distancetoedge() >= 5) # at least 50m from other habitats
+#XXX this ought to check for distance to forest and builtup,
+# but that's very expensive (see below)
+# @distanceto(forest) > 5 && # at least 50m from forest edges
+# @distanceto(builtup) > 5) # and from anthropogenic structures
"""
Skylark
@@ -30,32 +30,29 @@ At the moment, this implementation is still in development.
ISBN 3-89104-019-9
"""
@species Skylark begin
-
#XXX use Unitful.jl
- #TODO add type annotations
-
eggtime::Int64 = 11 # 11 days from laying to hatching
eggpredationmortality::Float64 = 0.03 # per-day egg mortality from predation
nestharvestmortality::Float64 = 0.9 # egg/nestling mortality after a harvest event (XXX guess)
- nestlingtime = 7:11 # 7-11 days from hatching to leaving nest
+ nestlingtime::Union{Int64,UnitRange{Int64}} = 7:11 # 7-11 days from hatching to leaving nest
nestlingpredationmortality::Float64 = 0.03 # per-day nestling mortality from predation
- fledglingtime = 25:30 # 25-30 days from hatching to independence
+ fledglingtime::Union{Int64,UnitRange{Int64}} = 25:30 # 25-30 days from hatching to independence
fledglingharvestmortality::Float64 = 0.5 # fledgling mortality after harvest
fledglingpredationmortality::Float64 = 0.01 # per-day fledgling mortality from predation
firstyearmortality::Float64 = 0.38 # total mortality in the first year after independence
- migrationdates = () # is defined by each individual in @create(Skylark)
+ migrationdates::Tuple = () # is defined by each individual in @create(Skylark)
migrationmortality::Float64 = 0.33 # chance of dying during the winter
mate::Int64 = -1 # the agent ID of the mate (-1 if none)
- nest = () # coordinates of current nest
- nestingbegin = (April, 10) # begin nesting in the middle of April
- nestbuildingtime = 4:5 # 4-5 days needed to build a nest (doubled for first nest)
+ nest::Tuple = () # coordinates of current nest
+ nestingbegin::Tuple{Int64,Int64} = (April, 10) # begin nesting in the middle of April
+ nestbuildingtime::Union{Int64,UnitRange{Int64}} = 4:5 # 4-5 days needed to build a nest (doubled for first nest)
nestcompletion::Int64 = 0 # days left until the nest is built
- eggsperclutch = 2:5 # 2-5 eggs laid per clutch
- clutch = [] # IDs of offspring in current clutch
+ eggsperclutch::Union{Int64,UnitRange{Int64}} = 2:5 # 2-5 eggs laid per clutch
+ clutch::Vector{Int64} = Vector{Int64}() # IDs of offspring in current clutch
breedingdelay::Int64 = 18 # wait 18 days after hatching to start a new brood
nestingend::Int64 = July # last month of nesting
@@ -68,7 +65,6 @@ As an egg, simply check for mortality and hatching.
@phase Skylark egg begin
@kill(self.eggpredationmortality, "predation")
@respond(harvesting, @kill(self.nestharvestmortality, "harvest"))
-
if self.age == self.eggtime
@setphase(nestling)
end
diff --git a/src/parameters.toml b/src/parameters.toml
index 272bb25..d956e37 100644
--- a/src/parameters.toml
+++ b/src/parameters.toml
@@ -10,7 +10,7 @@
configfile = "src/parameters.toml" # location of the configuration file
outdir = "results" # location and name of the output folder
overwrite = "ask" # overwrite the output directory? (true/false/"ask")
-logoutput = "both" # log output to screen/file/both
+logoutput = "both" # log output to screen/file/none/both
csvoutput = true # save collected data in CSV files
visualise = true # generate result graphs
storedata = true # keep collected data in memory
@@ -19,13 +19,14 @@ loglevel = "debug" # verbosity level: "debug", "info", "warn"
processors = 2 # number of processors to use on parallel runs
seed = 2 # seed value for the RNG (0 -> random value)
startdate = 2022-01-01 # first day of the simulation
-#enddate = 2022-12-31 # last day of the simulation
-enddate = 2022-03-31 # last day of the simulation (test value)
+enddate = 2022-12-31 # last day of the simulation
+#enddate = 2022-03-31 # last day of the simulation (test value)
[world]
-landcovermap = "data/regions/jena-small/landcover.tif" # location of the landcover map
-farmfieldsmap = "data/regions/jena-small/fields.tif" # location of the field geometry map
-weatherfile = "data/regions/jena-small/weather.csv" # location of the weather data file
+mapdirectory = "data/regions/jena-small" # the directory in which all geographic data are stored
+landcovermap = "landcover.tif" # name of the landcover map in the map directory
+farmfieldsmap = "fields.tif" # name of the field geometry map in the map directory
+weatherfile = "weather.csv" # name of the weather data file in the map directory
[farm]
farmmodel = "FieldManager" # which version of the farm model to use (not yet implemented)
diff --git a/src/world/landscape.jl b/src/world/landscape.jl
index f310cc6..36a47fe 100644
--- a/src/world/landscape.jl
+++ b/src/world/landscape.jl
@@ -38,13 +38,15 @@ mutable struct FarmEvent
end
"""
- initlandscape(landcovermap, farmfieldsmap)
+ initlandscape(directory, landcovermap, farmfieldsmap)
Initialise the model landscape based on the map files specified in the
configuration. Returns a matrix of pixels.
"""
-function initlandscape(landcovermap::String, farmfieldsmap::String)
+function initlandscape(directory::String, landcovermap::String, farmfieldsmap::String)
@debug "Initialising landscape"
+ landcovermap = joinpath(directory, landcovermap)
+ farmfieldsmap = joinpath(directory, farmfieldsmap)
#TODO replace errors with exception
!(isfile(landcovermap)) && Base.error("Landcover map $(landcovermap) doesn't exist.")
!(isfile(farmfieldsmap)) && Base.error("Field map $(farmfieldsmap) doesn't exist.")
diff --git a/test/runtests.jl b/test/runtests.jl
index db4870c..8540f05 100644
--- a/test/runtests.jl
+++ b/test/runtests.jl
@@ -31,10 +31,12 @@ function inittestmodel(smallmap=true)
if smallmap
landscape = smalltestlandscape()
else
- landscape = Ps.initlandscape(TESTSETTINGS["world.landcovermap"],
+ landscape = Ps.initlandscape(TESTSETTINGS["world.mapdirectory"],
+ TESTSETTINGS["world.landcovermap"],
TESTSETTINGS["world.farmfieldsmap"])
end
- weather = Ps.initweather(TESTSETTINGS["world.weatherfile"],
+ weather = Ps.initweather(joinpath(TESTSETTINGS["world.mapdirectory"],
+ TESTSETTINGS["world.weatherfile"]),
TESTSETTINGS["core.startdate"],
TESTSETTINGS["core.enddate"])
crops = Ps.readcropparameters(TESTSETTINGS["crop.cropfile"],
diff --git a/test/test_parameters.toml b/test/test_parameters.toml
index 3a24704..33413f8 100644
--- a/test/test_parameters.toml
+++ b/test/test_parameters.toml
@@ -21,6 +21,7 @@ startdate = 2022-02-01
enddate = 2022-03-31
[world]
+mapdirectory = "."
landcovermap = "landcover_jena.tif" # location of the landcover map
farmfieldsmap = "fields_jena.tif" # location of the field geometry map
weatherfile = "weather_jena.csv" # location of the weather data file
--
GitLab