From dc00b4a291a8b15b9b5b200f34118f0022b44318 Mon Sep 17 00:00:00 2001
From: Daniel Vedder <daniel.vedder@idiv.de>
Date: Fri, 6 Sep 2024 11:44:35 +0200
Subject: [PATCH] Check package directory for input files
---
CHANGELOG.md | 14 ++++++++++++++
src/Persefone.jl | 2 +-
src/analysis/makieplots.jl | 2 +-
src/core/input.jl | 11 ++++++++++-
src/core/output.jl | 19 +++++++++++++++++++
src/core/utils.jl | 4 ----
src/crop/farmplot.jl | 2 +-
src/nature/macros.jl | 19 -------------------
src/parameters.toml | 14 +++++++-------
src/world/landscape.jl | 1 -
test/nature_tests.jl | 2 +-
11 files changed, 54 insertions(+), 36 deletions(-)
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 83e12b9..02f4db6 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -14,6 +14,20 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
*Plan: decouple CairoMakie (#81), fix & test ALMaSS, set up first experiments*
+### Added
+
+### Changed
+
+- `preprocessparameters()` checks whether the map directory is reachable from the current working
+ directory. If not, it checks whether it can be reached from the package directory. This makes
+ running simulations easier when Persefone has been installed as a package.
+
+### Deprecated
+
+### Removed
+
+### Fixed
+
---
## [0.5.5] - 09-08-2024
diff --git a/src/Persefone.jl b/src/Persefone.jl
index f5aa7b4..2b51908 100644
--- a/src/Persefone.jl
+++ b/src/Persefone.jl
@@ -22,7 +22,7 @@ using
DataFramesMeta,
Distributed,
FileIO,
- GeoArrays, #XXX this is another big dependency
+ GeoArrays, #XXX this is another big dependency - replace with Rasters.jl?
Logging,
LoggingExtras,
Random,
diff --git a/src/analysis/makieplots.jl b/src/analysis/makieplots.jl
index 70ba8ce..d03c32e 100644
--- a/src/analysis/makieplots.jl
+++ b/src/analysis/makieplots.jl
@@ -25,7 +25,7 @@ function visualisemap(model::SimulationModel,date=nothing,landcover=nothing)
image!(f[1,1], landcover)
ax.aspect = DataAspect()
# check if there are individuals and plot them
- inds = @subset(@data("individuals"), :X .== -1) #remove migrants
+ inds = @subset(@data("individuals"), :X .!= -1) #remove migrants
if iszero(size(inds)[1])
@debug "No individual data to map"
return f
diff --git a/src/core/input.jl b/src/core/input.jl
index e233382..2647835 100644
--- a/src/core/input.jl
+++ b/src/core/input.jl
@@ -93,8 +93,17 @@ function preprocessparameters(settings::Dict{String,Any}, defaultoutdir::String)
if settings["core.startdate"] > settings["core.enddate"]
Base.error("Enddate is earlier than startdate.") #TODO replace with exception
end
+ if !isdir(settings["world.mapdirectory"])
+ #TODO do equivalent check for crop directory, once this is implemented
+ # check if it's relative to the package directory
+ if isdir(abspath(pkgdir(@__MODULE__), settings["world.mapdirectory"]))
+ settings["world.mapdirectory"] = abspath(pkgdir(@__MODULE__), settings["world.mapdirectory"])
+ else
+ Base.error("Couldn't find map directory $(settings["world.mapdirectory"]).")
+ end
+ end
settings["world.mapresolution"] = settings["world.mapresolution"] * 1m
- if ! (settings["crop.cropmodel"] in AVAILABLE_CROPMODELS)
+ if !(settings["crop.cropmodel"] in AVAILABLE_CROPMODELS)
error("crop.cropmodel = \"$(settings["crop.cropmodel"])\", but has to be one of: $AVAILABLE_CROPMODELS")
end
#FIXME enable parallelisation
diff --git a/src/core/output.jl b/src/core/output.jl
index 4b3fd97..4144d8f 100644
--- a/src/core/output.jl
+++ b/src/core/output.jl
@@ -245,6 +245,25 @@ function record!(model::SimulationModel, outputname::String, data::Vector)
!(outputname in keys(model.dataoutputs)) && return #XXX should this be a warning?
push!(model.dataoutputs[outputname].databuffer, data)
end
+
+"""
+ @record(outputname, data)
+
+Record an observation / data point. Only use in scopes where `model` is available.
+"""
+macro record(args...)
+ :(record!($(esc(:model)), $(map(esc, args)...)))
+end
+
+"""
+ @data(outputname)
+
+Return the data stored in the given output (assumes `core.storedata` is true).
+Only use in scopes where `model` is available.
+"""
+macro data(outputname)
+ :(data($(esc(:model)).dataoutputs[$(esc(outputname))]))
+end
"""
visualiseoutput(model)
diff --git a/src/core/utils.jl b/src/core/utils.jl
index 607cafd..25d1b1d 100644
--- a/src/core/utils.jl
+++ b/src/core/utils.jl
@@ -53,10 +53,6 @@ AnnualDate(ad::String) = AnnualDate(Date(ad, dateformat"d U"))
Base.convert(::Type{AnnualDate}, ad::String) = AnnualDate(ad)
Base.tryparse(::Type{AnnualDate}, ad::String) = AnnualDate(ad)
-# allow creating AnnualDates from a string of the format "8 August"
-AnnualDate(ad::String) = AnnualDate(Date(ad, dateformat"d U"))
-Base.convert(::Type{AnnualDate}, ad::String) = AnnualDate(ad)
-
# Interface with Dates
AnnualDate(date::Date) = AnnualDate(month(date), day(date))
Base.convert(::Type{AnnualDate}, ad::Date) = AnnualDate(ad)
diff --git a/src/crop/farmplot.jl b/src/crop/farmplot.jl
index ecd4baf..c44d6ad 100644
--- a/src/crop/farmplot.jl
+++ b/src/crop/farmplot.jl
@@ -84,7 +84,7 @@ function isgrassland(farmplot::FarmPlot, model::SimulationModel)
if proportiongrass > 0.8
return true
elseif proportiongrass > 0.2
- @warn "Unclear classification: farm plot $(farmplot.id) has $(proportiongrass*100)% grass."
+ @debug "Unclear classification: farm plot $(farmplot.id) has $(proportiongrass*100)% grass."
proportiongrass >= 0.5 && return true
end
return false
diff --git a/src/nature/macros.jl b/src/nature/macros.jl
index 53da2a6..eb7f25c 100644
--- a/src/nature/macros.jl
+++ b/src/nature/macros.jl
@@ -522,25 +522,6 @@ macro lastyear(annualdate)
:(lastyear($(esc(annualdate)), $(esc(:model))))
end
-"""
- @record(outputname, data)
-
-Record an observation / data point. Only use in scopes where `model` is available.
-"""
-macro record(args...)
- :(record!($(esc(:model)), $(map(esc, args)...)))
-end
-
-"""
- @data(outputname)
-
-Return the data stored in the given output (assumes `core.storedata` is true).
-Only use in scopes where `model` is available.
-"""
-macro data(outputname)
- :(data($(esc(:model)).dataoutputs[$(esc(outputname))]))
-end
-
"""
@destroynest(reason)
diff --git a/src/parameters.toml b/src/parameters.toml
index 484c1a9..5b742db 100644
--- a/src/parameters.toml
+++ b/src/parameters.toml
@@ -5,7 +5,7 @@
###
### DO NOT MODIFY THIS FILE FOR SIMULATION EXPERIMENTS!
### Instead, copy it to another directory and modify the copy.
-
+
[core]
configfile = "src/parameters.toml" # location of the configuration file
outdir = "results" # location and name of the output folder
@@ -36,12 +36,12 @@ fieldoutfreq = "daily" # output frequency for crop/field data, daily/monthly/yea
[nature]
#targetspecies = ["Wolpertinger", "Wyvern"] # list of target species to simulate - example species
-targetspecies = [] # XXX disable all species for farm model testing
-#targetspecies = ["Skylark"] # list of target species to simulate
-popoutfreq = "never" # output frequency population-level data, daily/monthly/yearly/end/never
-indoutfreq = "never" # output frequency individual-level data, daily/monthly/yearly/end/never
-#popoutfreq = "daily" # output frequency population-level data, daily/monthly/yearly/end/never
-#indoutfreq = "end" # output frequency individual-level data, daily/monthly/yearly/end/never
+#targetspecies = [] # XXX disable all species for farm model testing
+targetspecies = ["Skylark"] # list of target species to simulate
+#popoutfreq = "never" # output frequency population-level data, daily/monthly/yearly/end/never
+#indoutfreq = "never" # output frequency individual-level data, daily/monthly/yearly/end/never
+popoutfreq = "daily" # output frequency population-level data, daily/monthly/yearly/end/never
+indoutfreq = "end" # output frequency individual-level data, daily/monthly/yearly/end/never
insectmodel = ["season", "habitat", "pesticides", "weather"] # factors affecting insect growth
[crop]
diff --git a/src/world/landscape.jl b/src/world/landscape.jl
index afbc6d7..a9d0454 100644
--- a/src/world/landscape.jl
+++ b/src/world/landscape.jl
@@ -54,7 +54,6 @@ function initlandscape(directory::String, landcovermap::String, farmfieldsmap::S
#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.")
- #XXX can I read the files in using FileIO, to avoid the GeoArrays dependency?
# read in TIFFs, replacing missing values with 0
landcover = coalesce(GeoArrays.read(landcovermap), 0)
farmfields = coalesce(GeoArrays.read(farmfieldsmap), 0)
diff --git a/test/nature_tests.jl b/test/nature_tests.jl
index b0d7e3c..d4b723e 100644
--- a/test/nature_tests.jl
+++ b/test/nature_tests.jl
@@ -39,7 +39,7 @@ end
habitat = @habitat(@landcover() == water)
pairs=true
end
-
+
end) # end eval
## Test sets
--
GitLab