diff --git a/CHANGELOG.md b/CHANGELOG.md
index 02f4db6a62c29aed709a41a5f1fb5ae4922486db..a9d18b0df29d45fa82b13bec6b9c2fff70e7037c 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,22 +10,28 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
*Aim: 3 species, 2 crop growth models, farm model, GAEC scenarios, experimental analysis*
-## [0.6.0] - in planning
+## [0.6.0] - unreleased
*Plan: decouple CairoMakie (#81), fix & test ALMaSS, set up first experiments*
### Added
+- `crop.cropdirectory` parameter specifies folder in which all crop data files for the
+ selected crop model can be found.
+
### 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.
+- `preprocessparameters()` checks whether the map and crop directories are 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
+- `crop.cropfile` and `crop.growthfile` parameters -> user configuration is now done via
+ `crop.cropdirectory`, names of ALMaSS input files are specified as constants in `almass.jl`
+
### Fixed
---
diff --git a/data/crops/almass/almass_crop_growth_curves.csv b/data/crops/almass/crop_growth_curves.csv
similarity index 100%
rename from data/crops/almass/almass_crop_growth_curves.csv
rename to data/crops/almass/crop_growth_curves.csv
diff --git a/src/core/input.jl b/src/core/input.jl
index 26478351958dfaa3729f337ea9bc008a64034762..803c9ab8121aaec2abcbd9de2a6c6f0e620c5424 100644
--- a/src/core/input.jl
+++ b/src/core/input.jl
@@ -85,24 +85,35 @@ Take the raw input parameters and process them where necessary (e.g. convert typ
perform checks). This is a helper function for [`getsettings`](@ref).
"""
function preprocessparameters(settings::Dict{String,Any}, defaultoutdir::String)
+ # miscellaneous processing
(settings["core.seed"] == 0) && (settings["core.seed"] = abs(rand(RandomDevice(), Int32)))
+ settings["world.mapresolution"] = settings["world.mapresolution"] * 1m
+ # create a standardised name for the output directory
if settings["core.outdir"] == defaultoutdir
outdir = defaultoutdir*"_"*string(Dates.today())*"_s"*string(settings["core.seed"])
settings["core.outdir"] = outdir
end
- if settings["core.startdate"] > settings["core.enddate"]
- Base.error("Enddate is earlier than startdate.") #TODO replace with exception
- end
+ # check if input data are present in the working directory or the package directory
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"])
+ @debug "Using package directory to load map data: $(settings["world.mapdirectory"])".
else
Base.error("Couldn't find map directory $(settings["world.mapdirectory"]).")
end
end
- settings["world.mapresolution"] = settings["world.mapresolution"] * 1m
+ if !isdir(settings["crop.cropdirectory"])
+ if isdir(abspath(pkgdir(@__MODULE__), settings["crop.cropdirectory"]))
+ settings["crop.cropdirectory"] = abspath(pkgdir(@__MODULE__), settings["crop.cropdirectory"])
+ @debug "Using package directory to load crop data: $(settings["crop.cropdirectory"])".
+ else
+ Base.error("Couldn't find map directory $(settings["crop.cropdirectory"]).")
+ end
+ end
+ # sanity checks
+ if settings["core.startdate"] > settings["core.enddate"]
+ Base.error("Enddate is earlier than startdate.") #TODO replace with exception
+ end
if !(settings["crop.cropmodel"] in AVAILABLE_CROPMODELS)
error("crop.cropmodel = \"$(settings["crop.cropmodel"])\", but has to be one of: $AVAILABLE_CROPMODELS")
end
diff --git a/src/core/simulation.jl b/src/core/simulation.jl
index 5d150d541db8b52cf919c9e8c7bd0f2afebc8d82..4d227a07d636019a1a3aacfcf75a50d7c2d7ce8a 100644
--- a/src/core/simulation.jl
+++ b/src/core/simulation.jl
@@ -117,8 +117,7 @@ function initmodel(settings::Dict{String, Any})
settings["core.startdate"],
settings["core.enddate"])
crops, Tcroptype, Tcropstate = initcropmodel(settings["crop.cropmodel"],
- settings["crop.cropfile"],
- settings["crop.growthfile"])
+ settings["crop.cropdirectory"])
farmers = Vector{Farmer}()
farmplots = Vector{FarmPlot{Tcropstate}}()
model = AgricultureModel{Tcroptype,Tcropstate}(
diff --git a/src/crop/almass.jl b/src/crop/almass.jl
index eb7db59037c188e707de12c30e65eb43c0aacf49..a3d47c238c953b703ad3dccd72b6eac9d0efec7d 100644
--- a/src/crop/almass.jl
+++ b/src/crop/almass.jl
@@ -11,6 +11,10 @@
module ALMaSS
+## The two input files required by ALMaSS. Must be present in the crop directory.
+const CROPFILE = "crop_data_general.csv"
+const GROWTHFILE = "crop_growth_curves.csv"
+
using Persefone:
AnnualDate,
Management,
@@ -152,16 +156,16 @@ function buildgrowthcurve(data::Vector{CSV.Row})
end
"""
- readcropparameters(generalcropfile, cropgrowthfile)
+ readcropparameters(cropdirectory)
Parse a CSV file containing the required parameter values for each crop
(as produced from the original ALMaSS file by `convert_almass_data.py`).
"""
-function readcropparameters(generalcropfile::String, growthfile::String)
+function readcropparameters(cropdirectory::String)
@debug "Reading crop parameters"
- cropdata = CSV.File(generalcropfile, missingstring="NA",
+ cropdata = CSV.File(joinpath(cropdirectory, CROPFILE), missingstring="NA",
types=[String,AnnualDate,AnnualDate,AnnualDate,AnnualDate,Float64,String])
- growthdata = CSV.File(growthfile, missingstring="NA",
+ growthdata = CSV.File(joinpath(cropdirectory, GROWTHFILE), missingstring="NA",
types=[Int,String,String,GrowthPhase,String,
Float64,Float64,Float64,Float64])
croptypes = Dict{String,CropType}()
diff --git a/src/crop/cropmodels.jl b/src/crop/cropmodels.jl
index 8653a1439e8d0a5dcfe14b09c326ef9a4a0a3bad..83497fd176c08ea39f33e4c618fc37d624a57bcc 100644
--- a/src/crop/cropmodels.jl
+++ b/src/crop/cropmodels.jl
@@ -9,11 +9,11 @@
Initialise the crop model. Returns the crop types available in the
simulation, as well as the types `Tcroptype` and `Tcropstate`.
"""
-function initcropmodel(cropmodel::AbstractString, cropfile::AbstractString, growthfile::AbstractString)
+function initcropmodel(cropmodel::AbstractString, cropdirectory::AbstractString)
if cropmodel == "almass"
Tcroptype = ALMaSS.CropType
Tcropstate = ALMaSS.CropState
- crops = ALMaSS.readcropparameters(cropfile, growthfile)
+ crops = ALMaSS.readcropparameters(cropdirectory)
elseif cropmodel == "simple"
Tcroptype = SimpleCrop.CropType
Tcropstate = SimpleCrop.CropState
diff --git a/src/nature/species/skylark.jl b/src/nature/species/skylark.jl
index feaa063a7be5e538c88895f2bef913bc8d06e965..811301065aa4a51a0982c3da05003642d98ce2fc 100644
--- a/src/nature/species/skylark.jl
+++ b/src/nature/species/skylark.jl
@@ -163,7 +163,7 @@ Females returning from migration move around to look for a suitable partner with
# ...check if he is still alive and the female wants to stay with him
#XXX is mate-faithfulness decided by the female when she returns,
# or by the male taking whichever female comes to him first?
- @debug "$(animalid(self)) and $(animalid(n)) have mated again."
+ @debug "$(animalid(self)) and $(self.mate) have mated again."
@setphase(nesting)
return
else
diff --git a/src/parameters.toml b/src/parameters.toml
index 5b742db393bc02a17f13f33895adf18443b11cc0..0cb6ea75c6cce17d5fe3cf81f286801ca19f5732 100644
--- a/src/parameters.toml
+++ b/src/parameters.toml
@@ -46,6 +46,5 @@ insectmodel = ["season", "habitat", "pesticides", "weather"] # factors affecting
[crop]
cropmodel = "almass" # crop growth model to use, "almass", "aquacrop", or "simple"
-cropfile = "data/crops/almass/crop_data_general.csv" # file with general crop parameters
-growthfile = "data/crops/almass/almass_crop_growth_curves.csv" # file with crop growth parameters
+cropdirectory = "data/crops/almass" # the directory storing all data files for the selected crop model