Set up logging functionality

Manifest.toml

@@ -2,7 +2,7 @@
 
 julia_version = "1.8.2"
 manifest_format = "2.0"
-project_hash = "3094d3134b943670349bd9f535622ba576264330"
+project_hash = "410e4f52e8705498e2b8e0db499b81897c7f31a9"
 
 [[deps.AbstractFFTs]]
 deps = ["ChainRulesCore", "LinearAlgebra"]

Project.toml

@@ -9,5 +9,6 @@ ArgParse = "c7e460c6-2fb9-53a9-8c5b-16f535851c63"
 Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
 GeoArrays = "2fb1d81b-e6a0-5fc5-82e6-8e06903437ab"
 Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
+LoggingExtras = "e6f89c97-d47a-5376-807f-9c37f3926c36"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 TOML = "fa267f1f-6049-4f14-aa54-33bafae1ed76"

data/config.toml

-### Persephone - a socio-economic-ecological model of European agricultural landscapes.
-###
-### This is an example configuration file for development.
-### Note: the reference version is at src/parameters.toml
-###
-
-[core]
-configfile = "data/config.toml" # location of the configuration file
-mapfile = "data/region_hohenlohe.tif" # location of the map file
-outdir = "results" # location and name of the output folder
-logfile = "simulation.log" # name of the log file
-loglevel = "debug" # verbosity level: "debug", "normal", "errors"
-runtime = 5 # duration in days that the simulation will run for
-seed = 0 # seed value for the RNG (0 -> random value)
-
-[farm]
-
-
-[ecology]
-
-[crop]
-cropmodel = "linear" # crop growth model to use, "linear" or "aquacrop" (not yet implemented)
-

src/Persephone.jl

@@ -18,6 +18,7 @@ using
     Dates,
     GeoArrays,
     Logging,
+    LoggingExtras,
     Random,
     TOML
 

src/core/input.jl

@@ -83,10 +83,15 @@ end
 Certain software parameters can be set via the commandline.
 """
 function parsecommandline()
-    s = ArgParseSettings()
+    versionstring = """
+            Persephone $(@project_version), commit $(read(`git rev-parse HEAD`, String)[1:8])
+            © 2022 Daniel Vedder, Lea Kolb (MIT license)
+            https://git.idiv.de/xo30xoqa/persephone
+            """
+    s = ArgParseSettings(add_version=true, version=versionstring)
     @add_arg_table! s begin
         "--configfile", "-c"
-            help = "name of the config file"
+            help = "name of the configuration file"
             arg_type = String
             required = false
         "--seed", "-s"
@@ -101,13 +106,13 @@ function parsecommandline()
             arg_type = String
             required = false
         "--loglevel", "-l"
-            help = "verbosity: \"debug\", \"normal\", or \"errors\""
+            help = "verbosity: \"debug\", \"info\", or \"errors\""
             arg_type = String
             required = false
         "--runtime", "-r"
-           help = "duration in days that the simulation will run"
-           arg_type = Int
-           required = false
+            help = "duration in days that the simulation will run"
+            arg_type = Int
+            required = false
     end
     args = parse_args(s)
     for a in keys(args)

src/core/output.jl

@@ -3,7 +3,7 @@
 ### This file includes functions for saving the model output.
 ###
 
-## Note: some of this code was adapted from the GeMM model by Leidinger et al.
+## Note: `setupdatadir()` was adapted from the GeMM model by Leidinger et al.
 ## (https://github.com/CCTB-Ecomods/gemm/blob/master/src/output.jl)
 
 """
@@ -22,6 +22,17 @@ function setupdatadir()
     else
         mkpath(param("core.outdir"))
     end
+    # Setup the logging system and logfile
+    loglevel = Logging.Info
+    if param("core.loglevel") == "debug"
+        loglevel = Logging.Debug
+    elseif param("core.loglevel") == "quiet"
+        loglevel = Logging.Warn
+    end
+    logfile = open(joinpath(param("core.outdir"), "simulation.log"), "w+")
+    simulationlogger = TeeLogger(ConsoleLogger(logfile, loglevel),
+                                 ConsoleLogger(stdout, loglevel))
+    global_logger(simulationlogger)
     @info "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
@@ -35,6 +46,7 @@ function setupdatadir()
     end
     # Copy the map file to the output folder
     mapf = param("core.mapfile")
-    !(isfile(mapf)) && @error "The map file $(mapf) doesn't exist."
+    !(isfile(mapf)) && Base.error("The map file $(mapf) doesn't exist.")
     cp(mapf, joinpath(param("core.outdir"), basename(mapf)), force = true)
 end
+

src/core/simulation.jl

@@ -8,15 +8,16 @@ function initsim(config::String)
     Random.seed!(param("core.seed"))
     setupdatadir()
     #TODO create world
+    @info "Simulation initialised."
 end
 
 function stepsim()
-    println("Simulating another day.")
+    @info "Simulating another day."
     #TODO
 end
 
 function finalisesim()
-    println("Simulation ran. Nothing happened. But it will!")
+    @info "Simulation ran. Nothing happened. But it will!"
     #TODO
 end
 

src/parameters.toml

@@ -10,8 +10,7 @@
 configfile = "src/parameters.toml" # location of the configuration file
 mapfile = "data/region_jena.tif" # location of the map file
 outdir = "results" # location and name of the output folder
-logfile = "simulation.log" # name of the log file
-loglevel = "debug" # verbosity level: "debug", "normal", "errors"
+loglevel = "debug" # verbosity level: "debug", "info", "quiet"
 runtime = 10 # duration in days that the simulation will run for
 seed = 0 # seed value for the RNG (0 -> random value)