Merge pull request #5 from MRC-CSO-SPHSU/develop

Version 0.1.2

README.md

@@ -6,3 +6,4 @@ Releases
 
 - **V0.1.0 (28.11.2022)** : The lone parent model (corresponding to LoneParentsModel.jl Version 0.6.1) based on the SocioEconomics.jl package V0.1.0 
    - V0.1.1 (29.11.2022)  : Simplified usage of SocioEconomics Library 
+   - V0.1.2 ( 1.12.2022)  : "data parameters" and loading / handling parameters from command line and input files is now part of SE library within ParamTypes module

lpm.jl

@@ -3,7 +3,7 @@ include("libspath.jl")
 using SocioEconomicsX: SEVERSION 
 using SocioEconomicsX: SEPATH, SESRCPATH 
 
-@assert SEVERSION == v"0.1.1" 
+@assert SEVERSION == v"0.1.2" 
 
 using SocioEconomicsX.ParamTypes
 

main.jl

@@ -5,7 +5,7 @@ using Random
 include("lpm.jl")
 
 # create parameters
-const simPars, pars = loadParameters(ARGS)
+const simPars, dataPars, pars = loadParameters(ARGS)
 pars.poppars.initialPop = 500  # Quick ad-hoc adjustment 
 
 # Atiyah: for more DRY Code, you may consider using 
@@ -14,7 +14,7 @@ pars.poppars.initialPop = 500  # Quick ad-hoc adjustment
 Random.seed!(simPars.seed)
 
 # create model object
-const model = setupModel(pars)
+const model = setupModel(dataPars, pars)
 
 # like this for CSV output:
 # const logfile = setupLogging(simPars, FS=",")

mainGui.jl

@@ -19,10 +19,10 @@ function main(parOverrides...)
     end
 
     # need to do that first, otherwise it blocks the GUI
-    simPars, pars, args = loadParameters(args, 
+    simPars, datapars, pars, args = loadParameters(args, 
         ["--gui-scale"], 
         Dict(:help => "set gui scale", :default => 1.0, :arg_type => Float64))
-    model = setupModel(pars)
+    model = setupModel(datapars, pars)
     logfile = setupLogging(simPars)
 
     scale = args[:gui_scale]

mainHelpers.jl

@@ -1,17 +1,5 @@
-
-using ArgParse
-
 using Utilities
 
-
-# TODO put into module somewhere?
-# Atiyah: Suggestion: as it is related to ParamTypes, it fits there
-#                     or another module for Data (though currently 
-#                     not that significant amount of code)
-include("$(SESRCPATH)/socioeconomics/demography/demographydata.jl")
-
-include("$(SESRCPATH)/handleParams.jl")
-
 include("analysis.jl")
 
 mutable struct Model
@@ -24,7 +12,7 @@ mutable struct Model
     deathMale :: Matrix{Float64}
 end
 
-function createDemography!(pars)
+function createDemography!(datapars, pars)
     ukTowns = createTowns(pars.mappars)
 
     ukHouses = Vector{PersonHouse}()
@@ -33,14 +21,9 @@ function createDemography!(pars)
     #ukPopulation = createPopulation(pars.poppars)
     ukPopulation = createPyramidPopulation(pars.poppars)
 
-    # Atiyah: For more DRY code, you may want to consider calling 
-    #         loadDemographyData(datapars) 
-    datp = pars.datapars
-    dir = SEPATH * "/" * datp.datadir
-
-    ukDemoData   = loadDemographyData(dir * "/" * datp.fertFName, 
-                                      dir * "/" * datp.deathFFName,
-                                      dir * "/" * datp.deathMFName)
+    # temporarily solution , input files and command line arguments 
+    #   should be invistigated 
+    ukDemoData   = loadDemographyData(datapars)
 
     Model(ukTowns, ukHouses, ukPopulation, 
             ukDemoData.fertility , ukDemoData.deathFemale, ukDemoData.deathMale)
@@ -110,85 +93,11 @@ function stepModel!(model, time, simPars, pars)
     append!(model.pop, babies)
 end
 
-
-function loadParameters(argv, cmdl...)
-	arg_settings = ArgParseSettings("run simulation", autofix_names=true)
-
-	@add_arg_table! arg_settings begin
-		"--par-file", "-p"
-            help = "parameter file"
-            default = ""
-        "--par-out-file", "-P"
-			help = "file name for parameter output"
-			default = "parameters.run.yaml"
-	end
-
-    if ! isempty(cmdl)
-        add_arg_table!(arg_settings, cmdl...)
-    end
-
-    # setup command line arguments with docs 
-
-	add_arg_group!(arg_settings, "Simulation Parameters")
-	fieldsAsArgs!(arg_settings, SimulationPars)
-
-    for t in fieldtypes(DemographyPars)
-        groupName =  String(nameOfParType(t)) * " Parameters"
-        add_arg_group!(arg_settings, groupName)
-        fieldsAsArgs!(arg_settings, t)
-    end
-
-    # parse command line
-	args = parse_args(argv, arg_settings, as_symbols=true)
-
-    # read parameters from file if provided or set to default
-    simpars, pars = loadParametersFromFile(args[:par_file])
-
-    # override values that were provided on command line
-
-    overrideParsCmdl!(simpars, args)
-
-    @assert typeof(pars) == DemographyPars
-    for f in fieldnames(DemographyPars)
-        overrideParsCmdl!(getfield(pars, f), args)
-    end
-
-    # Atiyah: for more DRY Code, you may consider using 
-    # LPM.ParamTypes.{seed!,reseed0!} within mainHelpers.jl 
-    # and remove the following call & the using statement 
-    # set time dependent seed
-    if simpars.seed == 0
-        simpars.seed = floor(Int, time())
-    end
-
-    # keep a record of parameters used (including seed!)
-    saveParametersToFile(simpars, pars, args[:par_out_file])
-
-    simpars, pars, args
-end
-
-
-function setupModel(pars)
-    model = createDemography!(pars)
+function setupModel(datapars,pars)
+    model = createDemography!(datapars,pars)
 
     initializeDemography!(model, pars.poppars, pars.workpars, pars.mappars)
 
-    #= 
-    Atiyah: this portion is not need any more. But if useful, could be 
-            attached with Logging level. 
-    @show "Town Samples: \n"     
-    @show model.towns[1:10]
-    println(); println(); 
-                            
-    @show "Houses samples: \n"      
-    @show model.houses[1:10]
-    println(); println(); 
-                            
-    @show "population samples : \n" 
-    @show model.pop[1:10]
-    println(); println(); 
-    =# 
-
     model
 end
 

mainMA.jl

@@ -16,7 +16,7 @@ const mainConfig = Light()    # no input files, logging or flags (REPL Exec.)
 const lpmExample = LPMUKDemography()    # remove deads
 # lpmExample = LPMUKDemographyOpt()   # don't remove deads 
 
-const simPars, pars = loadParameters(mainConfig) 
+const simPars, dataPars, pars = loadParameters(mainConfig) 
 
 # Most significant simulation and model parameters 
 # The following works only with Light() configuration
@@ -29,11 +29,11 @@ if mainConfig == Light()
     pars.poppars.initialPop = 500
 end
 
-const model = setupModel(pars)
+const model = setupModel(dataPars, pars)
 
 const logfile = setupLogging(simPars,mainConfig)
 
-const demoData = loadDemographyData(pars.datapars,SEPATH)
+const demoData = loadDemographyData(dataPars)
 
 const ukDemography = MAModel(model,pars,demoData)
 

mainMAHelpers.jl

@@ -5,7 +5,7 @@ addToLoadPath!("../MultiAgents.jl")
 
 using SocioEconomics: SEVERSION, SEPATH, SESRCPATH 
 
-@assert SEVERSION == v"0.1.1" 
+@assert SEVERSION == v"0.1.2" 
 
 using SocioEconomics.ParamTypes
 
@@ -37,16 +37,17 @@ struct WithInputFiles <: MainSim end   # Input parameter files
 struct Light <: MainSim end            # no input files 
 
 function loadParameters(::WithInputFiles) 
-    simPars, pars = loadParameters(ARGS)
+    simPars, dataPars, pars = loadParameters(ARGS)
     seed!(simPars)
-    simPars, pars 
+    simPars, dataPars, pars 
 end  
 
 function loadParameters(::Light)
     simPars = SimulationPars()
     seed!(simPars)
+    dataPars = DataPars() 
     pars = DemographyPars()
-    simPars, pars 
+    simPars, dataPars, pars 
 end
 
 setupLogging(simPars,::WithInputFiles) = setupLogging(simPars)