code changes minor

src-old/MadsDocumentation.jl

@@ -19,7 +19,6 @@ function getfunctionargumentsold(f::Function, m::Base.MethodList, l::Integer=get
 	end
 	return sort(unique(mp))
 end
-
 @doc """
 Get function arguments
 
@@ -54,7 +53,6 @@ function getfunctionkeywordsold(f::Function, m::Base.MethodList, l::Integer=getm
 	end
 	return sort(unique(mp))
 end
-
 @doc """
 Get function keywords
 

src-old/MadsPlotPy.jl

@@ -63,7 +63,6 @@ function plotgrid(madsdata::AbstractDict, parameters::AbstractDict; addtitle::Bo
 		plotgrid(madsdata, s; addtitle=addtitle, title=title, filename=filename, format=format)
 	end
 end
-
 @doc """
 Plot a 3D grid solution based on model predictions in array `s`, initial parameters, or user provided parameter values
 

src/MadsAnasol.jl

@@ -507,7 +507,6 @@ function computemass(madsfiles::Union{Regex,String}; time::Number=0, path::Abstr
 	end
 	return lambda, mass_injected, mass_reduced
 end
-
 @doc """
 Compute injected/reduced contaminant mass (for a given set of mads input files when "path" is provided)
 

src/MadsBayesInfoGap.jl

@@ -41,7 +41,7 @@ function makebigdt!(madsdata::AbstractDict, choice::AbstractDict)
 		madsinfo("Decision parameter $(paramname) set to $c.")
 	end
 	makeloglikelihood = makearrayconditionalloglikelihood(madsdata)
-	logprior = makearrayfunction(madsdata, makelogprior(madsdata))
+	logprior = Mads.makearrayfunction(madsdata, makelogprior(madsdata))
 	nominalparams = getparamsinit(madsdata)
 	f = makemadscommandfunction(madsdata; calczeroweightobs=true, calcpredictions=true)
 	function likelihoodparamsmax(horizon::Real)

src/MadsCreate.jl

@@ -297,7 +297,6 @@ function createproblem(madsdata::AbstractDict, predictions::AbstractDict)
 	end
 	return madsdata_c
 end
-
 @doc """
 Create a new Mads problem where the observation targets are computed based on the model predictions
 

src/MadsDisplay.jl

@@ -137,7 +137,6 @@ function display(o; gwo=nothing, gho=nothing, gw=gwo, gh=gho)
 		print("\r")
 	end
 end
-
 @doc """
 Display image file
 

src/MadsExecute.jl

@@ -22,7 +22,6 @@ function checknodedir(dir::AbstractString, waittime::Float64=10.) # 10 seconds
 	end
 	return true
 end
-
 @doc """
 Check if a directory is readable
 
@@ -111,7 +110,6 @@ function runcmd(cmdstring::AbstractString; quiet::Bool=Mads.quiet, pipe::Bool=fa
 	end
 	return r
 end
-
 @doc """
 Run external command and pipe stdout and stderr
 

src/MadsFunc.jl

@@ -352,7 +352,6 @@ function makemadsreusablefunction(paramkeys::AbstractVector, obskeys::AbstractVe
 		return madscommandfunction
 	end
 end
-
 @doc """
 Make Reusable Mads function to execute a forward model simulation (automatically restarts if restart data exists)
 
@@ -382,8 +381,7 @@ Returns:
 
 - restart directory where reusable model results will be stored
 """
-function getrestartdir(madsdata::AbstractDict, suffix::AbstractString="")
-	restartdir = ""
+function getrestartdir(madsdata::AbstractDict, suffix::AbstractString="", restartdir::AbstractString="")
 	if haskey(madsdata, "RestartDir")
 		restartdir = madsdata["RestartDir"]
 		if !isdir(restartdir)
@@ -409,7 +407,11 @@ function getrestartdir(madsdata::AbstractDict, suffix::AbstractString="")
 		end
 	end
 	if restartdir == ""
-		restartdir = getmadsrootname(madsdata; version=true) * "_restart"
+		rdir = getmadsrootname(madsdata; version=true)
+		if rdir == ""
+			return rdir
+		end
+		restartdir = rdir * "_restart"
 		if !isdir(restartdir)
 			try
 				recursivemkdir(restartdir; filename=false)
@@ -419,7 +421,7 @@ function getrestartdir(madsdata::AbstractDict, suffix::AbstractString="")
 			end
 		end
 	end
-	if suffix != ""
+	if suffix != "" && restartdir != ""
 		restartdir = joinpath(restartdir, suffix)
 		recursivemkdir(restartdir; filename=false)
 	end

src/MadsHelp.jl

@@ -128,7 +128,6 @@ function functions(m::Union{Symbol, Module}, string::AbstractString=""; shortout
 	n > 0 && string == "" && @info("Number of functions in module $m: $n")
 	return functions
 end
-
 @doc """
 List available functions in the MADS modules:
 

src/MadsHelpers.jl

@@ -309,7 +309,6 @@ function haskeyword(madsdata::AbstractDict, class::AbstractString, keyword::Abst
 		return false
 	end
 end
-
 @doc """
 Check for a `keyword` in a `class` within the Mads dictionary `madsdata`
 
@@ -345,7 +344,6 @@ function addkeyword!(madsdata::AbstractDict, class::AbstractString, keyword::Abs
 		push!(madsdata[class], keyword)
 	end
 end
-
 @doc """
 Add a `keyword` in a `class` within the Mads dictionary `madsdata`
 
@@ -373,7 +371,6 @@ function deletekeyword!(madsdata::AbstractDict, class::AbstractString, keyword::
 		end
 	end
 end
-
 @doc """
 Delete a `keyword` in a `class` within the Mads dictionary `madsdata`
 

src/MadsIO.jl

@@ -808,7 +808,6 @@ function setnewmadsfilename(filename::AbstractString)
 	end
 	return joinpath(dir, filename)
 end
-
 @doc """
 Set new mads file name
 
@@ -1079,7 +1078,6 @@ end
 
 searchdir(key::Regex; path::AbstractString = ".") = filter(x->occursin(key, x), readdir(path))
 searchdir(key::AbstractString; path::AbstractString = ".") = filter(x->occursin(key, x), readdir(path))
-
 @doc """
 Get files in the current directory or in a directory defined by `path` matching pattern `key` which can be a string or regular expression
 
@@ -1102,7 +1100,6 @@ Examples:
 
 filterkeys(dict::AbstractDict, key::Regex) = key == r"" ? collect(keys(dict)) : filter(x->occursin(key, x), collect(keys(dict)))
 filterkeys(dict::AbstractDict, key::AbstractString = "") = key == "" ? collect(keys(dict)) : filter(x->occursin(key, x), collect(keys(dict)))
-
 @doc """
 Filter dictionary keys based on a string or regular expression
 
@@ -1113,7 +1110,6 @@ argtext=Dict("dict"=>"dictionary",
 
 indexkeys(dict::AbstractDict, key::Regex) = key == r"" ? findall(collect(keys(dict))) : findall(x->occursin(key, x), collect(keys(dict)))
 indexkeys(dict::AbstractDict, key::AbstractString = "") = key == "" ? findall(collect(keys(dict))) : findall(x->occursin(key, x), collect(keys(dict)))
-
 @doc """
 Find indexes for dictionary keys based on a string or regular expression
 
@@ -1124,7 +1120,6 @@ argtext=Dict("dict"=>"dictionary",
 
 getdictvalues(dict::AbstractDict, key::Regex) = map(y->(y, dict[y]), filterkeys(dict, key))
 getdictvalues(dict::AbstractDict, key::AbstractString = "") = map(y->(y, dict[y]), filterkeys(dict, key))
-
 @doc """
 Get dictionary values for keys based on a string or regular expression
 

src/MadsKriging.jl

@@ -205,7 +205,6 @@ end
 function estimationerror(w::AbstractVector, covmat::AbstractMatrix, covvec::AbstractVector, cov0::Number)
 	return cov0 + LinearAlgebra.dot(w, covmat * w) - 2 * LinearAlgebra.dot(w, covvec)
 end
-
 @doc """
 Estimate kriging error
 

src/MadsLevenbergMarquardt.jl

@@ -33,7 +33,6 @@ function residuals(madsdata::AbstractDict)
 	resultdict = Mads.forward(madsdata)
 	residuals(madsdata, collect(values(resultdict)))
 end
-
 @doc """
 Compute residuals
 
@@ -79,7 +78,6 @@ function of(madsdata::AbstractDict; filter::Union{AbstractVector,AbstractRange,C
 	resultdict = Mads.forward(madsdata)
 	of(madsdata, collect(values(resultdict)); filter=filter)
 end
-
 @doc """
 Compute objective function
 
@@ -249,7 +247,6 @@ function makelmfunctions(madsdata::AbstractDict; parallel_gradients::Bool=parall
 	end
 	return f_lm, g_lm, o_lm
 end
-
 @doc """
 Make forward model, gradient, objective functions needed for Levenberg-Marquardt optimization
 

src/MadsMisc.jl

@@ -3,16 +3,18 @@ import OrderedCollections
 import DocumentFunction
 import Printf
 
-#=
-function makearrayfunction_vector(madsdata::AbstractDict, f::Function=makemadscommandfunction(madsdata))
-	function arrayfunction(arrayparameters::AbstractVector)
-		return f(arrayparameters)
-	end
-	return arrayfunction
-end
-=#
+"""
+Make a version of the function `f` that accepts an array containing the optimal parameter values
 
-function makearrayfunction_dictionary(madsdata::AbstractDict, f::Function=makemadscommandfunction(madsdata))
+$(DocumentFunction.documentfunction(makearrayfunction;
+argtext=Dict("madsdata"=>"MADS problem dictionary",
+            "f"=>"function [default=`makemadscommandfunction(madsdata)`]")))
+
+Returns:
+
+- function accepting an array containing the optimal parameter values
+"""
+function makearrayfunction(madsdata::AbstractDict, f::Function=makemadscommandfunction(madsdata))
 	optparamkeys = getoptparamkeys(madsdata)
 	initparams = Mads.getparamdict(madsdata)
 	function arrayfunction_merge(arrayparameters::AbstractVector)
@@ -30,25 +32,8 @@ function makearrayfunction_dictionary(madsdata::AbstractDict, f::Function=makema
 	end
 end
 
-function makearrayfunction(madsdata::AbstractDict, f::Function=makemadscommandfunction(madsdata))
-	# arrayfunction = vectorflag ? makearrayfunction_vector(madsdata, f) : makearrayfunction_dictionary(madsdata, f)
-	makearrayfunction_dictionary(madsdata, f)
-end
-
-@doc """
-Make a version of the function `f` that accepts an array containing the optimal parameter values
-
-$(DocumentFunction.documentfunction(makearrayfunction;
-argtext=Dict("madsdata"=>"MADS problem dictionary",
-            "f"=>"function [default=`makemadscommandfunction(madsdata)`]")))
-
-Returns:
-
-- function accepting an array containing the optimal parameter values
-""" makearrayfunction
-
 function makedoublearrayfunction_vector(madsdata::AbstractDict, f::Function=makemadscommandfunction(madsdata))
-	arrayfunction = makearrayfunction(madsdata, f)
+	arrayfunction = Mads.makearrayfunction(madsdata, f)
 	function doublearrayfunction(arrayparameters::AbstractMatrix)
 		nr = size(arrayparameters, 2)
 		vectorresult = Array{Float64}(undef, nr)
@@ -61,7 +46,7 @@ function makedoublearrayfunction_vector(madsdata::AbstractDict, f::Function=make
 end
 
 function makedoublearrayfunction_dictionary(madsdata::AbstractDict, f::Function=makemadscommandfunction(madsdata))
-	arrayfunction = makearrayfunction(madsdata, f)
+	arrayfunction = Mads.makearrayfunction(madsdata, f)
 	obskeys = getobskeys(madsdata)
 	function doublearrayfunction(arrayparameters::AbstractVector)
 		dictresult = arrayfunction(arrayparameters)
@@ -75,11 +60,9 @@ function makedoublearrayfunction_dictionary(madsdata::AbstractDict, f::Function=
 	end
 	return doublearrayfunction
 end
-
 function makedoublearrayfunction(madsdata::AbstractDict, f::Function=makemadscommandfunction(madsdata))
 	doublearrayfunction = vectorflag ? makedoublearrayfunction_vector(madsdata, f) : makedoublearrayfunction_dictionary(madsdata, f)
 end
-
 @doc """
 Make a version of the function `f` that accepts an array containing the optimal parameter values, and returns an array of observations
 

src/MadsModules.jl

@@ -379,7 +379,6 @@ function tag(madsmodule::AbstractString, versionsym::Symbol=:patch)
 		@warn("$(madsmodule) cannot be tagged!")
 	end
 end
-
 @doc """
 Tag Mads modules with a default argument `:patch`
 

src/MadsMonteCarlo.jl

@@ -184,6 +184,9 @@ function emceesampling(madsdata::AbstractDict, p0::AbstractMatrix; filename::Abs
 		arrayloglikelihood = (x)->Core.eval(Main, :arrayloglikelihood_distributed)(x)
 	end
 	numsamples_perwalker_burnin = div(burnin, numwalkers)
+	if numsamples_perwalker_burnin == 0
+		numsamples_perwalker_burnin = 10
+	end
 	numsamples = numsamples_perwalker_burnin * numwalkers
 	@info("AffineInvariantMCMC burning stage (total number of executions $(numsamples), final burning chain size $(numsamples_perwalker_burnin * numwalkers))...")
 	burninchain, _ = AffineInvariantMCMC.sample(arrayloglikelihood, numwalkers, p0, numsamples_perwalker_burnin, 1; filename="", load=false, save=false, rng=Mads.rng)

src/MadsObservations.jl

@@ -274,7 +274,6 @@ function setobstime!(madsdata::AbstractDict, rx::Regex, obskeys::AbstractVector=
 		end
 	end
 end
-
 @doc """
 Set observation time based on the observation name in the MADS problem dictionary
 
@@ -301,7 +300,6 @@ function setobsweights!(madsdata::AbstractDict, v::AbstractVector, obskeys::Abst
 		setweight!(madsdata["Observations"][obskeys[i]], v[i])
 	end
 end
-
 @doc """
 Set observation weights in the MADS problem dictionary
 
@@ -530,7 +528,6 @@ function createobservations!(madsdata::AbstractDict, observation::AbstractDict;
 	end
 	madsdata["Observations"] = observationsdict
 end
-
 @doc """
 Create observations in the MADS problem dictionary based on `time` and `observation` vectors
 

src/MadsParallel.jl

@@ -252,7 +252,6 @@ function setdir()
 	dir = Distributed.remotecall_fetch(()->pwd(), 1)
 	setdir(dir)
 end
-
 @doc """
 Set the working directory (for parallel environments)
 

src/MadsParameters.jl

@@ -395,7 +395,6 @@ function getoptparams(madsdata::AbstractDict, parameterarray::AbstractArray=getp
 		return parameterarray
 	end
 end
-
 @doc """
 Get optimizable parameters
 
@@ -954,7 +953,6 @@ function boundparameters!(madsdata::AbstractDict, pardict::AbstractDict)
 	end
 	return nothing
 end
-
 @doc """
 Bound model parameters based on their ranges
 

src/MadsPlot.jl

@@ -381,7 +381,6 @@ function plotmatches(madsdata::AbstractDict, dict_in::AbstractDict; plotdata::Bo
 	end
 	return nothing
 end
-
 @doc """
 Plot the matches between model predictions and observations
 
@@ -585,7 +584,6 @@ function plotwellSAresults(madsdata::AbstractDict, result::AbstractDict, wellnam
 	!quiet && Mads.display(p; gw=8Gadfly.inch, gh=vsize)
 	return nothing
 end
-
 @doc """
 Plot the sensitivity analysis results for all the wells in the MADS problem dictionary (wells class expected)
 
@@ -836,7 +834,6 @@ function spaghettiplots(madsdata::AbstractDict, paramdictarray::OrderedCollectio
 	end
 	return nothing
 end
-
 @doc """
 Generate separate spaghetti plots for each `selected` (`type != null`) model parameter
 
@@ -1035,7 +1032,6 @@ function spaghettiplot(madsdata::AbstractDict, matrix::AbstractMatrix; plotdata:
 	!quiet && Mads.display(pl; gw=8Gadfly.inch, gh=vsize)
 	return nothing
 end
-
 @doc """
 Generate a combined spaghetti plot for the `selected` (`type != null`) model parameter
 
@@ -1112,7 +1108,6 @@ function plotseries(X::Union{AbstractMatrix,AbstractVector}, filename::AbstractS
 		plotseriesengine(m, filename; names=names, kw...)
 	end
 end
-
 @doc """
 Create plots of data series