Enable parallel execution of bootstraps and multi-model runs

6 files changed, 11 insertions, 40 deletions

diff --git a/.travis.yml b/.travis.yml
index 17165c9..ade2244 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -2,7 +2,6 @@ language: julia
 
 julia:
   - nightly
-  - 1.2
-  - 1.1
+  - 1.3
 
 codecov: true
diff --git a/examples/example_parallel.jl b/examples/example_parallel.jl
deleted file mode 100644
index 68eee4c..0000000
--- a/examples/example_parallel.jl
+++ /dev/null
@@ -1,31 +0,0 @@
-#export JULIA_NUM_THREADS=3 #in bash
-Threads.nthreads() #should be >1
-
-using Distributed, DataFrames
-addprocs(3);
-@everywhere using Unmarked
-
-
-
-ψ_formula = @formula(ψ~elev+forest);
-p_formula = @formula(p~precip+wind);
-β_truth = [0, -0.5, 1.2, -0.2, 0, 0.7];
-
-umd = simulate(Occu, ψ_formula, p_formula, [1000, 5], β_truth);
-
-fit = occu(ψ_formula, p_formula, umd);
-
-
-#bootstrap
-
-@everywhere function calc_stat(i, fit::Unmarked.UnmarkedModel)
-  s = simulate(fit)
-  sum(s.y)
-end
-
-@everywhere calc_stat2 = calc_stat2
-
-@time y = map(x -> calc_stat(x, fit), 1:5000);
-
-@time y2 = pmap(x -> calc_stat(x, fit), 1:5000);
-
diff --git a/src/Unmarked.jl b/src/Unmarked.jl
index 40d6ebe..4f192f8 100644
--- a/src/Unmarked.jl
+++ b/src/Unmarked.jl
@@ -4,7 +4,7 @@ using StatsBase, StatsModels, StatsFuns, Distributions, Random, Printf
 using LinearAlgebra, DataFrames, Optim, NLSolversBase, ForwardDiff
 using Combinatorics: combinations
 using PrettyTables: pretty_table, ft_printf
-using ProgressMeter: @showprogress
+using ProgressMeter: Progress, next!
 using Gadfly: plot, style, Guide, Geom, pt, vstack, hstack
 
 import Base: show, getindex, length
diff --git a/src/gof.jl b/src/gof.jl
index 60b62e1..392cdec 100644
--- a/src/gof.jl
+++ b/src/gof.jl
@@ -9,11 +9,12 @@ end
 function parboot(fit::UnmarkedModel, nsims::Int, statistic::Any)
 
   out = Array{Float64}(undef, nsims)
-
-  @showprogress 1 string("Bootstrap (",nsims," sims) ") for i = 1:nsims
+  p = Progress(nsims, desc=string("Bootstrap (",nsims," sims) "))
+  Threads.@threads for i = 1:nsims
     new_data = simulate(fit)
     new_fit = update(fit, new_data)
     out[i] = statistic(new_fit)
+    next!(p)
   end
 
   return out
diff --git a/src/nmix.jl b/src/nmix.jl
index 33551ab..dd7e54d 100644
--- a/src/nmix.jl
+++ b/src/nmix.jl
@@ -85,10 +85,11 @@ function nmix(λ_form::Union{Array,FormulaTerm},
               p_form::Union{Array,FormulaTerm}, 
               data::UmData, K::Union{Int,Nothing}=nothing)
   cf = combine_formulas(λ_form, p_form)
-  msg = string("Fitting ", length(cf), " models ")
   out = Array{UnmarkedModel}(undef, length(cf))
-  @showprogress 1 msg for i in 1:length(cf) 
+  p = Progress(length(cf), desc=string("Fitting ", length(cf), " models "))
+  Threads.@threads for i in 1:length(cf) 
     out[i] = nmix(cf[i][1],cf[i][2], data, K)
+    next!(p)
   end
   return UnmarkedModels(out)
 end
diff --git a/src/occupancy.jl b/src/occupancy.jl
index ff18ac1..39fccca 100644
--- a/src/occupancy.jl
+++ b/src/occupancy.jl
@@ -64,10 +64,11 @@ combinations. To fit all model subsets, wrap formula with `allsubs()`.
 function occu(ψ_form::Union{Array,FormulaTerm}, 
               p_form::Union{Array,FormulaTerm}, data::UmData)
   cf = combine_formulas(ψ_form, p_form)
-  msg = string("Fitting ", length(cf), " models ")
   out = Array{UnmarkedModel}(undef, length(cf))
-  @showprogress 1 msg for i in 1:length(cf)
+  p = Progress(length(cf), desc=string("Fitting ", length(cf), " models ")) 
+  Threads.@threads for i in 1:length(cf)
     out[i] = occu(cf[i][1], cf[i][2], data)
+    next!(p)
   end
   return UnmarkedModels(out)
 end