Merge branch 'master' into unify-step

# Conflicts:
#	src/samplers/gibbs.jl

Author: Hong Ge

README.md

@@ -81,8 +81,8 @@ c4 = sample(gdemo([1.5, 2]), Gibbs(1000, PG(10, 2, :m), HMC(2, 0.1, 5, :s)))
 describe(c3)
 
 # Plot results 
-p = plot(c3)
-draw(p, "gdemo-plot.svg")
+p = Turing.plot(c3)
+Turing.draw(p, fmt=:pdf, filename="gdemo-plot.pdf")
 ```
 
 The arguments for each sampler are

benchmarks/gauss-stan.run.jl

@@ -3,8 +3,8 @@ using Turing
 using Stan
 
 include(Pkg.dir("Turing")*"/benchmarks/benchmarkhelper.jl")
-include(Pkg.dir("Turing")*"/example-models/stan-models/simplegauss-stan.data.jl")
-include(Pkg.dir("Turing")*"/example-models/stan-models/simplegauss-stan.model.jl")
+include(Pkg.dir("Turing")*"/example-models/benchmarks/gdemo-stan.data.jl")
+include(Pkg.dir("Turing")*"/example-models/benchmarks/gdemo-stan.model.jl")
 
 stan_model_name = "simplegauss"
 simplegaussstan = Stanmodel(name=stan_model_name, model=simplegaussstanmodel, nchains=1);

benchmarks/gauss.run.jl

@@ -3,14 +3,14 @@ using Turing
 using Stan
 
 include(Pkg.dir("Turing")*"/benchmarks/benchmarkhelper.jl")
-include(Pkg.dir("Turing")*"/example-models/stan-models/simplegauss.data.jl")
-include(Pkg.dir("Turing")*"/example-models/stan-models/simplegauss.model.jl")
+include(Pkg.dir("Turing")*"/example-models/benchmarks/gdemo.data.jl")
+include(Pkg.dir("Turing")*"/example-models/benchmarks/gdemo.model.jl")
 
 bench_res = tbenchmark("HMC(2000, 0.1, 3)", "simplegaussmodel", "simplegaussdata")
 logd = build_logd("Simple Gaussian Model", bench_res...)
 logd["analytic"] = Dict("s" => 49/24, "m" => 7/6)
 
-include(Pkg.dir("Turing")*"/benchmarks/"*"simplegauss-stan.run.jl")
+include(Pkg.dir("Turing")*"/benchmarks/"*"gauss-stan.run.jl")
 
 logd["stan"] = Dict("s" => mean(s_stan), "m" => mean(m_stan))
 logd["time_stan"] = sg_time

example-models/notebooks/BayesHmm.ipynb

@@ -70,7 +70,7 @@ function sample(model::Function, alg::Gibbs)
     dprintln(2, "Gibbs stepping...")
 
     for local_spl in spl.info[:samplers]
-      local_spl.info[:progress] = spl.info[:progress]
+      if haskey(spl.info, :progress) local_spl.info[:progress] = spl.info[:progress] end
 
       dprintln(2, "$(typeof(local_spl)) stepping...")
 
@@ -100,7 +100,8 @@ function sample(model::Function, alg::Gibbs)
 
     if spl.alg.thin samples[i].value = Sample(varInfo).value end
 
-    ProgressMeter.next!(spl.info[:progress])
+    haskey(spl.info, :progress) &&
+        ProgressMeter.update!(spl.info[:progress], spl.info[:progress].counter+1)
   end
 
   Chain(0, samples)    # wrap the result by Chain