Rel 0.3.0 - Fixed cmdline() and stan_run() warnings

Project.toml

@@ -1,7 +1,7 @@
 name = "StanPathfinder"
 uuid = "e8ee4b5e-54b2-4408-8575-c3c89e582a15"
 authors = ["Rob J Goedman <[email protected]>"]
-version = "0.2.0"
+version = "0.3.0"
 
 [deps]
 CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"

examples/Bernoulli/bernoulli.jl

@@ -22,7 +22,7 @@ data = Dict("N" => 10, "y" => [0, 1, 0, 1, 0, 0, 0, 0, 0, 1])
 # Keep tmpdir across multiple runs to prevent re-compilation
 tmpdir = joinpath(@__DIR__, "tmp")
 
-sm = PathfinderModel("bernoulli", bernoulli_model, tmpdir)
+sm = PathfinderModel("bernoulli", bernoulli_model)
 rc = stan_pathfinder(sm; data, seed=rand(1:200000000, 1)[1], num_chains=2)
 
 if all(success.(rc))
@@ -37,3 +37,6 @@ if all(success.(rc))
     display(profile_df)
 
 end
+
+sm2 = PathfinderModel("bernoulli2", bernoulli_model, tmpdir)
+rc2 = stan_pathfinder(sm2; data, seed=rand(1:200000000, 1)[1], num_chains=2)

src/stanrun/cmdline.jl

@@ -40,7 +40,7 @@ function cmdline(m::PathfinderModel, id)
     cmd = `$cmd save_single_paths=$(m.save_single_paths)`
     cmd = `$cmd max_lbfgs_iters=$(m.max_lbfgs_iters)`
     cmd = `$cmd num_draws=$(m.num_draws)`
-    cmd = `$cmd num_draws=$(m.num_elbo_draws)`
+    cmd = `$cmd num_elbo_draws=$(m.num_elbo_draws)`
 
     cmd = `$cmd id=$(id)`
 

src/stanrun/stan_run.jl

@@ -56,9 +56,8 @@ function stan_run(m::PathfinderModel, use_json=true; kwargs...)
 
     handle_keywords!(m, kwargs)
 
-    if m.num_chains > 1 || m.num_threads > 1
-        @info "Currently running StanPathfinder with either \
-         num_chains>1 or num_threads>1 can lead to problematic results."
+    if m.num_threads > 1
+        @info "Currently running StanPathfinder with num_threads>1 can lead to problematic results."
      end
 
     setup_profiles(m, m.num_chains)

src/stansamples/read_pathfinder.jl

@@ -19,19 +19,26 @@ read_pathfinder(m::PathfinderModelodel)
 """
 function read_pathfinder(m::PathfinderModel)
 
-  local a3d, index, idx, indvec
+  local a3d, idx, indvec
 
   ftype = "chain"
 
   for i in 1:m.num_chains
-    if isfile("$(m.output_base)_$(ftype)_$(i).csv")
+
+    file = "$(m.output_base)_$(ftype)_$(i).csv"
+    if !(isfile(file))
+      println("Found file $file not found!")
+    end
+
+    if isfile(file)
       instream = open("$(m.output_base)_$(ftype)_$(i).csv")
       skipchars(isspace, instream, linecomment='#')
       line = Unicode.normalize(readline(instream), newline2lf=true)
       idx = split(strip(line), ",")
       index = [idx[k] for k in 1:length(idx)]
       indvec = 1:length(index)
       if i == 1
+        cnames = convert.(String, idx[indvec])
         a3d = fill(0.0, m.num_draws, length(indvec), m.num_chains)
       end
       skipchars(isspace, instream, linecomment='#')