Attach varname_to_symbol mapping to Chains

Project.toml

@@ -1,6 +1,6 @@
 name = "Turing"
 uuid = "fce5fe82-541a-59a6-adf8-730c64b5f9a0"
-version = "0.29"
+version = "0.29.1"
 
 [deps]
 AbstractMCMC = "80f14c24-f653-4e6a-9b94-39d6b0f70001"
@@ -56,7 +56,7 @@ Distributions = "0.23.3, 0.24, 0.25"
 DistributionsAD = "0.6"
 DocStringExtensions = "0.8, 0.9"
 DynamicHMC = "3.4"
-DynamicPPL = "0.23.15"
+DynamicPPL = "0.23.17"
 EllipticalSliceSampling = "0.5, 1"
 ForwardDiff = "0.10.3"
 Libtask = "0.7, 0.8"

ext/TuringOptimExt.jl

@@ -253,7 +253,7 @@ function _optimize(
         Turing.Inference.getparams(model, f.varinfo),
         DynamicPPL.getlogp(f.varinfo)
     )]
-    varnames, _ = Turing.Inference._params_to_array(model, ts)
+    varnames = map(Symbol, first(Turing.Inference._params_to_array(model, ts)))
 
     # Store the parameters and their names in an array.
     vmat = NamedArrays.NamedArray(vals, varnames)

src/mcmc/Inference.jl

@@ -310,18 +310,17 @@ end
 
 
 function _params_to_array(model::DynamicPPL.Model, ts::Vector)
-    # TODO: Do we really need to use `Symbol` here?
-    names_set = OrderedSet{Symbol}()
+    names_set = OrderedSet{VarName}()
     # Extract the parameter names and values from each transition.
     dicts = map(ts) do t
         nms_and_vs = getparams(model, t)
-        nms = map(Symbol ∘ first, nms_and_vs)
+        nms = map(first, nms_and_vs)
         vs = map(last, nms_and_vs)
         for nm in nms
             push!(names_set, nm)
         end
         # Convert the names and values to a single dictionary.
-        return Dict(nms[j] => vs[j] for j in 1:length(vs))
+        return OrderedDict(zip(nms, vs))
     end
     names = collect(names_set)
     vals = [get(dicts[i], key, missing) for i in eachindex(dicts),
@@ -379,29 +378,35 @@ function AbstractMCMC.bundle_samples(
     save_state = false,
     stats = missing,
     sort_chain = false,
+    include_varname_to_symbol = true,
     discard_initial = 0,
     thinning = 1,
     kwargs...
 )
     # Convert transitions to array format.
     # Also retrieve the variable names.
-    nms, vals = _params_to_array(model, ts)
+    varnames, vals = _params_to_array(model, ts)
+    varnames_symbol = map(Symbol, varnames)
 
     # Get the values of the extra parameters in each transition.
     extra_params, extra_values = get_transition_extras(ts)
 
     # Extract names & construct param array.
-    nms = [nms; extra_params]
+    nms = [varnames_symbol; extra_params]
     parray = hcat(vals, extra_values)
 
     # Get the average or final log evidence, if it exists.
     le = getlogevidence(ts, spl, state)
 
     # Set up the info tuple.
+    info = NamedTuple()
+
+    if include_varname_to_symbol
+        info = merge(info, (varname_to_symbol = OrderedDict(zip(varnames, varnames_symbol)),))
+    end
+
     if save_state
-        info = (model = model, sampler = spl, samplerstate = state)
-    else
-        info = NamedTuple()
+        info = merge(info, (model = model, sampler = spl, samplerstate = state))
     end
 
     # Merge in the timing info, if available

src/mcmc/emcee.jl

@@ -109,7 +109,8 @@ function AbstractMCMC.bundle_samples(
     params_vec = map(Base.Fix1(_params_to_array, model), samples)
 
     # Extract names and values separately.
-    nms = params_vec[1][1]
+    varnames = params_vec[1][1]
+    varnames_symbol = map(Symbol, varnames)
     vals_vec = [p[2] for p in params_vec]
 
     # Get the values of the extra parameters in each transition.
@@ -120,7 +121,7 @@ function AbstractMCMC.bundle_samples(
     extra_values_vec = [e[2] for e in extra_vec]
 
     # Extract names & construct param array.
-    nms = [nms; extra_params]
+    nms = [varnames_symbol; extra_params]
     # `hcat` first to ensure we get the right `eltype`.
     x = hcat(first(vals_vec), first(extra_values_vec))
     # Pre-allocate to minimize memory usage.
@@ -133,10 +134,9 @@ function AbstractMCMC.bundle_samples(
     le = getlogevidence(samples, state, spl)
 
     # Set up the info tuple.
+    info = (varname_to_symbol = OrderedDict(zip(varnames, varnames_symbol)),)
     if save_state
-        info = (model = model, sampler = spl, samplerstate = state)
-    else
-        info = NamedTuple()
+        info = merge(info, (model = model, sampler = spl, samplerstate = state))
     end
 
     # Concretize the array before giving it to MCMCChains.