TuringLang · cpfiffer · Mar 26, 2020 · Mar 25, 2020 · Mar 25, 2020 · Mar 26, 2020
diff --git a/HISTORY.md b/HISTORY.md
@@ -1,3 +1,6 @@
+# Release 0.10.1
+- Fix bug where arrays with mixed integers, floats, and missing values were not being passed to the `MCMCChains.Chains` constructor properly [#1180](https://github.com/TuringLang/Turing.jl/pull/1180).
+
 # Release 0.10.0
 - Update elliptical slice sampling to use [EllipticalSliceSampling.jl](https://github.com/TuringLang/EllipticalSliceSampling.jl) on the backend. [#1145](https://github.com/TuringLang/Turing.jl/pull/1145). Nothing should change from a front-end perspective -- you can still call `sample(model, ESS(), 1000)`.
 - Added default progress loggers in [#1149](https://github.com/TuringLang/Turing.jl/pull/1149).

diff --git a/Project.toml b/Project.toml
@@ -45,7 +45,7 @@ EllipticalSliceSampling = "0.2"
 ForwardDiff = "0.10.3"
 Libtask = "0.3.1"
 LogDensityProblems = "^0.9, 0.10"
-MCMCChains = "3"
+MCMCChains = "3.0.7"
 MacroTools = "0.5.1"
 PDMats = "0.9.9"
 ProgressLogging = "0.1"

diff --git a/src/contrib/inference/dynamichmc.jl b/src/contrib/inference/dynamichmc.jl
@@ -114,7 +114,7 @@ end
     model::AbstractModel,
     alg::DynamicNUTS,
     N::Integer;
-    chain_type=Chains,
+    chain_type=MCMCChains.Chains,
     resume_from=nothing,
     progress=PROGRESS[],
     kwargs...
@@ -136,7 +136,7 @@ function AbstractMCMC.psample(
     alg::DynamicNUTS,
     N::Integer,
     n_chains::Integer;
-    chain_type=Chains,
+    chain_type=MCMCChains.Chains,
     progress=PROGRESS[],
     kwargs...
 )

diff --git a/src/inference/AdvancedSMC.jl b/src/inference/AdvancedSMC.jl
@@ -246,14 +246,14 @@ function AbstractMCMC.sample_end!(
     loge = mean(t.le for t in ts)
 
     # If we already had a chain, grab the logevidence.
-    if resume_from isa Chains
+    if resume_from isa MCMCChains.Chains
         # pushfirst!(samples, resume_from.info[:samples]...)
         pre_loge = resume_from.logevidence
         # Calculate new log-evidence
         pre_n = length(resume_from)
         loge = (pre_loge * pre_n + loge * N) / (pre_n + N)
     elseif resume_from !== nothing
-        error("keyword argument `resume_from` has to be `nothing` or a `Chains` object")
+        error("keyword argument `resume_from` has to be `nothing` or a `MCMCChains.Chains` object")
     end
 
     # Store the logevidence.

diff --git a/src/inference/Inference.jl b/src/inference/Inference.jl
@@ -16,7 +16,6 @@ using Random: GLOBAL_RNG, AbstractRNG, randexp
 using DynamicPPL
 using AbstractMCMC: AbstractModel, AbstractSampler
 using Bijectors: _debug
-using MCMCChains: Chains
 
 import AbstractMCMC
 import AdvancedHMC; const AHMC = AdvancedHMC
@@ -26,6 +25,7 @@ import DynamicPPL: getspace, get_matching_type,
     VarName, _getranges, _getindex, getval, _getvns
 import EllipticalSliceSampling
 import Random
+import MCMCChains
 
 export  InferenceAlgorithm,
         Hamiltonian,
@@ -146,7 +146,7 @@ function AbstractMCMC.sample(
     model::AbstractModel,
     alg::InferenceAlgorithm,
     N::Integer;
-    chain_type=Chains,
+    chain_type=MCMCChains.Chains,
     resume_from=nothing,
     progress=PROGRESS[],
     kwargs...
@@ -175,7 +175,7 @@ function AbstractMCMC.psample(
     alg::InferenceAlgorithm,
     N::Integer,
     n_chains::Integer;
-    chain_type=Chains,
+    chain_type=MCMCChains.Chains,
     progress=PROGRESS[],
     kwargs...
 )
@@ -310,14 +310,14 @@ function get_transition_extras(ts::Vector)
     return extra_names, valmat
 end
 
-# Default Chains constructor.
+# Default MCMCChains.Chains constructor.
 function AbstractMCMC.bundle_samples(
     rng::AbstractRNG,
     model::Model,
     spl::Sampler,
     N::Integer,
     ts::Vector,
-    chain_type::Type{Chains};
+    chain_type::Type{MCMCChains.Chains};
     discard_adapt::Bool=true,
     save_state=false,
     kwargs...
@@ -358,8 +358,11 @@ function AbstractMCMC.bundle_samples(
         info = NamedTuple()
     end
 
+    # Conretize the array before giving it to MCMCChains.
+    parray = MCMCChains.concretize(parray)
+
     # Chain construction.
-    return Chains(
+    return MCMCChains.Chains(
         parray,
         string.(nms),
         deepcopy(TURING_INTERNAL_VARS);
@@ -398,12 +401,12 @@ function AbstractMCMC.bundle_samples(
     return map(identity, nts)
 end
 
-function save(c::Chains, spl::Sampler, model, vi, samples)
+function save(c::MCMCChains.Chains, spl::Sampler, model, vi, samples)
     nt = NamedTuple{(:spl, :model, :vi, :samples)}((spl, model, deepcopy(vi), samples))
     return setinfo(c, merge(nt, c.info))
 end
 
-function resume(c::Chains, n_iter::Int; chain_type=Chains, progress=PROGRESS[], kwargs...)
+function resume(c::MCMCChains.Chains, n_iter::Int; chain_type=MCMCChains.Chains, progress=PROGRESS[], kwargs...)
     @assert !isempty(c.info) "[Turing] cannot resume from a chain without state info"
 
     # Sample a new chain.
@@ -414,7 +417,7 @@ function resume(c::Chains, n_iter::Int; chain_type=Chains, progress=PROGRESS[],
         n_iter;
         resume_from=c,
         reuse_spl_n=n_iter,
-        chain_type=Chains,
+        chain_type=MCMCChains.Chains,
         progress=progress,
         kwargs...
     )
@@ -425,7 +428,7 @@ end
 
 function set_resume!(
     s::Sampler;
-    resume_from::Union{Chains, Nothing}=nothing,
+    resume_from::Union{MCMCChains.Chains, Nothing}=nothing,
     kwargs...
 )
     # If we're resuming, grab the sampler info.

diff --git a/src/utilities/Utilities.jl b/src/utilities/Utilities.jl
@@ -4,7 +4,6 @@ using DynamicPPL: AbstractSampler, Sampler
 using DynamicPPL: init, inittrans, reconstruct, reconstruct!, vectorize
 using Distributions, Bijectors
 using StatsFuns, SpecialFunctions
-using MCMCChains: Chains, setinfo
 import Distributions: sample
 
 export  vectorize,

diff --git a/test/runtests.jl b/test/runtests.jl
@@ -51,7 +51,7 @@ include("test_utils/AllUtils.jl")
     Turing.setadbackend(:forwarddiff)
     @testset "stdlib" begin
         include("stdlib/distributions.jl")
-        # include("stdlib/RandomMeasures.jl")
+        include("stdlib/RandomMeasures.jl")
     end
 
     @testset "utilities" begin