copy Turing over

Author: mohamed82008

src/compiler.jl

@@ -615,4 +615,4 @@ end
 Get the specialized version of type `T` for sampler `spl`. For example,
 if `T === Float64` and `spl::Hamiltonian`, the matching type is `eltype(vi[spl])`.
 """
-get_matching_type(spl, vi, ::Type{T}) where {T} = T
+function get_matching_type end

test/Turing/Turing.jl

@@ -8,16 +8,17 @@ module Turing
 #       to indicate that's not implemented inside Turing.jl            #
 ########################################################################
 
-using Requires, Reexport, ForwardDiff, DynamicPPL
+using Requires, Reexport, ForwardDiff
 using Bijectors, StatsFuns, SpecialFunctions
 using Statistics, LinearAlgebra, ProgressMeter
-using Markdown, Libtask
+using Markdown, Libtask, MacroTools
 using AbstractMCMC
 @reexport using Distributions, MCMCChains, Libtask
 using Tracker: Tracker
 
 import Base: ~, ==, convert, hash, promote_rule, rand, getindex, setindex!
 import MCMCChains: AbstractChains, Chains
+import DynamicPPL: getspace, runmodel!
 
 const PROGRESS = Ref(true)
 function turnprogress(switch::Bool)
@@ -30,7 +31,6 @@ const DEBUG = Bool(parse(Int, get(ENV, "DEBUG_TURING", "0")))
 # Random probability measures.
 include("stdlib/distributions.jl")
 include("stdlib/RandomMeasures.jl")
-
 include("utilities/Utilities.jl")
 using .Utilities
 include("core/Core.jl")

test/Turing/core/Core.jl

@@ -1,23 +1,29 @@
 module Core
 
-using Libtask, ForwardDiff, Random
+using MacroTools, Libtask, ForwardDiff, Random
 using Distributions, LinearAlgebra
 using ..Utilities, Reexport
 using Tracker: Tracker
-using ..Turing: Turing, Model, runmodel!,
+using ..Turing: Turing
+using DynamicPPL: Model, runmodel!,
     AbstractSampler, Sampler, SampleFromPrior
 using LinearAlgebra: copytri!
+using Bijectors: PDMatDistribution
+import Bijectors: link, invlink
 using DistributionsAD
 using StatsFuns: logsumexp, softmax
-using Bijectors: PDMatDistribution
-
-using DynamicPPL
+@reexport using DynamicPPL
 
 include("container.jl")
 include("ad.jl")
 
 export  @model,
         @varname,
+        generate_observe,
+        translate_tilde!,
+        get_vars,
+        get_data,
+        get_default_values,
         ParticleContainer,
         Particle,
         Trace,
@@ -45,6 +51,8 @@ export  @model,
         gradient_logp_reverse,
         @varinfo,
         @logpdf,
-        @sampler
+        @sampler,
+        @logprob_str,
+        @prob_str
 
 end # module

test/Turing/inference/Inference.jl

@@ -1,27 +1,26 @@
 module Inference
 
 using ..Core, ..Utilities
-using ..Utilities: init
-using DynamicPPL: Metadata, _tail, VarInfo, TypedVarInfo, istrans,
-    islinked, link!, invlink!, getlogp, tonamedtuple, VarName, getsym, vectorize, 
-    settrans!, split_var_str, Model, runmodel!, Sampler, SampleFromPrior,
-    SampleFromUniform, Selector, DefaultContext, PriorContext, LikelihoodContext,
-    MiniBatchContext, AbstractSampler, AbstractSamplerState, set_retained_vns_del_by_spl!
-using DynamicPPL
+using DynamicPPL: Metadata, _tail, VarInfo, TypedVarInfo, 
+    islinked, invlink!, getlogp, tonamedtuple, VarName, getsym, vectorize, 
+    settrans!, _getvns, getdist, split_var_str, CACHERESET, AbstractSampler,
+    Model, runmodel!, Sampler, SampleFromPrior, SampleFromUniform,
+    Selector, AbstractSamplerState, DefaultContext, PriorContext,
+    LikelihoodContext, MiniBatchContext, set_flag!, unset_flag!
 using Distributions, Libtask, Bijectors
 using ProgressMeter, LinearAlgebra
-using ..Turing: Turing, NamedDist, NoDist, PROGRESS
+using ..Turing: PROGRESS, NamedDist, NoDist, Turing
 using StatsFuns: logsumexp
 using Random: GLOBAL_RNG, AbstractRNG, randexp
-using AbstractMCMC
+using AbstractMCMC, DynamicPPL
 
 import MCMCChains: Chains
 import AdvancedHMC; const AHMC = AdvancedHMC
-import DynamicPPL: getspace, get_matching_type, tilde, dot_tilde
 import ..Core: getchunksize, getADtype
 import AbstractMCMC: AbstractTransition, sample, step!, sample_init!,
     transitions_init, sample_end!, AbstractSampler, transition_type,
     callback, init_callback, AbstractCallback, psample
+import DynamicPPL: tilde, dot_tilde, getspace, get_matching_type
 
 export  InferenceAlgorithm,
         Hamiltonian,

test/Turing/utilities/Utilities.jl

@@ -1,11 +1,20 @@
 module Utilities
 
-using ..Turing: AbstractSampler, Sampler
+using DynamicPPL: AbstractSampler, Sampler
 using Distributions, Bijectors
 using StatsFuns, SpecialFunctions
 using MCMCChains: AbstractChains, Chains, setinfo
 import Distributions: sample
 
+export  vectorize,
+        reconstruct,
+        reconstruct!,
+        Sample,
+        Chain,
+        init,
+        vectorize,
+        set_resume!
+
 include("robustinit.jl")
 
 end # module

test/Turing/variational/VariationalInference.jl

@@ -1,10 +1,10 @@
 module Variational
 
-using ..Core, DynamicPPL, ..Utilities
-using Distributions, Bijectors
+using ..Core, ..Utilities
+using Distributions, Bijectors, DynamicPPL
 using ProgressMeter, LinearAlgebra
 using ..Turing: PROGRESS
-using ..Turing: Model, SampleFromPrior, SampleFromUniform
+using DynamicPPL: Model, SampleFromPrior, SampleFromUniform
 using ..Turing: Turing
 using Random: AbstractRNG