rebase fixes

TuringLang · Mar 10, 2020 · 75d3e66 · 75d3e66
1 parent 784d055
commit 75d3e66
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Showing 4 changed files with 9 additions and 21 deletions.
diff --git a/Project.toml b/Project.toml
@@ -73,4 +73,4 @@ UnicodePlots = "b8865327-cd53-5732-bb35-84acbb429228"
 Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"
 
 [targets]
-test = ["Pkg", "TerminalLoggers", "Test", "UnicodePlots", "StatsBase", "SpecialFunctions", "FiniteDifferences", "DynamicHMC", "CmdStan", "BenchmarkTools", "Zygote"]
+test = ["Pkg", "TerminalLoggers", "Test", "UnicodePlots", "StatsBase", "FiniteDifferences", "DynamicHMC", "CmdStan", "BenchmarkTools", "Zygote"]
diff --git a/src/inference/AdvancedSMC.jl b/src/inference/AdvancedSMC.jl
@@ -283,7 +283,7 @@ function assume(spl::Sampler{<:Union{PG,SMC}}, dist::Distribution, vn::VarName,
             r = rand(dist)
             push!(vi, vn, r, dist, Selector(:invalid))
         end
-        acclogp!(vi, invlink_logpdf_trans(spl, dist, r, istrans(vi, vn)))
+        acclogp!(vi, logpdf_with_trans(dist, r, istrans(vi, vn)))
     end
     return r, 0
 end

diff --git a/src/inference/Inference.jl b/src/inference/Inference.jl
@@ -314,7 +314,7 @@ function AbstractMCMC.bundle_samples(
     model::Model,
     spl::Sampler,
     N::Integer,
-    ts::Vector{<:AbstractTransition},
+    ts::Vector,
     chain_type::Type{Chains};
     raw_output::Bool=false,
     discard_adapt::Bool=true,
@@ -613,7 +613,7 @@ function assume(
     #       r is genereated from some uniform distribution which is different from the prior
     # acclogp!(vi, logpdf_with_trans(dist, r, istrans(vi, vn)))
 
-    return r, invlink_logpdf_trans(spl, dist, r, istrans(vi, vn))
+    return r, logpdf_with_trans(dist, r, istrans(vi, vn))
 end
 
 function observe(
@@ -727,7 +727,7 @@ function dot_assume(
 )
     @assert length(dist) == size(var, 1)
     r = get_and_set_val!(vi, vns, dist, spl)
-    lp = sum(invlink_logpdf_trans(spl, dist, r, istrans(vi, vns[1])))
+    lp = sum(logpdf_with_trans(dist, r, istrans(vi, vns[1])))
     var .= r
     return var, lp
 end
@@ -740,7 +740,7 @@ function dot_assume(
 )
     r = get_and_set_val!(vi, vns, dists, spl)
     # Make sure `r` is not a matrix for multivariate distributions
-    lp = sum(invlink_logpdf_trans.(Ref(spl), dists, r, istrans(vi, vns[1])))
+    lp = sum(logpdf_with_trans.(dists, r, istrans(vi, vns[1])))
     var .= r
     return var, lp
 end
@@ -835,18 +835,6 @@ function set_val!(
     return val
 end
 
-function invlink_logpdf_trans(spl, dist, x, trans)
-    #if dist isa Dirichlet || dist isa VectorOfMultivariate{<:Any, <:Dirichlet}
-        if trans
-            return logpdf_with_trans(dist, invlink(dist, x), true)
-        else
-            return logpdf_with_trans(dist, x, false)
-        end
-    #else
-    #    return logpdf_with_trans(dist, x, trans)
-    #end
-end
-
 # observe
 function dot_tilde(ctx::DefaultContext, sampler, right, left, vi)
     return _dot_tilde(sampler, right, left, vi)

diff --git a/src/inference/hmc.jl b/src/inference/hmc.jl
@@ -447,7 +447,7 @@ function assume(
     Turing.DEBUG && _debug("dist = $dist")
     Turing.DEBUG && _debug("vn = $vn")
     Turing.DEBUG && _debug("r = $r, typeof(r)=$(typeof(r))")
-    return r, invlink_logpdf_trans(spl, dist, r, istrans(vi, vn))
+    return r, logpdf_with_trans(dist, r, istrans(vi, vn))
 end
 
 function dot_assume(
@@ -461,7 +461,7 @@ function dot_assume(
     updategid!.(Ref(vi), vns, Ref(spl))
     r = vi[vns]
     var .= r
-    return var, sum(invlink_logpdf_trans(spl, dist, r, istrans(vi, vns[1])))
+    return var, sum(logpdf_with_trans(dist, r, istrans(vi, vns[1])))
 end
 function dot_assume(
     spl::Sampler{<:Hamiltonian},
@@ -473,7 +473,7 @@ function dot_assume(
     updategid!.(Ref(vi), vns, Ref(spl))
     r = reshape(vi[vec(vns)], size(var))
     var .= r
-    return var, sum(invlink_logpdf_trans.(Ref(spl), dists, r, istrans(vi, vns[1])))
+    return var, sum(logpdf_with_trans.(dists, r, istrans(vi, vns[1])))
 end
 
 function observe(