Fix imports

Author: phipsgabler

src/DynamicPPL.jl

@@ -1,11 +1,8 @@
 module DynamicPPL
 
 using AbstractMCMC: AbstractSampler, AbstractChains, AbstractModel
-using Distributions: UnivariateDistribution,
-                     MultivariateDistribution,
-                     MatrixDistribution,
-                     Distribution
-using Bijectors: link, invlink
+using Distributions
+using Bijectors
 using MacroTools
 
 import Base: string,

src/context_implementations.jl

@@ -1,3 +1,9 @@
+using Distributions: UnivariateDistribution,
+                     MultivariateDistribution,
+                     MatrixDistribution,
+                     Distribution
+
+
 alg_str(spl::Sampler) = string(nameof(typeof(spl.alg)))
 
 # utility funcs for querying sampler information
@@ -93,9 +99,9 @@ function assume(
     end
     # NOTE: The importance weight is not correctly computed here because
     #       r is genereated from some uniform distribution which is different from the prior
-    # acclogp!(vi, logpdf_with_trans(dist, r, istrans(vi, vn)))
+    # acclogp!(vi, Bijectors.logpdf_with_trans(dist, r, istrans(vi, vn)))
 
-    return r, logpdf_with_trans(dist, r, istrans(vi, vn))
+    return r, Bijectors.logpdf_with_trans(dist, r, istrans(vi, vn))
 end
 
 function observe(
@@ -105,7 +111,7 @@ function observe(
     vi::VarInfo,
 )
     increment_num_produce!(vi)
-    return logpdf(dist, value)
+    return Distributions.logpdf(dist, value)
 end
 
 # .~ functions
@@ -209,7 +215,7 @@ function dot_assume(
 )
     @assert length(dist) == size(var, 1)
     r = get_and_set_val!(vi, vns, dist, spl)
-    lp = sum(logpdf_with_trans(dist, r, istrans(vi, vns[1])))
+    lp = sum(Bijectors.logpdf_with_trans(dist, r, istrans(vi, vns[1])))
     var .= r
     return var, lp
 end
@@ -222,7 +228,7 @@ function dot_assume(
 )
     r = get_and_set_val!(vi, vns, dists, spl)
     # Make sure `r` is not a matrix for multivariate distributions
-    lp = sum(logpdf_with_trans.(dists, r, istrans(vi, vns[1])))
+    lp = sum(Bijectors.logpdf_with_trans.(dists, r, istrans(vi, vns[1])))
     var .= r
     return var, lp
 end
@@ -353,7 +359,7 @@ function dot_observe(
     increment_num_produce!(vi)
     DynamicPPL.DEBUG && @debug "dist = $dist"
     DynamicPPL.DEBUG && @debug "value = $value"
-    return sum(logpdf(dist, value))
+    return sum(Distributions.logpdf(dist, value))
 end
 function dot_observe(
     spl::Union{SampleFromPrior, SampleFromUniform},
@@ -364,7 +370,7 @@ function dot_observe(
     increment_num_produce!(vi)
     DynamicPPL.DEBUG && @debug "dists = $dists"
     DynamicPPL.DEBUG && @debug "value = $value"
-    return sum(logpdf.(dists, value))
+    return sum(Distributions.logpdf.(dists, value))
 end
 function dot_observe(
     spl::Sampler,

src/varinfo.jl

@@ -772,7 +772,7 @@ function link!(vi::UntypedVarInfo, spl::Sampler)
         for vn in vns
             dist = getdist(vi, vn)
             # TODO: Use inplace versions to avoid allocations
-            setval!(vi, vectorize(dist, link(dist, reconstruct(dist, getval(vi, vn)))), vn)
+            setval!(vi, vectorize(dist, Bijectors.link(dist, reconstruct(dist, getval(vi, vn)))), vn)
             settrans!(vi, true, vn)
         end
     else
@@ -793,7 +793,7 @@ end
                     # Iterate over all `f_vns` and transform
                     for vn in f_vns
                         dist = getdist(vi, vn)
-                        setval!(vi, vectorize(dist, link(dist, reconstruct(dist, getval(vi, vn)))), vn)
+                        setval!(vi, vectorize(dist, Bijectors.link(dist, reconstruct(dist, getval(vi, vn)))), vn)
                         settrans!(vi, true, vn)
                     end
                 else
@@ -818,7 +818,7 @@ function invlink!(vi::UntypedVarInfo, spl::AbstractSampler)
     if istrans(vi, vns[1])
         for vn in vns
             dist = getdist(vi, vn)
-            setval!(vi, vectorize(dist, invlink(dist, reconstruct(dist, getval(vi, vn)))), vn)
+            setval!(vi, vectorize(dist, Bijectors.invlink(dist, reconstruct(dist, getval(vi, vn)))), vn)
             settrans!(vi, false, vn)
         end
     else
@@ -839,7 +839,7 @@ end
                     # Iterate over all `f_vns` and transform
                     for vn in f_vns
                         dist = getdist(vi, vn)
-                        setval!(vi, vectorize(dist, invlink(dist, reconstruct(dist, getval(vi, vn)))), vn)
+                        setval!(vi, vectorize(dist, Bijectors.invlink(dist, reconstruct(dist, getval(vi, vn)))), vn)
                         settrans!(vi, false, vn)
                     end
                 else
@@ -894,14 +894,14 @@ function getindex(vi::AbstractVarInfo, vn::VarName)
     @assert haskey(vi, vn) "[DynamicPPL] attempted to replay unexisting variables in VarInfo"
     dist = getdist(vi, vn)
     return istrans(vi, vn) ?
-        invlink(dist, reconstruct(dist, getval(vi, vn))) :
+        Bijectors.invlink(dist, reconstruct(dist, getval(vi, vn))) :
         reconstruct(dist, getval(vi, vn))
 end
 function getindex(vi::AbstractVarInfo, vns::Vector{<:VarName})
     @assert haskey(vi, vns[1]) "[DynamicPPL] attempted to replay unexisting variables in VarInfo"
     dist = getdist(vi, vns[1])
     return istrans(vi, vns[1]) ?
-        invlink(dist, reconstruct(dist, getval(vi, vns), length(vns))) :
+        Bijectors.invlink(dist, reconstruct(dist, getval(vi, vns), length(vns))) :
         reconstruct(dist, getval(vi, vns), length(vns))
 end