Merge branch 'master' into yebai-patch-1

Project.toml

@@ -1,6 +1,6 @@
 name = "DynamicPPL"
 uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8"
-version = "0.23.13"
+version = "0.23.14"
 
 [deps]
 AbstractMCMC = "80f14c24-f653-4e6a-9b94-39d6b0f70001"

src/simple_varinfo.jl

@@ -544,7 +544,7 @@ values_as(vi::SimpleVarInfo) = vi.values
 values_as(vi::SimpleVarInfo{<:T}, ::Type{T}) where {T} = vi.values
 function values_as(vi::SimpleVarInfo{<:Any,T}, ::Type{Vector}) where {T}
     isempty(vi) && return T[]
-    return mapreduce(v -> vec([v;]), vcat, values(vi.values))
+    return mapreduce(vectorize, vcat, values(vi.values))
 end
 function values_as(vi::SimpleVarInfo, ::Type{D}) where {D<:AbstractDict}
     return ConstructionBase.constructorof(D)(zip(keys(vi), values(vi.values)))

src/utils.jl

@@ -209,11 +209,10 @@ invlink_transform(dist) = inverse(link_transform(dist))
 # Helper functions for vectorize/reconstruct values #
 #####################################################
 
-vectorize(d, r) = vec(r)
-vectorize(d::UnivariateDistribution, r::Real) = [r]
-vectorize(d::MultivariateDistribution, r::AbstractVector{<:Real}) = copy(r)
-vectorize(d::MatrixDistribution, r::AbstractMatrix{<:Real}) = copy(vec(r))
-vectorize(d::Distribution{CholeskyVariate}, r::Cholesky) = copy(vec(r.UL))
+vectorize(d, r) = vectorize(r)
+vectorize(r::Real) = [r]
+vectorize(r::AbstractArray{<:Real}) = copy(vec(r))
+vectorize(r::Cholesky) = copy(vec(r.UL))
 
 # NOTE:
 # We cannot use reconstruct{T} because val is always Vector{Real} then T will be Real.
@@ -237,6 +236,15 @@ reconstruct(::UnivariateDistribution, val::Real) = val
 reconstruct(::MultivariateDistribution, val::AbstractVector{<:Real}) = copy(val)
 reconstruct(::MatrixDistribution, val::AbstractMatrix{<:Real}) = copy(val)
 reconstruct(::Inverse{Bijectors.VecCorrBijector}, ::LKJ, val::AbstractVector) = copy(val)
+
+function reconstruct(dist::LKJCholesky, val::AbstractVector{<:Real})
+    return reconstruct(dist, reshape(val, size(dist)))
+end
+function reconstruct(dist::LKJCholesky, val::AbstractMatrix{<:Real})
+    return Cholesky(val, dist.uplo, 0)
+end
+reconstruct(::LKJCholesky, val::Cholesky) = val
+
 function reconstruct(
     ::Inverse{Bijectors.VecCholeskyBijector}, ::LKJCholesky, val::AbstractVector
 )

src/varinfo.jl

@@ -325,7 +325,12 @@ Set the value(s) of `vn` in the metadata of `vi` to `val`.
 The values may or may not be transformed to Euclidean space.
 """
 setval!(vi::VarInfo, val, vn::VarName) = setval!(getmetadata(vi, vn), val, vn)
-setval!(md::Metadata, val, vn::VarName) = md.vals[getrange(md, vn)] = [val;]
+function setval!(md::Metadata, val::AbstractVector, vn::VarName)
+    return md.vals[getrange(md, vn)] = val
+end
+function setval!(md::Metadata, val, vn::VarName)
+    return md.vals[getrange(md, vn)] = vectorize(getdist(md, vn), val)
+end
 
 """
     getval(vi::VarInfo, vns::Vector{<:VarName})

test/linking.jl

@@ -91,16 +91,51 @@ end
         end
     end
 
+    @testset "LKJCholesky" begin
+        @testset "uplo=$uplo" for uplo in ['L', 'U']
+            @model demo_lkj(d) = x ~ LKJCholesky(d, 1.0, uplo)
+            @testset "d=$d" for d in [2, 3, 5]
+                model = demo_lkj(d)
+                dist = LKJCholesky(d, 1.0, uplo)
+                values_original = rand(model)
+                vis = DynamicPPL.TestUtils.setup_varinfos(
+                    model, values_original, (@varname(x),)
+                )
+                @testset "$(short_varinfo_name(vi))" for vi in vis
+                    val = vi[@varname(x), dist]
+                    # Ensure that `reconstruct` works as intended.
+                    @test val isa Cholesky
+                    @test val.uplo == uplo
+
+                    @test length(vi[:]) == d^2
+                    lp = logpdf(dist, val)
+                    lp_model = logjoint(model, vi)
+                    @test lp_model ≈ lp
+                    # Linked.
+                    vi_linked = DynamicPPL.link!!(deepcopy(vi), model)
+                    @test length(vi_linked[:]) == d * (d - 1) ÷ 2
+                    # Should now include the log-absdet-jacobian correction.
+                    @test !(getlogp(vi_linked) ≈ lp)
+                    # Invlinked.
+                    vi_invlinked = DynamicPPL.invlink!!(deepcopy(vi_linked), model)
+                    @test length(vi_invlinked[:]) == d^2
+                    @test getlogp(vi_invlinked) ≈ lp
+                end
+            end
+        end
+    end
+
     # Related: https://github.com/TuringLang/DynamicPPL.jl/issues/504
-    @testset "dirichlet" begin
+    @testset "Dirichlet" begin
         @model demo_dirichlet(d::Int) = x ~ Dirichlet(d, 1.0)
         @testset "d=$d" for d in [2, 3, 5]
             model = demo_dirichlet(d)
             vis = DynamicPPL.TestUtils.setup_varinfos(model, rand(model), (@varname(x),))
             @testset "$(short_varinfo_name(vi))" for vi in vis
                 lp = logpdf(Dirichlet(d, 1.0), vi[:])
                 @test length(vi[:]) == d
-                @test getlogp(vi) ≈ lp
+                lp_model = logjoint(model, vi)
+                @test lp_model ≈ lp
                 # Linked.
                 vi_linked = DynamicPPL.link!!(deepcopy(vi), model)
                 @test length(vi_linked[:]) == d - 1

test/test_util.jl

@@ -61,13 +61,18 @@ function test_setval!(model, chain; sample_idx=1, chain_idx=1)
     nt = DynamicPPL.tonamedtuple(var_info)
     for (k, (vals, names)) in pairs(nt)
         for (n, v) in zip(names, vals)
-            chain_val = if Symbol(n) ∉ keys(chain)
+            if Symbol(n) ∉ keys(chain)
                 # Assume it's a group
-                vec(MCMCChains.group(chain, Symbol(n)).value[sample_idx, :, chain_idx])
+                chain_val = vec(
+                    MCMCChains.group(chain, Symbol(n)).value[sample_idx, :, chain_idx]
+                )
+                v_true = vec(v)
             else
-                chain[sample_idx, n, chain_idx]
+                chain_val = chain[sample_idx, n, chain_idx]
+                v_true = v
             end
-            @test v == chain_val
+
+            @test v_true == chain_val
         end
     end
 end

test/turing/runtests.jl

@@ -10,6 +10,7 @@ setprogress!(false)
 Random.seed!(100)
 
 # load test utilities
+include(joinpath(pathof(DynamicPPL), "..", "..", "test", "test_util.jl"))
 include(joinpath(pathof(Turing), "..", "..", "test", "test_utils", "numerical_tests.jl"))
 
 @testset "Turing" begin