Fixes failing tests (#276)

Co-authored-by: Hong Ge <[email protected]>

Author: torfjelde

test/compat/ad.jl

@@ -8,7 +8,8 @@
 
             return logpdf(InverseGamma(2, 3), s) +
                    logpdf(Normal(0, sqrt(s)), m) +
-                   logpdf(dist, 1.5) + logpdf(dist, 2.0)
+                   logpdf(dist, 1.5) +
+                   logpdf(dist, 2.0)
         end
 
         test_model_ad(gdemo_default, logp_gdemo_default)

test/turing/loglikelihoods.jl

@@ -13,7 +13,9 @@
     y = randn()
     model = demo(xs, y)
     chain = sample(model, MH(), MCMCThreads(), 100, 2)
-    var_to_likelihoods = pointwise_loglikelihoods(model, chain)
+    var_to_likelihoods = pointwise_loglikelihoods(
+        model, MCMCChains.get_sections(chain, :parameters)
+    )
     @test haskey(var_to_likelihoods, "xs[1]")
     @test haskey(var_to_likelihoods, "xs[2]")
     @test haskey(var_to_likelihoods, "xs[3]")
@@ -32,8 +34,8 @@
     results = pointwise_loglikelihoods(model, var_info)
     var_to_likelihoods = Dict(string(vn) => ℓ for (vn, ℓ) in results)
     s, m = var_info[SampleFromPrior()]
-    @test logpdf(Normal(m, √s), xs[1]) == var_to_likelihoods["xs[1]"]
-    @test logpdf(Normal(m, √s), xs[2]) == var_to_likelihoods["xs[2]"]
-    @test logpdf(Normal(m, √s), xs[3]) == var_to_likelihoods["xs[3]"]
-    @test logpdf(Normal(m, √s), y) == var_to_likelihoods["y"]
+    @test [logpdf(Normal(m, √s), xs[1])] == var_to_likelihoods["xs[1]"]
+    @test [logpdf(Normal(m, √s), xs[2])] == var_to_likelihoods["xs[2]"]
+    @test [logpdf(Normal(m, √s), xs[3])] == var_to_likelihoods["xs[3]"]
+    @test [logpdf(Normal(m, √s), y)] == var_to_likelihoods["y"]
 end

test/turing/model.jl

@@ -30,11 +30,11 @@
         chain1 = sample(model1, MH(), 100)
         chain2 = sample(model2, MH(), 100)
 
-        res11 = generated_quantities(model1, chain1)
-        res21 = generated_quantities(model2, chain1)
+        res11 = generated_quantities(model1, MCMCChains.get_sections(chain1, :parameters))
+        res21 = generated_quantities(model2, MCMCChains.get_sections(chain1, :parameters))
 
-        res12 = generated_quantities(model1, chain2)
-        res22 = generated_quantities(model2, chain2)
+        res12 = generated_quantities(model1, MCMCChains.get_sections(chain2, :parameters))
+        res22 = generated_quantities(model2, MCMCChains.get_sections(chain2, :parameters))
 
         # Check that the two different models produce the same values for
         # the same chains.
@@ -43,8 +43,8 @@
         # Ensure that they're not all the same (some can be, because rejected samples)
         @test any(res12[1:(end - 1)] .!= res12[2:end])
 
-        test_setval!(model1, chain1)
-        test_setval!(model2, chain2)
+        test_setval!(model1, MCMCChains.get_sections(chain1, :parameters))
+        test_setval!(model2, MCMCChains.get_sections(chain2, :parameters))
 
         # Next level
         @model function demo3(xs, ::Type{TV}=Vector{Float64}) where {TV}
@@ -79,11 +79,11 @@
         chain3 = sample(model3, MH(), 100)
         chain4 = sample(model4, MH(), 100)
 
-        res33 = generated_quantities(model3, chain3)
-        res43 = generated_quantities(model4, chain3)
+        res33 = generated_quantities(model3, MCMCChains.get_sections(chain3, :parameters))
+        res43 = generated_quantities(model4, MCMCChains.get_sections(chain3, :parameters))
 
-        res34 = generated_quantities(model3, chain4)
-        res44 = generated_quantities(model4, chain4)
+        res34 = generated_quantities(model3, MCMCChains.get_sections(chain4, :parameters))
+        res44 = generated_quantities(model4, MCMCChains.get_sections(chain4, :parameters))
 
         # Check that the two different models produce the same values for
         # the same chains.

test/turing/prob_macro.jl

@@ -11,7 +11,9 @@
 
         model = demo(xval)
         varinfo = VarInfo(model)
-        chain = sample(model, IS(), iters; save_state=true)
+        chain = MCMCChains.get_sections(
+            sample(model, IS(), iters; save_state=true), :parameters
+        )
         chain2 = Chains(chain.value, chain.logevidence, chain.name_map, NamedTuple())
         lps = logpdf.(Normal.(chain["m"], 1), xval)
         @test logprob"x = xval | chain = chain" == lps
@@ -40,7 +42,9 @@
 
         model = demo(xval)
         varinfo = VarInfo(model)
-        chain = sample(model, HMC(0.5, 1), iters; save_state=true)
+        chain = MCMCChains.get_sections(
+            sample(model, HMC(0.5, 1), iters; save_state=true), :parameters
+        )
         chain2 = Chains(chain.value, chain.logevidence, chain.name_map, NamedTuple())
 
         names = namesingroup(chain, "m")
@@ -74,7 +78,10 @@
         group = rand(1:4, 100)
         n_groups = 4
 
-        chain1 = sample(model1(y, group, n_groups), NUTS(0.65), 2_000; save_state=true)
+        chain1 = MCMCChains.get_sections(
+            sample(model1(y, group, n_groups), NUTS(0.65), 2_000; save_state=true),
+            :parameters,
+        )
         logprob"y = y[[1]] | group = group[[1]], n_groups = n_groups, chain = chain1"
 
         @model function model2(y, group, n_groups)
@@ -85,7 +92,10 @@
             end
         end
 
-        chain2 = sample(model2(y, group, n_groups), NUTS(0.65), 2_000; save_state=true)
+        chain2 = MCMCChains.get_sections(
+            sample(model2(y, group, n_groups), NUTS(0.65), 2_000; save_state=true),
+            :parameters,
+        )
         logprob"y = y[[1]] | group = group[[1]], n_groups = n_groups, chain = chain2"
     end
 end