Merge branch 'master' into sunxd/remove_tonamedtuple

src/model.jl

@@ -1037,7 +1037,7 @@ function Base.rand(rng::Random.AbstractRNG, ::Type{T}, model::Model) where {T}
         evaluate!!(
             model,
             SimpleVarInfo{Float64}(OrderedDict()),
-            SamplingContext(rng, SampleFromPrior(), DefaultContext()),
+            SamplingContext(rng, SampleFromPrior(), model.context),
         ),
     )
     return values_as(x, T)

src/test_utils.jl

@@ -179,6 +179,15 @@ corresponding value using `get`, e.g. `get(posterior_mean(model), varname)`.
 """
 function posterior_mean end
 
+"""
+    rand_prior_true([rng::AbstractRNG, ]model::DynamicPPL.Model)
+
+Return a `NamedTuple` of realizations from the prior of `model` compatible with `varnames(model)`.
+"""
+function rand_prior_true(model::DynamicPPL.Model)
+    return rand_prior_true(Random.default_rng(), model)
+end
+
 """
     demo_dynamic_constraint()
 
@@ -263,10 +272,8 @@ function logprior_true_with_logabsdet_jacobian(
     return (x=x_unconstrained,), logprior_true(model, x) - Δlogp
 end
 
-function Random.rand(
-    rng::Random.AbstractRNG,
-    ::Type{NamedTuple},
-    model::Model{typeof(demo_one_variable_multiple_constraints)},
+function rand_prior_true(
+    rng::Random.AbstractRNG, model::Model{typeof(demo_one_variable_multiple_constraints)}
 )
     x = Vector{Float64}(undef, 5)
     x[1] = rand(rng, Normal())
@@ -310,9 +317,7 @@ function logprior_true_with_logabsdet_jacobian(model::Model{typeof(demo_lkjchol)
     return (x=x_unconstrained,), logprior_true(model, x) - Δlogp
 end
 
-function Random.rand(
-    rng::Random.AbstractRNG, ::Type{NamedTuple}, model::Model{typeof(demo_lkjchol)}
-)
+function rand_prior_true(rng::Random.AbstractRNG, model::Model{typeof(demo_lkjchol)})
     x = rand(rng, LKJCholesky(model.args.d, 1.0))
     return (x=x,)
 end
@@ -724,12 +729,6 @@ const DemoModels = Union{
     Model{typeof(demo_assume_matrix_dot_observe_matrix)},
 }
 
-# We require demo models to have explict impleentations of `rand` since we want
-# these to be considered as ground truth.
-function Random.rand(rng::Random.AbstractRNG, ::Type{NamedTuple}, model::DemoModels)
-    return error("demo models requires explicit implementation of rand")
-end
-
 const UnivariateAssumeDemoModels = Union{
     Model{typeof(demo_assume_dot_observe)},Model{typeof(demo_assume_literal_dot_observe)}
 }
@@ -743,9 +742,7 @@ function posterior_optima(::UnivariateAssumeDemoModels)
     # TODO: Figure out exact for `s`.
     return (s=0.907407, m=7 / 6)
 end
-function Random.rand(
-    rng::Random.AbstractRNG, ::Type{NamedTuple}, model::UnivariateAssumeDemoModels
-)
+function rand_prior_true(rng::Random.AbstractRNG, model::UnivariateAssumeDemoModels)
     s = rand(rng, InverseGamma(2, 3))
     m = rand(rng, Normal(0, sqrt(s)))
 
@@ -766,7 +763,7 @@ const MultivariateAssumeDemoModels = Union{
 }
 function posterior_mean(model::MultivariateAssumeDemoModels)
     # Get some containers to fill.
-    vals = Random.rand(model)
+    vals = rand_prior_true(model)
 
     vals.s[1] = 19 / 8
     vals.m[1] = 3 / 4
@@ -778,7 +775,7 @@ function posterior_mean(model::MultivariateAssumeDemoModels)
 end
 function likelihood_optima(model::MultivariateAssumeDemoModels)
     # Get some containers to fill.
-    vals = Random.rand(model)
+    vals = rand_prior_true(model)
 
     # NOTE: These are "as close to zero as we can get".
     vals.s[1] = 1e-32
@@ -791,7 +788,7 @@ function likelihood_optima(model::MultivariateAssumeDemoModels)
 end
 function posterior_optima(model::MultivariateAssumeDemoModels)
     # Get some containers to fill.
-    vals = Random.rand(model)
+    vals = rand_prior_true(model)
 
     # TODO: Figure out exact for `s[1]`.
     vals.s[1] = 0.890625
@@ -801,9 +798,7 @@ function posterior_optima(model::MultivariateAssumeDemoModels)
 
     return vals
 end
-function Random.rand(
-    rng::Random.AbstractRNG, ::Type{NamedTuple}, model::MultivariateAssumeDemoModels
-)
+function rand_prior_true(rng::Random.AbstractRNG, model::MultivariateAssumeDemoModels)
     # Get template values from `model`.
     retval = model(rng)
     vals = (s=retval.s, m=retval.m)
@@ -821,7 +816,7 @@ const MatrixvariateAssumeDemoModels = Union{
 }
 function posterior_mean(model::MatrixvariateAssumeDemoModels)
     # Get some containers to fill.
-    vals = Random.rand(model)
+    vals = rand_prior_true(model)
 
     vals.s[1, 1] = 19 / 8
     vals.m[1] = 3 / 4
@@ -833,7 +828,7 @@ function posterior_mean(model::MatrixvariateAssumeDemoModels)
 end
 function likelihood_optima(model::MatrixvariateAssumeDemoModels)
     # Get some containers to fill.
-    vals = Random.rand(model)
+    vals = rand_prior_true(model)
 
     # NOTE: These are "as close to zero as we can get".
     vals.s[1, 1] = 1e-32
@@ -846,7 +841,7 @@ function likelihood_optima(model::MatrixvariateAssumeDemoModels)
 end
 function posterior_optima(model::MatrixvariateAssumeDemoModels)
     # Get some containers to fill.
-    vals = Random.rand(model)
+    vals = rand_prior_true(model)
 
     # TODO: Figure out exact for `s[1]`.
     vals.s[1, 1] = 0.890625
@@ -856,9 +851,7 @@ function posterior_optima(model::MatrixvariateAssumeDemoModels)
 
     return vals
 end
-function Base.rand(
-    rng::Random.AbstractRNG, ::Type{NamedTuple}, model::MatrixvariateAssumeDemoModels
-)
+function rand_prior_true(rng::Random.AbstractRNG, model::MatrixvariateAssumeDemoModels)
     # Get template values from `model`.
     retval = model(rng)
     vals = (s=retval.s, m=retval.m)
@@ -954,6 +947,14 @@ function logprior_true_with_logabsdet_jacobian(
     return _demo_logprior_true_with_logabsdet_jacobian(model, s, m)
 end
 
+function rand_prior_true(
+    rng::Random.AbstractRNG, model::Model{typeof(demo_static_transformation)}
+)
+    s = rand(rng, InverseGamma(2, 3))
+    m = rand(rng, Normal(0, sqrt(s)))
+    return (s=s, m=m)
+end
+
 """
     marginal_mean_of_samples(chain, varname)
 

test/linking.jl

@@ -72,7 +72,8 @@ end
         @model demo() = m ~ dist
         model = demo()
 
-        vis = DynamicPPL.TestUtils.setup_varinfos(model, rand(model), (@varname(m),))
+        example_values = rand(NamedTuple, model)
+        vis = DynamicPPL.TestUtils.setup_varinfos(model, example_values, (@varname(m),))
         @testset "$(short_varinfo_name(vi))" for vi in vis
             # Evaluate once to ensure we have `logp` value.
             vi = last(DynamicPPL.evaluate!!(model, vi, DefaultContext()))
@@ -105,7 +106,7 @@ end
             @testset "d=$d" for d in [2, 3, 5]
                 model = demo_lkj(d)
                 dist = LKJCholesky(d, 1.0, uplo)
-                values_original = rand(model)
+                values_original = rand(NamedTuple, model)
                 vis = DynamicPPL.TestUtils.setup_varinfos(
                     model, values_original, (@varname(x),)
                 )
@@ -146,7 +147,8 @@ end
         @model demo_dirichlet(d::Int) = x ~ Dirichlet(d, 1.0)
         @testset "d=$d" for d in [2, 3, 5]
             model = demo_dirichlet(d)
-            vis = DynamicPPL.TestUtils.setup_varinfos(model, rand(model), (@varname(x),))
+            example_values = rand(NamedTuple, model)
+            vis = DynamicPPL.TestUtils.setup_varinfos(model, example_values, (@varname(x),))
             @testset "$(short_varinfo_name(vi))" for vi in vis
                 lp = logpdf(Dirichlet(d, 1.0), vi[:])
                 @test length(vi[:]) == d

test/logdensityfunction.jl

@@ -2,7 +2,7 @@ using Test, DynamicPPL, LogDensityProblems
 
 @testset "LogDensityFunction" begin
     @testset "$(nameof(model))" for model in DynamicPPL.TestUtils.DEMO_MODELS
-        example_values = rand(NamedTuple, model)
+        example_values = DynamicPPL.TestUtils.rand_prior_true(model)
         vns = DynamicPPL.TestUtils.varnames(model)
         varinfos = DynamicPPL.TestUtils.setup_varinfos(model, example_values, vns)
 

test/loglikelihoods.jl

@@ -1,6 +1,6 @@
 @testset "loglikelihoods.jl" begin
     @testset "$(m.f)" for m in DynamicPPL.TestUtils.DEMO_MODELS
-        example_values = rand(NamedTuple, m)
+        example_values = DynamicPPL.TestUtils.rand_prior_true(m)
 
         # Instantiate a `VarInfo` with the example values.
         vi = VarInfo(m)

test/model.jl

@@ -222,7 +222,7 @@ is_typed_varinfo(varinfo::DynamicPPL.SimpleVarInfo{<:NamedTuple}) = true
         Random.seed!(1776)
         s, m = model()
         sample_namedtuple = (; s=s, m=m)
-        sample_dict = Dict(@varname(s) => s, @varname(m) => m)
+        sample_dict = OrderedDict(@varname(s) => s, @varname(m) => m)
 
         # With explicit RNG
         @test rand(Random.seed!(1776), model) == sample_namedtuple
@@ -235,7 +235,7 @@ is_typed_varinfo(varinfo::DynamicPPL.SimpleVarInfo{<:NamedTuple}) = true
         Random.seed!(1776)
         @test rand(NamedTuple, model) == sample_namedtuple
         Random.seed!(1776)
-        @test rand(Dict, model) == sample_dict
+        @test rand(OrderedDict, model) == sample_dict
     end
 
     @testset "default arguments" begin
@@ -263,7 +263,21 @@ is_typed_varinfo(varinfo::DynamicPPL.SimpleVarInfo{<:NamedTuple}) = true
 
     @testset "TestUtils" begin
         @testset "$(model.f)" for model in DynamicPPL.TestUtils.DEMO_MODELS
-            x = rand(model)
+            x = DynamicPPL.TestUtils.rand_prior_true(model)
+            # `rand_prior_true` should return a `NamedTuple`.
+            @test x isa NamedTuple
+
+            # `rand` with a `AbstractDict` should have `varnames` as keys.
+            x_rand_dict = rand(OrderedDict, model)
+            for vn in DynamicPPL.TestUtils.varnames(model)
+                @test haskey(x_rand_dict, vn)
+            end
+            # `rand` with a `NamedTuple` should have `map(Symbol, varnames)` as keys.
+            x_rand_nt = rand(NamedTuple, model)
+            for vn in DynamicPPL.TestUtils.varnames(model)
+                @test haskey(x_rand_nt, Symbol(vn))
+            end
+
             # Ensure log-probability computations are implemented.
             @test logprior(model, x) ≈ DynamicPPL.TestUtils.logprior_true(model, x...)
             @test loglikelihood(model, x) ≈

test/simple_varinfo.jl

@@ -60,7 +60,7 @@
 
     @testset "link!! & invlink!! on $(nameof(model))" for model in
                                                           DynamicPPL.TestUtils.DEMO_MODELS
-        values_constrained = rand(NamedTuple, model)
+        values_constrained = DynamicPPL.TestUtils.rand_prior_true(model)
         @testset "$(typeof(vi))" for vi in (
             SimpleVarInfo(Dict()), SimpleVarInfo(values_constrained), VarInfo(model)
         )
@@ -112,7 +112,7 @@
 
         # We might need to pre-allocate for the variable `m`, so we need
         # to see whether this is the case.
-        svi_nt = SimpleVarInfo(rand(NamedTuple, model))
+        svi_nt = SimpleVarInfo(DynamicPPL.TestUtils.rand_prior_true(model))
         svi_dict = SimpleVarInfo(VarInfo(model), Dict)
 
         @testset "$(nameof(typeof(DynamicPPL.values_as(svi))))" for svi in (
@@ -121,7 +121,7 @@
             DynamicPPL.settrans!!(svi_nt, true),
             DynamicPPL.settrans!!(svi_dict, true),
         )
-            # Random seed is set in each `@testset`, so we need to sample
+            # RandOM seed is set in each `@testset`, so we need to sample
             # a new realization for `m` here.
             retval = model()
 
@@ -138,7 +138,7 @@
             @test getlogp(svi_new) != 0
 
             ### Evaluation ###
-            values_eval_constrained = rand(NamedTuple, model)
+            values_eval_constrained = DynamicPPL.TestUtils.rand_prior_true(model)
             if DynamicPPL.istrans(svi)
                 _values_prior, logpri_true = DynamicPPL.TestUtils.logprior_true_with_logabsdet_jacobian(
                     model, values_eval_constrained...
@@ -225,7 +225,7 @@
         model = DynamicPPL.TestUtils.demo_static_transformation()
 
         varinfos = DynamicPPL.TestUtils.setup_varinfos(
-            model, rand(NamedTuple, model), [@varname(s), @varname(m)]
+            model, DynamicPPL.TestUtils.rand_prior_true(model), [@varname(s), @varname(m)]
         )
         @testset "$(short_varinfo_name(vi))" for vi in varinfos
             # Initialize varinfo and link.

test/varinfo.jl

@@ -338,7 +338,7 @@ DynamicPPL.getspace(::DynamicPPL.Sampler{MySAlg}) = (:s,)
 
     @testset "values_as" begin
         @testset "$(nameof(model))" for model in DynamicPPL.TestUtils.DEMO_MODELS
-            example_values = rand(NamedTuple, model)
+            example_values = DynamicPPL.TestUtils.rand_prior_true(model)
             vns = DynamicPPL.TestUtils.varnames(model)
 
             # Set up the different instances of `AbstractVarInfo` with the desired values.
@@ -385,7 +385,7 @@ DynamicPPL.getspace(::DynamicPPL.Sampler{MySAlg}) = (:s,)
             DynamicPPL.TestUtils.demo_lkjchol(),
         ]
             @testset "mutating=$mutating" for mutating in [false, true]
-                value_true = rand(model)
+                value_true = DynamicPPL.TestUtils.rand_prior_true(model)
                 varnames = DynamicPPL.TestUtils.varnames(model)
                 varinfos = DynamicPPL.TestUtils.setup_varinfos(
                     model, value_true, varnames; include_threadsafe=true
@@ -541,7 +541,10 @@ DynamicPPL.getspace(::DynamicPPL.Sampler{MySAlg}) = (:s,)
         @testset "$(model.f)" for model in DynamicPPL.TestUtils.DEMO_MODELS
             vns = DynamicPPL.TestUtils.varnames(model)
             varinfos = DynamicPPL.TestUtils.setup_varinfos(
-                model, rand(model), vns; include_threadsafe=true
+                model,
+                DynamicPPL.TestUtils.rand_prior_true(model),
+                vns;
+                include_threadsafe=true,
             )
             @testset "$(short_varinfo_name(varinfo))" for varinfo in varinfos
                 @testset "with itself" begin
@@ -581,7 +584,7 @@ DynamicPPL.getspace(::DynamicPPL.Sampler{MySAlg}) = (:s,)
                 end
 
                 @testset "with different value" begin
-                    x = DynamicPPL.TestUtils.rand(model)
+                    x = DynamicPPL.TestUtils.rand_prior_true(model)
                     varinfo_changed = DynamicPPL.TestUtils.update_values!!(
                         deepcopy(varinfo), x, vns
                     )