Depreciate@submodel l ~ m in favour of l ~ to_submodel(m); rename generated_quantities to returned

docs/src/api.md

@@ -14,10 +14,18 @@ These statements are rewritten by `@model` as calls of [internal functions](@ref
 @model
 ```
 
-One can nest models and call another model inside the model function with [`@submodel`](@ref).
+One can nest models and call another model inside the model function with [`@submodel`](@ref) and [`@returned_quantities(model)`](@ref).
 
 ```@docs
 @submodel
+@returned_quantities(model)
+```
+
+In the context of nesting models, it's also useful to prefix the variables in sub-models to avoid variable names clashing:
+
+```@docs
+@prefix
+DynamicPPL.prefix
 ```
 
 ### Type
@@ -118,10 +126,11 @@ It is possible to manually increase (or decrease) the accumulated log density fr
 @addlogprob!
 ```
 
-Return values of the model function for a collection of samples can be obtained with [`generated_quantities`](@ref).
+Return values of the model function for a collection of samples can be obtained with [`@returned_quantities`](@ref).
 
 ```@docs
-generated_quantities
+@returned_quantities(model, input)
+DynamicPPL.returned_quantities
 ```
 
 For a chain of samples, one can compute the pointwise log-likelihoods of each observed random variable with [`pointwise_loglikelihoods`](@ref). Similarly, the log-densities of the priors using

ext/DynamicPPLMCMCChainsExt.jl

@@ -43,7 +43,7 @@ function DynamicPPL.varnames(c::MCMCChains.Chains)
 end
 
 """
-    generated_quantities(model::Model, chain::MCMCChains.Chains)
+    returned_quantities(model::Model, chain::MCMCChains.Chains)
 
 Execute `model` for each of the samples in `chain` and return an array of the values
 returned by the `model` for each sample.
@@ -63,7 +63,7 @@ m = demo(data)
 chain = sample(m, alg, n)
 # To inspect the `interesting_quantity(θ, x)` where `θ` is replaced by samples
 # from the posterior/`chain`:
-generated_quantities(m, chain) # <= results in a `Vector` of returned values
+returned_quantities(m, chain) # <= results in a `Vector` of returned values
                                #    from `interesting_quantity(θ, x)`
 ```
 ## Concrete (and simple)
@@ -87,7 +87,7 @@ julia> model = demo(randn(10));
 
 julia> chain = sample(model, MH(), 10);
 
-julia> generated_quantities(model, chain)
+julia> returned_quantities(model, chain)
 10×1 Array{Tuple{Float64},2}:
  (2.1964758025119338,)
  (2.1964758025119338,)
@@ -101,7 +101,7 @@ julia> generated_quantities(model, chain)
  (-0.16489786710222099,)
 ```
 """
-function DynamicPPL.generated_quantities(
+function DynamicPPL.returned_quantities(
     model::DynamicPPL.Model, chain_full::MCMCChains.Chains
 )
     chain = MCMCChains.get_sections(chain_full, :parameters)

src/DynamicPPL.jl

@@ -86,7 +86,6 @@ export AbstractVarInfo,
     Model,
     getmissings,
     getargnames,
-    generated_quantities,
     extract_priors,
     values_as_in_model,
     # Samplers
@@ -125,6 +124,8 @@ export AbstractVarInfo,
     # Convenience macros
     @addlogprob!,
     @submodel,
+    @returned_quantities,
+    @prefix,
     value_iterator_from_chain,
     check_model,
     check_model_and_trace,
@@ -196,6 +197,8 @@ include("values_as_in_model.jl")
 include("debug_utils.jl")
 using .DebugUtils
 
+include("deprecated.jl")
+
 if !isdefined(Base, :get_extension)
     using Requires
 end

src/contexts.jl

@@ -294,6 +294,60 @@ function prefix(::PrefixContext{Prefix}, vn::VarName{Sym}) where {Prefix,Sym}
     end
 end
 
+"""
+    prefix(model::Model, x)
+
+Return `model` but with all random variables prefixed by `x`.
+
+If `x` is known at compile-time, use `Val{x}()` to avoid runtime overheads for prefixing.
+
+# Examples
+
+```jldoctest
+julia> using DynamicPPL: prefix
+
+julia> @model demo() = x ~ Dirac(1)
+demo (generic function with 2 methods)
+
+julia> rand(prefix(demo(), :my_prefix))
+(var"my_prefix.x" = 1,)
+
+julia> # One can also use `Val` to avoid runtime overheads.
+       rand(prefix(demo(), Val(:my_prefix)))
+(var"my_prefix.x" = 1,)
+```
+"""
+prefix(model::Model, x) = contextualize(model, PrefixContext{Symbol(x)}(model.context))
+function prefix(model::Model, ::Val{x}) where {x}
+    return contextualize(model, PrefixContext{Symbol(x)}(model.context))
+end
+
+"""
+    @prefix(model, prefix_expr)
+
+Return `model` but with all random variables prefixed by `prefix_expr`.
+
+The result of `prefix_expr` must will be converted to a `Symbol` and used as the prefix.
+
+!!! note
+    This is effectively just a convenience macro for the method [`DynamicPPL.prefix(::Model, x)`](@ref),
+    which automatically converts the result of `prefix_expr` into a `Val` to avoid runtime overheads
+    for static prefixes. For more control over the prefixing, use the method directly.
+
+# Examples
+
+```jldoctest
+julia> @model demo() = x ~ Dirac(1)
+demo (generic function with 2 methods)
+
+julia> rand(@prefix(demo(), :my_prefix))
+(var"my_prefix.x" = 1,)
+```
+"""
+macro prefix(model, prefix_expr)
+    return :($prefix($(esc(model)), $Val{$Symbol($(esc(prefix_expr)))}()))
+end
+
 struct ConditionContext{Values,Ctx<:AbstractContext} <: AbstractContext
     values::Values
     context::Ctx

src/deprecated.jl

@@ -0,0 +1 @@
+@deprecate generated_quantities returned_quantities

src/model.jl

@@ -1051,7 +1051,9 @@ function Base.rand(rng::Random.AbstractRNG, ::Type{T}, model::Model) where {T}
         evaluate!!(
             model,
             SimpleVarInfo{Float64}(OrderedDict()),
-            SamplingContext(rng, SampleFromPrior(), model.context),
+            # NOTE: Use `leafcontext` here so we a) avoid overriding the leaf context of `model`,
+            # and b) avoid double-stacking the parent contexts.
+            SamplingContext(rng, SampleFromPrior(), leafcontext(model.context)),
         ),
     )
     return values_as(x, T)
@@ -1204,9 +1206,9 @@ function Distributions.loglikelihood(model::Model, chain::AbstractMCMC.AbstractC
 end
 
 """
-    generated_quantities(model::Model, parameters::NamedTuple)
-    generated_quantities(model::Model, values, keys)
-    generated_quantities(model::Model, values, keys)
+    returned_quantities(model::Model, parameters::NamedTuple)
+    returned_quantities(model::Model, values, keys)
+    returned_quantities(model::Model, values, keys)
 
 Execute `model` with variables `keys` set to `values` and return the values returned by the `model`.
 
@@ -1231,18 +1233,30 @@ julia> model = demo(randn(10));
 
 julia> parameters = (; s = 1.0, m_shifted=10.0);
 
-julia> generated_quantities(model, parameters)
+julia> returned_quantities(model, parameters)
 (0.0,)
 
-julia> generated_quantities(model, values(parameters), keys(parameters))
+julia> returned_quantities(model, values(parameters), keys(parameters))
 (0.0,)
 ```
 """
-function generated_quantities(model::Model, parameters::NamedTuple)
+function returned_quantities(model::Model, parameters::NamedTuple)
     fixed_model = fix(model, parameters)
     return fixed_model()
 end
 
-function generated_quantities(model::Model, values, keys)
-    return generated_quantities(model, NamedTuple{keys}(values))
+function returned_quantities(model::Model, values, keys)
+    return returned_quantities(model, NamedTuple{keys}(values))
+end
+
+"""
+    @returned_quantities(model, input)
+
+Execute `model` and extract the return-values of `model` for `input`.
+
+!!! note
+    This macro is in fact a simple wrapper around the method [`DynamicPPL.returned_quantities`](@ref).
+"""
+macro returned_quantities(model_expr, input_expr)
+    return :($returned_quantities($(esc(model_expr)), $(esc(input_expr))))
 end