[Merged by Bors] - Linearization/flattening of SimpleVarInfo

Project.toml

@@ -1,6 +1,6 @@
 name = "DynamicPPL"
 uuid = "366bfd00-2699-11ea-058f-f148b4cae6d8"
-version = "0.20.2"
+version = "0.21.0"
 
 [deps]
 AbstractMCMC = "80f14c24-f653-4e6a-9b94-39d6b0f70001"

docs/make.jl

@@ -3,7 +3,9 @@ using DynamicPPL
 using DynamicPPL: AbstractPPL
 
 # Doctest setup
-DocMeta.setdocmeta!(DynamicPPL, :DocTestSetup, :(using DynamicPPL); recursive=true)
+DocMeta.setdocmeta!(
+    DynamicPPL, :DocTestSetup, :(using DynamicPPL, Distributions); recursive=true
+)
 
 makedocs(;
     sitename="DynamicPPL",

docs/src/api.md

@@ -154,23 +154,56 @@ AbstractVarInfo
 
 ### Common API
 
+#### Accumulation of log-probabilities
+
 ```@docs
 getlogp
 setlogp!!
 acclogp!!
 resetlogp!!
 ```
 
+#### Variables and their realizations
+
 ```@docs
+keys
 getindex
+DynamicPPL.getindex_raw
 push!!
 empty!!
+isempty
 ```
 
 ```@docs
 values_as
 ```
 
+#### Transformations
+
+```@docs
+DynamicPPL.AbstractTransformation
+DynamicPPL.NoTransformation
+DynamicPPL.DynamicTransformation
+DynamicPPL.StaticTransformation
+```
+
+```@docs
+DynamicPPL.istrans
+DynamicPPL.settrans!!
+DynamicPPL.transformation
+DynamicPPL.link!!
+DynamicPPL.invlink!!
+DynamicPPL.default_transformation
+DynamicPPL.maybe_invlink_before_eval!!
+``` 
+
+#### Utils
+
+```@docs
+DynamicPPL.unflatten
+DynamicPPL.tonamedtuple
+```
+
 #### `SimpleVarInfo`
 
 ```@docs
@@ -189,10 +222,8 @@ TypedVarInfo
 One main characteristic of [`VarInfo`](@ref) is that samples are stored in a linearized form.
 
 ```@docs
-tonamedtuple
 link!
 invlink!
-istrans
 ```
 
 ```@docs

src/DynamicPPL.jl

@@ -59,7 +59,9 @@ export AbstractVarInfo,
     setorder!,
     istrans,
     link!,
+    link!!,
     invlink!,
+    invlink!!,
     tonamedtuple,
     values_as,
     # VarName (reexport from AbstractPPL)
@@ -125,27 +127,33 @@ export loglikelihood
 # Used here and overloaded in Turing
 function getspace end
 
-# Necessary forward declarations
 """
     AbstractVarInfo
 
 Abstract supertype for data structures that capture random variables when executing a
 probabilistic model and accumulate log densities such as the log likelihood or the
 log joint probability of the model.
 
-See also: [`VarInfo`](@ref)
+See also: [`VarInfo`](@ref), [`SimpleVarInfo`](@ref).
 """
 abstract type AbstractVarInfo <: AbstractModelTrace end
 
+const LEGACY_WARNING = """
+!!! warning
+    This method is considered legacy, and is likely to be deprecated in the future.
+"""
+
+# Necessary forward declarations
 include("utils.jl")
 include("selector.jl")
 include("model.jl")
 include("sampler.jl")
 include("varname.jl")
 include("distribution_wrappers.jl")
 include("contexts.jl")
-include("varinfo.jl")
+include("abstract_varinfo.jl")
 include("threadsafe.jl")
+include("varinfo.jl")
 include("simple_varinfo.jl")
 include("context_implementations.jl")
 include("compiler.jl")
@@ -154,5 +162,6 @@ include("compat/ad.jl")
 include("loglikelihoods.jl")
 include("submodel_macro.jl")
 include("test_utils.jl")
+include("transforming.jl")
 
 end # module