Replacing tonamedtuple (#526)

* added impl of varname_and_value_leaves

* added examples with cholesky to varname_and_value_leaves doctests

* added more descriptive docstring of iterate for Leaf

* added concrete example in comment of iterate for Leaf

* added small docstring to Leaf

* Update src/utils.jl

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

---------

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

Author: torfjelde

docs/src/api.md

@@ -255,6 +255,8 @@ DynamicPPL.reconstruct
 ```@docs
 DynamicPPL.unflatten
 DynamicPPL.tonamedtuple
+DynamicPPL.varname_leaves
+DynamicPPL.varname_and_value_leaves
 ```
 
 #### `SimpleVarInfo`

src/DynamicPPL.jl

@@ -15,7 +15,7 @@ using Setfield: Setfield
 using ZygoteRules: ZygoteRules
 using LogDensityProblems: LogDensityProblems
 
-using LinearAlgebra: Cholesky
+using LinearAlgebra: LinearAlgebra, Cholesky
 
 using DocStringExtensions
 

src/utils.jl

@@ -870,3 +870,155 @@ function varname_leaves(vn::VarName, val::NamedTuple)
     end
     return Iterators.flatten(iter)
 end
+
+"""
+    varname_and_value_leaves(vn::VarName, val)
+
+Return an iterator over all varname-value pairs that are represented by `vn` on `val`.
+
+# Examples
+```jldoctest varname-and-value-leaves
+julia> using DynamicPPL: varname_and_value_leaves
+
+julia> foreach(println, varname_and_value_leaves(@varname(x), 1:2))
+(x[1], 1)
+(x[2], 2)
+
+julia> foreach(println, varname_and_value_leaves(@varname(x[1:2]), 1:2))
+(x[1:2][1], 1)
+(x[1:2][2], 2)
+
+julia> x = (y = 1, z = [[2.0], [3.0]]);
+
+julia> foreach(println, varname_and_value_leaves(@varname(x), x))
+(x.y, 1)
+(x.z[1][1], 2.0)
+(x.z[2][1], 3.0)
+```
+
+There are also some special handling for certain types:
+
+```jldoctest varname-and-value-leaves
+julia> using LinearAlgebra
+
+julia> x = reshape(1:4, 2, 2);
+
+julia> # `LowerTriangular`
+       foreach(println, varname_and_value_leaves(@varname(x), LowerTriangular(x)))
+(x[1,1], 1)
+(x[2,1], 2)
+(x[2,2], 4)
+
+julia> # `UpperTriangular`
+       foreach(println, varname_and_value_leaves(@varname(x), UpperTriangular(x)))
+(x[1,1], 1)
+(x[1,2], 3)
+(x[2,2], 4)
+
+julia> # `Cholesky` with lower-triangular
+       foreach(println, varname_and_value_leaves(@varname(x), Cholesky([1.0 0.0; 0.0 1.0], 'L', 0)))
+(x[1,1], 1.0)
+(x[2,1], 0.0)
+(x[2,2], 1.0)
+
+julia> # `Cholesky` with upper-triangular
+       foreach(println, varname_and_value_leaves(@varname(x), Cholesky([1.0 0.0; 0.0 1.0], 'U', 0)))
+(x[1,1], 1.0)
+(x[1,2], 0.0)
+(x[2,2], 1.0)
+```
+"""
+function varname_and_value_leaves(vn::VarName, x)
+    return Iterators.map(value, Iterators.flatten(varname_and_value_leaves_inner(vn, x)))
+end
+
+"""
+    Leaf{T}
+
+A container that represents the leaf of a nested structure, implementing
+`iterate` to return itself.
+
+This is particularly useful in conjunction with `Iterators.flatten` to
+prevent flattening of nested structures.
+"""
+struct Leaf{T}
+    value::T
+end
+
+Leaf(xs...) = Leaf(xs)
+
+# Allow us to treat `Leaf` as an iterator containing a single element.
+# Something like an `[x]` would also be an iterator with a single element,
+# but when we call `flatten` on this, it would also iterate over `x`,
+# unflattening that too. By making `Leaf` a single-element iterator, which
+# returns itself, we can call `iterate` on this as many times as we like
+# without causing any change. The result is that `Iterators.flatten`
+# will _not_ unflatten `Leaf`s.
+# Note that this is similar to how `Base.iterate` is implemented for `Real`::
+#
+#    julia> iterate(1)
+#    (1, nothing)
+#
+# One immediate example where this becomes in our scenario is that we might
+# have `missing` values in our data, which does _not_ have an `iterate`
+# implemented. Calling `Iterators.flatten` on this would cause an error.
+Base.iterate(leaf::Leaf) = leaf, nothing
+Base.iterate(::Leaf, _) = nothing
+
+# Convenience.
+value(leaf::Leaf) = leaf.value
+
+# Leaf-types.
+varname_and_value_leaves_inner(vn::VarName, x::Real) = [Leaf(vn, x)]
+function varname_and_value_leaves_inner(
+    vn::VarName, val::AbstractArray{<:Union{Real,Missing}}
+)
+    return (
+        Leaf(
+            VarName(vn, DynamicPPL.getlens(vn) ∘ DynamicPPL.Setfield.IndexLens(Tuple(I))),
+            val[I],
+        ) for I in CartesianIndices(val)
+    )
+end
+# Containers.
+function varname_and_value_leaves_inner(vn::VarName, val::AbstractArray)
+    return Iterators.flatten(
+        varname_and_value_leaves_inner(
+            VarName(vn, DynamicPPL.getlens(vn) ∘ DynamicPPL.Setfield.IndexLens(Tuple(I))),
+            val[I],
+        ) for I in CartesianIndices(val)
+    )
+end
+function varname_and_value_leaves_inner(vn::DynamicPPL.VarName, val::NamedTuple)
+    iter = Iterators.map(keys(val)) do sym
+        lens = DynamicPPL.Setfield.PropertyLens{sym}()
+        varname_and_value_leaves_inner(vn ∘ lens, get(val, lens))
+    end
+
+    return Iterators.flatten(iter)
+end
+# Special types.
+function varname_and_value_leaves_inner(vn::VarName, x::Cholesky)
+    # TODO: Or do we use `PDMat` here?
+    return varname_and_value_leaves_inner(vn, x.UL)
+end
+function varname_and_value_leaves_inner(vn::VarName, x::LinearAlgebra.LowerTriangular)
+    return (
+        Leaf(
+            VarName(vn, DynamicPPL.getlens(vn) ∘ DynamicPPL.Setfield.IndexLens(Tuple(I))),
+            x[I],
+        )
+        # Iteration over the lower-triangular indices.
+        for I in CartesianIndices(x) if I[1] >= I[2]
+    )
+end
+function varname_and_value_leaves_inner(vn::VarName, x::LinearAlgebra.UpperTriangular)
+    return (
+        Leaf(
+            VarName(vn, DynamicPPL.getlens(vn) ∘ DynamicPPL.Setfield.IndexLens(Tuple(I))),
+            x[I],
+        )
+        # Iteration over the upper-triangular indices.
+        for I in CartesianIndices(x) if I[1] <= I[2]
+    )
+end