Merge branch 'jc/NamedArrayPartition' of https://github.com/jlchan/RecursiveArrayTools.jl into jc/NamedArrayPartition

Author: jlchan

Project.toml

@@ -39,7 +39,7 @@ RecipesBase = "0.7, 0.8, 1.0"
 Requires = "1.0"
 StaticArraysCore = "1.1"
 Statistics = "1"
-SymbolicIndexingInterface = "0.1, 0.2"
+SymbolicIndexingInterface = "0.3"
 Tables = "1"
 Zygote = "0.6.56"
 julia = "1.6"

docs/make.jl

@@ -6,13 +6,13 @@ cp("./docs/Project.toml", "./docs/src/assets/Project.toml", force = true)
 include("pages.jl")
 
 makedocs(sitename = "RecursiveArrayTools.jl",
-         authors = "Chris Rackauckas",
-         modules = [RecursiveArrayTools],
-         clean = true, doctest = false, linkcheck = true,
-         warnonly = [:missing_docs],
-         format = Documenter.HTML(assets = ["assets/favicon.ico"],
-                                  canonical = "https://docs.sciml.ai/RecursiveArrayTools/stable/"),
-         pages = pages)
+    authors = "Chris Rackauckas",
+    modules = [RecursiveArrayTools],
+    clean = true, doctest = false, linkcheck = true,
+    warnonly = [:missing_docs],
+    format = Documenter.HTML(assets = ["assets/favicon.ico"],
+        canonical = "https://docs.sciml.ai/RecursiveArrayTools/stable/"),
+    pages = pages)
 
 deploydocs(repo = "github.com/SciML/RecursiveArrayTools.jl.git";
-           push_preview = true)
+    push_preview = true)

ext/RecursiveArrayToolsMeasurementsExt.jl

@@ -4,8 +4,8 @@ import RecursiveArrayTools
 isdefined(Base, :get_extension) ? (import Measurements) : (import ..Measurements)
 
 function RecursiveArrayTools.recursive_unitless_bottom_eltype(a::Type{
-                                                                      <:Measurements.Measurement
-                                                                      })
+    <:Measurements.Measurement,
+})
     typeof(oneunit(a))
 end
 

ext/RecursiveArrayToolsMonteCarloMeasurementsExt.jl

@@ -1,15 +1,18 @@
 module RecursiveArrayToolsMonteCarloMeasurementsExt
 
 import RecursiveArrayTools
-isdefined(Base, :get_extension) ? (import MonteCarloMeasurements) : (import ..MonteCarloMeasurements)
+isdefined(Base, :get_extension) ? (import MonteCarloMeasurements) :
+(import ..MonteCarloMeasurements)
 
 function RecursiveArrayTools.recursive_unitless_bottom_eltype(a::Type{
-                                                                      <:MonteCarloMeasurements.Particles
-                                                                      })
+    <:MonteCarloMeasurements.Particles,
+})
     typeof(one(a))
 end
 
-function RecursiveArrayTools.recursive_unitless_eltype(a::Type{<:MonteCarloMeasurements.Particles})
+function RecursiveArrayTools.recursive_unitless_eltype(a::Type{
+    <:MonteCarloMeasurements.Particles,
+})
     typeof(one(a))
 end
 

ext/RecursiveArrayToolsTrackerExt.jl

@@ -4,12 +4,12 @@ import RecursiveArrayTools
 isdefined(Base, :get_extension) ? (import Tracker) : (import ..Tracker)
 
 function RecursiveArrayTools.recursivecopy!(b::AbstractArray{T, N},
-                                            a::AbstractArray{T2, N}) where {
-                                                                            T <:
-                                                                            Tracker.TrackedArray,
-                                                                            T2 <:
-                                                                            Tracker.TrackedArray,
-                                                                            N}
+    a::AbstractArray{T2, N}) where {
+    T <:
+    Tracker.TrackedArray,
+    T2 <:
+    Tracker.TrackedArray,
+    N}
     @inbounds for i in eachindex(a)
         b[i] = copy(a[i])
     end

ext/RecursiveArrayToolsZygoteExt.jl

@@ -14,7 +14,7 @@ end
 ChainRulesCore.ProjectTo(x::VectorOfArray) = ChainRulesCore.ProjectTo{VectorOfArray}()
 
 function ChainRulesCore.rrule(T::Type{<:RecursiveArrayTools.GPUArraysCore.AbstractGPUArray},
-                              xs::AbstractVectorOfArray)
+    xs::AbstractVectorOfArray)
     T(xs), ȳ -> (ChainRulesCore.NoTangent(), ȳ)
 end
 
@@ -28,7 +28,7 @@ end
 end
 
 @adjoint function getindex(VA::AbstractVectorOfArray,
-                           i::Union{BitArray, AbstractArray{Bool}})
+    i::Union{BitArray, AbstractArray{Bool}})
     function AbstractVectorOfArray_getindex_adjoint(Δ)
         Δ′ = [(i[j] ? Δ[j] : FillArrays.Fill(zero(eltype(x)), size(x)))
               for (x, j) in zip(VA.u, 1:length(VA))]
@@ -48,7 +48,7 @@ end
 end
 
 @adjoint function getindex(VA::AbstractVectorOfArray,
-                           i::Union{Int, AbstractArray{Int}})
+    i::Union{Int, AbstractArray{Int}})
     function AbstractVectorOfArray_getindex_adjoint(Δ)
         Δ′ = [(i[j] ? Δ[j] : FillArrays.Fill(zero(eltype(x)), size(x)))
               for (x, j) in zip(VA.u, 1:length(VA))]
@@ -65,8 +65,8 @@ end
 end
 
 @adjoint function getindex(VA::AbstractVectorOfArray, i::Int,
-                           j::Union{Int, AbstractArray{Int}, CartesianIndex,
-                                    Colon, BitArray, AbstractArray{Bool}}...)
+    j::Union{Int, AbstractArray{Int}, CartesianIndex,
+        Colon, BitArray, AbstractArray{Bool}}...)
     function AbstractVectorOfArray_getindex_adjoint(Δ)
         Δ′ = VectorOfArray([zero(x) for (x, j) in zip(VA.u, 1:length(VA))])
         Δ′[i, j...] = Δ
@@ -76,11 +76,11 @@ end
 end
 
 @adjoint function ArrayPartition(x::S,
-                                 ::Type{Val{copy_x}} = Val{false}) where {
-                                                                          S <:
-                                                                          Tuple,
-                                                                          copy_x
-                                                                          }
+    ::Type{Val{copy_x}} = Val{false}) where {
+    S <:
+    Tuple,
+    copy_x,
+}
     function ArrayPartition_adjoint(_y)
         y = Array(_y)
         starts = vcat(0, cumsum(reduce(vcat, length.(x))))
@@ -93,14 +93,21 @@ end
 
 @adjoint function VectorOfArray(u)
     VectorOfArray(u),
-    y -> (VectorOfArray([y[ntuple(x -> Colon(), ndims(y) - 1)..., i]
-                         for i in 1:size(y)[end]]),)
+    y -> begin
+        y isa Ref && (y = VectorOfArray(y[].u))
+        (VectorOfArray([y[ntuple(x -> Colon(), ndims(y.u) - 1)..., i]
+                        for i in 1:size(y.u)[end]]),)
+    end
 end
 
 @adjoint function DiffEqArray(u, t)
     DiffEqArray(u, t),
-    y -> (DiffEqArray([y[ntuple(x -> Colon(), ndims(y) - 1)..., i] for i in 1:size(y)[end]],
-                      t), nothing)
+    y -> begin
+        y isa Ref && (y = VectorOfArray(y[].u))
+        (DiffEqArray([y[ntuple(x -> Colon(), ndims(y.u) - 1)..., i]
+                       for i in 1:size(y.u)[end]],
+            t), nothing)
+    end
 end
 
 @adjoint function literal_getproperty(A::ArrayPartition, ::Val{:x})

src/RecursiveArrayTools.jl

@@ -6,14 +6,14 @@ module RecursiveArrayTools
 
 using DocStringExtensions
 using RecipesBase, StaticArraysCore, Statistics,
-      ArrayInterface, LinearAlgebra
+    ArrayInterface, LinearAlgebra
 using SymbolicIndexingInterface
 
 import Adapt
 
 import Tables, IteratorInterfaceExtensions
 
-abstract type AbstractVectorOfArray{T, N, A} <: AbstractArray{T, N} end
+abstract type AbstractVectorOfArray{T, N, A} end
 abstract type AbstractDiffEqArray{T, N, A} <: AbstractVectorOfArray{T, N, A} end
 
 include("utils.jl")
@@ -32,18 +32,24 @@ Base.convert(T::Type{<:GPUArraysCore.AbstractGPUArray}, VA::AbstractVectorOfArra
 import Requires
 @static if !isdefined(Base, :get_extension)
     function __init__()
-        Requires.@require Measurements="eff96d63-e80a-5855-80a2-b1b0885c5ab7" begin include("../ext/RecursiveArrayToolsMeasurementsExt.jl") end
-        Requires.@require Tracker="9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" begin include("../ext/RecursiveArrayToolsTrackerExt.jl") end
-        Requires.@require Zygote="e88e6eb3-aa80-5325-afca-941959d7151f" begin include("../ext/RecursiveArrayToolsZygoteExt.jl") end
+        Requires.@require Measurements="eff96d63-e80a-5855-80a2-b1b0885c5ab7" begin
+            include("../ext/RecursiveArrayToolsMeasurementsExt.jl")
+        end
+        Requires.@require Tracker="9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c" begin
+            include("../ext/RecursiveArrayToolsTrackerExt.jl")
+        end
+        Requires.@require Zygote="e88e6eb3-aa80-5325-afca-941959d7151f" begin
+            include("../ext/RecursiveArrayToolsZygoteExt.jl")
+        end
     end
 end
 
 export VectorOfArray, DiffEqArray, AbstractVectorOfArray, AbstractDiffEqArray,
-       AllObserved, vecarr_to_vectors, tuples
+    AllObserved, vecarr_to_vectors, tuples
 
 export recursivecopy, recursivecopy!, recursivefill!, vecvecapply, copyat_or_push!,
-       vecvec_to_mat, recursive_one, recursive_mean, recursive_bottom_eltype,
-       recursive_unitless_bottom_eltype, recursive_unitless_eltype
+    vecvec_to_mat, recursive_one, recursive_mean, recursive_bottom_eltype,
+    recursive_unitless_bottom_eltype, recursive_unitless_eltype
 
 export ArrayPartition, NamedArrayPartition