More precise deprecations of linear indexing

Noticed in SciML/Catalyst.jl#1248, the linear indexing is actually fine when done on scalar arrays because that matches the linear indexing that you get from an AbstractArray interface. So instead the deprecations are made more precise to be just about the array of array case.

Author: ChrisRackauckas

src/vector_of_array.jl

@@ -388,29 +388,32 @@ end
 @inline Base.IteratorSize(::Type{<:AbstractVectorOfArray}) = Base.HasLength()
 @inline Base.first(VA::AbstractVectorOfArray) = first(VA.u)
 @inline Base.last(VA::AbstractVectorOfArray) = last(VA.u)
-function Base.firstindex(VA::AbstractVectorOfArray)
-    Base.depwarn(
+function Base.firstindex(VA::AbstractVectorOfArray{T,N,A}) where {T,N,A}
+    N > 1 && Base.depwarn(
         "Linear indexing of `AbstractVectorOfArray` is deprecated. Change `A[i]` to `A.u[i]` ",
         :firstindex)
     return firstindex(VA.u)
 end
 
-function Base.lastindex(VA::AbstractVectorOfArray)
-    Base.depwarn(
+function Base.lastindex(VA::AbstractVectorOfArray{T,N,A}) where {T,N,A}
+     N > 1 && Base.depwarn(
         "Linear indexing of `AbstractVectorOfArray` is deprecated. Change `A[i]` to `A.u[i]` ",
         :lastindex)
     return lastindex(VA.u)
 end
 
-@deprecate Base.getindex(A::AbstractVectorOfArray, I::Int) Base.getindex(A, :, I) false
+Base.getindex(A::AbstractVectorOfArray, I::Int) = A.u[I]
+Base.getindex(A::AbstractVectorOfArray, I::AbstractArray{Int}) = A.u[I]
+Base.getindex(A::AbstractDiffEqArray, I::Int) = A.u[I]
+Base.getindex(A::AbstractDiffEqArray, I::AbstractArray{Int}) = A.u[I]
 
-@deprecate Base.getindex(A::AbstractVectorOfArray, I::AbstractArray{Int}) Base.getindex(
-    A, :, I) false
+@deprecate Base.getindex(A::AbstractVectorOfArray{T,N,A}, I::Int) where {T,N,A<:Union{AbstractArray, AbstractVectorOfArray}} A.u[I] false
 
-@deprecate Base.getindex(A::AbstractDiffEqArray, I::AbstractArray{Int}) Base.getindex(
-    A, :, I) false
+@deprecate Base.getindex(A::AbstractVectorOfArray{T,N,A}, I::AbstractArray{Int}) where {T,N,A<:Union{AbstractArray, AbstractVectorOfArray}} A.u[I] false
 
-@deprecate Base.getindex(A::AbstractDiffEqArray, i::Int) Base.getindex(A, :, i) false
+@deprecate Base.getindex(A::AbstractDiffEqArray{T,N,A}, I::AbstractArray{Int}) where {T,N,A<:Union{AbstractArray, AbstractVectorOfArray}} A.u[I] false
+
+@deprecate Base.getindex(A::AbstractDiffEqArray{T,N,A}, i::Int) where {T,N,A<:Union{AbstractArray, AbstractVectorOfArray}} A.u[i] false
 
 __parameterless_type(T) = Base.typename(T).wrapper
 
@@ -520,22 +523,25 @@ Base.@propagate_inbounds function Base.setindex!(VA::AbstractVectorOfArray{T, N}
     VA.u[I] = v
 end
 
-@deprecate Base.setindex!(VA::AbstractVectorOfArray, v, I::Int) Base.setindex!(VA, v, :, I) false
+Base.@propagate_inbounds Base.setindex!(VA::AbstractVectorOfArray, v, I::Int) = Base.setindex!(VA.u, v, I)
+@deprecate Base.setindex!(VA::AbstractVectorOfArray{T,N,A}, v, I::Int) where {T,N,A<:Union{AbstractArray, AbstractVectorOfArray}} Base.setindex!(VA.u, v, I) false
 
 Base.@propagate_inbounds function Base.setindex!(VA::AbstractVectorOfArray{T, N}, v,
         ::Colon, I::Colon) where {T, N}
     VA.u[I] = v
 end
 
-@deprecate Base.setindex!(VA::AbstractVectorOfArray, v, I::Colon) Base.setindex!(
-    VA, v, :, I) false
+Base.@propagate_inbounds Base.setindex!(VA::AbstractVectorOfArray, v, I::Colon) = Base.setindex!(VA.u, v, I)
+@deprecate Base.setindex!(VA::AbstractVectorOfArray{T,N,A}, v, I::Colon)  where {T,N,A<:Union{AbstractArray, AbstractVectorOfArray}} Base.setindex!(
+    VA.u, v, I) false
 
 Base.@propagate_inbounds function Base.setindex!(VA::AbstractVectorOfArray{T, N}, v,
         ::Colon, I::AbstractArray{Int}) where {T, N}
     VA.u[I] = v
 end
 
-@deprecate Base.setindex!(VA::AbstractVectorOfArray, v, I::AbstractArray{Int}) Base.setindex!(
+Base.@propagate_inbounds Base.setindex!(VA::AbstractVectorOfArray, v, I::AbstractArray{Int}) = Base.setindex!(VA.u, v, I)
+@deprecate Base.setindex!(VA::AbstractVectorOfArray{T,N,A}, v, I::AbstractArray{Int}) where {T,N,A<:Union{AbstractArray, AbstractVectorOfArray}} Base.setindex!(
     VA, v, :, I) false
 
 Base.@propagate_inbounds function Base.setindex!(