dont pirate convert: fix mauro3/Parameters.jl#73 (#20)

* dont pirate convert

* add helper functions

* docs

* drop shiftedabstractarray and generalize

Author: Pietro Vertechi

NEWS.md

@@ -1,3 +1,10 @@
+## ShiftedArrays 0.4 release notes
+
+### Breaking changes
+
+- Now conversion of `AbstractArray{<:ShiftedArray}` to `Array` or `OffsetArray` is done via `ShiftedArray.to_array` and `ShiftedArray.to_offsetarray` respectively rather than `Base.convert` to avoid type piracy.
+
+
 ## ShiftedArrays 0.3.1 release notes
 
 ### New features

README.md

@@ -246,19 +246,19 @@ mapreduce_vec(f, g, s, range, filter = isfinite)
 To collect a `Vector` of `ShiftedArrays` into a normal `Array`, simply:
 
 ```julia
-convert(Array, s, inds...)
+ShiftedArray.to_array(s, inds...)
 ```
 
 where you need as many `inds` as the dimensions of your `ShiftedArrays`. The output `Array` first few dimensions will be indexed by `inds` (though starting from `1`) and the last one will correspond to the index of the `ShiftedArray` within the `Array` of `ShiftedArrays`.
 
 Similarly, to collect a `Vector` of `ShiftedArrays` into an `OffseyArray` (if you want to preserve the `inds` as offset indices), simply:
 
 ```julia
-convert(OffsetArray, s, inds...)
+ShiftedArray.to_offsetarray(s, inds...)
 ```
 
 The output `OffsetArray` first few dimensions will be indexed by `inds` and the last one will correspond to the index of the `ShiftedArray` within the `Array` of `ShiftedArrays`.
 
 ## Warning
 
-This package uses `Missings` for missing data. `Missings` are known to be inefficient in Julia 0.6 and still have some problems when used in combination with `map`, `broadcast` or `collect` in the development version of Julia 0.7 (see [#25553](https://github.com/JuliaLang/julia/pull/25553) for a potential fix).
+This package uses `Missings` for missing data. `Missings` are known to be inefficient in Julia 0.6, but should work better in Julia 1.0.

src/offset.jl

@@ -1,9 +1,23 @@
-function Base.convert(::Type{<:Array}, ss::AbstractArray{<:ShiftedAbstractArray{<:Any, N}}, I::Vararg{<:AbstractArray, N}) where N
+"""
+`to_array(ss::AbstractArray{<:AbstractArray{<:Any, N}}, I::Vararg{<:AbstractArray, N}) where N`
+
+Collect a `AbstractArray` of `AbstractArrays` into a normal `Array` selecting indices `I` (can take negative values if inner `AbstractArrays` allow it).
+The output `Array` first few dimensions will be indexed by `I` (though starting from `1`)
+and the last one will correspond to the index of the inner `AbstractArray` within the `AbstractArray` of `AbstractArrays`.
+"""
+function to_array(ss::AbstractArray{<:AbstractArray{<:Any, N}}, I::Vararg{<:AbstractArray, N}) where N
     v = VectorOfArray([view(s, I...) for s in ss])
     Array(v)
 end
 
-function Base.convert(::Type{<:OffsetArray}, ss::AbstractArray{<:ShiftedAbstractArray{<:Any, N}}, I::Vararg{<:AbstractArray, N}) where N
-    m = convert(Array, ss, I...)
+"""
+`to_offsetarray(ss::AbstractArray{<:AbstractArray{<:Any, N}}, I::Vararg{<:AbstractArray, N}) where N`
+
+Collect a `AbstractArray` of `ShiftedArrays` into an `OffsetArray` selecting indices `I` (can take negative values if inner `AbstractArrays` allow it).
+The output `OffsetArray` first few dimensions will be indexed by `I`
+and the last one will correspond to the index of the inner `AbstractArray` within the `AbstractArray` of `AbstractArrays`.
+"""
+function to_offsetarray(ss::AbstractArray{<:AbstractArray{<:Any, N}}, I::Vararg{<:AbstractArray, N}) where N
+    m = to_array(ss, I...)
     OffsetArray(m, I..., last(Compat.axes(m)))
 end

src/reduce.jl

@@ -157,13 +157,13 @@ for (_mapreduce, mapreduce, reduce) in [(:_mapreduce, :mapreduce, :reduce), (:_m
         end
 
         # align the shifted arrays and apply _mapreduce
-        function ($mapreduce)(g, f, ss::AbstractArray{<:ShiftedAbstractArray{<:Any, N}}, args::Vararg{<:AbstractArray, N}; kwargs...) where{N}
+        function ($mapreduce)(g, f, ss::AbstractArray{<:ShiftedArray{<:Any, <:Any, N}}, args::Vararg{<:AbstractArray, N}; kwargs...) where{N}
             inds = Base.product(args...)
             [($_mapreduce)(g, f, (s[CartesianIndex(i)] for s in ss); kwargs...) for i in inds]
         end
 
         # define corresponding reduce methods
-        ($reduce)(op, ss::AbstractArray{<:ShiftedAbstractArray{<:Any, N}}, args::Vararg{<:AbstractArray, N}; kwargs...) where{N} =
+        ($reduce)(op, ss::AbstractArray{<:ShiftedArray{<:Any, <:Any, N}}, args::Vararg{<:AbstractArray, N}; kwargs...) where{N} =
             ($mapreduce)(identity, op, ss, args...; kwargs...)
     end
 end

src/shiftedarray.jl

@@ -59,8 +59,6 @@ struct ShiftedArray{T, M, N, S<:AbstractArray} <: AbstractArray{Union{T, M}, N}
     default::M
 end
 
-const ShiftedAbstractArray{T, N} = ShiftedArray{T, <:Any, N, <:Any}
-
 ShiftedArray(v::AbstractArray{T, N}, n = Tuple(0 for i in 1:N); default::M = missing) where {T, N, M} =
      ShiftedArray{T, M, N, typeof(v)}(v, _padded_tuple(v, n), default)
 

test/runtests.jl

@@ -115,6 +115,6 @@ end
 @testset "offset" begin
     v = [1, 3, 5, 6, 7, 8, 9, 11]
     ss = ShiftedArray.((v,), [-1, -3, -6])
-    @test isequal(convert(Array, ss, -1:2), [missing 3 7; 1 5 8; 3 6 9; 5 7 11])
-    @test isequal(convert(OffsetArray, ss, -1:2), OffsetArray([missing 3 7; 1 5 8; 3 6 9; 5 7 11], -1:2, 1:3))
+    @test isequal(ShiftedArrays.to_array(ss, -1:2), [missing 3 7; 1 5 8; 3 6 9; 5 7 11])
+    @test isequal(ShiftedArrays.to_offsetarray(ss, -1:2), OffsetArray([missing 3 7; 1 5 8; 3 6 9; 5 7 11], -1:2, 1:3))
 end