Change signature of pairwise! and colwise! (#239)

Author: devmotion

README.md

@@ -132,14 +132,29 @@ If the vector/matrix to store the results are pre-allocated, you may use the
 storage (without creating a new array) using the following syntax
 (`i` being either `1` or `2`):
 
+```julia
+colwise!(dist, r, X, Y)
+pairwise!(dist, R, X, Y, dims=i)
+pairwise!(dist, R, X, dims=i)
+```
+
+Please pay attention to the difference, the functions for inplace computation are
+`colwise!` and `pairwise!` (instead of `colwise` and `pairwise`).
+
+#### Deprecated alternative syntax
+
+The syntax
+
 ```julia
 colwise!(r, dist, X, Y)
 pairwise!(R, dist, X, Y, dims=i)
 pairwise!(R, dist, X, dims=i)
 ```
 
-Please pay attention to the difference, the functions for inplace computation are
-`colwise!` and `pairwise!` (instead of `colwise` and `pairwise`).
+with the first two arguments (metric and results) interchanged is supported as well.
+However, its use is discouraged since
+[it is deprecated](https://github.com/JuliaStats/Distances.jl/pull/239) and will be
+removed in a future release.
 
 ## Distance type hierarchy
 

src/Distances.jl

@@ -118,4 +118,6 @@ include("mahalanobis.jl")
 include("bhattacharyya.jl")
 include("bregman.jl")
 
+include("deprecated.jl")
+
 end # module end

src/deprecated.jl

@@ -0,0 +1,69 @@
+Base.@deprecate pairwise!(r::AbstractMatrix, dist::PreMetric, a) pairwise!(dist, r, a)
+Base.@deprecate pairwise!(r::AbstractMatrix, dist::PreMetric, a, b) pairwise!(dist, r, a, b)
+
+Base.@deprecate pairwise!(
+    r::AbstractMatrix, dist::PreMetric, a::AbstractMatrix;
+    dims::Union{Nothing,Integer}=nothing
+) pairwise!(dist, r, a; dims=dims)
+Base.@deprecate pairwise!(
+    r::AbstractMatrix, dist::PreMetric, a::AbstractMatrix, b::AbstractMatrix;
+    dims::Union{Nothing,Integer}=nothing
+) pairwise!(dist, r, a, b; dims=dims)
+
+Base.@deprecate colwise!(r::AbstractArray, dist::PreMetric, a, b) colwise!(dist, r, a, b)
+
+# docstrings for deprecated methods
+@doc """
+    pairwise!(r::AbstractMatrix, dist::PreMetric, a)
+
+Same as `pairwise!(dist, r, a)`.
+
+!!! warning
+    Since this alternative syntax is deprecated and will be removed in a future release of
+    Distances.jl, its use is discouraged. Please call `pairwise!(dist, r, a)` instead.
+""" pairwise!(r::AbstractMatrix, dist::PreMetric, a)
+@doc """
+    pairwise!(r::AbstractMatrix, dist::PreMetric, a, b)
+
+Same as `pairwise!(dist, r, a, b)`.
+
+!!! warning
+    Since this alternative syntax is deprecated and will be removed in a future release of
+    Distances.jl, its use is discouraged. Please call `pairwise!(dist, r, a, b)` instead.
+""" pairwise!(r::AbstractMatrix, dist::PreMetric, a, b)
+
+@doc """
+    pairwise!(r::AbstractMatrix, dist::PreMetric, a::AbstractMatrix; dims)
+
+Same as `pairwise!(dist, r, a; dims)`.
+
+    !!! warning
+    Since this alternative syntax is deprecated and will be removed in a future release of
+    Distances.jl, its use is discouraged. Please call `pairwise!(dist, r, a; dims)` instead.
+""" pairwise!(
+    r::AbstractMatrix, dist::PreMetric, a::AbstractMatrix;
+    dims::Union{Nothing,Integer}
+)
+@doc """
+    pairwise!(r::AbstractMatrix, dist::PreMetric, a::AbstractMatrix, b::AbstractMatrix; dims)
+
+Same as `pairwise!(dist, r, a, b; dims)`.
+
+!!! warning
+    Since this alternative syntax is deprecated and will be removed in a future release of
+    Distances.jl, its use is discouraged. Please call `pairwise!(dist, r, a, b; dims)`
+    instead.
+""" pairwise!(
+    r::AbstractMatrix, dist::PreMetric, a::AbstractMatrix, b::AbstractMatrix;
+    dims::Union{Nothing,Integer}
+)
+
+@doc """
+    colwise!(r::AbstractArray, dist::PreMetric, a, b)
+
+Same as `colwise!(dist, r, a, b)`.
+
+!!! warning
+    Since this alternative syntax is deprecated and will be removed in a future release of
+    Distances.jl, its use is discouraged. Please call `colwise!(dist, r, a, b)` instead.
+""" colwise!(r::AbstractArray, dist::PreMetric, a, b)

src/generic.jl

@@ -46,15 +46,15 @@ __eltype(::Base.EltypeUnknown, a) = _eltype(typeof(first(a)))
 # Generic column-wise evaluation
 
 """
-    colwise!(r::AbstractArray, metric::PreMetric, a, b)
+    colwise!(metric::PreMetric, r::AbstractArray, a, b)
 
 Compute distances between corresponding elements of the iterable collections
 `a` and `b` according to distance `metric`, and store the result in `r`.
 
 `a` and `b` must have the same number of elements, `r` must be an array of length
 `length(a) == length(b)`.
 """
-function colwise!(r::AbstractArray, metric::PreMetric, a, b)
+function colwise!(metric::PreMetric, r::AbstractArray, a, b)
     require_one_based_indexing(r)
     n = length(a)
     length(b) == n || throw(DimensionMismatch("iterators have different lengths"))
@@ -65,7 +65,7 @@ function colwise!(r::AbstractArray, metric::PreMetric, a, b)
     r
 end
 
-function colwise!(r::AbstractArray, metric::PreMetric, a::AbstractVector, b::AbstractMatrix)
+function colwise!(metric::PreMetric, r::AbstractArray, a::AbstractVector, b::AbstractMatrix)
     require_one_based_indexing(r)
     n = size(b, 2)
     length(r) == n || throw(DimensionMismatch("Incorrect size of r."))
@@ -75,7 +75,7 @@ function colwise!(r::AbstractArray, metric::PreMetric, a::AbstractVector, b::Abs
     r
 end
 
-function colwise!(r::AbstractArray, metric::PreMetric, a::AbstractMatrix, b::AbstractVector)
+function colwise!(metric::PreMetric, r::AbstractArray, a::AbstractMatrix, b::AbstractVector)
     require_one_based_indexing(r)
     n = size(a, 2)
     length(r) == n || throw(DimensionMismatch("Incorrect size of r."))
@@ -86,11 +86,11 @@ function colwise!(r::AbstractArray, metric::PreMetric, a::AbstractMatrix, b::Abs
 end
 
 """
-    colwise!(r::AbstractArray, metric::PreMetric,
+    colwise!(metric::PreMetric, r::AbstractArray,
              a::AbstractMatrix, b::AbstractMatrix)
-    colwise!(r::AbstractArray, metric::PreMetric,
+    colwise!(metric::PreMetric, r::AbstractArray,
              a::AbstractVector, b::AbstractMatrix)
-    colwise!(r::AbstractArray, metric::PreMetric,
+    colwise!(metric::PreMetric, r::AbstractArray,
              a::AbstractMatrix, b::AbstractVector)
 
 Compute distances between each corresponding columns of `a` and `b` according
@@ -105,7 +105,7 @@ vector. `r` must be an array of length `maximum(size(a, 2), size(b, 2))`.
     If both `a` and `b` are vectors, the generic, iterator-based method of
     `colwise` applies.
 """
-function colwise!(r::AbstractArray, metric::PreMetric, a::AbstractMatrix, b::AbstractMatrix)
+function colwise!(metric::PreMetric, r::AbstractArray, a::AbstractMatrix, b::AbstractMatrix)
     require_one_based_indexing(r, a, b)
     n = get_common_ncols(a, b)
     length(r) == n || throw(DimensionMismatch("Incorrect size of r."))
@@ -126,7 +126,7 @@ Compute distances between corresponding elements of the iterable collections
 function colwise(metric::PreMetric, a, b)
     n = get_common_length(a, b)
     r = Vector{result_type(metric, a, b)}(undef, n)
-    colwise!(r, metric, a, b)
+    colwise!(metric, r, a, b)
 end
 
 """
@@ -148,25 +148,25 @@ vector.
 function colwise(metric::PreMetric, a::AbstractMatrix, b::AbstractMatrix)
     n = get_common_ncols(a, b)
     r = Vector{result_type(metric, a, b)}(undef, n)
-    colwise!(r, metric, a, b)
+    colwise!(metric, r, a, b)
 end
 
 function colwise(metric::PreMetric, a::AbstractVector, b::AbstractMatrix)
     n = size(b, 2)
     r = Vector{result_type(metric, a, b)}(undef, n)
-    colwise!(r, metric, a, b)
+    colwise!(metric, r, a, b)
 end
 
 function colwise(metric::PreMetric, a::AbstractMatrix, b::AbstractVector)
     n = size(a, 2)
     r = Vector{result_type(metric, a, b)}(undef, n)
-    colwise!(r, metric, a, b)
+    colwise!(metric, r, a, b)
 end
 
 
 # Generic pairwise evaluation
 
-function _pairwise!(r::AbstractMatrix, metric::PreMetric, a, b=a)
+function _pairwise!(metric::PreMetric, r::AbstractMatrix, a, b=a)
     require_one_based_indexing(r)
     na = length(a)
     nb = length(b)
@@ -177,7 +177,7 @@ function _pairwise!(r::AbstractMatrix, metric::PreMetric, a, b=a)
     r
 end
 
-function _pairwise!(r::AbstractMatrix, metric::PreMetric,
+function _pairwise!(metric::PreMetric, r::AbstractMatrix,
                     a::AbstractMatrix, b::AbstractMatrix=a)
     require_one_based_indexing(r, a, b)
     na = size(a, 2)
@@ -192,7 +192,7 @@ function _pairwise!(r::AbstractMatrix, metric::PreMetric,
     r
 end
 
-function _pairwise!(r::AbstractMatrix, metric::SemiMetric, a)
+function _pairwise!(metric::SemiMetric, r::AbstractMatrix, a)
     require_one_based_indexing(r)
     n = length(a)
     size(r) == (n, n) || throw(DimensionMismatch("Incorrect size of r."))
@@ -208,7 +208,7 @@ function _pairwise!(r::AbstractMatrix, metric::SemiMetric, a)
     r
 end
 
-function _pairwise!(r::AbstractMatrix, metric::SemiMetric, a::AbstractMatrix)
+function _pairwise!(metric::SemiMetric, r::AbstractMatrix, a::AbstractMatrix)
     require_one_based_indexing(r)
     n = size(a, 2)
     size(r) == (n, n) || throw(DimensionMismatch("Incorrect size of r."))
@@ -237,7 +237,7 @@ function deprecated_dims(dims::Union{Nothing,Integer})
 end
 
 """
-    pairwise!(r::AbstractMatrix, metric::PreMetric,
+    pairwise!(metric::PreMetric, r::AbstractMatrix,
               a::AbstractMatrix, b::AbstractMatrix=a; dims)
 
 Compute distances between each pair of rows (if `dims=1`) or columns (if `dims=2`)
@@ -247,7 +247,7 @@ If a single matrix `a` is provided, compute distances between its rows or column
 `a` and `b` must have the same numbers of columns if `dims=1`, or of rows if `dims=2`.
 `r` must be a matrix with size `size(a, dims) × size(b, dims)`.
 """
-function pairwise!(r::AbstractMatrix, metric::PreMetric,
+function pairwise!(metric::PreMetric, r::AbstractMatrix,
                    a::AbstractMatrix, b::AbstractMatrix;
                    dims::Union{Nothing,Integer}=nothing)
     dims = deprecated_dims(dims)
@@ -266,13 +266,13 @@ function pairwise!(r::AbstractMatrix, metric::PreMetric,
     size(r) == (na, nb) ||
         throw(DimensionMismatch("Incorrect size of r (got $(size(r)), expected $((na, nb)))."))
     if dims == 1
-        _pairwise!(r, metric, permutedims(a), permutedims(b))
+        _pairwise!(metric, r, permutedims(a), permutedims(b))
     else
-        _pairwise!(r, metric, a, b)
+        _pairwise!(metric, r, a, b)
     end
 end
 
-function pairwise!(r::AbstractMatrix, metric::PreMetric, a::AbstractMatrix;
+function pairwise!(metric::PreMetric, r::AbstractMatrix, a::AbstractMatrix;
                    dims::Union{Nothing,Integer}=nothing)
     dims = deprecated_dims(dims)
     dims in (1, 2) || throw(ArgumentError("dims should be 1 or 2 (got $dims)"))
@@ -284,23 +284,23 @@ function pairwise!(r::AbstractMatrix, metric::PreMetric, a::AbstractMatrix;
     size(r) == (n, n) ||
         throw(DimensionMismatch("Incorrect size of r (got $(size(r)), expected $((n, n)))."))
     if dims == 1
-        _pairwise!(r, metric, permutedims(a))
+        _pairwise!(metric, r, permutedims(a))
     else
-        _pairwise!(r, metric, a)
+        _pairwise!(metric, r, a)
     end
 end
 
 """
-    pairwise!(r::AbstractMatrix, metric::PreMetric, a, b=a)
+    pairwise!(metric::PreMetric, r::AbstractMatrix, a, b=a)
 
 Compute distances between each element of collection `a` and each element of
 collection `b` according to distance `metric`, and store the result in `r`.
 If a single iterable `a` is provided, compute distances between its elements.
 
 `r` must be a matrix with size `length(a) × length(b)`.
 """
-pairwise!(r::AbstractMatrix, metric::PreMetric, a, b) = _pairwise!(r, metric, a, b)
-pairwise!(r::AbstractMatrix, metric::PreMetric, a) = _pairwise!(r, metric, a)
+pairwise!(metric::PreMetric, r::AbstractMatrix, a, b) = _pairwise!(metric, r, a, b)
+pairwise!(metric::PreMetric, r::AbstractMatrix, a) = _pairwise!(metric, r, a)
 
 """
     pairwise(metric::PreMetric, a::AbstractMatrix, b::AbstractMatrix=a; dims)
@@ -318,7 +318,7 @@ function pairwise(metric::PreMetric, a::AbstractMatrix, b::AbstractMatrix;
     m = size(a, dims)
     n = size(b, dims)
     r = Matrix{result_type(metric, a, b)}(undef, m, n)
-    pairwise!(r, metric, a, b, dims=dims)
+    pairwise!(metric, r, a, b, dims=dims)
 end
 
 function pairwise(metric::PreMetric, a::AbstractMatrix;
@@ -327,7 +327,7 @@ function pairwise(metric::PreMetric, a::AbstractMatrix;
     dims in (1, 2) || throw(ArgumentError("dims should be 1 or 2 (got $dims)"))
     n = size(a, dims)
     r = Matrix{result_type(metric, a, a)}(undef, n, n)
-    pairwise!(r, metric, a, dims=dims)
+    pairwise!(metric, r, a, dims=dims)
 end
 
 """
@@ -341,11 +341,11 @@ function pairwise(metric::PreMetric, a, b)
     m = length(a)
     n = length(b)
     r = Matrix{result_type(metric, a, b)}(undef, m, n)
-    _pairwise!(r, metric, a, b)
+    _pairwise!(metric, r, a, b)
 end
 
 function pairwise(metric::PreMetric, a)
     n = length(a)
     r = Matrix{result_type(metric, a, a)}(undef, n, n)
-    _pairwise!(r, metric, a)
+    _pairwise!(metric, r, a)
 end

src/mahalanobis.jl

@@ -95,34 +95,34 @@ end
 sqmahalanobis(a::AbstractVector, b::AbstractVector, Q::AbstractMatrix) = SqMahalanobis(Q)(a, b)
 mahalanobis(a::AbstractVector, b::AbstractVector, Q::AbstractMatrix) = Mahalanobis(Q)(a, b)
 
-function _colwise!(r, dist, a, b)
+function _colwise!(dist, r, a, b)
     Q = dist.qmat
     get_colwise_dims(size(Q, 1), r, a, b)
     z = a .- b
     dot_percol!(r, Q * z, z)
 end
 
-function colwise!(r::AbstractArray, dist::SqMahalanobis, a::AbstractMatrix, b::AbstractMatrix)
-    _colwise!(r, dist, a, b)
+function colwise!(dist::SqMahalanobis, r::AbstractArray, a::AbstractMatrix, b::AbstractMatrix)
+    _colwise!(dist, r, a, b)
 end
-function colwise!(r::AbstractArray, dist::SqMahalanobis, a::AbstractVector, b::AbstractMatrix)
-    _colwise!(r, dist, a, b)
+function colwise!(dist::SqMahalanobis, r::AbstractArray, a::AbstractVector, b::AbstractMatrix)
+    _colwise!(dist, r, a, b)
 end
-function colwise!(r::AbstractArray, dist::SqMahalanobis, a::AbstractMatrix, b::AbstractVector)
-    _colwise!(r, dist, a, b)
+function colwise!(dist::SqMahalanobis, r::AbstractArray, a::AbstractMatrix, b::AbstractVector)
+    _colwise!(dist, r, a, b)
 end
 
-function colwise!(r::AbstractArray, dist::Mahalanobis, a::AbstractMatrix, b::AbstractMatrix)
-    sqrt!(_colwise!(r, dist, a, b))
+function colwise!(dist::Mahalanobis, r::AbstractArray, a::AbstractMatrix, b::AbstractMatrix)
+    sqrt!(_colwise!(dist, r, a, b))
 end
-function colwise!(r::AbstractArray, dist::Mahalanobis, a::AbstractVector, b::AbstractMatrix)
-    sqrt!(_colwise!(r, dist, a, b))
+function colwise!(dist::Mahalanobis, r::AbstractArray, a::AbstractVector, b::AbstractMatrix)
+    sqrt!(_colwise!(dist, r, a, b))
 end
-function colwise!(r::AbstractArray, dist::Mahalanobis, a::AbstractMatrix, b::AbstractVector)
-    sqrt!(_colwise!(r, dist, a, b))
+function colwise!(dist::Mahalanobis, r::AbstractArray, a::AbstractMatrix, b::AbstractVector)
+    sqrt!(_colwise!(dist, r, a, b))
 end
 
-function _pairwise!(r::AbstractMatrix, dist::Union{SqMahalanobis,Mahalanobis}, a::AbstractMatrix, b::AbstractMatrix)
+function _pairwise!(dist::Union{SqMahalanobis,Mahalanobis}, r::AbstractMatrix, a::AbstractMatrix, b::AbstractMatrix)
     Q = dist.qmat
     m, na, nb = get_pairwise_dims(size(Q, 1), r, a, b)
 
@@ -140,7 +140,7 @@ function _pairwise!(r::AbstractMatrix, dist::Union{SqMahalanobis,Mahalanobis}, a
     r
 end
 
-function _pairwise!(r::AbstractMatrix, dist::Union{SqMahalanobis,Mahalanobis}, a::AbstractMatrix)
+function _pairwise!(dist::Union{SqMahalanobis,Mahalanobis}, r::AbstractMatrix, a::AbstractMatrix)
     Q = dist.qmat
     m, n = get_pairwise_dims(size(Q, 1), r, a)