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move SparseArrays to stdlib #25249

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Jan 12, 2018
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move SparseArrays to stdlib #25249

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2 changes: 2 additions & 0 deletions NEWS.md
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Expand Up @@ -881,6 +881,8 @@ Deprecated or removed
* The functions `eigs` and `svds` have been moved to the `IterativeEigensolvers` standard
library module ([#24714]).

* Sparse array functionality has moved to the `SparseArrays` standard library module ([#25249]).

* `@printf` and `@sprintf` have been moved to the `Printf` standard library ([#23929],[#25056]).

* `isnumber` has been deprecated in favor of `isnumeric`, `is_assigned_char`
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7 changes: 0 additions & 7 deletions base/asyncmap.jl
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Expand Up @@ -260,13 +260,6 @@ function asyncmap(f, b::BitArray; kwargs...)
return b2
end

# TODO: Optimize for sparse arrays
# For now process as regular arrays and convert back
function asyncmap(f, s::AbstractSparseArray...; kwargs...)
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I deprecated this in stdlib/SparseArrays/src/deprecated.jl since it is better to be transparent to the user that we don't have an optimized method for this anyway.

sa = map(Array, s)
return sparse(asyncmap(f, sa...; kwargs...))
end

mutable struct AsyncCollector
f
results
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247 changes: 30 additions & 217 deletions base/deprecated.jl
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27 changes: 1 addition & 26 deletions base/exports.jl
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Expand Up @@ -433,15 +433,13 @@ export
minimum,
minmax,
ndims,
nonzeros,
ones,
parent,
parentindices,
partialsort,
partialsort!,
partialsortperm,
partialsortperm!,
permute,
permute!,
permutedims,
permutedims!,
Expand Down Expand Up @@ -512,7 +510,6 @@ export
# linear algebra
bkfact!,
bkfact,
blkdiag,
chol,
cholfact!,
cholfact,
Expand Down Expand Up @@ -593,10 +590,6 @@ export
⋅,
×,

# sparse
dropzeros,
dropzeros!,

# bitarrays
falses,
flipbits!,
Expand Down Expand Up @@ -1183,22 +1176,4 @@ export
@goto,
@view,
@views,
@static,

# SparseArrays module re-exports
SparseArrays,
AbstractSparseArray,
AbstractSparseMatrix,
AbstractSparseVector,
SparseMatrixCSC,
SparseVector,
issparse,
sparse,
sparsevec,
spdiagm,
sprand,
sprandn,
spzeros,
rowvals,
nzrange,
nnz
@static
3 changes: 2 additions & 1 deletion base/linalg/bidiag.jl
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Expand Up @@ -178,7 +178,8 @@ broadcast(::typeof(big), B::Bidiagonal) = Bidiagonal(big.(B.dv), big.(B.ev), B.u
# On the other hand, similar(B, [neweltype,] shape...) should yield a sparse matrix.
# The first method below effects the former, and the second the latter.
similar(B::Bidiagonal, ::Type{T}) where {T} = Bidiagonal(similar(B.dv, T), similar(B.ev, T), B.uplo)
similar(B::Bidiagonal, ::Type{T}, dims::Union{Dims{1},Dims{2}}) where {T} = spzeros(T, dims...)
# The method below is moved to SparseArrays for now
# similar(B::Bidiagonal, ::Type{T}, dims::Union{Dims{1},Dims{2}}) where {T} = spzeros(T, dims...)


###################
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2 changes: 0 additions & 2 deletions base/linalg/dense.jl
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Expand Up @@ -303,8 +303,6 @@ Vector `kv.second` will be placed on the `kv.first` diagonal.
versions with fast arithmetic, see [`Diagonal`](@ref), [`Bidiagonal`](@ref)
[`Tridiagonal`](@ref) and [`SymTridiagonal`](@ref).

See also: [`spdiagm`](@ref)

# Examples
```jldoctest
julia> diagm(1 => [1,2,3])
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3 changes: 2 additions & 1 deletion base/linalg/diagonal.jl
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Expand Up @@ -59,7 +59,8 @@ Array(D::Diagonal) = Matrix(D)
# On the other hand, similar(D, [neweltype,] shape...) should yield a sparse matrix.
# The first method below effects the former, and the second the latter.
similar(D::Diagonal, ::Type{T}) where {T} = Diagonal(similar(D.diag, T))
similar(D::Diagonal, ::Type{T}, dims::Union{Dims{1},Dims{2}}) where {T} = spzeros(T, dims...)
# The method below is moved to SparseArrays for now
# similar(D::Diagonal, ::Type{T}, dims::Union{Dims{1},Dims{2}}) where {T} = spzeros(T, dims...)

copyto!(D1::Diagonal, D2::Diagonal) = (copyto!(D1.diag, D2.diag); D1)

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2 changes: 1 addition & 1 deletion base/linalg/lapack.jl
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Expand Up @@ -3759,7 +3759,7 @@ for (stev, stebz, stegr, stein, elty) in
chklapackerror(info[])
if any(ifail .!= 0)
# TODO: better error message / type
error("failed to converge eigenvectors:\n$(nonzeros(ifail))")
error("failed to converge eigenvectors:\n$(find(!iszero, ifail))")
end
z
end
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6 changes: 4 additions & 2 deletions base/linalg/tridiag.jl
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Expand Up @@ -111,7 +111,8 @@ end
# On the other hand, similar(S, [neweltype,] shape...) should yield a sparse matrix.
# The first method below effects the former, and the second the latter.
similar(S::SymTridiagonal, ::Type{T}) where {T} = SymTridiagonal(similar(S.dv, T), similar(S.ev, T))
similar(S::SymTridiagonal, ::Type{T}, dims::Union{Dims{1},Dims{2}}) where {T} = spzeros(T, dims...)
# The method below is moved to SparseArrays for now
# similar(S::SymTridiagonal, ::Type{T}, dims::Union{Dims{1},Dims{2}}) where {T} = spzeros(T, dims...)

#Elementary operations
broadcast(::typeof(abs), M::SymTridiagonal) = SymTridiagonal(abs.(M.dv), abs.(M.ev))
Expand Down Expand Up @@ -497,7 +498,8 @@ Array(M::Tridiagonal) = Matrix(M)
# On the other hand, similar(M, [neweltype,] shape...) should yield a sparse matrix.
# The first method below effects the former, and the second the latter.
similar(M::Tridiagonal, ::Type{T}) where {T} = Tridiagonal(similar(M.dl, T), similar(M.d, T), similar(M.du, T))
similar(M::Tridiagonal, ::Type{T}, dims::Union{Dims{1},Dims{2}}) where {T} = spzeros(T, dims...)
# The method below is moved to SparseArrays for now
# similar(M::Tridiagonal, ::Type{T}, dims::Union{Dims{1},Dims{2}}) where {T} = spzeros(T, dims...)

# Operations on Tridiagonal matrices
copyto!(dest::Tridiagonal, src::Tridiagonal) = (copyto!(dest.dl, src.dl); copyto!(dest.d, src.d); copyto!(dest.du, src.du); dest)
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18 changes: 14 additions & 4 deletions base/sysimg.jl
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Expand Up @@ -447,10 +447,6 @@ using .LinAlg
const ⋅ = dot
const × = cross

# sparse matrices, vectors, and sparse linear algebra
include("sparse/sparse.jl")
using .SparseArrays

include("asyncmap.jl")

include("multimedia.jl")
Expand Down Expand Up @@ -504,6 +500,7 @@ Base.require(:IterativeEigensolvers)
Base.require(:Mmap)
Base.require(:Profile)
Base.require(:SharedArrays)
Base.require(:SparseArrays)
Base.require(:SuiteSparse)
Base.require(:Test)
Base.require(:Unicode)
Expand All @@ -518,6 +515,19 @@ Base.require(:Libdl)
@deprecate_binding Profile root_module(:Profile) true ", run `using Profile` instead"
@deprecate_binding Dates root_module(:Dates) true ", run `using Dates` instead"
@deprecate_binding Distributed root_module(:Distributed) true ", run `using Distributed` instead"

# PR #25249
@deprecate_binding SparseArrays root_module(:SparseArrays) true ", run `using SparseArrays` instead"
@deprecate_binding(AbstractSparseArray, root_module(:SparseArrays).AbstractSparseArray, true,
", run `using SparseArrays` to load sparse array functionality")
@deprecate_binding(AbstractSparseMatrix, root_module(:SparseArrays).AbstractSparseMatrix, true,
", run `using SparseArrays` to load sparse array functionality")
@deprecate_binding(AbstractSparseVector, root_module(:SparseArrays).AbstractSparseVector, true,
", run `using SparseArrays` to load sparse array functionality")
@deprecate_binding(SparseMatrixCSC, root_module(:SparseArrays).SparseMatrixCSC, true,
", run `using SparseArrays` to load sparse array functionality")
@deprecate_binding(SparseVector, root_module(:SparseArrays).SparseVector, true,
", run `using SparseArrays` to load sparse array functionality")
end

empty!(LOAD_PATH)
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27 changes: 0 additions & 27 deletions doc/src/base/arrays.md
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Expand Up @@ -188,30 +188,3 @@ and can be converted to/from the latter via `Array(bitarray)` and `BitArray(arra
```@docs
Base.flipbits!
```

## [Sparse Vectors and Matrices](@id stdlib-sparse-arrays)

Sparse vectors and matrices largely support the same set of operations as their dense counterparts.
The following functions are specific to sparse arrays.

```@docs
Base.SparseArrays.SparseVector
Base.SparseArrays.SparseMatrixCSC
Base.SparseArrays.sparse
Base.SparseArrays.sparsevec
Base.SparseArrays.issparse
Base.SparseArrays.nnz
Base.SparseArrays.spzeros
Base.SparseArrays.spdiagm
Base.SparseArrays.sprand
Base.SparseArrays.sprandn
Base.SparseArrays.nonzeros
Base.SparseArrays.rowvals
Base.SparseArrays.nzrange
Base.SparseArrays.dropzeros!(::SparseMatrixCSC, ::Bool)
Base.SparseArrays.dropzeros(::SparseMatrixCSC, ::Bool)
Base.SparseArrays.dropzeros!(::SparseVector, ::Bool)
Base.SparseArrays.dropzeros(::SparseVector, ::Bool)
Base.SparseArrays.permute
Base.permute!{Tv, Ti, Tp <: Integer, Tq <: Integer}(::SparseMatrixCSC{Tv,Ti}, ::SparseMatrixCSC{Tv,Ti}, ::AbstractArray{Tp,1}, ::AbstractArray{Tq,1})
```
1 change: 0 additions & 1 deletion doc/src/base/base.md
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Expand Up @@ -97,7 +97,6 @@ Base.Markdown
Base.Meta
Base.Pkg
Base.Serializer
Base.SparseArrays
Base.StackTraces
Base.Sys
Base.Threads
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1 change: 1 addition & 0 deletions doc/src/base/index.md
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Expand Up @@ -31,5 +31,6 @@
* [Memory-mapped I/O](@ref)
* [Base64](@ref)
* [File Events](@ref lib-filewatching)
* [Sparse Arrays](@ref)
* [Iterative Eigensolvers](@ref lib-itereigen)
* [Printf](@ref)
1 change: 0 additions & 1 deletion doc/src/base/linalg.md
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Expand Up @@ -91,7 +91,6 @@ Base.LinAlg.pinv
Base.LinAlg.nullspace
Base.repmat
Base.kron
Base.SparseArrays.blkdiag
Base.LinAlg.linreg
Base.LinAlg.exp(::StridedMatrix{<:Base.LinAlg.BlasFloat})
Base.LinAlg.log(::StridedMatrix)
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1 change: 1 addition & 0 deletions doc/src/index.md
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Expand Up @@ -81,6 +81,7 @@
* [Delimited Files](@ref)
* [Distributed Computing](@ref)
* [File Events](@ref lib-filewatching)
* [Sparse Arrays](@ref)
* [Iterative Eigensolvers](@ref lib-itereigen)
* [Memory-mapped I/O](@ref)
* [Printf](@ref)
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