wip move SparseArrays to stdlib [ci skip] [bsd skip]

JuliaLang · Jan 9, 2018 · 10763d5 · 10763d5
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diff --git a/NEWS.md b/NEWS.md
@@ -871,6 +871,8 @@ 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 ([#TBD]).
+
   * `@printf` and `@sprintf` have been moved to the `Printf` standard library ([#23929],[#25056]).
 
   * `isnumber` has been deprecated in favor of `isnumeric`, `is_assigned_char`

diff --git a/base/asyncmap.jl b/base/asyncmap.jl
@@ -262,10 +262,10 @@ end
 
 # TODO: Optimize for sparse arrays
 # For now process as regular arrays and convert back
-function asyncmap(f, s::AbstractSparseArray...; kwargs...)
-    sa = map(Array, s)
-    return sparse(asyncmap(f, sa...; kwargs...))
-end
+# function asyncmap(f, s::AbstractSparseArray...; kwargs...)
+#     sa = map(Array, s)
+#     return sparse(asyncmap(f, sa...; kwargs...))
+# end
 
 mutable struct AsyncCollector
     f

diff --git a/base/deprecated.jl b/base/deprecated.jl
diff --git a/base/exports.jl b/base/exports.jl
@@ -434,15 +434,13 @@ export
     minimum,
     minmax,
     ndims,
-    nonzeros,
     ones,
     parent,
     parentindices,
     partialsort,
     partialsort!,
     partialsortperm,
     partialsortperm!,
-    permute,
     permute!,
     permutedims,
     permutedims!,
@@ -513,7 +511,6 @@ export
 # linear algebra
     bkfact!,
     bkfact,
-    blkdiag,
     chol,
     cholfact!,
     cholfact,
@@ -594,10 +591,6 @@ export
     ⋅,
     ×,
 
-# sparse
-    dropzeros,
-    dropzeros!,
-
 # bitarrays
     falses,
     flipbits!,
@@ -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
diff --git a/base/linalg/bidiag.jl b/base/linalg/bidiag.jl
@@ -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...)
 
 
 ###################

diff --git a/base/linalg/dense.jl b/base/linalg/dense.jl
@@ -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])

diff --git a/base/linalg/diagonal.jl b/base/linalg/diagonal.jl
@@ -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)
 

diff --git a/base/linalg/tridiag.jl b/base/linalg/tridiag.jl
@@ -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))
@@ -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)

diff --git a/base/sysimg.jl b/base/sysimg.jl
@@ -428,8 +428,8 @@ include("libgit2/libgit2.jl")
 include("pkg/pkg.jl")
 
 # sparse matrices, vectors, and sparse linear algebra
-include("sparse/sparse.jl")
-using .SparseArrays
+# include("sparse/sparse.jl")
+# using .SparseArrays
 
 include("asyncmap.jl")
 
@@ -499,6 +499,7 @@ Base.require(:IterativeEigensolvers)
 Base.require(:Mmap)
 Base.require(:Profile)
 Base.require(:SharedArrays)
+Base.require(:SparseArrays)
 Base.require(:SuiteSparse)
 Base.require(:Test)
 Base.require(:Unicode)

diff --git a/doc/make.jl b/doc/make.jl
@@ -30,6 +30,7 @@ if Sys.iswindows()
     cp_q("../stdlib/FileWatching/docs/src/index.md",          "src/stdlib/filewatching.md")
     cp_q("../stdlib/CRC32c/docs/src/index.md",                "src/stdlib/crc32c.md")
     cp_q("../stdlib/Dates/docs/src/index.md",                 "src/stdlib/dates.md")
+    cp_q("../stdlib/SparseArrays/docs/src/index.md",          "src/stdlib/sparsearrays.md")
     cp_q("../stdlib/IterativeEigensolvers/docs/src/index.md", "src/stdlib/iterativeeigensolvers.md")
     cp_q("../stdlib/Unicode/docs/src/index.md",               "src/stdlib/unicode.md")
     cp_q("../stdlib/Distributed/docs/src/index.md",           "src/stdlib/distributed.md")
@@ -44,6 +45,7 @@ else
     symlink_q("../../../stdlib/FileWatching/docs/src/index.md",          "src/stdlib/filewatching.md")
     symlink_q("../../../stdlib/CRC32c/docs/src/index.md",                "src/stdlib/crc32c.md")
     symlink_q("../../../stdlib/Dates/docs/src/index.md",                 "src/stdlib/dates.md")
+    symlink_q("../../../stdlib/SparseArrays/docs/src/index.md",          "src/stdlib/sparsearrays.md")
     symlink_q("../../../stdlib/IterativeEigensolvers/docs/src/index.md", "src/stdlib/iterativeeigensolvers.md")
     symlink_q("../../../stdlib/Unicode/docs/src/index.md",               "src/stdlib/unicode.md")
     symlink_q("../../../stdlib/Distributed/docs/src/index.md",           "src/stdlib/distributed.md")
@@ -125,6 +127,7 @@ const PAGES = [
         "stdlib/sharedarrays.md",
         "stdlib/filewatching.md",
         "stdlib/crc32c.md",
+        "stdlib/sparsearrays.md",
         "stdlib/iterativeeigensolvers.md",
         "stdlib/unicode.md",
         "stdlib/printf.md",
@@ -163,12 +166,13 @@ const PAGES = [
 ]
 
 using DelimitedFiles, Test, Mmap, SharedArrays, Profile, Base64, FileWatching, CRC32c,
-      Dates, IterativeEigensolvers, Unicode, Distributed, Printf
+      Dates, SparseArrays, IterativeEigensolvers, Unicode, Distributed, Printf
 
 makedocs(
     build     = joinpath(pwd(), "_build/html/en"),
     modules   = [Base, Core, BuildSysImg, DelimitedFiles, Test, Mmap, SharedArrays, Profile,
-                 Base64, FileWatching, Dates, IterativeEigensolvers, Unicode, Distributed, Printf],
+                 Base64, FileWatching, Dates, SparseArrays, IterativeEigensolvers, Unicode,
+                 Distributed, Printf],
     clean     = false,
     doctest   = "doctest" in ARGS,
     linkcheck = "linkcheck" in ARGS,

diff --git a/doc/src/index.md b/doc/src/index.md
@@ -74,6 +74,7 @@
   * [Memory-mapped I/O](@ref)
   * [Base64](@ref)
   * [File Events](@ref lib-filewatching)
+  * [Sparse Arrays](@ref)
   * [Iterative Eigensolvers](@ref lib-itereigen)
   * [Unicode](@ref)
   * [Printf](@ref)

diff --git a/doc/src/manual/arrays.md b/doc/src/manual/arrays.md
@@ -762,195 +762,3 @@ julia> r
  -1.58553  -0.921517
   0.0       0.866567
 ```
-
-## Sparse Vectors and Matrices
-
-Julia has built-in support for sparse vectors and
-[sparse matrices](https://en.wikipedia.org/wiki/Sparse_matrix). Sparse arrays are arrays
-that contain enough zeros that storing them in a special data structure leads to savings
-in space and execution time, compared to dense arrays.
-
-### [Compressed Sparse Column (CSC) Sparse Matrix Storage](@id man-csc)
-
-In Julia, sparse matrices are stored in the [Compressed Sparse Column (CSC) format](https://en.wikipedia.org/wiki/Sparse_matrix#Compressed_sparse_column_.28CSC_or_CCS.29).
-Julia sparse matrices have the type [`SparseMatrixCSC{Tv,Ti}`](@ref), where `Tv` is the
-type of the stored values, and `Ti` is the integer type for storing column pointers and
-row indices. The internal representation of `SparseMatrixCSC` is as follows:
-
-```julia
-struct SparseMatrixCSC{Tv,Ti<:Integer} <: AbstractSparseMatrix{Tv,Ti}
-    m::Int                  # Number of rows
-    n::Int                  # Number of columns
-    colptr::Vector{Ti}      # Column i is in colptr[i]:(colptr[i+1]-1)
-    rowval::Vector{Ti}      # Row indices of stored values
-    nzval::Vector{Tv}       # Stored values, typically nonzeros
-end
-```
-
-The compressed sparse column storage makes it easy and quick to access the elements in the column
-of a sparse matrix, whereas accessing the sparse matrix by rows is considerably slower. Operations
-such as insertion of previously unstored entries one at a time in the CSC structure tend to be slow. This is
-because all elements of the sparse matrix that are beyond the point of insertion have to be moved
-one place over.
-
-All operations on sparse matrices are carefully implemented to exploit the CSC data structure
-for performance, and to avoid expensive operations.
-
-If you have data in CSC format from a different application or library, and wish to import it
-in Julia, make sure that you use 1-based indexing. The row indices in every column need to be
-sorted. If your `SparseMatrixCSC` object contains unsorted row indices, one quick way to sort
-them is by doing a double transpose.
-
-In some applications, it is convenient to store explicit zero values in a `SparseMatrixCSC`. These
-*are* accepted by functions in `Base` (but there is no guarantee that they will be preserved in
-mutating operations). Such explicitly stored zeros are treated as structural nonzeros by many
-routines. The [`nnz`](@ref) function returns the number of elements explicitly stored in the
-sparse data structure, including structural nonzeros. In order to count the exact number of
-numerical nonzeros, use [`count(!iszero, x)`](@ref), which inspects every stored element of a sparse
-matrix. [`dropzeros`](@ref), and the in-place [`dropzeros!`](@ref), can be used to
-remove stored zeros from the sparse matrix.
-
-```jldoctest
-julia> A = sparse([1, 2, 3], [1, 2, 3], [0, 2, 0])
-3×3 SparseMatrixCSC{Int64,Int64} with 3 stored entries:
-  [1, 1]  =  0
-  [2, 2]  =  2
-  [3, 3]  =  0
-
-julia> dropzeros(A)
-3×3 SparseMatrixCSC{Int64,Int64} with 1 stored entry:
-  [2, 2]  =  2
-```
-
-### Sparse Vector Storage
-
-Sparse vectors are stored in a close analog to compressed sparse column format for sparse
-matrices. In Julia, sparse vectors have the type [`SparseVector{Tv,Ti}`](@ref) where `Tv`
-is the type of the stored values and `Ti` the integer type for the indices. The internal
-representation is as follows:
-
-```julia
-struct SparseVector{Tv,Ti<:Integer} <: AbstractSparseVector{Tv,Ti}
-    n::Int              # Length of the sparse vector
-    nzind::Vector{Ti}   # Indices of stored values
-    nzval::Vector{Tv}   # Stored values, typically nonzeros
-end
-```
-
-As for [`SparseMatrixCSC`](@ref), the `SparseVector` type can also contain explicitly
-stored zeros. (See [Sparse Matrix Storage](@ref man-csc).).
-
-### Sparse Vector and Matrix Constructors
-
-The simplest way to create a sparse array is to use a function equivalent to the [`zeros`](@ref)
-function that Julia provides for working with dense arrays. To produce a
-sparse array instead, you can use the same name with an `sp` prefix:
-
-```jldoctest
-julia> spzeros(3)
-3-element SparseVector{Float64,Int64} with 0 stored entries
-```
-
-The [`sparse`](@ref) function is often a handy way to construct sparse arrays. For
-example, to construct a sparse matrix we can input a vector `I` of row indices, a vector
-`J` of column indices, and a vector `V` of stored values (this is also known as the
-[COO (coordinate) format](https://en.wikipedia.org/wiki/Sparse_matrix#Coordinate_list_.28COO.29)).
-`sparse(I,J,V)` then constructs a sparse matrix such that `S[I[k], J[k]] = V[k]`. The
-equivalent sparse vector constructor is [`sparsevec`](@ref), which takes the (row) index
-vector `I` and the vector `V` with the stored values and constructs a sparse vector `R`
-such that `R[I[k]] = V[k]`.
-
-```jldoctest sparse_function
-julia> I = [1, 4, 3, 5]; J = [4, 7, 18, 9]; V = [1, 2, -5, 3];
-
-julia> S = sparse(I,J,V)
-5×18 SparseMatrixCSC{Int64,Int64} with 4 stored entries:
-  [1 ,  4]  =  1
-  [4 ,  7]  =  2
-  [5 ,  9]  =  3
-  [3 , 18]  =  -5
-
-julia> R = sparsevec(I,V)
-5-element SparseVector{Int64,Int64} with 4 stored entries:
-  [1]  =  1
-  [3]  =  -5
-  [4]  =  2
-  [5]  =  3
-```
-
-The inverse of the [`sparse`](@ref) and [`sparsevec`](@ref) functions is
-[`findnz`](@ref), which retrieves the inputs used to create the sparse array.
-There is also a [`findn`](@ref) function which only returns the index vectors.
-
-```jldoctest sparse_function
-julia> findnz(S)
-([1, 4, 5, 3], [4, 7, 9, 18], [1, 2, 3, -5])
-
-julia> findn(S)
-([1, 4, 5, 3], [4, 7, 9, 18])
-
-julia> findnz(R)
-([1, 3, 4, 5], [1, -5, 2, 3])
-
-julia> find(!iszero, R)
-4-element Array{Int64,1}:
- 1
- 3
- 4
- 5
-```
-
-Another way to create a sparse array is to convert a dense array into a sparse array using
-the [`sparse`](@ref) function:
-
-```jldoctest
-julia> sparse(Matrix(1.0I, 5, 5))
-5×5 SparseMatrixCSC{Float64,Int64} with 5 stored entries:
-  [1, 1]  =  1.0
-  [2, 2]  =  1.0
-  [3, 3]  =  1.0
-  [4, 4]  =  1.0
-  [5, 5]  =  1.0
-
-julia> sparse([1.0, 0.0, 1.0])
-3-element SparseVector{Float64,Int64} with 2 stored entries:
-  [1]  =  1.0
-  [3]  =  1.0
-```
-
-You can go in the other direction using the [`Array`](@ref) constructor. The [`issparse`](@ref)
-function can be used to query if a matrix is sparse.
-
-```jldoctest
-julia> issparse(spzeros(5))
-true
-```
-
-### Sparse matrix operations
-
-Arithmetic operations on sparse matrices also work as they do on dense matrices. Indexing of,
-assignment into, and concatenation of sparse matrices work in the same way as dense matrices.
-Indexing operations, especially assignment, are expensive, when carried out one element at a time.
-In many cases it may be better to convert the sparse matrix into `(I,J,V)` format using [`findnz`](@ref),
-manipulate the values or the structure in the dense vectors `(I,J,V)`, and then reconstruct
-the sparse matrix.
-
-### Correspondence of dense and sparse methods
-
-The following table gives a correspondence between built-in methods on sparse matrices and their
-corresponding methods on dense matrix types. In general, methods that generate sparse matrices
-differ from their dense counterparts in that the resulting matrix follows the same sparsity pattern
-as a given sparse matrix `S`, or that the resulting sparse matrix has density `d`, i.e. each matrix
-element has a probability `d` of being non-zero.
-
-Details can be found in the [Sparse Vectors and Matrices](@ref stdlib-sparse-arrays)
-section of the standard library reference.
-
-| Sparse                     | Dense                  | Description                                                                                                                                                           |
-|:-------------------------- |:---------------------- |:--------------------------------------------------------------------------------------------------------------------------------------------------------------------- |
-| [`spzeros(m,n)`](@ref)     | [`zeros(m,n)`](@ref)   | Creates a *m*-by-*n* matrix of zeros. ([`spzeros(m,n)`](@ref) is empty.)                                                                                              |
-| [`sparse(I, n, n)`](@ref)  | [`Matrix(I,n,n)`](@ref)| Creates a *n*-by-*n* identity matrix.                                                                                                                                 |
-| [`Array(S)`](@ref)         | [`sparse(A)`](@ref)    | Interconverts between dense and sparse formats.                                                                                                                       |
-| [`sprand(m,n,d)`](@ref)    | [`rand(m,n)`](@ref)    | Creates a *m*-by-*n* random matrix (of density *d*) with iid non-zero elements distributed uniformly on the half-open interval ``[0, 1)``.                            |
-| [`sprandn(m,n,d)`](@ref)   | [`randn(m,n)`](@ref)   | Creates a *m*-by-*n* random matrix (of density *d*) with iid non-zero elements distributed according to the standard normal (Gaussian) distribution.                  |
-| [`sprandn(m,n,d,X)`](@ref) | [`randn(m,n,X)`](@ref) | Creates a *m*-by-*n* random matrix (of density *d*) with iid non-zero elements distributed according to the *X* distribution. (Requires the `Distributions` package.) |