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

JuliaLang · Jan 9, 2018 · 11e778b · 11e778b
1 parent 9b5eed2
commit 11e778b
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diff --git a/NEWS.md b/NEWS.md
@@ -872,6 +872,8 @@ 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 ([#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`

diff --git a/base/asyncmap.jl b/base/asyncmap.jl
@@ -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...)
-    sa = map(Array, s)
-    return sparse(asyncmap(f, sa...; kwargs...))
-end
-
 mutable struct AsyncCollector
     f
     results

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/lapack.jl b/base/linalg/lapack.jl
@@ -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(x->x != 0, ifail))")
             end
             z
         end

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
@@ -427,10 +427,6 @@ include("libgit2/libgit2.jl")
 # package manager
 include("pkg/pkg.jl")
 
-# sparse matrices, vectors, and sparse linear algebra
-include("sparse/sparse.jl")
-using .SparseArrays
-
 include("asyncmap.jl")
 
 # worker threads
@@ -499,6 +495,7 @@ Base.require(:IterativeEigensolvers)
 Base.require(:Mmap)
 Base.require(:Profile)
 Base.require(:SharedArrays)
+Base.require(:SparseArrays)
 Base.require(:SuiteSparse)
 Base.require(:Test)
 Base.require(:Unicode)
@@ -512,6 +509,19 @@ Base.require(:Future)
     @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)

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)