Merge pull request #25571 from fredrikekre/so-long-and-thanks-for-all…

…-the-fish

Base.LinAlg to LinearAlgebra stdlib

NEWS.md

@@ -899,6 +899,9 @@ Deprecated or removed
 
   * Sparse array functionality has moved to the `SparseArrays` standard library module ([#25249]).
 
+  * Linear algebra functionality, and specifically the `LinAlg` module has moved to the
+    `LinearAlgebra` standard library module ([#25571]).
+
   * `@printf` and `@sprintf` have been moved to the `Printf` standard library ([#23929],[#25056]).
 
   * The aliases `Complex32`, `Complex64` and `Complex128` have been deprecated in favor of `ComplexF16`,

base/array.jl

@@ -391,7 +391,12 @@ end
 function _one(unit::T, x::AbstractMatrix) where T
     m,n = size(x)
     m==n || throw(DimensionMismatch("multiplicative identity defined only for square matrices"))
-    Matrix{T}(I, m, m)
+    # Matrix{T}(I, m, m)
+    I = zeros(T, m, m)
+    for i in 1:m
+        I[i,i] = 1
+    end
+    I
 end
 
 one(x::AbstractMatrix{T}) where {T} = _one(one(T), x)

base/exports.jl

@@ -8,9 +8,6 @@ export
     StackTraces,
     Sys,
     Libc,
-    LinAlg,
-    BLAS,
-    LAPACK,
     Serializer,
     Docs,
     Markdown,
@@ -29,7 +26,6 @@ export
     AbstractVecOrMat,
     Array,
     AbstractDict,
-    Bidiagonal,
     BigFloat,
     BigInt,
     BitArray,
@@ -46,22 +42,16 @@ export
     ComplexF64,
     ComplexF32,
     ComplexF16,
-    ConjVector,
-    ConjMatrix,
     DenseMatrix,
     DenseVecOrMat,
     DenseVector,
     DevNull,
-    Diagonal,
     Dict,
     Dims,
     EachLine,
     Enum,
     Enumerate,
     ExponentialBackOff,
-    Factorization,
-    Hermitian,
-    UniformScaling,
     IndexCartesian,
     IndexLinear,
     IndexStyle,
@@ -70,7 +60,6 @@ export
     IOBuffer,
     IOStream,
     LinSpace,
-    LowerTriangular,
     Irrational,
     Matrix,
     MergeSort,
@@ -94,8 +83,6 @@ export
     RoundNearestTiesUp,
     RoundToZero,
     RoundUp,
-    Adjoint,
-    Transpose,
     AbstractSerializer,
     SerializationState,
     Set,
@@ -108,12 +95,8 @@ export
     StridedVector,
     SubArray,
     SubString,
-    Symmetric,
-    SymTridiagonal,
     Timer,
-    Tridiagonal,
     UnitRange,
-    UpperTriangular,
     Val,
     VecOrMat,
     Vector,
@@ -178,7 +161,6 @@ export
     im,
     π, pi,
     ℯ,
-    I,
 
 # Operators
     !,
@@ -501,87 +483,9 @@ export
     startswith,
 
 # linear algebra
-    bkfact!,
-    bkfact,
-    chol,
-    cholfact!,
-    cholfact,
-    cond,
-    condskeel,
-    cross,
-    adjoint!,
     adjoint,
-    det,
-    diag,
-    diagind,
-    diagm,
-    diff,
-    dot,
-    eig,
-    eigfact!,
-    eigfact,
-    eigmax,
-    eigmin,
-    eigvals,
-    eigvals!,
-    eigvecs,
-    factorize,
-    givens,
-    hessfact!,
-    hessfact,
-    isdiag,
-    ishermitian,
-    isposdef!,
-    isposdef,
-    issymmetric,
-    istril,
-    istriu,
-    kron,
-    ldltfact,
-    ldltfact!,
-    linreg,
-    logabsdet,
-    logdet,
-    lu,
-    lufact!,
-    lufact,
-    lyap,
-    norm,
-    normalize,
-    normalize!,
-    nullspace,
-    ordschur!,
-    ordschur,
-    peakflops,
-    pinv,
-    qr,
-    qrfact!,
-    qrfact,
-    lq,
-    lqfact!,
-    lqfact,
-    rank,
-    scale!,
-    schur,
-    schurfact!,
-    schurfact,
-    svd,
-    svdfact!,
-    svdfact,
-    svdvals!,
-    svdvals,
-    sylvester,
-    trace,
-    transpose!,
     transpose,
-    tril!,
-    tril,
-    triu!,
-    triu,
-    vecdot,
-    vecnorm,
-    ⋅,
-    ×,
+    kron,
 
 # bitarrays
     falses,

base/interactiveutil.jl

@@ -322,13 +322,6 @@ function versioninfo(io::IO=STDOUT; verbose::Bool=false, packages::Bool=false)
         println(io)
     end
     println(io, "  WORD_SIZE: ", Sys.WORD_SIZE)
-    if Base.libblas_name == "libopenblas" || BLAS.vendor() == :openblas || BLAS.vendor() == :openblas64
-        openblas_config = BLAS.openblas_get_config()
-        println(io, "  BLAS: libopenblas (", openblas_config, ")")
-    else
-        println(io, "  BLAS: ",libblas_name)
-    end
-    println(io, "  LAPACK: ",liblapack_name)
     println(io, "  LIBM: ",libm_name)
     println(io, "  LLVM: libLLVM-",libllvm_version," (", Sys.JIT, ", ", Sys.CPU_NAME, ")")
 

base/math.jl

@@ -506,7 +506,7 @@ end
 
 Compute the hypotenuse ``\\sqrt{\\sum x_i^2}`` avoiding overflow and underflow.
 """
-hypot(x::Number...) = vecnorm(x)
+hypot(x::Number...) = sqrt(sum(abs2(y) for y in x))
 
 """
     atan2(y, x)

base/precompile.jl

@@ -1234,7 +1234,6 @@ precompile(Tuple{typeof(Base.join), Base.GenericIOBuffer{Array{UInt8, 1}}, Tuple
 precompile(Tuple{typeof(Base.setindex!), Base.Dict{Int64, Nothing}, Nothing, Int64})
 precompile(Tuple{Type{Array{Union{Tuple{Any, Int64}, Tuple{Tuple{}, Any, Bool}}, 1}}, Tuple{Int64}})
 precompile(Tuple{typeof(Base.eachindex), Array{Union{Tuple{Any, Int64}, Tuple{Tuple{}, Any, Bool}}, 1}})
-precompile(Tuple{typeof(Base.LinAlg.BLAS.set_num_threads), Int64})
 precompile(Tuple{typeof(Base.eltype), Type{Base.Union{IO, Nothing}}})
 precompile(Tuple{Type{Base.Union{IO, Nothing}}})
 precompile(Tuple{typeof(Base.eltype), Type{Base.Union{AbstractString, Nothing}}})

base/statistics.jl

@@ -59,7 +59,8 @@ julia> mean!([1. 1.], v)
 """
 function mean!(R::AbstractArray, A::AbstractArray)
     sum!(R, A; init=true)
-    scale!(R, max(1, _length(R)) // _length(A))
+    x = max(1, _length(R)) // _length(A)
+    R .= R .* x
     return R
 end
 
@@ -175,7 +176,8 @@ function varm!(R::AbstractArray{S}, A::AbstractArray, m::AbstractArray; correcte
         fill!(R, convert(S, NaN))
     else
         rn = div(_length(A), _length(R)) - Int(corrected)
-        scale!(centralize_sumabs2!(R, A, m), 1//rn)
+        centralize_sumabs2!(R, A, m)
+        R .= R .* (1 // rn)
     end
     return R
 end
@@ -328,7 +330,7 @@ unscaled_covzm(x::AbstractVector{<:Number})    = sum(abs2, x)
 unscaled_covzm(x::AbstractVector)              = sum(t -> t*t', x)
 unscaled_covzm(x::AbstractMatrix, vardim::Int) = (vardim == 1 ? _conj(x'x) : x * x')
 
-unscaled_covzm(x::AbstractVector, y::AbstractVector) = dot(y, x)
+unscaled_covzm(x::AbstractVector, y::AbstractVector) = sum(conj(y[i])*x[i] for i in eachindex(y, x))
 unscaled_covzm(x::AbstractVector, y::AbstractMatrix, vardim::Int) =
     (vardim == 1 ? *(transpose(x), _conj(y)) : *(transpose(x), transpose(_conj(y))))
 unscaled_covzm(x::AbstractMatrix, y::AbstractVector, vardim::Int) =
@@ -342,14 +344,20 @@ covzm(x::AbstractVector; corrected::Bool=true) = unscaled_covzm(x) / (_length(x)
 function covzm(x::AbstractMatrix, vardim::Int=1; corrected::Bool=true)
     C = unscaled_covzm(x, vardim)
     T = promote_type(typeof(first(C) / 1), eltype(C))
-    return scale!(convert(AbstractMatrix{T}, C), 1//(size(x, vardim) - corrected))
+    A = convert(AbstractMatrix{T}, C)
+    b = 1//(size(x, vardim) - corrected)
+    A .= A .* b
+    return A
 end
 covzm(x::AbstractVector, y::AbstractVector; corrected::Bool=true) =
     unscaled_covzm(x, y) / (_length(x) - Int(corrected))
 function covzm(x::AbstractVecOrMat, y::AbstractVecOrMat, vardim::Int=1; corrected::Bool=true)
     C = unscaled_covzm(x, y, vardim)
     T = promote_type(typeof(first(C) / 1), eltype(C))
-    return scale!(convert(AbstractArray{T}, C), 1//(_getnobs(x, y, vardim) - corrected))
+    A = convert(AbstractArray{T}, C)
+    b = 1//(_getnobs(x, y, vardim) - corrected)
+    A .= A .* b
+    return A
 end
 
 # covm (with provided mean)
@@ -467,7 +475,7 @@ end
 corzm(x::AbstractVector{T}) where {T} = one(real(T))
 function corzm(x::AbstractMatrix, vardim::Int=1)
     c = unscaled_covzm(x, vardim)
-    return cov2cor!(c, sqrt!(diag(c)))
+    return cov2cor!(c, collect(sqrt(c[i,i]) for i in 1:min(size(c)...)))
 end
 corzm(x::AbstractVector, y::AbstractMatrix, vardim::Int=1) =
     cov2cor!(unscaled_covzm(x, y, vardim), sqrt(sum(abs2, x)), sqrt!(sum(abs2, y, vardim)))

base/sysimg.jl

@@ -460,12 +460,6 @@ import Base64
 
 INCLUDE_STATE = 2
 
-# dense linear algebra
-include("linalg/linalg.jl")
-using .LinAlg
-const ⋅ = dot
-const × = cross
-
 include("asyncmap.jl")
 
 include("multimedia.jl")
@@ -520,6 +514,7 @@ Base.require(:FileWatching)
 Base.require(:Future)
 Base.require(:IterativeEigensolvers)
 Base.require(:Libdl)
+Base.require(:LinearAlgebra)
 Base.require(:Logging)
 Base.require(:Mmap)
 Base.require(:Printf)
@@ -551,6 +546,9 @@ Base.require(:Unicode)
         ", run `using SparseArrays` to load sparse array functionality")
     @deprecate_binding(SparseVector, root_module(:SparseArrays).SparseVector, true,
         ", run `using SparseArrays` to load sparse array functionality")
+
+    # PR #25571
+    @deprecate_binding LinAlg root_module(:LinearAlgebra) true ", run `using LinearAlgebra` instead"
 end
 
 empty!(LOAD_PATH)

doc/make.jl

@@ -68,7 +68,6 @@ const PAGES = [
         "manual/documentation.md",
         "manual/metaprogramming.md",
         "manual/arrays.md",
-        "manual/linear-algebra.md",
         "manual/missing.md",
         "manual/networking-and-streams.md",
         "manual/parallel-computing.md",
@@ -98,7 +97,6 @@ const PAGES = [
         "base/arrays.md",
         "base/parallel.md",
         "base/multi-threading.md",
-        "base/linalg.md",
         "base/constants.md",
         "base/file.md",
         "base/io-network.md",

doc/src/base/arrays.md

@@ -50,7 +50,6 @@ Base.IndexStyle
 Base.conj!
 Base.stride
 Base.strides
-Base.LinAlg.checksquare
 ```
 
 ## Broadcast and vectorization
@@ -148,7 +147,7 @@ Base.cumprod
 Base.cumprod!
 Base.cumsum
 Base.cumsum!
-Base.LinAlg.diff
+LinearAlgebra.diff
 Base.repeat(::AbstractArray)
 Base.rot180
 Base.rotl90

doc/src/base/base.md

@@ -86,13 +86,10 @@ primitive type
 
 ## Base Modules
 ```@docs
-Base.BLAS
 Base.Docs
 Base.Iterators
-Base.LAPACK
 Base.LibGit2
 Base.Libc
-Base.LinAlg
 Base.Markdown
 Base.Meta
 Base.Pkg

doc/src/base/index.md

@@ -10,7 +10,6 @@
   * [Distributed Computing](@ref)
   * [Shared Arrays](@ref)
   * [Multi-Threading](@ref)
-  * [Linear Algebra](@ref)
   * [Constants](@ref lib-constants)
   * [Filesystem](@ref)
   * [Delimited Files](@ref)