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Base.LinAlg to LinearAlgebra stdlib #25571

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Jan 18, 2018
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Base.LinAlg to LinearAlgebra stdlib #25571

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3 changes: 3 additions & 0 deletions NEWS.md
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Expand Up @@ -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`,
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7 changes: 6 additions & 1 deletion base/array.jl
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Expand Up @@ -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)
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This function should probably be moved too, but can stay for now.

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)
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1,525 changes: 147 additions & 1,378 deletions base/deprecated.jl
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98 changes: 1 addition & 97 deletions base/exports.jl
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Expand Up @@ -8,9 +8,6 @@ export
StackTraces,
Sys,
Libc,
LinAlg,
BLAS,
LAPACK,
Serializer,
Docs,
Markdown,
Expand All @@ -29,7 +26,6 @@ export
AbstractVecOrMat,
Array,
AbstractDict,
Bidiagonal,
BigFloat,
BigInt,
BitArray,
Expand All @@ -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,
Expand All @@ -70,7 +60,6 @@ export
IOBuffer,
IOStream,
LinSpace,
LowerTriangular,
Irrational,
Matrix,
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Maybe we want to define these aliases in LinearAlgebra

MergeSort,
Expand All @@ -94,8 +83,6 @@ export
RoundNearestTiesUp,
RoundToZero,
RoundUp,
Adjoint,
Transpose,
AbstractSerializer,
SerializationState,
Set,
Expand All @@ -108,12 +95,8 @@ export
StridedVector,
SubArray,
SubString,
Symmetric,
SymTridiagonal,
Timer,
Tridiagonal,
UnitRange,
UpperTriangular,
Val,
VecOrMat,
Vector,
Expand Down Expand Up @@ -178,7 +161,6 @@ export
im,
π, pi,
ℯ,
I,

# Operators
!,
Expand Down Expand Up @@ -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,
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7 changes: 0 additions & 7 deletions base/interactiveutil.jl
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Expand Up @@ -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, ")")

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2 changes: 1 addition & 1 deletion base/math.jl
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Expand Up @@ -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))
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One of two places which uses a LinearAlgebra owned function... I hope this hack is fine for now.

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We should consider deprecating this function or just move it since the raison d'être of hypot is to handle potential overflow which vecnorm does but this implementation doesn't


"""
atan2(y, x)
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1 change: 0 additions & 1 deletion base/precompile.jl
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Expand Up @@ -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}}})
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20 changes: 14 additions & 6 deletions base/statistics.jl
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Expand Up @@ -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
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I believe this could R .*= x

return R
end

Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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))
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The second place where a LinearAlgebra owned function is used. This should be ok for now...

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This is not equivalent for all element types. Should we move statistics to stdlib first?

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This indeed turned out to be a problem in some cases. See https://github.com/JuliaLang/Statistics.jl/pull/85.

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) =
Expand All @@ -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)
Expand Down Expand Up @@ -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)...)))
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I imagine cov2cor! returns c, so that the potential type change under this transformation should not matter much? If so, collect -> Vector? :)

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Does that work for a generator? I get:
MethodError: no method matching Array{T,1} where T(::Base.Generator{UnitRange{Int64},getfield(Base, Symbol("##691#692")){Array{Float64,2}}})

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Ah yes, not implemented yet :).

end
corzm(x::AbstractVector, y::AbstractMatrix, vardim::Int=1) =
cov2cor!(unscaled_covzm(x, y, vardim), sqrt(sum(abs2, x)), sqrt!(sum(abs2, y, vardim)))
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10 changes: 4 additions & 6 deletions base/sysimg.jl
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Expand Up @@ -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")
Expand Down Expand Up @@ -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)
Expand Down Expand Up @@ -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)
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2 changes: 0 additions & 2 deletions doc/make.jl
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Expand Up @@ -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",
Expand Down Expand Up @@ -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",
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3 changes: 1 addition & 2 deletions doc/src/base/arrays.md
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Expand Up @@ -50,7 +50,6 @@ Base.IndexStyle
Base.conj!
Base.stride
Base.strides
Base.LinAlg.checksquare
```

## Broadcast and vectorization
Expand Down Expand Up @@ -148,7 +147,7 @@ Base.cumprod
Base.cumprod!
Base.cumsum
Base.cumsum!
Base.LinAlg.diff
LinearAlgebra.diff
Base.repeat(::AbstractArray)
Base.rot180
Base.rotl90
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3 changes: 0 additions & 3 deletions doc/src/base/base.md
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Expand Up @@ -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
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1 change: 0 additions & 1 deletion doc/src/base/index.md
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Expand Up @@ -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)
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