Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Base.LinAlg to LinearAlgebra stdlib #25571

Merged
merged 1 commit into from
Jan 18, 2018
Merged

Base.LinAlg to LinearAlgebra stdlib #25571

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
3 changes: 3 additions & 0 deletions NEWS.md
View file
Open in desktop
Original file line number Diff line number Diff line change
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`,
Expand Down
7 changes: 6 additions & 1 deletion base/array.jl
View file
Open in desktop
Original file line number Diff line number Diff line change
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)
Copy link
Member Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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)
Expand Down
1,525 changes: 147 additions & 1,378 deletions base/deprecated.jl
View file
Open in desktop

Large diffs are not rendered by default.

98 changes: 1 addition & 97 deletions base/exports.jl
View file
Open in desktop
Original file line number Diff line number Diff line change
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,
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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,
Expand Down
7 changes: 0 additions & 7 deletions base/interactiveutil.jl
View file
Open in desktop
Original file line number Diff line number Diff line change
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, ")")

Expand Down
2 changes: 1 addition & 1 deletion base/math.jl
View file
Open in desktop
Original file line number Diff line number Diff line change
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))
Copy link
Member Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

One of two places which uses a LinearAlgebra owned function... I hope this hack is fine for now.

Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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)
Expand Down
1 change: 0 additions & 1 deletion base/precompile.jl
View file
Open in desktop
Original file line number Diff line number Diff line change
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}}})
Expand Down
20 changes: 14 additions & 6 deletions base/statistics.jl
View file
Open in desktop
Original file line number Diff line number Diff line change
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
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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))
Copy link
Member Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

The second place where a LinearAlgebra owned function is used. This should be ok for now...

Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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

Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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)...)))
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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

Copy link
Member Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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}}})

Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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)))
Expand Down
10 changes: 4 additions & 6 deletions base/sysimg.jl
View file
Open in desktop
Original file line number Diff line number Diff line change
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)
Expand Down
2 changes: 0 additions & 2 deletions doc/make.jl
View file
Open in desktop
Original file line number Diff line number Diff line change
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",
Expand Down
3 changes: 1 addition & 2 deletions doc/src/base/arrays.md
View file
Open in desktop
Original file line number Diff line number Diff line change
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
Expand Down
3 changes: 0 additions & 3 deletions doc/src/base/base.md
View file
Open in desktop
Original file line number Diff line number Diff line change
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
Expand Down
1 change: 0 additions & 1 deletion doc/src/base/index.md
View file
Open in desktop
Original file line number Diff line number Diff line change
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)
Expand Down
Loading