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Merge branch 'main' of github.com:JuliaSparse/SparseArrays.jl into so…
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@SobhanMP
SobhanMP committed Aug 2, 2022
2 parents 4d473c7 + 7bf0c5c commit fa199bb
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6 changes: 3 additions & 3 deletions README.md
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Expand Up @@ -22,11 +22,11 @@ SparseArrays.jl provides functionality for working with sparse arrays in Julia.

## Using newer version of this package with julia master

You need to build Julia from scratch to use the git version (or other version) of this package. The build process is the same, but `DEPS_GIT` should be set when building i.e. `make DEPS_GIT="SparseArrays" ...`. The other option is to manually select the commit in `stdlib/SparseArrays.version`.
To use a newer version of this package, you need to build Julia from scratch. The build process is the same as any other build except that `DEPS_GIT="SparseArrays"` should be passed to `make` i.e. `make DEPS_GIT="SparseArrays"`. Then after the build is complete, the git repo in `stdlib/SparseArrays` can be used to check out the desired commit/branch. Alternatively, you need to change the commit used in `stdlib/SparseArrays.version`. It is also possible to do both to get an up to date git repo directly. There is no need to rebuild julia in case of changes in `stdlib/SparseArrays` (or `SparseArrays-<sha1>` if `DEPS_GIT` was not used) as the package is not in the sysimage but having a git repo is convenient.

It's also possible to load a development version of the package using [the trick used in the Section named "Using the development version of Pkg.jl" in the `Pkg.jl` repo](https://github.com/JuliaLang/Pkg.jl#using-the-development-version-of-pkgjl) but the capabilities are limited as all other packages will depend on the stdlib version of the package and will not work with the modified package.
It's also possible to load a development version of the package using [the trick used in the Section named "Using the development version of Pkg.jl" in the `Pkg.jl` repo](https://github.com/JuliaLang/Pkg.jl#using-the-development-version-of-pkgjl), but the capabilities are limited as all other packages will depend on the stdlib version of the package and will not work with the modified package.

The main environment may become inconsistent so you might need to run `Pkg.instantiate()` and/or `Pkg.resolve()` in the main or project environments if Julia complains about missing `Serialization` in this package's dependencies.
The main environment may become inconsistent so you might need to run `Pkg.instantiate()` and/or `Pkg.resolve()` in the main or project environments if Julia complains about missing `Serialization.jl` in this package's dependencies.

For older (1.8 and before) `SuiteSparse.jl` needs to be bumped too.

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8 changes: 8 additions & 0 deletions src/SparseArrays.jl
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Expand Up @@ -32,6 +32,14 @@ export AbstractSparseArray, AbstractSparseMatrix, AbstractSparseVector,
sprand, sprandn, spzeros, nnz, permute, findnz, fkeep!, ftranspose!,
sparse_hcat, sparse_vcat, sparse_hvcat

# helper function needed in sparsematrix, sparsevector and higherorderfns
@inline _iszero(x) = x == 0
@inline _iszero(x::Number) = Base.iszero(x)
@inline _iszero(x::AbstractArray) = Base.iszero(x)
@inline _isnotzero(x) = (x != 0) !== false # like `x != 0`, but handles `x::Missing`
@inline _isnotzero(x::Number) = !iszero(x)
@inline _isnotzero(x::AbstractArray) = !iszero(x)

include("abstractsparse.jl")
include("sparsematrix.jl")
include("sparseconvert.jl")
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36 changes: 20 additions & 16 deletions src/higherorderfns.jl
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Expand Up @@ -7,9 +7,16 @@ module HigherOrderFns
import Base: map, map!, broadcast, copy, copyto!

using Base: front, tail, to_shape
<<<<<<< HEAD
using ..SparseArrays: SparseVector, SparseMatrixCSC, FixedSparseCSC, AbstractSparseVector, AbstractSparseMatrixCSC,
AbstractSparseMatrix, AbstractSparseArray, AbstractFixedCSC, SorF, indtype, nnz, nzrange, spzeros,
SparseVectorUnion, AdjOrTransSparseVectorUnion, nonzeroinds, nonzeros, rowvals, getcolptr, widelength
=======
using ..SparseArrays: SparseVector, SparseMatrixCSC, AbstractSparseVector, AbstractSparseMatrixCSC,
AbstractSparseMatrix, AbstractSparseArray, indtype, nnz, nzrange, spzeros,
SparseVectorUnion, AdjOrTransSparseVectorUnion, nonzeroinds, nonzeros,
rowvals, getcolptr, widelength, _iszero, _isnotzero
>>>>>>> 7bf0c5cc6d6015137ca7ddcc8093d575ba860eed
using Base.Broadcast: BroadcastStyle, Broadcasted, flatten
using LinearAlgebra

Expand Down Expand Up @@ -210,9 +217,6 @@ end
# helper functions for map[!]/broadcast[!] entry points (and related methods below)
@inline _sumnnzs(A) = nnz(A)
@inline _sumnnzs(A, Bs...) = nnz(A) + _sumnnzs(Bs...)
@inline _iszero(x) = x == 0
@inline _iszero(x::Number) = Base.iszero(x)
@inline _iszero(x::AbstractArray) = Base.iszero(x)
@inline _zeros_eltypes(A) = (zero(eltype(A)),)
@inline _zeros_eltypes(A, Bs...) = (zero(eltype(A)), _zeros_eltypes(Bs...)...)
@inline _promote_indtype(A) = indtype(A)
Expand Down Expand Up @@ -252,7 +256,7 @@ function _map_zeropres!(f::Tf, C::SparseVecOrMat, A::SparseVecOrMat) where Tf
setcolptr!(C, j, Ck)
for Ak in colrange(A, j)
Cx = f(storedvals(A)[Ak])
if isa(C, AbstractFixedCSC) || isa(A, AbstractFixedCSC) || !_iszero(Cx)
if isa(C, AbstractFixedCSC) || isa(A, AbstractFixedCSC) || _isnotzero(Cx)
Ck > spaceC && (spaceC = expandstorage!(C, Ck + nnz(A) - (Ak - 1)))
storedinds(C)[Ck] = storedinds(A)[Ak]
storedvals(C)[Ck] = Cx
Expand Down Expand Up @@ -334,7 +338,7 @@ function _map_zeropres!(f::Tf, C::SparseVecOrMat, A::SparseVecOrMat, B::SparseVe
# cases are equally or more likely than the Ai < Bi and Bi < Ai cases. Hence
# the ordering of the conditional chain above differs from that in the
# corresponding broadcast code (below).
if !_iszero(Cx)
if _isnotzero(Cx)
Ck > spaceC && (spaceC = expandstorage!(C, Ck + (nnz(A) - (Ak - 1)) + (nnz(B) - (Bk - 1))))
storedinds(C)[Ck] = Ci
storedvals(C)[Ck] = Cx
Expand Down Expand Up @@ -395,7 +399,7 @@ function _map_zeropres!(f::Tf, C::SparseVecOrMat, As::Vararg{SparseVecOrMat,N})
while activerow < rowsentinel
vals, ks, rows = _fusedupdate_all(rowsentinel, activerow, rows, ks, stopks, As)
Cx = f(vals...)
if !_iszero(Cx)
if _isnotzero(Cx)
Ck > spaceC && (spaceC = expandstorage!(C, Int(min(widelength(C), Ck + _sumnnzs(As...) - (sum(ks) - N)))))
storedinds(C)[Ck] = activerow
storedvals(C)[Ck] = Cx
Expand Down Expand Up @@ -486,7 +490,7 @@ function _broadcast_zeropres!(f::Tf, C::SparseVecOrMat, A::SparseVecOrMat) where
bccolrangejA = numcols(A) == 1 ? colrange(A, 1) : colrange(A, j)
for Ak in bccolrangejA
Cx = f(storedvals(A)[Ak])
if !_iszero(Cx)
if _isnotzero(Cx)
Ck > spaceC && (spaceC = expandstorage!(C, _unchecked_maxnnzbcres(size(C), A)))
storedinds(C)[Ck] = storedinds(A)[Ak]
storedvals(C)[Ck] = Cx
Expand All @@ -505,7 +509,7 @@ function _broadcast_zeropres!(f::Tf, C::SparseVecOrMat, A::SparseVecOrMat) where
# contains a nonzero value x but f(Ax) is nonetheless zero, so we need store
# nothing in C's jth column. if to the contrary fofAx is nonzero, then we must
# densely populate C's jth column with fofAx.
if !_iszero(fofAx)
if _isnotzero(fofAx)
for Ci::indtype(C) in 1:numrows(C)
Ck > spaceC && (spaceC = expandstorage!(C, _unchecked_maxnnzbcres(size(C), A)))
storedinds(C)[Ck] = Ci
Expand Down Expand Up @@ -608,7 +612,7 @@ function _broadcast_zeropres!(f::Tf, C::SparseVecOrMat, A::SparseVecOrMat, B::Sp
# pattern) the Ai < Bi and Bi < Ai cases are equally or more likely than the
# Ai == Bi and termination cases. Hence the ordering of the conditional
# chain above differs from that in the corresponding map code.
if !_iszero(Cx)
if _isnotzero(Cx)
Ck > spaceC && (spaceC = expandstorage!(C, _unchecked_maxnnzbcres(size(C), A, B)))
storedinds(C)[Ck] = Ci
storedvals(C)[Ck] = Cx
Expand All @@ -625,7 +629,7 @@ function _broadcast_zeropres!(f::Tf, C::SparseVecOrMat, A::SparseVecOrMat, B::Sp
Ax = Ak < stopAk ? storedvals(A)[Ak] : zero(eltype(A))
Bx = Bk < stopBk ? storedvals(B)[Bk] : zero(eltype(B))
Cx = f(Ax, Bx)
if !_iszero(Cx)
if _isnotzero(Cx)
for Ci::indtype(C) in 1:numrows(C)
Ck > spaceC && (spaceC = expandstorage!(C, _unchecked_maxnnzbcres(size(C), A, B)))
storedinds(C)[Ck] = Ci
Expand All @@ -647,7 +651,7 @@ function _broadcast_zeropres!(f::Tf, C::SparseVecOrMat, A::SparseVecOrMat, B::Sp
# B's jth column without storing every entry in C's jth column
while Bk < stopBk
Cx = f(Ax, storedvals(B)[Bk])
if !_iszero(Cx)
if _isnotzero(Cx)
Ck > spaceC && (spaceC = expandstorage!(C, _unchecked_maxnnzbcres(size(C), A, B)))
storedinds(C)[Ck] = storedinds(B)[Bk]
storedvals(C)[Ck] = Cx
Expand All @@ -666,7 +670,7 @@ function _broadcast_zeropres!(f::Tf, C::SparseVecOrMat, A::SparseVecOrMat, B::Sp
else
Cx = fvAzB
end
if !_iszero(Cx)
if _isnotzero(Cx)
Ck > spaceC && (spaceC = expandstorage!(C, _unchecked_maxnnzbcres(size(C), A, B)))
storedinds(C)[Ck] = Ci
storedvals(C)[Ck] = Cx
Expand All @@ -688,7 +692,7 @@ function _broadcast_zeropres!(f::Tf, C::SparseVecOrMat, A::SparseVecOrMat, B::Sp
# A's jth column without storing every entry in C's jth column
while Ak < stopAk
Cx = f(storedvals(A)[Ak], Bx)
if !_iszero(Cx)
if _isnotzero(Cx)
Ck > spaceC && (spaceC = expandstorage!(C, _unchecked_maxnnzbcres(size(C), A, B)))
storedinds(C)[Ck] = storedinds(A)[Ak]
storedvals(C)[Ck] = Cx
Expand All @@ -707,7 +711,7 @@ function _broadcast_zeropres!(f::Tf, C::SparseVecOrMat, A::SparseVecOrMat, B::Sp
else
Cx = fzAvB
end
if !_iszero(Cx)
if _isnotzero(Cx)
Ck > spaceC && (spaceC = expandstorage!(C, _unchecked_maxnnzbcres(size(C), A, B)))
storedinds(C)[Ck] = Ci
storedvals(C)[Ck] = Cx
Expand Down Expand Up @@ -897,7 +901,7 @@ function _broadcast_zeropres!(f::Tf, C::SparseVecOrMat, As::Vararg{SparseVecOrMa
while activerow < rowsentinel
args, ks, rows = _fusedupdatebc_all(rowsentinel, activerow, rows, defargs, ks, stopks, As)
Cx = f(args...)
if !_iszero(Cx)
if _isnotzero(Cx)
Ck > spaceC && (spaceC = expandstorage!(C, _unchecked_maxnnzbcres(size(C), As)))
storedinds(C)[Ck] = activerow
storedvals(C)[Ck] = Cx
Expand All @@ -914,7 +918,7 @@ function _broadcast_zeropres!(f::Tf, C::SparseVecOrMat, As::Vararg{SparseVecOrMa
else
Cx = defaultCx
end
if !_iszero(Cx)
if _isnotzero(Cx)
Ck > spaceC && (spaceC = expandstorage!(C, _unchecked_maxnnzbcres(size(C), As)))
storedinds(C)[Ck] = Ci
storedvals(C)[Ck] = Cx
Expand Down
2 changes: 1 addition & 1 deletion src/solvers/spqr.jl
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Expand Up @@ -324,7 +324,7 @@ _ret_size(F::QRSparse, b::AbstractVector) = (size(F, 2),)
_ret_size(F::QRSparse, B::AbstractMatrix) = (size(F, 2), size(B, 2))

LinearAlgebra.rank(F::QRSparse) = reduce(max, view(rowvals(F.R), 1:nnz(F.R)), init = eltype(rowvals(F.R))(0))
LinearAlgebra.rank(S::SparseMatrixCSC) = rank(qr(S))
LinearAlgebra.rank(S::SparseMatrixCSC; tol=_default_tol(S)) = rank(qr(S; tol))

function (\)(F::QRSparse{T}, B::VecOrMat{Complex{T}}) where T<:LinearAlgebra.BlasReal
# |z1|z3| reinterpret |x1|x2|x3|x4| transpose |x1|y1| reshape |x1|y1|x3|y3|
Expand Down
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