Merge pull request #27 from gridap/release-0.6.8

Release 0.6.8

.github/dependabot.yml

@@ -0,0 +1,7 @@
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "monthly"

.github/workflows/ci.yml

@@ -8,41 +8,37 @@ jobs:
       fail-fast: false
       matrix:
         version:
+          - '1.8'
           - '1.9'
+          - '1.10'
         os:
           - ubuntu-latest
+          - windows-latest
         arch:
           - x64
     steps:
-      - uses: actions/checkout@v2
-      - uses: julia-actions/setup-julia@v1
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
-      - uses: actions/cache@v1
-        env:
-          cache-name: cache-artifacts
-        with:
-          path: ~/.julia/artifacts
-          key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
-          restore-keys: |
-            ${{ runner.os }}-test-${{ env.cache-name }}-
-            ${{ runner.os }}-test-
-            ${{ runner.os }}-
+      - uses: julia-actions/cache@v2
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-runtest@v1
       - uses: julia-actions/julia-processcoverage@v1
-      - uses: codecov/codecov-action@v1
+      - uses: codecov/codecov-action@v4
         with:
           file: lcov.info
+          verbose: true
+
   docs:
     name: Documentation
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v2
       - uses: julia-actions/setup-julia@v1
         with:
-          version: '1.9'
+          version: '1.10'
       - run: |
           julia --project=docs -e '
             using Pkg
@@ -52,3 +48,30 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}
+
+  downgrade:
+    name: Downgrade ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        version:
+          - '1.10'
+        os:
+          - ubuntu-latest
+        arch:
+          - x64
+    steps:
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
+        with:
+          version: ${{ matrix.version }}
+          arch: ${{ matrix.arch }}
+      - uses: julia-actions/cache@v2
+      - uses: julia-actions/julia-downgrade-compat@v1
+        with: # As per documentation, we exclude packages within the Julia standard library
+          skip: LinearAlgebra,SparseArrays
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-runtest@v1
+        with:
+          coverage: false

NEWS.md

@@ -1,30 +1,41 @@
 # Changelog
+
 All notable changes to this project will be documented in this file.
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
 ## [0.6.8] - 2024.08.29
 
+### Added
+
+- Added `SparseMatrixCSC` and `AbstractMatrix` constructors.
+
 ### Fixed
-- Fixed show method for SparseMatrixCSR
+
+- Fixed show method for SparseMatrixCSR.
+- Fixes related to `TransposeFactorization` (see https://github.com/JuliaLang/julia/pull/46874).
 
 ## [0.6.6] - 2021.11.26
 
 ### Added
+
 - Implemented `Base.setindex!`.
 
 ## [0.6.5] - 2021.10.20
 
 ### Fixed
+
 - Return value of `LinearAlbegra.fillstored!`.
 
 ### Added
+
 - Implemented `LinearAlbegra.rmul!`.
 
 ## [0.6.4] - 2021.10.20
 
 ### Added
+
 - Implemented `LinearAlbegra.fillstored!`.
 
 *Previous releases are not included in this Changelog*

README.md

@@ -7,5 +7,3 @@ Sparse matrices in CSR format (symmetric and non-symmetric) for Julia computatio
 | [![](https://img.shields.io/badge/docs-stable-blue.svg)](https://gridap.github.io/SparseMatricesCSR.jl/stable) [![](https://img.shields.io/badge/docs-dev-blue.svg)](https://gridap.github.io/SparseMatricesCSR.jl/dev) |
 |**Build Status** |
 | [![Build Status](https://github.com/gridap/SparseMatricesCSR.jl/workflows/CI/badge.svg?branch=master)](https://github.com/gridap/SparseMatricesCSR.jl/actions?query=workflow%3ACI) [![Codecov](https://codecov.io/gh/gridap/SparseMatricesCSR.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/gridap/SparseMatricesCSR.jl) |
-
-

docs/.gitignore

@@ -0,0 +1,2 @@
+Manifest.toml
+build

docs/Project.toml

@@ -1,3 +1,4 @@
 [deps]
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+DocumenterInterLinks = "d12716ef-a0f6-4df4-a9f1-a5a34e75c656"
 SparseMatricesCSR = "a0a7dd2c-ebf4-11e9-1f05-cf50bc540ca1"

docs/make.jl

@@ -1,4 +1,9 @@
-using Documenter, SparseMatricesCSR
+using Documenter, DocumenterInterLinks
+using SparseMatricesCSR
+
+links = InterLinks(
+    "SparseArrays" => "https://docs.julialang.org/en/v1/"
+)
 
 makedocs(;
     modules=[SparseMatricesCSR],
@@ -9,6 +14,7 @@ makedocs(;
     repo="https://github.com/gridap/SparseMatricesCSR.jl/blob/{commit}{path}#L{line}",
     sitename="SparseMatricesCSR.jl",
     authors="Víctor Sande <[email protected]> and Francesc Verdugo <[email protected]>",
+    plugins=[links],
 )
 
 deploydocs(;

src/SparseMatricesCSR.jl

@@ -6,7 +6,7 @@ using SuiteSparse
 
 import Base: convert, copy, size, getindex, setindex!, show, count, *, IndexStyle
 import LinearAlgebra: mul!, lu, lu!
-import SparseArrays: nnz, getnzval, nonzeros, nzrange
+import SparseArrays: nnz, getnzval, nonzeros, nzvalview, nzrange
 import SparseArrays: findnz, rowvals, getnzval, issparse
 
 export SparseMatrixCSR

src/SparseMatrixCSR.jl

@@ -55,6 +55,20 @@ function SparseMatrixCSR(a::Transpose{Tv,<:SparseMatrixCSC} where Tv)
   SparseMatrixCSR{1}(size(a,1),size(a,2),at.colptr,rowvals(at),nonzeros(at))
 end
 
+"""
+    SparseMatrixCSR(a::SparseMatrixCSC}
+
+Build a 1-based `SparseMatrixCSR` from a `SparseMatrixCSC`. 
+"""
+SparseMatrixCSR(a::SparseMatrixCSC) = SparseMatrixCSR(transpose(sparse(transpose(a))))
+
+"""
+    SparseMatrixCSR(a::AbstractMatrix}
+
+Build a 1-based `SparseMatrixCSR` from an `AbstractMatrix`. 
+"""
+SparseMatrixCSR(a::AbstractMatrix) = SparseMatrixCSR(sparse(a))
+
 """
     SparseMatrixCSR{Bi}(a::Transpose{Tv,<:SparseMatrixCSC} where Tv) where Bi
 
@@ -77,7 +91,7 @@ SparseMatrixCSR{1}(a::Transpose{Tv,<:SparseMatrixCSC} where Tv) = SparseMatrixCS
 
 Create  a `SparseMatrixCSR` with `Bi`-based indexing (1 by default)
 from the same `args...` as one constructs a `SparseMatrixCSC`
-with the [`sparse`](@ref) function.
+with the [`SparseArrays.sparse`](@extref) function.
 """
 sparsecsr(I,J,V) = SparseMatrixCSR(transpose(sparse(J,I,V,dimlub(J),dimlub(I))))
 sparsecsr(I,J,V,m,n) = SparseMatrixCSR(transpose(sparse(J,I,V,n,m)))
@@ -133,27 +147,31 @@ end
 function LinearAlgebra.lu(a::SparseMatrixCSR{0})
   rowptr = _copy_and_increment(a.rowptr)
   colval = _copy_and_increment(a.colval)
-  Transpose(lu(SparseMatrixCSC(a.m,a.n,rowptr,colval,a.nzval)))
+  transpose(lu(SparseMatrixCSC(a.m,a.n,rowptr,colval,a.nzval)))
 end
 
 function LinearAlgebra.lu(a::SparseMatrixCSR{1})
-  Transpose(lu(SparseMatrixCSC(a.m,a.n,a.rowptr,a.colval,a.nzval)))
+  transpose(lu(SparseMatrixCSC(a.m,a.n,a.rowptr,a.colval,a.nzval)))
 end
 
 if Base.USE_GPL_LIBS
 
+const TransposeFact = isdefined(LinearAlgebra, :TransposeFactorization) ?
+  LinearAlgebra.TransposeFactorization :
+  Transpose
+
 function LinearAlgebra.lu!(
-    translu::Transpose{T,<:SuiteSparse.UMFPACK.UmfpackLU{T}},
+    translu::TransposeFact{T,<:SuiteSparse.UMFPACK.UmfpackLU{T}},
     a::SparseMatrixCSR{1}) where {T}
-  Transpose(lu!(translu.parent,SparseMatrixCSC(a.m,a.n,a.rowptr,a.colval,a.nzval)))
+  transpose(lu!(translu.parent,SparseMatrixCSC(a.m,a.n,a.rowptr,a.colval,a.nzval)))
 end
 
 function LinearAlgebra.lu!(
-  translu::Transpose{T,<:SuiteSparse.UMFPACK.UmfpackLU{T}},
+  translu::TransposeFact{T,<:SuiteSparse.UMFPACK.UmfpackLU{T}},
   a::SparseMatrixCSR{0}) where {T}
   rowptr = _copy_and_increment(a.rowptr)
   colval = _copy_and_increment(a.colval)
-  Transpose(lu!(translu.parent,SparseMatrixCSC(a.m,a.n,rowptr,colval,a.nzval)))
+  transpose(lu!(translu.parent,SparseMatrixCSC(a.m,a.n,rowptr,colval,a.nzval)))
 end
 
 end # Base.USE_GPL_LIBS
@@ -223,7 +241,7 @@ issparse(S::SparseMatrixCSR) = true
 
 Returns the number of stored (filled) elements in a sparse array.
 """
-nnz(S::SparseMatrixCSR) = length(nonzeros(S))
+nnz(S::SparseMatrixCSR{Bi}) where Bi = Int(S.rowptr[size(S, 1) + 1] - Bi)
 
 """
     nonzeros(S::SparseMatrixCSR)
@@ -235,6 +253,8 @@ and any modifications to the returned vector will mutate S as well.
 """
 nonzeros(S::SparseMatrixCSR) = S.nzval
 
+nzvalview(S::SparseMatrixCSR) = view(nonzeros(S), 1:nnz(S))
+
 """
     colvals(S::SparseMatrixCSR{Bi}) where {Bi}
 
@@ -289,8 +309,8 @@ end
 Count the number of elements in `nonzeros(S)` for which predicate `pred` returns `true`.
 If  `pred` not given, it counts the number of `true` values.
 """
-count(pred, S::SparseMatrixCSR) = count(pred, nonzeros(S))
-count(S::SparseMatrixCSR) = count(i->true, nonzeros(S))
+count(pred, S::SparseMatrixCSR) = count(pred, nzvalview(S))
+count(S::SparseMatrixCSR) = count(i->true, nzvalview(S))
 
 function mul!(y::AbstractVector,A::SparseMatrixCSR,v::AbstractVector, α::Number, β::Number)
   A.n == size(v, 1) || throw(DimensionMismatch())

test/SparseMatrixCSR.jl

@@ -79,7 +79,7 @@ function test_csr(Bi,Tv,Ti)
   @test getBi(CSR) == Bi
   @test getoffset(CSR) == 1-Bi
   @test nnz(CSR) == nnz(CSC)
-  @test length(nonzeros(CSR)) == nnz(CSR)
+  @test length(SparseArrays.nzvalview(CSR)) == nnz(CSR)
   @test nonzeros(CSR) === CSR.nzval
   @test colvals(CSR) === CSR.colval
   i,j,v = findnz(CSR)
@@ -106,11 +106,22 @@ function test_csr(Bi,Tv,Ti)
   mul!(z,CSC,x)
   @test y ≈ z
 
+  # test constructors
+  @test CSR == SparseMatrixCSR(CSC)
+  @test CSR == SparseMatrixCSR(Matrix(CSC))
+
   _CSR = copy(CSR)
   out = LinearAlgebra.rmul!(CSR,-1)
   @test out === CSR
   @test _CSR ≈ -1*CSR
 
+  # Test overlong buffers
+  let A = sparsecsr([1, 2, 3], [1, 2, 3], [4., 5, 6])
+    push!(A.nzval, 4.0)
+    push!(A.rowptr, -1)
+    @test nnz(A) == length(SparseArrays.nzvalview(A)) == 3
+    @test SparseArrays.nzvalview(A) == [4., 5, 6]
+  end
 end
 
 function test_lu(Bi,I,J,V)
@@ -135,13 +146,13 @@ for Bi in (0,1)
 end
 
 if Base.USE_GPL_LIBS  # `lu!` requires `SuiteSparse.UMFPACK`
-    I = [1,1,2,2,2,3,3]
-    J = [1,2,1,2,3,2,3]
-    V = [4.0,1.0,-1.0,4.0,1.0,-1.0,4.0]
-    test_lu(0,I,J,V)
-    test_lu(1,I,J,V)
+  I = [1,1,2,2,2,3,3]
+  J = [1,2,1,2,3,2,3]
+  V = [4.0,1.0,-1.0,4.0,1.0,-1.0,4.0]
+  test_lu(0,I,J,V)
+  test_lu(1,I,J,V)
 else
-    @warn "Tests run without GPL libraries."
+  @warn "Tests run without GPL libraries."
 end
 
 end # module