Merge branch 'main' into lh/hardcode-backlinks

.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/CompatHelper.yml

@@ -0,0 +1,45 @@
+name: CompatHelper
+on:
+  schedule:
+    - cron: 0 0 * * *
+  workflow_dispatch:
+permissions:
+  contents: write
+  pull-requests: write
+jobs:
+  CompatHelper:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check if Julia is already available in the PATH
+        id: julia_in_path
+        run: which julia
+        continue-on-error: true
+      - name: Install Julia, but only if it is not already available in the PATH
+        uses: julia-actions/setup-julia@v1
+        with:
+          version: '1'
+          arch: ${{ runner.arch }}
+        if: steps.julia_in_path.outcome != 'success'
+      - name: "Add the General registry via Git"
+        run: |
+          import Pkg
+          ENV["JULIA_PKG_SERVER"] = ""
+          Pkg.Registry.add("General")
+        shell: julia --color=yes {0}
+      - name: "Install CompatHelper"
+        run: |
+          import Pkg
+          name = "CompatHelper"
+          uuid = "aa819f21-2bde-4658-8897-bab36330d9b7"
+          version = "3"
+          Pkg.add(; name, uuid, version)
+        shell: julia --color=yes {0}
+      - name: "Run CompatHelper"
+        run: |
+          import CompatHelper
+          CompatHelper.main()
+        shell: julia --color=yes {0}
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          COMPATHELPER_PRIV: ${{ secrets.DOCUMENTER_KEY }}
+          # COMPATHELPER_PRIV: ${{ secrets.COMPATHELPER_PRIV }}

.github/workflows/backport.yml

@@ -11,6 +11,6 @@ jobs:
     if: github.event.pull_request.merged
     steps:
       - name: Backport
-        uses: tibdex/backport@v1
+        uses: tibdex/backport@v2
         with:
           github_token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/ci.yml

@@ -34,12 +34,12 @@ jobs:
           - os: macOS-latest
             arch: x86
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@v1
         with:
           version: ${{ matrix.version }}
           arch: ${{ matrix.arch }}
-      - uses: actions/cache@v1
+      - uses: actions/cache@v3
         env:
           cache-name: cache-artifacts
         with:
@@ -52,14 +52,16 @@ jobs:
       - run: julia --color=yes .ci/test_and_change_uuid.jl
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-runtest@v1
+        env:
+          SPARSEARRAYS_AQUA_TEST: true
       - uses: julia-actions/julia-processcoverage@v1
-      - uses: codecov/codecov-action@v1
+      - uses: codecov/codecov-action@v3
         with:
           file: lcov.info
   docs:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@latest
         with:
           # version: '1.6'

.gitignore

@@ -1 +1,2 @@
 Manifest.toml
+docs/build

Project.toml

@@ -10,7 +10,17 @@ Serialization = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
 SuiteSparse_jll = "bea87d4a-7f5b-5778-9afe-8cc45184846c"
 
 [compat]
-SuiteSparse_jll = "7.2"
+Aqua = "0.8"
+Dates = "<0.0.1, 1"
+InteractiveUtils = "<0.0.1, 1"
+Libdl = "<0.0.1, 1"
+LinearAlgebra = "<0.0.1, 1"
+Pkg = "<0.0.1, 1"
+Printf = "<0.0.1, 1"
+Random = "<0.0.1, 1"
+Serialization = "<0.0.1, 1"
+SuiteSparse_jll = "7.4.0"
+Test = "<0.0.1, 1"
 julia = "1.11"
 
 [extras]

docs/Project.toml

@@ -1,2 +1,5 @@
 [deps]
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+
+[compat]
+Documenter = "1"

docs/make.jl

@@ -10,8 +10,7 @@ makedocs(
         "SparseArrays" => "index.md",
         "Sparse Linear Algebra" => "solvers.md",
         ];
-    # strict = true,
-    strict = Symbol[:doctest],
+    warnonly = [:missing_docs, :cross_references],
     )
 
 deploydocs(repo = "github.com/JuliaSparse/SparseArrays.jl.git")

docs/src/index.md

@@ -125,9 +125,9 @@ julia> R = sparsevec(I,V)
 ```
 
 The inverse of the [`sparse`](@ref) and [`sparsevec`](@ref) functions is
-[`findnz`](@ref), which retrieves the inputs used to create the sparse array.
+[`findnz`](@ref), which retrieves the inputs used to create the sparse array (including stored entries equal to zero).
 [`findall(!iszero, x)`](@ref) returns the Cartesian indices of non-zero entries in `x`
-(including stored entries equal to zero).
+(not including stored entries equal to zero).
 
 ```jldoctest sparse_function
 julia> findnz(S)
@@ -262,3 +262,5 @@ Several other Julia packages provide sparse matrix implementations that should b
 6. [LuxurySparse.jl](https://github.com/QuantumBFS/LuxurySparse.jl) provides static sparse array formats, as well as a coordinate format.
 
 7. [ExtendableSparse.jl](https://github.com/j-fu/ExtendableSparse.jl) enables fast insertion into sparse matrices using a lazy approach to new stored indices.
+
+8. [Finch.jl](https://github.com/willow-ahrens/Finch.jl) supports extensive multidimensional sparse array formats and operations through a mini tensor language and compiler, all in native Julia. Support for COO, CSF, CSR, CSC and more, as well as operations like broadcast, reduce, etc. and custom operations.

docs/src/solvers.md

@@ -14,7 +14,10 @@ Sparse matrix solvers call functions from [SuiteSparse](http://suitesparse.com).
 
 Other solvers such as [Pardiso.jl](https://github.com/JuliaSparse/Pardiso.jl/) are available as external packages. [Arpack.jl](https://julialinearalgebra.github.io/Arpack.jl/stable/) provides `eigs` and `svds` for iterative solution of eigensystems and singular value decompositions.
 
-These factorizations are described in more detail in [`Linear Algebra`](https://docs.julialang.org/en/v1/stdlib/LinearAlgebra/) section of the manual:
+These factorizations are described in more detail in the
+[`Linear Algebra`](https://docs.julialang.org/en/v1/stdlib/LinearAlgebra/)
+section of the manual:
+
 1. [`cholesky`](@ref SparseArrays.CHOLMOD.cholesky)
 2. [`ldlt`](@ref SparseArrays.CHOLMOD.ldlt)
 3. [`lu`](@ref SparseArrays.UMFPACK.lu)