Merge main into gd/structured3

.buildkite/pipeline.yml

@@ -0,0 +1,18 @@
+env:
+  SECRET_CODECOV_TOKEN: "l7PxpMgxHEiz2l3UDDj5122Xirv5du1QFQiTf09YISC8VOz/nXeQC2yYY6iTMbccQG3xrumfWke9vtLbAc9LPH75kw3zQODuWMbz0eGSf9wtw7foqO6KAo5neMTeZJ0ZFgFMa2Q89T5SNIQsi4b5Zs7BVto6qB9Z/3QEs/BpsR25cYkY4Y6JBU6XuqZ6GRAc6BtlB4OmBEp3BBsXatx6y64zF0qbp4rocmcBQEoeQkcXtxf0dfA0KNAHpweWPrzIAMZ0aUYp6iEikxwLY5TjVFhOIcpVXUlxIdhl2qaaDF6b6WlgGXiGLpBjsLQfvlOgIlXH59Ddg0IVxboF2a37OA==;U2FsdGVkX19MveWMe1aasYZoJwaeiKO5XqwMZ/utOFj7h1CE9UX4nduBMXTyJ77tpNmCBYsQNJ/PadbX2224hQ=="
+
+steps:
+  - label: "Julia v1"
+    plugins:
+      - JuliaCI/julia#v1:
+          version: "1"
+      - JuliaCI/julia-test#v1: ~
+      - JuliaCI/julia-coverage#v1:
+          codecov: true
+    agents:
+      queue: "juliagpu"
+      cuda: "*"
+    if: build.message !~ /\[skip tests\]/
+    timeout_in_minutes: 60
+    env:
+      JULIA_SMC_TEST_GROUP: 'GPU'

.github/workflows/Benchmark.yml

@@ -12,11 +12,11 @@ jobs:
         runs-on: ubuntu-latest
         if: contains(github.event.pull_request.labels.*.name, 'benchmark')
         steps:
-            - uses: actions/checkout@v4
-            - uses: julia-actions/setup-julia@v2
+            - uses: actions/checkout@v6
+            - uses: julia-actions/setup-julia@v3
               with:
                 version: "1"
-            - uses: julia-actions/cache@v2
+            - uses: julia-actions/cache@v3
             - name: Extract Package Name from Project.toml
               id: extract-package-name
               run: |
@@ -46,14 +46,14 @@ jobs:
                 echo '' >> body.md
                 echo '' >> body.md
             - name: Find Comment
-              uses: peter-evans/find-comment@v3
+              uses: peter-evans/find-comment@v4
               id: fcbenchmark
               with:
                 issue-number: ${{ github.event.pull_request.number }}
                 comment-author: 'github-actions[bot]'
                 body-includes: Benchmark Results
             - name: Comment on PR
-              uses: peter-evans/create-or-update-comment@v4
+              uses: peter-evans/create-or-update-comment@v5
               with:
                 comment-id: ${{ steps.fcbenchmark.outputs.comment-id }}
                 issue-number: ${{ github.event.pull_request.number }}

.github/workflows/CompatHelper.yml

@@ -15,7 +15,7 @@ jobs:
         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@v2
+        uses: julia-actions/setup-julia@v3
         with:
           version: '1'
           arch: ${{ runner.arch }}

.github/workflows/Documentation.yml

@@ -19,11 +19,11 @@ jobs:
       statuses: write
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
-      - uses: julia-actions/setup-julia@v2
+      - uses: actions/checkout@v6
+      - uses: julia-actions/setup-julia@v3
         with:
           version: '1'
-      - uses: julia-actions/cache@v2
+      - uses: julia-actions/cache@v3
       - name: Install dependencies
         run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
       - name: Build and deploy

.github/workflows/Format.yml

@@ -0,0 +1,12 @@
+name: Format suggestions
+on:
+  pull_request:
+    # this argument is not required if you don't use the `suggestion-label` input
+    types: [opened, reopened, synchronize, labeled, unlabeled]
+jobs:
+  code-style:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: julia-actions/julia-format@v4
+        with:
+          version: '1' # Set `version` to '1.0.54' if you need to use JuliaFormatter.jl v1.0.54 (default: '1')

.github/workflows/Test.yml

@@ -20,24 +20,24 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        julia-version: ['1.10', '1']
+        julia-version: ['1.10', '1.11', '1.12']
 
     steps:
-      - uses: actions/checkout@v4
-      - uses: julia-actions/setup-julia@v2
+      - uses: actions/checkout@v6
+      - uses: julia-actions/setup-julia@v3
         with:
           version: ${{ matrix.julia-version }}
           arch: x64
-      - uses: julia-actions/julia-downgrade-compat@v1
+      - uses: julia-actions/julia-downgrade-compat@v2
         if: ${{ matrix.version == '1.10' }}
         with:
           skip: LinearAlgebra, Random, SparseArrays
-      - uses: julia-actions/cache@v2
+      - uses: julia-actions/cache@v3
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-runtest@v1
       - uses: julia-actions/julia-processcoverage@v1
-      - uses: codecov/codecov-action@v5
+      - uses: codecov/codecov-action@v6
         with:
           files: lcov.info
           token: ${{ secrets.CODECOV_TOKEN }}
-          fail_ci_if_error: false
+          fail_ci_if_error: false

CITATION.cff

@@ -18,7 +18,7 @@ identifiers:
   - type: doi
     value: 10.5281/zenodo.11314275
     description: Zenodo
-repository-code: 'https://github.com/gdalle/SparseMatrixColorings.jl'
+repository-code: 'https://github.com/JuliaDiff/SparseMatrixColorings.jl'
 abstract: >-
   Coloring algorithms for sparse Jacobian and Hessian
   matrices

Project.toml

@@ -1,7 +1,7 @@
 name = "SparseMatrixColorings"
 uuid = "0a514795-09f3-496d-8182-132a7b665d35"
+version = "0.4.27"
 authors = ["Guillaume Dalle", "Alexis Montoison"]
-version = "0.4.22"
 
 [deps]
 ADTypes = "47edcb42-4c32-4615-8424-f2b9edc5f35b"
@@ -18,25 +18,35 @@ BlockBandedMatrices = "ffab5731-97b5-5995-9138-79e8c1846df0"
 CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"
 CliqueTrees = "60701a23-6482-424a-84db-faee86b9b1f8"
 Colors = "5ae59095-9a9b-59fe-a467-6f913c188581"
+GPUArrays = "0c68f7d7-f131-5f86-a1c3-88cf8149b2d7"
+JuMP = "4076af6c-e467-56ae-b986-b466b2749572"
+MathOptInterface = "b8f27783-ece8-5eb3-8dc8-9495eed66fee"
+cuSPARSE = "b26da814-b3bc-49ef-b0ee-c816305aa060"
 
 [extensions]
 SparseMatrixColoringsBandedMatricesExt = "BandedMatrices"
 SparseMatrixColoringsBlockBandedMatricesExt = ["BlockArrays", "BlockBandedMatrices"]
-SparseMatrixColoringsCUDAExt = "CUDA"
+SparseMatrixColoringsCUDAExt = ["CUDA", "cuSPARSE"]
 SparseMatrixColoringsCliqueTreesExt = "CliqueTrees"
 SparseMatrixColoringsColorsExt = "Colors"
+SparseMatrixColoringsGPUArraysExt = "GPUArrays"
+SparseMatrixColoringsJuMPExt = ["JuMP", "MathOptInterface"]
 
 [compat]
 ADTypes = "1.2.1"
 BandedMatrices = "1.9.4"
 BlockArrays = "1.6.3"
 BlockBandedMatrices = "0.13.1"
-CUDA = "5.8.2"
+CUDA = "6.0.0"
 CliqueTrees = "1"
 Colors = "0.12.11, 0.13"
 DocStringExtensions = "0.8,0.9"
-LinearAlgebra = "<0.0.1, 1"
+GPUArrays = "11.5.0"
+JuMP = "1.29.1"
+LinearAlgebra = "1"
+MathOptInterface = "1.45.0"
 PrecompileTools = "1.2.1"
-Random = "<0.0.1, 1"
-SparseArrays = "<0.0.1, 1"
+Random = "1"
+SparseArrays = "1"
+cuSPARSE = "6.0.0"
 julia = "1.10"

README.md

@@ -1,9 +1,11 @@
 # SparseMatrixColorings.jl
 
-[![Build Status](https://github.com/gdalle/SparseMatrixColorings.jl/actions/workflows/Test.yml/badge.svg?branch=main)](https://github.com/gdalle/SparseMatrixColorings.jl/actions/workflows/Test.yml?query=branch%3Amain)
-[![Stable Documentation](https://img.shields.io/badge/docs-stable-blue.svg)](https://gdalle.github.io/SparseMatrixColorings.jl/stable/)
-[![Dev Documentation](https://img.shields.io/badge/docs-dev-blue.svg)](https://gdalle.github.io/SparseMatrixColorings.jl/dev/)
-[![Coverage](https://codecov.io/gh/gdalle/SparseMatrixColorings.jl/branch/main/graph/badge.svg)](https://app.codecov.io/gh/gdalle/SparseMatrixColorings.jl)
+[![Build Status](https://github.com/juliadiff/SparseMatrixColorings.jl/actions/workflows/Test.yml/badge.svg?branch=main)](https://github.com/juliadiff/SparseMatrixColorings.jl/actions/workflows/Test.yml?query=branch%3Amain)
+[![GPU build status](https://badge.buildkite.com/7d8ed289d7bdb5a25ae48b2c778a202ce4990b7ee558cdfef8.svg?branch=main)](https://buildkite.com/julialang/sparsematrixcolorings-dot-jl)
+[![Coverage](https://codecov.io/gh/juliadiff/SparseMatrixColorings.jl/branch/main/graph/badge.svg)](https://app.codecov.io/gh/juliadiff/SparseMatrixColorings.jl)
+
+[![Stable Documentation](https://img.shields.io/badge/docs-stable-blue.svg)](https://juliadiff.org/SparseMatrixColorings.jl/stable/)
+[![Dev Documentation](https://img.shields.io/badge/docs-dev-blue.svg)](https://juliadiff.org/SparseMatrixColorings.jl/dev/)
 [![Code Style: Blue](https://img.shields.io/badge/code%20style-blue-4495d1.svg)](https://github.com/JuliaDiff/BlueStyle)
 [![arXiv](https://img.shields.io/badge/arXiv-2505.07308-b31b1b.svg)](https://arxiv.org/abs/2505.07308)
 [![DOI](https://zenodo.org/badge/801999408.svg)](https://zenodo.org/doi/10.5281/zenodo.11314275)

docs/make.jl

@@ -24,5 +24,7 @@ makedocs(;
 )
 
 deploydocs(;
-    repo="github.com/gdalle/SparseMatrixColorings.jl", push_preview=true, devbranch="main"
+    repo="github.com/JuliaDiff/SparseMatrixColorings.jl",
+    push_preview=true,
+    devbranch="main",
 )

docs/src/api.md

@@ -24,6 +24,7 @@ ColoringProblem
 ```@docs
 GreedyColoringAlgorithm
 ConstantColoringAlgorithm
+OptimalColoringAlgorithm
 StructuredColoringAlgorithm
 ```
 

docs/src/dev.md

@@ -41,6 +41,7 @@ SparseMatrixColorings.TreeSetColoringResult
 SparseMatrixColorings.LinearSystemColoringResult
 SparseMatrixColorings.BicoloringResult
 SparseMatrixColorings.remap_colors
+SparseMatrixColorings.decompress_csc!
 ```
 
 ## Testing
@@ -50,6 +51,9 @@ SparseMatrixColorings.directly_recoverable_columns
 SparseMatrixColorings.symmetrically_orthogonal_columns
 SparseMatrixColorings.structurally_orthogonal_columns
 SparseMatrixColorings.structurally_biorthogonal
+SparseMatrixColorings.substitutable_columns
+SparseMatrixColorings.substitutable_bidirectional
+SparseMatrixColorings.rank_nonzeros_from_trees
 SparseMatrixColorings.valid_dynamic_order
 ```
 
@@ -58,7 +62,7 @@ SparseMatrixColorings.valid_dynamic_order
 ```@docs
 SparseMatrixColorings.respectful_similar
 SparseMatrixColorings.matrix_versions
-SparseMatrixColorings.same_pattern
+SparseMatrixColorings.compatible_pattern
 ```
 
 ## Visualization

docs/src/tutorial.md

@@ -31,7 +31,7 @@ problem = ColoringProblem()
 
 The algorithm defines how you want to solve it. It can be either a [`GreedyColoringAlgorithm`](@ref) or a [`ConstantColoringAlgorithm`](@ref). For `GreedyColoringAlgorithm`, you can select options such as
 
-- the order in which vertices are processed (a subtype of [`AbstractOrder`](@ref SparseMatrixColorings.AbstractOrder))
+- the order in which vertices are processed (a subtype of [`AbstractOrder`](@ref SparseMatrixColorings.AbstractOrder) , or a tuple of such objects)
 - the type of decompression you want (`:direct` or `:substitution`)
 
 ```@example tutorial

ext/SparseMatrixColoringsCUDAExt.jl

@@ -3,23 +3,7 @@ module SparseMatrixColoringsCUDAExt
 import SparseMatrixColorings as SMC
 using SparseArrays: SparseMatrixCSC, rowvals, nnz, nzrange
 using CUDA: CuVector, CuMatrix
-using CUDA.CUSPARSE: AbstractCuSparseMatrix, CuSparseMatrixCSC, CuSparseMatrixCSR
-
-SMC.matrix_versions(A::AbstractCuSparseMatrix) = (A,)
-
-## Compression (slow, through CPU)
-
-function SMC.compress(
-    A::AbstractCuSparseMatrix, result::SMC.AbstractColoringResult{structure,:column}
-) where {structure}
-    return CuMatrix(SMC.compress(SparseMatrixCSC(A), result))
-end
-
-function SMC.compress(
-    A::AbstractCuSparseMatrix, result::SMC.AbstractColoringResult{structure,:row}
-) where {structure}
-    return CuMatrix(SMC.compress(SparseMatrixCSC(A), result))
-end
+using cuSPARSE: AbstractCuSparseMatrix, CuSparseMatrixCSC, CuSparseMatrixCSR
 
 ## CSC Result
 

ext/SparseMatrixColoringsColorsExt.jl

@@ -271,9 +271,8 @@ function show_colors!(
     A_ccolor_indices = mod1.(column_colors(res), length(colorscheme))
     A_rcolor_indices = mod1.(row_shift .+ row_colors(res), length(colorscheme))
     B_ccolor_indices = mod1.(1:maximum(column_colors(res)), length(colorscheme))
-    B_rcolor_indices = mod1.(
-        (row_shift + 1):(row_shift + maximum(row_colors(res))), length(colorscheme)
-    )
+    B_rcolor_indices =
+        mod1.((row_shift + 1):(row_shift + maximum(row_colors(res))), length(colorscheme))
     A_ccolors = colorscheme[A_ccolor_indices]
     A_rcolors = colorscheme[A_rcolor_indices]
     B_ccolors = colorscheme[B_ccolor_indices]

ext/SparseMatrixColoringsGPUArraysExt.jl

@@ -0,0 +1,29 @@
+module SparseMatrixColoringsGPUArraysExt
+
+using GPUArrays: AbstractGPUSparseMatrix, dense_array_type
+using SparseArrays: SparseMatrixCSC
+import SparseMatrixColorings as SMC
+
+SMC.matrix_versions(A::AbstractGPUSparseMatrix) = (A,)
+
+## Compression (slow, through CPU)
+
+function SMC.compress(
+    A::AbstractGPUSparseMatrix, result::SMC.AbstractColoringResult{structure,:column}
+) where {structure}
+    A_cpu = SparseMatrixCSC(A)
+    B_cpu = SMC.compress(A_cpu, result)
+    B = dense_array_type(A)(B_cpu)
+    return B
+end
+
+function SMC.compress(
+    A::AbstractGPUSparseMatrix, result::SMC.AbstractColoringResult{structure,:row}
+) where {structure}
+    A_cpu = SparseMatrixCSC(A)
+    B_cpu = SMC.compress(A_cpu, result)
+    B = dense_array_type(A)(B_cpu)
+    return B
+end
+
+end