Use SparseMatrixColorings (#270)

* Use SparseMatrixColorings

* Add docs

* Fix

* Compat

* Fix signature

* Docs

* Clean up tests

* Name tests

* Fix

* Shorten

* Fixes

* Fix

* Add out of place sparse stuff

* Update SCT

Author: gdalle

.github/workflows/Test.yml

@@ -17,7 +17,7 @@ concurrency:
 jobs:
 
   test-DI:
-    name: DI (${{ matrix.group }}) - Julia ${{ matrix.version }}
+    name: DI (${{ matrix.group }}) - ${{ matrix.version }}
     runs-on: ubuntu-latest
     timeout-minutes: 60
     permissions: # needed to allow julia-actions/cache to proactively delete old caches that it has created
@@ -77,6 +77,8 @@ jobs:
           arch: x64
       - uses: julia-actions/cache@v2
       - uses: julia-actions/julia-buildpkg@v1
+      - name: Update registry
+        run: julia -e 'using Pkg; Pkg.Registry.update()'
       - uses: julia-actions/julia-runtest@v1
         with:
           project: ./DifferentiationInterface
@@ -92,7 +94,7 @@ jobs:
           fail_ci_if_error: true
 
   test-DIT:
-    name: DIT - Julia ${{ matrix.version }}
+    name: DIT (${{ matrix.group }}) - ${{ matrix.version }}
     runs-on: ubuntu-latest
     timeout-minutes: 60
     permissions: # needed to allow julia-actions/cache to proactively delete old caches that it has created
@@ -104,6 +106,13 @@ jobs:
         version:
           - '1'
           - '1.6'
+        group:
+          - Formalities
+          - Zero
+          - ForwardDiff
+        exclude:
+          - version: '1.6'
+            group: Formalities
 
     steps:
       - uses: actions/checkout@v4
@@ -122,6 +131,8 @@ jobs:
       - uses: julia-actions/julia-runtest@v1
         with:
           project: ./DifferentiationInterfaceTest
+        env:
+          JULIA_DI_TEST_GROUP: ${{ matrix.group }}
       - uses: julia-actions/julia-processcoverage@v1
         with:
           directories: ./DifferentiationInterfaceTest/src,./DifferentiationInterfaceTest/ext

DifferentiationInterface/Project.toml

@@ -11,6 +11,7 @@ FillArrays = "1a297f60-69ca-5386-bcde-b61e274b549b"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 PackageExtensionCompat = "65ce6f38-6b18-4e1d-a461-8949797d7930"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
+SparseMatrixColorings = "0a514795-09f3-496d-8182-132a7b665d35"
 
 [weakdeps]
 ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
@@ -59,6 +60,8 @@ PackageExtensionCompat = "1.0.2"
 PolyesterForwardDiff = "0.1.1"
 ReverseDiff = "1.15.1"
 SparseArrays = "<0.0.1,1"
+SparseConnectivityTracer = "0.4.2"
+SparseMatrixColorings = "0.3.1"
 Symbolics = "5.27.1"
 Tapir = "0.2.4"
 Tracker = "0.2.33"
@@ -84,22 +87,12 @@ PolyesterForwardDiff = "98d1487c-24ca-40b6-b7ab-df2af84e126b"
 ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 SparseConnectivityTracer = "9f842d2f-2579-4b1d-911e-f412cf18a3f5"
+SparseMatrixColorings = "0a514795-09f3-496d-8182-132a7b665d35"
 Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7"
 Tapir = "07d77754-e150-4737-8c94-cd238a1fb45b"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c"
 Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"
 
 [targets]
-test = [
-    "ADTypes",
-    "Aqua",
-    "DataFrames",
-    "DifferentiationInterfaceTest",
-    "JET",
-    "JuliaFormatter",
-    "Pkg",
-    "SparseArrays",
-    "SparseConnectivityTracer",
-    "Test",
-]
+test = ["ADTypes", "Aqua", "DataFrames", "DifferentiationInterfaceTest", "JET", "JuliaFormatter", "Pkg", "SparseArrays", "SparseConnectivityTracer", "SparseMatrixColorings", "Test"]

DifferentiationInterface/docs/Project.toml

@@ -18,6 +18,7 @@ PolyesterForwardDiff = "98d1487c-24ca-40b6-b7ab-df2af84e126b"
 PrettyTables = "08abe8d2-0d0c-5749-adfa-8a2ac140af0d"
 ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267"
 SparseConnectivityTracer = "9f842d2f-2579-4b1d-911e-f412cf18a3f5"
+SparseMatrixColorings = "0a514795-09f3-496d-8182-132a7b665d35"
 Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7"
 Tapir = "07d77754-e150-4737-8c94-cd238a1fb45b"
 Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c"

DifferentiationInterface/docs/make.jl

@@ -22,6 +22,7 @@ using Zygote: Zygote
 links = InterLinks(
     "ADTypes" => "https://sciml.github.io/ADTypes.jl/stable/",
     "SparseConnectivityTracer" => "https://adrianhill.de/SparseConnectivityTracer.jl/stable/",
+    "SparseMatrixColorings" => "https://gdalle.github.io/SparseMatrixColorings.jl/stable/",
 )
 
 cp(joinpath(@__DIR__, "..", "README.md"), joinpath(@__DIR__, "src", "index.md"); force=true)

DifferentiationInterface/docs/src/api.md

@@ -96,7 +96,6 @@ check_hessian
 
 ```@docs
 DifferentiateWith
-GreedyColoringAlgorithm
 ```
 
 ## Internals

DifferentiationInterface/docs/src/tutorial.md

@@ -148,13 +148,14 @@ To compute sparse Jacobians or Hessians, you need three ingredients (read [this
     - [`TracerSparsityDetector`](@extref SparseConnectivityTracer.TracerSparsityDetector), implemented by [SparseConnectivityTracer.jl](https://github.com/adrhill/SparseConnectivityTracer.jl) (our default recommendation)
     - [`SymbolicsSparsityDetector`](@ref DifferentiationInterface.SymbolicsSparsityDetector), implemented by DifferentiationInterface.jl with [Symbolics.jl](https://github.com/JuliaSymbolics/Symbolics.jl) but not exported nor part of the public API (it will soon be [transferred](https://github.com/JuliaSymbolics/Symbolics.jl/pull/1134))
 3. A coloring algorithm like:
-    - [`GreedyColoringAlgorithm`](@ref), implemented by DifferentiationInterface.jl
+    - `GreedyColoringAlgorithm`, implemented by [SparseMatrixColorings.jl](https://github.com/gdalle/SparseMatrixColorings.jl) and re-exported by DifferentiationInterface.jl
 
 ADTypes.jl v1.0 provides the [`AutoSparse`](@extref ADTypes.AutoSparse) wrapper to combine these three ingredients, and DifferentiationInterface.jl re-exports it.
 Here's an example:
 
 ```@example tuto
-using SparseConnectivityTracer
+using SparseConnectivityTracer: TracerSparsityDetector
+using SparseMatrixColorings: GreedyColoringAlgorithm
 
 dense_backend = AutoForwardDiff()
 

DifferentiationInterface/src/DifferentiationInterface.jl

@@ -34,6 +34,13 @@ using FillArrays: OneElement
 using LinearAlgebra: Symmetric, Transpose, dot, parent, transpose
 using PackageExtensionCompat: @require_extensions
 using SparseArrays: SparseMatrixCSC, nonzeros, nzrange, rowvals, sparse
+using SparseMatrixColorings:
+    GreedyColoringAlgorithm,
+    color_groups,
+    decompress_columns!,
+    decompress_columns,
+    decompress_rows!,
+    decompress_rows
 
 abstract type Extras end
 
@@ -57,10 +64,8 @@ include("second_order/hvp.jl")
 include("second_order/hessian.jl")
 
 include("sparse/detector.jl")
-include("sparse/matrices.jl")
-include("sparse/coloring.jl")
-include("sparse/compressed_matrix.jl")
 include("sparse/fallbacks.jl")
+include("sparse/matrices.jl")
 include("sparse/jacobian.jl")
 include("sparse/hessian.jl")