Merge branch 'main' into gd/diffwith

gdalle · gdalle · commit 2905246b4601 · 2026-03-18T08:41:00.000+01:00
diff --git a/.github/workflows/Documentation.yml b/.github/workflows/Documentation.yml
@@ -39,7 +39,7 @@ jobs:
       - uses: julia-actions/setup-julia@v2
         with:
           version: '1'  # TODO: 1
-      - uses: julia-actions/cache@v1
+      - uses: julia-actions/cache@v3
       - name: Install dependencies
         run: julia --project=${{ matrix.pkg.dir}}/docs/ --color=yes -e '
           using Pkg;
diff --git a/.github/workflows/PreCommit.yml b/.github/workflows/PreCommit.yml
@@ -20,7 +20,7 @@ jobs:
     steps:
       - uses: actions/checkout@v6
       - uses: julia-actions/setup-julia@v2
-      - uses: julia-actions/cache@v2
+      - uses: julia-actions/cache@v3
       - run: julia -e 'using Pkg; Pkg.add("Runic")'
       - uses: astral-sh/setup-uv@v7
       - run: uv tool install pre-commit
diff --git a/.github/workflows/Test.yml b/.github/workflows/Test.yml
@@ -54,7 +54,7 @@ jobs:
         with:
           version: ${{ matrix.version }}
           arch: x64
-      - uses: julia-actions/cache@v2
+      - uses: julia-actions/cache@v3
       - name: Install dependencies & run tests
         run: julia --color=yes -e '
           using Pkg;
@@ -139,7 +139,7 @@ jobs:
         with:
           version: ${{ matrix.version }}
           arch: x64
-      - uses: julia-actions/cache@v2
+      - uses: julia-actions/cache@v3
       - name: Install dependencies & run tests
         run: julia --code-coverage=user --color=yes -e '
           using Pkg;
@@ -195,7 +195,7 @@ jobs:
         with:
           version: ${{ matrix.version }}
           arch: x64
-      - uses: julia-actions/cache@v2
+      - uses: julia-actions/cache@v3
       - name: Install dependencies & run tests
         run: julia --project=./DifferentiationInterfaceTest --color=yes -e '
           using Pkg;
diff --git a/DifferentiationInterface/README.md b/DifferentiationInterface/README.md
@@ -2,16 +2,13 @@
 
 # DifferentiationInterface
 
-[![Build Status](https://github.com/JuliaDiff/DifferentiationInterface.jl/actions/workflows/Test.yml/badge.svg?branch=main)](https://github.com/JuliaDiff/DifferentiationInterface.jl/actions/workflows/Test.yml?query=branch%3Amain)
-[![Coverage](https://codecov.io/gh/JuliaDiff/DifferentiationInterface.jl/branch/main/graph/badge.svg?flag=DI)](https://app.codecov.io/gh/JuliaDiff/DifferentiationInterface.jl)
-[![code style: runic](https://img.shields.io/badge/code_style-%E1%9A%B1%E1%9A%A2%E1%9A%BE%E1%9B%81%E1%9A%B2-black)](https://github.com/fredrikekre/Runic.jl)
-[![ColPrac: Contributor's Guide on Collaborative Practices for Community Packages](https://img.shields.io/badge/ColPrac-Contributor%27s%20Guide-blueviolet)](https://github.com/SciML/ColPrac)
-[![DOI](https://zenodo.org/badge/740973714.svg)](https://zenodo.org/doi/10.5281/zenodo.11092033)
-
-|           Package            |                                                                                                                                                 Docs                                                                                                                                                 |
-| :--------------------------: | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: |
-|   DifferentiationInterface   |   [![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://juliadiff.org/DifferentiationInterface.jl/DifferentiationInterface/stable/)     [![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://juliadiff.org/DifferentiationInterface.jl/DifferentiationInterface/dev/)   |
-| DifferentiationInterfaceTest | [![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://juliadiff.org/DifferentiationInterface.jl/DifferentiationInterfaceTest/stable/) [![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://juliadiff.org/DifferentiationInterface.jl/DifferentiationInterfaceTest/dev/) |
+| Category | Badges |
+|---|---|
+| Build status | [![Tests](https://github.com/JuliaDiff/DifferentiationInterface.jl/actions/workflows/Test.yml/badge.svg?branch=main)](https://github.com/JuliaDiff/DifferentiationInterface.jl/actions/workflows/Test.yml?query=branch%3Amain) [![Coverage](https://codecov.io/gh/JuliaDiff/DifferentiationInterface.jl/branch/main/graph/badge.svg?flag=DI)](https://app.codecov.io/gh/JuliaDiff/DifferentiationInterface.jl) |
+| Documentation | [![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://juliadiff.org/DifferentiationInterface.jl/DifferentiationInterface/stable/)     [![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://juliadiff.org/DifferentiationInterface.jl/DifferentiationInterface/dev/) [![ColPrac: Contributor's Guide on Collaborative Practices for Community Packages](https://img.shields.io/badge/ColPrac-Contributor%27s%20Guide-blueviolet)](https://github.com/SciML/ColPrac) |
+| Code quality | [![code style: runic](https://img.shields.io/badge/code_style-%E1%9A%B1%E1%9A%A2%E1%9A%BE%E1%9B%81%E1%9A%B2-black)](https://github.com/fredrikekre/Runic.jl) [![Aqua QA](https://juliatesting.github.io/Aqua.jl/dev/assets/badge.svg)](https://github.com/JuliaTesting/Aqua.jl) |
+| Downloads | [![Downloads](https://img.shields.io/badge/dynamic/json?url=http%3A%2F%2Fjuliapkgstats.com%2Fapi%2Fv2%2Fmonthly_downloads%2FDifferentiationInterface&query=total_requests&suffix=%2Fmonth&label=Downloads)](http://juliapkgstats.com/pkg/DifferentiationInterface) [![Dependents](https://juliahub.com/docs/General/DifferentiationInterface/stable/deps.svg)](https://juliahub.com/ui/Packages/General/DifferentiationInterface?#dependents) |
+| References | [![DOI](https://zenodo.org/badge/740973714.svg)](https://zenodo.org/doi/10.5281/zenodo.11092033) |
 
 An interface to various automatic differentiation (AD) backends in Julia.
 
@@ -94,7 +91,7 @@ Whenever you refer to this package or the ideas it contains, please cite:
 
  1. our JMLR paper [*A Common Interface for Automatic Differentiation*](https://jmlr.org/papers/v27/25-1024.html);
  2. our inspiration [AbstractDifferentiation.jl](https://github.com/JuliaDiff/AbstractDifferentiation.jl).
- 3. if you use sparse differentiation capabilities, our companion packages [SparseConnectivityTracer.jl](https://github.com/adrhill/SparseConnectivityTracer.jl) and [SparseMatrixColorings.jl](https://github.com/gdalle/SparseMatrixColorings.jl) which provide these capabilities (see their respective repositories for guidelines).
+ 3. if you use sparse differentiation capabilities, our companion packages [SparseConnectivityTracer.jl](https://github.com/adrhill/SparseConnectivityTracer.jl) and [SparseMatrixColorings.jl](https://github.com/JuliaDiff/SparseMatrixColorings.jl) which provide these capabilities (see their respective repositories for guidelines).
 
 For the first two items, you can use the provided [`CITATION.cff`](https://github.com/JuliaDiff/DifferentiationInterface.jl/blob/main/CITATION.cff) file or the following BibTeX entries:
 
diff --git a/DifferentiationInterface/docs/make.jl b/DifferentiationInterface/docs/make.jl
@@ -11,7 +11,7 @@ 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/",
+    "SparseMatrixColorings" => "https://juliadiff.org/SparseMatrixColorings.jl/stable/",
     "Symbolics" => "https://symbolics.juliasymbolics.org/stable/",
 )
 
diff --git a/DifferentiationInterface/docs/src/explanation/advanced.md b/DifferentiationInterface/docs/src/explanation/advanced.md
@@ -23,7 +23,7 @@ An `AutoSparse` backend must be constructed from three ingredients:
       + [`DenseSparsityDetector`](@ref) from DifferentiationInterface.jl (beware that this detector only gives a locally valid pattern)
       + [`KnownJacobianSparsityDetector`](@extref ADTypes.KnownJacobianSparsityDetector) or [`KnownHessianSparsityDetector`](@extref ADTypes.KnownHessianSparsityDetector) from [ADTypes.jl](https://github.com/SciML/ADTypes.jl) (if you already know the pattern)
 
- 3. A coloring algorithm following the [`ADTypes.AbstractColoringAlgorithm`](@extref ADTypes.AbstractColoringAlgorithm) interface, such as those from [SparseMatrixColorings.jl](https://github.com/gdalle/SparseMatrixColorings.jl):
+ 3. A coloring algorithm following the [`ADTypes.AbstractColoringAlgorithm`](@extref ADTypes.AbstractColoringAlgorithm) interface, such as those from [SparseMatrixColorings.jl](https://github.com/JuliaDiff/SparseMatrixColorings.jl):
 
       + [`GreedyColoringAlgorithm`](@extref SparseMatrixColorings.GreedyColoringAlgorithm) (our generic recommendation, don't forget to tune the `order` parameter)
       + [`ConstantColoringAlgorithm`](@extref SparseMatrixColorings.ConstantColoringAlgorithm) (if you have already computed the optimal coloring and always want to return it)
@@ -48,7 +48,7 @@ But after preparation, the more zeros are present in the matrix, the greater the
 The complexity of sparse Jacobians or Hessians grows with the number of distinct colors in a coloring of the sparsity pattern.
 To reduce this number of colors, [`GreedyColoringAlgorithm`](@extref SparseMatrixColorings.GreedyColoringAlgorithm) has two main settings: the order used for vertices and the decompression method.
 Depending on your use case, you may want to modify either of these options to increase performance.
-See the documentation of [SparseMatrixColorings.jl](https://github.com/gdalle/SparseMatrixColorings.jl) for details.
+See the documentation of [SparseMatrixColorings.jl](https://github.com/JuliaDiff/SparseMatrixColorings.jl) for details.
 
 ### Mixed mode
 
diff --git a/DifferentiationInterface/docs/src/tutorials/advanced.md b/DifferentiationInterface/docs/src/tutorials/advanced.md
@@ -127,7 +127,7 @@ In the examples above, we didn't use preparation.
 Sparse preparation is more costly than dense preparation, but it is even more essential.
 Indeed, once preparation is done, sparse differentiation is much faster than dense differentiation, because it makes fewer calls to the underlying function.
 
-Some result analysis functions from [SparseMatrixColorings.jl](https://github.com/gdalle/SparseMatrixColorings.jl) can help you figure out what the preparation contains.
+Some result analysis functions from [SparseMatrixColorings.jl](https://github.com/JuliaDiff/SparseMatrixColorings.jl) can help you figure out what the preparation contains.
 First, it records the sparsity pattern itself (the one returned by the detector).
 
 ```@example tuto_advanced
diff --git a/DifferentiationInterface/test/Back/Mooncake/test.jl b/DifferentiationInterface/test/Back/Mooncake/test.jl
@@ -7,6 +7,8 @@ using Test
 using ExplicitImports
 check_no_implicit_imports(DifferentiationInterface)
 
+nomatrix(scens) = filter(s -> !(s.x isa AbstractMatrix) && !(s.y isa AbstractMatrix), scens)
+
 backends = [
     AutoMooncake(),
     AutoMooncakeForward(),
@@ -20,14 +22,21 @@ for backend in backends
 end
 
 test_differentiation(
-    backends,
+    backends[3:4],
     default_scenarios(;
         include_constantified = true, include_cachified = true, use_tuples = true
     );
     excluded = SECOND_ORDER,
     logging = LOGGING,
 );
 
+test_differentiation(
+    backends[1:2],
+    nomatrix(default_scenarios());
+    excluded = SECOND_ORDER,
+    logging = LOGGING,
+);
+
 EXCLUDED = @static if VERSION ≥ v"1.11-" && VERSION ≤ v"1.12-"
     # testing only :hessian on 1.11 due to an opaque closure bug.
     # this is potentially the same issue as discussed in
@@ -54,7 +63,7 @@ end
 
 test_differentiation(
     backends[3:4],
-    static_scenarios();
+    nomatrix(static_scenarios());
     logging = LOGGING,
     excluded = SECOND_ORDER
 )
diff --git a/DifferentiationInterfaceTest/README.md b/DifferentiationInterfaceTest/README.md
@@ -1,32 +1,28 @@
 # DifferentiationInterfaceTest
 
-[![Build Status](https://github.com/JuliaDiff/DifferentiationInterface.jl/actions/workflows/Test.yml/badge.svg?branch=main)](https://github.com/JuliaDiff/DifferentiationInterface.jl/actions/workflows/Test.yml?query=branch%3Amain)
-[![Coverage](https://codecov.io/gh/JuliaDiff/DifferentiationInterface.jl/branch/main/graph/badge.svg?flag=DIT)](https://app.codecov.io/gh/JuliaDiff/DifferentiationInterface.jl)
-[![code style: runic](https://img.shields.io/badge/code_style-%E1%9A%B1%E1%9A%A2%E1%9A%BE%E1%9B%81%E1%9A%B2-black)](https://github.com/fredrikekre/Runic.jl)
-[![ColPrac: Contributor's Guide on Collaborative Practices for Community Packages](https://img.shields.io/badge/ColPrac-Contributor%27s%20Guide-blueviolet)](https://github.com/SciML/ColPrac)
-[![DOI](https://zenodo.org/badge/740973714.svg)](https://zenodo.org/doi/10.5281/zenodo.11092033)
-
-|           Package            |                                                                                                                                                 Docs                                                                                                                                                 |
-| :--------------------------: | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: |
-|   DifferentiationInterface   |   [![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://juliadiff.org/DifferentiationInterface.jl/DifferentiationInterface/stable/)     [![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://juliadiff.org/DifferentiationInterface.jl/DifferentiationInterface/dev/)   |
-| DifferentiationInterfaceTest | [![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://juliadiff.org/DifferentiationInterface.jl/DifferentiationInterfaceTest/stable/) [![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://juliadiff.org/DifferentiationInterface.jl/DifferentiationInterfaceTest/dev/) |
+| Category | Badges |
+|---|---|
+| Build status | [![Tests](https://github.com/JuliaDiff/DifferentiationInterface.jl/actions/workflows/Test.yml/badge.svg?branch=main)](https://github.com/JuliaDiff/DifferentiationInterface.jl/actions/workflows/Test.yml?query=branch%3Amain) [![Coverage](https://codecov.io/gh/JuliaDiff/DifferentiationInterface.jl/branch/main/graph/badge.svg?flag=DIT)](https://app.codecov.io/gh/JuliaDiff/DifferentiationInterface.jl) |
+| Documentation | [![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://juliadiff.org/DifferentiationInterface.jl/DifferentiationInterfaceTest/stable/)     [![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://juliadiff.org/DifferentiationInterface.jl/DifferentiationInterfaceTest/dev/) [![ColPrac: Contributor's Guide on Collaborative Practices for Community Packages](https://img.shields.io/badge/ColPrac-Contributor%27s%20Guide-blueviolet)](https://github.com/SciML/ColPrac) |
+| Code quality | [![code style: runic](https://img.shields.io/badge/code_style-%E1%9A%B1%E1%9A%A2%E1%9A%BE%E1%9B%81%E1%9A%B2-black)](https://github.com/fredrikekre/Runic.jl) [![Aqua QA](https://juliatesting.github.io/Aqua.jl/dev/assets/badge.svg)](https://github.com/JuliaTesting/Aqua.jl) |
+| References | [![DOI](https://zenodo.org/badge/740973714.svg)](https://zenodo.org/doi/10.5281/zenodo.11092033) |
 
 Testing and benchmarking utilities for automatic differentiation (AD) in Julia, based on [DifferentiationInterface](https://github.com/JuliaDiff/DifferentiationInterface.jl/tree/main/DifferentiationInterface).
 
 ## Goal
 
 Make it easy to know, for a given function:
 
-  - which AD backends can differentiate it
-  - how fast they can do it
+- which AD backends can differentiate it
+- how fast they can do it
 
 ## Features
 
-  - Definition of custom test scenarios
-  - Correctness tests
-  - Type stability tests
-  - Count calls to the function
-  - Benchmark runtime and allocations
+- Definition of custom test scenarios
+- Correctness tests
+- Type stability tests
+- Count calls to the function
+- Benchmark runtime and allocations
 
 ## Installation
 
@@ -53,3 +49,7 @@ Pkg.add(;
     subdir="DifferentiationInterfaceTest",
 )
 ```
+
+## Citation
+
+See the citation instructions for [DifferentiationInterface](https://github.com/JuliaDiff/DifferentiationInterface.jl/tree/main/DifferentiationInterface).

Original file line number	Diff line number	Diff line change
`@@ -11,7 +11,7 @@ using Zygote: Zygote`
`11`	`11`	`links = InterLinks(`
`12`	`12`	`"ADTypes" => "https://sciml.github.io/ADTypes.jl/stable/",`
`13`	`13`	`"SparseConnectivityTracer" => "https://adrianhill.de/SparseConnectivityTracer.jl/stable/",`
`14`		`- "SparseMatrixColorings" => "https://gdalle.github.io/SparseMatrixColorings.jl/stable/",`
	`14`	`+ "SparseMatrixColorings" => "https://juliadiff.org/SparseMatrixColorings.jl/stable/",`
`15`	`15`	`"Symbolics" => "https://symbolics.juliasymbolics.org/stable/",`
`16`	`16`	`)`
`17`	`17`