Raise Mooncake compat floor to 0.5.36 (fix Downgrade resolution)

.github/dependabot.yml

@@ -5,6 +5,14 @@ updates:
     directory: "/" # Location of package manifests
     schedule:
       interval: "weekly"
-    ignore:
-      - dependency-name: "crate-ci/typos"
-        update-types: ["version-update:semver-patch", "version-update:semver-minor"]
+  - package-ecosystem: "julia"
+    directories:
+      - "/"
+      - "/docs"
+      - "/test"
+    schedule:
+      interval: "daily"
+    groups:
+      all-julia-packages:
+        patterns:
+          - "*"

.github/workflows/DependabotAutoMerge.yml

@@ -0,0 +1,9 @@
+name: "Dependabot Auto-merge"
+on: pull_request
+permissions:
+  contents: write
+  pull-requests: write
+jobs:
+  automerge:
+    uses: "SciML/.github/.github/workflows/dependabot-automerge.yml@v1"
+    secrets: "inherit"

.github/workflows/DocPreviewCleanup.yml

@@ -0,0 +1,10 @@
+name: "Doc Preview Cleanup"
+on:
+  pull_request:
+    types: [closed]
+permissions:
+  contents: write
+jobs:
+  cleanup:
+    uses: "SciML/.github/.github/workflows/docs-preview-cleanup.yml@v1"
+    secrets: "inherit"

.github/workflows/FormatCheck.yml

@@ -0,0 +1,17 @@
+name: Format Check
+on:
+  push:
+    branches:
+      - 'master'
+      - 'main'
+      - 'release-'
+    tags: '*'
+  pull_request:
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ github.ref != 'refs/heads/main' }}
+jobs:
+  runic:
+    name: Format Check
+    uses: "SciML/.github/.github/workflows/runic.yml@v1"
+    secrets: "inherit"

.github/workflows/RunicSuggestions.yml

@@ -0,0 +1,9 @@
+name: "Runic Suggestions"
+on: pull_request
+permissions:
+  contents: read
+  pull-requests: write
+jobs:
+  runic-suggestions:
+    uses: "SciML/.github/.github/workflows/runic-suggestions-on-pr.yml@v1"
+    secrets: "inherit"

.github/workflows/SpellCheck.yml

@@ -0,0 +1,10 @@
+name: Spell Check
+on: [pull_request]
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ github.ref != 'refs/heads/main' }}
+jobs:
+  typos-check:
+    name: Spell Check with Typos
+    uses: "SciML/.github/.github/workflows/spellcheck.yml@v1"
+    secrets: "inherit"

.github/workflows/TagBot.yml

@@ -1,15 +1,9 @@
-name: TagBot
+name: "TagBot"
 on:
   issue_comment:
-    types:
-      - created
+    types: [created]
   workflow_dispatch:
 jobs:
-  TagBot:
-    if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'
-    runs-on: ubuntu-latest
-    steps:
-      - uses: JuliaRegistries/TagBot@v1
-        with:
-          token: ${{ secrets.GITHUB_TOKEN }}
-          ssh: ${{ secrets.DOCUMENTER_KEY }}
+  tagbot:
+    uses: "SciML/.github/.github/workflows/tagbot.yml@v1"
+    secrets: "inherit"

.github/workflows/ci.yml

@@ -7,40 +7,10 @@ on:
     branches:
       - main
     tags: '*'
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ github.ref != 'refs/heads/main' }}
 jobs:
-  test:
-    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
-    runs-on: ${{ matrix.os }}
-    strategy:
-      fail-fast: false
-      matrix:
-        version:
-          - 'lts'
-          - '1' # Leave this line unchanged. '1' will automatically expand to the latest stable 1.x release of Julia.
-          - 'pre'
-        os:
-          - ubuntu-latest
-        arch:
-          - x64
-    steps:
-      - uses: actions/checkout@v4
-      - uses: julia-actions/setup-julia@v2
-        with:
-          version: ${{ matrix.version }}
-          arch: ${{ matrix.arch }}
-      - uses: actions/cache@v4
-        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/julia-buildpkg@v1
-      - uses: julia-actions/julia-runtest@v1
-      - uses: julia-actions/julia-processcoverage@v1
-      - uses: codecov/codecov-action@v5
-        with:
-          file: lcov.info
+  tests:
+    uses: "SciML/.github/.github/workflows/grouped-tests.yml@v1"
+    secrets: "inherit"

.github/workflows/docs.yml

@@ -1,24 +1,16 @@
 name: Documentation
-
 on:
   push:
-    branches:
-      - master
+    branches: [main]
     tags: '*'
   pull_request:
-
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ github.ref != 'refs/heads/main' }}
 jobs:
-  build:
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-      - uses: julia-actions/setup-julia@latest
-        with:
-          version: '1.10'
-      - name: Install dependencies
-        run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
-      - name: Build and deploy
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # For authentication with GitHub Actions token
-          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # For authentication with SSH deploy key
-        run: julia --project=docs/ docs/make.jl
+  docs:
+    name: Documentation
+    uses: "SciML/.github/.github/workflows/documentation.yml@v1"
+    with:
+      coverage: false
+    secrets: "inherit"

.github/workflows/downgrade.yml

@@ -2,35 +2,27 @@ name: Downgrade
 on:
   pull_request:
     branches:
-      - master
+      - main
     paths-ignore:
       - 'docs/**'
   push:
     branches:
-      - master
+      - main
     paths-ignore:
       - 'docs/**'
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ github.ref != 'refs/heads/main' }}
 jobs:
-  test:
-    runs-on: ubuntu-latest
+  downgrade:
+    name: Downgrade
     strategy:
+      fail-fast: false
       matrix:
         group:
           - Core
-        downgrade_mode: ['alldeps']
-        julia-version: ['1.10']
-    steps:
-      - uses: actions/checkout@v4
-      - uses: julia-actions/setup-julia@v2
-        with:
-          version: ${{ matrix.julia-version }}
-      - uses: julia-actions/julia-downgrade-compat@v2
-#        if: ${{ matrix.version == '1.6' }}
-        with:
-          skip: Pkg,TOML
-      - uses: julia-actions/julia-buildpkg@v1
-      - uses: julia-actions/julia-runtest@v1
-        with:
-          ALLOW_RERESOLVE: false
-        env:
-          GROUP: ${{ matrix.group }}
+    uses: "SciML/.github/.github/workflows/downgrade.yml@v1"
+    with:
+      group: "${{ matrix.group }}"
+      julia-version: "lts"
+    secrets: "inherit"

.typos.toml

@@ -0,0 +1,3 @@
+[default.extend-words]
+# `temp_noth` test variable (component array holding a `nothing` field)
+noth = "noth"

Project.toml

@@ -1,7 +1,7 @@
 name = "ComponentArrays"
 uuid = "b0b7db55-cfe3-40fc-9ded-d10e2dbeff66"
 authors = ["Jonnie Diegelman <47193959+jonniedie@users.noreply.github.com>"]
-version = "0.15.29"
+version = "0.15.41"
 
 [deps]
 Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
@@ -16,6 +16,7 @@ StaticArraysCore = "1e83bf80-4336-4d27-bf5d-d5a4f845583c"
 [weakdeps]
 GPUArrays = "0c68f7d7-f131-5f86-a1c3-88cf8149b2d7"
 KernelAbstractions = "63c18a36-062a-441e-b654-da1e3ab1ce7c"
+Mooncake = "da2b9cff-9c12-43a0-ae48-6db2b0edb7d6"
 Optimisers = "3bd65402-5787-11e9-1adc-39752487f4e2"
 Reactant = "3c362404-f566-11ee-1572-e11a4b42c853"
 RecursiveArrayTools = "731186ca-8d62-57ce-b412-fbd966d074cd"
@@ -27,6 +28,7 @@ Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"
 [extensions]
 ComponentArraysGPUArraysExt = "GPUArrays"
 ComponentArraysKernelAbstractionsExt = "KernelAbstractions"
+ComponentArraysMooncakeExt = "Mooncake"
 ComponentArraysOptimisersExt = "Optimisers"
 ComponentArraysReactantExt = "Reactant"
 ComponentArraysRecursiveArrayToolsExt = "RecursiveArrayTools"
@@ -36,19 +38,20 @@ ComponentArraysTrackerExt = "Tracker"
 ComponentArraysZygoteExt = "Zygote"
 
 [compat]
-Adapt = "4.1"
-ArrayInterface = "7.17.1"
+Adapt = "4.1.1"
+ArrayInterface = "7.25.0"
 ChainRulesCore = "1.25"
-ConstructionBase = "1"
-Functors = "0.4.12, 0.5"
+ConstructionBase = "1.5.0"
+Functors = "0.5.2"
 GPUArrays = "10.3.1, 11"
 KernelAbstractions = "0.9.29"
 LinearAlgebra = "1.10"
 Optimisers = "0.3, 0.4"
+Mooncake = "0.5.36"
 Reactant = "0.2.15"
-RecursiveArrayTools = "3.8"
+RecursiveArrayTools = "3.36.0, 4"
 ReverseDiff = "1.15"
-SciMLBase = "2"
+SciMLBase = "2, 3"
 StaticArrayInterface = "1"
 StaticArraysCore = "1.4"
 Tracker = "0.2.37"

docs/Project.toml

@@ -4,3 +4,4 @@ StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 
 [compat]
 Documenter = "1.3"
+StaticArrays = "1.9.16"

docs/make.jl

@@ -17,9 +17,10 @@ makedocs(;
         "Examples" => [
             "examples/DiffEqFlux.md",
             "examples/adaptive_control.md",
-            "examples/ODE_jac.md"
+            "examples/ODE_jac.md",
+            "examples/coulomb_control.md",
         ],
-        "API" => "api.md"
+        "API" => "api.md",
     ],
     repo = GitHub("SciML/ComponentArrays.jl"),
     sitename = "ComponentArrays.jl",

docs/src/examples/DiffEqFlux.md

@@ -83,10 +83,10 @@ cb(θ, loss_n_ode(θ)...)
 
 data = Iterators.repeated((), 1000)
 
-res1 = sciml_train(loss_n_ode, θ, ADAM(0.05); cb = cb, maxiters = 100)
+res1 = sciml_train(loss_n_ode, θ, ADAM(0.05); cb, maxiters = 100)
 cb(res1.minimizer, loss_n_ode(res1.minimizer)...; doplot = true)
 
-res2 = sciml_train(loss_n_ode, res1.minimizer, LBFGS(); cb = cb)
+res2 = sciml_train(loss_n_ode, res1.minimizer, LBFGS(); cb)
 cb(res2.minimizer, loss_n_ode(res2.minimizer)...; doplot = true)
 ```
 

docs/src/examples/adaptive_control.md

@@ -107,9 +107,9 @@ plot!(step_p, solve(ODEProblem(apply_inputs(nominal_sim!; u = 1), nominal_ic, (0
     vars = 1, label = "nominal model")
 
 u = (x, p, t) -> sin(3t)
-sin_p = plot(solve(ODEProblem(apply_inputs(truth_sim!; u = u), truth_ic, (0.0, 10.0)));
+sin_p = plot(solve(ODEProblem(apply_inputs(truth_sim!; u), truth_ic, (0.0, 10.0)));
     vars = 1, label = "truth model")
-plot!(sin_p, solve(ODEProblem(apply_inputs(nominal_sim!; u = u), nominal_ic, (0.0, 10.0)));
+plot!(sin_p, solve(ODEProblem(apply_inputs(nominal_sim!; u), nominal_ic, (0.0, 10.0)));
     vars = 1, label = "nominal model")
 
 plot(step_p, sin_p; layout = (2, 1), size = (800, 800))
@@ -155,11 +155,11 @@ function feedback_sys!(D, vars, p, t; ym, r, n)
     regressor = [r, plant_model[1]]
 
     u = control(parameter_estimates, regressor)
-    yp = p.plant_fun(D.plant_model, plant_model, (), t; u = u)
+    yp = p.plant_fun(D.plant_model, plant_model, (), t; u)
     ŷ = sensor_sim!(D.sensor, sensor, (), t; u = yp[1]) + n
     e = ŷ .- ym
     regressor[2] = ŷ
-    adapt!(D.parameter_estimates, parameter_estimates, γ, t; e = e, w = regressor)
+    adapt!(D.parameter_estimates, parameter_estimates, γ, t; e, w = regressor)
     return yp
 end
 ```
@@ -172,7 +172,7 @@ function system!(D, vars, p, t; r = 0.0, n = 0.0)
     @unpack reference_model, feedback_loop = vars
 
     ym = ref_sim!(D.reference_model, reference_model, (), t; u = r)
-    yp = feedback_sys!(D.feedback_loop, feedback_loop, p, t; ym = ym, r = r, n = n)
+    yp = feedback_sys!(D.feedback_loop, feedback_loop, p, t; ym, r, n)
     return yp
 end
 ```
@@ -219,10 +219,7 @@ function simulate(plant_fun, plant_ic;
     )
 
     # Model parameters
-    p = (
-        gamma = adapt_gain,
-        plant_fun = plant_fun
-    )
+    p = (; gamma = adapt_gain, plant_fun)
 
     sim_fun = apply_inputs(system!; r = input_signal, n = deterministic_noise)