Merge branch 'master' into arraypart_zero

Author: ChrisRackauckas

.github/dependabot.yml

@@ -1,5 +1,6 @@
 # https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
 version: 2
+enable-beta-ecosystems: true # Julia ecosystem
 updates:
   - package-ecosystem: "github-actions"
     directory: "/" # Location of package manifests
@@ -8,3 +9,14 @@ updates:
     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/CompatHelper.yml

@@ -15,18 +15,22 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        version: ['1']
         group:
           - Core
-          - Downstream
+        downgrade_mode: ['alldeps']
+        julia-version: ['1.10']
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
       - uses: julia-actions/setup-julia@v2
         with:
-          version: ${{ matrix.version }}
-      - uses: julia-actions/julia-downgrade-compat@v1
+          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 }}

.github/workflows/Downgrade.yml

@@ -33,14 +33,14 @@ jobs:
           - {user: SciML, repo: SciMLSensitivity.jl, group: Core6}
           - {user: SciML, repo: LabelledArrays.jl, group: RecursiveArrayTools}
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v6
       - uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.julia-version }}
           arch: x64
       - uses: julia-actions/julia-buildpkg@latest
       - name: Clone Downstream
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           repository: ${{ matrix.package.user }}/${{ matrix.package.repo }}
           path: downstream

.github/workflows/Downstream.yml

@@ -8,6 +8,6 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout Actions Repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
       - name: Check spelling
         uses: crate-ci/typos@v1.18.0 

.github/workflows/Invalidations.yml

@@ -1 +1,73 @@
-[default.extend-words]
+[default.extend-words]
+# Julia-specific functions
+indexin = "indexin"
+findfirst = "findfirst"
+findlast = "findlast"
+eachindex = "eachindex"
+setp = "setp"
+getp = "getp"
+setu = "setu"
+getu = "getu"
+
+# Mathematical/scientific terms
+jacobian = "jacobian"
+hessian = "hessian" 
+eigenvalue = "eigenvalue"
+eigenvector = "eigenvector"
+discretization = "discretization"
+linearization = "linearization"
+parameterized = "parameterized"
+discretized = "discretized"
+vectorized = "vectorized"
+
+# Common variable patterns in Julia/SciML
+ists = "ists"
+ispcs = "ispcs"
+osys = "osys"
+rsys = "rsys"
+usys = "usys"
+fsys = "fsys"
+eqs = "eqs"
+rhs = "rhs"
+lhs = "lhs"
+ode = "ode"
+pde = "pde"
+sde = "sde"
+dde = "dde"
+bvp = "bvp"
+ivp = "ivp"
+
+# Common abbreviations
+tol = "tol"
+rtol = "rtol"
+atol = "atol"
+idx = "idx"
+jdx = "jdx"
+prev = "prev"
+curr = "curr"
+init = "init"
+tmp = "tmp"
+vec = "vec"
+arr = "arr"
+dt = "dt"
+du = "du"
+dx = "dx"
+dy = "dy"
+dz = "dz"
+
+# Algorithm/type suffixes
+alg = "alg"
+prob = "prob"
+sol = "sol"
+cb = "cb"
+opts = "opts"
+args = "args"
+kwargs = "kwargs"
+
+# Scientific abbreviations
+ND = "ND"
+nd = "nd"
+MTK = "MTK"
+ODE = "ODE"
+PDE = "PDE"
+SDE = "SDE"

.github/workflows/SpellCheck.yml

@@ -1,79 +1,82 @@
 name = "RecursiveArrayTools"
 uuid = "731186ca-8d62-57ce-b412-fbd966d074cd"
 authors = ["Chris Rackauckas <accounts@chrisrackauckas.com>"]
-version = "3.33.0"
+version = "3.39.0"
 
 [deps]
 Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
 ArrayInterface = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9"
 DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
 GPUArraysCore = "46192b85-c4d5-4398-a991-12ede77f4527"
-IteratorInterfaceExtensions = "82899510-4779-5014-852e-03e436cf321d"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 RecipesBase = "3cdcf5f2-1ef4-517c-9805-6587b60abb01"
 StaticArraysCore = "1e83bf80-4336-4d27-bf5d-d5a4f845583c"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 SymbolicIndexingInterface = "2efcf032-c050-4f8e-a9bb-153293bab1f5"
-Tables = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
 
 [weakdeps]
 FastBroadcast = "7034ab61-46d4-4ed7-9d0f-46aef9175898"
 ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
+KernelAbstractions = "63c18a36-062a-441e-b654-da1e3ab1ce7c"
 Measurements = "eff96d63-e80a-5855-80a2-b1b0885c5ab7"
 MonteCarloMeasurements = "0987c9cc-fe09-11e8-30f0-b96dd679fdca"
 ReverseDiff = "37e2e3b7-166d-5795-8a7a-e32c996b4267"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 StructArrays = "09ab397b-f2b6-538f-b94a-2f83cf4a842a"
+Tables = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
 Tracker = "9f7883ad-71c0-57eb-9f7f-b5c9e6d3789c"
 Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"
 
 [extensions]
 RecursiveArrayToolsFastBroadcastExt = "FastBroadcast"
 RecursiveArrayToolsForwardDiffExt = "ForwardDiff"
+RecursiveArrayToolsKernelAbstractionsExt = "KernelAbstractions"
 RecursiveArrayToolsMeasurementsExt = "Measurements"
 RecursiveArrayToolsMonteCarloMeasurementsExt = "MonteCarloMeasurements"
 RecursiveArrayToolsReverseDiffExt = ["ReverseDiff", "Zygote"]
 RecursiveArrayToolsSparseArraysExt = ["SparseArrays"]
 RecursiveArrayToolsStructArraysExt = "StructArrays"
+RecursiveArrayToolsTablesExt = ["Tables"]
 RecursiveArrayToolsTrackerExt = "Tracker"
 RecursiveArrayToolsZygoteExt = "Zygote"
 
 [compat]
-Adapt = "3.4, 4"
+Adapt = "4"
 Aqua = "0.8"
-ArrayInterface = "7.6"
-DocStringExtensions = "0.9"
-FastBroadcast = "0.2.8, 0.3"
-ForwardDiff = "0.10.19, 1"
-GPUArraysCore = "0.1.1, 0.2"
-IteratorInterfaceExtensions = "1"
+ArrayInterface = "7.16"
+DocStringExtensions = "0.9.3"
+FastBroadcast = "0.3.5"
+ForwardDiff = "0.10.38, 1"
+GPUArraysCore = "0.2"
+KernelAbstractions = "0.9.36"
 LinearAlgebra = "1.10"
-Measurements = "2.3"
-MonteCarloMeasurements = "1.1"
+Measurements = "2.11"
+MonteCarloMeasurements = "1.2"
 NLsolve = "4.5"
 Pkg = "1"
 Random = "1"
-RecipesBase = "1.1"
+RecipesBase = "1.3.4"
 ReverseDiff = "1.15"
 SafeTestsets = "0.1"
-SciMLBase = "2"
+SciMLBase = "2.103"
 SparseArrays = "1.10"
 StaticArrays = "1.6"
-StaticArraysCore = "1.4"
+StaticArraysCore = "1.4.2"
 Statistics = "1.10, 1.11"
-StructArrays = "0.6.11, 0.7"
-SymbolicIndexingInterface = "0.3.25"
-Tables = "1.11"
+StructArrays = "0.7"
+SymbolicIndexingInterface = "0.3.42"
+Tables = "1.12"
 Test = "1"
-Tracker = "0.2.15"
+Tracker = "0.2.34"
 Unitful = "1"
-Zygote = "0.6.67, 0.7"
+Zygote = "0.7.10"
 julia = "1.10"
 
 [extras]
 Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
 FastBroadcast = "7034ab61-46d4-4ed7-9d0f-46aef9175898"
 ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
+KernelAbstractions = "63c18a36-062a-441e-b654-da1e3ab1ce7c"
 Measurements = "eff96d63-e80a-5855-80a2-b1b0885c5ab7"
 MonteCarloMeasurements = "0987c9cc-fe09-11e8-30f0-b96dd679fdca"
 NLsolve = "2774e3e8-f4cf-5e23-947b-6d7e65073b56"
@@ -90,4 +93,4 @@ Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"
 
 [targets]
-test = ["Aqua", "FastBroadcast", "ForwardDiff", "Measurements", "NLsolve", "Pkg", "Random", "SafeTestsets", "SciMLBase", "SparseArrays", "StaticArrays", "StructArrays", "Test", "Unitful", "Zygote"]
+test = ["Aqua", "FastBroadcast", "ForwardDiff", "KernelAbstractions", "Measurements", "NLsolve", "Pkg", "Random", "SafeTestsets", "SciMLBase", "SparseArrays", "StaticArrays", "StructArrays", "Tables", "Test", "Unitful", "Zygote"]

.typos.toml

@@ -22,6 +22,8 @@ the documentation, which contains the unreleased features.
 
 ## Example
 
+### VectorOfArray
+
 ```julia
 using RecursiveArrayTools
 a = [[1, 2, 3], [4, 5, 6], [7, 8, 9]]
@@ -30,11 +32,30 @@ vA = VectorOfArray(a)
 vB = VectorOfArray(b)
 
 vA .* vB # Now all standard array stuff works!
+```
 
+### ArrayPartition
+
+```julia
 a = (rand(5), rand(5))
 b = (rand(5), rand(5))
 pA = ArrayPartition(a)
 pB = ArrayPartition(b)
 
 pA .* pB # Now all standard array stuff works!
+
+# or do:
+x0 = rand(3, 3)
+v0 = rand(3, 3)
+a0 = rand(3, 3)
+u0 = ArrayPartition(x0, v0, a0)
+u0.x[1] == x0 # true
+
+u0 .+= 1
+u0.x[2] == v0 # still true
+
+# do some calculations creating a new partitioned array
+unew = u0 * 10
+# easily access the individual components without having to rely on complicated indexing
+xnew, vnew, anew = unew.x
 ```

Project.toml

@@ -1,6 +1,6 @@
 # The AbstractVectorOfArray and AbstractDiffEqArray Interfaces
 
-```@doc
+```@docs
 AbstractVectorOfArray
 AbstractDiffEqArray
 ```