Uniformize monorepo structure to OrdinaryDiffEq canonical style

.github/workflows/Tests.yml → .github/workflows/CI.yml

@@ -1,4 +1,4 @@
-name: "Tests"
+name: CI
 
 on:
   pull_request:
@@ -23,23 +23,40 @@ jobs:
       fail-fast: false
       matrix:
         version:
-          - "1"
           - "lts"
+          - "1"
           - "pre"
         group:
           - "Core"
-          - "RaggedArrays"
-          - "ArrayPartitionAnyAll"
-          - "ShorthandConstructors"
+          - "QA"
+          - "SymbolicIndexingInterface"
           - "Downstream"
-          - "nopre"
+          - "NoPre"
         exclude:
+          # JET (NoPre) is not run on prereleases.
           - version: "pre"
-            group: "nopre"
+            group: "NoPre"
+          # QA (Aqua) runs only on lts and 1, never on prereleases.
+          - version: "pre"
+            group: "QA"
     uses: "SciML/.github/.github/workflows/tests.yml@v1"
     with:
       julia-version: "${{ matrix.version }}"
       group: "${{ matrix.group }}"
       num-threads: "2"
+      check-bounds: "auto"
+      coverage-directories: "src,ext"
+    secrets: "inherit"
+
+  # GPU tests are a dep-adding group (test/GPU/Project.toml) that runs on the
+  # self-hosted GPU runner. Folded in from the former bespoke GPU.yml.
+  gpu:
+    name: "GPU Tests"
+    uses: "SciML/.github/.github/workflows/tests.yml@v1"
+    with:
+      julia-version: "1"
+      group: "GPU"
+      runner: '["self-hosted", "Linux", "X64", "gpu"]'
+      timeout-minutes: 60
       coverage-directories: "src,ext"
     secrets: "inherit"

.github/workflows/Downgrade.yml

@@ -20,7 +20,5 @@ jobs:
           - Core
     uses: "SciML/.github/.github/workflows/downgrade.yml@v1"
     with:
-      julia-version: "1.10"
       group: "${{ matrix.group }}"
-      skip: "Pkg,TOML"
     secrets: "inherit"

.github/workflows/DowngradeSublibraries.yml

@@ -19,4 +19,6 @@ jobs:
     secrets: "inherit"
     with:
       julia-version: "lts"
-      skip: "RecursiveArrayTools, Pkg, TOML, Statistics, LinearAlgebra, SparseArrays, InteractiveUtils, Random, Test"
+      group-env-name: "RECURSIVEARRAYTOOLS_TEST_GROUP"
+      group-env-value: "Core"
+      # Every lib/* sublibrary is downgrade-tested (projects auto-discovered, no exclusions).

.github/workflows/SublibraryCI.yml

@@ -19,4 +19,7 @@ concurrency:
 jobs:
   sublibraries:
     uses: "SciML/.github/.github/workflows/sublibrary-project-tests.yml@v1"
+    with:
+      group-env-name: RECURSIVEARRAYTOOLS_TEST_GROUP
+      check-bounds: auto
     secrets: "inherit"

.github/workflows/TagBot.yml

@@ -1,15 +1,21 @@
-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: ${{ secrets.DOCUMENTER_KEY }}
+  tagbot:
+    uses: "SciML/.github/.github/workflows/tagbot.yml@v1"
+    secrets: "inherit"
+  tagbot-subpackages:
+    strategy:
+      fail-fast: false
+      matrix:
+        subdir:
+          - "lib/RecursiveArrayToolsArrayPartitionAnyAll"
+          - "lib/RecursiveArrayToolsRaggedArrays"
+          - "lib/RecursiveArrayToolsShorthandConstructors"
+    uses: "SciML/.github/.github/workflows/tagbot.yml@v1"
+    with:
+      subdir: "${{ matrix.subdir }}"
+    secrets: "inherit"

.gitignore

@@ -1,5 +1,13 @@
 *.jl.cov
 *.jl.*.cov
 *.jl.mem
+*.jl.*.mem
 Manifest.toml
+*.DS_Store
 .vscode
+profile.pb.gz
+.*.swp
+LocalPreferences.toml
+
+docs/build
+.claude/

Project.toml

@@ -50,7 +50,6 @@ RecursiveArrayToolsZygoteExt = "Zygote"
 
 [compat]
 Adapt = "4"
-Aqua = "0.8"
 ArrayInterface = "7.17.0"
 CUDA = "5, 6.0"
 DocStringExtensions = "0.9.3"
@@ -62,12 +61,12 @@ LinearAlgebra = "1.10"
 Measurements = "2.11"
 MonteCarloMeasurements = "1.2"
 Mooncake = "0.5"
-NLsolve = "4.5"
 Pkg = "1"
 Polyester = "0.7.16"
 PrecompileTools = "1.2.1"
 Random = "1"
 RecipesBase = "1.3.4"
+RecursiveArrayToolsShorthandConstructors = "1"
 ReverseDiff = "1.15"
 SafeTestsets = "0.1"
 SparseArrays = "1.10"
@@ -84,17 +83,16 @@ Zygote = "0.7"
 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"
 Mooncake = "da2b9cff-9c12-43a0-ae48-6db2b0edb7d6"
 MonteCarloMeasurements = "0987c9cc-fe09-11e8-30f0-b96dd679fdca"
-NLsolve = "2774e3e8-f4cf-5e23-947b-6d7e65073b56"
 Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 Polyester = "f517fe37-dbe3-4b94-8317-1923a5111588"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+RecursiveArrayToolsShorthandConstructors = "39fb7555-b4ad-4efd-8abe-30331df017d3"
 SafeTestsets = "1bc83da4-3b8d-516f-aca4-4fe02f6d838f"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
@@ -106,4 +104,4 @@ Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"
 
 [targets]
-test = ["Aqua", "FastBroadcast", "ForwardDiff", "KernelAbstractions", "Measurements", "Mooncake", "NLsolve", "Pkg", "Polyester", "Random", "ReverseDiff", "SafeTestsets", "SparseArrays", "StaticArrays", "Statistics", "StructArrays", "Tables", "Test", "Unitful", "Zygote"]
+test = ["FastBroadcast", "ForwardDiff", "KernelAbstractions", "Measurements", "Mooncake", "Pkg", "Polyester", "Random", "RecursiveArrayToolsShorthandConstructors", "ReverseDiff", "SafeTestsets", "SparseArrays", "StaticArrays", "Statistics", "StructArrays", "Tables", "Test", "Unitful", "Zygote"]

lib/RecursiveArrayToolsArrayPartitionAnyAll/Project.toml

@@ -5,6 +5,9 @@ version = "1.0.0"
 [deps]
 RecursiveArrayTools = "731186ca-8d62-57ce-b412-fbd966d074cd"
 
+[sources]
+RecursiveArrayTools = {path = "../.."}
+
 [compat]
 RecursiveArrayTools = "4"
 julia = "1.10"

lib/RecursiveArrayToolsArrayPartitionAnyAll/README.md

@@ -1,8 +1,13 @@
 # RecursiveArrayToolsArrayPartitionAnyAll.jl
 
-Optimized `any` and `all` for
-[RecursiveArrayTools.jl](https://github.com/SciML/RecursiveArrayTools.jl)'s
-`ArrayPartition` type.
+[![Join the chat at https://julialang.zulipchat.com #sciml-bridged](https://img.shields.io/static/v1?label=Zulip&message=chat&color=9558b2&labelColor=389826)](https://julialang.zulipchat.com/#narrow/stream/279055-sciml-bridged)
+[![Global Docs](https://img.shields.io/badge/docs-SciML-blue.svg)](https://docs.sciml.ai/RecursiveArrayTools/stable/)
+
+[![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)
+[![SciML Code Style](https://img.shields.io/static/v1?label=code%20style&message=SciML&color=9558b2&labelColor=389826)](https://github.com/SciML/SciMLStyle)
+
+RecursiveArrayToolsArrayPartitionAnyAll.jl is a component of the [RecursiveArrayTools.jl](https://github.com/SciML/RecursiveArrayTools.jl) monorepo. Optimized `any` and `all` for the `ArrayPartition` type.
+While completely independent and usable on its own, users wanting the full functionality should use [RecursiveArrayTools.jl](https://github.com/SciML/RecursiveArrayTools.jl).
 
 `ArrayPartition` stores data as a tuple of arrays. The default `AbstractArray`
 `any`/`all` iterates element-by-element through the partition, which incurs

lib/RecursiveArrayToolsArrayPartitionAnyAll/test/runtests.jl

@@ -1,34 +1,38 @@
 using RecursiveArrayTools, RecursiveArrayToolsArrayPartitionAnyAll, Test
 
-@testset "Optimized any" begin
-    ap = ArrayPartition(collect(1:5), collect(6:10), collect(11:15))
-    @test any(x -> x == 4, ap)
-    @test any(x -> x == 15, ap)
-    @test !any(x -> x == 17, ap)
-    @test any(ap .> 10)
-    @test !any(ap .> 20)
-end
+const TEST_GROUP = get(ENV, "RECURSIVEARRAYTOOLS_TEST_GROUP", "Core")
 
-@testset "Optimized all" begin
-    ap = ArrayPartition(ones(5), ones(5), ones(5))
-    @test all(x -> x == 1.0, ap)
-    @test !all(x -> x == 2.0, ap)
-    @test all(ap .> 0)
+if TEST_GROUP == "Core" || TEST_GROUP == "All"
+    @testset "Optimized any" begin
+        ap = ArrayPartition(collect(1:5), collect(6:10), collect(11:15))
+        @test any(x -> x == 4, ap)
+        @test any(x -> x == 15, ap)
+        @test !any(x -> x == 17, ap)
+        @test any(ap .> 10)
+        @test !any(ap .> 20)
+    end
 
-    ap2 = ArrayPartition(ones(5), [1.0, 1.0, 0.0, 1.0, 1.0], ones(5))
-    @test !all(x -> x == 1.0, ap2)
-end
+    @testset "Optimized all" begin
+        ap = ArrayPartition(ones(5), ones(5), ones(5))
+        @test all(x -> x == 1.0, ap)
+        @test !all(x -> x == 2.0, ap)
+        @test all(ap .> 0)
+
+        ap2 = ArrayPartition(ones(5), [1.0, 1.0, 0.0, 1.0, 1.0], ones(5))
+        @test !all(x -> x == 1.0, ap2)
+    end
 
-@testset "Matches AbstractArray default results" begin
-    ap = ArrayPartition(rand(100), rand(100), rand(100))
-    f = x -> x > 0.5
+    @testset "Matches AbstractArray default results" begin
+        ap = ArrayPartition(rand(100), rand(100), rand(100))
+        f = x -> x > 0.5
 
-    # Results must match
-    @test any(f, ap) == any(f, collect(ap))
-    @test all(f, ap) == all(f, collect(ap))
+        # Results must match
+        @test any(f, ap) == any(f, collect(ap))
+        @test all(f, ap) == all(f, collect(ap))
 
-    # Edge case: empty
-    ap_empty = ArrayPartition(Float64[], Float64[])
-    @test !any(x -> true, ap_empty)
-    @test all(x -> true, ap_empty)
+        # Edge case: empty
+        ap_empty = ArrayPartition(Float64[], Float64[])
+        @test !any(x -> true, ap_empty)
+        @test all(x -> true, ap_empty)
+    end
 end

lib/RecursiveArrayToolsArrayPartitionAnyAll/test/test_groups.toml

@@ -0,0 +1,2 @@
+[Core]
+versions = ["lts", "1", "pre"]

lib/RecursiveArrayToolsRaggedArrays/Project.toml

@@ -10,6 +10,9 @@ RecursiveArrayTools = "731186ca-8d62-57ce-b412-fbd966d074cd"
 StaticArraysCore = "1e83bf80-4336-4d27-bf5d-d5a4f845583c"
 SymbolicIndexingInterface = "2efcf032-c050-4f8e-a9bb-153293bab1f5"
 
+[sources]
+RecursiveArrayTools = {path = "../.."}
+
 [compat]
 Adapt = "4"
 ArrayInterface = "7.17.0"

lib/RecursiveArrayToolsRaggedArrays/README.md

@@ -1,7 +1,13 @@
 # RecursiveArrayToolsRaggedArrays.jl
 
-True ragged (non-rectangular) array types for
-[RecursiveArrayTools.jl](https://github.com/SciML/RecursiveArrayTools.jl).
+[![Join the chat at https://julialang.zulipchat.com #sciml-bridged](https://img.shields.io/static/v1?label=Zulip&message=chat&color=9558b2&labelColor=389826)](https://julialang.zulipchat.com/#narrow/stream/279055-sciml-bridged)
+[![Global Docs](https://img.shields.io/badge/docs-SciML-blue.svg)](https://docs.sciml.ai/RecursiveArrayTools/stable/)
+
+[![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)
+[![SciML Code Style](https://img.shields.io/static/v1?label=code%20style&message=SciML&color=9558b2&labelColor=389826)](https://github.com/SciML/SciMLStyle)
+
+RecursiveArrayToolsRaggedArrays.jl is a component of the [RecursiveArrayTools.jl](https://github.com/SciML/RecursiveArrayTools.jl) monorepo. True ragged (non-rectangular) array types for `RaggedVectorOfArray` and `RaggedDiffEqArray`.
+While completely independent and usable on its own, users wanting the full functionality should use [RecursiveArrayTools.jl](https://github.com/SciML/RecursiveArrayTools.jl).
 
 This subpackage provides `RaggedVectorOfArray` and `RaggedDiffEqArray`, which
 preserve the exact ragged structure of collections of differently-sized arrays