Merge pull request #505 from ChrisRackauckas-Claude/uniformize-monorepo-structure

Uniformize monorepo structure to OrdinaryDiffEq.jl canonical style

Author: ChrisRackauckas

.github/workflows/CI.yml

@@ -0,0 +1,78 @@
+name: CI
+on:
+  pull_request:
+    branches:
+      - master
+  push:
+    branches:
+      - master
+concurrency:
+  # Skip intermediate builds: always.
+  # Cancel intermediate builds: only if it is a pull request build.
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
+jobs:
+  test:
+    permissions:
+      actions: write
+      contents: read
+    runs-on: ubuntu-latest
+    timeout-minutes: 120
+    strategy:
+      fail-fast: false
+      matrix:
+        # Root BoundaryValueDiffEq's own test groups only. The lib/* sublibraries
+        # are covered by SublibraryCI.yml (project model); do not double-test them
+        # through the root matrix.
+        group:
+          - Misc
+          - Wrappers
+          - QA
+        version:
+          - 'lts'
+          - '1'
+          - 'pre'
+        exclude:
+          # QA (Aqua + JET) runs on release + LTS Julia only (not pre-release).
+          - group: QA
+            version: 'pre'
+    steps:
+      - uses: actions/checkout@v6
+      - uses: julia-actions/setup-julia@v3
+        with:
+          version: ${{ matrix.version }}
+      - uses: julia-actions/cache@v3
+      - name: Develop local path deps (Julia < 1.11)
+        shell: julia --color=yes --project=. {0}
+        run: |
+          using Pkg
+          if VERSION < v"1.11.0-DEV.0"
+            toml = Pkg.TOML.parsefile("Project.toml")
+            if haskey(toml, "sources")
+              specs = Pkg.PackageSpec[]
+              for (dep, spec) in toml["sources"]
+                if spec isa Dict && haskey(spec, "path") && isdir(spec["path"])
+                  @info "Developing" dep spec["path"]
+                  push!(specs, Pkg.PackageSpec(path=spec["path"]))
+                end
+              end
+              # Batch the develop call so Pkg resolves all path deps together.
+              isempty(specs) || Pkg.develop(specs)
+            end
+          end
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-runtest@v1
+        with:
+          coverage: true
+          check_bounds: auto
+        env:
+          GROUP: ${{ matrix.group }}
+      - uses: julia-actions/julia-processcoverage@v1
+        with:
+          directories: src,ext
+      - uses: codecov/codecov-action@v6
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: lcov.info
+          fail_ci_if_error: false
+          disable_safe_directory: true

.github/workflows/CI_BoundaryValueDiffEq.yml

@@ -17,6 +17,6 @@ jobs:
     name: "Downgrade"
     uses: "SciML/.github/.github/workflows/downgrade.yml@v1"
     with:
-      julia-version: "1.11"
-      skip: "Pkg,TOML"
+      julia-version: "lts"
+      group: "Misc"
     secrets: "inherit"

.github/workflows/Downgrade.yml

@@ -22,5 +22,6 @@ jobs:
     uses: "SciML/.github/.github/workflows/sublibrary-downgrade.yml@v1"
     secrets: "inherit"
     with:
-      julia-version: "1.11"
-      skip: "Pkg,TOML"
+      julia-version: "lts"
+      group-env-name: "BOUNDARYVALUEDIFFEQ_TEST_GROUP"
+      group-env-value: "Core"

.github/workflows/DowngradeSublibraries.yml

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

.github/workflows/QA.yml

@@ -1,55 +1,24 @@
-name: TagBot
+name: "TagBot"
 on:
   issue_comment:
-    types:
-      - created
+    types: [created]
   workflow_dispatch:
-    inputs:
-      lookback:
-        default: "3"
-
-permissions:
-  actions: read
-  checks: read
-  contents: write
-  deployments: read
-  issues: read
-  discussions: read
-  packages: read
-  pages: read
-  pull-requests: read
-  repository-projects: read
-  security-events: read
-  statuses: read
-
 jobs:
-  TagBot-BoundaryValueDiffEq:
-    if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'
-    runs-on: ubuntu-latest
-    steps:
-      - name: Tag BoundaryValueDiffEq
-        uses: JuliaRegistries/TagBot@v1
-        with:
-          token: ${{ secrets.GITHUB_TOKEN }}
-          ssh: ${{ secrets.DOCUMENTER_KEY }}
-
-  TagBot-Subpackages:
-    if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'
-    runs-on: ubuntu-latest
+  tagbot:
+    uses: "SciML/.github/.github/workflows/tagbot.yml@v1"
+    secrets: "inherit"
+  tagbot-subpackages:
     strategy:
       fail-fast: false
       matrix:
-        package:
-          - BoundaryValueDiffEqCore
-          - BoundaryValueDiffEqMIRK
-          - BoundaryValueDiffEqFIRK
-          - BoundaryValueDiffEqMIRKN
-          - BoundaryValueDiffEqAscher
-          - BoundaryValueDiffEqShooting
-    steps:
-      - name: Tag ${{ matrix.package }}
-        uses: JuliaRegistries/TagBot@v1
-        with:
-          token: ${{ secrets.GITHUB_TOKEN }}
-          ssh: ${{ secrets.DOCUMENTER_KEY }}
-          subdir: "lib/${{ matrix.package }}"
+        subdir:
+          - "lib/BoundaryValueDiffEqCore"
+          - "lib/BoundaryValueDiffEqMIRK"
+          - "lib/BoundaryValueDiffEqFIRK"
+          - "lib/BoundaryValueDiffEqMIRKN"
+          - "lib/BoundaryValueDiffEqAscher"
+          - "lib/BoundaryValueDiffEqShooting"
+    uses: "SciML/.github/.github/workflows/tagbot.yml@v1"
+    with:
+      subdir: "${{ matrix.subdir }}"
+    secrets: "inherit"

.github/workflows/SublibraryCI.yml

@@ -34,7 +34,6 @@ BoundaryValueDiffEqODEInterfaceExt = "ODEInterface"
 
 [compat]
 ADTypes = "1.14"
-Aqua = "0.8.11"
 BoundaryValueDiffEqAscher = "1"
 BoundaryValueDiffEqCore = "2"
 BoundaryValueDiffEqFIRK = "1"
@@ -46,7 +45,6 @@ DiffEqDevTools = "2.48, 3"
 DifferentiationInterface = "0.7.13"
 FastClosures = "0.3.2"
 ForwardDiff = "0.10.38, 1"
-Hwloc = "3.3"
 InteractiveUtils = "<0.0.1, 1"
 LinearAlgebra = "1.10"
 LinearSolve = "3.12"
@@ -58,35 +56,32 @@ OrdinaryDiffEqTsit5 = "1.1, 2"
 OptimizationBase = "5"
 Pkg = "1.10.0"
 Random = "1.10"
-ReTestItems = "1.29"
 RecursiveArrayTools = "3.31.2, 4"
 Reexport = "1.2"
+SafeTestsets = "0.1.0"
 SciMLBase = "3"
 Sparspak = "0.3.11"
 StaticArrays = "1.9.8"
 Test = "1.10"
 julia = "1.10"
 
 [extras]
-Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
 DiffEqDevTools = "f3b72e0c-5b89-59e1-b016-84e28bfd966d"
 DifferentiationInterface = "a0c0ee7d-e4b9-4e03-894e-1c5f64a51d63"
-Hwloc = "0e44f5e4-bd66-52a0-8798-143a42290a1d"
 InteractiveUtils = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
 LinearSolve = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae"
 NonlinearSolveBase = "be0214bd-f91f-a760-ac4e-3421ce2b2da0"
 NonlinearSolveFirstOrder = "5959db7a-ea39-4486-b5fe-2dd0bf03d60d"
-ODEInterface = "54ca160b-1b9f-5127-a996-1867f4bc2a2c"
 OrdinaryDiffEqLowOrderRK = "1344f307-1e59-4825-a18e-ace9aa3fa4c6"
 OrdinaryDiffEqTsit5 = "b1df2697-797e-41e3-8120-5422d3b24e4a"
 OptimizationBase = "bca83a33-5cc9-4baa-983d-23429ab6bcbb"
 Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
-ReTestItems = "817f1d60-ba6b-4fd5-9520-3cf149f6a823"
 RecursiveArrayTools = "731186ca-8d62-57ce-b412-fbd966d074cd"
+SafeTestsets = "1bc83da4-3b8d-516f-aca4-4fe02f6d838f"
 Sparspak = "e56a9233-b9d6-4f03-8d0f-1825330902ac"
 StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["Aqua", "DiffEqDevTools", "DifferentiationInterface", "Hwloc", "InteractiveUtils", "LinearSolve", "NonlinearSolveFirstOrder", "ODEInterface", "OrdinaryDiffEqLowOrderRK", "OrdinaryDiffEqTsit5", "Pkg", "Random", "ReTestItems", "RecursiveArrayTools", "Sparspak", "StaticArrays", "Test", "OptimizationBase", "NonlinearSolveBase"]
+test = ["DiffEqDevTools", "DifferentiationInterface", "InteractiveUtils", "LinearSolve", "NonlinearSolveFirstOrder", "OrdinaryDiffEqLowOrderRK", "OrdinaryDiffEqTsit5", "Pkg", "Random", "RecursiveArrayTools", "SafeTestsets", "Sparspak", "StaticArrays", "Test", "OptimizationBase", "NonlinearSolveBase"]