Uniformize monorepo structure to OrdinaryDiffEq canonical style

.github/workflows/CI.yml

@@ -19,12 +19,11 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
+        # Root-only test groups. The lib/* sublibraries (DataDrivenDMD, DataDrivenSR,
+        # DataDrivenSparse, DataDrivenLux) are covered by SublibraryCI.yml via the
+        # project model and must not be double-tested through the root matrix.
         group:
           - Core
-          - DataDrivenDMD
-          - DataDrivenSR
-          - DataDrivenSparse
-          - DataDrivenLux
           - nopre
         version:
           - '1'
@@ -37,5 +36,5 @@ jobs:
     with:
       julia-version: "${{ matrix.version }}"
       group: "${{ matrix.group }}"
-      coverage-directories: "src,lib/DataDrivenDMD/src,lib/DataDrivenSparse/src,lib/DataDrivenSR/src,lib/DataDrivenLux/src"
+      coverage-directories: "src"
     secrets: "inherit"

.github/workflows/Downgrade.yml

@@ -10,11 +10,13 @@ on:
       - master
     paths-ignore:
       - 'docs/**'
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
 jobs:
   test:
     name: "Downgrade"
     uses: "SciML/.github/.github/workflows/downgrade.yml@v1"
     with:
-      julia-version: "1.10"
-      skip: "Pkg,TOML"
+      group: "Core"
     secrets: "inherit"

.github/workflows/DowngradeSublibraries.yml

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

.github/workflows/Downstream.yml

@@ -0,0 +1,62 @@
+name: IntegrationTest
+on:
+  push:
+    branches: [master]
+    tags: [v*]
+  pull_request:
+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:
+    name: ${{ matrix.package.repo }}/${{ matrix.package.group }}/${{ matrix.julia-version }}
+    runs-on: ${{ matrix.os }}
+    env:
+      GROUP: ${{ matrix.package.group }}
+    strategy:
+      fail-fast: false
+      matrix:
+        julia-version: ['1.10']
+        os: [ubuntu-latest]
+        package:
+          - {user: SciML, repo: SymbolicNumericIntegration.jl, group: All}
+          - {user: ODINN-SciML, repo: ODINN.jl, group: Core1}
+
+    steps:
+      - uses: actions/checkout@v6
+      - uses: julia-actions/setup-julia@v3
+        with:
+          version: ${{ matrix.julia-version }}
+          arch: x64
+      - name: Clone Downstream
+        uses: actions/checkout@v6
+        with:
+          repository: ${{ matrix.package.user }}/${{ matrix.package.repo }}
+          path: downstream
+      - name: Load this and run the downstream tests
+        shell: julia --color=yes --project=downstream {0}
+        run: |
+          using Pkg
+          try
+            # Develop the root umbrella DataDrivenDiffEq plus every lib/* sublibrary
+            # so the downstream tests run against this checkout rather than releases.
+            Pkg.develop(PackageSpec(path="."));
+            Pkg.develop(map(path ->Pkg.PackageSpec.(;path="lib/$(path)"), readdir("./lib")));
+            Pkg.test(coverage=true)  # resolver may fail with test time deps
+          catch err
+            err isa Pkg.Resolve.ResolverError || rethrow()
+            # If we can't resolve that means this is incompatible by SemVer and this is fine
+            # It means we marked this as a breaking change, so we don't need to worry about
+            # mistakenly introducing a breaking change, as we have intentionally made one
+            @info "Not compatible with this release. No problem." exception=err
+            exit(0)  # Exit immediately, as a success
+          end
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: codecov/codecov-action@v6
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          files: lcov.info
+          fail_ci_if_error: false
+          disable_safe_directory: true

.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: DATADRIVENDIFFEQ_TEST_GROUP
+      check-bounds: auto
     secrets: "inherit"

.github/workflows/TagBot.yml

@@ -1,15 +1,22 @@
-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: ${{ secrets.DOCUMENTER_KEY }}
+  tagbot:
+    uses: "SciML/.github/.github/workflows/tagbot.yml@v1"
+    secrets: "inherit"
+  tagbot-subpackages:
+    strategy:
+      fail-fast: false
+      matrix:
+        subdir:
+          - "lib/DataDrivenDMD"
+          - "lib/DataDrivenLux"
+          - "lib/DataDrivenSparse"
+          - "lib/DataDrivenSR"
+    uses: "SciML/.github/.github/workflows/tagbot.yml@v1"
+    with:
+      subdir: "${{ matrix.subdir }}"
+    secrets: "inherit"

Project.toml

@@ -31,22 +31,27 @@ CommonSolve = "0.2"
 DataInterpolations = "4, 5, 6, 7, 8"
 DiffEqBase = "6.211, 7"
 DocStringExtensions = "0.7, 0.8, 0.9"
+LinearAlgebra = "1"
 MLUtils = "0.3, 0.4"
 ModelingToolkit = "11.21.0"
 OrdinaryDiffEqTsit5 = "1, 2"
 Parameters = "0.12.1"
+Pkg = "1"
 PrecompileTools = "1"
 ProgressMeter = "1.6"
 QuadGK = "2.4"
+Random = "1"
 RecipesBase = "1"
 Reexport = "1.0"
+SafeTestsets = "0.1"
 SciMLBase = "2.155, 3"
 SciMLStructures = "1"
 Setfield = "1"
 Statistics = "1"
 StatsBase = "0.32.0, 0.33, 0.34"
 SymbolicUtils = "4"
 Symbolics = "7"
+Test = "1"
 julia = "1.10"
 
 [extras]

lib/DataDrivenDMD/Project.toml

@@ -7,10 +7,18 @@ version = "0.1.3"
 DataDrivenDiffEq = "2445eb08-9709-466a-b3fc-47e12bd697a2"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 
+[sources]
+DataDrivenDiffEq = {path = "../.."}
+
 [compat]
-DataDrivenDiffEq = "1.14"
+DataDrivenDiffEq = "1.15"
+LinearAlgebra = "1.10"
 OrdinaryDiffEq = "6, 7"
 OrdinaryDiffEqFunctionMap = "1, 2"
+SafeTestsets = "0.1"
+StableRNGs = "1"
+StatsBase = "0.34"
+Test = "1.10"
 julia = "1.10"
 
 [extras]

lib/DataDrivenDMD/README.md

@@ -0,0 +1,12 @@
+# DataDrivenDMD.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/DataDrivenDiffEq/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)
+
+DataDrivenDMD.jl is a component of the [DataDrivenDiffEq.jl](https://github.com/SciML/DataDrivenDiffEq.jl) monorepo. Dynamic Mode Decomposition (DMD) and Koopman-based methods for discovering linear operator approximations of dynamical systems from data.
+While completely independent and usable on its own, users wanting the full data-driven modeling suite should use [DataDrivenDiffEq.jl](https://github.com/SciML/DataDrivenDiffEq.jl).
+
+For a full description of the methods and their options, see the [DataDrivenDiffEq documentation](https://docs.sciml.ai/DataDrivenDiffEq/stable/).

lib/DataDrivenDMD/test/runtests.jl

@@ -5,21 +5,21 @@ using Test
 
 @info "Finished loading packages"
 
-const GROUP = get(ENV, "GROUP", "All")
+const GROUP = get(ENV, "DATADRIVENDIFFEQ_TEST_GROUP", get(ENV, "GROUP", "All"))
 
 @time begin
-    if GROUP == "All" || GROUP == "DataDrivenDMD"
+    if GROUP == "All" || GROUP == "Core" || GROUP == "DataDrivenDMD"
         @safetestset "Linear autonomous" begin
-            include("./linear_autonomous.jl")
+            include("./Core/linear_autonomous.jl")
         end
         @safetestset "Linear forced" begin
-            include("./linear_forced.jl")
+            include("./Core/linear_forced.jl")
         end
         @safetestset "Nonlinear autonomous" begin
-            include("./nonlinear_autonomous.jl")
+            include("./Core/nonlinear_autonomous.jl")
         end
         @safetestset "Nonlinear forced" begin
-            include("./nonlinear_forced.jl")
+            include("./Core/nonlinear_forced.jl")
         end
     end
 end

lib/DataDrivenDMD/test/test_groups.toml

@@ -0,0 +1,4 @@
+# Each sublibrary only defines functional ("Core") tests; there are no QA
+# (Aqua/JET/AllocCheck) suites here, so the default QA group is not declared.
+[Core]
+versions = ["lts", "1", "pre"]

lib/DataDrivenLux/Project.toml

@@ -30,27 +30,37 @@ StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
 TransformVariables = "84d833dd-6860-57f9-a1a7-6da5db126cff"
 WeightInitializers = "d49dbf32-c5c2-4618-8acc-27bb2598ef2d"
 
+[sources]
+DataDrivenDiffEq = {path = "../.."}
+
 [compat]
 AbstractDifferentiation = "0.6"
 ChainRulesCore = "1.15"
 CommonSolve = "0.2.4"
 ComponentArrays = "0.15"
 ConcreteStructs = "0.2.3"
-DataDrivenDiffEq = "1.14"
-OrdinaryDiffEq = "6, 7"
+DataDrivenDiffEq = "1.15"
+Distributed = "1.10"
 Distributions = "0.25"
 DistributionsAD = "0.6"
 DocStringExtensions = "0.9.3"
 ForwardDiff = "0.10, 1"
 IntervalArithmetic = "0.22, 0.23, 1"
 InverseFunctions = "0.1"
+LinearAlgebra = "1.10"
+Logging = "1.10"
 Lux = "1"
 LuxCore = "1"
 Optim = "1.7, 2"
 Optimisers = "0.3, 0.4"
+OrdinaryDiffEq = "6, 7"
 ProgressMeter = "1.7"
+Random = "1.10"
+SafeTestsets = "0.1"
 Setfield = "1"
+StableRNGs = "1"
 StatsBase = "0.34.3"
+Test = "1.10"
 TransformVariables = "0.8"
 WeightInitializers = "1"
 julia = "1.10"

lib/DataDrivenLux/README.md

@@ -0,0 +1,12 @@
+# DataDrivenLux.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/DataDrivenDiffEq/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)
+
+DataDrivenLux.jl is a component of the [DataDrivenDiffEq.jl](https://github.com/SciML/DataDrivenDiffEq.jl) monorepo. Deep-learning-based structure search, built on Lux.jl, for discovering governing equations via differentiable directed-acyclic-graph candidate models.
+While completely independent and usable on its own, users wanting the full data-driven modeling suite should use [DataDrivenDiffEq.jl](https://github.com/SciML/DataDrivenDiffEq.jl).
+
+For a full description of the methods and their options, see the [DataDrivenDiffEq documentation](https://docs.sciml.ai/DataDrivenDiffEq/stable/).

lib/DataDrivenLux/test/runtests.jl

@@ -5,25 +5,25 @@ using Test
 
 @info "Finished loading packages"
 
-const GROUP = get(ENV, "GROUP", "All")
+const GROUP = get(ENV, "DATADRIVENDIFFEQ_TEST_GROUP", get(ENV, "GROUP", "All"))
 
 @testset "DataDrivenLux" begin
-    if GROUP == "All" || GROUP == "DataDrivenLux"
+    if GROUP == "All" || GROUP == "Core" || GROUP == "DataDrivenLux"
         @testset "Lux" begin
-            @safetestset "Nodes" include("nodes.jl")
-            @safetestset "Layers" include("layers.jl")
-            @safetestset "Graphs" include("graphs.jl")
+            @safetestset "Nodes" include("Core/nodes.jl")
+            @safetestset "Layers" include("Core/layers.jl")
+            @safetestset "Graphs" include("Core/graphs.jl")
         end
 
         @testset "Caches" begin
-            @safetestset "Candidate" include("candidate.jl")
-            @safetestset "Cache" include("cache.jl")
+            @safetestset "Candidate" include("Core/candidate.jl")
+            @safetestset "Cache" include("Core/cache.jl")
         end
 
         @testset "Algorithms" begin
-            @safetestset "RandomSearch" include("randomsearch_solve.jl")
-            @safetestset "Reinforce" include("reinforce_solve.jl")
-            @safetestset "CrossEntropy" include("crossentropy_solve.jl")
+            @safetestset "RandomSearch" include("Core/randomsearch_solve.jl")
+            @safetestset "Reinforce" include("Core/reinforce_solve.jl")
+            @safetestset "CrossEntropy" include("Core/crossentropy_solve.jl")
         end
     end
 end

lib/DataDrivenLux/test/test_groups.toml

@@ -0,0 +1,4 @@
+# Each sublibrary only defines functional ("Core") tests; there are no QA
+# (Aqua/JET/AllocCheck) suites here, so the default QA group is not declared.
+[Core]
+versions = ["lts", "1", "pre"]

lib/DataDrivenSR/Project.toml

@@ -8,10 +8,16 @@ DataDrivenDiffEq = "2445eb08-9709-466a-b3fc-47e12bd697a2"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 SymbolicRegression = "8254be44-1295-4e6a-a16d-46603ac705cb"
 
+[sources]
+DataDrivenDiffEq = {path = "../.."}
+
 [compat]
+DataDrivenDiffEq = "1.15"
 Reexport = "1.2"
-DataDrivenDiffEq = "1.14"
+StableRNGs = "1"
+StatsBase = "0.34"
 SymbolicRegression = "1"
+Test = "1.10"
 julia = "1.10"
 
 [extras]

lib/DataDrivenSR/README.md

@@ -0,0 +1,12 @@
+# DataDrivenSR.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/DataDrivenDiffEq/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)
+
+DataDrivenSR.jl is a component of the [DataDrivenDiffEq.jl](https://github.com/SciML/DataDrivenDiffEq.jl) monorepo. Symbolic regression methods, built on SymbolicRegression.jl, for discovering closed-form governing equations from data.
+While completely independent and usable on its own, users wanting the full data-driven modeling suite should use [DataDrivenDiffEq.jl](https://github.com/SciML/DataDrivenDiffEq.jl).
+
+For a full description of the methods and their options, see the [DataDrivenDiffEq documentation](https://docs.sciml.ai/DataDrivenDiffEq/stable/).