Merge branch 'master' into offset_indices

Author: hersle

.github/workflows/Downstream.yml

@@ -32,7 +32,7 @@ jobs:
           - {user: SciML, repo: NeuralPDE.jl, group: NNPDE}
           - {user: SciML, repo: DataDrivenDiffEq.jl, group: Downstream}
           - {user: SciML, repo: StructuralIdentifiability.jl, group: All}
-          - {user: SciML, repo: ModelingToolkitStandardLibrary.jl}
+          - {user: SciML, repo: ModelingToolkitStandardLibrary.jl, group: Core}
           - {user: SciML, repo: ModelOrderReduction.jl, group: All}
           - {user: SciML, repo: MethodOfLines.jl, group: Interface}
           - {user: SciML, repo: MethodOfLines.jl, group: 2D_Diffusion}

.github/workflows/FormatCheck.yml

@@ -0,0 +1,13 @@
+name: "Format Check"
+
+on:
+  push:
+    branches:
+      - 'master'
+    tags: '*'
+  pull_request:
+
+jobs:
+  format-check:
+    name: "Format Check"
+    uses: "SciML/.github/.github/workflows/format-suggestions-on-pr.yml@v1"

.github/workflows/Invalidations.yml

@@ -1,9 +1,9 @@
-name: Invalidations
+name: "Invalidations"
 
 on:
   pull_request:
     paths-ignore:
-        - 'docs/**'
+      - 'docs/**'
 
 concurrency:
   # Skip intermediate builds: always.
@@ -12,31 +12,6 @@ concurrency:
   cancel-in-progress: true
 
 jobs:
-  evaluate:
-    # Only run on PRs to the default branch.
-    # In the PR trigger above branches can be specified only explicitly whereas this check should work for master, main, or any other default branch
-    if: github.base_ref == github.event.repository.default_branch
-    runs-on: ubuntu-latest
-    steps:
-    - uses: julia-actions/setup-julia@v1
-      with:
-        version: '1'
-    - uses: actions/checkout@v4
-    - uses: julia-actions/julia-buildpkg@v1
-    - uses: julia-actions/julia-invalidations@v1
-      id: invs_pr
-
-    - uses: actions/checkout@v4
-      with:
-        ref: ${{ github.event.repository.default_branch }}
-    - uses: julia-actions/julia-buildpkg@v1
-    - uses: julia-actions/julia-invalidations@v1
-      id: invs_default
-
-    - name: Report invalidation counts
-      run: |
-        echo "Invalidations on default branch: ${{ steps.invs_default.outputs.total }} (${{ steps.invs_default.outputs.deps }} via deps)" >> $GITHUB_STEP_SUMMARY
-        echo "This branch: ${{ steps.invs_pr.outputs.total }} (${{ steps.invs_pr.outputs.deps }} via deps)" >> $GITHUB_STEP_SUMMARY
-    - name: Check if the PR does increase number of invalidations
-      if: steps.invs_pr.outputs.total > steps.invs_default.outputs.total
-      run: exit 1
+  evaluate-invalidations:
+    name: "Evaluate Invalidations"
+    uses: "SciML/.github/.github/workflows/invalidations.yml@v1"

.github/workflows/Tests.yml

@@ -0,0 +1,39 @@
+name: "Tests"
+
+on:
+  pull_request:
+    branches:
+      - master
+      - 'release-'
+    paths-ignore:
+      - 'docs/**'
+  push:
+    branches:
+      - master
+    paths-ignore:
+      - 'docs/**'
+
+concurrency:
+  # Skip intermediate builds: always, but for the master branch.
+  # Cancel intermediate builds: always, but for the master branch.
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: ${{ github.ref != 'refs/heads/master' }}
+
+jobs:
+  tests:
+    name: "Tests"
+    strategy:
+      fail-fast: false
+      matrix:
+        group:
+          - InterfaceI
+          - InterfaceII
+          - SymbolicIndexingInterface
+          - Extended
+          - Extensions
+          - Downstream
+          - RegressionI
+    uses: "SciML/.github/.github/workflows/tests.yml@v1"
+    with:
+      group: "${{ matrix.group }}"
+    secrets: "inherit"

.github/workflows/ci.yml

@@ -1,39 +1,43 @@
 name = "ModelingToolkit"
 uuid = "961ee093-0014-501f-94e3-6117800e7a78"
 authors = ["Yingbo Ma <[email protected]>", "Chris Rackauckas <[email protected]> and contributors"]
-version = "9.12.1"
+version = "9.42.0"
 
 [deps]
 AbstractTrees = "1520ce14-60c1-5f80-bbc7-55ef81b5835c"
 ArrayInterface = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9"
+BlockArrays = "8e7c35d0-a365-5155-bbbb-fb81a777f24e"
 Combinatorics = "861a8166-3701-5b0c-9a16-15d98fcdc6aa"
 Compat = "34da2185-b29b-5c13-b0c7-acf172513d20"
 ConstructionBase = "187b0558-2788-49d3-abe0-74a17ed4e7c9"
 DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
 DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e"
 DiffEqCallbacks = "459566f4-90b8-5000-8ac3-15dfb0a30def"
+DiffEqNoiseProcess = "77a26b50-5914-5dd7-bc55-306e6241c503"
 DiffRules = "b552c78f-8df3-52c6-915a-8e097449b14b"
 Distributed = "8ba89e20-285c-5b6f-9357-94700520ee1b"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
 DomainSets = "5b8099bc-c8ec-5219-889f-1d9e522a28bf"
 DynamicQuantities = "06fc5a27-2a28-4c7c-a15d-362465fb6821"
 ExprTools = "e2ba6199-217a-4e67-a87a-7c52f15ade04"
+Expronicon = "6b7a57c9-7cc1-4fdf-b7f5-e857abae3636"
 FindFirstFunctions = "64ca27bc-2ba2-4a57-88aa-44e436879224"
 ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
+FunctionWrappers = "069b7b12-0de2-55c6-9aab-29f3d0a68a2e"
 FunctionWrappersWrappers = "77dc65aa-8811-40c2-897b-53d922fa7daf"
 Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
 InteractiveUtils = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
 JuliaFormatter = "98e50ef6-434e-11e9-1051-2b60c6c9e899"
 JumpProcesses = "ccbc3e58-028d-4f4c-8cd5-9ae44345cda5"
-LabelledArrays = "2ee39098-c373-598a-b85f-a56591580800"
 Latexify = "23fbe1c1-3f47-55db-b15f-69d7ec21a316"
 Libdl = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 MLStyle = "d8e11817-5142-5d16-987a-aa16d5891078"
 NaNMath = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3"
+NonlinearSolve = "8913a72c-1f9b-4ce2-8d82-65094dcecaec"
 OffsetArrays = "6fe1bfb0-de20-5000-8ca7-80f57d26f881"
-OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
+OrderedCollections = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
 PrecompileTools = "aea7be01-6a6a-4083-8856-8a6e6704d82a"
 RecursiveArrayTools = "731186ca-8d62-57ce-b412-fbd966d074cd"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
@@ -55,57 +59,71 @@ Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 
 [weakdeps]
 BifurcationKit = "0f109fa4-8a5d-4b75-95aa-f515264e7665"
+ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
 DeepDiffs = "ab62b9b5-e342-54a8-a765-a90f495de1a6"
+LabelledArrays = "2ee39098-c373-598a-b85f-a56591580800"
 
 [extensions]
 MTKBifurcationKitExt = "BifurcationKit"
+MTKChainRulesCoreExt = "ChainRulesCore"
 MTKDeepDiffsExt = "DeepDiffs"
+MTKLabelledArraysExt = "LabelledArrays"
 
 [compat]
 AbstractTrees = "0.3, 0.4"
 ArrayInterface = "6, 7"
+BifurcationKit = "0.3"
+BlockArrays = "1.1"
+ChainRulesCore = "1"
 Combinatorics = "1"
 Compat = "3.42, 4"
 ConstructionBase = "1"
+DataInterpolations = "6.4"
 DataStructures = "0.17, 0.18"
+DeepDiffs = "1"
 DiffEqBase = "6.103.0"
-DiffEqCallbacks = "2.16, 3"
+DiffEqCallbacks = "2.16, 3, 4"
+DiffEqNoiseProcess = "5"
 DiffRules = "0.1, 1.0"
 Distributed = "1"
 Distributions = "0.23, 0.24, 0.25"
 DocStringExtensions = "0.7, 0.8, 0.9"
 DomainSets = "0.6, 0.7"
-DynamicQuantities = "^0.11.2, 0.12, 0.13"
+DynamicQuantities = "^0.11.2, 0.12, 0.13, 1"
 ExprTools = "0.1.10"
+Expronicon = "0.8"
 FindFirstFunctions = "1"
 ForwardDiff = "0.10.3"
+FunctionWrappers = "1.1"
 FunctionWrappersWrappers = "0.1"
 Graphs = "1.5.2"
 InteractiveUtils = "1"
 JuliaFormatter = "1.0.47"
-JumpProcesses = "9.1"
+JumpProcesses = "9.13.1"
 LabelledArrays = "1.3"
 Latexify = "0.11, 0.12, 0.13, 0.14, 0.15, 0.16"
 Libdl = "1"
 LinearAlgebra = "1"
 MLStyle = "0.4.17"
 NaNMath = "0.3, 1"
-OrdinaryDiffEq = "6.73.0"
+NonlinearSolve = "3.14"
+OrderedCollections = "1"
+OrdinaryDiffEq = "6.82.0"
 PrecompileTools = "1"
-RecursiveArrayTools = "2.3, 3"
+RecursiveArrayTools = "3.26"
 Reexport = "0.2, 1"
 RuntimeGeneratedFunctions = "0.5.9"
-SciMLBase = "2.28.0"
+SciMLBase = "2.55"
 SciMLStructures = "1.0"
 Serialization = "1"
 Setfield = "0.7, 0.8, 1"
 SimpleNonlinearSolve = "0.1.0, 1"
 SparseArrays = "1"
 SpecialFunctions = "0.7, 0.8, 0.9, 0.10, 1.0, 2"
 StaticArrays = "0.10, 0.11, 0.12, 1.0"
-SymbolicIndexingInterface = "0.3.12"
-SymbolicUtils = "1.0"
-Symbolics = "5.26"
+SymbolicIndexingInterface = "0.3.31"
+SymbolicUtils = "3.7"
+Symbolics = "6.12"
 URIs = "1"
 UnPack = "0.1, 1.0"
 Unitful = "1.1"
@@ -115,6 +133,7 @@ julia = "1.9"
 AmplNLWriter = "7c4d4715-977e-5154-bfe0-e096adeac482"
 BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
 ControlSystemsBase = "aaaaaaaa-a6ca-5380-bf3e-84a91bcd477e"
+DataInterpolations = "82cc6244-b520-54b8-b5a6-8a565e85f1d0"
 DeepDiffs = "ab62b9b5-e342-54a8-a765-a90f495de1a6"
 DelayDiffEq = "bcd4f6db-9728-5f36-b5f7-82caef46ccdb"
 ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
@@ -126,6 +145,7 @@ NonlinearSolve = "8913a72c-1f9b-4ce2-8d82-65094dcecaec"
 Optimization = "7f7a1694-90dd-40f0-9382-eb1efda571ba"
 OptimizationMOI = "fd9f6733-72f4-499f-8506-86b2bdd0dea1"
 OptimizationOptimJL = "36348300-93cb-4f02-beb5-3c3902f8871e"
+OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
 Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 ReferenceTests = "324d217c-45ce-50fc-942e-d289b448e8cf"
@@ -139,4 +159,4 @@ Sundials = "c3572dad-4567-51f8-b174-8c6c989267f4"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["AmplNLWriter", "BenchmarkTools", "ControlSystemsBase", "DelayDiffEq", "NonlinearSolve", "ForwardDiff", "Ipopt", "Ipopt_jll", "ModelingToolkitStandardLibrary", "Optimization", "OptimizationOptimJL", "OptimizationMOI", "Random", "ReferenceTests", "SafeTestsets", "StableRNGs", "Statistics", "SteadyStateDiffEq", "Test", "StochasticDiffEq", "Sundials", "StochasticDelayDiffEq", "Pkg", "JET"]
+test = ["AmplNLWriter", "BenchmarkTools", "ControlSystemsBase", "DataInterpolations", "DelayDiffEq", "NonlinearSolve", "ForwardDiff", "Ipopt", "Ipopt_jll", "ModelingToolkitStandardLibrary", "Optimization", "OptimizationOptimJL", "OptimizationMOI", "OrdinaryDiffEq", "Random", "ReferenceTests", "SafeTestsets", "StableRNGs", "Statistics", "SteadyStateDiffEq", "Test", "StochasticDiffEq", "Sundials", "StochasticDelayDiffEq", "Pkg", "JET"]

Project.toml

@@ -83,13 +83,13 @@ eqs = [D(x) ~ σ * (y - x),
     D(y) ~ x * (ρ - z) - y,
     D(z) ~ x * y - β * z]
 
-@mtkbuild lorenz1 = ODESystem(eqs)
-@mtkbuild lorenz2 = ODESystem(eqs)
+@named lorenz1 = ODESystem(eqs, t)
+@named lorenz2 = ODESystem(eqs, t)
 
 @variables a(t)
 @parameters γ
 connections = [0 ~ lorenz1.x + lorenz2.y + a * γ]
-@mtkbuild connected = ODESystem(connections, t, [a], [γ], systems = [lorenz1, lorenz2])
+@mtkbuild connected = ODESystem(connections, t, systems = [lorenz1, lorenz2])
 
 u0 = [lorenz1.x => 1.0,
     lorenz1.y => 0.0,

README.md

@@ -26,9 +26,9 @@ BifurcationKit = "0.3"
 DifferentialEquations = "7.6"
 Distributions = "0.25"
 Documenter = "1"
-DynamicQuantities = "^0.11.2, 0.12"
+DynamicQuantities = "^0.11.2, 0.12, 1"
 ModelingToolkit = "8.33, 9"
-NonlinearSolve = "0.3, 1, 2, 3"
+NonlinearSolve = "3"
 Optim = "1.7"
 Optimization = "3.9"
 OptimizationOptimJL = "0.1"
@@ -37,6 +37,6 @@ Plots = "1.36"
 SciMLStructures = "1.1"
 StochasticDiffEq = "6"
 SymbolicIndexingInterface = "0.3.1"
-SymbolicUtils = "1"
-Symbolics = "5"
+SymbolicUtils = "3"
+Symbolics = "6"
 Unitful = "1.12"

docs/Project.toml

@@ -1,4 +1,5 @@
 using Documenter, ModelingToolkit
+using ModelingToolkit: SciMLBase
 
 # Make sure that plots don't throw a bunch of warnings / errors!
 ENV["GKSwstype"] = "100"