Merge branch 'master' into ChrisRackauckas-patch-5

.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 +1,37 @@
+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: ${{ github.ref != 'refs/heads/master' }}
+
+jobs:
+  tests:
+    name: "Tests"
+    strategy:
+      fail-fast: false
+      matrix:
+        group:
+          - InterfaceI
+          - InterfaceII
+          - Extensions
+          - Downstream
+          - RegressionI
+    uses: "SciML/.github/.github/workflows/tests.yml@v1"
+    with:
+      group: "${{ matrix.group }}"
+    secrets: "inherit"

Project.toml

@@ -1,11 +1,12 @@
 name = "ModelingToolkit"
 uuid = "961ee093-0014-501f-94e3-6117800e7a78"
 authors = ["Yingbo Ma <[email protected]>", "Chris Rackauckas <[email protected]> and contributors"]
-version = "9.27.0"
+version = "9.33.1"
 
 [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"
@@ -28,7 +29,6 @@ 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"
@@ -57,16 +57,22 @@ 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"
@@ -89,14 +95,14 @@ 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"
-NonlinearSolve = "3.12"
+NonlinearSolve = "3.14"
 OrderedCollections = "1"
 OrdinaryDiffEq = "6.82.0"
 PrecompileTools = "1"
@@ -111,9 +117,9 @@ 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 = "0.3.26"
-SymbolicUtils = "2.1"
-Symbolics = "5.32"
+SymbolicIndexingInterface = "0.3.28"
+SymbolicUtils = "3.2"
+Symbolics = "6"
 URIs = "1"
 UnPack = "0.1, 1.0"
 Unitful = "1.1"
@@ -129,6 +135,7 @@ ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
 Ipopt = "b6b21f68-93f8-5de0-b562-5493be1d77c9"
 Ipopt_jll = "9cc047cb-c261-5740-88fc-0cf96f7bdcc7"
 JET = "c3a54625-cd67-489e-a8e7-0a5a0ff4e31b"
+LabelledArrays = "2ee39098-c373-598a-b85f-a56591580800"
 ModelingToolkitStandardLibrary = "16a59e39-deab-5bd0-87e4-056b12336739"
 NonlinearSolve = "8913a72c-1f9b-4ce2-8d82-65094dcecaec"
 Optimization = "7f7a1694-90dd-40f0-9382-eb1efda571ba"
@@ -148,4 +155,4 @@ 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", "OrdinaryDiffEq", "Random", "ReferenceTests", "SafeTestsets", "StableRNGs", "Statistics", "SteadyStateDiffEq", "Test", "StochasticDiffEq", "Sundials", "StochasticDelayDiffEq", "Pkg", "JET"]
+test = ["AmplNLWriter", "BenchmarkTools", "ControlSystemsBase", "DelayDiffEq", "NonlinearSolve", "ForwardDiff", "Ipopt", "Ipopt_jll", "ModelingToolkitStandardLibrary", "Optimization", "OptimizationOptimJL", "OptimizationMOI", "OrdinaryDiffEq", "Random", "ReferenceTests", "SafeTestsets", "StableRNGs", "Statistics", "SteadyStateDiffEq", "Test", "StochasticDiffEq", "Sundials", "StochasticDelayDiffEq", "Pkg", "JET", "LabelledArrays"]

README.md

@@ -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,

docs/Project.toml

@@ -37,6 +37,6 @@ Plots = "1.36"
 SciMLStructures = "1.1"
 StochasticDiffEq = "6"
 SymbolicIndexingInterface = "0.3.1"
-SymbolicUtils = "2, 3"
-Symbolics = "5"
+SymbolicUtils = "3"
+Symbolics = "6"
 Unitful = "1.12"

docs/make.jl

@@ -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"

docs/pages.jl

@@ -28,6 +28,7 @@ pages = [
         "basics/Composition.md",
         "basics/Events.md",
         "basics/Linearization.md",
+        "basics/InputOutput.md",
         "basics/MTKLanguage.md",
         "basics/Validation.md",
         "basics/DependencyGraphs.md",

docs/src/basics/Events.md

@@ -336,3 +336,45 @@ one must still use a vector
 ```julia
 discrete_events = [[2.0] => [v ~ -v]]
 ```
+
+## Saving discrete values
+
+Time-dependent parameters which are updated in callbacks are termed as discrete variables.
+ModelingToolkit enables automatically saving the timeseries of these discrete variables,
+and indexing the solution object to obtain the saved timeseries. Consider the following
+example:
+
+```@example events
+@variables x(t)
+@parameters c(t)
+
+@mtkbuild sys = ODESystem(
+    D(x) ~ c * cos(x), t, [x], [c]; discrete_events = [1.0 => [c ~ c + 1]])
+
+prob = ODEProblem(sys, [x => 0.0], (0.0, 2pi), [c => 1.0])
+sol = solve(prob, Tsit5())
+sol[c]
+```
+
+The solution object can also be interpolated with the discrete variables
+
+```@example events
+sol([1.0, 2.0], idxs = [c, c * cos(x)])
+```
+
+Note that only time-dependent parameters will be saved. If we repeat the above example with
+this change:
+
+```@example events
+@variables x(t)
+@parameters c
+
+@mtkbuild sys = ODESystem(
+    D(x) ~ c * cos(x), t, [x], [c]; discrete_events = [1.0 => [c ~ c + 1]])
+
+prob = ODEProblem(sys, [x => 0.0], (0.0, 2pi), [c => 1.0])
+sol = solve(prob, Tsit5())
+sol.ps[c] # sol[c] will error, since `c` is not a timeseries value
+```
+
+It can be seen that the timeseries for `c` is not saved.