Merge branch 'master' into myb/state_machine

Author: YingboMa

.github/dependabot.yml

@@ -7,4 +7,4 @@ updates:
       interval: "weekly"
     ignore:
       - dependency-name: "crate-ci/typos"
-        update-types: ["version-update:semver-patch"]
+        update-types: ["version-update:semver-patch", "version-update:semver-minor"]

.github/workflows/Documentation.yml

@@ -30,6 +30,8 @@ jobs:
           DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # For authentication with SSH deploy key
         run: DISPLAY=:0 xvfb-run -s '-screen 0 1024x768x24' julia --project=docs/ --code-coverage=user docs/make.jl
       - uses: julia-actions/julia-processcoverage@v1
-      - uses: codecov/codecov-action@v3
+      - uses: codecov/codecov-action@v4
         with:
           file: lcov.info
+          token: ${{ secrets.CODECOV_TOKEN }}
+          fail_ci_if_error: true

.github/workflows/Downstream.yml

@@ -68,6 +68,8 @@ jobs:
             exit(0)  # Exit immediately, as a success
           end
       - uses: julia-actions/julia-processcoverage@v1
-      - uses: codecov/codecov-action@v3
+      - uses: codecov/codecov-action@v4
         with:
           file: lcov.info
+          token: ${{ secrets.CODECOV_TOKEN }}
+          fail_ci_if_error: true

.github/workflows/FormatCheck.yml

@@ -10,4 +10,4 @@ jobs:
       - name: Checkout Actions Repository
         uses: actions/checkout@v4
       - name: Check spelling
-        uses: crate-ci/typos@v1.17.0 
+        uses: crate-ci/typos@v1.18.0 

.github/workflows/SpellCheck.yml

@@ -3,6 +3,7 @@ on:
   pull_request:
     branches:
       - master
+      - 'release-'
     paths-ignore:
       - 'docs/**'
   push:
@@ -18,7 +19,39 @@ concurrency:
   cancel-in-progress: ${{ github.ref != 'refs/heads/master' }}
 
 jobs:
+  formatter:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        julia-version: [1]
+        julia-arch: [x86]
+        os: [ubuntu-latest]
+    steps:
+      - uses: julia-actions/setup-julia@latest
+        with:
+          version: ${{ matrix.julia-version }}
+
+      - uses: actions/checkout@v4
+      - name: Install JuliaFormatter and format
+        # This will use the latest version by default but you can set the version like so:
+        #
+        # julia  -e 'using Pkg; Pkg.add(PackageSpec(name="JuliaFormatter", version="0.13.0"))'
+        run: |
+          julia  -e 'using Pkg; Pkg.add(PackageSpec(name="JuliaFormatter"))'
+          julia  -e 'using JuliaFormatter; format(".", verbose=true)'
+      - name: Format check
+        run: |
+          julia -e '
+          out = Cmd(`git diff`) |> read |> String
+          if out == ""
+              exit(0)
+          else
+              @error "Some files have not been formatted !!!"
+              write(stdout, out)
+              exit(1)
+          end'
   test:
+    needs: formatter
     runs-on: ubuntu-latest
     strategy:
       fail-fast: false
@@ -27,6 +60,8 @@ jobs:
           - InterfaceI
           - InterfaceII
           - Extensions
+          - Downstream
+          - RegressionI
         version:
           - '1'
     steps:
@@ -49,6 +84,8 @@ jobs:
         env:
           GROUP: ${{ matrix.group }}
       - uses: julia-actions/julia-processcoverage@v1
-      - uses: codecov/codecov-action@v3
+      - uses: codecov/codecov-action@v4
         with:
           file: lcov.info
+          token: ${{ secrets.CODECOV_TOKEN }}
+          fail_ci_if_error: true

.github/workflows/ci.yml

@@ -1,9 +1,44 @@
-# ModelingToolkit v8 Release Notes
+# ModelingToolkit v9 Release Notes
 
 ### Upgrade guide
 
-  - `connect` should not be overloaded by users anymore. `[connect = Flow]`
-    informs ModelingToolkit that particular variable in a connector ought to sum
-    to zero, and by default, variables are equal in a connection. Please check out
-    [acausal components tutorial](https://docs.sciml.ai/ModelingToolkit/stable/tutorials/acausal_components/)
-    for examples.
+  - The function `states` is renamed to `unknowns`. In a similar vein:
+    
+      + `unknown_states` is now `solved_unknowns`.
+      + `get_states` is `get_unknowns`.
+      + `get_unknown_states` is now `get_solved_unknowns`.
+
+  - The default backend for using units in models is now `DynamicQuantities.jl` instead of
+    `Unitful.jl`.
+  - ModelingToolkit.jl now exports common definitions of `t` (time independent variable)
+    and `D` (the first derivative with respect to `t`). Any models made using ModelingToolkit.jl
+    should leverage these common definitions. There are three variants:
+    
+      + `t` and `D` use DynamicQuantities.jl units. This is the default for standard library
+        components.
+      + `t_unitful` and `D_unitful` use Unitful.jl units.
+      + `t_nounits` and `D_nounits` are unitless.
+  - `ODAEProblem` is deprecated in favor of `ODEProblem`.
+  - Specifying the independent variable for an `ODESystem` is now mandatory. The `ODESystem(eqs)`
+    constructor is removed.
+  - Systems must be marked as `complete` before creating `*Function`/`*FunctionExpr`/`*Problem`/
+    `*ProblemExpr`. Typically this involved using `@mtkbuild` to create the system or calling
+    `structural_simplify` on an existing system.
+  - All systems will perform parameter splitting by default. Problems created using ModelingToolkit.jl
+    systems will have a custom struct instead of a `Vector` of parameters. The internals of this
+    type are undocumented and subject to change without notice or a breaking release. Parameter values
+    can be queried, updated or manipulated using SciMLStructures.jl or SymbolicIndexingInterface.jl.
+    This also requires that the symbolic type of a parameter match its assigned value. For example,
+    `@parameters p` will always use a `Float64` value for `p`. To use `Int` instead, use
+    `@parameters p::Int`. Array-valued parameters must be array symbolics; `@parameters p = [1.0, 2.0]`
+    is now invalid and must be changed to `@parameters p[1:2] = [1.0, 2.0]`. The index of a parameter
+    in the system is also not guaranteed to be an `Int`, and will instead be a custom undocumented type.
+    To restore the old behavior:
+    
+      + Pass the `split = false` keyword to `structural_simplify`. E.g. `ss = structural_simplify(sys; split = false)`.
+      + Pass `split = false` to `@mtkbuild`. E.g. `@mtkbuild sys = ODESystem(...) split = false`.
+  - Discrete-time system using `Difference` are unsupported. Instead, use the new `Clock`-based syntax.
+  - Automatic scalarization has been removed, meaning that vector variables need to be treated with proper vector
+    equations. For example, `[p[1] => 1.0, p[2] => 2.0]` is no longer allowed in default equations, use
+    `[p => [1.0, 2.0]]` instead. Also, array equations like for `@variables u[1:2]` have `D(u) ~ A*u` as an
+    array equation. If the scalarized version is desired, use `scalarize(u)`.

NEWS.md

@@ -1,7 +1,7 @@
 name = "ModelingToolkit"
 uuid = "961ee093-0014-501f-94e3-6117800e7a78"
 authors = ["Yingbo Ma <[email protected]>", "Chris Rackauckas <[email protected]> and contributors"]
-version = "9.0.0"
+version = "8.76.0"
 
 [deps]
 AbstractTrees = "1520ce14-60c1-5f80-bbc7-55ef81b5835c"
@@ -18,6 +18,7 @@ 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"
 FindFirstFunctions = "64ca27bc-2ba2-4a57-88aa-44e436879224"
 ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
 FunctionWrappersWrappers = "77dc65aa-8811-40c2-897b-53d922fa7daf"
@@ -31,14 +32,14 @@ Latexify = "23fbe1c1-3f47-55db-b15f-69d7ec21a316"
 Libdl = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 MLStyle = "d8e11817-5142-5d16-987a-aa16d5891078"
-MacroTools = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09"
 NaNMath = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3"
 OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
 PrecompileTools = "aea7be01-6a6a-4083-8856-8a6e6704d82a"
 RecursiveArrayTools = "731186ca-8d62-57ce-b412-fbd966d074cd"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 RuntimeGeneratedFunctions = "7e49a35a-f44a-4d26-94aa-eba1b4ca6b47"
 SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
+SciMLStructures = "53ae85a6-f571-4167-b2af-e1d143709226"
 Serialization = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
 Setfield = "efcf1570-3423-57d1-acb7-fd33fddbac46"
 SimpleNonlinearSolve = "727e6d20-b764-4bd8-a329-72de5adea6c7"
@@ -73,22 +74,22 @@ DiffRules = "0.1, 1.0"
 Distributed = "1"
 Distributions = "0.23, 0.24, 0.25"
 DocStringExtensions = "0.7, 0.8, 0.9"
-DomainSets = "0.6"
+DomainSets = "0.6, 0.7"
 DynamicQuantities = "^0.11.2"
+ExprTools = "0.1.10"
 FindFirstFunctions = "1"
 ForwardDiff = "0.10.3"
 FunctionWrappersWrappers = "0.1"
 Graphs = "1.5.2"
 IfElse = "0.1"
 InteractiveUtils = "1"
-JuliaFormatter = "1"
+JuliaFormatter = "1.0.47"
 JumpProcesses = "9.1"
 LabelledArrays = "1.3"
 Latexify = "0.11, 0.12, 0.13, 0.14, 0.15, 0.16"
 Libdl = "1"
 LinearAlgebra = "1"
 MLStyle = "0.4.17"
-MacroTools = "0.5"
 NaNMath = "0.3, 1"
 OrdinaryDiffEq = "6"
 PrecompileTools = "1"
@@ -99,6 +100,7 @@ SciMLBase = "2.0.1"
 Serialization = "1"
 Setfield = "0.7, 0.8, 1"
 SimpleNonlinearSolve = "0.1.0, 1"
+SciMLStructures = "1.0"
 SparseArrays = "1"
 SpecialFunctions = "0.7, 0.8, 0.9, 0.10, 1.0, 2"
 StaticArrays = "0.10, 0.11, 0.12, 1.0"

Project.toml

@@ -16,7 +16,7 @@ mathengine = MathJax3(Dict(:loader => Dict("load" => ["[tex]/require", "[tex]/ma
             "ams",
             "autoload",
             "mathtools",
-            "require",
+            "require"
         ])))
 
 makedocs(sitename = "ModelingToolkit.jl",

docs/make.jl

@@ -10,7 +10,8 @@ pages = [
         "tutorials/parameter_identifiability.md",
         "tutorials/bifurcation_diagram_computation.md",
         "tutorials/domain_connections.md"],
-    "Examples" => Any["Basic Examples" => Any["examples/higher_order.md",
+    "Examples" => Any[
+        "Basic Examples" => Any["examples/higher_order.md",
             "examples/spring_mass.md",
             "examples/modelingtoolkitize_index_reduction.md",
             "examples/parsing.md"],
@@ -32,8 +33,7 @@ pages = [
         "systems/JumpSystem.md",
         "systems/NonlinearSystem.md",
         "systems/OptimizationSystem.md",
-        "systems/DiscreteSystem.md",
         "systems/PDESystem.md"],
     "comparison.md",
-    "internals.md",
+    "internals.md"
 ]