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"
 ]

docs/pages.jl

@@ -22,7 +22,7 @@ Generally, it follows the order of:
 
  1. Equations
  2. Independent Variables
- 3. Dependent Variables (or States)
+ 3. Dependent Variables (or Unknowns)
  4. Parameters
 
 All other pieces are handled via keyword arguments. `AbstractSystem`s share the
@@ -37,19 +37,19 @@ same keyword arguments, which are:
 ## Composition and Accessor Functions
 
 Each `AbstractSystem` has lists of variables in context, such as distinguishing
-parameters vs states. In addition, an `AbstractSystem` can also hold other
-`AbstractSystem` types. Direct accessing of the values, such as `sys.states`,
-gives the immediate list, while the accessor functions `states(sys)` gives the
+parameters vs unknowns. In addition, an `AbstractSystem` can also hold other
+`AbstractSystem` types. Direct accessing of the values, such as `sys.unknowns`,
+gives the immediate list, while the accessor functions `unknowns(sys)` gives the
 total set, which includes that of all systems held inside.
 
 The values which are common to all `AbstractSystem`s are:
 
   - `equations(sys)`: All equations that define the system and its subsystems.
-  - `states(sys)`: All the states in the system and its subsystems.
+  - `unknowns(sys)`: All the unknowns in the system and its subsystems.
   - `parameters(sys)`: All parameters of the system and its subsystems.
   - `nameof(sys)`: The name of the current-level system.
   - `get_eqs(sys)`: Equations that define the current-level system.
-  - `get_states(sys)`: States that are in the current-level system.
+  - `get_unknowns(sys)`: Unknowns that are in the current-level system.
   - `get_ps(sys)`: Parameters that are in the current-level system.
   - `get_systems(sys)`: Subsystems of the current-level system.
 
@@ -129,7 +129,7 @@ pairs `var=>value`, which allows the user to designate the values without having
 to know the order that ModelingToolkit is internally using.
 
 For the value maps, the parameters are allowed to be functions of each other,
-and value maps of states can be functions of the parameters, i.e. you can do:
+and value maps of unknowns can be functions of the parameters, i.e. you can do:
 
 ```
 u0 = [