Merge branch 'master' into discretedocs

Author: baggepinnen

.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

@@ -28,8 +28,11 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # For authentication with GitHub Actions token
           DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # For authentication with SSH deploy key
+          JULIA_DEBUG: "Documenter"
         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@v1.16.25 
+        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
@@ -27,14 +60,16 @@ jobs:
           - InterfaceI
           - InterfaceII
           - Extensions
+          - Downstream
+          - RegressionI
         version:
           - '1'
     steps:
       - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@v1
         with:
           version: ${{ matrix.version }}
-      - uses: actions/cache@v3
+      - uses: actions/cache@v4
         env:
           cache-name: cache-artifacts
         with:
@@ -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

@@ -3,4 +3,5 @@ nin = "nin"
 nd = "nd"
 Strat = "Strat"
 eles = "eles"
-ser = "ser"
+ser = "ser"
+isconnection = "isconnection"

.typos.toml

@@ -1,9 +1,60 @@
-# 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. Use `ODESystem(eqs,t)` instead.
+  - 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.
+    Parameters that have a default value depending on other parameters are now treated as dependent
+    parameters. Their value cannot be modified directly. Whenever a parameter value is changed, dependent
+    parameter values are recalculated. For example, if `@parameters p1 p2 = 3p1` then `p2` can not be
+    modified directly. If `p1` is changed, then `p2` will be updated accordingly. 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)`.
+  - Parameter dependencies are now supported. They can be specified using the syntax
+    `(single_parameter => expression_involving_other_parameters)` and a `Vector` of these can be passed to
+    the `parameter_dependencies` keyword argument of `ODESystem`, `SDESystem` and `JumpSystem`. The dependent
+    parameters are updated whenever other parameters are modified, e.g. in callbacks.
+  - Support for `IfElse.jl` has been dropped. `Base.ifelse` can be used instead.
+  - DAE initialization and the solving for consistent initial conditions has been changed to use a customized
+    initialization solve. This change adds `guess` semantics which are clearly delinated from the behavior of
+    the defaults, where `default` (and `u0`) is designed to be always satisfied and error if unsatisfiable,
+    while `guess` is an initial guess to the initializer. In previous iterations, initialization with the
+    default (`BrownBasicInit`) would treat the initial condition to the algebraic variables as a `guess`,
+    and with `ShampineCollocationInit` would treat all initial conditions as a `guess`. To return to the
+    previous behavior, use the keyword argument `initializealg` in the solve, i.e.
+    `solve(prob;initializealg = BrownBasicInit())`.

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 = "8.75.0"
+version = "9.3.0"
 
 [deps]
 AbstractTrees = "1520ce14-60c1-5f80-bbc7-55ef81b5835c"
@@ -17,10 +17,12 @@ 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"
+FindFirstFunctions = "64ca27bc-2ba2-4a57-88aa-44e436879224"
 ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
 FunctionWrappersWrappers = "77dc65aa-8811-40c2-897b-53d922fa7daf"
 Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
-IfElse = "615f187c-cbe4-4ef1-ba3b-2fcf58d6d173"
 InteractiveUtils = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
 JuliaFormatter = "98e50ef6-434e-11e9-1051-2b60c6c9e899"
 JumpProcesses = "ccbc3e58-028d-4f4c-8cd5-9ae44345cda5"
@@ -29,14 +31,14 @@ 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"
@@ -66,32 +68,34 @@ Compat = "3.42, 4"
 ConstructionBase = "1"
 DataStructures = "0.17, 0.18"
 DiffEqBase = "6.103.0"
-DiffEqCallbacks = "2.16"
+DiffEqCallbacks = "2.16, 3"
 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, 0.12"
+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"
+OrdinaryDiffEq = "6.73.0"
 PrecompileTools = "1"
 RecursiveArrayTools = "2.3, 3"
 Reexport = "0.2, 1"
 RuntimeGeneratedFunctions = "0.5.9"
-SciMLBase = "2.0.1"
+SciMLBase = "2.28.0"
+SciMLStructures = "1.0"
 Serialization = "1"
 Setfield = "0.7, 0.8, 1"
 SimpleNonlinearSolve = "0.1.0, 1"
@@ -100,7 +104,7 @@ SpecialFunctions = "0.7, 0.8, 0.9, 0.10, 1.0, 2"
 StaticArrays = "0.10, 0.11, 0.12, 1.0"
 SymbolicIndexingInterface = "0.3.1"
 SymbolicUtils = "1.0"
-Symbolics = "5.7"
+Symbolics = "5.20.1"
 URIs = "1"
 UnPack = "0.1, 1.0"
 Unitful = "1.1"
@@ -109,7 +113,7 @@ julia = "1.9"
 [extras]
 AmplNLWriter = "7c4d4715-977e-5154-bfe0-e096adeac482"
 BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
-ControlSystemsMTK = "687d7614-c7e5-45fc-bfc3-9ee385575c88"
+ControlSystemsBase = "aaaaaaaa-a6ca-5380-bf3e-84a91bcd477e"
 DeepDiffs = "ab62b9b5-e342-54a8-a765-a90f495de1a6"
 ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
 Ipopt = "b6b21f68-93f8-5de0-b562-5493be1d77c9"
@@ -132,4 +136,4 @@ Sundials = "c3572dad-4567-51f8-b174-8c6c989267f4"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["AmplNLWriter", "BenchmarkTools", "ControlSystemsMTK", "NonlinearSolve", "ForwardDiff", "Ipopt", "Ipopt_jll", "ModelingToolkitStandardLibrary", "Optimization", "OptimizationOptimJL", "OptimizationMOI", "Random", "ReferenceTests", "SafeTestsets", "StableRNGs", "Statistics", "SteadyStateDiffEq", "Test", "StochasticDiffEq", "Sundials", "StochasticDelayDiffEq", "Pkg"]
+test = ["AmplNLWriter", "BenchmarkTools", "ControlSystemsBase", "NonlinearSolve", "ForwardDiff", "Ipopt", "Ipopt_jll", "ModelingToolkitStandardLibrary", "Optimization", "OptimizationOptimJL", "OptimizationMOI", "Random", "ReferenceTests", "SafeTestsets", "StableRNGs", "Statistics", "SteadyStateDiffEq", "Test", "StochasticDiffEq", "Sundials", "StochasticDelayDiffEq", "Pkg"]