Merge branch 'master' into spatial___internal_restructure

Author: TorkelE

.github/workflows/CI.yml

@@ -37,7 +37,7 @@ jobs:
         with:
           file: lcov.info
           token: ${{ secrets.CODECOV_TOKEN }}
-          fail_ci_if_error: true
+          fail_ci_if_error: false
       - uses: coverallsapp/github-action@master
         with:
           github-token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/Documentation.yml

@@ -28,4 +28,4 @@ jobs:
         with:
           file: lcov.info
           token: ${{ secrets.CODECOV_TOKEN }}
-          fail_ci_if_error: true
+          fail_ci_if_error: false

.github/workflows/Invalidations.yml

@@ -4,37 +4,10 @@ on:
   pull_request:
 
 concurrency:
-  # Skip intermediate builds: always.
-  # Cancel intermediate builds: always.
   group: ${{ github.workflow }}-${{ github.ref }}
   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@v2
-      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"

Project.toml

@@ -1,8 +1,9 @@
 name = "Catalyst"
 uuid = "479239e8-5488-4da2-87a7-35f2df7eef83"
-version = "13.5.1"
+version = "14.0.0-DEV"
 
 [deps]
+Combinatorics = "861a8166-3701-5b0c-9a16-15d98fcdc6aa"
 DataStructures = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
 DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e"
 DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
@@ -21,7 +22,6 @@ Requires = "ae029012-a4dd-5104-9daa-d747884805df"
 RuntimeGeneratedFunctions = "7e49a35a-f44a-4d26-94aa-eba1b4ca6b47"
 Setfield = "efcf1570-3423-57d1-acb7-fd33fddbac46"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
-SymbolicUtils = "d1185830-fcd6-423d-90d6-eec64667417b"
 Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7"
 Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 
@@ -37,6 +37,7 @@ CatalystStructuralIdentifiabilityExtension = "StructuralIdentifiability"
 
 [compat]
 BifurcationKit = "0.3"
+Combinatorics = "1.0.2"
 DataStructures = "0.18"
 DiffEqBase = "6.83.0"
 DocStringExtensions = "0.8, 0.9"
@@ -48,15 +49,14 @@ JumpProcesses = "9.3.2"
 LaTeXStrings = "1.3.0"
 Latexify = "0.14, 0.15, 0.16"
 MacroTools = "0.5.5"
-ModelingToolkit = "9.11.0"
+ModelingToolkit = "9.16.0"
 Parameters = "0.12"
 Reexport = "0.2, 1.0"
 Requires = "1.0"
 RuntimeGeneratedFunctions = "0.5.12"
 Setfield = "1"
-StructuralIdentifiability = "0.5.1"
-SymbolicUtils = "1.0.3"
-Symbolics = "5.27"
+StructuralIdentifiability = "0.5.8"
+Symbolics = "5.30.1"
 Unitful = "1.12.4"
 julia = "1.10"
 
@@ -67,6 +67,7 @@ DomainSets = "5b8099bc-c8ec-5219-889f-1d9e522a28bf"
 Graphviz_jll = "3c863552-8265-54e4-a6dc-903eb78fde85"
 HomotopyContinuation = "f213a82b-91d6-5c5d-acf7-10f1c761b327"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
 NonlinearSolve = "8913a72c-1f9b-4ce2-8d82-65094dcecaec"
 OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
@@ -83,4 +84,4 @@ Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 
 [targets]
-test = ["BifurcationKit", "DiffEqCallbacks", "DomainSets", "Graphviz_jll", "HomotopyContinuation", "NonlinearSolve", "OrdinaryDiffEq", "Plots", "Random", "SafeTestsets", "SciMLBase", "SciMLNLSolve", "StableRNGs", "Statistics", "SteadyStateDiffEq", "StochasticDiffEq", "StructuralIdentifiability", "Test", "Unitful"]
+test = ["BifurcationKit", "DiffEqCallbacks", "DomainSets", "Graphviz_jll", "HomotopyContinuation", "Logging", "NonlinearSolve", "OrdinaryDiffEq", "Plots", "Random", "SafeTestsets", "SciMLBase", "SciMLNLSolve", "StableRNGs", "Statistics", "SteadyStateDiffEq", "StochasticDiffEq", "StructuralIdentifiability", "Test", "Unitful"]

docs/Project.toml

@@ -51,7 +51,7 @@ IncompleteLU = "0.2"
 JumpProcesses = "9.11"
 Latexify = "0.16"
 LinearSolve = "2.30"
-ModelingToolkit = "9.15"
+ModelingToolkit = "9.16.0"
 NonlinearSolve = "3.12"
 Optim = "1.9"
 Optimization = "3.25"
@@ -68,5 +68,5 @@ SpecialFunctions = "2.4"
 StaticArrays = "1.9"
 SteadyStateDiffEq = "2.2"
 StochasticDiffEq = "6.65"
-StructuralIdentifiability = "0.5.7"
-Symbolics = "5.28"
+StructuralIdentifiability = "0.5.8"
+Symbolics = "5.30.1"

docs/make.jl

@@ -31,17 +31,17 @@ include("pages.jl")
 #          pages = pages)
 
 makedocs(sitename = "Catalyst.jl",
-         authors = "Samuel Isaacson",
-         format = Documenter.HTML(; analytics = "UA-90474609-3",
-                                  prettyurls = (get(ENV, "CI", nothing) == "true"),
-                                  assets = ["assets/favicon.ico"],
-                                  canonical = "https://docs.sciml.ai/Catalyst/stable/"),
-         modules = [Catalyst, ModelingToolkit],
-         doctest = false,
-         clean = true,
-         pages = pages,
-         pagesonly = true,
-         warnonly = true)
+    authors = "Samuel Isaacson",
+    format = Documenter.HTML(; analytics = "UA-90474609-3",
+        prettyurls = (get(ENV, "CI", nothing) == "true"),
+        assets = ["assets/favicon.ico"],
+        canonical = "https://docs.sciml.ai/Catalyst/stable/"),
+    modules = [Catalyst, ModelingToolkit],
+    doctest = false,
+    clean = true,
+    pages = pages,
+    pagesonly = true,
+    warnonly = [:missing_docs])
 
 deploydocs(repo = "github.com/SciML/Catalyst.jl.git";
-           push_preview = true)
+    push_preview = true)

docs/pages.jl

@@ -2,70 +2,50 @@ pages = Any[
     "Home" => "index.md",
     "Introduction to Catalyst" => Any[
         "introduction_to_catalyst/catalyst_for_new_julia_users.md",
-        # "introduction_to_catalyst/introduction_to_catalyst.md"
-        # Advanced introduction.
+        "introduction_to_catalyst/introduction_to_catalyst.md"
     ],
     "Model Creation and Properties" => Any[
         "model_creation/dsl_basics.md",
         "model_creation/dsl_advanced.md",
-        #"model_creation/programmatic_CRN_construction.md",
+        "model_creation/programmatic_CRN_construction.md",
         "model_creation/compositional_modeling.md",
-        #"model_creation/constraint_equations.md",
-        # Events.
-        "model_creation/parametric_stoichiometry.md",# Distributed parameters, rates, and initial conditions.
-        "model_creation/model_file_loading_and_export.md",# Distributed parameters, rates, and initial conditions.
-        # Loading and writing models to files.
+        "model_creation/constraint_equations.md",
+        "model_creation/parametric_stoichiometry.md",
+        "model_creation/model_file_loading_and_export.md",
         "model_creation/model_visualisation.md",
-        #"model_creation/network_analysis.md",
+        "model_creation/network_analysis.md",
         "model_creation/chemistry_related_functionality.md",
         "Model creation examples" => Any[
             "model_creation/examples/basic_CRN_library.md",
             "model_creation/examples/programmatic_generative_linear_pathway.md",
             "model_creation/examples/hodgkin_huxley_equation.md",
-            #"model_creation/examples/smoluchowski_coagulation_equation.md"
+            "model_creation/examples/smoluchowski_coagulation_equation.md"
         ]
     ],
     "Model simulation" => Any[
         "model_simulation/simulation_introduction.md",
         "model_simulation/simulation_plotting.md",
         "model_simulation/simulation_structure_interfacing.md",
         "model_simulation/ensemble_simulations.md",
-        # Stochastic simulation statistical analysis.
-        "model_simulation/ode_simulation_performance.md",
-        # SDE Performance considerations/advice.
-        # Jump Performance considerations/advice.
-        # Finite state projection
+        "model_simulation/ode_simulation_performance.md"
     ],
     "Steady state analysis" => Any[
         "steady_state_functionality/homotopy_continuation.md",
         "steady_state_functionality/nonlinear_solve.md",
-        "steady_state_functionality/steady_state_stability_computation.md",        
+        "steady_state_functionality/steady_state_stability_computation.md",
         "steady_state_functionality/bifurcation_diagrams.md",
         "steady_state_functionality/dynamical_systems.md"
     ],
     "Inverse Problems" => Any[
-        # Inverse problems introduction.
         "inverse_problems/optimization_ode_param_fitting.md",
         # "inverse_problems/petab_ode_param_fitting.md",
-        # ODE parameter fitting using Turing.
-        # SDE/Jump fitting.
         "inverse_problems/behaviour_optimisation.md",
-        "inverse_problems/structural_identifiability.md", # Broken on Julia v1.10.3, requires v1.10.2 or 1.10.4.
-        # Practical identifiability.
+        "inverse_problems/structural_identifiability.md",
         "inverse_problems/global_sensitivity_analysis.md",
         "Inverse problem examples" => Any[
             "inverse_problems/examples/ode_fitting_oscillation.md"
         ]
     ],
-    "Spatial modelling" => Any[
-        # Intro.
-        # Lattice ODEs.
-        # Lattice Jumps.
-    ],
-    # "Developer Documentation" => Any[
-    #     # Contributor's guide.
-    #     # Repository structure.
-    # ],
     "FAQs" => "faqs.md",
     "API" => "api.md"
 ]

docs/src/api.md

@@ -272,6 +272,7 @@ hillar
 ```@docs
 Base.convert
 ModelingToolkit.structural_simplify
+set_default_noise_scaling
 ```
 
 ## Chemistry-related functionalities

docs/src/assets/Project.toml

@@ -5,7 +5,6 @@ CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
 Catalyst = "479239e8-5488-4da2-87a7-35f2df7eef83"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 DiffEqParamEstim = "1130ab10-4a5a-5621-a13d-e4788d82bd4c"
-DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 DynamicalSystems = "61744808-ddfa-5f27-97ff-6e42cc95d634"
@@ -38,7 +37,7 @@ Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7"
 
 [compat]
 BenchmarkTools = "1.5"
-BifurcationKit = "0.3"
+BifurcationKit = "0.3.4"
 CairoMakie = "0.12"
 Catalyst = "13"
 DataFrames = "1.6"
@@ -52,7 +51,7 @@ IncompleteLU = "0.2"
 JumpProcesses = "9.11"
 Latexify = "0.16"
 LinearSolve = "2.30"
-ModelingToolkit = "9.15"
+ModelingToolkit = "9.16.0"
 NonlinearSolve = "3.12"
 Optim = "1.9"
 Optimization = "3.25"
@@ -69,5 +68,5 @@ SpecialFunctions = "2.4"
 StaticArrays = "1.9"
 SteadyStateDiffEq = "2.2"
 StochasticDiffEq = "6.65"
-StructuralIdentifiability = "0.5.7"
-Symbolics = "5.28"
+StructuralIdentifiability = "0.5.8"
+Symbolics = "5.30.1"

docs/src/faqs.md

@@ -59,7 +59,7 @@ plot(sol; idxs = [A, B])
 ```
 
 ## How to disable rescaling of reaction rates in rate laws?
-As explained in the [Reaction rate laws used in simulations](@ref) section, for
+As explained in the [Reaction rate laws used in simulations](@ref introduction_to_catalyst_ratelaws) section, for
 a reaction such as `k, 2X --> 0`, the generated rate law will rescale the rate
 constant, giving `k*X^2/2` instead of `k*X^2` for ODEs and `k*X*(X-1)/2` instead
 of `k*X*(X-1)` for jumps. This can be disabled when directly `convert`ing a
@@ -96,7 +96,7 @@ Note, when using `convert(ODESystem, mixedsys; combinatoric_ratelaws=false)` the
 calling `ODEProblem(mixedsys,...; combinatoric_ratelaws=false)`. As described
 above, this disables Catalyst's standard rescaling of reaction rates when
 generating reaction rate laws, see also the [Reaction rate laws used in
-simulations](@ref) section. Leaving this keyword out for systems with floating
+simulations](@ref introduction_to_catalyst_ratelaws) section. Leaving this keyword out for systems with floating
 point stoichiometry will give an error message.
 
 For a more extensive documentation of using non-integer stoichiometric
@@ -105,7 +105,7 @@ parametric_stoichiometry) section.
 
 ## How to set default values for initial conditions and parameters?
 How to set defaults when using the `@reaction_network` macro is described in
-more detail [here](@ref dsl_description_defaults). There are several ways to do
+more detail [here](@ref dsl_advanced_options_default_vals). There are several ways to do
 this. Using the DSL, one can use the `@species` and `@parameters` options:
 ```@example faq3
 using Catalyst