Merge branch 'master' into dsl_file_improvements

Author: TorkelE

.github/workflows/CI.yml

@@ -14,7 +14,7 @@ jobs:
         group:
           - Core
         version:
-          - '1.10.2'
+          - '1'
     steps:
       - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@v2
@@ -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/FormatCheck.yml

@@ -1,4 +1,4 @@
-name: format-check
+name: "Format Check"
 
 on:
   push:
@@ -9,34 +9,6 @@ on:
   pull_request:
 
 jobs:
-  build:
-    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", version="1.0.32"))'
-          julia  -e 'using JuliaFormatter; format(".", verbose=true)'
-      - name: Format check
-        run: |
-          julia -e '
-          out = Cmd(`git diff --name-only`) |> read |> String
-          if out == ""
-              exit(0)
-          else
-              @error "Some files have not been formatted !!!"
-              write(stdout, out)
-              exit(1)
-          end'
+  format-check:
+    name: "Format Check"
+    uses: "SciML/.github/.github/workflows/format-check.yml@v1"

.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"

HISTORY.md

@@ -24,7 +24,7 @@ rn = @reaction_network begin
     @parameters η
     k, 2X --> X2, [noise_scaling=η]
 end
-get_noise_scaling(rn)
+getnoisescaling(rn)
 ```
 - `SDEProblem` no longer takes the `noise_scaling` argument (see above for new approach to handle noise scaling).
 - Changed fields of internal `Reaction` structure. `ReactionSystems`s saved using `serialize` on previous Catalyst versions cannot be loaded using this (or later) versions.

Project.toml

@@ -3,6 +3,7 @@ uuid = "479239e8-5488-4da2-87a7-35f2df7eef83"
 version = "13.5.1"
 
 [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"
 
@@ -37,27 +37,28 @@ CatalystStructuralIdentifiabilityExtension = "StructuralIdentifiability"
 
 [compat]
 BifurcationKit = "0.3"
+Combinatorics = "1.0.2"
 DataStructures = "0.18"
 DiffEqBase = "6.83.0"
 DocStringExtensions = "0.8, 0.9"
+DynamicPolynomials = "0.5"
 DynamicQuantities = "0.13.2"
 Graphs = "1.4"
 HomotopyContinuation = "2.9"
 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 = "1.9"
+julia = "1.10"
 
 [extras]
 BifurcationKit = "0f109fa4-8a5d-4b75-95aa-f515264e7665"
@@ -66,6 +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"
@@ -82,4 +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

@@ -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"
@@ -29,45 +28,45 @@ Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 QuasiMonteCarlo = "8a4e6c94-4038-4cdc-81c3-7e6ffdb2a71b"
 SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
 SciMLSensitivity = "1ed8b502-d754-442c-8d5d-10ac956f44a1"
-Setfield = "efcf1570-3423-57d1-acb7-fd33fddbac46"
 SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
+StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
 SteadyStateDiffEq = "9672c7b4-1e72-59bd-8a11-6ac3964bc41f"
 StochasticDiffEq = "789caeaf-c7a9-5a7d-9973-96adeb23e2a0"
 StructuralIdentifiability = "220ca800-aa68-49bb-acd8-6037fa93a544"
 Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7"
 
 [compat]
-BenchmarkTools = "1"
-BifurcationKit = "0.3"
+BenchmarkTools = "1.5"
+BifurcationKit = "0.3.4"
 CairoMakie = "0.12"
 Catalyst = "13"
-DataFrames = "1"
-DiffEqParamEstim = "2.1"
-DifferentialEquations = "7.7"
+DataFrames = "1.6"
+DiffEqParamEstim = "2.2"
 Distributions = "0.25"
 Documenter = "1.4.1"
-DynamicalSystems = "3"
-GlobalSensitivity = "2.4.0"
-HomotopyContinuation = "2.6"
+DynamicalSystems = "3.3"
+GlobalSensitivity = "2.6"
+HomotopyContinuation = "2.9"
 IncompleteLU = "0.2"
-JumpProcesses = "9"
-Latexify = "0.15, 0.16"
-LinearSolve = "2"
-ModelingToolkit = "9.5"
-NonlinearSolve = "3.4.0"
-Optim = "1"
-Optimization = "3.19"
-OptimizationBBO = "0.1.5, 0.2"
-OptimizationNLopt = "0.1.8"
-OptimizationOptimJL = "0.1.14"
-OptimizationOptimisers = "0.1.1"
-OrdinaryDiffEq = "6"
-Plots = "1.36"
-SciMLBase = "2.13"
-SciMLSensitivity = "7.19"
-Setfield = "1.1"
-SpecialFunctions = "2.1"
-SteadyStateDiffEq = "2.0.1"
-StochasticDiffEq = "6"
-StructuralIdentifiability = "0.5.1"
-Symbolics = "5.14"
+JumpProcesses = "9.11"
+Latexify = "0.16"
+LinearSolve = "2.30"
+ModelingToolkit = "9.16.0"
+NonlinearSolve = "3.12"
+Optim = "1.9"
+Optimization = "3.25"
+OptimizationBBO = "0.2.1"
+OptimizationNLopt = "0.2.1"
+OptimizationOptimJL = "0.3.1"
+OptimizationOptimisers = "0.2.1"
+OrdinaryDiffEq = "6.80.1"
+Plots = "1.40"
+QuasiMonteCarlo = "0.3"
+SciMLBase = "2.39"
+SciMLSensitivity = "7.60"
+SpecialFunctions = "2.4"
+StaticArrays = "1.9"
+SteadyStateDiffEq = "2.2"
+StochasticDiffEq = "6.65"
+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

@@ -1,20 +1,18 @@
 pages = Any[
-    "Home" => "home.md",
+    "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.
     ],
     "Model Creation and Properties" => Any[
         "model_creation/dsl_basics.md",
         "model_creation/dsl_advanced.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.
-        # Loading and writing models to files.
-        # Model visualisation.
+        "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/chemistry_related_functionality.md",
         "Model creation examples" => Any[
@@ -26,47 +24,28 @@ pages = Any[
     ],
     "Model simulation" => Any[
         "model_simulation/simulation_introduction.md",
-        # Simulation introduction.
         "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",
-        # ODE Performance considerations/advice.
-        # 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",
-        # Practical identifiability.
         "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"
-]
+]