Merge branch 'master' into symbolics_fixes

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

.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"

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

@@ -41,6 +41,7 @@ BifurcationKit = "0.3"
 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"
@@ -58,7 +59,7 @@ StructuralIdentifiability = "0.5.1"
 SymbolicUtils = "1.0.3"
 Symbolics = "5.27"
 Unitful = "1.12.4"
-julia = "1.9"
+julia = "1.10"
 
 [extras]
 BifurcationKit = "0f109fa4-8a5d-4b75-95aa-f515264e7665"

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 = "9.15"
+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 = "0.5.7"
+Symbolics = "5.28"

docs/pages.jl

@@ -1,38 +1,37 @@
 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"
+        # "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/programmatic_CRN_construction.md",
         "model_creation/compositional_modeling.md",
-        "model_creation/constraint_equations.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 visualisation.
-        "model_creation/network_analysis.md",
+        "model_creation/model_visualisation.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",
-        # 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
@@ -51,7 +50,7 @@ pages = Any[
         # ODE parameter fitting using Turing.
         # SDE/Jump fitting.
         "inverse_problems/behaviour_optimisation.md",
-        "inverse_problems/structural_identifiability.md",
+        "inverse_problems/structural_identifiability.md", # Broken on Julia v1.10.3, requires v1.10.2 or 1.10.4.
         # Practical identifiability.
         "inverse_problems/global_sensitivity_analysis.md",
         "Inverse problem examples" => Any[
@@ -69,4 +68,4 @@ pages = Any[
     # ],
     "FAQs" => "faqs.md",
     "API" => "api.md"
-]
+]

docs/src/api.md

@@ -35,37 +35,41 @@ corresponding chemical reaction ODE models, chemical Langevin equation SDE
 models, and stochastic chemical kinetics jump process models.
 
 ```@example ex1
-using Catalyst, DifferentialEquations, Plots
+using Catalyst, OrdinaryDiffEq, StochasticDiffEq, JumpProcesses, Plots
 t = default_t()
 @parameters β γ
 @species S(t) I(t) R(t)
 
 rxs = [Reaction(β, [S,I], [I], [1,1], [2])
        Reaction(γ, [I], [R])]
 @named rs = ReactionSystem(rxs, t)
+rs = complete(rs)
 
 u₀map    = [S => 999.0, I => 1.0, R => 0.0]
 parammap = [β => 1/10000, γ => 0.01]
 tspan    = (0.0, 250.0)
 
 # solve as ODEs
 odesys = convert(ODESystem, rs)
+odesys = complete(odesys)
 oprob = ODEProblem(odesys, u₀map, tspan, parammap)
 sol = solve(oprob, Tsit5())
 p1 = plot(sol, title = "ODE")
 
 # solve as SDEs
 sdesys = convert(SDESystem, rs)
+sdesys = complete(sdesys)
 sprob = SDEProblem(sdesys, u₀map, tspan, parammap)
-sol = solve(sprob, EM(), dt=.01)
+sol = solve(sprob, EM(), dt=.01, saveat = 2.0)
 p2 = plot(sol, title = "SDE")
 
 # solve as jump process
 jumpsys = convert(JumpSystem, rs)
+jumpsys = complete(jumpsys)
 u₀map    = [S => 999, I => 1, R => 0]
 dprob = DiscreteProblem(jumpsys, u₀map, tspan, parammap)
-jprob = JumpProblem(jumpsys, dprob, Direct())
-sol = solve(jprob, SSAStepper())
+jprob = JumpProblem(jumpsys, dprob, Direct(); save_positions = (false,false))
+sol = solve(jprob, SSAStepper(), saveat = 2.0)
 p3 = plot(sol, title = "jump")
 
 plot(p1, p2, p3; layout = (3,1))
@@ -152,16 +156,13 @@ accessor functions.
 ```@docs
 species
 nonspecies
-reactionsystemparams
 reactions
 nonreactions
 numspecies
 numparams
 numreactions
-numreactionsystemparams
 speciesmap
 paramsmap
-reactionsystemparamsmap
 isspecies
 isautonomous
 Catalyst.isconstant

docs/src/assets/Project.toml

@@ -1,18 +1,26 @@
 [deps]
+BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
 BifurcationKit = "0f109fa4-8a5d-4b75-95aa-f515264e7665"
+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"
+GlobalSensitivity = "af5da776-676b-467e-8baf-acd8249e4f0f"
 HomotopyContinuation = "f213a82b-91d6-5c5d-acf7-10f1c761b327"
+IncompleteLU = "40713840-3770-5561-ab4c-a76e7d0d7895"
+JumpProcesses = "ccbc3e58-028d-4f4c-8cd5-9ae44345cda5"
 Latexify = "23fbe1c1-3f47-55db-b15f-69d7ec21a316"
+LinearSolve = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae"
 Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
 ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"
 NonlinearSolve = "8913a72c-1f9b-4ce2-8d82-65094dcecaec"
 Optim = "429524aa-4258-5aef-a3af-852621145aeb"
 Optimization = "7f7a1694-90dd-40f0-9382-eb1efda571ba"
+OptimizationBBO = "3e6eede4-6085-4f62-9a71-46d9bc1eb92b"
 OptimizationNLopt = "4e6fcdb7-1186-4e1f-a706-475e75c168bb"
 OptimizationOptimJL = "36348300-93cb-4f02-beb5-3c3902f8871e"
 OptimizationOptimisers = "42dfb2eb-d2b4-4451-abcd-913932933ac1"
@@ -21,37 +29,45 @@ 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 = "1.5"
 BifurcationKit = "0.3"
+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"
-HomotopyContinuation = "2.6"
-Latexify = "0.15, 0.16"
-ModelingToolkit = "9.5"
-NonlinearSolve = "3.4.0"
-Optim = "1"
-Optimization = "3.19"
-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"
+DynamicalSystems = "3.3"
+GlobalSensitivity = "2.6"
+HomotopyContinuation = "2.9"
+IncompleteLU = "0.2"
+JumpProcesses = "9.11"
+Latexify = "0.16"
+LinearSolve = "2.30"
+ModelingToolkit = "9.15"
+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 = "0.5.7"
+Symbolics = "5.28"