Merge branch 'master' into change_equation_inference

Author: TorkelE

.github/workflows/DocsCleanup.yml

@@ -0,0 +1,33 @@
+name: Doc Preview Cleanup
+
+on:
+  pull_request:
+    types: [closed]
+
+# Ensure that only one "Doc Preview Cleanup" workflow is force pushing at a time
+concurrency:
+  group: doc-preview-cleanup
+  cancel-in-progress: false
+
+jobs:
+  doc-preview-cleanup:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    steps:
+      - name: Checkout gh-pages branch
+        uses: actions/checkout@v4
+        with:
+          ref: gh-pages
+      - name: Delete preview and history + push changes
+        run: |
+          if [ -d "${preview_dir}" ]; then
+              git config user.name "Documenter.jl"
+              git config user.email "[email protected]"
+              git rm -rf "${preview_dir}"
+              git commit -m "delete preview"
+              git branch gh-pages-new $(echo "delete history" | git commit-tree HEAD^{tree})
+              git push --force origin gh-pages-new:gh-pages
+          fi
+        env:
+          preview_dir: previews/PR${{ github.event.number }}

.github/workflows/Documentation.yml

@@ -12,8 +12,8 @@ permissions:
   contents: read
 
 concurrency:
-  group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
-  cancel-in-progress: true
+  group: docs-${{ github.ref }} # Group name for concurrency control
+  cancel-in-progress: true # Ensures only one doc build runs at a time for each branch/ref, regardless of the trigger
 
 jobs:
   build:
@@ -22,11 +22,21 @@ jobs:
       - name: Checkout
         uses: actions/checkout@v4
 
-      # Install binary dependencies needed for GLMakie to run in a headless environment
-      # xvfb: Creates a virtual frame buffer to simulate a display
-      # libgl1, mesa-utils, freeglut3-dev, xorg-dev, libxrandr-dev, libxinerama-dev, libxcursor-dev, libxi-dev, libxext-dev: Required libraries for OpenGL rendering
-      - name: Install binary dependencies
-        run: sudo apt-get update && sudo apt-get install -y xvfb libgl1 mesa-utils freeglut3-dev xorg-dev libxrandr-dev libxinerama-dev libxcursor-dev libxi-dev libxext-dev
+      # # Install all required X11 and OpenGL libraries
+      # # These are needed for GLMakie to work in a headless environment
+      # - name: Install binary dependencies
+      #   run: |
+      #     sudo apt-get update
+      #     sudo apt-get install -y xvfb libgl1 mesa-utils freeglut3-dev xorg-dev \
+      #       libxrandr-dev libxinerama-dev libxcursor-dev libxi-dev libxext-dev
+
+      # # Start Xvfb explicitly instead of using xvfb-run
+      # # This gives us more control and visibility into the virtual display setup
+      # - name: Setup virtual framebuffer
+      #   run: |
+      #     # Start Xvfb and wait for it to be ready
+      #     /usr/bin/Xvfb :99 -screen 0 1024x768x24
+      #     echo "DISPLAY=:99" >> $GITHUB_ENV
 
       - name: Install Julia
         uses: julia-actions/setup-julia@latest
@@ -38,22 +48,22 @@ jobs:
         with:
           cache-name: docs-cache
 
-      # Install Julia package dependencies for the documentation project
+      # Install dependencies with the virtual display already running
       - name: Install dependencies
-        run: >
-          DISPLAY=:0 xvfb-run -s '-screen 0 1024x768x24' julia --project=docs/ -e 'ENV["JULIA_PKG_SERVER"] = ""; using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
+        run: |
+          julia --project=docs/ -e '
+            ENV["JULIA_PKG_SERVER"] = "";
+            using Pkg;
+            Pkg.develop(PackageSpec(path=pwd()));
+            Pkg.instantiate()'
 
-      # Build and deploy the documentation using xvfb to simulate a display for GLMakie
-      # xvfb-run: Runs Julia with a virtual display to support OpenGL rendering
-      # --server-args: Configures the virtual display resolution and color depth
+      # Build documentation with the stable virtual display
       - name: Build and deploy
         env:
-          GKSwstype: "100" # Specifies the workstation type for GR framework rendering, https://discourse.julialang.org/t/generation-of-documentation-fails-qt-qpa-xcb-could-not-connect-to-display/60988/7
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # Required for permissions to deploy documentation
-          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # For authentication with SSH deploy key
-        run: >
-          DISPLAY=:0 xvfb-run -s '-screen 0 1024x768x24' 
-          julia --project=docs --color=yes --code-coverage=user docs/make.jl
+          GKSwstype: "100"
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}
+        run: xvfb-run julia --project=docs --color=yes --code-coverage=user docs/make.jl
 
       - name: Upload site as artifact
         uses: actions/upload-artifact@v4
@@ -66,9 +76,8 @@ jobs:
 
       - uses: julia-actions/julia-processcoverage@v1
 
-      - uses: codecov/codecov-action@v4
+      - uses: codecov/codecov-action@v5
         with:
-          file: lcov.info
+          files: lcov.info
           token: ${{ secrets.CODECOV_TOKEN }}
           fail_ci_if_error: false
-

HISTORY.md

@@ -25,7 +25,34 @@
   StructuralIdentifiability has with Julia 1.10.5 and 1.11.
 - A tutorial on making interactive plot displays using Makie has been added.
 - The BifurcationKit extension has been updated to v.4.
-
+- There is a new DSL option `@require_declaration` that will turn off automatic inferring for species, parameters, and variables in the DSL. For example, the following will now error:
+  ```julia
+  rn = @reaction_network begin
+    @require_declaration
+    (k1, k2), A <--> B
+  end
+  ```
+  When this flag is set, all symbolics must be explicitly declared. 
+  ```julia
+  rn = @reaction_network begin
+    @species A(t) B(t)
+    @parameters k1 k2
+    @require_declaration
+    (k1, k2), A <--> B
+  end
+  ```
+- Catalyst's network visualization capability has shifted from using Graphviz to [GraphMakie.jl](https://graph.makie.org/stable/). To use this functionality, load the GraphMakie extension by installing `Catalyst` and `GraphMakie`, along with a Makie backend like `GLMakie`. There are two new methods for visualizing graphs: `plot_network` and `plot_complexes`, which respectively display the species-reaction graph and complex graph.
+  ```julia
+  using Catalyst, GraphMakie, GLMakie
+  brusselator = @reaction_network begin
+     A, ∅ --> X
+     1, 2X + Y --> 3X
+     B, X --> Y
+     1, X --> ∅
+  end
+  plot_network(brusselator)
+  ```
+ 
 ## Catalyst 14.4.1
 - Support for user-defined functions on the RHS when providing coupled equations 
   for CRNs using the @equations macro. For example, the following now works: 

Project.toml

@@ -32,12 +32,13 @@ BifurcationKit = "0f109fa4-8a5d-4b75-95aa-f515264e7665"
 CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
 GraphMakie = "1ecd5474-83a3-4783-bb4f-06765db800d2"
 HomotopyContinuation = "f213a82b-91d6-5c5d-acf7-10f1c761b327"
+NetworkLayout = "46757867-2c16-5918-afeb-47bfcb05e46a"
 # StructuralIdentifiability = "220ca800-aa68-49bb-acd8-6037fa93a544"
 
 [extensions]
 CatalystBifurcationKitExtension = "BifurcationKit"
 CatalystCairoMakieExtension = "CairoMakie"
-CatalystGraphMakieExtension = "GraphMakie"
+CatalystGraphMakieExtension = ["GraphMakie", "NetworkLayout"]
 CatalystHomotopyContinuationExtension = "HomotopyContinuation"
 # CatalystStructuralIdentifiabilityExtension = "StructuralIdentifiability"
 
@@ -46,7 +47,7 @@ BifurcationKit = "0.4.4"
 CairoMakie = "0.12"
 Combinatorics = "1.0.2"
 DataStructures = "0.18"
-DiffEqBase = "< 6.159.0"
+DiffEqBase = "6.159.0"
 DocStringExtensions = "0.8, 0.9"
 DynamicPolynomials = "0.5, 0.6"
 DynamicQuantities = "0.13.2, 1"
@@ -57,27 +58,31 @@ JumpProcesses = "9.13.2"
 LaTeXStrings = "1.3.0"
 Latexify = "0.16.5"
 MacroTools = "0.5.5"
-ModelingToolkit = "9.32"
+ModelingToolkit = "< 9.60"
+NetworkLayout = "0.4.7"
 Parameters = "0.12"
 Reexport = "0.2, 1.0"
 Requires = "1.0"
 RuntimeGeneratedFunctions = "0.5.12"
-SciMLBase = "< 2.57.2"
+SciMLBase = "2.57.2"
 Setfield = "1"
 # StructuralIdentifiability = "0.5.8"
-SymbolicUtils = "2.1.2, 3.3.0"
-Symbolics = "5.30.1, 6"
+SymbolicUtils = "3.8.1"
+Symbolics = "6.22"
 Unitful = "1.12.4"
 julia = "1.10"
 
 [extras]
 DiffEqCallbacks = "459566f4-90b8-5000-8ac3-15dfb0a30def"
 DomainSets = "5b8099bc-c8ec-5219-889f-1d9e522a28bf"
-Graphviz_jll = "3c863552-8265-54e4-a6dc-903eb78fde85"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
 NonlinearSolve = "8913a72c-1f9b-4ce2-8d82-65094dcecaec"
-OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
+OrdinaryDiffEqBDF = "6ad6398a-0878-4a85-9266-38940aa047c8"
+OrdinaryDiffEqDefault = "50262376-6c5a-4cf5-baba-aaf4f84d72d7"
+OrdinaryDiffEqRosenbrock = "43230ef6-c299-4910-a778-202eb28ce4ce"
+OrdinaryDiffEqTsit5 = "b1df2697-797e-41e3-8120-5422d3b24e4a"
+OrdinaryDiffEqVerner = "79d7bb75-1356-48c1-b8c0-6832512096c2"
 Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
@@ -93,7 +98,4 @@ Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 
 [targets]
-test = ["DiffEqCallbacks", "DomainSets", "Graphviz_jll", "Logging", "NonlinearSolve", 
-        "OrdinaryDiffEq", "Pkg", "Plots", "Random", "SafeTestsets", "SciMLBase", "SciMLNLSolve", 
-        "StableRNGs", "StaticArrays", "Statistics", "SteadyStateDiffEq", "StochasticDiffEq", 
-        "Test", "Unitful"]
+test = ["DiffEqCallbacks", "DomainSets", "Logging", "NonlinearSolve", "OrdinaryDiffEqBDF", "OrdinaryDiffEqDefault", "OrdinaryDiffEqRosenbrock", "OrdinaryDiffEqTsit5", "OrdinaryDiffEqVerner", "Pkg", "Plots", "Random", "SafeTestsets", "SciMLBase", "SciMLNLSolve", "StableRNGs", "StaticArrays", "Statistics", "SteadyStateDiffEq", "StochasticDiffEq", "Test", "Unitful"]

README.md

@@ -72,10 +72,10 @@ be found in its corresponding research paper, [Catalyst: Fast and flexible model
 - Model steady states can be [computed through homotopy continuation](https://docs.sciml.ai/Catalyst/stable/steady_state_functionality/homotopy_continuation/) using [HomotopyContinuation.jl](https://github.com/JuliaHomotopyContinuation/HomotopyContinuation.jl) (which can find *all* steady states of systems with multiple ones), by [forward ODE simulations](https://docs.sciml.ai/Catalyst/stable/steady_state_functionality/nonlinear_solve/#steady_state_solving_simulation) using [SteadyStateDiffEq.jl](https://github.com/SciML/SteadyStateDiffEq.jl), or by [numerically solving steady-state nonlinear equations](https://docs.sciml.ai/Catalyst/stable/steady_state_functionality/nonlinear_solve/#steady_state_solving_nonlinear) using [NonlinearSolve.jl](https://github.com/SciML/NonlinearSolve.jl).
 - [BifurcationKit.jl](https://github.com/bifurcationkit/BifurcationKit.jl) can be used to [compute bifurcation diagrams](https://docs.sciml.ai/Catalyst/stable/steady_state_functionality/bifurcation_diagrams/) of model steady states (including finding periodic orbits).
 - [DynamicalSystems.jl](https://github.com/JuliaDynamics/DynamicalSystems.jl) can be used to compute model [basins of attraction](https://docs.sciml.ai/Catalyst/stable/steady_state_functionality/dynamical_systems/#dynamical_systems_basins_of_attraction), [Lyapunov spectrums](https://docs.sciml.ai/Catalyst/stable/steady_state_functionality/dynamical_systems/#dynamical_systems_lyapunov_exponents), and other dynamical system properties.
-- [StructuralIdentifiability.jl](https://github.com/SciML/StructuralIdentifiability.jl) can be used to [perform structural identifiability analysis](https://docs.sciml.ai/Catalyst/stable/inverse_problems/structural_identifiability/).
 - [Optimization.jl](https://github.com/SciML/Optimization.jl), [DiffEqParamEstim.jl](https://github.com/SciML/DiffEqParamEstim.jl), and [PEtab.jl](https://github.com/sebapersson/PEtab.jl) can all be used to [fit model parameters to data](https://sebapersson.github.io/PEtab.jl/stable/Define_in_julia/).
 - [GlobalSensitivity.jl](https://github.com/SciML/GlobalSensitivity.jl) can be used to perform [global sensitivity analysis](https://docs.sciml.ai/Catalyst/stable/inverse_problems/global_sensitivity_analysis/) of model behaviors.
 - [SciMLSensitivity.jl](https://github.com/SciML/SciMLSensitivity.jl) can be used to compute local sensitivities of functions containing forward model simulations.
+<!-- - [StructuralIdentifiability.jl](https://github.com/SciML/StructuralIdentifiability.jl) can be used to [perform structural identifiability analysis](https://docs.sciml.ai/Catalyst/stable/inverse_problems/structural_identifiability/). -->
 
 #### Features of packages built upon Catalyst
 - Catalyst [`ReactionSystem`](@ref)s can be [imported from SBML files](https://docs.sciml.ai/Catalyst/stable/model_creation/model_file_loading_and_export/#Loading-SBML-files-using-SBMLImporter.jl-and-SBMLToolkit.jl) via [SBMLImporter.jl](https://github.com/sebapersson/SBMLImporter.jl) and [SBMLToolkit.jl](https://github.com/SciML/SBMLToolkit.jl), and [from BioNetGen .net files](https://docs.sciml.ai/Catalyst/stable/model_creation/model_file_loading_and_export/#file_loading_rni_net) and various stoichiometric matrix network representations using [ReactionNetworkImporters.jl](https://github.com/SciML/ReactionNetworkImporters.jl).
@@ -92,7 +92,7 @@ an ordinary differential equation.
 
 ```julia
 # Fetch required packages.
-using Catalyst, OrdinaryDiffEq, Plots
+using Catalyst, OrdinaryDiffEqDefault, Plots
 
 # Create model.
 model = @reaction_network begin

docs/Project.toml

@@ -5,11 +5,9 @@ CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
 Catalyst = "479239e8-5488-4da2-87a7-35f2df7eef83"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e"
-DiffEqParamEstim = "1130ab10-4a5a-5621-a13d-e4788d82bd4c"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 DynamicalSystems = "61744808-ddfa-5f27-97ff-6e42cc95d634"
-GLMakie = "e9467ef8-e4e7-5192-8a1a-b1aee30e663a"
 GlobalSensitivity = "af5da776-676b-467e-8baf-acd8249e4f0f"
 GraphMakie = "1ecd5474-83a3-4783-bb4f-06765db800d2"
 Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
@@ -20,10 +18,12 @@ Latexify = "23fbe1c1-3f47-55db-b15f-69d7ec21a316"
 LinearSolve = "7ed4a6bd-45f5-4d41-b270-4a48e9bafcae"
 Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
 ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"
+NetworkLayout = "46757867-2c16-5918-afeb-47bfcb05e46a"
 NonlinearSolve = "8913a72c-1f9b-4ce2-8d82-65094dcecaec"
 Optim = "429524aa-4258-5aef-a3af-852621145aeb"
 Optimization = "7f7a1694-90dd-40f0-9382-eb1efda571ba"
 OptimizationBBO = "3e6eede4-6085-4f62-9a71-46d9bc1eb92b"
+OptimizationEvolutionary = "cb963754-43f6-435e-8d4b-99009ff27753"
 OptimizationNLopt = "4e6fcdb7-1186-4e1f-a706-475e75c168bb"
 OptimizationOptimJL = "36348300-93cb-4f02-beb5-3c3902f8871e"
 OptimizationOptimisers = "42dfb2eb-d2b4-4451-abcd-913932933ac1"
@@ -33,6 +33,7 @@ OrdinaryDiffEqRosenbrock = "43230ef6-c299-4910-a778-202eb28ce4ce"
 OrdinaryDiffEqSDIRK = "2d112036-d095-4a1e-ab9a-08536f3ecdbf"
 OrdinaryDiffEqTsit5 = "b1df2697-797e-41e3-8120-5422d3b24e4a"
 OrdinaryDiffEqVerner = "79d7bb75-1356-48c1-b8c0-6832512096c2"
+PEtab = "48d54b35-e43e-4a66-a5a1-dde6b987cf69"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 QuasiMonteCarlo = "8a4e6c94-4038-4cdc-81c3-7e6ffdb2a71b"
 SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
@@ -49,12 +50,10 @@ BifurcationKit = "0.4.4"
 CairoMakie = "0.12"
 Catalyst = "14.4"
 DataFrames = "1.6"
-DiffEqBase = "< 6.159.0"
-DiffEqParamEstim = "2.2"
+DiffEqBase = "6.159.0"
 Distributions = "0.25"
 Documenter = "1.4.1"
 DynamicalSystems = "3.3"
-GLMakie = "0.10"
 GlobalSensitivity = "2.6"
 GraphMakie = "0.5"
 Graphs = "1.11.1"
@@ -63,11 +62,13 @@ IncompleteLU = "0.2"
 JumpProcesses = "9.13.2"
 Latexify = "0.16.5"
 LinearSolve = "2.30"
-ModelingToolkit = "9.32"
+ModelingToolkit = "< 9.60"
+NetworkLayout = "0.4"
 NonlinearSolve = "3.12, 4"
 Optim = "1.9"
 Optimization = "4"
 OptimizationBBO = "0.4"
+OptimizationEvolutionary = "0.4"
 OptimizationNLopt = "0.3"
 OptimizationOptimJL = "0.4"
 OptimizationOptimisers = "0.3"
@@ -77,6 +78,7 @@ OrdinaryDiffEqRosenbrock = "1"
 OrdinaryDiffEqSDIRK = "1"
 OrdinaryDiffEqTsit5 = "1"
 OrdinaryDiffEqVerner = "1"
+PEtab = "3.5"
 Plots = "1.40"
 QuasiMonteCarlo = "0.3"
 SciMLBase = "2.46"
@@ -85,4 +87,4 @@ SpecialFunctions = "2.4"
 StaticArrays = "1.9"
 SteadyStateDiffEq = "2.2"
 StochasticDiffEq = "6.65"
-Symbolics = "5.30.1, 6"
+Symbolics = "6.22"

docs/make.jl

@@ -1,5 +1,7 @@
 using Documenter
 using Catalyst, ModelingToolkit
+# Add packages for plotting
+using GraphMakie, CairoMakie
 
 docpath = Base.source_dir()
 assetpath = joinpath(docpath, "src", "assets")
@@ -37,7 +39,9 @@ makedocs(sitename = "Catalyst.jl",
         collapselevel = 1,
         assets = ["assets/favicon.ico"],
         canonical = "https://docs.sciml.ai/Catalyst/stable/"),
-    modules = [Catalyst, ModelingToolkit],
+    modules = [Catalyst, ModelingToolkit, 
+               isdefined(Base, :get_extension) ? Base.get_extension(Catalyst, :CatalystGraphMakieExtension) :
+               Catalyst.CatalystGraphMakieExtension],
     doctest = false,
     clean = true,
     pages = pages,

docs/pages.jl

@@ -40,13 +40,13 @@ pages = Any[
     "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/petab_ode_param_fitting.md",
         "inverse_problems/optimization_ode_param_fitting.md",
-        # "inverse_problems/petab_ode_param_fitting.md",
         "inverse_problems/behaviour_optimisation.md",
         # "inverse_problems/structural_identifiability.md",
         "inverse_problems/global_sensitivity_analysis.md",

docs/src/api.md

@@ -271,7 +271,7 @@ isequivalent
 ==(rn1::ReactionSystem, rn2::ReactionSystem)
 ```
 
-## Network visualization
+## [Network visualization](@id network_visualization)
 [Latexify](https://korsbo.github.io/Latexify.jl/stable/) can be used to convert
 networks to LaTeX equations by
 ```julia
@@ -292,13 +292,10 @@ displayed as the ODE form)
 
 Finally, another optional argument (`expand_functions=true`) automatically expands functions defined by Catalyst (such as `mm`). To disable this, set `expand_functions=false`.
 
-If [Graphviz](https://graphviz.org/) is installed and commandline accessible, it
-can be used to create and save network diagrams using [`Graph`](@ref) and
-[`savegraph`](@ref).
+Reaction networks can be plotted using the `GraphMakie` extension, which is loaded whenever all of `Catalyst`, `GraphMakie`, and `NetworkLayout` are loaded (note that a Makie backend, like `CairoMakie`, must be loaded as well). The two functions for plotting networks are `plot_network` and `plot_complexes`, which are two distinct representations. 
 ```@docs
-Graph
-complexgraph
-savegraph
+plot_network(::ReactionSystem)
+plot_complexes(::ReactionSystem)
 ```
 
 ## [Rate laws](@id api_rate_laws)