Merge branch 'master' into pdmps

Author: isaacsas

.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

@@ -7,6 +7,29 @@
   (at the time the release is made). If you need a dependency version increased,
   please open an issue and we can update it and make a new Catalyst release once
   testing against the newer dependency version is complete. 
+- New formula for inferring variables from equations (declared using the `@equations` options) in the DSL. The order of inference of species/variables/parameters is now:
+    (1) Every symbol explicitly declared using `@species`, `@variables`, and `@parameters` are assigned to the correct category.
+    (2) Every symbol used as a reaction reactant is inferred as a species.
+    (3) Every symbol not declared in (1) or (2) that occurs in an expression provided after `@equations` is inferred as a variable.
+    (4) Every symbol not declared in (1), (2), or (3) that occurs either as a reaction rate or stoichiometric coefficient is inferred to be a parameter.
+E.g. in
+```julia
+@reaction_network begin
+    @equations V1 + S ~ V2^2
+    (p + S + V1), S --> 0
+end
+```
+`S` is inferred as a species, `V1` and `V2` as variables, and `p` as a parameter. The previous special cases for the `@observables`, `@compounds`, and `@differentials` options still hold. Finally, the `@require_declaration` options (described in more detail below) can now be used to require everything to be explicitly declared.
+- New formula for determining whether the default differentials have been used within an `@equations` option. Now, if any expression `D(...)` is encountered (where `...` can be anything), this is inferred as usage of the default differential D. E.g. in the following equations `D` is inferred as a differential with respect to the default independent variable:
+```julia
+@reaction_network begin
+  @equations D(V) + V ~ 1
+end
+@reaction_network begin
+  @equations D(D(V)) ~ 1
+end
+```
+Please note that this cannot be used at the same time as `D` is used to represent a species, variable, or parameter (including is these are implicitly designated as such by e.g. appearing as a reaction reactant). 
 - Array symbolics support is more consistent with ModelingToolkit v9. Parameter
   arrays are no longer scalarized by Catalyst, while species and variables
   arrays still are (as in ModelingToolkit). As such, parameter arrays should now
@@ -25,7 +48,34 @@
   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

@@ -33,53 +33,54 @@ BifurcationKit = "0f109fa4-8a5d-4b75-95aa-f515264e7665"
 CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
 GraphMakie = "1ecd5474-83a3-4783-bb4f-06765db800d2"
 HomotopyContinuation = "f213a82b-91d6-5c5d-acf7-10f1c761b327"
-# StructuralIdentifiability = "220ca800-aa68-49bb-acd8-6037fa93a544"
+NetworkLayout = "46757867-2c16-5918-afeb-47bfcb05e46a"
 
 [extensions]
 CatalystBifurcationKitExtension = "BifurcationKit"
 CatalystCairoMakieExtension = "CairoMakie"
-CatalystGraphMakieExtension = "GraphMakie"
+CatalystGraphMakieExtension = ["GraphMakie", "NetworkLayout"]
 CatalystHomotopyContinuationExtension = "HomotopyContinuation"
-# CatalystStructuralIdentifiabilityExtension = "StructuralIdentifiability"
 
 [compat]
 BifurcationKit = "0.4.4"
-CairoMakie = "0.12"
+CairoMakie = "0.12, 0.13"
 Combinatorics = "1.0.2"
 DataStructures = "0.18"
-DiffEqBase = "< 6.159.0"
-DocStringExtensions = "0.9"
-DynamicPolynomials = "0.6"
-DynamicQuantities = "1"
-EnumX = "1.0.4"
+DiffEqBase = "6.159.0"
+DocStringExtensions = "0.8, 0.9"
+DynamicPolynomials = "0.5, 0.6"
+DynamicQuantities = "0.13.2, 1"
 GraphMakie = "0.5"
 Graphs = "1.4"
 HomotopyContinuation = "2.9"
 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 = "1.0"
 Requires = "1.0"
 RuntimeGeneratedFunctions = "0.5.12"
-SciMLBase = "< 2.57.2"
+SciMLBase = "2.57.2"
 Setfield = "1"
-# StructuralIdentifiability = "0.5.8"
-SymbolicUtils = "3.3.0"
-Symbolics = "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"
@@ -95,4 +96,4 @@ 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"
@@ -46,15 +47,13 @@ Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7"
 [compat]
 BenchmarkTools = "1.5"
 BifurcationKit = "0.4.4"
-CairoMakie = "0.12"
+CairoMakie = "0.12, 0.13"
 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,