Merge branch 'master' into tests___new___vector_valued

Author: TorkelE

.github/workflows/CI.yml

@@ -3,11 +3,9 @@ on:
   pull_request:
     branches:
       - master
-      - Catalyst_version_14
   push:
     branches:
       - master
-      - Catalyst_version_14
 jobs:
   test:
     runs-on: ubuntu-latest
@@ -19,7 +17,7 @@ jobs:
           - '1'
     steps:
       - uses: actions/checkout@v4
-      - uses: julia-actions/setup-julia@v1
+      - uses: julia-actions/setup-julia@v2
         with:
           version: ${{ matrix.version }}
       - uses: actions/cache@v4
@@ -35,9 +33,11 @@ jobs:
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-runtest@v1
       - uses: julia-actions/julia-processcoverage@v1
-      - uses: codecov/codecov-action@v3
+      - uses: codecov/codecov-action@v4
         with:
           file: lcov.info
+          token: ${{ secrets.CODECOV_TOKEN }}
+          fail_ci_if_error: false
       - uses: coverallsapp/github-action@master
         with:
           github-token: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/CompatHelper.yml

@@ -15,7 +15,7 @@ jobs:
         run: which julia
         continue-on-error: true
       - name: Install Julia, but only if it is not already available in the PATH
-        uses: julia-actions/setup-julia@v1
+        uses: julia-actions/setup-julia@v2
         with:
           version: '1'
           arch: ${{ runner.arch }}

.github/workflows/Documentation.yml

@@ -24,7 +24,8 @@ jobs:
           GKSwstype: "100" # https://discourse.julialang.org/t/generation-of-documentation-fails-qt-qpa-xcb-could-not-connect-to-display/60988
         run: julia --project=docs/ --code-coverage=user docs/make.jl
       - uses: julia-actions/julia-processcoverage@v1
-      - uses: codecov/codecov-action@v3
+      - uses: codecov/codecov-action@v4
         with:
           file: lcov.info
-
+          token: ${{ secrets.CODECOV_TOKEN }}
+          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@v1
-      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

@@ -3,6 +3,8 @@
 ## Catalyst unreleased (master branch)
 
 ## Catalyst 14.0
+- The `reactionparams`, `numreactionparams`, and `reactionparamsmap`  functions have been removed.
+- To be more consistent with ModelingToolkit's immutability requirement for systems, we have removed API functions that mutate `ReactionSystem`s such as `addparam!`, `addreaction!`, `addspecies`, `@add_reactions`, and `merge!`. Please use `ModelingToolkit.extend` and `ModelingToolkit.compose` to generate new merged and/or composed `ReactionSystem`s from multiple component systems.
 - Added CatalystStructuralIdentifiabilityExtension, which permits StructuralIdentifiability.jl function to be applied directly to Catalyst systems. E.g. use
 ```julia
 using Catalyst, StructuralIdentifiability
@@ -22,7 +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.
@@ -84,6 +86,20 @@ plot(bif_dia; xguide="k1", yguide="X")
 ```
 - Automatically handles elimination of conservation laws for computing bifurcation diagrams.
 - Updated Bifurcation documentation with respect to this new feature.
+- Added function `isautonomous` to check if a `ReactionSystem` is autonomous.
+- Added function `steady_state_stability` to compute stability for steady states. Example:
+```julia
+# Creates model.
+rn = @reaction_network begin
+    (p,d), 0 <--> X
+end
+p = [:p => 1.0, :d => 0.5]
+
+# Finds (the trivial) steady state, and computes stability.
+steady_state = [2.0]
+steady_state_stability(steady_state, rn, p)
+```
+Here, `steady_state_stability` take an optional argument `tol = 10*sqrt(eps())`, which is used to determine whether a eigenvalue real part is reliably less that 0.
 
 ## Catalyst 13.5
 - Added a CatalystHomotopyContinuationExtension extension, which exports the `hc_steady_state` function if HomotopyContinuation is exported. `hc_steady_state` finds the steady states of a reaction system using the homotopy continuation method. This feature is only available for julia versions 1.9+. Example:

Project.toml

@@ -1,11 +1,13 @@
 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"
+DynamicPolynomials = "7c1d4256-1411-5781-91ec-d7bc3513ac07"
 DynamicQuantities = "06fc5a27-2a28-4c7c-a15d-362465fb6821"
 Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
 JumpProcesses = "ccbc3e58-028d-4f4c-8cd5-9ae44345cda5"
@@ -20,7 +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"
 
@@ -36,34 +37,37 @@ 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 = "9.7.1"
+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 = "5.14"
+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"
+DiffEqCallbacks = "459566f4-90b8-5000-8ac3-15dfb0a30def"
 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"
@@ -80,4 +84,4 @@ Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 
 [targets]
-test = ["BifurcationKit", "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"]

README.md

@@ -3,8 +3,8 @@
 [![Join the chat at https://julialang.zulipchat.com #sciml-bridged](https://img.shields.io/static/v1?label=Zulip&message=chat&color=9558b2&labelColor=389826)](https://julialang.zulipchat.com/#narrow/stream/279055-sciml-bridged)
 [![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://docs.sciml.ai/Catalyst/stable/)
 [![API Stable](https://img.shields.io/badge/API-stable-blue.svg)](https://docs.sciml.ai/Catalyst/stable/api/catalyst_api/)
-[![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://docs.sciml.ai/Catalyst/dev/)
-[![API Dev](https://img.shields.io/badge/API-dev-blue.svg)](https://docs.sciml.ai/Catalyst/dev/api/catalyst_api/)
+<!---  [![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://docs.sciml.ai/Catalyst/dev/)
+[![API Dev](https://img.shields.io/badge/API-dev-blue.svg)](https://docs.sciml.ai/Catalyst/dev/api/catalyst_api/) -->
 
 [![Build Status](https://github.com/SciML/Catalyst.jl/workflows/CI/badge.svg)](https://github.com/SciML/Catalyst.jl/actions?query=workflow%3ACI)
 [![codecov.io](https://codecov.io/gh/SciML/Catalyst.jl/branch/master/graph/badge.svg)](https://codecov.io/gh/SciML/Catalyst.jl)

docs/Project.toml

@@ -1,18 +1,25 @@
 [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 +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]
-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 = "0.27"
-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"
+Documenter = "1.4.1"
+DynamicalSystems = "3.3"
+GlobalSensitivity = "2.6"
+HomotopyContinuation = "2.9"
+IncompleteLU = "0.2"
+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

@@ -31,15 +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)
+    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)