Merge remote-tracking branch 'origin/master' into pr/1101

SciML · Nov 14, 2024 · 2443365 · 2443365
2 parents 98c86eb + a5ebaeb
commit 2443365
Show file tree

Hide file tree

Showing 5 changed files with 8 additions and 5 deletions.
diff --git a/Project.toml b/Project.toml
@@ -46,7 +46,7 @@ BifurcationKit = "0.4.3"
 CairoMakie = "0.12"
 Combinatorics = "1.0.2"
 DataStructures = "0.18"
-DiffEqBase = "6.83.0"
+DiffEqBase = "< 6.159.0"
 DocStringExtensions = "0.8, 0.9"
 DynamicPolynomials = "0.5, 0.6"
 DynamicQuantities = "0.13.2, 1"

diff --git a/docs/Project.toml b/docs/Project.toml
@@ -4,6 +4,7 @@ BifurcationKit = "0f109fa4-8a5d-4b75-95aa-f515264e7665"
 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"
@@ -46,8 +47,9 @@ Symbolics = "0c5d862f-8b57-4792-8d23-62f2024744c7"
 BenchmarkTools = "1.5"
 BifurcationKit = "0.4"
 CairoMakie = "0.12"
-Catalyst = "14.2"
+Catalyst = "14.4"
 DataFrames = "1.6"
+DiffEqBase = "< 6.159.0"
 DiffEqParamEstim = "2.2"
 Distributions = "0.25"
 Documenter = "1.4.1"

diff --git a/docs/make.jl b/docs/make.jl
@@ -34,13 +34,14 @@ makedocs(sitename = "Catalyst.jl",
     authors = "Samuel Isaacson",
     format = Documenter.HTML(; analytics = "UA-90474609-3",
         prettyurls = (get(ENV, "CI", nothing) == "true"),
+        collapselevel = 1,
         assets = ["assets/favicon.ico"],
         canonical = "https://docs.sciml.ai/Catalyst/stable/"),
     modules = [Catalyst, ModelingToolkit],
     doctest = false,
     clean = true,
     pages = pages,
-    pagesonly = false,
+    pagesonly = true,
     warnonly = [:missing_docs])
 
 deploydocs(repo = "github.com/SciML/Catalyst.jl.git";

diff --git a/docs/pages.jl b/docs/pages.jl
@@ -41,7 +41,7 @@ pages = Any[
         "steady_state_functionality/homotopy_continuation.md",
         "steady_state_functionality/nonlinear_solve.md",
         "steady_state_functionality/steady_state_stability_computation.md",
-        "steady_state_functionality/bifurcation_diagrams.md",
+        #"steady_state_functionality/bifurcation_diagrams.md",
         "steady_state_functionality/dynamical_systems.md"
     ],
     "Inverse problems" => Any[

diff --git a/docs/src/index.md b/docs/src/index.md
@@ -39,7 +39,7 @@ etc).
 - [Latexify](https://korsbo.github.io/Latexify.jl/stable/) can be used to [generate LaTeX expressions](@ref visualisation_latex) corresponding to generated mathematical models or the underlying set of reactions.
 - [Graphviz](https://graphviz.org/) can be used to generate and [visualize reaction network graphs](@ref visualisation_graphs) (reusing the Graphviz interface created in [Catlab.jl](https://algebraicjulia.github.io/Catlab.jl/stable/)).
 - Model steady states can be [computed through homotopy continuation](@ref 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](@ref steady_state_solving_simulation) using [SteadyStateDiffEq.jl)](https://github.com/SciML/SteadyStateDiffEq.jl), or by [numerically solving steady-state nonlinear equations](@ref 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](@ref bifurcation_diagrams) of model steady states (including finding periodic orbits).
+<!--- [BifurcationKit.jl](https://github.com/bifurcationkit/BifurcationKit.jl) can be used to compute 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](@ref dynamical_systems_basins_of_attraction), [Lyapunov spectrums](@ref 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.-->
 - [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/).