diff --git a/Project.toml b/Project.toml index 4f8d24569..0d3103ff0 100644 --- a/Project.toml +++ b/Project.toml @@ -46,7 +46,7 @@ BifurcationKit = "0.3" 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 index 96d9feed0..a18db09ea 100644 --- 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 = "0.3.4" 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 index 0d354c641..a877fb5d5 100644 --- 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 index 79525e3f8..c72f578bb 100644 --- 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 index 7c4588faf..163df5ae8 100644 --- 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). + - [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. - [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/).