Merge pull request #768 from SciML/doc_updates

TorkelE · web-flow · commit 235ad85b5a47 · 2024-01-24T23:53:51.000+01:00
Doc updates
diff --git a/HISTORY.md b/HISTORY.md
@@ -1,6 +1,8 @@
 # Breaking updates and feature summaries across releases
 
 ## Catalyst unreleased (master branch)
+
+## Catalyst 14.0
 - Simulation of spatial ODEs now supported. For full details, please see https://github.com/SciML/Catalyst.jl/pull/644 and upcoming documentation. Note that these methods are currently considered alpha, with the interface and approach changing even in non-breaking Catalyst releases.
 - LatticeReactionSystem structure represents a spatial reaction network:
   ```julia
@@ -35,7 +37,6 @@ wilhelm_2009_model = @reaction_network begin
     k5, 0 --> X
 end
 
-
 using BifurcationKit
 bif_par = :k1
 u_guess = [:X => 5.0, :Y => 2.0]
diff --git a/Project.toml b/Project.toml
@@ -49,7 +49,7 @@ Requires = "1.0"
 RuntimeGeneratedFunctions = "0.5.12"
 Setfield = "1"
 SymbolicUtils = "1.0.3"
-Symbolics = "5.0.3"
+Symbolics = "5.14"
 Unitful = "1.12.4"
 julia = "1.9"
 
diff --git a/README.md b/README.md
@@ -31,10 +31,7 @@ etc).
 
 ## Breaking changes and new features
 
-**NOTE:** version 13 is a breaking release, with changes to simplify the DSL
-notation while also adding more features, changes to how chemical species are
-specified symbolically when directly building `ReactionSystem`s, and changes that
-simplify how to include ODE or algebraic constraint equation.
+**NOTE:** version 14 is a breaking release, prompted by the release of ModelingToolkit.jl version 9. This caused several breaking changes in how Catalyst models are represented and interfaced with.
 
 Breaking changes and new functionality are summarized in the
 [HISTORY.md](HISTORY.md) file.
@@ -48,6 +45,8 @@ the current master branch.
 
 Several Youtube video tutorials and overviews are also available, but note these use older 
 Catalyst versions with slightly different notation (for example, in building reaction networks):
+- From JuliaCon 2023: A short 15 minute overview of Catalyst as of version 13 is
+available in the talk [Catalyst.jl, Modeling Chemical Reaction Networks](https://www.youtube.com/watch?v=yreW94n98eM&ab_channel=TheJuliaProgrammingLanguage).
 - From JuliaCon 2022: A three hour tutorial workshop overviewing how to use
   Catalyst and its more advanced features as of version 12.1. [Workshop
   video](https://youtu.be/tVfxT09AtWQ), [Workshop Pluto.jl
@@ -60,6 +59,8 @@ Catalyst.jl](https://www.youtube.com/watch?v=5p1PJE5A5Jw).
   Modelling of Biochemical Reaction
   Networks](https://www.youtube.com/watch?v=s1e72k5XD6s)
 
+Finally, an overview of the package and its features (as of version 13) can also be found in its corresponding research paper, [Catalyst: Fast and flexible modeling of reaction networks](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011530).
+
 ## Features
 
 - A DSL provides a simple and readable format for manually specifying chemical
diff --git a/docs/Project.toml b/docs/Project.toml
@@ -34,17 +34,17 @@ Documenter = "0.27"
 HomotopyContinuation = "2.6"
 Latexify = "0.15, 0.16"
 ModelingToolkit = "8.47"
-NonlinearSolve = "1.6.0, 2"
+NonlinearSolve = "3.4.0"
 Optim = "1"
 Optimization = "3.19"
 OptimizationOptimisers = "0.1.1"
 OrdinaryDiffEq = "6"
 PEtab = "2"
 Plots = "1.36"
-SciMLBase = "~2.5"
+SciMLBase = "2.13"
 SciMLSensitivity = "7.19"
 Setfield = "1.1"
 SpecialFunctions = "2.1"
-SteadyStateDiffEq = "1"
+SteadyStateDiffEq = "2.0.1"
 StochasticDiffEq = "6"
-Symbolics = "5.0.3"
+Symbolics = "5.14"
diff --git a/docs/src/catalyst_applications/bifurcation_diagrams.md b/docs/src/catalyst_applications/bifurcation_diagrams.md
@@ -1,6 +1,6 @@
 # [Bifurcation Diagrams](@id bifurcation_diagrams)
 
-Bifurcation diagrams describe how, for a dynamical system, the quantity and type of its steady states change as a parameter is varied[^1]. When using Catalyst-generated models, these can be computed with the [BifurcationKit.jl](https://github.com/bifurcationkit/BifurcationKit.jl) package. Catalyst provides a simple interface for creating BifurcationKit compatible `BifurcationProblem`s from `ReactionSystem`s. If you use this feature in your research, please [cite the BifurcationKit.jl](@ref bifurcation_kit_citation) and [Catalyst.jl](@ref catalyst_citation) publications.
+Bifurcation diagrams describe how, for a dynamical system, the quantity and type of its steady states change as a parameter is varied[^1]. When using Catalyst-generated models, these can be computed with the [BifurcationKit.jl](https://github.com/bifurcationkit/BifurcationKit.jl) package. Catalyst provides a simple interface for creating BifurcationKit compatible `BifurcationProblem`s from `ReactionSystem`s.
 
 This tutorial briefly introduces how to use Catalyst with BifurcationKit through basic examples, with BifurcationKit.jl providing [a more extensive documentation](https://bifurcationkit.github.io/BifurcationKitDocs.jl/stable/). Especially for more complicated systems, where careful tuning of algorithm options might be required, reading the BifurcationKit documentation is recommended. Finally, BifurcationKit provides many additional features not described here, including [computation of periodic orbits](https://bifurcationkit.github.io/BifurcationKitDocs.jl/stable/periodicOrbit/), [tracking of bifurcation points along secondary parameters](https://bifurcationkit.github.io/BifurcationKitDocs.jl/dev/branchswitching/), and [bifurcation computations for PDEs](https://bifurcationkit.github.io/BifurcationKitDocs.jl/dev/tutorials/tutorials/#PDEs:-bifurcations-of-equilibria).
 
diff --git a/docs/src/catalyst_applications/homotopy_continuation.md b/docs/src/catalyst_applications/homotopy_continuation.md
@@ -9,7 +9,7 @@ integer Hill exponents). The roots of these can reliably be found through a
 *homotopy continuation* algorithm. This is implemented in Julia through the
 [HomotopyContinuation.jl](https://www.juliahomotopycontinuation.org/) package.
 
-Catalyst contains a special homotopy continuation extension that is loaded whenever HomotopyContinuation.jl is. This exports a single function, `hc_steady_states`, that can be used to find the steady states of any `ReactionSystem` structure. If you use this in your research, please [cite the HomotopyContinuation.jl](@ref homotopy_continuation_citation) and [Catalyst.jl](@ref catalyst_citation) publications.
+Catalyst contains a special homotopy continuation extension that is loaded whenever HomotopyContinuation.jl is. This exports a single function, `hc_steady_states`, that can be used to find the steady states of any `ReactionSystem` structure.
 
 ## Basic example
 For this tutorial, we will use a model from Wilhelm (2009)[^1] (which
diff --git a/docs/src/catalyst_applications/nonlinear_solve.md b/docs/src/catalyst_applications/nonlinear_solve.md
@@ -6,7 +6,7 @@ We have previously described how `ReactionSystem` steady states can be found thr
 
 However, if all (or multiple) steady states are sought, using homotopy continuation is better.
 
-This tutorial describes how to create `NonlinearProblem`s from Catalyst's `ReactionSystemn`s, and how to solve them using NonlinearSolve. More extensive descriptions of available solvers and options can be found in [NonlinearSolve's documentation](https://docs.sciml.ai/NonlinearSolve/stable/). If you use this in your research, please [cite the NonlinearSolve.jl](@ref nonlinear_solve_citation) and [Catalyst.jl](@ref catalyst_citation) publications.
+This tutorial describes how to create `NonlinearProblem`s from Catalyst's `ReactionSystemn`s, and how to solve them using NonlinearSolve. More extensive descriptions of available solvers and options can be found in [NonlinearSolve's documentation](https://docs.sciml.ai/NonlinearSolve/stable/).
 
 ## Basic example
 Let us consider a simple dimerisation network, where a protein ($P$) can exist in a monomer and a dimer form. The protein is produced at a constant rate from its mRNA, which is also produced at a constant rate.
diff --git a/docs/src/introduction_to_catalyst/catalyst_for_new_julia_users.md b/docs/src/introduction_to_catalyst/catalyst_for_new_julia_users.md
diff --git a/docs/src/inverse_problems/petab_ode_param_fitting.md b/docs/src/inverse_problems/petab_ode_param_fitting.md
