Merge pull request #592 from SciML/minor_doc_changes

Various docs fixes

HISTORY.md

@@ -151,7 +151,7 @@
 
 ## Catalyst 11.0
 - **BREAKING:** Added the ability to eliminate conserved species when generating
-  ODEs, nonlinear problems, SDEs, and steady-state problems via the
+  ODEs, nonlinear problems, SDEs, and steady state problems via the
   `remove_conserved=true` keyword that can be passed to `convert` or to
   `ODEProblem`, `NonlinearProblem`, `SDEProblem`, or `SteadyStateProblem` when
   called with a `ReactionSystem`. For example,
@@ -287,7 +287,7 @@
   when calling `ODEProblem(mixedsys,...; combinatoric_ratelaws=false)`. This
   disables Catalyst's standard rescaling of reaction rates when generating
   reaction rate laws, see the
-  [docs](https://catalyst.sciml.ai/dev/tutorials/using_catalyst/#Reaction-rate-laws-used-in-simulations).
+  [docs](https://catalyst.sciml.ai/dev/tutorials/introduction_to_catalyst/#Reaction-rate-laws-used-in-simulations).
   Leaving this out for systems with floating point stoichiometry will give an
   error message.
 

README.md

@@ -13,7 +13,7 @@
 
 Catalyst.jl is a symbolic modeling package for analysis and high performance
 simulation of chemical reaction networks. Catalyst defines symbolic
-[`ReactionSystem`](https://docs.sciml.ai/Catalyst/stable/tutorials/reaction_systems/)s,
+[`ReactionSystem`](https://docs.sciml.ai/Catalyst/stable/catalyst_functionality/programmatic_CRN_construction/)s,
 which can be created programmatically or easily
 specified using Catalyst's domain specific language (DSL). Leveraging
 [ModelingToolkit](/~https://github.com/SciML/ModelingToolkit.jl) and
@@ -27,12 +27,12 @@ Generated models can be used with solvers throughout the broader
 for sensitivity analysis, parameter estimation, machine learning applications,
 etc).
 
-## Breaking Changes and New Features
+## Breaking changes and new features
 
 Breaking changes and new functionality are summarized in the
 [HISTORY.md](HISTORY.md) file.
 
-## Tutorials and Documentation
+## Tutorials and documentation
 
 For tutorials and information on using the package, [see the stable
 documentation](https://docs.sciml.ai/Catalyst/stable/). The [in-development
@@ -47,44 +47,43 @@ Several Youtube video tutorials and overviews are also available:
 
 ## Features
 
-- DSL provides a simple and readable format for manually specifying chemical
+- A DSL provides a simple and readable format for manually specifying chemical
   reactions.
 - Catalyst `ReactionSystem`s provide a symbolic representation of reaction networks,
-  built on [ModelingToolkit.jl](https://github.com/SciML/ModelingToolkit.jl) and
-  [Symbolics.jl](https://github.com/JuliaSymbolics/Symbolics.jl).
+  built on [ModelingToolkit.jl](https://docs.sciml.ai/ModelingToolkit/stable/) and
+  [Symbolics.jl](https://docs.sciml.ai/Symbolics/stable/).
 - Non-integer (e.g. `Float64`) stoichiometric coefficients are supported for generating
   ODE models, and symbolic expressions for stoichiometric coefficients are supported for
   all system types.
-- The [Catalyst.jl API](http://docs.sciml.ai/Catalyst/stable/api/catalyst_api) provides
-  functionality for extending networks, building networks programmatically,
-  network analysis, and for composing multiple networks together.
+- The [Catalyst.jl API](http://docs.sciml.ai/Catalyst/stable/api/catalyst_api) provides functionality for extending networks,
+  building networks programmatically, network analysis, and for composing multiple
+  networks together.
 - `ReactionSystem`s generated by the DSL can be converted to a variety of
-  `ModelingToolkit.AbstractSystem`s, including symbolic ODE, SDE, and jump process
+  `ModelingToolkit.AbstractSystem`s, including symbolic ODE, SDE and jump process
   representations.
 - Conservation laws can be detected and applied to reduce system sizes, and generate
-  non-singular Jacobians, during conversion to ODEs, SDEs, and steady-state equations.
+  non-singular Jacobians, during conversion to ODEs, SDEs, and steady state equations.
 - By leveraging ModelingToolkit, users have a variety of options for generating
   optimized system representations to use in solvers. These include construction
   of dense or sparse Jacobians, multithreading or parallelization of generated
   derivative functions, automatic classification of reactions into optimized
-  jump types for Gillespie-type simulations, automatic construction of
+  jump types for Gillespie type simulations, automatic construction of
   dependency graphs for jump systems, and more.
 - Generated systems can be solved using any
-  [DifferentialEquations.jl](https://github.com/SciML/DifferentialEquations.jl)
+  [DifferentialEquations.jl](https://docs.sciml.ai/DiffEqDocs/stable/)
   ODE/SDE/jump solver, and can be used within `EnsembleProblem`s for carrying
   out parallelized parameter sweeps and statistical sampling. Plot recipes
   are available for visualizing the solutions.
-- [Symbolics.jl](/~https://github.com/JuliaSymbolics/Symbolics.jl) symbolic expressions
-  and Julia `Expr`s can be obtained for all rate laws and functions determining the
-  deterministic and stochastic terms within resulting ODE, SDE, or jump models.
-- [Latexify](/~https://github.com/korsbo/Latexify.jl) can be used to generate
+- Symbolic Julia `Expr`s (implemented through [Symbolics.jl](/~https://github.com/JuliaSymbolics/Symbolics.jl)) can be obtained for all rate laws and functions determining the
+  deterministic and stochastic terms within resulting ODE, SDE or jump models.
+- [Latexify](https://korsbo.github.io/Latexify.jl/stable/) can be used to generate
   LaTeX expressions 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. (Reusing the Graphviz interface created in
-  [Catlab.jl](https://github.com/AlgebraicJulia/Catlab.jl/).)
+  [Catlab.jl](https://algebraicjulia.github.io/Catlab.jl/stable/).)
 
-## Packages Supporting Catalyst
+## Packages supporting Catalyst
 - Catalyst [`ReactionSystem`](@ref)s can be imported from SBML files via
   [SBMLToolkit.jl](/~https://github.com/SciML/SBMLToolkit.jl), and from BioNetGen .net
   files and various stoichiometric matrix network representations using
@@ -101,8 +100,8 @@ Several Youtube video tutorials and overviews are also available:
   resulting stochastic chemical kinetics with delays models.
 
 
-## Illustrative Examples
-#### Gillespie Simulations of Michaelis-Menten Enzyme Kinetics
+## Illustrative examples
+#### Gillespie simulations of Michaelis-Menten enzyme kinetics
 
 ```julia
 using Catalyst, Plots, JumpProcesses
@@ -124,7 +123,7 @@ plot(jsol,lw=2,title="Gillespie: Michaelis-Menten Enzyme Kinetics")
 
 ![](https://user-images.githubusercontent.com/1814174/87864114-3bf9dd00-c932-11ea-83a0-58f38aee8bfb.png)
 
-#### Adaptive SDEs for A Birth-Death Process
+#### Adaptive time stepping SDEs for a birth-death process
 
 ```julia
 using Catalyst, Plots, StochasticDiffEq
@@ -143,13 +142,13 @@ plot(ssol,lw=2,title="Adaptive SDE: Birth-Death Process")
 
 ![](https://user-images.githubusercontent.com/1814174/87864113-3bf9dd00-c932-11ea-8275-f903eef90b91.png)
 
-## Getting Help
+## Getting help
 Catalyst developers are active on the [Julia
 Discourse](https://discourse.julialang.org/), the [Julia Slack](https://julialang.slack.com) channels \#sciml-bridged and \#sciml-sysbio, and the [Julia Zulip sciml-bridged channel](https://julialang.zulipchat.com/#narrow/stream/279055-sciml-bridged).
 For bugs or feature requests [open an issue](/~https://github.com/SciML/Catalyst.jl/issues).
 
 
-## Supporting and Citing Catalyst.jl
+## Supporting and citing Catalyst.jl
 The software in this ecosystem was developed as part of academic research. If you would like to help support it, 
 please star the repository as such metrics may help us secure funding in the future. If you use Catalyst as part 
 of your research, teaching, or other activities, we would be grateful if you could cite our work:

docs/Project.toml

@@ -1,9 +1,11 @@
 [deps]
 BifurcationKit = "0f109fa4-8a5d-4b75-95aa-f515264e7665"
 Catalyst = "479239e8-5488-4da2-87a7-35f2df7eef83"
+DiffEqFlux = "aae7a2af-3d4f-5e19-a356-7da93b79d9d0"
 DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+Flux = "587475ba-b771-5e3f-ad9e-33799f191a9c"
 HomotopyContinuation = "f213a82b-91d6-5c5d-acf7-10f1c761b327"
 Latexify = "23fbe1c1-3f47-55db-b15f-69d7ec21a316"
 ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"

docs/old_files/unused_tutorials/models.md

@@ -39,7 +39,7 @@ plot(sol, lw=2)
 ```
 ![models1](../assets/models1.svg)
 
-To solve for a steady-state starting from the guess `u0`, one can use
+To solve for a steady state starting from the guess `u0`, one can use
 ```julia
 using SteadyStateDiffEq
 prob = SteadyStateProblem(rn,u0,p)

docs/pages.jl

@@ -1,15 +1,15 @@
 pages = Any["Home" => "index.md",
-            "Introduction to Catalyst" => Any["intro_to_catalyst/catalyst_for_new_julia_users.md",
-                                              "intro_to_catalyst/using_catalyst.md"],
+            "Introduction to Catalyst" => Any["introduction_to_catalyst/catalyst_for_new_julia_users.md",
+                                              "introduction_to_catalyst/introduction_to_catalyst.md"],
             "Catalyst Functionality" => Any["catalyst_functionality/dsl_description.md",
                                             "catalyst_functionality/programmatic_CRN_construction.md",
                                             "catalyst_functionality/compositional_modeling.md",
                                             "catalyst_functionality/parametric_stoichiometry.md",
                                             "catalyst_functionality/network_analysis.md"],
-            "Catalyst Applications" => Any["tutorials/advanced_simulations.md",
-                                           "tutorials/homotopy_continuation.md",
-                                           "tutorials/bifurcation_diagrams.md",
-                                           "tutorials/parameter_estimation.md"],
+            "Catalyst Applications" => Any["catalyst_applications/advanced_simulations.md",
+                                           "catalyst_applications/homotopy_continuation.md",
+                                           "catalyst_applications/bifurcation_diagrams.md",
+                                           "catalyst_applications/parameter_estimation.md"],
             "Example Networks" => Any["example_networks/basic_CRN_examples.md",
                                       "example_networks/smoluchowski_coagulation_equation.md"],
             "FAQs" => "faqs.md",

docs/src/api/catalyst_api.md

@@ -3,7 +3,7 @@
 CurrentModule = Catalyst
 ```
 
-## Reaction Network Generation and Representation
+## Reaction network generation and representation
 Catalyst provides the [`@reaction_network`](@ref) macro for generating a
 complete network, stored as a [`ReactionSystem`](@ref), which in turn is
 composed of [`Reaction`](@ref)s. `ReactionSystem`s can be converted to other
@@ -79,7 +79,7 @@ Reaction
 ReactionSystem
 ```
 
-## ModelingToolkit and Catalyst Accessor Functions
+## [ModelingToolkit and Catalyst accessor functions](@id api_accessor_functions)
 A [`ReactionSystem`](@ref) is an instance of a
 `ModelingToolkit.AbstractTimeDependentSystem`, and has a number of fields that
 can be accessed using the Catalyst API and the [ModelingToolkit.jl Abstract
@@ -149,9 +149,9 @@ In the latter case `equations` is equivalent to `get_eqs`.
 Below we list the remainder of the Catalyst API accessor functions mentioned
 above.
 
-## Basic System Properties
+## Basic system properties
 See [Programmatic Construction of Symbolic Reaction Systems](@ref programmatic_CRN_construction) for examples and [ModelingToolkit and
-Catalyst Accessor Functions](@ref) for more details on the basic accessor
+Catalyst Accessor Functions](@ref api_accessor_functions) for more details on the basic accessor
 functions.
 
 ```@docs
@@ -168,7 +168,7 @@ Catalyst.isconstant
 Catalyst.isbc
 ```
 
-## Basic Reaction Properties
+## Basic reaction properties
 ```@docs
 ismassaction
 dependents
@@ -179,7 +179,7 @@ netstoichmat
 reactionrates
 ```
 
-## Functions to Extend or Modify a Network
+## Functions to extend or modify a network
 `ReactionSystem`s can be programmatically extended using [`addspecies!`](@ref),
 [`addparam!`](@ref), [`addreaction!`](@ref), [`@add_reactions`](@ref), or
 composed using [`ModelingToolkit.extend`](@ref) and
@@ -198,7 +198,7 @@ Catalyst.flatten
 merge!(network1::ReactionSystem, network2::ReactionSystem)
 ```
 
-## Network Analysis and Representations
+## Network analysis and representations
 Note, currently API functions for network analysis and conservation law analysis
 do not work with constant species (currently only generated by SBMLToolkit).
 
@@ -224,20 +224,28 @@ isweaklyreversible
 reset_networkproperties!
 ```
 
-## Network Comparison
+## Network comparison
 ```@docs
 ==(rn1::Reaction, rn2::Reaction)
 isequal_ignore_names
 ==(rn1::ReactionSystem, rn2::ReactionSystem)
 ```
 
-## Network Visualization
+## Network visualization
 [Latexify](https://korsbo.github.io/Latexify.jl/stable/) can be used to convert
 networks to LaTeX mhchem equations by
 ```julia
 using Latexify
 latexify(rn)
 ```
+An optional argument, `form` allows using `latexify` to display a reaction network's ODE (as generated by the reaction rate equation) or SDE (as generated by the chemical Langevin equation) form:
+```julia
+latexify(rn; form=:ode)
+```
+```julia
+latexify(rn; form=:sde)
+```
+(As of writing this, an upstream bug causes the SDE form to be erroneously displayed as the ODE form)
 
 If [Graphviz](https://graphviz.org/) is installed and commandline accessible, it
 can be used to create and save network diagrams using [`Graph`](@ref) and
@@ -248,7 +256,7 @@ complexgraph
 savegraph
 ```
 
-## Rate Laws
+## [Rate laws](@id api_rate_laws)
 As the underlying [`ReactionSystem`](@ref) is comprised of `ModelingToolkit`
 expressions, one can directly access the generated rate laws, and using
 `ModelingToolkit` tooling generate functions or Julia `Expr`s from them.
@@ -268,13 +276,13 @@ Base.convert
 ModelingToolkit.structural_simplify
 ```
 
-## Unit Validation
+## Unit validation
 ```@docs
 validate(rx::Reaction; info::String = "")
 validate(rs::ReactionSystem, info::String="")
 ```
 
-## Utility Functions
+## Utility functions
 ```@docs
 symmap_to_varmap
 ```