Api update

docs/src/api.md

@@ -84,6 +84,22 @@ Reaction
 ReactionSystem
 ```
 
+## [Options for the `@reaction_network` DSL](@id api_dsl_options)
+We have [previously described](@ref dsl_advanced_options) how options permits the user to supply non-reaction information to [`ReactionSystem`](@ref) created through the DSL. Here follows a list 
+of all options currently available.
+- [`parameters`]:(@ref dsl_advanced_options_declaring_species_and_parameters) Allows the designation of a set of symbols as system parameter. 
+- [`species`](@ref dsl_advanced_options_declaring_species_and_parameters): Allows the designation of a set of symbols as system species.
+- [`variables`](@ref dsl_advanced_options_declaring_species_and_parameters): Allows the designation of a set of symbols as system non-species variables. 
+- [`ivs`](@ref dsl_advanced_options_ivs): Allows the designation of a set of symbols as system independent variables.
+- [`compounds`](@ref chemistry_functionality_compounds): Allows the designation of compound species.
+- [`observables`](@ref dsl_advanced_options_observables): Allows the designation of compound observables. 
+- [`default_noise_scaling`](@ref simulation_intro_SDEs_noise_saling): Enables the setting of a default noise scaling expression.
+- [`differentials`](@ref constraint_equations_coupling_constraints): Allows the designation of differentials. 
+- [`equations`](@ref constraint_equations_coupling_constraints): Allows the creation of algebraic and/or differential equations. 
+- [`continuous_events`](@ref constraint_equations_events): Allows the creation of continuous events. 
+- [`discrete_events`](@ref constraint_equations_events): Allows the creation of discrete events.  
+- [`combinatoric_ratelaws`](@ref faq_combinatoric_ratelaws): Takes a single option (`true` or `false`), which sets whether to use combinatorial rate laws.
+
 ## [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
@@ -156,18 +172,36 @@ accessor functions.
 
 ```@docs
 species
+Catalyst.get_species
 nonspecies
 reactions
+Catalyst.get_rxs
 nonreactions
 numspecies
 numparams
 numreactions
 speciesmap
 paramsmap
-isspecies
 isautonomous
+```
+
+## Coupled reaction/equation system properties
+The following system property accessor functions are primarily relevant to reaction system [coupled 
+to differential and/or algebraic equations](@ref constraint_equations).
+```@docs
+ModelingToolkit.has_alg_equations
+ModelingToolkit.alg_equations
+ModelingToolkit.has_diff_equations
+ModelingToolkit.diff_equations
+```
+
+## Basic species properties
+The following functions permits the querying of species properties.
+```@docs
+isspecies
 Catalyst.isconstant
 Catalyst.isbc
+Catalyst.isvalidreactant
 ```
 
 ## Basic reaction properties
@@ -181,6 +215,17 @@ netstoichmat
 reactionrates
 ```
 
+## [Reaction metadata](@id api_rx_metadata)
+The following functions permits the retrieval of [reaction metadata](@ref dsl_advanced_options_reaction_metadata).
+```@docs
+Catalyst.hasnoisescaling
+Catalyst.getnoisescaling
+Catalyst.hasdescription
+Catalyst.getdescription
+Catalyst.hasmisc
+Catalyst.getmisc
+```
+
 ## [Functions to extend or modify a network](@id api_network_extension_and_modification)
 `ReactionSystem`s can be programmatically extended using [`ModelingToolkit.extend`](@ref) and
 [`ModelingToolkit.compose`](@ref).
@@ -307,23 +352,22 @@ LatticeReactionSystem
 The following functions can be used to querying the properties of `LatticeReactionSystem`s:
 ```@docs
 reactionsystem
-spatial_reactions
-lattice
-num_verts
-num_edges
-num_species
-spatial_species
-vertex_parameters
-edge_parameters
-edge_iterator
-is_transport_system
+Catalyst.spatial_reactions
+Catalyst.lattice
+Catalyst.num_verts
+Catalyst.num_edges
+Catalyst.num_species
+Catalyst.spatial_species
+Catalyst.vertex_parameters
+Catalyst.edge_parameters
+Catalyst.edge_iterator
+Catalyst.is_transport_system
 has_cartesian_lattice
 has_masked_lattice
 has_grid_lattice
 has_graph_lattice
 grid_size
 grid_dims
-get_lattice_graph
 ```
 In addition, most accessor functions for normal `ReactionSystem`s (such as `species` and `parameters`) works when applied to `LatticeReactionSystem`s as well.
 

docs/src/faqs.md

@@ -58,7 +58,7 @@ like
 plot(sol; idxs = [A, B])
 ```
 
-## How to disable rescaling of reaction rates in rate laws?
+## [How to disable rescaling of reaction rates in rate laws?](@id faq_combinatoric_ratelaws)
 As explained in the [Reaction rate laws used in simulations](@ref introduction_to_catalyst_ratelaws) section, for
 a reaction such as `k, 2X --> 0`, the generated rate law will rescale the rate
 constant, giving `k*X^2/2` instead of `k*X^2` for ODEs and `k*X*(X-1)/2` instead
@@ -71,6 +71,16 @@ osys = convert(ODESystem, rn; combinatoric_ratelaws=false)
 Disabling these rescalings should work for all conversions of `ReactionSystem`s
 to other `ModelingToolkit.AbstractSystem`s.
 
+When creating a [`ReactionSystem`](@ref) using the DSL, combinatoric rate laws can be disabled (for 
+the created system, and all systems derived from it) using the `@combinatoric_ratelaws` option (providing `false` as its only input):
+```@example faq1
+rn = @reaction_network begin
+    @combinatoric_ratelaws false
+    k, 2X --> 0
+end
+nothing # hide
+```
+
 ## How to use non-integer stoichiometric coefficients?
 ```@example faq2
 using Catalyst

docs/src/model_creation/chemistry_related_functionality.md

@@ -5,7 +5,7 @@ While Catalyst has primarily been designed around the modelling of biological sy
 - The `balance_reaction` function, which enables the user to balance a reaction so the same number of components occur on both sides.
 
 
-## Modelling with compound species
+## [Modelling with compound species](@id chemistry_functionality_compounds)
 
 ### Creating compound species programmatically
 We will first show how to create compound species through [programmatic model construction](@ref programmatic_CRN_construction), and then demonstrate using the DSL. To create a compound species, use the `@compound` macro, first designating the compound, followed by its components (and their stoichiometries). In this example, we will create a CO₂ molecule, consisting of one C atom and two O atoms. First, we create species corresponding to the components:

docs/src/model_creation/dsl_advanced.md

@@ -464,6 +464,8 @@ rx = @reaction p, 0 --> X, [description="A production reaction"]
 Catalyst.getdescription(rx)
 ```
 
+A list of all available reaction metadata can be found [in the api](@ref api_rx_metadata).
+
 ## [Working with symbolic variables and the DSL](@id dsl_advanced_options_symbolics_and_DSL)
 We have previously described how Catalyst represents its models symbolically (enabling e.g. symbolic differentiation of expressions stored in models). While Catalyst utilises this for many internal operation, these symbolic representations can also be accessed and harnessed by the user. Primarily, doing so is much easier during programmatic (as opposed to DSL-based) modelling. Indeed, the section on [programmatic modelling](@ref programmatic_CRN_construction) goes into more details about symbolic representation in models, and how these can be used. It is, however, also ways to utilise these methods during DSL-based modelling. Below we briefly describe two methods for doing so.
 

src/spatial_reaction_systems/spatial_reactions.jl

@@ -10,6 +10,11 @@ struct EdgeParameter end
 Symbolics.option_to_metadata_type(::Val{:edgeparameter}) = EdgeParameter
 
 # Implements the isedgeparameter check function.
+"""
+    isedgeparameter(p)
+
+Returns `true` if the parameter `p` is an edge parameter (else `false`).
+"""
 isedgeparameter(x::Num, args...) = isedgeparameter(Symbolics.unwrap(x), args...)
 function isedgeparameter(x, default = false)
     p = Symbolics.getparent(x, nothing)