Merge e082f6c into 1f8b6b0

HISTORY.md

@@ -3,11 +3,22 @@
 ## Catalyst unreleased (master branch) 
 - **BREAKING:** added a dependency on Nemo.jl for integer matrix linear algebra methods.
 - Added `incidencematgraph`, `linkageclasses`, `deficiency`, `subnetworks`, `linkagedeficiency`, `isreversible` and `isweaklyreversible` API functions.
+- Added the ability to compose `ReactionSystem`s via subsystems, and include
+  either `ODESystem`s or `NonlinearSystem`s as subsystems. Note, if using
+  subsystems it is not currently possible to convert to a `JumpSystem`. It is
+  also not possible to include either `SDESystem`s or `JumpSystems` as
+  subsystems.
+- Depreciated `merge`, use `ModelingToolkit.extend` instead.
+- Depreciated `params` and `numparams` (use `ModelingToolkit.parameters` to get
+  all parameters of a system and all subsystems, or use `reactionparams` to get
+  all parameters of a system and all `ReactionSystem` subsystems. The latter
+  correspond to those parameters used within `Reaction`s.)
 
 ## Catalyst 9.0
-*1.* **BREAKING:** `netstoichmat`, `prodstoichmat` and `substoichmat` are now transposed to be
-number of species by number of reactions. This is more consistent with the chemical
-reaction network literature for stoichiometry matrices.
+*1.* **BREAKING:** `netstoichmat`, `prodstoichmat` and `substoichmat` are now
+transposed to be number of species by number of reactions. This is more
+consistent with the chemical reaction network literature for stoichiometry
+matrices.
 
 *2.* `reactioncomplexmap` added to provide a mapping from reaction complexes to
 reactions they participate in.

Project.toml

@@ -37,6 +37,7 @@ julia = "1.5"
 [extras]
 Graphviz_jll = "3c863552-8265-54e4-a6dc-903eb78fde85"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+NonlinearSolve = "8913a72c-1f9b-4ce2-8d82-65094dcecaec"
 OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 SafeTestsets = "1bc83da4-3b8d-516f-aca4-4fe02f6d838f"
@@ -48,4 +49,4 @@ Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
 
 [targets]
-test = ["Graphviz_jll", "LinearAlgebra", "OrdinaryDiffEq", "Random", "SafeTestsets", "StableRNGs", "Statistics", "SteadyStateDiffEq", "StochasticDiffEq", "Test", "Unitful"]
+test = ["Graphviz_jll", "LinearAlgebra", "NonlinearSolve", "OrdinaryDiffEq", "Random", "SafeTestsets", "StableRNGs", "Statistics", "SteadyStateDiffEq", "StochasticDiffEq", "Test", "Unitful"]

docs/src/api/catalyst_api.md

@@ -79,14 +79,25 @@ ReactionSystem
 ```@docs
 species
 speciesmap
-params
+ModelingToolkit.parameters
+reactionparams
 paramsmap
 reactions
 numspecies
 numparams
-numreactions
+numreactionparams
 ```
 
+## ModelingToolkit-Inherited Accessor Functions
+- `ModelingToolkit.get_eqs(sys)`: The reactions of the system (ignores subsystems).
+- `ModelingToolkit.equations(sys)`: Collects all reactions and equations from
+  the system and all subsystems.
+- `ModelingToolkit.get_states(sys)`: The set of chemical species in the system (ignores subsystems).
+- `ModelingToolkit.states(sys)`: Collects all species and states from the system and all subsystems.
+- `ModelingToolkit.get_ps(sys)`: The parameters of the system (ignores subsystems).
+- `ModelingToolkit.parameters(sys)`: Collects all parameters from the system and all subsystems.
+- `ModelingToolkit.get_iv(sys)`: The independent variable of the system, usually time.
+
 ## Basic Reaction Properties
 ```@docs
 ismassaction
@@ -98,21 +109,14 @@ netstoichmat
 reactionrates
 ```
 
-## Composition and Accessor Functions for [`ReactionSystem`](@ref)s
-- `ModelingToolkit.get_eqs(sys)` or `equations(sys)`: The reactions that define the system.
-- `ModelingToolkit.get_states(sys)` or `states(sys)`: The set of chemical species in the system.
-- `ModelingToolkit.get_ps(sys)` or `parameters(sys)`: The parameters of the system.
-- `ModelingToolkit.get_iv(sys)`: The independent variable of the reaction
-  system, usually time.
-
 ## Functions to Extend a Network
 ```@docs
 @add_reactions
 addspecies!
 addparam!
 addreaction!
-merge!(network1::ReactionSystem, network2::ReactionSystem)
-merge(network1::ReactionSystem, network2::ReactionSystem)
+ModelingToolkit.extend
+ModelingToolkit.compose
 ```
 
 ## Network Analysis and Representations
@@ -136,8 +140,9 @@ isweaklyreversible
 
 ## Network Comparison 
 ```@docs
-==(rn1::ReactionSystem, rn2::ReactionSystem)
 ==(rn1::Reaction, rn2::Reaction)
+isequal_without_names
+==(rn1::ReactionSystem, rn2::ReactionSystem)
 ```
 
 ## Network Visualization

docs/src/tutorials/advanced_examples.md

@@ -21,7 +21,7 @@ tspan = (0.,4.)
 u0    = [5.]   
 osys  = convert(ODESystem, rs)
 u0map = map((x,y) -> Pair(x,y), species(rs), u0)
-pmap  = map((x,y) -> Pair(x,y), params(rs), p)
+pmap  = map((x,y) -> Pair(x,y), parameters(rs), p)
 oprob = ODEProblem(osys, u0map, tspan, pmap)
 sol   = solve(oprob, Tsit5())
 ```

docs/src/tutorials/basics.md

@@ -35,7 +35,7 @@ called `rn`). The generated `ReactionSystem` can be converted to a differential
 equation model via
 ```julia
 osys = convert(ODESystem, rn)
-oprob = ODEProblem(osys, Pair.(species(rn),u0), tspan, Pair.(params(rn),p))
+oprob = ODEProblem(osys, Pair.(species(rn),u0), tspan, Pair.(parameters(rn),p))
 ```
 or more directly via
 ```julia

docs/src/tutorials/generated_systems.md

@@ -6,7 +6,7 @@ API method listed first:
 
 * [`species(rn)`](@ref) and `states(rn)` is a vector of all the chemical
   species within the system, each represented as a `ModelingToolkit.Term`.
-* [`params(rn)`](@ref) and `parameters(rn)` is a vector of all the parameters
+* [`parameters(rn)`](@ref) is a vector of all the parameters
   within the system, each represented as a `ModelingToolkit.Sym`.
 * [`reactions(rn)`](@ref) and `equations(rn)` is a vector of all the
   `Reaction`s within the system.
@@ -37,4 +37,5 @@ Empty `ReactionSystem`s can be generated via [`make_empty_network`](@ref) or
 [`@reaction_network`](@ref) with no arguments (giving one argument to the latter
 will specify a system name). `ReactionSystem`s can be programmatically extended
 using [`addspecies!`](@ref), [`addparam!`](@ref), [`addreaction!`](@ref),
-[`@add_reactions`](@ref), or composed using `merge` and `merge!`.
+[`@add_reactions`](@ref), or composed using [`ModelingToolkit.extend`](@ref) and
+`ModelingToolkit.compose`](@ref).

docs/src/tutorials/models.md

@@ -25,7 +25,7 @@ sol = solve(prob, Tsit5())
 ```
 Here, the order of unknowns in `u0` and `p` matches the order that species and
 parameters first appear within the DSL. They can also be determined by examining
-the ordering within the [`species(rn)`](@ref) and [`params(rn)`](@ref) vectors,
+the ordering within the [`species(rn)`](@ref) and [`parameters(rn)`](@ref) vectors,
 or accessed more explicitly through the [`speciesmap(rn)`](@ref) and
 [`paramsmap(rn)`](@ref) dictionaries, which map the ModelingToolkit `Term`s
 and/or `Sym`s corresponding to each species or parameter to their integer id.

docs/src/tutorials/using_catalyst.md

@@ -163,7 +163,7 @@ species(repressilator)
  P₃(t)
 ```
 ```julia
-params(repressilator)
+parameters(repressilator)
 ```
 ```julia
 7-element Array{Sym{ModelingToolkit.Parameter{Real}},1}:
@@ -198,7 +198,7 @@ instead pass `odesys` directly, provided we construct mappings from each species
 to their initial value, and each parameter to their value like:
 ```julia
 u₀map  = Pair.(species(repressilator), u₀)
-pmap   = Pair.(params(repressilator), p)
+pmap   = Pair.(parameters(repressilator), p)
 oprob2 = ODEProblem(osys, u₀map, tspan, pmap)
 ```
 `oprob` and `oprob2` are functionally equivalent, each representing the same

src/Catalyst.jl

@@ -4,27 +4,31 @@ $(DocStringExtensions.README)
 module Catalyst
 
 using DocStringExtensions
-using SparseArrays, DiffEqBase, Reexport, ModelingToolkit, DiffEqJump
+using SparseArrays, DiffEqBase, Reexport, DiffEqJump
 using Latexify, Requires
 
 # ModelingToolkit imports and convenience functions we use
+using ModelingToolkit; 
 using Symbolics
 using ModelingToolkit: Symbolic, value, istree, get_states, get_ps, get_iv, get_systems, 
-                       get_eqs, get_defaults, toparam
+                       get_eqs, get_defaults, toparam, get_defaults, get_observed
 import ModelingToolkit: get_variables, namespace_expr, namespace_equation, get_variables!, 
-                        modified_states!, validate
+                        modified_states!, validate, namespace_variables, namespace_parameters
 
 # internal but needed ModelingToolkit functions
 import ModelingToolkit: check_variables, check_parameters, _iszero, _merge, check_units, get_unit
 
 const DEFAULT_IV = (@parameters t)[1]
 @reexport using ModelingToolkit
 
-import Base: (==), merge!, merge, hash, size, getindex, setindex, isless, Sort.defalg, length, show
+import Base: (==), hash, size, getindex, setindex, isless, Sort.defalg, length, show
 import MacroTools, LightGraphs
-const LG = LightGraphs
 import Nemo: FlintZZ, matrix, nullspace, rank
 
+# convenience shorthands for packages
+const MT = ModelingToolkit
+const LG = LightGraphs
+
 # as used in Catlab
 const USE_GV_JLL = Ref(false)
 function __init__()
@@ -54,7 +58,7 @@ include("registered_functions.jl")
 
 # functions to query network properties
 include("networkapi.jl")
-export species, params, reactions, speciesmap, paramsmap, numspecies, numreactions, numparams
+export species, reactionparams, reactions, speciesmap, paramsmap, numspecies, numreactions, numparams
 export make_empty_network, addspecies!, addparam!, addreaction!
 export dependants, dependents, substoichmat, prodstoichmat, netstoichmat
 export conservationlaws, conservedquantities