Merge branch 'master' into uniting, with fixed conflicts.

# Conflicts:
#	src/ModelingToolkit.jl
#	src/systems/diffeqs/odesystem.jl
#	src/systems/pde/pdesystem.jl
#	src/systems/reaction/reactionsystem.jl

Author: Lucas Morton

Project.toml

@@ -1,7 +1,7 @@
 name = "ModelingToolkit"
 uuid = "961ee093-0014-501f-94e3-6117800e7a78"
 authors = ["Chris Rackauckas <[email protected]>"]
-version = "5.26.0"
+version = "6.2.2"
 
 [deps]
 AbstractTrees = "1520ce14-60c1-5f80-bbc7-55ef81b5835c"
@@ -73,7 +73,7 @@ Setfield = "0.7"
 SpecialFunctions = "0.7, 0.8, 0.9, 0.10, 1.0"
 StaticArrays = "0.10, 0.11, 0.12, 1.0"
 SymbolicUtils = "0.12, 0.13"
-Symbolics = "1.4.1"
+Symbolics = "3.0"
 UnPack = "0.1, 1.0"
 Unitful = "1.1"
 julia = "1.2"

docs/make.jl

@@ -40,7 +40,6 @@ makedocs(
             "systems/NonlinearSystem.md",
             "systems/OptimizationSystem.md",
             "systems/ControlSystem.md",
-            "systems/ReactionSystem.md",
             "systems/PDESystem.md",
         ],
         "comparison.md",

docs/src/basics/AbstractSystem.md

@@ -4,9 +4,16 @@
 
 The `AbstractSystem` interface is the core of the system level of ModelingToolkit.jl.
 It establishes a common set of functionality that is used between systems
-from ODEs and chemical reactions, allowing users to have a common framework for
+representing ODEs, PDEs, SDEs and more, allowing users to have a common framework for
 model manipulation and compilation.
 
+### Subtypes
+
+There are three immediate subtypes of `AbstractSystem`, classified by how many independent variables each type has:
+* `AbstractTimeIndependentSystem`: has no independent variable (eg: `NonlinearSystem`)
+* `AbstractTimeDependentSystem`: has a single independent variable (eg: `ODESystem`)
+* `AbstractMultivariateSystem`: may have multiple independent variables (eg: `PDESystem`)
+
 ## Constructors and Naming
 
 The `AbstractSystem` interface has a consistent method for constructing systems.
@@ -50,12 +57,11 @@ Optionally, a system could have:
 - `observed(sys)`: All observed equations of the system and its subsystems.
 - `get_observed(sys)`: Observed equations of the current-level system.
 - `get_defaults(sys)`: A `Dict` that maps variables into their default values.
-- `independent_variable(sys)`: The independent variable of a system.
+- `independent_variables(sys)`: The independent variables of a system.
 - `get_noiseeqs(sys)`: Noise equations of the current-level system.
 
-Note that there's `get_iv(sys)`, but it is not advised to use, since it errors
-when the system has no field `iv`. `independent_variable(sys)` returns `nothing`
-for `NonlinearSystem`s.
+Note that if you know a system is an `AbstractTimeDependentSystem` you could use `get_iv` to get the 
+unique independent variable directly, rather than using `independenent_variables(sys)[1]`, which is clunky and may cause problems if `sys` is an `AbstractMultivariateSystem` because there may be more than one independent variable. `AbstractTimeIndependentSystem`s do not have a method `get_iv`, and `independent_variables(sys)` will return a size-zero result for such. For an `AbstractMultivariateSystem`, `get_ivs` is equivalent.
 
 A system could also have caches:
 

docs/src/index.md

@@ -72,7 +72,7 @@ is built on, consult the
 - Nonlinear systems
 - Optimization problems
 - Continuous-Time Markov Chains
-- Chemical Reactions
+- Chemical Reactions (via [Catalyst.jl](https://github.com/SciML/Catalyst.jl))
 - Nonlinear Optimal Control
 
 ## Model Import Formats

docs/src/systems/JumpSystem.md

@@ -11,7 +11,7 @@ JumpSystem
 - `get_eqs(sys)` or `equations(sys)`: The equations that define the jump system.
 - `get_states(sys)` or `states(sys)`: The set of states in the jump system.
 - `get_ps(sys)` or `parameters(sys)`: The parameters of the jump system.
-- `independent_variable(sys)`: The independent variable of the jump system.
+- `get_iv(sys)`: The independent variable of the jump system.
 
 ## Transformations
 

docs/src/systems/ODESystem.md

@@ -11,7 +11,7 @@ ODESystem
 - `get_eqs(sys)` or `equations(sys)`: The equations that define the ODE.
 - `get_states(sys)` or `states(sys)`: The set of states in the ODE.
 - `get_ps(sys)` or `parameters(sys)`: The parameters of the ODE.
-- `independent_variable(sys)`: The independent variable of the ODE.
+- `get_iv(sys)`: The independent variable of the ODE.
 
 ## Transformations
 

docs/src/systems/ReactionSystem.md

@@ -17,7 +17,7 @@ sde = SDESystem(ode, noiseeqs)
 - `get_eqs(sys)` or `equations(sys)`: The equations that define the SDE.
 - `get_states(sys)` or `states(sys)`: The set of states in the SDE.
 - `get_ps(sys)` or `parameters(sys)`: The parameters of the SDE.
-- `independent_variable(sys)`: The independent variable of the SDE.
+- `get_iv(sys)`: The independent variable of the SDE.
 
 ## Transformations
 

docs/src/systems/SDESystem.md

@@ -14,7 +14,7 @@ equalities before solving. Let's see this in action.
 ```julia
 using ModelingToolkit, Plots, DifferentialEquations
 
-@parameters t
+@variables t
 @connector function Pin(;name)
     sts = @variables v(t)=1.0 i(t)=1.0
     ODESystem(Equation[], t, sts, []; name=name)
@@ -95,7 +95,8 @@ rc_eqs = [
           connect(capacitor.n, source.n, ground.g)
          ]
 
-@named rc_model = compose(ODESystem(rc_eqs, t),
+@named _rc_model = ODESystem(rc_eqs, t)
+@named rc_model = compose(_rc_model,
                           [resistor, capacitor, source, ground])
 sys = structural_simplify(rc_model)
 u0 = [
@@ -288,7 +289,8 @@ rc_eqs = [
 Finally we build our four component model with these connection rules:
 
 ```julia
-@named rc_model = compose(ODESystem(rc_eqs, t)
+@named _rc_model = ODESystem(rc_eqs, t)
+@named rc_model = compose(_rc_model,
                           [resistor, capacitor, source, ground])
 ```
 

docs/src/tutorials/acausal_components.md

@@ -13,15 +13,15 @@ We utilize the derivative operator twice here to define the second order:
 ```julia
 using ModelingToolkit, OrdinaryDiffEq
 
-@parameters t σ ρ β
-@variables x(t) y(t) z(t)
+@parameters σ ρ β
+@variables t x(t) y(t) z(t)
 D = Differential(t)
 
 eqs = [D(D(x)) ~ σ*(y-x),
        D(y) ~ x*(ρ-z)-y,
        D(z) ~ x*y - β*z]
 
-sys = ODESystem(eqs)
+@named sys = ODESystem(eqs)
 ```
 
 Note that we could've used an alternative syntax for 2nd order, i.e.