major docs cleanup

Author: ChrisRackauckas

docs/src/systems/SDESystem.md

@@ -18,9 +18,9 @@ SDESystem
 ## Function Calculation and Generation
 
 ```@docs
-calculate_jacobian
-calculate_tgrad
-calculate_factorized_W
+calculate_jacobian(sys::ModelingToolkit.AbstractODESystem)
+calculate_tgrad(sys::ModelingToolkit.AbstractODESystem)
+calculate_factorized_W(sys::ModelingToolkit.AbstractODESystem, simplify)
 generate_jacobian
 generate_tgrad
 generate_factorized_W

src/ModelingToolkit.jl

@@ -66,9 +66,9 @@ function independent_variables end
 """
 $(TYPEDSIGNATURES)
 
-Get the set of dependent variables for the given system.
+Get the set of states for the given system.
 """
-function dependent_variables end
+function states end
 
 """
 $(TYPEDSIGNATURES)

src/systems/diffeqs/abstractodesystem.jl

@@ -173,6 +173,12 @@ function DiffEqBase.ODEProblem(sys::AbstractODESystem, args...; kwargs...)
     ODEProblem{true}(sys, args...; kwargs...)
 end
 
+"""
+$(TYPEDEF)
+
+Generates an ODEProblem from an ODESystem and allows for automatically
+symbolically calculating numerical enhancements.
+"""
 function DiffEqBase.ODEProblem{iip}(sys::AbstractODESystem,u0map,tspan,
                                     parammap=DiffEqBase.NullParameters();
                                     version = nothing, tgrad=false,

src/systems/diffeqs/first_order_transform.jl

@@ -13,7 +13,7 @@ function flatten_differential(O::Operation)
 end
 
 """
-ode_order_lowering(sys::ODESystem)
+$(TYPEDSIGNATURES)
 
 Takes a Nth order ODESystem and returns a new ODESystem written in first order
 form by defining new variables which represent the N-1 derivatives.

src/systems/diffeqs/modelingtoolkitize.jl

@@ -1,5 +1,5 @@
 """
-$(SIGNATURES)
+$(TYPEDSIGNATURES)
 
 Generate `ODESystem`, dependent variables, and parameters from an `ODEProblem`.
 """

src/systems/diffeqs/odesystem.jl

@@ -4,9 +4,9 @@ $(TYPEDEF)
 A system of ordinary differential equations.
 
 # Fields
-* `eqs` - The ODEs defining the system.
+$(FIELDS)
 
-# Examples
+# Example
 
 ```
 using ModelingToolkit
@@ -19,7 +19,7 @@ eqs = [D(x) ~ σ*(y-x),
        D(y) ~ x*(ρ-z)-y,
        D(z) ~ x*y - β*z]
 
-de = ODESystem(eqs)
+de = ODESystem(eqs,[x,y,z],[σ,ρ,β])
 ```
 """
 struct ODESystem <: AbstractODESystem

src/systems/diffeqs/sdesystem.jl

@@ -1,8 +1,36 @@
+"""
+$(TYPEDEF)
+
+A system of stochastic differential equations.
+
+# Fields
+$(FIELDS)
+
+# Example
+
+```
+using ModelingToolkit
+
+@parameters t σ ρ β
+@variables x(t) y(t) z(t)
+@derivatives D'~t
+
+eqs = [D(x) ~ σ*(y-x),
+       D(y) ~ x*(ρ-z)-y,
+       D(z) ~ x*y - β*z]
+
+noiseeqs = [0.1*x,
+            0.1*y,
+            0.1*z]
+
+de = SDESystem(eqs,noiseeqs,t,[x,y,z],[σ,ρ,β])
+```
+"""
 struct SDESystem <: AbstractODESystem
     """The expressions defining the drift term."""
     eqs::Vector{Equation}
     """The expressions defining the diffusion term."""
-    noiseeqs
+    noiseeqs::AbstractArray{Operation}
     """Independent variable."""
     iv::Variable
     """Dependent (state) variables."""
@@ -122,6 +150,12 @@ function rename(sys::SDESystem,name)
     ODESystem(sys.eqs, sys.noiseeqs, sys.iv, sys.states, sys.ps, sys.tgrad, sys.jac, sys.Wfact, sys.Wfact_t, name, sys.systems)
 end
 
+"""
+$(TYPEDEF)
+
+Generates an SDEProblem from an SDESystem and allows for automatically
+symbolically calculating numerical enhancements.
+"""
 function DiffEqBase.SDEProblem{iip}(sys::SDESystem,u0map,tspan,p=parammap;
                                     version = nothing, tgrad=false,
                                     jac = false, Wfact = false,

src/systems/nonlinear/nonlinearsystem.jl

@@ -4,7 +4,7 @@ $(TYPEDEF)
 A nonlinear system of equations.
 
 # Fields
-* `eqs` - Vector of equations defining the system.
+$(FIELDS)
 
 # Examples
 
@@ -76,6 +76,12 @@ function generate_function(sys::NonlinearSystem, vs = states(sys), ps = paramete
     return build_function(rhss, vs′, ps′, (), NLSysToExpr(sys), expression; kwargs...)
 end
 
+"""
+$(TYPEDEF)
+
+Generates an NonlinearProblem from a NonlinearSystem and allows for automatically
+symbolically calculating numerical enhancements.
+"""
 function DiffEqBase.NonlinearProblem{iip}(sys::NonlinearSystem,u0map,tspan,
                                           parammap=DiffEqBase.NullParameters();
                                           jac = false, sparse=false,

src/systems/optimization/optimizationsystem.jl

@@ -4,7 +4,7 @@ $(TYPEDEF)
 A scalar equation for optimization.
 
 # Fields
-* `op` - The objective function
+$(FIELDS)
 
 # Examples
 
@@ -70,6 +70,12 @@ end
 equations(sys::OptimizationSystem) = isempty(sys.systems) ? sys.op : sys.op + reduce(+,namespace_operation.(sys.systems))
 namespace_operation(sys::OptimizationSystem) = namespace_operation(sys.op,sys.name,nothing)
 
+"""
+$(TYPEDEF)
+
+Generates an OptimizationProblem from an OptimizationSystem and allows for automatically
+symbolically calculating numerical enhancements.
+"""
 function DiffEqBase.OptimizationProblem{iip}(sys::OptimizationSystem,
                                           parammap=DiffEqBase.NullParameters();
                                           u0=nothing, lb=nothing, ub=nothing,