Merge pull request #1096 from SciML/myb/inh

Namespacing change & default variable syntax

Author: YingboMa

Project.toml

@@ -16,6 +16,7 @@ Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
 DomainSets = "5b8099bc-c8ec-5219-889f-1d9e522a28bf"
 IfElse = "615f187c-cbe4-4ef1-ba3b-2fcf58d6d173"
+InteractiveUtils = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
 JuliaFormatter = "98e50ef6-434e-11e9-1051-2b60c6c9e899"
 LabelledArrays = "2ee39098-c373-598a-b85f-a56591580800"
 Latexify = "23fbe1c1-3f47-55db-b15f-69d7ec21a316"

docs/src/basics/Composition.md

@@ -32,10 +32,10 @@ end
 
 @parameters t
 D = Differential(t)
-@named connected = ODESystem([
+@named connected = compose(ODESystem([
                         decay2.f ~ decay1.x
                         D(decay1.f) ~ 0
-                      ], t, systems=[decay1, decay2])
+                      ], t), decay1, decay2)
 
 equations(connected)
 
@@ -81,7 +81,7 @@ subsystems. A model is the composition of itself and its subsystems.
 For example, if we have:
 
 ```julia
-@named sys = ODESystem(eqs,indepvar,states,ps,system=[subsys])
+@named sys = compose(ODESystem(eqs,indepvar,states,ps),subsys)
 ```
 
 the `equations` of `sys` is the concatenation of `get_eqs(sys)` and
@@ -191,7 +191,7 @@ N = S + I + R
 @named ieqn = ODESystem([D(I) ~ β*S*I/N-γ*I])
 @named reqn = ODESystem([D(R) ~ γ*I])
 
-@named sir = ODESystem([   
+@named sir = compose(ODESystem([
                     S ~ ieqn.S,
                     I ~ seqn.I,
                     R ~ ieqn.R,
@@ -200,13 +200,12 @@ N = S + I + R
                     seqn.R ~ reqn.R,
                     ieqn.R ~ reqn.R,
                     reqn.I ~ ieqn.I], t, [S,I,R], [β,γ],
-                    systems=[seqn,ieqn,reqn],
-                    default_p = [
+                    defaults = [
                         seqn.β => β
                         ieqn.β => β
                         ieqn.γ => γ
                         reqn.γ => γ
-                    ])
+                    ]), seqn, ieqn, reqn)
 ```
 
 Note that the states are forwarded by an equality relationship, while
@@ -241,14 +240,6 @@ sol = solve(prob,Tsit5())
 sol[reqn.R]
 ```
 
-However, one can similarly simplify this process of inheritance by
-using `combine` which concatenates all of the vectors within the
-systems. For example, we could equivalently have done:
-
-```julia
-@named sir = combine([seqn,ieqn,reqn])
-```
-
 ## Tearing Problem Construction
 
 Some system types, specifically `ODESystem` and `NonlinearSystem`, can be further
@@ -259,12 +250,3 @@ strongly connected components calculated during the process of simplification
 as the basis for building pre-simplified nonlinear systems in the implicit
 solving. In summary: these problems are structurally modified, but could be
 more efficient and more stable.
-
-## Automatic Model Promotion (TODO)
-
-In many cases one might want to compose models of different types. For example,
-one may want to include a `NonlinearSystem` as a set of algebraic equations
-within an `ODESystem`, or one may want to use an `ODESystem` as a subsystem of
-an `SDESystem`. In these cases, the compostion works automatically by promoting
-the model via `promote_system`. System promotions exist in the cases where a
-mathematically-trivial definition of the promotion exists.

docs/src/systems/SDESystem.md

@@ -10,7 +10,7 @@ SDESystem
 
 - `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)s` or `parameters(sys)`: The parameters of the SDE.
+- `get_ps(sys)` or `parameters(sys)`: The parameters of the SDE.
 - `independent_variable(sys)`: The independent variable of the SDE.
 
 ## Transformations