Merge pull request #1231 from isaacsas/drop_symmap_in_docs

Drop symmap in docs

Author: isaacsas

docs/src/faqs.md

@@ -188,38 +188,11 @@ nothing  # hide
 while using ModelingToolkit symbolic variables we have
 ```@example faq4
 t = default_t()
-@parameters α β
-@species S(t) I(t) R(t)
-u0 = [S => 999.0, I => 1.0, R => 0.0]
-p  = (α => 1e-4, β => .01)
+u0 = [rn.S => 999.0, rn.I => 1.0, rn.R => 0.0]
+p  = (rn.α => 1e-4, rn.β => .01)
 op2  = ODEProblem(rn, u0, (0.0, 250.0), p)
 nothing  # hide
 ```
-*Note,* while symbolic mappings as in the last example will work with *any*
-`ModelingToolkit.AbstractSystem`, for example if one `convert`s `rn` to an
-`ODESystem`, `Symbol`-based mappings only work when passing a `ReactionSystem`
-directly into a problem type. That is, the following does not work
-```@julia
-osys = convert(ODESystem, rn)
-
-# this fails
-u0 = [:S => 999.0, :I => 1.0, :R => 0.0]
-p  = (:α => 1e-4, :β => .01)
-op  = ODEProblem(osys, u0, (0.0, 250.0), p)
-```
-In this case one must either use a symbolic mapping as was used to make `op2` in
-the second example, or one can use the `symmap_to_varmap` function to convert the
-`Symbol` mapping to a symbolic mapping. I.e. this works
-```@example faq4
-osys = convert(ODESystem, rn)
-osys = complete(osys)
-
-# this works
-u0 = symmap_to_varmap(rn, [:S => 999.0, :I => 1.0, :R => 0.0])
-p  = symmap_to_varmap(rn, (:α => 1e-4, :β => .01))
-op  = ODEProblem(osys, u0, (0.0, 250.0), p)
-nothing # hide
-```
 
 ## How to include non-reaction terms in equations for a chemical species?
 One method to add non-reaction terms into an ODE or algebraic equation for a

docs/src/introduction_to_catalyst/introduction_to_catalyst.md

@@ -117,7 +117,6 @@ Let's now use our `ReactionSystem` to generate and solve a corresponding mass
 action ODE model. We first convert the system to a `ModelingToolkit.ODESystem`
 by
 ```@example tut1
-rn = complete(rn)
 odesys = convert(ODESystem, rn)
 ```
 (Here Latexify is used automatically to display `odesys` in Latex within Markdown
@@ -144,7 +143,8 @@ u₀symmap = [rn.m₁ => 0., rn.m₂ => 0., rn.m₃ => 0., rn.P₁ => 20.,
     rn.P₂ => 0., rn.P₃ => 0.]
 nothing   # hide
 ```
-Knowing these mappings we can set up the `ODEProblem` we want to solve:
+Knowing one of the preceding mappings we can set up the `ODEProblem` we want to
+solve:
 
 ```@example tut1
 # time interval to solve on
@@ -159,22 +159,14 @@ By passing `rn` directly to the `ODEProblem`, Catalyst has to
 symbolic ODEs. We could instead pass `odesys` directly like
 ```@example tut1
 odesys = complete(odesys)
-oprob2 = ODEProblem(odesys, u₀symmap, tspan, psymmap)
+oprob2 = ODEProblem(odesys, u₀map, tspan, pmap)
 nothing   # hide
 ```
 `oprob` and `oprob2` are functionally equivalent, each representing the same
 underlying problem.
 
 !!! note
-    When passing `odesys` to `ODEProblem` we needed to use the symbolic
-    variable-based parameter mappings, `u₀symmap` and `psymmap`, while when
-    directly passing `rn` we could use either those or the
-    `Symbol`-based mappings, `u₀map` and `pmap`. `Symbol`-based mappings can
-    always be converted to `symbolic` mappings using [`symmap_to_varmap`](@ref).
-
-
-!!! note
-    Above we have used `rn = complete(rn)` and `odesys = complete(odesys)` to mark these systems as *complete*, indicating to Catalyst and ModelingToolkit that these models are finalized. This must be done before any system is given as input to a `convert` call or some problem type. `ReactionSystem` models created through the `@reaction_network` DSL (which is introduced elsewhere, and primarily used throughout these documentation) are always marked as complete when generated. Hence `complete` does not need to be called on them. Symbolically generated `ReactionSystem`s, `ReactionSystem`s generated via the `@network_component` macro, and any ModelingToolkit system generated by `convert` always needs to be manually marked as `complete` as we do for `odesys` above. An expanded description on *completeness* can be found [here](@ref completeness_note).
+    Above we have used `odesys = complete(odesys)` to mark the `ODESystem` as *complete*, indicating to Catalyst and ModelingToolkit that these models are finalized. This must be done before any system is given as input to a `convert` call or some problem type. `ReactionSystem` models created through the `@reaction_network` DSL, like `rn` above, are always marked as complete when generated. Hence `complete` does not need to be called on them. Symbolically generated `ReactionSystem`s, `ReactionSystem`s generated via the `@network_component` macro, and any ModelingToolkit system generated by `convert` always needs to be manually marked as `complete` as we do for `odesys` above. An expanded description on *completeness* can be found [here](@ref completeness_note).
 
 At this point we are all set to solve the ODEs. We can now use any ODE solver
 from within the

docs/src/model_creation/parametric_stoichiometry.md

@@ -173,9 +173,8 @@ bval = 70
 k₋val = 0.001
 k₊val = 0.05
 kₚval = pmean * γₚval * (k₋val * pmean^2 + k₊val) / (k₊val * bval)
-p = symmap_to_varmap(jsys, (:k₊ => k₊val, :k₋ => k₋val, :kₚ => kₚval,
-                            :γₚ => γₚval, :b => bval))
-u₀ = symmap_to_varmap(jsys, [:G₊ => 1, :G₋ => 0, :P => 1])
+p = (:k₊ => k₊val, :k₋ => k₋val, :kₚ => kₚval, :γₚ => γₚval, :b => bval)
+u₀ = [:G₊ => 1, :G₋ => 0, :P => 1]
 tspan = (0., 6.0)   # time interval to solve over
 dprob = DiscreteProblem(jsys, u₀, tspan, p)
 jprob = JumpProblem(jsys, dprob, Direct())