refactor: rename getu/setu to getsym/setsym

docs/src/api.md

@@ -46,7 +46,7 @@ is_markovian
 
 If the index provider contains parameters that change during the course of the simulation
 at discrete time points, it must implement the following methods to ensure correct
-functioning of [`getu`](@ref) and [`getp`](@ref) for value providers that save the parameter
+functioning of [`getsym`](@ref) and [`getp`](@ref) for value providers that save the parameter
 timeseries. Note that there can be multiple parameter timeseries, in case different parameters
 may change at different times.
 
@@ -69,10 +69,13 @@ is_timeseries
 state_values
 set_state!
 current_time
-getu
-setu
+getsym
+setsym
 ```
 
+!!! note
+    `getu` and `setu` have been renamed to [`getsym`](@ref) and [`setsym`](@ref) respectively.
+
 #### Historical value providers
 
 ```@docs
@@ -95,7 +98,7 @@ ParameterIndexingProxy
 
 If a solution object saves a timeseries of parameter values that are updated during the
 simulation (such as by callbacks), it must implement the following methods to ensure
-correct functioning of [`getu`](@ref) and [`getp`](@ref).
+correct functioning of [`getsym`](@ref) and [`getp`](@ref).
 
 Parameter timeseries support requires that the value provider store the different
 timeseries in a [`ParameterTimeseriesCollection`](@ref).

docs/src/complete_sii.md

@@ -174,9 +174,9 @@ end
 ```
 
 If a type contains the value of state variables, it can define [`state_values`](@ref) to
-enable the usage of [`getu`](@ref) and [`setu`](@ref). These methods retturn getter/
+enable the usage of [`getsym`](@ref) and [`setsym`](@ref). These methods retturn getter/
 setter functions to access or update the value of a state variable (or a collection of
-them). If the type also supports generating [`observed`](@ref) functions, `getu` also
+them). If the type also supports generating [`observed`](@ref) functions, `getsym` also
 enables returning functions to access the value of arbitrary expressions involving
 the system's symbols. This also requires that the type implement
 [`parameter_values`](@ref) and [`current_time`](@ref) (if the system is time-dependent).
@@ -202,21 +202,21 @@ Then the following example would work:
 ```julia
 sys = ExampleSystem(Dict(:x => 1, :y => 2, :z => 3), Dict(:a => 1, :b => 2), :t, Dict())
 integrator = ExampleIntegrator([1.0, 2.0, 3.0], [4.0, 5.0], 6.0, sys)
-getx = getu(sys, :x)
+getx = getsym(sys, :x)
 getx(integrator) # 1.0
 
-get_expr = getu(sys, :(x + y + t))
+get_expr = getsym(sys, :(x + y + t))
 get_expr(integrator) # 13.0
 
-setx! = setu(sys, :y)
+setx! = setsym(sys, :y)
 setx!(integrator, 0.0)
 getx(integrator) # 0.0
 ```
 
 In case a type stores timeseries data (such as solutions), then it must also implement
 the [`Timeseries`](@ref) trait. The type would then return a timeseries from
 [`state_values`](@ref) and [`current_time`](@ref) and the function returned from
-[`getu`](@ref) would then return a timeseries as well. For example, consider the
+[`getsym`](@ref) would then return a timeseries as well. For example, consider the
 `ExampleSolution` below:
 
 ```julia
@@ -242,20 +242,20 @@ Then the following example would work:
 ```julia
 # using the same system that the ExampleIntegrator used
 sol = ExampleSolution([[1.0, 2.0, 3.0], [1.5, 2.5, 3.5]], [4.0, 5.0], [6.0, 7.0], sys)
-getx = getu(sys, :x)
+getx = getsym(sys, :x)
 getx(sol) # [1.0, 1.5]
 
-get_expr = getu(sys, :(x + y + t))
+get_expr = getsym(sys, :(x + y + t))
 get_expr(sol) # [9.0, 11.0]
 
-get_arr = getu(sys, [:y, :(x + a)])
+get_arr = getsym(sys, [:y, :(x + a)])
 get_arr(sol) # [[2.0, 5.0], [2.5, 5.5]]
 
-get_tuple = getu(sys, (:z, :(z * t)))
+get_tuple = getsym(sys, (:z, :(z * t)))
 get_tuple(sol) # [(3.0, 18.0), (3.5, 24.5)]
 ```
 
-Note that `setu` is not designed to work for `Timeseries` objects.
+Note that `setsym` is not designed to work for `Timeseries` objects.
 
 If a type needs to perform some additional actions when updating the state/parameters
 or if it is not possible to return a mutable reference to the state/parameter vector
@@ -315,7 +315,7 @@ setp(integrator, :b)(integrator, 3.0) # functionally the same as above
 
 If a solution object includes modified parameter values (such as through callbacks) during the
 simulation, it must implement several additional functions for correct functioning of
-[`getu`](@ref) and [`getp`](@ref). [`ParameterTimeseriesCollection`](@ref) helps in
+[`getsym`](@ref) and [`getp`](@ref). [`ParameterTimeseriesCollection`](@ref) helps in
 implementing parameter timeseries objects. The following mockup gives an example of
 correct implementation of these functions and the indexing syntax they enable.
 
@@ -457,12 +457,12 @@ sol.ps[:(b + c)] # observed quantities work too
 ```
 
 ```@example param_timeseries
-getu(sol, :b)(sol) # works
+getsym(sol, :b)(sol) # works
 ```
 
 ```@example param_timeseries
 try
-  getu(sol, [:b, :d])(sol) # errors since :b and :d belong to different timeseries
+  getsym(sol, [:b, :d])(sol) # errors since :b and :d belong to different timeseries
 catch e
   showerror(stdout, e)
 end

docs/src/usage.md

@@ -123,11 +123,11 @@ sol[allvariables] # equivalent to sol[all_variable_symbols(sol)]
 
 ### Evaluating expressions
 
-`getu` also generates functions for expressions if the object passed to it supports
+`getsym` also generates functions for expressions if the object passed to it supports
 [`observed`](@ref). For example:
 
 ```@example Usage
-getu(prob, x + y + z)(prob)
+getsym(prob, x + y + z)(prob)
 ```
 
 To evaluate this function using values other than the ones contained in `prob`, we need
@@ -137,7 +137,7 @@ which has trivial implementations of the above functions. We can thus do:
 
 ```@example Usage
 temp_state = ProblemState(; u = [0.1, 0.2, 0.3, 0.4], p = parameter_values(prob))
-getu(prob, x + y + z)(temp_state)
+getsym(prob, x + y + z)(temp_state)
 ```
 
 Note that providing all of the state vector, parameter object and time may not be

src/SymbolicIndexingInterface.jl

@@ -35,7 +35,7 @@ include("parameter_timeseries_collection.jl")
 export getp, setp, setp_oop
 include("parameter_indexing.jl")
 
-export getu, setu
+export getsym, setsym, getu, setu
 include("state_indexing.jl")
 
 export BatchedInterface, setsym_oop, associated_systems

src/batched_interface.jl

@@ -2,7 +2,7 @@
     struct BatchedInterface{S <: AbstractVector, I}
     function BatchedInterface(indp_syms::Tuple...)
 
-A struct which stores information for batched calls to [`getu`](@ref) or [`setu`](@ref).
+A struct which stores information for batched calls to [`getsym`](@ref) or [`setsym`](@ref).
 Given `Tuple`s, where the first element of each tuple is an index provider and the second
 an array of symbolic variables (either states or parameters) in the index provider,
 `BatchedInterface` will compute the union of all symbols and associate each symbol with
@@ -17,7 +17,7 @@ be retained internally.
 `BatchedInterface` implements [`variable_symbols`](@ref), [`is_variable`](@ref),
 [`variable_index`](@ref) to query the order of symbols in the union.
 
-See [`getu`](@ref) and [`setu`](@ref) for further details.
+See [`getsym`](@ref) and [`setsym`](@ref) for further details.
 
 See also: [`associated_systems`](@ref).
 """
@@ -118,7 +118,7 @@ is the index of the index provider associated with the corresponding symbol in
 associated_systems(bi::BatchedInterface) = bi.associated_systems
 
 """
-    getu(bi::BatchedInterface)
+    getsym(bi::BatchedInterface)
 
 Given a [`BatchedInterface`](@ref) composed from `n` index providers (and corresponding
 symbols), return a function which takes `n` corresponding value providers and returns an
@@ -127,7 +127,7 @@ an `AbstractArray` of the appropriate `eltype` and size as its first argument, i
 case the operation will populate the array in-place with the values of the symbols in the
 union.
 
-Note that all of the value providers passed to the function returned by `getu` must satisfy
+Note that all of the value providers passed to the function returned by `getsym` must satisfy
 `is_timeseries(prob) === NotTimeseries()`.
 
 The value of the `i`th symbol in the union (obtained through `variable_symbols(bi)[i]`) is
@@ -137,7 +137,7 @@ provider at index `associated_systems(bi)[i]`).
 See also: [`variable_symbols`](@ref), [`associated_systems`](@ref), [`is_timeseries`](@ref),
 [`NotTimeseries`](@ref).
 """
-function getu(bi::BatchedInterface)
+function getsym(bi::BatchedInterface)
     numprobs = length(bi.system_to_symbol_subset)
     probnames = [Symbol(:prob, i) for i in 1:numprobs]
 
@@ -189,13 +189,13 @@ function getu(bi::BatchedInterface)
 end
 
 """
-    setu(bi::BatchedInterface)
+    setsym(bi::BatchedInterface)
 
 Given a [`BatchedInterface`](@ref) composed from `n` index providers (and corresponding
 symbols), return a function which takes `n` corresponding problems and an array of the
 values, and updates each of the problems with the values of the corresponding symbols.
 
-Note that all of the value providers passed to the function returned by `setu` must satisfy
+Note that all of the value providers passed to the function returned by `setsym` must satisfy
 `is_timeseries(prob) === NotTimeseries()`.
 
 Note that if any subset of the `n` index providers share common symbols (among those passed
@@ -204,7 +204,7 @@ updated with the values of the common symbols.
 
 See also: [`is_timeseries`](@ref), [`NotTimeseries`](@ref).
 """
-function setu(bi::BatchedInterface)
+function setsym(bi::BatchedInterface)
     numprobs = length(bi.system_to_symbol_subset)
     probnames = [Symbol(:prob, i) for i in 1:numprobs]
 

src/problem_state.jl

@@ -3,7 +3,7 @@
     function ProblemState(; u = nothing, p = nothing, t = nothing)
 
 A value provider struct which can be used as an argument to the function returned by
-[`getu`](@ref) or [`setu`](@ref). It stores the state vector, parameter object and
+[`getsym`](@ref) or [`setsym`](@ref). It stores the state vector, parameter object and
 current time, and forwards calls to [`state_values`](@ref), [`parameter_values`](@ref),
 [`current_time`](@ref), [`set_state!`](@ref), [`set_parameter!`](@ref) to the contained
 objects.

src/remake.jl

@@ -46,7 +46,7 @@ function remake_buffer(sys, oldbuffer::AbstractArray, idxs, vals)
             else
                 v = elT(v)
             end
-            setu(sys, k)(newbuffer, v)
+            setsym(sys, k)(newbuffer, v)
         end
     else
         mutbuffer = remake_buffer(sys, collect(oldbuffer), idxs, vals)
@@ -80,7 +80,7 @@ end
 function remake_buffer(sys, oldbuffer::Tuple, idxs, vals)
     wrap = TupleRemakeWrapper(oldbuffer)
     for (idx, val) in zip(idxs, vals)
-        setu(sys, idx)(wrap, val)
+        setsym(sys, idx)(wrap, val)
     end
     return wrap.t
 end