Merge pull request #72 from SciML/as/hotfix

fix: observed getu generation, tuple wrapper

Author: ChrisRackauckas

Project.toml

@@ -1,7 +1,7 @@
 name = "SymbolicIndexingInterface"
 uuid = "2efcf032-c050-4f8e-a9bb-153293bab1f5"
 authors = ["Aayush Sabharwal <[email protected]> and contributors"]
-version = "0.3.19"
+version = "0.3.20"
 
 [deps]
 Accessors = "7d9f7c33-5ae7-4f3b-8dc6-eff91059b697"

docs/pages.jl

@@ -2,6 +2,7 @@
 
 pages = [
     "Home" => "index.md",
+    "Terminology" => "terminology.md",
     "Tutorials" => [
         "Using the SciML Symbolic Indexing Interface" => "usage.md",
         "Simple Demonstration of a Symbolic System Structure" => "simple_sii_sys.md",

docs/src/api.md

@@ -1,6 +1,8 @@
 # Interface Functions
 
-## Mandatory methods
+## Index provider interface
+
+### Mandatory methods
 
 ```@docs
 symbolic_container
@@ -22,14 +24,16 @@ solvedvariables
 allvariables
 ```
 
-## Optional Methods
+### Optional Methods
 
-### Observed equation handling
+#### Observed equation handling
 
 ```@docs
 observed
 ```
 
+## Value provider interface
+
 ### Parameter indexing
 
 ```@docs
@@ -41,6 +45,19 @@ setp
 ParameterIndexingProxy
 ```
 
+#### Parameter timeseries
+
+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).
+
+```@docs
+parameter_timeseries
+parameter_values_at_time
+parameter_values_at_state_time
+```
+
+
 ### State indexing
 
 ```@docs
@@ -54,22 +71,17 @@ getu
 setu
 ```
 
-## Container objects
+### Batched Queries and Updates
 
 ```@docs
-remake_buffer
+BatchedInterface
+associated_systems
 ```
 
-### Parameter timeseries
-
-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).
+## Container objects
 
 ```@docs
-parameter_timeseries
-parameter_values_at_time
-parameter_values_at_state_time
+remake_buffer
 ```
 
 # Symbolic Trait
@@ -90,10 +102,3 @@ symbolic_evaluate
 SymbolCache
 ProblemState
 ```
-
-### Batched Queries and Updates
-
-```@docs
-BatchedInterface
-associated_systems
-```

docs/src/terminology.md

@@ -0,0 +1,61 @@
+# Terminology
+
+SymbolicIndexingInterface.jl uses various library-specific terminology throughout its
+documentation. This page attempts to provide comprehensive explanations of the terms
+used.
+
+## Indexes
+
+An index is an object that defines how to extract specific data from a data structure.
+Indexes may be anything from integer indexes into arrays, to custom types that contain
+information specific to a particular data structure.
+
+In code samples, an index is typically denoted with the name `idx` or `i`.
+
+## Symbolic variables
+
+Symbolic variables are objects that represent quantities (states, parameters, time, etc.)
+or collections of quantities used in a numerical simulation in a more human-accessible
+manner. Typically the values of these quantities are stored in custom data structures
+and referred to using indexes that do not convey any semantic meaning to users. Symbolic
+variables cannot directly be used to access values from these data structures and need
+to be translated into indexes.
+
+In code samples, a symbolic variable is typically denoted with the name `sym`.
+
+Symbolic variables are also sometimes referred to as "symbolic indices".
+
+## Index providers
+
+Index providers translate symbolic variables into indexes. In general, an "index" can
+be anything from integer indexes into an array, or custom types that define how to
+index into complicated data structures. `nothing` is reserved to denote the absence of
+an index, in cases where the index provider is unaware of a particular symbolic variable.
+It cannot be used as an index. ModelingToolkit.jl systems are examples of index providers.
+
+In code samples, an index provider is typically denoted with the name `indp`.
+
+## Value providers
+
+Value providers store values of symbolic variables. Given an appropriate index from an
+index provider, value providers return the value (or values) stored at that index. The
+problem, integrator and solution types in SciML are all examples of value providers.
+Each value provider is (directly or indirectly) associated with an index provider that
+defines the set of valid symbolic variables for that value provider, and the corresponding
+indexes.
+
+A value provider may not store values for all symbolic variables in the corresponding index
+provider. For example, a parameter object (even a plain `Array` storing parameter values)
+is a value provider specifically for the symbolic variables referring to parameters.
+
+In code samples, a value provider is typically denoted with the name `valp`.
+
+!!! note
+    It is important to note that an object may be both a value- and index- provider. For
+    example, SciML's problem, integrator and solution types are both value- and index-
+    providers. This allows for several syntactic improvements. The [`symbolic_container`](@ref)
+    function is useful in defining such objects.
+
+!!! note "Timeseries objects"
+    The documentation uses "Timeseries objects" to refer to value providers which implement
+    the [`Timeseries`](@ref) variant of the [`is_timeseries`](@ref) trait.

src/SymbolicIndexingInterface.jl

@@ -17,7 +17,7 @@ export is_variable, variable_index, variable_symbols, is_parameter, parameter_in
        observed, is_time_dependent, constant_structure, symbolic_container,
        all_variable_symbols,
        all_symbols, solvedvariables, allvariables, default_values, symbolic_evaluate
-include("interface.jl")
+include("index_provider_interface.jl")
 
 export SymbolCache
 include("symbol_cache.jl")

src/batched_interface.jl

@@ -1,14 +1,14 @@
 """
     struct BatchedInterface{S <: AbstractVector, I}
-    function BatchedInterface(syssyms::Tuple...)
+    function BatchedInterface(indp_syms::Tuple...)
 
 A struct which stores information for batched calls to [`getu`](@ref) or [`setu`](@ref).
-Given `Tuple`s, where the first element of each tuple is a system and the second an
-array of symbols (either variables or parameters) in the system, `BatchedInterface` will
-compute the union of all symbols and associate each symbol with the first system with
-which it occurs.
+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
+the first index provider with which it occurs.
 
-For example, given two systems `s1 = SymbolCache([:x, :y, :z])` and
+For example, given two index providers `s1 = SymbolCache([:x, :y, :z])` and
 `s2 = SymbolCache([:y, :z, :w])`, `BatchedInterface((s1, [:x, :y]), (s2, [:y, :z]))` will
 associate `:x` and `:y` with `s1` and `:z` with `s2`. The information that `s1` had
 associated symbols `:x` and `:y` and `s2` had associated symbols `:y` and `:z` will also
@@ -24,17 +24,17 @@ See also: [`associated_systems`](@ref).
 struct BatchedInterface{S <: AbstractVector, I, T}
     "Order of symbols in the union."
     symbol_order::S
-    "Index of the system each symbol in the union is associated with."
+    "Index of the index provider each symbol in the union is associated with."
     associated_systems::Vector{Int}
-    "Index of symbol in the system it is associated with."
+    "Index of symbol in the index provider it is associated with."
     associated_indexes::I
-    "Whether the symbol is a state in the system it is associated with."
+    "Whether the symbol is a state in the index provider it is associated with."
     isstate::BitVector
-    "Map from system to indexes of its symbols in the union."
+    "Map from index provider to indexes of its symbols in the union."
     system_to_symbol_subset::Vector{Vector{Int}}
-    "Map from system to indexes of its symbols in the system."
+    "Map from index provider to indexes of its symbols in the index provider."
     system_to_symbol_indexes::Vector{Vector{T}}
-    "Map from system to whether each of its symbols is a state in the system."
+    "Map from index provider to whether each of its symbols is a state in the index provider."
     system_to_isstate::Vector{BitVector}
 end
 
@@ -102,26 +102,27 @@ is_variable(bi::BatchedInterface, sym) = variable_index(bi, sym) !== nothing
     associated_systems(bi::BatchedInterface)
 
 Return an array of integers of the same length as `variable_symbols(bi)` where each value
-is the index of the system associated with the corresponding symbol in
+is the index of the index provider associated with the corresponding symbol in
 `variable_symbols(bi)`.
 """
 associated_systems(bi::BatchedInterface) = bi.associated_systems
 
 """
     getu(bi::BatchedInterface)
 
-Given a [`BatchedInterface`](@ref) composed from `n` systems (and corresponding symbols),
-return a function which takes `n` corresponding problems and returns an array of the values
-of the symbols in the union. The returned function can also be passed an `AbstractArray` of
-the appropriate `eltype` and size as its first argument, in which case the operation will
-populate the array in-place with the values of the symbols in the union.
+Given a [`BatchedInterface`](@ref) composed from `n` index providers (and corresponding
+symbols), return a function which takes `n` corresponding value providers and returns an
+array of the values of the symbols in the union. The returned function can also be passed
+an `AbstractArray` of the appropriate `eltype` and size as its first argument, in which
+case the operation will populate the array in-place with the values of the symbols in the
+union.
 
-Note that all of the problems passed to the function returned by `getu` must satisfy
+Note that all of the value providers passed to the function returned by `getu` must satisfy
 `is_timeseries(prob) === NotTimeseries()`.
 
 The value of the `i`th symbol in the union (obtained through `variable_symbols(bi)[i]`) is
-obtained from the problem corresponding to the associated system (i.e. the problem at
-index `associated_systems(bi)[i]`).
+obtained from the problem corresponding to the associated index provider (i.e. the value
+provider at index `associated_systems(bi)[i]`).
 
 See also: [`variable_symbols`](@ref), [`associated_systems`](@ref), [`is_timeseries`](@ref),
 [`NotTimeseries`](@ref).
@@ -180,16 +181,16 @@ end
 """
     setu(bi::BatchedInterface)
 
-Given a [`BatchedInterface`](@ref) composed from `n` systems (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.
+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 problems passed to the function returned by `setu` must satisfy
+Note that all of the value providers passed to the function returned by `setu` must satisfy
 `is_timeseries(prob) === NotTimeseries()`.
 
-Note that if any subset of the `n` systems share common symbols (among those passed to
-`BatchedInterface`) then all of the corresponding problems in the subset will be updated
-with the values of the common symbols.
+Note that if any subset of the `n` index providers share common symbols (among those passed
+to `BatchedInterface`) then all of the corresponding value providers in the subset will be
+updated with the values of the common symbols.
 
 See also: [`is_timeseries`](@ref), [`NotTimeseries`](@ref).
 """