Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

@require_declaration docs edits #1131

Merged
merged 7 commits into from
Nov 21, 2024
Merged
Changes from 2 commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
23 changes: 10 additions & 13 deletions docs/src/model_creation/dsl_advanced.md
Original file line number Diff line number Diff line change
Expand Up @@ -272,22 +272,19 @@ sol = solve(oprob)
plot(sol)
```

### [Turning off species, parameter, and variable inferring](@id dsl_advanced_options_require_dec)
In some cases it may be desirable for Catalyst to not infer species and parameters from the DSL, as in the case of reaction networks with very many variables, or as a sanity check that variable names are written correctly. To turn off inferring, simply add the `@require_declaration` macro to one of the lines of the `@reaction_network` declaration. Having this macro means that every single variable, species, or parameter will have to be explicitly declared using the `@variable`, `@species`, or `@parameter` macro. In the case that the DSL parser encounters an undeclared symbolic, it will error with an `UndeclaredSymbolicError` and print the reaction or equation that the undeclared symbolic was found in.
### [Turning off species, parameter, and variable inference](@id dsl_advanced_options_require_dec)
In some cases it may be desirable for Catalyst to not infer species and parameters from the DSL, as in the case of reaction networks with very many variables, or as a sanity check that variable names are written correctly. To turn off inference, simply use the `@require_declaration` option when using the `@reaction_network` DSL. This will require every single variable, species, or parameter used within the DSL to be explicitly declared using the `@variable`, `@species`, or `@parameter` options. In the case that the DSL parser encounters an undeclared symbolic, it will error with an `UndeclaredSymbolicError` and print the reaction or equation that the undeclared symbolic was found in.

```@example dsl_advanced_no_infer
```julia
using Catalyst
# The following case will throw an UndeclaredSymbolicError.
try @macroexpand @reaction_network begin
rn = @reaction_network begin
isaacsas marked this conversation as resolved.
Show resolved Hide resolved
@require_declaration
(k1, k2), A <--> B
end
catch e
println(e.msg)
end
```
In order to avoid an error in this case all the relevant species and parameters will have to be declared.
```
```@example dsl_advanced_require_dec
# The following case will not error.
t = default_t()
rn = @reaction_network begin
Expand All @@ -299,11 +296,11 @@ end
```

The following cases in which the DSL would normally infer variables will all throw errors if `@require_declaration` is set and the variables are not explicitly declared.
- Inferring a species in a reaction, as in the example above
- Inferring a parameter in a reaction rate expression, as in the reaction line `k*n, A --> B`
- Inferring a parameter in the stoichiometry of a species, as in the reaction line `k, n*A --> B`
- Inferring a differential variable on the LHS of a coupled differential equation, as in `A` in `@equations D(A) ~ A^2`
- Inferring an [observable](@ref dsl_advanced_options_observables) that is declared using `@observables`
- Occurrence of an undeclared species in a reaction, as in the example above.
- Occurrence of an undeclared parameter in a reaction rate expression, as in the reaction line `k*n, A --> B`.
- Occurrence of an undeclared parameter in the stoichiometry of a species, as in the reaction line `k, n*A --> B`.
- Occurrence of an undeclared differential variable on the LHS of a coupled differential equation, as in `A` in `@equations D(A) ~ A^2`.
- Occurrence of an undeclared [observable](@ref dsl_advanced_options_observables) in an `@observables` expression, such as `@observables X1 ~ A + B`.

## [Naming reaction networks](@id dsl_advanced_options_naming)
Each reaction network model has a name. It can be accessed using the `nameof` function. By default, some generic name is used:
Expand Down
Loading