up

Author: TorkelE

docs/src/catalyst_functionality/dsl_description.md

@@ -623,4 +623,4 @@ Finally, some general rules for creating observables:
 - The left-hand side of the observables expression must be a single symbol, indicating the observable's name.
 - Metadata can, however, be provided, e.g through `@observables (Xtot, [description="Total amount of X"]) ~ X + XY`.
 - The right-hand side of the observables expression can be any valid algebraic expression.
-- Observables are (by default, but this can be changed) considered `variables` (and not `species`).
+- Observables are (by default, but this can be changed) considered `variables` (and not `species`). This can be changed by e.g. pre-declaring them using the `@species` option.

src/reactionsystem.jl

@@ -516,6 +516,10 @@ struct ReactionSystem{V <: NetworkProperties} <:
     function ReactionSystem(eqs, rxs, iv, sivs, states, spcs, ps, var_to_name, observed,
                             name, systems, defaults, connection_type, nps, cls, cevs, devs,
                             complete::Bool = false; checks::Bool = true)
+        # Filters away any potential obervables from `states` and `spcs`.
+        obs_vars = [obs_eq.lhs for obs_eq in observed]
+        states = filter(state -> !in(state, obs_vars), states)
+        spcs = filter(spc -> !in(spc, obs_vars), spcs)
 
         # unit checks are for ODEs and Reactions only currently
         nonrx_eqs = Equation[eq for eq in eqs if eq isa Equation]