PEtab import: Fix potentially incorrect sensitivities with state-depe…

…ndent sigmas (#2562)

Due to PEtab not allowing and observables in noiseFormula and
AMICI not allowing state variables in sigma expressions, we are trying
to replace any state variables by matching observables during PEtab import.

However, if there were multiple observables with the same observableFormula,
or one observableFormula was contained in another one, the substition
of observableFormula for observableId could - depending on the ordering -
result in noiseFormulas depending on other observables, which could lead to
incorrect sensitivities due to #2561.

This change ensures that we are only using the observableId from the same
row of the observable table as the noiseFormula.

---------

Co-authored-by: Dilan Pathirana <[email protected]>

python/sdist/amici/petab/import_helpers.py

@@ -47,29 +47,27 @@ def get_observation_model(
 
     observables = {}
     sigmas = {}
-
     nan_pat = r"^[nN]a[nN]$"
+
     for _, observable in observable_df.iterrows():
         oid = str(observable.name)
         # need to sanitize due to https://github.com/PEtab-dev/PEtab/issues/447
         name = re.sub(nan_pat, "", str(observable.get(OBSERVABLE_NAME, "")))
         formula_obs = re.sub(nan_pat, "", str(observable[OBSERVABLE_FORMULA]))
         formula_noise = re.sub(nan_pat, "", str(observable[NOISE_FORMULA]))
         observables[oid] = {"name": name, "formula": formula_obs}
-        sigmas[oid] = formula_noise
-
-    # PEtab does currently not allow observables in noiseFormula and AMICI
-    #  cannot handle states in sigma expressions. Therefore, where possible,
-    #  replace species occurring in error model definition by observableIds.
-    replacements = {
-        sp.sympify(observable["formula"], locals=_clash): sp.Symbol(
-            observable_id
+        formula_noise_sym = sp.sympify(formula_noise, locals=_clash)
+        formula_obs_sym = sp.sympify(formula_obs, locals=_clash)
+        # PEtab does currently not allow observables in noiseFormula, and
+        #  AMICI cannot handle state variables in sigma expressions.
+        #  Therefore, where possible, replace state variables occurring in
+        #  the error model definition by equivalent observableIds.
+        #  Do not use observableIds from other rows
+        #  (https://github.com/AMICI-dev/AMICI/issues/2561).
+        formula_noise_sym = formula_noise_sym.subs(
+            formula_obs_sym, sp.Symbol(oid)
         )
-        for observable_id, observable in observables.items()
-    }
-    for observable_id, formula in sigmas.items():
-        repl = sp.sympify(formula, locals=_clash).subs(replacements)
-        sigmas[observable_id] = str(repl)
+        sigmas[oid] = str(formula_noise_sym)
 
     noise_distrs = petab_noise_distributions_to_amici(observable_df)