Don't eliminate parameters that are initial assignment targets (pt2) (#2305)

Currently, parameters that are targets of initial assignments don't show up as parameters or expressions in the amici model. This is rather not what most users would expect.

Therefore, treat all SBML parameters that are initial assignment targets and whose initial assignment does not evaluate to a number (for those that do, see #2304) as amici expressions.
Those static expressions will be handled more efficiently after #2303.

Related to #2150.

See also #2304.

Author: dweindl

python/sdist/amici/sbml_import.py

@@ -722,7 +722,7 @@ def _gather_base_locals(
             "INF": sp.oo,
             "NaN": sp.nan,
             "rem": sp.Mod,
-            "time": symbol_with_assumptions("time"),
+            "time": sbml_time_symbol,
             # SBML L3 explicitly defines this value, which is not equal
             # to the most recent SI definition.
             "avogadro": sp.Float(6.02214179e23),
@@ -1108,11 +1108,13 @@ def _process_parameters(
                 }
 
         # Parameters that need to be turned into expressions
-        #  so far, this concerns parameters with initial assignments containing rateOf(.)
-        #  (those have been skipped above)
+        #  so far, this concerns parameters with symbolic initial assignments
+        #  (those have been skipped above) that are not rate rule targets
         for par in self.sbml.getListOfParameters():
-            if (ia := par_id_to_ia.get(par.getId())) is not None and ia.find(
-                sp.core.function.UndefinedFunction("rateOf")
+            if (
+                (ia := par_id_to_ia.get(par.getId())) is not None
+                and not ia.is_Number
+                and not self.is_rate_rule_target(par)
             ):
                 self.symbols[SymbolId.EXPRESSION][
                     _get_identifier_symbol(par)
@@ -1890,6 +1892,7 @@ def _process_initial_assignments(self):
             if identifier in itt.chain(
                 self.symbols[SymbolId.SPECIES],
                 self.compartments,
+                self.symbols[SymbolId.EXPRESSION],
                 self.symbols[SymbolId.PARAMETER],
                 self.symbols[SymbolId.FIXED_PARAMETER],
             ):
@@ -1965,9 +1968,7 @@ def _make_initial(
             if "init" in species:
                 sym_math = smart_subs(sym_math, species_id, species["init"])
 
-        sym_math = smart_subs(
-            sym_math, self._local_symbols["time"], sp.Float(0)
-        )
+        sym_math = smart_subs(sym_math, sbml_time_symbol, sp.Float(0))
 
         sym_math = _dummy_to_rateof(sym_math, rateof_to_dummy)
 

tests/testSBMLSuite.py

@@ -130,10 +130,12 @@ def verify_results(settings, rdata, expected, wrapper, model, atol, rtol):
     # collect parameters
     for par in model.getParameterIds():
         simulated[par] = rdata["ts"] * 0 + model.getParameterById(par)
-    # collect fluxes
+    # collect fluxes and other expressions
     for expr_idx, expr_id in enumerate(model.getExpressionIds()):
         if expr_id.startswith("flux_"):
             simulated[expr_id.removeprefix("flux_")] = rdata.w[:, expr_idx]
+        elif expr_id.removeprefix("amici_") not in simulated.columns:
+            simulated[expr_id] = rdata.w[:, expr_idx]
     # handle renamed reserved symbols
     simulated.rename(
         columns={c: c.replace("amici_", "") for c in simulated.columns},