Merge branch 'develop' into feature_1269_split_exprs

dweindl · Feb 27, 2024 · f87ddc3 · f87ddc3
2 parents e58a09e + 5e386ee
commit f87ddc3
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Showing 2 changed files with 12 additions and 9 deletions.
diff --git a/python/sdist/amici/sbml_import.py b/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)
 

diff --git a/tests/testSBMLSuite.py b/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},