Fix SBML import for parameters with piecewise initial assignments

python/sdist/amici/de_model.py

@@ -1305,18 +1305,36 @@ def parse_events(self) -> None:
         and replaces the formulae of the found roots by identifiers of AMICI's
         Heaviside function implementation in the right-hand side
         """
+        # toposorted w_sym -> w_expr for substitution of 'w' in trigger function
+        #  do only once. `w` is not modified during this function.
+        w_toposorted = toposort_symbols(
+            dict(
+                zip(
+                    [expr.get_id() for expr in self._expressions],
+                    [expr.get_val() for expr in self._expressions],
+                    strict=True,
+                )
+            )
+        )
+
         # Track all roots functions in the right-hand side
         roots = copy.deepcopy(self._events)
         for state in self._differential_states:
-            state.set_dt(self._process_heavisides(state.get_dt(), roots))
+            state.set_dt(
+                self._process_heavisides(state.get_dt(), roots, w_toposorted)
+            )
 
         for expr in self._expressions:
-            expr.set_val(self._process_heavisides(expr.get_val(), roots))
+            expr.set_val(
+                self._process_heavisides(expr.get_val(), roots, w_toposorted)
+            )
 
         # remove all possible Heavisides from roots, which may arise from
         # the substitution of `'w'` in `_collect_heaviside_roots`
         for root in roots:
-            root.set_val(self._process_heavisides(root.get_val(), roots))
+            root.set_val(
+                self._process_heavisides(root.get_val(), roots, w_toposorted)
+            )
 
         # Now add the found roots to the model components
         for root in roots:
@@ -1326,6 +1344,11 @@ def parse_events(self) -> None:
             # add roots of heaviside functions
             self.add_component(root)
 
+        # Substitute 'w' expressions into root expressions, to avoid rewriting
+        # 'root.cpp' and 'stau.cpp' headers to include 'w.h'.
+        for event in self.events():
+            event.set_val(event.get_val().subs(w_toposorted))
+
         # re-order events - first those that require root tracking, then the others
         constant_syms = set(self.sym("k")) | set(self.sym("p"))
         self._events = list(
@@ -2391,7 +2414,7 @@ def _expr_is_time_dependent(self, expr: sp.Expr) -> bool:
         expr_syms = {str(sym) for sym in expr.free_symbols}
 
         # Check if the time variable is in the expression.
-        if "t" in expr_syms:
+        if amici_time_symbol.name in expr_syms:
             return True
 
         # Check if any time-dependent states are in the expression.
@@ -2464,33 +2487,11 @@ def _collect_heaviside_roots(
 
         return root_funs
 
-    def _substitute_w_in_roots(
-        self,
-        root_funs: list[tuple[sp.Expr, sp.Expr]],
-    ) -> list[tuple[sp.Expr, sp.Expr]]:
-        """
-        Substitute 'w' expressions into root expressions, to avoid rewriting
-        'root.cpp' and 'stau.cpp' headers to include 'w.h'.
-        """
-        w_sorted = toposort_symbols(
-            dict(
-                zip(
-                    [expr.get_id() for expr in self._expressions],
-                    [expr.get_val() for expr in self._expressions],
-                    strict=True,
-                )
-            )
-        )
-        root_funs = [
-            (r[0].subs(w_sorted), r[1].subs(w_sorted)) for r in root_funs
-        ]
-
-        return root_funs
-
     def _process_heavisides(
         self,
         dxdt: sp.Expr,
         roots: list[Event],
+        w_toposorted: dict[sp.Symbol, sp.Expr],
     ) -> sp.Expr:
         """
         Parses the RHS of a state variable, checks for Heaviside functions,
@@ -2502,7 +2503,8 @@ def _process_heavisides(
             right-hand side of state variable
         :param roots:
             list of known root functions with identifier
-
+        :param w_toposorted:
+            `w` symbols->expressions sorted in topological order
         :returns:
             dxdt with Heaviside functions replaced by amici helper variables
         """
@@ -2511,7 +2513,15 @@ def _process_heavisides(
         heavisides = []
         # run through the expression tree and get the roots
         tmp_roots_old = self._collect_heaviside_roots((dxdt,))
-        tmp_roots_old = self._substitute_w_in_roots(tmp_roots_old)
+        # substitute 'w' symbols in the root expression by their equations,
+        #  because currently,
+        #  1) root functions must not depend on 'w'
+        #  2) the check for time-dependence currently assumes only state
+        #     variables are implicitly time-dependent
+        tmp_roots_old = [
+            (a.subs(w_toposorted), b.subs(w_toposorted))
+            for a, b in tmp_roots_old
+        ]
         for tmp_root_old, tmp_x0_old in unique_preserve_order(tmp_roots_old):
             # we want unique identifiers for the roots
             tmp_root_new = self._get_unique_root(tmp_root_old, roots)

python/sdist/amici/import_utils.py

@@ -17,7 +17,17 @@
 from sympy.logic.boolalg import BooleanAtom
 from toposort import toposort
 
-RESERVED_SYMBOLS = ["x", "k", "p", "y", "w", "h", "t", "AMICI_EMPTY_BOLUS"]
+RESERVED_SYMBOLS = [
+    "x",
+    "k",
+    "p",
+    "y",
+    "w",
+    "h",
+    "t",
+    "AMICI_EMPTY_BOLUS",
+    "NULL",
+]
 
 try:
     import pysb

python/tests/test_bngl.py

@@ -1,6 +1,5 @@
 import os
 
-import amici
 import numpy as np
 import pytest
 
@@ -10,6 +9,7 @@
 from amici.testing import TemporaryDirectoryWinSafe, skip_on_valgrind
 from pysb.importers.bngl import model_from_bngl
 from pysb.simulator import ScipyOdeSimulator
+from contextlib import suppress
 
 tests = [
     "CaOscillate_Func",
@@ -39,6 +39,13 @@
 @skip_on_valgrind
 @pytest.mark.parametrize("example", tests)
 def test_compare_to_pysb_simulation(example):
+    import amici.import_utils
+
+    # allow "NULL" as model symbol
+    # (used in CaOscillate_Func and Repressilator examples)
+    with suppress(ValueError):
+        amici.import_utils.RESERVED_SYMBOLS.remove("NULL")
+
     atol = 1e-8
     rtol = 1e-8