..

Author: dweindl

python/sdist/amici/de_model.py

@@ -12,6 +12,7 @@
 from typing import TYPE_CHECKING
 
 import numpy as np
+import pysb
 import sympy as sp
 from sympy import ImmutableDenseMatrix, MutableDenseMatrix
 
@@ -1295,36 +1296,22 @@ 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_sym() 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, w_toposorted)
-            )
+            state.set_dt(self._process_heavisides(state.get_dt(), roots))
 
         for expr in self._expressions:
-            expr.set_val(
-                self._process_heavisides(expr.get_val(), roots, w_toposorted)
-            )
+            expr.set_val(self._process_heavisides(expr.get_val(), roots))
+            if isinstance((pysb_component := expr.get_sym()), pysb.Expression):
+                # Make sure pysb Expression definitions stay in sync.
+                #  Remove with https://github.com/AMICI-dev/AMICI/issues/3035
+                pysb_component.expr = expr.get_val()
 
         # 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, w_toposorted)
-            )
+            root.set_val(self._process_heavisides(root.get_val(), roots))
 
         # Now add the found roots to the model components
         for root in roots:
@@ -2461,9 +2448,6 @@ def _get_unique_root(
             unique identifier for root, or ``None`` if the root is not
             time-dependent
         """
-        if not self._expr_is_time_dependent(root_found):
-            return None
-
         for root in roots:
             if (difference := (root_found - root.get_val())).is_zero or (
                 self._simplify and self._simplify(difference).is_zero
@@ -2481,6 +2465,12 @@ def _get_unique_root(
                 use_values_from_trigger_time=True,
             )
         )
+
+        if not self._expr_is_time_dependent(root_found):
+            # Not time-dependent. Return None, but we still need to create
+            # the event above
+            return None
+
         return roots[-1].get_sym()
 
     def _collect_heaviside_roots(
@@ -2511,7 +2501,6 @@ 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,
@@ -2523,8 +2512,6 @@ 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
         """
@@ -2533,9 +2520,9 @@ def _process_heavisides(
         heavisides = []
         # run through the expression tree and get the roots
         tmp_roots_old = self._collect_heaviside_roots((dxdt,))
-        # substitute 'w' symbols in the root expression by their equations,
+        # TODO remove: substitute 'w' symbols in the root expression by their equations,
         #  because currently,
-        # #  1) root functions must not depend on 'w'
+        #    1) root functions must not depend on 'w'
         # FIXME 2) the check for time-dependence currently assumes only state
         #     variables are implicitly time-dependent
         for tmp_root_old, tmp_x0_old in unique_preserve_order(tmp_roots_old):

python/sdist/amici/importers/pysb/__init__.py

@@ -669,12 +669,18 @@ def _add_expression(
             name == str(channel.sigma)
             for channel in observation_model.values()
         ):
-            component = SigmaY
+            component_type = SigmaY
         else:
-            component = Expression
-        ode_model.add_component(
-            component(sym, name, _parse_special_functions(expr))
-        )
+            component_type = Expression
+
+        component = component_type(sym, name, _parse_special_functions(expr))
+
+        if isinstance(sym, pysb.Expression):
+            # Make sure pysb Expression definitions stay in sync.
+            # Remove with https://github.com/AMICI-dev/AMICI/issues/3035
+            expr.expr = component.get_val()
+
+        ode_model.add_component(component)
 
     if name in observation_model:
         noise_dist = observation_model[name].noise_distribution