Fix piecewise/Heaviside handling (#2234)

* Fixes a bug where Heaviside functions weren't correctly substituted, potentially resulting in DiracDelta's in the model equations. The problem was, the substitution targets were collected from an expanded expression, but the actual substitution was attempted on the non-expanded expression, which did not always succeed.

  Fixed by *not* expanding the expressions beforehand. Closes #2231
  
* Fixes redundant trigger-function processing

#2234

python/sdist/amici/de_export.py

@@ -58,8 +58,8 @@
     generate_flux_symbol,
     smart_subs_dict,
     strip_pysb,
-    symbol_with_assumptions,
     toposort_symbols,
+    unique_preserve_order,
 )
 from .logging import get_logger, log_execution_time, set_log_level
 
@@ -2745,16 +2745,12 @@ def _process_heavisides(
         :returns:
             dxdt with Heaviside functions replaced by amici helper variables
         """
-
-        # expanding the rhs will in general help to collect the same
-        # heaviside function
-        dt_expanded = dxdt.expand()
         # track all the old Heaviside expressions in tmp_roots_old
         # replace them later by the new expressions
         heavisides = []
         # run through the expression tree and get the roots
-        tmp_roots_old = self._collect_heaviside_roots(dt_expanded.args)
-        for tmp_old in tmp_roots_old:
+        tmp_roots_old = self._collect_heaviside_roots(dxdt.args)
+        for tmp_old in unique_preserve_order(tmp_roots_old):
             # we want unique identifiers for the roots
             tmp_new = self._get_unique_root(tmp_old, roots)
             # `tmp_new` is None if the root is not time-dependent.

python/sdist/amici/import_utils.py

@@ -734,5 +734,20 @@ def strip_pysb(symbol: sp.Basic) -> sp.Basic:
         return symbol
 
 
+def unique_preserve_order(seq: Sequence) -> list:
+    """Return a list of unique elements in Sequence, keeping only the first
+    occurrence of each element
+
+    Parameters:
+        seq: Sequence to prune
+
+    Returns:
+        List of unique elements in ``seq``
+    """
+    seen = set()
+    seen_add = seen.add
+    return [x for x in seq if not (x in seen or seen_add(x))]
+
+
 sbml_time_symbol = symbol_with_assumptions("time")
 amici_time_symbol = symbol_with_assumptions("t")

python/sdist/amici/sbml_import.py

@@ -38,7 +38,6 @@
     DEModel,
     _default_simplify,
     smart_is_zero_matrix,
-    symbol_with_assumptions,
 )
 from .import_utils import (
     RESERVED_SYMBOLS,
@@ -54,6 +53,7 @@
     sbml_time_symbol,
     smart_subs,
     smart_subs_dict,
+    symbol_with_assumptions,
     toposort_symbols,
 )
 from .logging import get_logger, log_execution_time, set_log_level