Handle reserved names during code-printing

python/sdist/amici/cxxcodeprinter.py

@@ -30,6 +30,7 @@ class AmiciCxxCodePrinter(CXX11CodePrinter):
     """
 
     optimizations: Iterable[Optimization] = ()
+    RESERVED_SYMBOLS = ["x", "k", "p", "y", "w", "h", "t", "AMICI_EMPTY_BOLUS"]
 
     def __init__(self):
         """Create code printer"""
@@ -67,6 +68,12 @@ def doprint(self, expr: sp.Expr, assign_to: str | None = None) -> str:
                 f'Encountered unsupported function in expression "{expr}"'
             ) from e
 
+    def _print_Symbol(self, expr):
+        name = super()._print_Symbol(expr)
+        if name in self.RESERVED_SYMBOLS:
+            return f"amici_{name}"
+        return name
+
     def _print_min_max(self, expr, cpp_fun: str, sympy_fun):
         # C++ doesn't like mixing int and double for arguments for min/max,
         #  therefore, we just always convert to float

python/sdist/amici/de_export.py

@@ -394,6 +394,12 @@ def _write_index_files(self, name: str) -> None:
         lines = []
         for index, symbol in enumerate(symbols):
             symbol_name = strip_pysb(symbol)
+            # symbol_name is a mix of symbols and strings
+            symbol_name = self._code_printer._print_Symbol(
+                sp.Symbol(symbol_name)
+                if isinstance(symbol_name, str)
+                else symbol_name
+            )
             if str(symbol) == "0":
                 continue
             if str(symbol_name) == "":
@@ -1221,7 +1227,7 @@ def _get_symbol_id_initializer_list(self, name: str) -> str:
             Template initializer list of ids
         """
         return "\n".join(
-            f'"{self._code_printer.doprint(symbol)}", // {name}[{idx}]'
+            f'"{symbol}", // {name}[{idx}]'
             for idx, symbol in enumerate(self.model.sym(name))
         )
 

python/sdist/amici/de_model_components.py

@@ -7,7 +7,6 @@
 import sympy as sp
 
 from .import_utils import (
-    RESERVED_SYMBOLS,
     ObservableTransformation,
     amici_time_symbol,
     cast_to_sym,
@@ -66,13 +65,6 @@ def __init__(
                 f"identifier must be sympy.Symbol, was " f"{type(identifier)}"
             )
 
-        if str(identifier) in RESERVED_SYMBOLS or (
-            hasattr(identifier, "name") and identifier.name in RESERVED_SYMBOLS
-        ):
-            raise ValueError(
-                f'Cannot add model quantity with name "{name}", '
-                f"please rename."
-            )
         self._identifier: sp.Symbol = identifier
 
         if not isinstance(name, str):

python/sdist/amici/import_utils.py

@@ -18,8 +18,6 @@
 from sympy.logic.boolalg import BooleanAtom
 from toposort import toposort
 
-RESERVED_SYMBOLS = ["x", "k", "p", "y", "w", "h", "t", "AMICI_EMPTY_BOLUS"]
-
 try:
     import pysb
 except ImportError:

python/sdist/amici/sbml_import.py

@@ -35,7 +35,6 @@
 from .de_model_components import symbol_to_type, Expression
 from .sympy_utils import smart_is_zero_matrix, smart_multiply
 from .import_utils import (
-    RESERVED_SYMBOLS,
     _check_unsupported_functions,
     _get_str_symbol_identifiers,
     _parse_special_functions,
@@ -523,7 +522,6 @@ def _build_ode_model(
         )
         self._replace_compartments_with_volumes()
 
-        self._clean_reserved_symbols()
         self._process_time()
 
         ode_model = DEModel(
@@ -2596,24 +2594,6 @@ def _replace_in_all_expressions(
         for spline in self.splines:
             spline._replace_in_all_expressions(old, new)
 
-    def _clean_reserved_symbols(self) -> None:
-        """
-        Remove all reserved symbols from self.symbols
-        """
-        for sym in RESERVED_SYMBOLS:
-            old_symbol = symbol_with_assumptions(sym)
-            new_symbol = symbol_with_assumptions(f"amici_{sym}")
-            self._replace_in_all_expressions(
-                old_symbol, new_symbol, replace_identifiers=True
-            )
-            for symbols_ids, symbols in self.symbols.items():
-                if old_symbol in symbols:
-                    # reconstitute the whole dict in order to keep the ordering
-                    self.symbols[symbols_ids] = {
-                        new_symbol if k is old_symbol else k: v
-                        for k, v in symbols.items()
-                    }
-
     def _sympy_from_sbml_math(
         self, var_or_math: [sbml.SBase, str]
     ) -> sp.Expr | float | None:

python/tests/test_sbml_import.py

@@ -773,3 +773,39 @@ def test_constraints():
                 amici_solver.getAbsoluteTolerance(),
             )
         )
+
+
+def test_reserved_symbols():
+    """Test handling of reserved one-letter names."""
+    from amici.antimony_import import antimony2amici
+
+    ant_model = """
+    model test_non_negative_species
+        t = 0.1
+        x = 0.2
+        y = 0.3
+        w = 0.4
+        h = 0.5
+        p = 0.6
+        k = 0.7
+        x' = k + x + p + y + w + h + t
+    end
+    """
+    module_name = "test_reserved_symbols"
+    with TemporaryDirectory(prefix=module_name) as outdir:
+        antimony2amici(
+            ant_model,
+            model_name=module_name,
+            output_dir=outdir,
+            compute_conservation_laws=False,
+        )
+        # ensure it compiled successfully and can be imported
+        model_module = amici.import_model_module(
+            module_name=module_name, module_path=outdir
+        )
+        model = model_module.get_model()
+        ids = list(model.getParameterIds())
+        ids.extend(model.getStateIds())
+        # all symbols should be present with their original IDs
+        for symbol in "txywhpk":
+            assert symbol in ids