Add petab_symbol

Add `petab.v1.math.petab_symbol` (also available from `petab.v2.math`),
which creates a sympy symbol with the same assumptions as the symbols
created by `sympify_petab` (currently `real=True`).

Use it in the parser and in `calculate`, instead of repeating
`real=True`.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

Author: dweindl

CHANGELOG.md

@@ -69,6 +69,9 @@
 * `petab.v2.Problem.get_unused_id` returns an identifier that is not yet
   used in the problem or its model
   (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/561)
+* `petab.v1.math.petab_symbol` (also in `petab.v2.math`) creates sympy
+  symbols with the same assumptions as `sympify_petab`
+  (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/563)
 
 ## 0.9 series
 

petab/v1/calculate.py

@@ -11,7 +11,7 @@
 import petab.v1 as petab
 
 from .C import *
-from .math import sympify_petab
+from .math import petab_symbol, sympify_petab
 
 __all__ = [
     "calculate_chi2",
@@ -202,18 +202,16 @@ def evaluate_noise_formula(
     )
     # fill in measurement specific parameters
     overrides = {
-        sp.Symbol(
-            f"noiseParameter{i_obs_par + 1}_{observable_id}", real=True
-        ): obs_par
+        petab_symbol(f"noiseParameter{i_obs_par + 1}_{observable_id}"): obs_par
         for i_obs_par, obs_par in enumerate(observable_parameter_overrides)
     }
 
     # fill in observables
-    overrides[sp.Symbol(observable_id, real=True)] = simulation
+    overrides[petab_symbol(observable_id)] = simulation
 
     # fill in general parameters
     for row in parameter_df.itertuples():
-        overrides[sp.Symbol(row.Index, real=True)] = row.nominalValue
+        overrides[petab_symbol(row.Index)] = row.nominalValue
 
     # replace parametric measurement specific parameters
     for key, value in overrides.items():

petab/v1/math/SympyVisitor.py

@@ -6,7 +6,7 @@
 from ._generated.PetabMathExprParser import PetabMathExprParser
 from ._generated.PetabMathExprParserVisitor import PetabMathExprParserVisitor
 
-__all__ = ["MathVisitorSympy"]
+__all__ = ["MathVisitorSympy", "petab_symbol"]
 
 # Mappings of PEtab math functions to sympy functions
 
@@ -65,6 +65,18 @@
 }
 
 
+def petab_symbol(name: str) -> sp.Symbol:
+    """Create a sympy symbol for a PEtab identifier.
+
+    The symbol has the same assumptions as the symbols created by
+    :func:`sympify_petab`.
+
+    :param name: The identifier.
+    :return: The symbol.
+    """
+    return sp.Symbol(name, real=True)
+
+
 class MathVisitorSympy(PetabMathExprParserVisitor):
     """
     ANTLR4 visitor for PEtab-math-to-sympy conversion.
@@ -101,7 +113,7 @@ def visitVar(self, ctx: PetabMathExprParser.VarContext) -> sp.Symbol:
         """Convert identifier to sympy Symbol."""
         if ctx.getText().lower() in _reserved_names:
             raise ValueError(f"Use of reserved name {ctx.getText()!r}")
-        return sp.Symbol(ctx.getText(), real=True)
+        return petab_symbol(ctx.getText())
 
     def visitMultExpr(
         self, ctx: PetabMathExprParser.MultExprContext

petab/v1/math/__init__.py

@@ -2,3 +2,4 @@
 
 from .printer import PetabStrPrinter, petab_math_str  # noqa: F401
 from .sympify import sympify_petab  # noqa: F401
+from .SympyVisitor import petab_symbol  # noqa: F401

petab/v1/math/sympify.py

@@ -34,7 +34,7 @@ def sympify_petab(
         .. note::
 
           All symbols in the returned expression will have the ``real=True``
-          assumption.
+          assumption, as created by :func:`petab_symbol`.
 
     :example:
     >>> from petab.v1.math import sympify_petab

petab/v2/calculate.py

@@ -11,7 +11,7 @@
 from petab.v1 import is_empty, split_parameter_replacement_list
 
 from .C import *
-from .math import sympify_petab
+from .math import petab_symbol, sympify_petab
 
 __all__ = [
     "calculate_chi2",
@@ -226,7 +226,7 @@ def evaluate_noise_formula(
 
     # fill in measurement specific parameters
     overrides = {
-        sp.Symbol(placeholder, real=True): override
+        petab_symbol(placeholder): override
         for placeholder, override in zip(
             [
                 p.strip()
@@ -240,11 +240,11 @@ def evaluate_noise_formula(
     }
 
     # fill in observables
-    overrides[sp.Symbol(observable_id, real=True)] = simulation
+    overrides[petab_symbol(observable_id)] = simulation
 
     # fill in general parameters
     for row in parameter_df.itertuples():
-        overrides[sp.Symbol(row.Index, real=True)] = row.nominalValue
+        overrides[petab_symbol(row.Index)] = row.nominalValue
 
     # replace parametric measurement specific parameters
     for key, value in overrides.items():

tests/v1/math/test_math.py

@@ -8,7 +8,7 @@
 from sympy.abc import _clash
 from sympy.logic.boolalg import Boolean, BooleanFalse, BooleanTrue
 
-from petab.v1.math import petab_math_str, sympify_petab
+from petab.v1.math import petab_math_str, petab_symbol, sympify_petab
 
 
 def test_sympify_numpy():
@@ -36,6 +36,10 @@ def test_assumptions():
     # non-real symbols are changed to real
     assert sympify_petab(sp.Symbol("x", real=False)).is_real
 
+    # `petab_symbol` creates the same symbols as the parser
+    assert petab_symbol("x") == sympify_petab("x")
+    assert petab_symbol("x") != sp.Symbol("x")
+
 
 def test_printer():
     a, b, c, d = sp.symbols("a b c d", real=True)