..

Author: dweindl

petab/v1/math/sympify.py

@@ -5,6 +5,7 @@
 from antlr4 import CommonTokenStream, InputStream
 from antlr4.error.ErrorListener import ErrorListener
 
+from . import petab_math_str
 from ._generated.PetabMathExprLexer import PetabMathExprLexer
 from ._generated.PetabMathExprParser import PetabMathExprParser
 from .SympyVisitor import MathVisitorSympy, bool2num
@@ -32,8 +33,7 @@ def sympify_petab(expr: str | int | float) -> sp.Expr | sp.Basic:
         Boolean values are converted to numeric values.
     """
     if isinstance(expr, sp.Expr):
-        # TODO: check if only PEtab-compatible symbols and functions are used
-        return expr
+        return sympify_petab(petab_math_str(expr))
 
     if isinstance(expr, int) or isinstance(expr, np.integer):
         return sp.Integer(expr)

petab/v2/core.py

@@ -25,7 +25,7 @@
 from typing_extensions import Self
 
 from ..v1.lint import is_valid_identifier
-from ..v1.math import sympify_petab
+from ..v1.math import petab_math_str, sympify_petab
 from . import C, get_observable_df
 
 __all__ = [
@@ -273,23 +273,8 @@ def to_df(self) -> pd.DataFrame:
         for record in records:
             obs = record[C.OBSERVABLE_FORMULA]
             noise = record[C.NOISE_FORMULA]
-            record[C.OBSERVABLE_FORMULA] = (
-                None
-                if obs is None
-                # TODO: we need a custom printer for sympy expressions
-                #  to avoid '**'
-                #  https://github.com/PEtab-dev/libpetab-python/issues/362
-                else str(obs)
-                if not obs.is_number
-                else float(obs)
-            )
-            record[C.NOISE_FORMULA] = (
-                None
-                if noise is None
-                else str(noise)
-                if not noise.is_number
-                else float(noise)
-            )
+            record[C.OBSERVABLE_FORMULA] = petab_math_str(obs)
+            record[C.NOISE_FORMULA] = petab_math_str(noise)
         return pd.DataFrame(records).set_index([C.OBSERVABLE_ID])
 
     @classmethod

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.math import petab_math_str, sympify_petab
+from petab.v1.math import petab_math_str, sympify_petab
 
 
 def test_sympify_numpy():
@@ -24,6 +24,15 @@ def test_parse_simple():
     assert float(sympify_petab("1 + 2 * (3 + 4) / 2")) == 8
 
 
+def test_assumptions():
+    # in PEtab, all symbols are expected to be real-valued
+    assert sympify_petab("x").is_real
+
+    # non-real symbols are changed to real
+    # TODO: should we raise an error instead?
+    assert sympify_petab(sp.Symbol("x", real=False)).is_real
+
+
 def test_printer():
     assert petab_math_str(BooleanTrue()) == "true"
     assert petab_math_str(BooleanFalse()) == "false"
@@ -87,9 +96,8 @@ def test_ids():
     assert sympify_petab("bla * 2") == 2.0 * sp.Symbol("bla", real=True)
 
     # test that sympy expressions that are invalid in PEtab raise an error
-    # TODO: handle these cases after
-    #   https://github.com/PEtab-dev/libpetab-python/pull/364
-    # sympify_petab(sp.Symbol("föö"))
+    with pytest.raises(ValueError):
+        sympify_petab(sp.Symbol("föö"))
 
 
 def test_syntax_error():