..

Author: dweindl

petab/v1/math/printer.py

@@ -74,13 +74,17 @@ def _print_Max(self, expr):
         return f"max({', '.join(map(self._print, expr.args))})"
 
 
-def petab_math_str(expr: sp.Expr) -> str:
+def petab_math_str(expr: sp.Basic | sp.Expr | None) -> str:
     """Convert a sympy expression to a PEtab-compatible math expression string.
 
     :example:
     >>> expr = sp.sympify("x**2 + sin(y)")
     >>> petab_math_str(expr)
     'x ^ 2 + sin(y)'
+    >>> petab_math_str(expr)
+    'x ^ 2 + sin(y)'
     """
+    if expr is None:
+        return ""
 
     return PetabStrPrinter().doprint(expr)

petab/v1/math/sympify.py

@@ -13,7 +13,7 @@
 __all__ = ["sympify_petab"]
 
 
-def sympify_petab(expr: str | int | float) -> sp.Expr | sp.Basic:
+def sympify_petab(expr: str | int | float | sp.Basic) -> sp.Expr | sp.Basic:
     """Convert PEtab math expression to sympy expression.
 
     .. note::
@@ -32,7 +32,7 @@ def sympify_petab(expr: str | int | float) -> sp.Expr | sp.Basic:
         The sympy expression corresponding to `expr`.
         Boolean values are converted to numeric values.
     """
-    if isinstance(expr, sp.Expr):
+    if isinstance(expr, sp.Basic):
         return sympify_petab(petab_math_str(expr))
 
     if isinstance(expr, int) or isinstance(expr, np.integer):

tests/v1/math/test_math.py

@@ -34,6 +34,7 @@ def test_assumptions():
 
 
 def test_printer():
+    assert petab_math_str(None) == ""
     assert petab_math_str(BooleanTrue()) == "true"
     assert petab_math_str(BooleanFalse()) == "false"
 

tests/v2/test_problem.py

@@ -133,7 +133,9 @@ def test_modify_problem():
         }
     ).set_index([OBSERVABLE_ID])
     assert_frame_equal(
-        problem.observable_df[[OBSERVABLE_FORMULA, NOISE_FORMULA]],
+        problem.observable_df[[OBSERVABLE_FORMULA, NOISE_FORMULA]].map(
+            lambda x: float(x) if x != "" else None
+        ),
         exp_observable_df,
         check_dtype=False,
     )