Add petab-compatible sympy string-printer

Add a sympy Printer to stringify sympy expressions in a petab-compatible way.
For example, we need to avoid `str(sympy.sympify("x^2"))` -> `'x**2'`.

Closes #362.

Author: dweindl

petab/v1/math/__init__.py

@@ -1,3 +1,4 @@
 """Functions for parsing and evaluating mathematical expressions."""
 
+from .printer import PetabStrPrinter, petab_math_str  # noqa: F401
 from .sympify import sympify_petab  # noqa: F401

petab/v1/math/printer.py

@@ -0,0 +1,33 @@
+"""A PEtab-compatible sympy string-printer."""
+
+import sympy as sp
+from sympy.printing.str import StrPrinter
+
+
+class PetabStrPrinter(StrPrinter):
+    """A PEtab-compatible sympy string-printer."""
+
+    def _print_Pow(self, expr: sp.Pow):
+        """Custom printing for the power operator"""
+        base, exp = expr.as_base_exp()
+        return f"{self._print(base)} ^ {self._print(exp)}"
+
+    def _print_Infinity(self, expr):
+        """Custom printing for infinity"""
+        return "inf"
+
+    def _print_NegativeInfinity(self, expr):
+        """Custom printing for negative infinity"""
+        return "-inf"
+
+
+def petab_math_str(expr: sp.Expr) -> 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)'
+    """
+
+    return PetabStrPrinter().doprint(expr)

tests/v1/math/test_math.py

@@ -8,7 +8,7 @@
 from sympy.abc import _clash
 from sympy.logic.boolalg import Boolean
 
-from petab.math import sympify_petab
+from petab.math import petab_math_str, sympify_petab
 
 
 def test_sympify_numpy():
@@ -55,20 +55,27 @@ def read_cases():
 @pytest.mark.parametrize("expr_str, expected", read_cases())
 def test_parse_cases(expr_str, expected):
     """Test PEtab math expressions for the PEtab test suite."""
-    result = sympify_petab(expr_str)
-    if isinstance(result, Boolean):
-        assert result == expected
+    sym_expr = sympify_petab(expr_str)
+    if isinstance(sym_expr, Boolean):
+        assert sym_expr == expected
     else:
         try:
-            result = float(result.evalf())
+            result = float(sym_expr.evalf())
             assert np.isclose(result, expected), (
                 f"{expr_str}: Expected {expected}, got {result}"
             )
         except TypeError:
-            assert result == expected, (
+            assert sym_expr == expected, (
                 f"{expr_str}: Expected {expected}, got {result}"
             )
 
+    # test parsing, printing, and parsing again
+    resympified = sympify_petab(petab_math_str(sym_expr))
+    if sym_expr.is_number:
+        assert np.isclose(float(resympified), float(sym_expr))
+    else:
+        assert resympified.equals(sym_expr), (sym_expr, resympified)
+
 
 def test_ids():
     """Test symbols in expressions."""