Implement BNG boolean treatment within expressions (#494)

* Implement BNG boolean treatment within expressions

BNG treats booleans as integers within expressions (1=True,
0=False), so an expression like `(2 > 1) * 4` will get evaluated
to `4`. Sometimes these expressions get produced by BNG
local functions and may be present in other imported models as
well. However, doesn't implement multiplication of
BooleanAtoms, which causes a TypeError.

* Implement Boolean multiplication fix proposed by @jmuhlich

Co-authored-by: Jeremy Muhlich <jmuhlich@bitflood.org>

pysb/bng.py

@@ -18,7 +18,7 @@
 import pysb.pathfinder as pf
 import tokenize
 from pysb.logging import get_logger, EXTENDED_DEBUG
-
+from sympy.logic.boolalg import BooleanTrue, BooleanFalse, BooleanAtom
 try:
     from cStringIO import StringIO
 except ImportError:
@@ -933,6 +933,19 @@ def _convert_tokens(tokens, local_dict, global_dict):
     return tokens
 
 
+def _is_bool_expr(e):
+    return isinstance(e, sympy.boolalg.Boolean) and not \
+        isinstance(e, sympy.AtomicExpr)
+
+
+def _fix_boolean_multiplication(*args):
+    args = [
+        sympy.Piecewise((1, a), (0, True)) if _is_bool_expr(a) else a
+        for a in args
+    ]
+    return sympy.Mul(*args)
+
+
 def parse_bngl_expr(text, *args, **kwargs):
     """Convert a BNGL math expression string to a sympy Expr."""
 
@@ -944,7 +957,13 @@ def parse_bngl_expr(text, *args, **kwargs):
         sympy_parser.standard_transformations
         + (sympy_parser.convert_equals_signs, _convert_tokens)
     )
-    expr = sympy_parser.parse_expr(text, *args, transformations=trans, **kwargs)
+    expr = sympy_parser.parse_expr(text, *args, transformations=trans,
+                                   evaluate=False, **kwargs)
+
+    # Replace Boolean multiplications, e.g. `2 * (3 > 0)`
+    # See https://github.com/pysb/pysb/pull/494
+    expr = expr.replace(sympy.Mul, _fix_boolean_multiplication)
+
     # Transforming 'if' to Piecewise requires subexpression rearrangement, so we
     # use sympy's replace functionality rather than attempt it using text
     # replacements above.

pysb/importers/bngl.py

@@ -67,8 +67,7 @@ def _eval_in_model_env(self, expression):
 
         # Quick security check on the expression
         if re.match(r'^[\w\s()/+\-._*^]*$', expression):
-            return parse_bngl_expr(expression, local_dict=self._model_env,
-                                   evaluate=False)
+            return parse_bngl_expr(expression, local_dict=self._model_env)
         else:
             self._warn_or_except('Security check on expression "%s" failed' %
                                  expression)

pysb/tests/test_bng.py

@@ -329,3 +329,8 @@ def test_parse_bngl_expression_and_or_equals():
     assert parse_bngl_expr('x and y') == sympy.And(x, y)
     assert parse_bngl_expr('x or y') == sympy.Or(x, y)
     assert parse_bngl_expr('x == y') == sympy.Eq(x, y)
+
+
+def test_bng_boolean_multiply_number():
+    assert parse_bngl_expr('(2 > 1) * 4') == 4
+    assert parse_bngl_expr('4 * (2 > 1)') == 4