Fix Sympy 1.6 Incompatibility (#505)

* fix string sympification
* Fix drug_binding macro for sympy 1.6

Co-authored-by: Alex Lubbock <code@alexlubbock.com>

pysb/bng.py

@@ -953,7 +953,7 @@ def parse_bngl_expr(text, *args, **kwargs):
         lambda cond, t, f: sympy.Piecewise((t, cond), (f, True))
     )
     # Check for unsupported constructs.
-    if expr.has('time'):
+    if expr.has(sympy.Symbol('time')):
         raise ValueError(
             "Expressions referencing simulation time are not supported"
         )

pysb/macros.py

@@ -33,13 +33,12 @@
 """
 
 
-import inspect
 from pysb import *
-import pysb.core
-from pysb.core import ComponentSet, as_reaction_pattern, as_complex_pattern, MonomerPattern, ComplexPattern
+from pysb.core import ComponentSet, as_complex_pattern, MonomerPattern, ComplexPattern
 import numbers
 import functools
 import itertools
+from sympy import Piecewise
 
 __all__ = ['equilibrate',
            'bind', 'bind_table',
@@ -953,8 +952,8 @@ def drug_binding(drug, d_site, substrate, s_site, t_action, klist):
          Monomer('__t'),
          Parameter('__k_t', 1.0),
          Observable('t', __t()),
-         Expression('kf_expr_drug_substrate', kf_drug_substrate*(t > 10)),
-         Expression('kr_expr_drug_substrate', kr_drug_substrate*(t > 10)),
+         Expression('kf_expr_drug_substrate', Piecewise((kf_drug_substrate, t > 10), (0, True))),
+         Expression('kr_expr_drug_substrate', Piecewise((kr_drug_substrate, t > 10), (0, True))),
          ])
 
     """
@@ -992,9 +991,9 @@ def drug_binding(drug, d_site, substrate, s_site, t_action, klist):
         raise ValueError("klist must contain Parameters, Expressions, or numbers.")
 
     kf_expr = Expression('kf_expr_{0}_{1}'.format(drug_monomer_name,
-                                                  substrate_monomer_name), (time_obs > t_action) * k1)
+                                                  substrate_monomer_name), Piecewise((k1, time_obs > t_action), (0, True)))
     kr_expr = Expression('kr_expr_{0}_{1}'.format(drug_monomer_name,
-                                                  substrate_monomer_name), (time_obs > t_action) * k2)
+                                                  substrate_monomer_name), Piecewise((k2, time_obs > t_action), (0, True)))
     bind_kpars = [kf_expr, kr_expr]
 
     components_added_macro = components_time_obs