Merge pull request #175 from jmuhlich/macro_expressions

Allow Expressions in addition to Parameters in macro calls

pysb/macros.py

@@ -8,9 +8,9 @@
 * All components created by the macro are implicitly added to the current model
   and explicitly returned in a ComponentSet.
 
-* Parameters may be passed as Parameter objects, or as plain numbers for which
-  Parameter objects will be automatically created using an appropriate naming
-  convention.
+* Parameters may be passed as Parameter or Expression objects, or as plain
+  numbers for which Parameter objects will be automatically created using an
+  appropriate naming convention.
 
 * Arguments which accept a MonomerPattern should also accept Monomers, which are
   to be interpreted as MonomerPatterns on that Monomer with an empty condition
@@ -95,18 +95,18 @@ def _macro_rule(rule_prefix, rule_expression, klist, ksuffixes,
     rule_expression : RuleExpression
         An expression specifying the form of the rule; gets passed directly
         to the Rule constructor.
-    klist : list of Parameters or list of numbers
+    klist : list of Parameters or Expressions, or list of numbers
         If the rule is unidirectional, the list must contain one element
-        (either a Parameter or number); if the rule is reversible, it must
-        contain two elements. If the rule is reversible, the first element
-        in the list is taken to be the forward rate, and the second element
-        is taken as the reverse rate. 
+        (either a Parameter/Expression or number); if the rule is reversible,
+        it must contain two elements. If the rule is reversible, the first
+        element in the list is taken to be the forward rate, and the second
+        element is taken as the reverse rate. 
     ksuffixes : list of strings
-        If klist contains numbers rather than Parameters, the strings in
-        ksuffixes are used to automatically generate the necessary Parameter
-        objects. The suffixes are appended to the rule name to generate the
-        associated parameter name. ksuffixes must contain one element if the
-        rule is unidirectional, two if it is reversible.
+        If klist contains numbers rather than Parameters or Expressions, the
+        strings in ksuffixes are used to automatically generate the necessary
+        Parameter objects. The suffixes are appended to the rule name to
+        generate the associated parameter name. ksuffixes must contain one
+        element if the rule is unidirectional, two if it is reversible.
     name_func : function, optional
         A function which takes a RuleExpression and returns a string label for
         it, to be called as part of the automatic rule name generation. If not
@@ -167,7 +167,7 @@ def _macro_rule(rule_prefix, rule_expression, klist, ksuffixes,
         if len(klist) != 2 or len(ksuffixes) != 2:
             raise ValueError("A bidirectional rule must have two parameters.")
 
-    if all(isinstance(x, Parameter) for x in klist):
+    if all(isinstance(x, (Parameter, Expression)) for x in klist):
         k1 = klist[0]
         if rule_expression.is_reversible:
             k2 = klist[1]
@@ -181,7 +181,7 @@ def _macro_rule(rule_prefix, rule_expression, klist, ksuffixes,
                            klist[1])
             params_created.add(k2)
     else:
-        raise ValueError("klist must contain Parameter objects or numbers.")
+        raise ValueError("klist must contain Parameters, Expressions, or numbers.")
 
     if rule_expression.is_reversible:
         r = Rule(r_name, rule_expression, k1, k2)