rename parameters in stratify and other MIRA changes (#148)

src/askem_beaker/contexts/mira_model_edit/procedures/python3/replace_ratelaw.py

@@ -1,3 +1,4 @@
+import sympy
 def replace_rate_law_sympy(model, template_name, new_rate_law):
     """Replace the rate law of transition. The new rate law passed in will be a sympy.Expr object
 
@@ -8,8 +9,6 @@ def replace_rate_law_sympy(model, template_name, new_rate_law):
         typically the name of the transition
     new_rate_law :
         The new rate law to replace the existing rate law with
-    local_dict :
-        A dictionary of local variables to use when parsing.
 
     Returns
     -------
@@ -18,9 +17,13 @@ def replace_rate_law_sympy(model, template_name, new_rate_law):
     """
     assert isinstance(model, TemplateModel)
     tm = model
+    local_dict = { key:sympy.Symbol(key) for key, _value in tm.parameters.items() }
+    for k, v in tm.get_concepts_name_map().items():
+        local_dict[k] = sympy.Symbol(k)
+
     for template in tm.templates:
         if template.name == template_name:
-            template.set_rate_law(new_rate_law, local_dict=None)
+            template.set_rate_law(new_rate_law, local_dict=local_dict)
     return tm
 
 model = replace_rate_law_sympy(model, "{{ template_name }}", "{{ new_rate_law }}")

src/askem_beaker/contexts/mira_model_edit/procedures/python3/stratify.py

@@ -7,5 +7,6 @@
     cartesian_control={{ cartesian_control|default(False) }},
     modify_names={{ modify_names|default(True) }},
     concepts_to_stratify={{ concepts_to_stratify|default(None) }}, #If none given, will stratify all concepts.
-	params_to_stratify= {{ params_to_stratify|default(None) }} #If none given, will stratify all parameters.
-)
+    params_to_stratify= {{ params_to_stratify|default(None) }}, #If none given, will stratify all parameters.
+    param_renaming_uses_strata_names = True
+)