Add observables to models

gyorilab · Jul 13, 2023 · e1a4eba · e1a4eba
1 parent 8c7207e
commit e1a4eba
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Showing 10 changed files with 5,923 additions and 29 deletions.
diff --git a/mira/metamodel/ops.py b/mira/metamodel/ops.py
@@ -208,7 +208,7 @@ def stratify(
 
     observables = {}
     for observable_key, observable in template_model.observables.items():
-        syms = set(observable.expression.args[0].free_symbols)
+        syms = {s.name for s in observable.expression.args[0].free_symbols}
         expr = deepcopy(observable.expression.args[0])
         for sym in (syms & concept_names) - exclude_concepts:
             new_symbols = []
@@ -217,7 +217,7 @@ def stratify(
                     do_rename=modify_names, **{key: stratum},
                 )
                 new_symbols.append(sympy.Symbol(new_concept.name))
-            expr = expr.args[0].subs(sym, sympy.Add(*new_symbols))
+            expr = expr.subs(sympy.Symbol(sym), sympy.Add(*new_symbols))
         observables[observable_key] = deepcopy(observable)
         observables[observable_key].expression = SympyExprStr(expr)
 

diff --git a/mira/modeling/askenet/petrinet.py b/mira/modeling/askenet/petrinet.py
@@ -75,7 +75,8 @@ def __init__(self, model: Model):
                 states_dict['units'] = {
                     'expression': str(var.concept.units.expression),
                     'expression_mathml': expression_to_mathml(
-                        var.concept.units.expression.args[0]),
+                        var.concept.units.expression.args[0]
+                    ),
                 }
 
             self.states.append(states_dict)

diff --git a/notebooks/hackathon_2023.07/scenario1.ipynb b/notebooks/hackathon_2023.07/scenario1.ipynb