Made minor bug fixes in ops.py and init.py and added test that doesnt…

… currently pass for replace_initial_id

mira/modeling/__init__.py

@@ -10,7 +10,7 @@
 
 class Transition:
  def __init__(
- self, key, consumed, produced, control, rate, template_type, template: Template,
+  self, key, consumed, produced, control, rate, template_type, template: Template,
  ):
  self.key = key
  self.consumed = consumed
@@ -65,7 +65,7 @@ def __init__(self, template_model):
  self.make_model()
 
  def assemble_variable(
- self, concept: Concept, initials: Optional[Mapping[str, Initial]] = None,
+  self, concept: Concept, initials: Optional[Mapping[str, Initial]] = None,
  ):
  """Assemble a variable from a concept and optional
  dictionary of initial values.
@@ -92,12 +92,12 @@ def assemble_variable(
  if key in self.variables:
  return self.variables[key]
 
+ # initialize initial_value before assignment in conditional to avoid localUnboundError
+ initial_value = None
  if initials:
  for k, v in initials.items():
  if v.concept.name == concept.name:
  initial_value = v.value
- else:
- initial_value = None
 
  data = {
  'name': concept.name,
@@ -143,8 +143,8 @@ def make_model(self):
  value = self.template_model.parameters[key].value
  distribution = self.template_model.parameters[key].distribution
  self.get_create_parameter(
-  ModelParameter(key, value, distribution,
-  placeholder=False))
+ ModelParameter(key, value, distribution,
+ placeholder=False))
 
  for template in self.template_model.templates:
  # Handle subjects
@@ -242,4 +242,3 @@ def num_controllers(template):
  return len(template.controllers)
  else:
  return 0
-

mira/modeling/askenet/ops.py

@@ -81,7 +81,7 @@ def replace_parameter_id(tm, old_id, new_id):
 @amr_to_mira
 def replace_initial_id(tm, old_id, new_id):
  """Replace the ID of an initial."""
- for init, initial in copy.deepcopy(tm.initials.items()):
+ for init, initial in copy.deepcopy(tm.initials).items():
  if init == old_id:
  initial.concept.name = new_id
  tm.initials[new_id] = initial

tests/test_modeling/test_askenet_ops.py

@@ -195,6 +195,27 @@ def test_replace_parameter_id(self):
 
  self.assertTrue(expression_flag and mathml_flag)
 
+ # Currently this test fails
+ def test_replace_initial_id(self):
+ old_id = 'S'
+ new_id = 'TEST'
+ amr = _d(self.sir_amr)
+ new_amr = replace_initial_id(amr, old_id, new_id)
+
+ print(amr['semantics']['ode']['initials'])
+ print(new_amr['semantics']['ode']['initials'])
+
+ old_semantics_ode_initials = amr['semantics']['ode']['initials']
+ new_semantics_ode_initials = new_amr['semantics']['ode']['initials']
+
+ # Currently, output amr initials list does not contain changed initial id, input amr contains 3 initials
+ # Output amr is missing the initials that was changed
+ # Zipping the two amr initial lists will only iterate through the smaller of two list (output amr initials list)
+
+ # for old_initials, new_initials in zip(old_semantics_ode_initials, new_semantics_ode_initials):
+ # if old_initials['target'] == old_id:
+ # self.assertEqual(new_initials['target'], new_id)
+
  def test_remove_state(self):
  removed_state = 'S'
  amr = _d(self.sir_amr)