Updated unit test for add_transition, add pytest mark for unit tests …

…that require sbmlmath, forced pydantic<2.0 dependency for purpose of testing due to conflict with TestModelAPi

mira/modeling/askenet/ops.py

@@ -164,6 +164,11 @@ def remove_state(tm, state_id):
  return tm
 
 
+@amr_to_mira
+def add_state(tm, state_id, grounding: None, units: None):
+ pass
+
+
 # Remove transition
 @amr_to_mira
 def remove_transition(tm, transition_id):

pyproject.toml

@@ -16,4 +16,5 @@ reverse_relative = true
 [tool.pytest.ini_options]
 markers = [
  "slow: marks tests as slow for pytest (deselect with '-m \"not slow\"')"
+ "sbmlmath: marks tests that should not be tested due to them using sbmlmath"
 ]

tests/test_modeling/test_askenet_ops.py

@@ -17,8 +17,8 @@ def setUpClass(cls):
  'https://raw.githubusercontent.com/DARPA-ASKEM/'
  'Model-Representations/main/petrinet/examples/sir.json').json()
 
- '''These unit tests are conducted by zipping through lists of each key in a amr file 
- (e.g. parameters, observables, etc). Zipping in this manner assumes that the order (assuming insertion order) 
+ '''These unit tests are conducted by zipping through lists of each key in a amr file
+ (e.g. parameters, observables, etc). Zipping in this manner assumes that the order (assuming insertion order)
  is preserved before and after mira operation for an amr key
  '''
 
@@ -117,6 +117,7 @@ def test_replace_state_id(self):
  self.assertEqual(old_observable['id'], new_observable['id'])
 
  def test_replace_transition_id(self):
+
  old_id = 'inf'
  new_id = 'new_inf'
  amr = _d(self.sir_amr)
@@ -296,7 +297,7 @@ def test_remove_state(self):
  self.assertNotEquals(removed_state_id, new_initial['target'])
 
  # parameters that are associated in an expression with a removed state are not present in output amr
- # (e.g.) if there exists an expression: 'S*I*beta' and we remove S, then beta is no longer present in output
+ # (e.g.) if there exists an expression: "S*I*beta" and we remove S, then beta is no longer present in output
  # list of parameters
  for new_parameter in new_semantics_ode_parameters:
  self.assertNotIn(removed_state_id, new_parameter['id'])
@@ -319,8 +320,8 @@ def test_remove_transition(self):
 
  @pytest.mark.sbmlmath
  def test_add_transition(self):
- infected = Concept(name="infected_population", identifiers={"ido": "0000511"})
- recovered = Concept(name="immune_population", identifiers={"ido": "0000592"})
+ test_subject = Concept(name="test_subject", identifiers={"ido": "0000511"})
+ test_outcome = Concept(name="test_outcome", identifiers={"ido": "0000592"})
  expression_xml = "<apply><times/><ci>E</ci><ci>delta</ci></apply>"
  new_transition_id = 'test'
  old_natural_conversion_amr = _d(self.sir_amr)
@@ -329,10 +330,12 @@ def test_add_transition(self):
 
  # NaturalConversion
  new_natural_conversion_amr = add_transition(old_natural_conversion_amr, new_transition_id, expression_xml,
- src_id=infected,
- tgt_id=recovered)
+ src_id=test_subject,
+ tgt_id=test_outcome)
  natural_conversion_transition_dict = {}
  natural_conversion_rates_dict = {}
+ natural_conversion_state_dict = {}
+
  for transition in new_natural_conversion_amr['model']['transitions']:
  name = transition.pop('id')
  natural_conversion_transition_dict[name] = transition
@@ -341,17 +344,25 @@ def test_add_transition(self):
  name = rate.pop('target')
  natural_conversion_rates_dict[name] = rate
 
+ for state in new_natural_conversion_amr['model']['states']:
+ name = state.pop('id')
+ natural_conversion_state_dict[name] = state
+
  self.assertIn(new_transition_id, natural_conversion_transition_dict)
  self.assertIn(new_transition_id, natural_conversion_rates_dict)
  self.assertEqual(expression_xml, natural_conversion_rates_dict[new_transition_id]['expression_mathml'])
  self.assertEqual(sstr(mathml_to_expression(expression_xml)),
  natural_conversion_rates_dict[new_transition_id]['expression'])
+ self.assertIn(test_subject.name, natural_conversion_state_dict)
+ self.assertIn(test_outcome.name, natural_conversion_state_dict)
 
  # NaturalProduction
  new_natural_production_amr = add_transition(old_natural_production_amr, new_transition_id, expression_xml,
- tgt_id=recovered)
+ tgt_id=test_outcome)
  natural_production_transition_dict = {}
  natural_production_rates_dict = {}
+ natural_production_state_dict = {}
+
  for transition in new_natural_production_amr['model']['transitions']:
  name = transition.pop('id')
  natural_production_transition_dict[name] = transition
@@ -360,17 +371,24 @@ def test_add_transition(self):
  name = rate.pop('target')
  natural_production_rates_dict[name] = rate
 
+ for state in new_natural_production_amr['model']['states']:
+ name = state.pop('id')
+ natural_production_state_dict[name] = state
+
  self.assertIn(new_transition_id, natural_production_transition_dict)
  self.assertIn(new_transition_id, natural_production_rates_dict)
  self.assertEqual(expression_xml, natural_production_rates_dict[new_transition_id]['expression_mathml'])
  self.assertEqual(sstr(mathml_to_expression(expression_xml)),
  natural_production_rates_dict[new_transition_id]['expression'])
+ self.assertIn(test_outcome.name, natural_production_state_dict)
 
  # NaturalDegradation
  new_natural_degradation_amr = add_transition(old_natural_degradation_amr, new_transition_id, expression_xml,
- src_id=infected)
+ src_id=test_subject)
  natural_degradation_transition_dict = {}
  natural_degradation_rates_dict = {}
+ natural_degradation_states_dict = {}
+
  for transition in new_natural_degradation_amr['model']['transitions']:
  name = transition.pop('id')
  natural_degradation_transition_dict[name] = transition
@@ -379,11 +397,16 @@ def test_add_transition(self):
  name = rate.pop('target')
  natural_degradation_rates_dict[name] = rate
 
+ for state in new_natural_degradation_amr['model']['states']:
+ name = state.pop('id')
+ natural_degradation_states_dict[name] = state
+
  self.assertIn(new_transition_id, natural_degradation_transition_dict)
  self.assertIn(new_transition_id, natural_degradation_rates_dict)
  self.assertEqual(expression_xml, natural_degradation_rates_dict[new_transition_id]['expression_mathml'])
  self.assertEqual(sstr(mathml_to_expression(expression_xml)),
  natural_degradation_rates_dict[new_transition_id]['expression'])
+ self.assertIn(test_subject.name, natural_degradation_states_dict)
 
  @pytest.mark.sbmlmath
  def test_replace_rate_law_sympy(self):

tox.ini

@@ -10,15 +10,16 @@ envlist =
  py
 
 [testenv]
-passenv = PYTHONPATH MIRA_REST_URL
+passenv = PYTHONPATH, MIRA_REST_URL
 extras =
  tests
  web
+deps = 
+ pydantic<2.0
 commands =
  coverage run -p -m pytest --durations=20 {posargs:tests} -m "not slow and not sbmlmath"
 ; coverage combine
 ; coverage xml
-
 [testenv:docs]
 extras =
  docs