Added comments in ops.py showing next possible steps for test_transit…

…ion and added decorator to all unit tests that require sbmlmath

mira/modeling/askenet/ops.py

@@ -172,6 +172,8 @@ def remove_transition(tm, transition_id):
 
 
 @amr_to_mira
+# option 1 take in optional parameters dict if rate law contains parameters that aren't already present
+# option 2, reverse engineer rate law and find parameters and states within the rate law and add to model
 def add_transition(tm, new_transition_id, rate_law_mathml, src_id=None, tgt_id=None):
  rate_law_sympy = SympyExprStr(mathml_to_expression(rate_law_mathml))
  if src_id is None and tgt_id is None:

tests/test_modeling/test_askenet_ops.py

@@ -1,5 +1,6 @@
 import unittest
 import requests
+import pytest
 from copy import deepcopy as _d
 from mira.modeling.askenet.ops import *
 from sympy import *
@@ -185,6 +186,7 @@ def test_remove_observable_or_parameter(self):
 
  self.assertEqual(old_obs['id'], new_obs['id'])
 
+ @pytest.mark.sbmlmath
  def test_add_observable(self):
  amr = _d(self.sir_amr)
  new_id = 'testinf'
@@ -203,6 +205,7 @@ def test_add_observable(self):
  self.assertEqual(xml_expression, new_observable_dict[new_id]['expression_mathml'])
  self.assertEqual(sstr(mathml_to_expression(xml_expression)), new_observable_dict[new_id]['expression'])
 
+ @pytest.mark.sbmlmath
  def test_replace_parameter_id(self):
  old_id = 'beta'
  new_id = 'TEST'
@@ -252,6 +255,7 @@ def test_replace_parameter_id(self):
  self.assertEqual(mathml_to_expression(old_parameter['units']['expression_mathml']),
  mathml_to_expression(new_parameter['units']['expression_mathml']))
 
+ @pytest.mark.sbmlmath
  def test_add_parameter(self):
  amr = _d(self.sir_amr)
 
@@ -313,6 +317,7 @@ def test_remove_transition(self):
  for new_transition in new_model_transition:
  self.assertNotEquals(removed_transition, new_transition['id'])
 
+ @pytest.mark.sbmlmath
  def test_add_transition(self):
  infected = Concept(name="infected_population", identifiers={"ido": "0000511"})
  recovered = Concept(name="immune_population", identifiers={"ido": "0000592"})
@@ -380,6 +385,7 @@ def test_add_transition(self):
  self.assertEqual(sstr(mathml_to_expression(expression_xml)),
  natural_degradation_rates_dict[new_transition_id]['expression'])
 
+ @pytest.mark.sbmlmath
  def test_replace_rate_law_sympy(self):
  transition_id = 'inf'
  target_expression_xml_str = '<apply><plus/><ci>X</ci><cn>8</cn></apply>'
@@ -394,6 +400,7 @@ def test_replace_rate_law_sympy(self):
  self.assertEqual(sstr(target_expression_sympy), new_rate['expression'])
  self.assertEqual(target_expression_xml_str, new_rate['expression_mathml'])
 
+ @pytest.mark.sbmlmath
  def test_replace_rate_law_mathml(self):
  amr = _d(self.sir_amr)
  transition_id = 'inf'
@@ -409,6 +416,7 @@ def test_replace_rate_law_mathml(self):
  self.assertEqual(sstr(target_expression_sympy), new_rate['expression'])
  self.assertEqual(target_expression_xml_str, new_rate['expression_mathml'])
 
+ @pytest.mark.sbmlmath
  # Following 2 unit tests only test for replacing expressions in observables, not initials
  def test_replace_expression_sympy(self):
  object_id = 'noninf'
@@ -422,6 +430,7 @@ def test_replace_expression_sympy(self):
  self.assertEqual(sstr(target_expression_sympy), new_obs['expression'])
  self.assertEqual(target_expression_xml_str, new_obs['expression_mathml'])
 
+ @pytest.mark.sbmlmath
  def test_replace_expression_mathml(self):
  object_id = 'noninf'
  amr = _d(self.sir_amr)