Alternate sbmlmath testing

pyproject.toml

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

setup.cfg

@@ -17,6 +17,7 @@ install_requires =
     typing_extensions
     networkx
     tqdm
+    sbmlmath; python_version >= "3.10"
 
 zip_safe = false
 include_package_data = True

tests/test_metamodel.py

@@ -16,6 +16,15 @@
     template_model_from_askenet_json
 from tests import expression_yielder, remove_all_sympy, sorted_json_str
 
+try:
+    import sbmlmath
+except ImportError:
+    sbmlmath_available = False
+else:
+    sbmlmath_available = True
+
+SBMLMATH_REQUIRED = unittest.skipUnless(sbmlmath_available, reason="SBMLMath package is not available")
+
 
 class TestMetaModel(unittest.TestCase):
     """A test case for the metamodel."""
@@ -31,7 +40,6 @@ def setUp(self) -> None:
         self.asymptomatic = Concept(name="asymptomatic infected population", identifiers={"ido": "0000511"})
         self.immune = Concept(name="immune population", identifiers={"ido": "0000592"})
 
-
     def test_schema(self):
         """Test that the schema is up to date."""
         self.assertTrue(SCHEMA_PATH.is_file())
@@ -105,7 +113,7 @@ def test_rate_law_to_mathml():
                       '<ci>b1</ci></apply>')
 
 
-@pytest.mark.sbmlmath
+@SBMLMATH_REQUIRED
 def test_mathml_to_sympy():
     # 1
     xml_str = """<apply>
@@ -181,11 +189,10 @@ def test_mathml_to_sympy():
     assert expression_to_mathml(sympy_expr) == expression_mathml
 
 
-
-@pytest.mark.sbmlmath
+@SBMLMATH_REQUIRED
 def test_from_askenet_petri():
     source_url = "https://raw.githubusercontent.com/DARPA-ASKEM/Model" \
-         "-Representations/main/petrinet/examples/sir.json"
+                 "-Representations/main/petrinet/examples/sir.json"
     resp = requests.get(source_url)
     assert resp.status_code == 200
     model_json = resp.json()
@@ -208,11 +215,11 @@ def test_from_askenet_petri():
                sympy.parse_expr(expression_str, local_dict=local_dict)
 
 
-@pytest.mark.sbmlmath
+@SBMLMATH_REQUIRED
 def test_from_askenet_petri_mathml():
     # Get model
     source_url = "https://raw.githubusercontent.com/DARPA-ASKEM/Model" \
-         "-Representations/main/petrinet/examples/sir.json"
+                 "-Representations/main/petrinet/examples/sir.json"
     resp = requests.get(source_url)
     assert resp.status_code == 200
     model_json_mathml = resp.json()

tests/test_model_api.py

@@ -34,6 +34,15 @@
 from tests import sorted_json_str, remove_all_sympy
 import requests
 
+try:
+    import sbmlmath
+except ImportError:
+    sbmlmath_available = False
+else:
+    sbmlmath_available = True
+
+SBMLMATH_REQUIRED = unittest.skipUnless(sbmlmath_available, reason="SBMLMath package is not available")
+
 
 class RequestsWrapper:
     base_url = "http://localhost:8771"
@@ -77,9 +86,9 @@ def _get_sir_templatemodel() -> TemplateModel:
 class MockNeo4jClient:
     @staticmethod
     def query_relations(
-        source_curie: str,
-        relation_type: Union[str, List[str]],
-        target_curie: str,
+            source_curie: str,
+            relation_type: Union[str, List[str]],
+            target_curie: str,
     ) -> List:
         rq = RelationQuery(
             source_curie=source_curie,
@@ -151,7 +160,7 @@ def test_petri_distribution(self):
         pm = response.json()
         assert pm['T'][0]['tprop']['parameter_distribution'] == distr.json()
         assert json.loads(pm['T'][0]['tprop']['mira_parameter_distributions']) == \
-            {'beta': distr.dict()}
+               {'beta': distr.dict()}
         self.assertEqual(200, response.status_code, msg=response.content)
 
     def test_petri_to_template_model(self):
@@ -179,7 +188,7 @@ def test_askenet_to_template_model(self):
         template_model = TemplateModel.from_json(response.json())
         self.assertIsInstance(template_model, TemplateModel)
 
-    @pytest.mark.sbmlmath
+    @SBMLMATH_REQUIRED
     def test_askenet_to_template_model_no_sympy(self):
         askenet_json = AskeNetPetriNetModel(Model(
             sir_parameterized_init)).to_json()
@@ -248,7 +257,7 @@ def test_stratify_observable_api(self):
         expr = sympy.Add(*[sympy.Symbol(s) for s in symbols])
         tm.observables = {'half_population': Observable(
             name='half_population',
-            expression=SympyExprStr(expr/2))
+            expression=SympyExprStr(expr / 2))
         }
 
         strata_options = dict(key='age',
@@ -665,4 +674,3 @@ def test_reconstruct_ode_semantics_endpoint(self):
         assert len(flux_span_tm.templates) == 10
         assert len(flux_span_tm.parameters) == 11
         assert all(t.rate_law for t in flux_span_tm.templates)
-

tests/test_modeling/test_askenet_ops.py

@@ -1,12 +1,21 @@
 import unittest
 import requests
-import pytest
 from copy import deepcopy as _d
 from mira.modeling.askenet.ops import *
 from sympy import *
 from mira.metamodel.io import mathml_to_expression
 from mira.metamodel.templates import Concept
 
+try:
+    import sbmlmath
+except ImportError:
+    sbmlmath_available = False
+else:
+    sbmlmath_available = True
+
+
+SBMLMATH_REQUIRED = unittest.skipUnless(sbmlmath_available, reason="SBMLMath package is not available")
+
 
 class TestAskenetOperations(unittest.TestCase):
     """A test case for operations on template models."""
@@ -188,7 +197,7 @@ def test_remove_observable_or_parameter(self):
 
                 self.assertEqual(old_obs['id'], new_obs['id'])
 
-    @pytest.mark.sbmlmath
+    @SBMLMATH_REQUIRED
     def test_add_observable(self):
         amr = _d(self.sir_amr)
         new_id = 'testinf'
@@ -207,7 +216,7 @@ 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
+    @SBMLMATH_REQUIRED
     def test_replace_parameter_id(self):
         old_id = 'beta'
         new_id = 'TEST'
@@ -311,7 +320,7 @@ def test_remove_transition(self):
         for new_transition in new_model_transition:
             self.assertNotEquals(removed_transition, new_transition['id'])
 
-    @pytest.mark.sbmlmath
+    @SBMLMATH_REQUIRED
     def test_add_transition(self):
         test_subject = Concept(name="test_subject", identifiers={"ido": "0000511"})
         test_outcome = Concept(name="test_outcome", identifiers={"ido": "0000592"})
@@ -404,7 +413,7 @@ def test_add_transition(self):
                          natural_degradation_rates_dict[new_transition_id]['expression'])
         self.assertIn(test_subject.name, natural_degradation_states_dict)
 
-    @pytest.mark.sbmlmath
+    @SBMLMATH_REQUIRED
     def test_replace_rate_law_sympy(self):
         transition_id = 'inf'
         target_expression_xml_str = '<apply><plus/><ci>X</ci><cn>8</cn></apply>'
@@ -419,7 +428,7 @@ 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
+    @SBMLMATH_REQUIRED
     def test_replace_rate_law_mathml(self):
         amr = _d(self.sir_amr)
         transition_id = 'inf'
@@ -435,7 +444,7 @@ 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
+    @SBMLMATH_REQUIRED
     # Following 2 unit tests only test for replacing expressions in observables, not initials
     def test_replace_observable_expression_sympy(self):
         object_id = 'noninf'
@@ -449,7 +458,7 @@ def test_replace_observable_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
+    @SBMLMATH_REQUIRED
     def test_replace_observable_expression_mathml(self):
         object_id = 'noninf'
         amr = _d(self.sir_amr)

tox.ini

@@ -17,7 +17,7 @@ extras =
 deps = 
     anyio<4
 commands =
-    coverage run -p -m pytest --durations=20 {posargs:tests} -m "not slow and not sbmlmath"
+    coverage run -p -m pytest --durations=20 {posargs:tests} -m "not slow"
 ;    coverage combine
 ;    coverage xml
 [testenv:docs]