Update tests to work with Pytest v8 (#1275)

Author: matt-graham

tests/test_consumables.py

@@ -96,7 +96,7 @@ def test_unrecognised_item_code_is_recorded(seed):
     assert cons._not_recognised_item_codes  # Some item_codes recorded as not recognised.
 
     # Check warning is issued at end of simulation
-    with pytest.warns(None) as recorded_warnings:
+    with pytest.warns(UserWarning) as recorded_warnings:
         cons.on_simulation_end()
 
     assert any_warnings_about_item_code(recorded_warnings)
@@ -479,35 +479,34 @@ def test_check_format_of_consumables_file():
 
 
 @pytest.mark.slow
-def test_every_declared_consumable_for_every_possible_hsi_using_actual_data():
+def test_every_declared_consumable_for_every_possible_hsi_using_actual_data(recwarn):
     """Check that every item_code that is declared can be requested from a person at every district and facility_level.
     """
 
     sim = get_sim_with_dummy_module_registered(run=True)
     hs = sim.modules['HealthSystem']
     item_codes = hs.consumables.item_codes
 
-    with pytest.warns(None) as recorded_warnings:
-        for month in range(1, 13):
-            sim.date = Date(2010, month, 1)
-            hs.consumables._refresh_availability_of_consumables(date=sim.date)
+    for month in range(1, 13):
+        sim.date = Date(2010, month, 1)
+        hs.consumables._refresh_availability_of_consumables(date=sim.date)
 
-            for _district in sim.modules['Demography'].PROPERTIES['district_of_residence'].categories:
-                # Change the district of person 0 (for whom the HSI is created.)
-                sim.population.props.at[0, 'district_of_residence'] = _district
-                for _facility_id in fac_ids:
-                    hsi_event = get_dummy_hsi_event_instance(
-                        module=sim.modules['DummyModule'],
-                        facility_id=_facility_id
-                    )
-                    for _item_code in item_codes:
-                        hsi_event.get_consumables(item_codes=_item_code)
+        for _district in sim.modules['Demography'].PROPERTIES['district_of_residence'].categories:
+            # Change the district of person 0 (for whom the HSI is created.)
+            sim.population.props.at[0, 'district_of_residence'] = _district
+            for _facility_id in fac_ids:
+                hsi_event = get_dummy_hsi_event_instance(
+                    module=sim.modules['DummyModule'],
+                    facility_id=_facility_id
+                )
+                for _item_code in item_codes:
+                    hsi_event.get_consumables(item_codes=_item_code)
 
-        sim.modules['HealthSystem'].on_simulation_end()
+    sim.modules['HealthSystem'].on_simulation_end()
 
     # Check that no warnings raised or item_codes recorded as being not recogised.
     assert not sim.modules['HealthSystem'].consumables._not_recognised_item_codes
-    assert not any_warnings_about_item_code(recorded_warnings)
+    assert not any_warnings_about_item_code(recwarn)
 
 
 def test_get_item_code_from_item_name():

tests/test_core.py

@@ -51,7 +51,7 @@ class TestLoadParametersFromDataframe:
 
     No explicit tests for correct parsing of boolean because of how python evaluates truthiness
     """
-    def setup(self):
+    def setup_method(self):
         class ParameterModule(Module):
             def __init__(self):
                 super().__init__(name=None)
@@ -169,7 +169,7 @@ def test_bools(self):
 
 class TestLoadParametersFromDataframe_Bools_From_Csv:
     """Tests for the load_parameters_from_dataframe method, including handling of bools when loading from csv"""
-    def setup(self):
+    def setup_method(self):
         class ParameterModule(Module):
             def __init__(self):
                 super().__init__(name=None)

tests/test_logging.py

@@ -137,7 +137,7 @@ def test_messages_lower_level(self, simulation_configuration, message_level):
 
 
 class TestConvertLogData:
-    def setup(self):
+    def setup_method(self):
         self.expected_output = {'item_1': 1, 'item_2': 2}
         self.logger = logging.getLogger('tlo.test.logger')
 

tox.ini

@@ -27,9 +27,7 @@ passenv =
 usedevelop = false
 deps =
     -r{toxinidir}/requirements/base.txt
-    ; Pin pytest version as some tests use features deprecated in v8
-    ; See https://github.com/UCL/TLOmodel/issues/1264
-    pytest==7.4.4
+    pytest
     pytest-cov
 commands =
     {posargs:pytest --cov --cov-report=term-missing -vv tests}
@@ -40,9 +38,7 @@ deps =
     pandas15: pandas==1.5.3
     pandas20: pandas==2.0.0
     pandas21: pandas==2.1.0
-    ; Pin pytest version as some tests use features deprecated in v8
-    ; See https://github.com/UCL/TLOmodel/issues/1264
-    pytest==7.4.4
+    pytest
     pytest-cov
 
 [testenv:spell]