Example vaccine pytest

Author: jmafoster1

examples/covasim_/vaccinating_elderly/example_vaccine.py

@@ -14,7 +14,7 @@
 ROOT = os.path.realpath(os.path.dirname(__file__))
 
 
-def setup_test_case(verbose: bool = False):
+def run_test_case(verbose: bool = False):
     """Run the causal test case for the effect of changing vaccine to prioritise elderly from observational
     data that was previously simulated.
 
@@ -23,7 +23,7 @@ def setup_test_case(verbose: bool = False):
     """
 
     # 1. Read in the Causal DAG
-    causal_dag = CausalDAG(f"{ROOT}/dag.dot")
+    causal_dag = CausalDAG(os.path.join(ROOT, "dag.dot"))
 
     # 2. Create variables
     vaccine = Input("vaccine", int)
@@ -33,7 +33,7 @@ def setup_test_case(verbose: bool = False):
     max_doses = Output("max_doses", int)
 
     # 5. Read the previously simulated data
-    obs_df = pd.read_csv("simulated_data.csv")
+    obs_df = pd.read_csv(os.path.join(ROOT, "simulated_data.csv"))
 
     # 6. Express expected outcomes
     expected_outcome_effects = {
@@ -82,8 +82,12 @@ def setup_test_case(verbose: bool = False):
     return results_dict
 
 
+def test_example_vaccine():
+    run_test_case()
+
+
 if __name__ == "__main__":
 
-    test_results = setup_test_case(verbose=True)
+    test_results = run_test_case(verbose=True)
 
     logging.info("%s", test_results)