fix broken repro test (#447)

src/vivarium/component.py

@@ -341,9 +341,9 @@ def __init__(self) -> None:
         self._name: str = ""
         self._sub_components: List["Component"] = []
         self.logger: Optional[Logger] = None
-        self.get_value_columns: Optional[Callable[[Union[str, pd.DataFrame]], List[str]]] = (
-            None
-        )
+        self.get_value_columns: Optional[
+            Callable[[Union[str, pd.DataFrame]], List[str]]
+        ] = None
         self.configuration: Optional[LayeredConfigTree] = None
         self.population_view: Optional[PopulationView] = None
         self.lookup_tables: Dict[str, LookupTable] = {}

src/vivarium/examples/disease_model/observer.py

@@ -2,11 +2,11 @@
 
 import pandas as pd
 
-from vivarium import Component
 from vivarium.framework.engine import Builder
+from vivarium.framework.results import Observer as Observer_
 
 
-class Observer(Component):
+class Observer(Observer_):
     ##############
     # Properties #
     ##############
@@ -23,6 +23,26 @@ def configuration_defaults(self) -> Dict[str, Any]:
     def columns_required(self) -> Optional[List[str]]:
         return ["age", "alive"]
 
+    def register_observations(self, builder: Builder) -> None:
+        builder.results.register_adding_observation(
+            name="total_population_alive",
+            requires_columns=["alive"],
+            pop_filter='alive == "alive"',
+        )
+        builder.results.register_adding_observation(
+            name="total_population_dead",
+            requires_columns=["alive"],
+            pop_filter='alive == "dead"',
+        )
+        builder.results.register_adding_observation(
+            name="years_of_life_lost",
+            requires_columns=["age", "alive"],
+            aggregator=self.calculate_ylls,
+        )
+
+    def calculate_ylls(self, df: pd.DataFrame) -> float:
+        return (self.life_expectancy - df.loc[df["alive"] == "dead", "age"]).sum()
+
     #####################
     # Lifecycle methods #
     #####################

tests/framework/randomness/test_reproducibility.py

@@ -22,9 +22,11 @@ def test_reproducibility(tmp_path, disease_model_spec):
         check=True,
     )
 
-    files = [file for file in results_dir.rglob("**/*.hdf")]
-    assert len(files) == 2
-    df1 = pd.read_hdf(files[0]).drop(columns="simulation_run_time")
-    df2 = pd.read_hdf(files[1]).drop(columns="simulation_run_time")
-
-    assert df1.equals(df2)
+    files = [file for file in results_dir.rglob("**/*.parquet")]
+    assert len(files) == 6
+    for filename in ["total_population_alive", "total_population_dead", "years_of_life_lost"]:
+        df_paths = [file for file in files if file.stem == filename]
+        df1 = pd.read_parquet(df_paths[0])
+        df2 = pd.read_parquet(df_paths[1])
+
+        assert df1.equals(df2)