drop python 3.9 changes (#540)

Category: CI
JIRA issue: https://jira.ihme.washington.edu/browse/MIC-5536

Changes and notes
Modernize type hinting
Remove unnecessary "from future import annotation" imports

Testing
Ran pytest.

CHANGELOG.rst

@@ -1,6 +1,8 @@
-**3.2.1 - TBD/TBD/TBD**
+**3.2.1 - 11/13/24**
 
   - Fix mypy errors in vivarium/framework/results/context.py
+  - Modernize type hinting
+  - Remove unnecessary "from future import annotation" imports
 
 **3.2.0 - 11/12/24**
 

docs/source/concepts/results.rst

@@ -66,7 +66,7 @@ to the existing number of people who have died from previous time steps.
 
 .. testcode::
 
-  from typing import Any, Optional
+  from typing import Any
 
   import pandas as pd
 
@@ -84,7 +84,7 @@ to the existing number of people who have died from previous time steps.
       }
 
     @property
-    def columns_required(self) -> Optional[list[str]]:
+    def columns_required(self) -> list[str] | None:
       return ["age", "alive"]
 
     def register_observations(self, builder: Builder) -> None:

src/vivarium/component.py

@@ -13,12 +13,12 @@
 import re
 import warnings
 from abc import ABC
-from collections.abc import Sequence
+from collections.abc import Callable, Sequence
 from datetime import datetime, timedelta
 from importlib import import_module
 from inspect import signature
 from numbers import Number
-from typing import TYPE_CHECKING, Any, Callable, Dict, List, Optional, Union
+from typing import TYPE_CHECKING, Any
 
 import pandas as pd
 from layered_config_tree import ConfigurationError, LayeredConfigTree
@@ -87,7 +87,7 @@ class Component(ABC):
 
     """
 
-    CONFIGURATION_DEFAULTS: Dict[str, Any] = {}
+    CONFIGURATION_DEFAULTS: dict[str, Any] = {}
     """A dictionary containing the defaults for any configurations managed by this
     component. An empty dictionary indicates no managed configurations.
     """
@@ -187,7 +187,7 @@ def population_view(self) -> PopulationView:
         return self._population_view
 
     @property
-    def sub_components(self) -> List["Component"]:
+    def sub_components(self) -> list["Component"]:
         """Provide components managed by this component.
 
         Returns
@@ -198,7 +198,7 @@ def sub_components(self) -> List["Component"]:
         return self._sub_components
 
     @property
-    def configuration_defaults(self) -> Dict[str, Any]:
+    def configuration_defaults(self) -> dict[str, Any]:
         """Provides a dictionary containing the defaults for any configurations
         managed by this component.
 
@@ -213,7 +213,7 @@ def configuration_defaults(self) -> Dict[str, Any]:
         return self.CONFIGURATION_DEFAULTS
 
     @property
-    def columns_created(self) -> List[str]:
+    def columns_created(self) -> list[str]:
         """Provides names of columns created by the component.
 
         Returns
@@ -224,7 +224,7 @@ def columns_created(self) -> List[str]:
         return []
 
     @property
-    def columns_required(self) -> Optional[List[str]]:
+    def columns_required(self) -> list[str] | None:
         """Provides names of columns required by the component.
 
         Returns
@@ -244,7 +244,7 @@ def initialization_requirements(
         return []
 
     @property
-    def population_view_query(self) -> Optional[str]:
+    def population_view_query(self) -> str | None:
         """Provides a query to use when filtering the component's `PopulationView`.
 
         Returns
@@ -334,14 +334,12 @@ def __init__(self) -> None:
         """
         self._repr: str = ""
         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.configuration: Optional[LayeredConfigTree] = None
-        self._population_view: Optional[PopulationView] = None
-        self.lookup_tables: Dict[str, LookupTable] = {}
+        self._sub_components: list["Component"] = []
+        self.logger: Logger | None = None
+        self.get_value_columns: Callable[[str | pd.DataFrame], list[str]] | None = None
+        self.configuration: LayeredConfigTree | None = None
+        self._population_view: PopulationView | None = None
+        self.lookup_tables: dict[str, LookupTable] = {}
 
     def setup_component(self, builder: "Builder") -> None:
         """Sets up the component for a Vivarium simulation.
@@ -501,7 +499,7 @@ def on_simulation_end(self, event: Event) -> None:
     # Helper methods #
     ##################
 
-    def get_initialization_parameters(self) -> Dict[str, Any]:
+    def get_initialization_parameters(self) -> dict[str, Any]:
         """Retrieves the values of all parameters specified in the `__init__` that
         have an attribute with the same name.
 
@@ -521,7 +519,7 @@ def get_initialization_parameters(self) -> Dict[str, Any]:
             if hasattr(self, parameter_name)
         }
 
-    def get_configuration(self, builder: "Builder") -> Optional[LayeredConfigTree]:
+    def get_configuration(self, builder: "Builder") -> LayeredConfigTree | None:
         """Retrieves the configuration for this component from the builder.
 
         This method retrieves the configuration for this component from the

src/vivarium/examples/boids/forces.py

@@ -1,6 +1,6 @@
 # mypy: ignore-errors
 from abc import ABC, abstractmethod
-from typing import Any, Dict
+from typing import Any
 
 import numpy as np
 import pandas as pd
@@ -14,7 +14,7 @@ class Force(Component, ABC):
     # Properties #
     ##############
     @property
-    def configuration_defaults(self) -> Dict[str, Any]:
+    def configuration_defaults(self) -> dict[str, Any]:
         return {
             self.__class__.__name__.lower(): {
                 "max_force": 0.03,

src/vivarium/examples/disease_model/disease.py

@@ -1,6 +1,4 @@
 # mypy: ignore-errors
-from __future__ import annotations
-
 import pandas as pd
 
 from vivarium import Component

src/vivarium/examples/disease_model/intervention.py

@@ -1,5 +1,5 @@
 # mypy: ignore-errors
-from typing import Any, Dict
+from typing import Any
 
 import pandas as pd
 
@@ -8,7 +8,7 @@
 
 
 class TreatmentIntervention(Component):
-    CONFIGURATION_DEFAULTS: Dict[str, Any] = {
+    CONFIGURATION_DEFAULTS: dict[str, Any] = {
         "intervention": {
             "effect_size": 0.5,
         }
@@ -19,7 +19,7 @@ class TreatmentIntervention(Component):
     ##############
 
     @property
-    def configuration_defaults(self) -> Dict[str, Any]:
+    def configuration_defaults(self) -> dict[str, Any]:
         return {self.intervention: self.CONFIGURATION_DEFAULTS["intervention"]}
 
     #####################

src/vivarium/examples/disease_model/mortality.py

@@ -1,5 +1,5 @@
 # mypy: ignore-errors
-from typing import Any, Dict, List, Optional
+from typing import Any
 
 import numpy as np
 import pandas as pd
@@ -15,7 +15,7 @@ class Mortality(Component):
     ##############
 
     @property
-    def configuration_defaults(self) -> Dict[str, Any]:
+    def configuration_defaults(self) -> dict[str, Any]:
         """A set of default configuration values for this component.
 
         These can be overwritten in the simulation model specification or by
@@ -28,7 +28,7 @@ def configuration_defaults(self) -> Dict[str, Any]:
         }
 
     @property
-    def columns_required(self) -> Optional[List[str]]:
+    def columns_required(self) -> list[str] | None:
         return ["tracked", "alive"]
 
     #####################

src/vivarium/examples/disease_model/observer.py

@@ -1,4 +1,4 @@
-from typing import Any, Optional
+from typing import Any
 
 import pandas as pd
 
@@ -14,7 +14,7 @@ class DeathsObserver(Observer):
     ##############
 
     @property
-    def columns_required(self) -> Optional[list[str]]:
+    def columns_required(self) -> list[str] | None:
         return ["alive"]
 
     #################
@@ -39,7 +39,7 @@ class YllsObserver(Observer):
     ##############
 
     @property
-    def columns_required(self) -> Optional[list[str]]:
+    def columns_required(self) -> list[str] | None:
         return ["age", "alive"]
 
     @property

src/vivarium/examples/disease_model/population.py

@@ -1,5 +1,5 @@
 # mypy: ignore-errors
-from typing import Any, Dict, List
+from typing import Any
 
 import pandas as pd
 
@@ -17,7 +17,7 @@ class BasePopulation(Component):
     ##############
 
     @property
-    def configuration_defaults(self) -> Dict[str, Any]:
+    def configuration_defaults(self) -> dict[str, Any]:
         """A set of default configuration values for this component.
 
         These can be overwritten in the simulation model specification or by
@@ -33,7 +33,7 @@ def configuration_defaults(self) -> Dict[str, Any]:
         }
 
     @property
-    def columns_created(self) -> List[str]:
+    def columns_created(self) -> list[str]:
         return ["age", "sex", "alive", "entrance_time"]
 
     #####################

src/vivarium/examples/disease_model/risk.py

@@ -1,7 +1,7 @@
 # mypy: ignore-errors
 from __future__ import annotations
 
-from typing import TYPE_CHECKING, Any, Dict, List
+from typing import TYPE_CHECKING, Any
 
 import pandas as pd
 
@@ -24,11 +24,11 @@ class Risk(Component):
     ##############
 
     @property
-    def configuration_defaults(self) -> Dict[str, Any]:
+    def configuration_defaults(self) -> dict[str, Any]:
         return {self.risk: self.CONFIGURATION_DEFAULTS["risk"]}
 
     @property
-    def columns_created(self) -> List[str]:
+    def columns_created(self) -> list[str]:
         return [self.propensity_column]
 
     @property
@@ -91,7 +91,7 @@ class RiskEffect(Component):
     ##############
 
     @property
-    def configuration_defaults(self) -> Dict[str, Any]:
+    def configuration_defaults(self) -> dict[str, Any]:
         return {self.risk: self.CONFIGURATION_DEFAULTS["risk_effect"]}
 
     #####################

src/vivarium/framework/artifact/artifact.py

@@ -10,8 +10,6 @@
 archive file for convenient access and inspection.
 
 """
-from __future__ import annotations
-
 import re
 import warnings
 from collections import defaultdict