Merge pull request #291 from ihmeuw/develop

Release v1.1.0
ihmeuw · May 3, 2023 · 53b7d1f · 53b7d1f
2 parents 6f8dd07 + 2b64612
commit 53b7d1f
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diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -1,3 +1,10 @@
+**1.1.0 - 05/03/23**
+
+ - Clean up randomness system
+ - Fix a bug in stratification when a stratum is empty
+ - Create a dedicated logging system
+ - Fix bug in preventing passing an Iterable to `rate_to_probability`
+
 **1.0.4 - 01/25/23**
 
  - Bugfixes for ResultsContext

diff --git a/docs/nitpick-exceptions b/docs/nitpick-exceptions
@@ -7,6 +7,9 @@ py:class pandas.core.frame.DataFrame
 py:class pandas.core.series.Series
 py:class pandas.core.generic.PandasObject
 
+# loguru
+py:class loguru._logger.Logger
+
 # vivarium
 # Type aliases don't play nicely with sphinx when you import them
 # elsewhere.  Works fine for static type checker though.  I think this

diff --git a/docs/source/api_reference/framework/logging/index.rst b/docs/source/api_reference/framework/logging/index.rst
@@ -0,0 +1,7 @@
+.. automodule:: vivarium.framework.logging
+
+.. toctree::
+   :maxdepth: 2
+   :glob:
+
+   *
diff --git a/docs/source/api_reference/framework/logging/manager.rst b/docs/source/api_reference/framework/logging/manager.rst
@@ -0,0 +1 @@
+.. automodule:: vivarium.framework.logging.manager
diff --git a/docs/source/api_reference/framework/logging/utilities.rst b/docs/source/api_reference/framework/logging/utilities.rst
@@ -0,0 +1 @@
+.. automodule:: vivarium.framework.logging.utilities
diff --git a/docs/source/api_reference/framework/population/index.rst b/docs/source/api_reference/framework/population/index.rst
@@ -1,3 +1,7 @@
+=====================
+Population Management
+=====================
+
 .. automodule:: vivarium.framework.population
 
 .. toctree::

diff --git a/docs/source/api_reference/framework/randomness/core.rst b/docs/source/api_reference/framework/randomness/core.rst
diff --git a/docs/source/api_reference/framework/randomness/index.rst b/docs/source/api_reference/framework/randomness/index.rst
@@ -1,3 +1,7 @@
+========================
+Random Number Generation
+========================
+
 .. automodule:: vivarium.framework.randomness
 
 .. toctree::

diff --git a/docs/source/concepts/logging.rst b/docs/source/concepts/logging.rst
@@ -0,0 +1,9 @@
+.. _logging_concept:
+
+=================
+Framework Logging
+=================
+
+.. todo::
+
+   Everything here.
diff --git a/setup.py b/setup.py
@@ -20,7 +20,6 @@
 from setuptools import find_packages, setup
 
 if __name__ == "__main__":
-
     base_dir = Path(__file__).parent
     src_dir = base_dir / "src"
 
@@ -33,7 +32,7 @@
 
     install_requirements = [
         "numpy",
-        "pandas",
+        "pandas<2.0.0",
         "pyyaml>=5.1",
         "scipy",
         "click",

diff --git a/src/vivarium/__about__.py b/src/vivarium/__about__.py
@@ -13,7 +13,7 @@
 __summary__ = "vivarium is a microsimulation framework built on top of the standard scientific python stack."
 __uri__ = "https://github.com/ihmeuw/vivarium"
 
-__version__ = "1.0.4"
+__version__ = "1.1.0"
 
 __author__ = "The vivarium developers"
 __email__ = "vivarium.dev@gmail.com"

diff --git a/src/vivarium/examples/boids/location.py b/src/vivarium/examples/boids/location.py
@@ -3,7 +3,6 @@
 
 
 class Location:
-
     configuration_defaults = {
         "location": {
             "width": 1000,  # Width of our field

diff --git a/src/vivarium/examples/boids/neighbors.py b/src/vivarium/examples/boids/neighbors.py
@@ -3,7 +3,6 @@
 
 
 class Neighbors:
-
     configuration_defaults = {"neighbors": {"radius": 10}}
 
     def __init__(self):

diff --git a/src/vivarium/examples/boids/population.py b/src/vivarium/examples/boids/population.py
@@ -3,7 +3,6 @@
 
 
 class Population:
-
     configuration_defaults = {
         "population": {
             "colors": ["red", "blue"],

diff --git a/src/vivarium/examples/disease_model/disease.py b/src/vivarium/examples/disease_model/disease.py
@@ -150,7 +150,6 @@ def metrics(self, index, metrics):
 
 
 class SISDiseaseModel:
-
     configuration_defaults = {
         "disease": {
             "incidence_rate": 0.005,

diff --git a/src/vivarium/examples/disease_model/intervention.py b/src/vivarium/examples/disease_model/intervention.py
@@ -4,7 +4,6 @@
 
 
 class TreatmentIntervention:
-
     configuration_defaults = {
         "intervention": {
             "effect_size": 0.5,

diff --git a/src/vivarium/examples/disease_model/observer.py b/src/vivarium/examples/disease_model/observer.py
@@ -6,7 +6,6 @@
 
 
 class Observer:
-
     configuration_defaults = {
         "mortality": {
             "life_expectancy": 80,
@@ -24,7 +23,6 @@ def setup(self, builder: Builder):
         builder.value.register_value_modifier("metrics", self.metrics)
 
     def metrics(self, index: pd.Index, metrics: Dict):
-
         pop = self.population_view.get(index)
         metrics["total_population_alive"] = len(pop[pop.alive == "alive"])
         metrics["total_population_dead"] = len(pop[pop.alive == "dead"])

diff --git a/src/vivarium/examples/disease_model/population.py b/src/vivarium/examples/disease_model/population.py
@@ -55,7 +55,7 @@ def setup(self, builder: Builder):
             )
 
         self.age_randomness = builder.randomness.get_stream(
-            "age_initialization", for_initialization=self.with_common_random_numbers
+            "age_initialization", initializes_crn_attributes=self.with_common_random_numbers
         )
         self.sex_randomness = builder.randomness.get_stream("sex_initialization")
 

diff --git a/src/vivarium/examples/disease_model/risk.py b/src/vivarium/examples/disease_model/risk.py
@@ -2,7 +2,6 @@
 
 
 class Risk:
-
     configuration_defaults = {
         "risk": {
             "proportion_exposed": 0.3,
@@ -50,7 +49,6 @@ def __repr__(self):
 
 
 class RiskEffect:
-
     configuration_defaults = {
         "risk_effect": {
             "relative_risk": 2,

diff --git a/src/vivarium/framework/artifact/hdf.py b/src/vivarium/framework/artifact/hdf.py
@@ -359,7 +359,6 @@ def _write_pandas_data(path: Path, entity_key: EntityKey, data: Union[PandasObj]
 def _write_json_blob(path: Path, entity_key: EntityKey, data: Any):
     """Writes a Python object as json to the HDF file at the given path."""
     with tables.open_file(str(path), "a") as store:
-
         if entity_key.group_prefix not in store:
             store.create_group("/", entity_key.type)
 

diff --git a/src/vivarium/framework/artifact/manager.py b/src/vivarium/framework/artifact/manager.py
@@ -12,7 +12,6 @@
 from typing import Any, Sequence, Union
 
 import pandas as pd
-from loguru import logger
 
 from vivarium.config_tree import ConfigTree
 from vivarium.framework.artifact.artifact import Artifact
@@ -37,6 +36,7 @@ def name(self):
 
     def setup(self, builder):
         """Performs this component's simulation setup."""
+        self.logger = builder.logging.get_logger(self.name)
         # because not all columns are accessible via artifact filter terms, apply config filters separately
         self.config_filter_term = validate_filter_term(
             builder.configuration.input_data.artifact_filter_term
@@ -63,9 +63,9 @@ def _load_artifact(self, configuration: ConfigTree) -> Union[Artifact, None]:
             return None
         artifact_path = parse_artifact_path_config(configuration)
         base_filter_terms = get_base_filter_terms(configuration)
-        logger.debug(f"Running simulation from artifact located at {artifact_path}.")
-        logger.debug(f"Artifact base filter terms are {base_filter_terms}.")
-        logger.debug(f"Artifact additional filter terms are {self.config_filter_term}.")
+        self.logger.info(f"Running simulation from artifact located at {artifact_path}.")
+        self.logger.info(f"Artifact base filter terms are {base_filter_terms}.")
+        self.logger.info(f"Artifact additional filter terms are {self.config_filter_term}.")
         return Artifact(artifact_path, base_filter_terms)
 
     def load(self, entity_key: str, **column_filters: _Filter) -> Any:
@@ -233,7 +233,6 @@ def parse_artifact_path_config(config: ConfigTree) -> str:
     path = Path(config.input_data.artifact_path)
 
     if not path.is_absolute():
-
         path_config = config.input_data.metadata("artifact_path")[-1]
         if path_config["source"] is None:
             raise ValueError("Insufficient information provided to find artifact.")