From 7912512c7c05ebf6bf9ce78fe21f8ed68d58ad64 Mon Sep 17 00:00:00 2001
From: hyi <hongyi@renci.org>
Date: Wed, 5 Nov 2025 22:44:56 -0500
Subject: [PATCH 01/12] dependency update as well as update code to conform to
 ruff linter

---
 biasanalyzer/api.py                           |  14 +-
 biasanalyzer/background/threading_utils.py    |   1 +
 biasanalyzer/cohort.py                        |  18 +-
 biasanalyzer/cohort_query_builder.py          |  13 +-
 biasanalyzer/concept.py                       |   7 +-
 biasanalyzer/config.py                        |   3 +-
 biasanalyzer/database.py                      |  39 ++--
 biasanalyzer/models.py                        |   4 +-
 biasanalyzer/module_test.py                   |  23 +-
 biasanalyzer/utils.py                         |   8 +-
 poetry.lock                                   | 206 +++++++++++++++++-
 pyproject.toml                                |  60 ++++-
 scripts/ingest_csvs_to_omop_duckdb.py         |   5 +-
 tests/conftest.py                             |  19 +-
 tests/query_based/test_cohort_creation.py     |   7 +-
 .../test_hierarchical_prevalence.py           |   6 +-
 tests/test_biasanalyzer_api.py                |   7 +-
 tests/test_config.py                          |  18 +-
 tests/test_database.py                        |   7 +-
 19 files changed, 363 insertions(+), 102 deletions(-)

diff --git a/biasanalyzer/api.py b/biasanalyzer/api.py
index 90a688e..8af9a65 100644
--- a/biasanalyzer/api.py
+++ b/biasanalyzer/api.py
@@ -1,13 +1,15 @@
 import time
-from pydantic import ValidationError
 from typing import List
-from biasanalyzer.database import OMOPCDMDatabase, BiasDatabase
+
+from IPython.display import display
+from ipytree import Tree
+from ipywidgets import Label, VBox
+from pydantic import ValidationError
+
 from biasanalyzer.cohort import CohortAction
 from biasanalyzer.config import load_config
-from ipywidgets import VBox, Label
-from ipytree import Tree
-from IPython.display import display
-from biasanalyzer.utils import get_direction_arrow, notify_users, build_concept_tree
+from biasanalyzer.database import BiasDatabase, OMOPCDMDatabase
+from biasanalyzer.utils import build_concept_tree, get_direction_arrow, notify_users
 
 
 class BIAS:
diff --git a/biasanalyzer/background/threading_utils.py b/biasanalyzer/background/threading_utils.py
index b65198f..a6fb9a9 100644
--- a/biasanalyzer/background/threading_utils.py
+++ b/biasanalyzer/background/threading_utils.py
@@ -1,6 +1,7 @@
 import threading
 import traceback
 
+
 class BackgroundResult:
     def __init__(self):
         self.value = None
diff --git a/biasanalyzer/cohort.py b/biasanalyzer/cohort.py
index 00166d7..691a112 100644
--- a/biasanalyzer/cohort.py
+++ b/biasanalyzer/cohort.py
@@ -1,15 +1,17 @@
+from datetime import datetime
 from functools import reduce
+from typing import List
+
 import pandas as pd
-from datetime import datetime
-from tqdm.auto import tqdm
 from pydantic import ValidationError
-from typing import List
-from biasanalyzer.models import CohortDefinition
-from biasanalyzer.config import load_cohort_creation_config
-from biasanalyzer.database import OMOPCDMDatabase, BiasDatabase
-from biasanalyzer.utils import hellinger_distance, clean_string, notify_users
+from tqdm.auto import tqdm
+
 from biasanalyzer.cohort_query_builder import CohortQueryBuilder
 from biasanalyzer.concept import ConceptHierarchy
+from biasanalyzer.config import load_cohort_creation_config
+from biasanalyzer.database import BiasDatabase, OMOPCDMDatabase
+from biasanalyzer.models import CohortDefinition
+from biasanalyzer.utils import clean_string, hellinger_distance, notify_users
 
 
 class CohortData:
@@ -147,7 +149,7 @@ def create_cohort(self, cohort_name: str, description: str, query_or_yaml_file:
                 return CohortData(cohort_id=cohort_def_id, bias_db=self.bias_db, omop_db=self.omop_db)
             else:
                 progress.update(2)
-                notify_users(f"No cohort is created due to empty results being returned from query")
+                notify_users("No cohort is created due to empty results being returned from query")
                 return None
         except Exception as e:
             progress.update(2)
diff --git a/biasanalyzer/cohort_query_builder.py b/biasanalyzer/cohort_query_builder.py
index 6c3f82a..755f6b0 100644
--- a/biasanalyzer/cohort_query_builder.py
+++ b/biasanalyzer/cohort_query_builder.py
@@ -1,9 +1,11 @@
+import importlib.resources
 import os
 import sys
-import importlib.resources
-from biasanalyzer.models import TemporalEventGroup, DOMAIN_MAPPING
+
 from jinja2 import Environment, FileSystemLoader
 
+from biasanalyzer.models import DOMAIN_MAPPING, TemporalEventGroup
+
 
 class CohortQueryBuilder:
     def __init__(self, cohort_creation=True):
@@ -12,7 +14,7 @@ def __init__(self, cohort_creation=True):
             if sys.version_info >= (3, 9): # pragma: no cover
                 # Python 3.9+: Use importlib.resources.files()
                 template_path = importlib.resources.files("biasanalyzer").joinpath("sql_templates")
-            else:
+            else: # pragma: no cover
                 # Python 3.8: Use importlib.resources.path() (context manager)
                 with importlib.resources.path("biasanalyzer", "sql_templates") as p:
                     template_path = str(p)
@@ -63,7 +65,7 @@ def build_query_cohort_creation(self, cohort_config: dict) -> str:
             # For demographic only inclusion criteria, filter DOMAIN_MAPPING to exclude domains with table: None
             ranked_domains = valid_domains
 
-        template = self.env.get_template(f"cohort_creation_query.sql.j2")
+        template = self.env.get_template("cohort_creation_query.sql.j2")
         return template.render(
             inclusion_criteria=inclusion_criteria,
             exclusion_criteria=exclusion_criteria,
@@ -259,7 +261,8 @@ def render_event_group(event_group, alias_prefix="evt"):
                                     AND {e1_alias}.event_start_date < {e2_alias}.event_start_date
                                     {interval_sql}
                                     UNION ALL
-                                    SELECT {e2_alias}.person_id, {e2_alias}.event_start_date, {e2_alias}.event_end_date, 
+                                    SELECT {e2_alias}.person_id, {e2_alias}.event_start_date, 
+                                           {e2_alias}.event_end_date, 
                                            {e2_alias}.adjusted_start, {e2_alias}.adjusted_end
                                     FROM ({queries[1]}) AS {e2_alias}
                                     JOIN ({queries[0]}) AS {e1_alias}
diff --git a/biasanalyzer/concept.py b/biasanalyzer/concept.py
index 1c98504..7aa77f5 100644
--- a/biasanalyzer/concept.py
+++ b/biasanalyzer/concept.py
@@ -1,6 +1,7 @@
-import networkx as nx
-from typing import List, Optional, Union
 from _collections import deque
+from typing import List, Optional, Union
+
+import networkx as nx
 
 
 class ConceptNode:
@@ -153,7 +154,7 @@ def get_root_nodes(self, serialization: bool = False) -> List:
 
     def get_leaf_nodes(self, serialization: bool = False) -> List:
         leaves = [n for n in self.graph.nodes if self.graph.out_degree(n) == 0]
-        leave_nodes = [ConceptNode(l, self) for l in leaves]
+        leave_nodes = [ConceptNode(lv, self) for lv in leaves]
         if serialization:
             return [ln.to_dict(include_children=False) for ln in leave_nodes]
         else:
diff --git a/biasanalyzer/config.py b/biasanalyzer/config.py
index 141a047..657a2ab 100644
--- a/biasanalyzer/config.py
+++ b/biasanalyzer/config.py
@@ -1,5 +1,6 @@
 import yaml
-from biasanalyzer.models import Configuration, CohortCreationConfig
+
+from biasanalyzer.models import CohortCreationConfig, Configuration
 
 
 def load_config(config_file):
diff --git a/biasanalyzer/database.py b/biasanalyzer/database.py
index b40674e..6eda39c 100644
--- a/biasanalyzer/database.py
+++ b/biasanalyzer/database.py
@@ -1,16 +1,24 @@
-import duckdb
-import pandas as pd
 import gc
-from typing import Optional
 from datetime import datetime
-from tqdm.auto import tqdm
-from sqlalchemy.orm import sessionmaker
-from sqlalchemy.exc import SQLAlchemyError
+from typing import Optional
+
+import duckdb
+import pandas as pd
 from sqlalchemy import create_engine, text
+from sqlalchemy.exc import SQLAlchemyError
+from sqlalchemy.orm import sessionmaker
+from tqdm.auto import tqdm
+
 from biasanalyzer.models import CohortDefinition
-from biasanalyzer.sql import (AGE_DISTRIBUTION_QUERY, GENDER_DISTRIBUTION_QUERY, AGE_STATS_QUERY,
-                              GENDER_STATS_QUERY, RACE_STATS_QUERY, ETHNICITY_STATS_QUERY)
-from biasanalyzer.utils import build_concept_hierarchy, print_hierarchy, find_roots, notify_users
+from biasanalyzer.sql import (
+    AGE_DISTRIBUTION_QUERY,
+    AGE_STATS_QUERY,
+    ETHNICITY_STATS_QUERY,
+    GENDER_DISTRIBUTION_QUERY,
+    GENDER_STATS_QUERY,
+    RACE_STATS_QUERY,
+)
+from biasanalyzer.utils import build_concept_hierarchy, find_roots, notify_users, print_hierarchy
 
 
 class BiasDatabase:
@@ -27,7 +35,7 @@ class BiasDatabase:
     _instance = None  # indicating a singleton with only one instance of the class ever created
     def __new__(cls, *args, **kwargs):
         if cls._instance is None:
-            cls._instance = super(BiasDatabase, cls).__new__(cls)
+            cls._instance = super().__new__(cls)
             cls._instance._initialize(*args, **kwargs)  # Initialize only once
         return cls._instance
 
@@ -176,7 +184,8 @@ def get_cohort_basic_stats(self, cohort_definition_id: int, variable=''):
                 if query_str is None:
                     raise ValueError(f"Statistics for variable '{variable}' is not available. "
                                      f"Valid variables are {self.__class__.stats_queries.keys()}")
-                stats_query = query_str.format(ba_schema=self.schema, omop=self.omop_alias, cohort_definition_id=cohort_definition_id)
+                stats_query = query_str.format(ba_schema=self.schema, omop=self.omop_alias,
+                                               cohort_definition_id=cohort_definition_id)
             else:
                 # Query the cohort data to get basic statistics
                 stats_query = f'''
@@ -268,8 +277,7 @@ def get_cohort_concept_stats(self, cohort_definition_id: int, qry_builder,
                     print_hierarchy(hierarchy, parent=root, level=0, parent_details=root_detail)
             return concept_stats
         except Exception as e:
-            err_msg = f"Error computing cohort concept stats: {e}"
-            raise ValueError(err_msg)
+            raise ValueError("Error computing cohort concept stats") from e
 
     def close(self):
         if self.conn:
@@ -283,7 +291,7 @@ class OMOPCDMDatabase:
     _database_type = None
     def __new__(cls, *args, **kwargs):
         if cls._instance is None:
-            cls._instance = super(OMOPCDMDatabase, cls).__new__(cls)
+            cls._instance = super().__new__(cls)
             cls._instance._initialize(*args, **kwargs)  # Initialize only once
         return cls._instance
 
@@ -475,7 +483,8 @@ def get_concept_hierarchy(self, concept_id: int):
 
         progress.set_postfix_str(stages[1])
         # Collect all unique concept IDs involved in the hierarchy using set comprehension
-        concept_ids = {row['ancestor_concept_id'] for row in results} | {row['descendant_concept_id'] for row in results}
+        concept_ids = {row['ancestor_concept_id'] for row in results} | {row['descendant_concept_id']
+                                                                         for row in results}
         # Fetch details of each concept
         concept_details = {}
         if concept_ids:
diff --git a/biasanalyzer/models.py b/biasanalyzer/models.py
index 72790fa..d935f73 100644
--- a/biasanalyzer/models.py
+++ b/biasanalyzer/models.py
@@ -1,7 +1,7 @@
-from pydantic import BaseModel, StrictStr, ConfigDict, field_validator, model_validator
-from typing import Optional, Literal, List, Union
 from datetime import date
+from typing import List, Literal, Optional, Union
 
+from pydantic import BaseModel, ConfigDict, StrictStr, field_validator, model_validator
 
 DOMAIN_MAPPING = {
     "condition_occurrence": {
diff --git a/biasanalyzer/module_test.py b/biasanalyzer/module_test.py
index cacc79d..fd1f572 100644
--- a/biasanalyzer/module_test.py
+++ b/biasanalyzer/module_test.py
@@ -1,9 +1,11 @@
+import os
 import pprint
-from biasanalyzer.api import BIAS
 import time
-import os
+
 import pandas as pd
 
+from biasanalyzer.api import BIAS
+
 
 def cohort_creation_template_test(bias_obj):
     cohort_data = bias_obj.create_cohort('COVID-19 patients', 'COVID-19 patients',
@@ -64,18 +66,21 @@ def condition_cohort_test(bias_obj):
         print(f"Root: {root}", flush=True)
         print(f"Leaves: {leaves}", flush=True)
         for node in cohort_concept_hierarchy.iter_nodes(root_nodes[0].id, serialization=True):
-          print(node)
+            print(node)
 
         hier_dict = cohort_concept_hierarchy.to_dict()
-        pprint.pprint(hier_dict, indent=2)
+        with open('diabetics_condition_occurrence_hierarchy_dict.txt', 'w') as cof:
+            pprint.pprint(hier_dict, indent=2, stream=cof)
 
 
         _, cohort_de_concept_hierarchy = cohort_data.get_concept_stats(concept_type='drug_exposure',
                                                                        filter_count=500)
         de_hier_dict = cohort_de_concept_hierarchy.to_dict()
-        pprint.pprint(de_hier_dict, indent=2)
-        compare_stats = bias_obj.compare_cohorts(cohort_data.metadata['id'], cohort_data.metadata['id'])
-        print(f'compare_stats: {compare_stats}')
+        with open('diabetics_drug_exposure_hierarchy_dict.txt', 'w') as dof:
+            pprint.pprint(de_hier_dict, indent=2, stream=dof)
+        # compare_stats = bias_obj.compare_cohorts(cohort_data.metadata['id'], cohort_data.metadata['id'])
+        # print(f'compare_stats: {compare_stats}')
+        print(f'times taken for computing cohort concept hierarcy: {time.time() - t1}')
     return
 
 
@@ -95,9 +100,9 @@ def concept_test(bias_obj):
     print(bias_obj.display_concept_tree(parent_concept_tree))
     print('children concept hierarchy for COVID-19 in text format:')
     print(bias_obj.display_concept_tree(children_concept_tree))
-    print(f'parent concept hierarchy for COVID-19 in widget tree format:')
+    print('parent concept hierarchy for COVID-19 in widget tree format:')
     bias_obj.display_concept_tree(parent_concept_tree, show_in_text_format=False)
-    print(f'children concept hierarchy for COVID-19 in widget tree format:')
+    print('children concept hierarchy for COVID-19 in widget tree format:')
     bias_obj.display_concept_tree(children_concept_tree, show_in_text_format=False)
     return
 
diff --git a/biasanalyzer/utils.py b/biasanalyzer/utils.py
index c2a2e2b..5bf257b 100644
--- a/biasanalyzer/utils.py
+++ b/biasanalyzer/utils.py
@@ -1,8 +1,8 @@
-import numpy as np
-import re
-from ipytree import Node
 import logging
+import re
 
+import numpy as np
+from ipytree import Node
 
 logger = logging.getLogger(__name__)
 
@@ -111,5 +111,5 @@ def print_hierarchy(hierarchy, parent=None, level=0, parent_details=None):
         print(parent_details)
         level += 1
     for child, details in hierarchy[parent]:
-        print(f"  " * level + details)
+        print("  " * level + details)
         print_hierarchy(hierarchy, parent=child, level=level + 1)
diff --git a/poetry.lock b/poetry.lock
index 8224fb5..28cf8c9 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand.
+# This file is automatically @generated by Poetry 2.2.1 and should not be changed by hand.
 
 [[package]]
 name = "annotated-types"
@@ -6,6 +6,7 @@ version = "0.7.0"
 description = "Reusable constraint types to use with typing.Annotated"
 optional = false
 python-versions = ">=3.8"
+groups = ["main"]
 files = [
     {file = "annotated_types-0.7.0-py3-none-any.whl", hash = "sha256:1f02e8b43a8fbbc3f3e0d4f0f4bfc8131bcb4eebe8849b8e5c773f3a1c582a53"},
     {file = "annotated_types-0.7.0.tar.gz", hash = "sha256:aff07c09a53a08bc8cfccb9c85b05f1aa9a2a6f23728d790723543408344ce89"},
@@ -20,6 +21,8 @@ version = "0.1.4"
 description = "Disable App Nap on macOS >= 10.9"
 optional = false
 python-versions = ">=3.6"
+groups = ["main"]
+markers = "sys_platform == \"darwin\""
 files = [
     {file = "appnope-0.1.4-py2.py3-none-any.whl", hash = "sha256:502575ee11cd7a28c0205f379b525beefebab9d161b7c964670864014ed7213c"},
     {file = "appnope-0.1.4.tar.gz", hash = "sha256:1de3860566df9caf38f01f86f65e0e13e379af54f9e4bee1e66b48f2efffd1ee"},
@@ -31,6 +34,7 @@ version = "3.0.0"
 description = "Annotate AST trees with source code positions"
 optional = false
 python-versions = ">=3.8"
+groups = ["main"]
 files = [
     {file = "asttokens-3.0.0-py3-none-any.whl", hash = "sha256:e3078351a059199dd5138cb1c706e6430c05eff2ff136af5eb4790f9d28932e2"},
     {file = "asttokens-3.0.0.tar.gz", hash = "sha256:0dcd8baa8d62b0c1d118b399b2ddba3c4aff271d0d7a9e0d4c1681c79035bbc7"},
@@ -46,6 +50,7 @@ version = "0.2.0"
 description = "Specifications for callback functions passed in to an API"
 optional = false
 python-versions = "*"
+groups = ["main"]
 files = [
     {file = "backcall-0.2.0-py2.py3-none-any.whl", hash = "sha256:fbbce6a29f263178a1f7915c1940bde0ec2b2a967566fe1c65c1dfb7422bd255"},
     {file = "backcall-0.2.0.tar.gz", hash = "sha256:5cbdbf27be5e7cfadb448baf0aa95508f91f2bbc6c6437cd9cd06e2a4c215e1e"},
@@ -57,10 +62,12 @@ version = "0.4.6"
 description = "Cross-platform colored terminal text."
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*,>=2.7"
+groups = ["main", "dev"]
 files = [
     {file = "colorama-0.4.6-py2.py3-none-any.whl", hash = "sha256:4f1d9991f5acc0ca119f9d443620b77f9d6b33703e51011c16baf57afb285fc6"},
     {file = "colorama-0.4.6.tar.gz", hash = "sha256:08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44"},
 ]
+markers = {main = "sys_platform == \"win32\" or platform_system == \"Windows\"", dev = "sys_platform == \"win32\""}
 
 [[package]]
 name = "comm"
@@ -68,6 +75,7 @@ version = "0.2.2"
 description = "Jupyter Python Comm implementation, for usage in ipykernel, xeus-python etc."
 optional = false
 python-versions = ">=3.8"
+groups = ["main"]
 files = [
     {file = "comm-0.2.2-py3-none-any.whl", hash = "sha256:e6fb86cb70ff661ee8c9c14e7d36d6de3b4066f1441be4063df9c5009f0a64d3"},
     {file = "comm-0.2.2.tar.gz", hash = "sha256:3fd7a84065306e07bea1773df6eb8282de51ba82f77c72f9c85716ab11fe980e"},
@@ -85,6 +93,7 @@ version = "7.6.1"
 description = "Code coverage measurement for Python"
 optional = false
 python-versions = ">=3.8"
+groups = ["dev"]
 files = [
     {file = "coverage-7.6.1-cp310-cp310-macosx_10_9_x86_64.whl", hash = "sha256:b06079abebbc0e89e6163b8e8f0e16270124c154dc6e4a47b413dd538859af16"},
     {file = "coverage-7.6.1-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:cf4b19715bccd7ee27b6b120e7e9dd56037b9c0681dcc1adc9ba9db3d417fa36"},
@@ -164,7 +173,7 @@ files = [
 tomli = {version = "*", optional = true, markers = "python_full_version <= \"3.11.0a6\" and extra == \"toml\""}
 
 [package.extras]
-toml = ["tomli"]
+toml = ["tomli ; python_full_version <= \"3.11.0a6\""]
 
 [[package]]
 name = "decorator"
@@ -172,6 +181,7 @@ version = "5.1.1"
 description = "Decorators for Humans"
 optional = false
 python-versions = ">=3.5"
+groups = ["main"]
 files = [
     {file = "decorator-5.1.1-py3-none-any.whl", hash = "sha256:b8c3f85900b9dc423225913c5aace94729fe1fa9763b38939a95226f02d37186"},
     {file = "decorator-5.1.1.tar.gz", hash = "sha256:637996211036b6385ef91435e4fae22989472f9d571faba8927ba8253acbc330"},
@@ -183,6 +193,7 @@ version = "1.1.3"
 description = "DuckDB in-process database"
 optional = false
 python-versions = ">=3.7.0"
+groups = ["main"]
 files = [
     {file = "duckdb-1.1.3-cp310-cp310-macosx_12_0_arm64.whl", hash = "sha256:1c0226dc43e2ee4cc3a5a4672fddb2d76fd2cf2694443f395c02dd1bea0b7fce"},
     {file = "duckdb-1.1.3-cp310-cp310-macosx_12_0_universal2.whl", hash = "sha256:7c71169fa804c0b65e49afe423ddc2dc83e198640e3b041028da8110f7cd16f7"},
@@ -244,6 +255,7 @@ version = "0.13.6"
 description = "SQLAlchemy driver for duckdb"
 optional = false
 python-versions = "<4,>=3.8"
+groups = ["main"]
 files = [
     {file = "duckdb_engine-0.13.6-py3-none-any.whl", hash = "sha256:cedd44252cce5f42de88752026925154a566c407987116a242d250642904ba84"},
     {file = "duckdb_engine-0.13.6.tar.gz", hash = "sha256:221ec7759e157fd8d4fcb0bd64f603c5a4b1889186f30d805a91b10a73f8c59a"},
@@ -260,6 +272,8 @@ version = "1.2.2"
 description = "Backport of PEP 654 (exception groups)"
 optional = false
 python-versions = ">=3.7"
+groups = ["dev"]
+markers = "python_version <= \"3.10\""
 files = [
     {file = "exceptiongroup-1.2.2-py3-none-any.whl", hash = "sha256:3111b9d131c238bec2f8f516e123e14ba243563fb135d3fe885990585aa7795b"},
     {file = "exceptiongroup-1.2.2.tar.gz", hash = "sha256:47c2edf7c6738fafb49fd34290706d1a1a2f4d1c6df275526b62cbb4aa5393cc"},
@@ -274,13 +288,14 @@ version = "2.2.0"
 description = "Get the currently executing AST node of a frame, and other information"
 optional = false
 python-versions = ">=3.8"
+groups = ["main"]
 files = [
     {file = "executing-2.2.0-py2.py3-none-any.whl", hash = "sha256:11387150cad388d62750327a53d3339fad4888b39a6fe233c3afbb54ecffd3aa"},
     {file = "executing-2.2.0.tar.gz", hash = "sha256:5d108c028108fe2551d1a7b2e8b713341e2cb4fc0aa7dcf966fa4327a5226755"},
 ]
 
 [package.extras]
-tests = ["asttokens (>=2.1.0)", "coverage", "coverage-enable-subprocess", "ipython", "littleutils", "pytest", "rich"]
+tests = ["asttokens (>=2.1.0)", "coverage", "coverage-enable-subprocess", "ipython", "littleutils", "pytest", "rich ; python_version >= \"3.11\""]
 
 [[package]]
 name = "greenlet"
@@ -288,6 +303,8 @@ version = "3.1.1"
 description = "Lightweight in-process concurrent programming"
 optional = false
 python-versions = ">=3.7"
+groups = ["main"]
+markers = "platform_machine == \"aarch64\" or platform_machine == \"ppc64le\" or platform_machine == \"x86_64\" or platform_machine == \"amd64\" or platform_machine == \"AMD64\" or platform_machine == \"win32\" or platform_machine == \"WIN32\""
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@@ -374,6 +391,7 @@ version = "2.0.0"
 description = "brain-dead simple config-ini parsing"
 optional = false
 python-versions = ">=3.7"
+groups = ["dev"]
 files = [
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@@ -385,6 +403,7 @@ version = "8.12.3"
 description = "IPython: Productive Interactive Computing"
 optional = false
 python-versions = ">=3.8"
+groups = ["main"]
 files = [
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@@ -424,6 +443,7 @@ version = "0.2.2"
 description = "A Tree Widget using jsTree"
 optional = false
 python-versions = "*"
+groups = ["main"]
 files = [
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@@ -438,6 +458,7 @@ version = "8.1.5"
 description = "Jupyter interactive widgets"
 optional = false
 python-versions = ">=3.7"
+groups = ["main"]
 files = [
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@@ -459,6 +480,7 @@ version = "0.19.2"
 description = "An autocompletion tool for Python that can be used for text editors."
 optional = false
 python-versions = ">=3.6"
+groups = ["main"]
 files = [
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@@ -478,6 +500,7 @@ version = "3.1.6"
 description = "A very fast and expressive template engine."
 optional = false
 python-versions = ">=3.7"
+groups = ["main"]
 files = [
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@@ -495,6 +518,7 @@ version = "3.0.13"
 description = "Jupyter interactive widgets for JupyterLab"
 optional = false
 python-versions = ">=3.7"
+groups = ["main"]
 files = [
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@@ -506,6 +530,7 @@ version = "2.1.5"
 description = "Safely add untrusted strings to HTML/XML markup."
 optional = false
 python-versions = ">=3.7"
+groups = ["main"]
 files = [
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@@ -575,6 +600,7 @@ version = "0.1.7"
 description = "Inline Matplotlib backend for Jupyter"
 optional = false
 python-versions = ">=3.8"
+groups = ["main"]
 files = [
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@@ -589,6 +615,7 @@ version = "3.1"
 description = "Python package for creating and manipulating graphs and networks"
 optional = false
 python-versions = ">=3.8"
+groups = ["main"]
 files = [
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@@ -607,6 +634,8 @@ version = "1.24.4"
 description = "Fundamental package for array computing in Python"
 optional = false
 python-versions = ">=3.8"
+groups = ["main"]
+markers = "python_version < \"3.12\""
 files = [
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@@ -638,12 +667,60 @@ files = [
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 ]
 
+[[package]]
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+optional = false
+python-versions = ">=3.9"
+groups = ["main"]
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+]
+
 [[package]]
 name = "packaging"
 version = "24.2"
 description = "Core utilities for Python packages"
 optional = false
 python-versions = ">=3.8"
+groups = ["main", "dev"]
 files = [
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@@ -655,6 +732,7 @@ version = "2.0.3"
 description = "Powerful data structures for data analysis, time series, and statistics"
 optional = false
 python-versions = ">=3.8"
+groups = ["main"]
 files = [
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@@ -687,7 +765,7 @@ files = [
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     {version = ">=1.23.2", markers = "python_version >= \"3.11\""},
-    {version = ">=1.21.0", markers = "python_version >= \"3.10\" and python_version < \"3.11\""},
+    {version = ">=1.21.0", markers = "python_version == \"3.10\""},
 ]
 python-dateutil = ">=2.8.2"
 pytz = ">=2020.1"
@@ -722,6 +800,7 @@ version = "0.8.4"
 description = "A Python Parser"
 optional = false
 python-versions = ">=3.6"
+groups = ["main"]
 files = [
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@@ -737,6 +816,8 @@ version = "4.9.0"
 description = "Pexpect allows easy control of interactive console applications."
 optional = false
 python-versions = "*"
+groups = ["main"]
+markers = "sys_platform != \"win32\""
 files = [
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@@ -751,6 +832,7 @@ version = "0.7.5"
 description = "Tiny 'shelve'-like database with concurrency support"
 optional = false
 python-versions = "*"
+groups = ["main"]
 files = [
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@@ -762,6 +844,7 @@ version = "1.5.0"
 description = "plugin and hook calling mechanisms for python"
 optional = false
 python-versions = ">=3.8"
+groups = ["dev"]
 files = [
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@@ -777,6 +860,7 @@ version = "3.0.50"
 description = "Library for building powerful interactive command lines in Python"
 optional = false
 python-versions = ">=3.8.0"
+groups = ["main"]
 files = [
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@@ -791,6 +875,7 @@ version = "2.9.10"
 description = "psycopg2 - Python-PostgreSQL Database Adapter"
 optional = false
 python-versions = ">=3.8"
+groups = ["main"]
 files = [
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@@ -809,6 +894,8 @@ version = "0.7.0"
 description = "Run a subprocess in a pseudo terminal"
 optional = false
 python-versions = "*"
+groups = ["main"]
+markers = "sys_platform != \"win32\""
 files = [
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@@ -820,6 +907,7 @@ version = "0.2.3"
 description = "Safely evaluate AST nodes without side effects"
 optional = false
 python-versions = "*"
+groups = ["main"]
 files = [
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@@ -834,6 +922,7 @@ version = "2.10.6"
 description = "Data validation using Python type hints"
 optional = false
 python-versions = ">=3.8"
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 files = [
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@@ -846,7 +935,7 @@ typing-extensions = ">=4.12.2"
 
 [package.extras]
 email = ["email-validator (>=2.0.0)"]
-timezone = ["tzdata"]
+timezone = ["tzdata ; python_version >= \"3.9\" and platform_system == \"Windows\""]
 
 [[package]]
 name = "pydantic-core"
@@ -854,6 +943,7 @@ version = "2.27.2"
 description = "Core functionality for Pydantic validation and serialization"
 optional = false
 python-versions = ">=3.8"
+groups = ["main"]
 files = [
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@@ -966,6 +1056,7 @@ version = "2.19.1"
 description = "Pygments is a syntax highlighting package written in Python."
 optional = false
 python-versions = ">=3.8"
+groups = ["main"]
 files = [
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@@ -980,6 +1071,7 @@ version = "8.3.4"
 description = "pytest: simple powerful testing with Python"
 optional = false
 python-versions = ">=3.8"
+groups = ["dev"]
 files = [
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@@ -1002,6 +1094,7 @@ version = "5.0.0"
 description = "Pytest plugin for measuring coverage."
 optional = false
 python-versions = ">=3.8"
+groups = ["dev"]
 files = [
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@@ -1020,6 +1113,7 @@ version = "2.9.0.post0"
 description = "Extensions to the standard Python datetime module"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
+groups = ["main"]
 files = [
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@@ -1034,6 +1128,7 @@ version = "2024.2"
 description = "World timezone definitions, modern and historical"
 optional = false
 python-versions = "*"
+groups = ["main"]
 files = [
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@@ -1045,6 +1140,7 @@ version = "6.0.2"
 description = "YAML parser and emitter for Python"
 optional = false
 python-versions = ">=3.8"
+groups = ["main"]
 files = [
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@@ -1101,12 +1197,43 @@ files = [
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 ]
 
+[[package]]
+name = "ruff"
+version = "0.14.3"
+description = "An extremely fast Python linter and code formatter, written in Rust."
+optional = false
+python-versions = ">=3.7"
+groups = ["dev"]
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+]
+
 [[package]]
 name = "scipy"
 version = "1.10.1"
 description = "Fundamental algorithms for scientific computing in Python"
 optional = false
 python-versions = "<3.12,>=3.8"
+groups = ["main"]
+markers = "python_version < \"3.12\""
 files = [
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@@ -1139,12 +1266,65 @@ dev = ["click", "doit (>=0.36.0)", "flake8", "mypy", "pycodestyle", "pydevtool",
 doc = ["matplotlib (>2)", "numpydoc", "pydata-sphinx-theme (==0.9.0)", "sphinx (!=4.1.0)", "sphinx-design (>=0.2.0)"]
 test = ["asv", "gmpy2", "mpmath", "pooch", "pytest", "pytest-cov", "pytest-timeout", "pytest-xdist", "scikit-umfpack", "threadpoolctl"]
 
+[[package]]
+name = "scipy"
+version = "1.14.1"
+description = "Fundamental algorithms for scientific computing in Python"
+optional = false
+python-versions = ">=3.10"
+groups = ["main"]
+markers = "python_version == \"3.12\""
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+[package.dependencies]
+numpy = ">=1.23.5,<2.3"
+
+[package.extras]
+dev = ["cython-lint (>=0.12.2)", "doit (>=0.36.0)", "mypy (==1.10.0)", "pycodestyle", "pydevtool", "rich-click", "ruff (>=0.0.292)", "types-psutil", "typing_extensions"]
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+test = ["Cython", "array-api-strict (>=2.0)", "asv", "gmpy2", "hypothesis (>=6.30)", "meson", "mpmath", "ninja ; sys_platform != \"emscripten\"", "pooch", "pytest", "pytest-cov", "pytest-timeout", "pytest-xdist", "scikit-umfpack", "threadpoolctl"]
+
 [[package]]
 name = "six"
 version = "1.17.0"
 description = "Python 2 and 3 compatibility utilities"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
+groups = ["main"]
 files = [
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@@ -1156,6 +1336,7 @@ version = "2.0.37"
 description = "Database Abstraction Library"
 optional = false
 python-versions = ">=3.7"
+groups = ["main"]
 files = [
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@@ -1251,6 +1432,7 @@ version = "0.6.3"
 description = "Extract data from python stack frames and tracebacks for informative displays"
 optional = false
 python-versions = "*"
+groups = ["main"]
 files = [
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@@ -1270,6 +1452,8 @@ version = "2.2.1"
 description = "A lil' TOML parser"
 optional = false
 python-versions = ">=3.8"
+groups = ["dev"]
+markers = "python_version <= \"3.10\""
 files = [
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@@ -1311,6 +1495,7 @@ version = "4.67.1"
 description = "Fast, Extensible Progress Meter"
 optional = false
 python-versions = ">=3.7"
+groups = ["main"]
 files = [
     {file = "tqdm-4.67.1-py3-none-any.whl", hash = "sha256:26445eca388f82e72884e0d580d5464cd801a3ea01e63e5601bdff9ba6a48de2"},
     {file = "tqdm-4.67.1.tar.gz", hash = "sha256:f8aef9c52c08c13a65f30ea34f4e5aac3fd1a34959879d7e59e63027286627f2"},
@@ -1332,6 +1517,7 @@ version = "5.14.3"
 description = "Traitlets Python configuration system"
 optional = false
 python-versions = ">=3.8"
+groups = ["main"]
 files = [
     {file = "traitlets-5.14.3-py3-none-any.whl", hash = "sha256:b74e89e397b1ed28cc831db7aea759ba6640cb3de13090ca145426688ff1ac4f"},
     {file = "traitlets-5.14.3.tar.gz", hash = "sha256:9ed0579d3502c94b4b3732ac120375cda96f923114522847de4b3bb98b96b6b7"},
@@ -1347,6 +1533,7 @@ version = "4.12.2"
 description = "Backported and Experimental Type Hints for Python 3.8+"
 optional = false
 python-versions = ">=3.8"
+groups = ["main"]
 files = [
     {file = "typing_extensions-4.12.2-py3-none-any.whl", hash = "sha256:04e5ca0351e0f3f85c6853954072df659d0d13fac324d0072316b67d7794700d"},
     {file = "typing_extensions-4.12.2.tar.gz", hash = "sha256:1a7ead55c7e559dd4dee8856e3a88b41225abfe1ce8df57b7c13915fe121ffb8"},
@@ -1358,6 +1545,7 @@ version = "2025.1"
 description = "Provider of IANA time zone data"
 optional = false
 python-versions = ">=2"
+groups = ["main"]
 files = [
     {file = "tzdata-2025.1-py2.py3-none-any.whl", hash = "sha256:7e127113816800496f027041c570f50bcd464a020098a3b6b199517772303639"},
     {file = "tzdata-2025.1.tar.gz", hash = "sha256:24894909e88cdb28bd1636c6887801df64cb485bd593f2fd83ef29075a81d694"},
@@ -1369,6 +1557,7 @@ version = "0.2.13"
 description = "Measures the displayed width of unicode strings in a terminal"
 optional = false
 python-versions = "*"
+groups = ["main"]
 files = [
     {file = "wcwidth-0.2.13-py2.py3-none-any.whl", hash = "sha256:3da69048e4540d84af32131829ff948f1e022c1c6bdb8d6102117aac784f6859"},
     {file = "wcwidth-0.2.13.tar.gz", hash = "sha256:72ea0c06399eb286d978fdedb6923a9eb47e1c486ce63e9b4e64fc18303972b5"},
@@ -1380,12 +1569,13 @@ version = "4.0.13"
 description = "Jupyter interactive widgets for Jupyter Notebook"
 optional = false
 python-versions = ">=3.7"
+groups = ["main"]
 files = [
     {file = "widgetsnbextension-4.0.13-py3-none-any.whl", hash = "sha256:74b2692e8500525cc38c2b877236ba51d34541e6385eeed5aec15a70f88a6c71"},
     {file = "widgetsnbextension-4.0.13.tar.gz", hash = "sha256:ffcb67bc9febd10234a362795f643927f4e0c05d9342c727b65d2384f8feacb6"},
 ]
 
 [metadata]
-lock-version = "2.0"
-python-versions = ">=3.8.10,<3.12"
-content-hash = "7ef5e6a3bec2bcef8429f74816408f554f0d021da19349481077a67065489833"
+lock-version = "2.1"
+python-versions = ">=3.8.10,<3.13"
+content-hash = "a588906e6e90991a51af15f24a95ed2841c834dc72b79872e843b54e889f56c5"
diff --git a/pyproject.toml b/pyproject.toml
index 7600f55..34f0901 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -10,28 +10,74 @@ include = [
     {path = "biasanalyzer/sql_templates/*.sql", format=["sdist", "wheel"]}
 ]
 [tool.poetry.dependencies]
-python = ">=3.8.10,<3.12"
+python = ">=3.8.10,<3.13"
 duckdb = "^1.1.1"
 pandas = "2.0.3"
-scipy = "1.10.1"
-numpy = "1.24.4"
+
+scipy = [
+    {version = ">=1.10.1,<1.11", markers = "python_version<'3.12'"},
+    {version = ">=1.14.1,<1.15", markers = "python_version>='3.12'"}
+]
+numpy = [
+    {version = ">=1.24.4,<1.25", markers = "python_version<'3.12'"},
+    {version = ">=1.25.0,<=1.26.4", markers = "python_version>='3.12'"}
+]
 duckdb-engine = "^0.13.2"
 sqlalchemy = "^2.0.35"
 pyyaml = "^6.0.2"
 pydantic = "^2.9.2"
-psycopg2 = "^2.9.1"
+psycopg2 = "^2.9.9"
 ipytree = "^0.2.2"
 ipywidgets = "^8.1.5"
 jinja2 = "3.1.6"
 tqdm = "4.67.1"
 networkx = "3.1"
 
-[tool.poetry.dev-dependencies]
-pytest = "^8.3.3"
-
 [tool.poetry.group.dev.dependencies]
+pytest = "^8.3.3"
 pytest-cov = "5.0.0"
+ruff = "^0.14.3"
 
 [build-system]
 requires = ["poetry-core>=1.0.0"]
 build-backend = "poetry.core.masonry.api"
+
+# ----------------------------
+# Ruff configuration
+# ----------------------------
+[tool.ruff]
+# Linting targets your source and test code
+target-version = "py38"
+src = ["biasanalyzer", "tests", "scripts"]
+line-length = 120
+
+# Enable full linting set roughly equivalent to Flake8 + isort + pyupgrade
+lint.select = [
+    "E",  # pycodestyle errors
+    "F",  # pyflakes
+    "I",  # isort-style import sorting
+    "B",  # flake8-bugbear
+    "UP", # pyupgrade
+    "N",  # pep8-naming
+    "S",  # security (flake8-bandit subset)
+]
+lint.ignore = ["S101", "N805", "S701"]
+
+# Automatically fix simple issues on save (optional)
+fix = true
+
+# Exclude build/test caches and notebooks
+exclude = [
+    ".venv",
+    ".git",
+    "__pycache__",
+    "build",
+    "dist",
+    "notebooks",
+]
+
+[tool.ruff.format]
+# Ruff's built-in formatter replaces Black
+indent-style = "space"
+docstring-code-format = true
+docstring-code-line-length = "dynamic"
diff --git a/scripts/ingest_csvs_to_omop_duckdb.py b/scripts/ingest_csvs_to_omop_duckdb.py
index f4d8525..dbebe38 100644
--- a/scripts/ingest_csvs_to_omop_duckdb.py
+++ b/scripts/ingest_csvs_to_omop_duckdb.py
@@ -8,12 +8,13 @@
         --output data/omop.duckdb
 """
 
-import duckdb
-import time
 import argparse
 import sys
+import time
 from pathlib import Path
 
+import duckdb
+
 
 def load_csv_to_duckdb(con, csv_path: Path, table_name: str):
     """Load a single CSV file into DuckDB."""
diff --git a/tests/conftest.py b/tests/conftest.py
index 1ae39cc..be1cb6b 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -1,8 +1,9 @@
-import pytest
+import os
+
 import duckdb
+import pytest
 from biasanalyzer.api import BIAS
 from biasanalyzer.config import load_config
-import os
 
 
 @pytest.fixture
@@ -145,7 +146,7 @@ def test_db():
                     (37311061, 'COVID-19', '2012-04-01', '2020-04-01', '840539006', 'SNOMED', 'Condition'),
                     (4041664, 'Difficulty breathing', '2012-04-01', '2020-04-01', '230145002', 'SNOMED', 'Condition'),
                     (316139, 'Heart failure', '2012-04-01', '2020-04-01', '84114007', 'SNOMED', 'Condition'),
-                    (201826, 'Type 2 diabetes mellitus', '2012-04-01', '2020-04-01', '44054006', 'SNOMED', 'Condition');                    
+                    (201826, 'Type 2 diabetes mellitus', '2012-04-01', '2020-04-01', '44054006', 'SNOMED', 'Condition')
             """)
 
     # Insert hierarchical relationships as needed
@@ -175,7 +176,8 @@ def test_db():
     result = conn.execute("SELECT COUNT(*) FROM condition_occurrence").fetchone()
     if result[0] == 0:
         conn.execute("""
-                INSERT INTO condition_occurrence (person_id, condition_concept_id, condition_start_date, condition_end_date)
+                INSERT INTO condition_occurrence (person_id, condition_concept_id, condition_start_date, 
+                                                  condition_end_date)
                 VALUES
                     (101, 2, '2023-01-01', '2023-01-31'), -- Patient 101 has Type 1 Diabetes
                     (101, 3, '2023-01-01', '2023-02-27'), -- Patient 101 has Type 2 Diabetes
@@ -215,7 +217,8 @@ def test_db():
     result = conn.execute("SELECT COUNT(*) FROM visit_occurrence").fetchone()
     if result[0] == 0:
         conn.execute("""
-                    INSERT INTO visit_occurrence (person_id, visit_occurrence_id, visit_concept_id, visit_start_date, visit_end_date)
+                    INSERT INTO visit_occurrence (person_id, visit_occurrence_id, visit_concept_id, visit_start_date, 
+                                                  visit_end_date)
                     VALUES 
                         (108, 1, 9201, '2020-04-13', '2020-04-14'), -- Inpatient Visit
                         (108, 2, 9201, '2020-04-16', '2020-04-27'), -- Second inpatient visit (meets criteria)
@@ -239,7 +242,8 @@ def test_db():
         result = conn.execute("SELECT COUNT(*) FROM procedure_occurrence").fetchone()
         if result[0] == 0:
             conn.execute("""
-                        INSERT INTO procedure_occurrence (person_id, procedure_occurrence_id, procedure_concept_id, procedure_date)
+                        INSERT INTO procedure_occurrence (person_id, procedure_occurrence_id, procedure_concept_id, 
+                                                          procedure_date)
                         VALUES 
                             (1, 1, 4048609, '2020-06-20'),  -- Person 1: Blood test
                             (2, 2, 4048609, '2020-06-20'),  -- Person 2: Blood test
@@ -255,7 +259,8 @@ def test_db():
         result = conn.execute("SELECT COUNT(*) FROM drug_exposure").fetchone()
         if result[0] == 0:
             conn.execute("""
-                            INSERT INTO drug_exposure (person_id, drug_concept_id, drug_exposure_start_date, drug_exposure_end_date)
+                            INSERT INTO drug_exposure (person_id, drug_concept_id, drug_exposure_start_date, 
+                                                       drug_exposure_end_date)
                             VALUES 
                                 (1, 4285892, '2020-06-15', '2020-06-15'),  -- Person 1: Insulin 14 days after
                                 (2, 4285892, '2020-06-15', '2020-06-15'),  -- Person 2: Insulin
diff --git a/tests/query_based/test_cohort_creation.py b/tests/query_based/test_cohort_creation.py
index 8f82190..c13878e 100644
--- a/tests/query_based/test_cohort_creation.py
+++ b/tests/query_based/test_cohort_creation.py
@@ -1,10 +1,11 @@
-import os
 import datetime
 import logging
+import os
+
 import pytest
-from sqlalchemy.exc import SQLAlchemyError
-from numpy.ma.testutils import assert_equal
 from biasanalyzer.models import DemographicsCriteria, TemporalEvent, TemporalEventGroup
+from numpy.ma.testutils import assert_equal
+from sqlalchemy.exc import SQLAlchemyError
 
 
 def test_cohort_yaml_validation(test_db):
diff --git a/tests/query_based/test_hierarchical_prevalence.py b/tests/query_based/test_hierarchical_prevalence.py
index a12d173..66893b3 100644
--- a/tests/query_based/test_hierarchical_prevalence.py
+++ b/tests/query_based/test_hierarchical_prevalence.py
@@ -1,6 +1,6 @@
+
 import pytest
-from functools import reduce
-from biasanalyzer.concept import ConceptHierarchy, ConceptNode
+from biasanalyzer.concept import ConceptHierarchy
 
 
 def test_cohort_concept_hierarchical_prevalence(test_db, caplog):
@@ -77,7 +77,7 @@ def test_identifier_normalization_and_cache():
     assert h1 is h2  # cache reuse even though results2 is different from results1
     assert h1.identifier == "1-condition_occurrence-0-None"
     h2 = ConceptHierarchy.build_concept_hierarchy_from_results(1, 'drug_exposure', results2)
-    assert not h1 is h2  # cache is not used since drug_exposure concept_name is different than the cached
+    assert h1 is not h2  # cache is not used since drug_exposure concept_name is different than the cached
     # condition_occurrence
     assert h2.identifier == "1-drug_exposure-0-None"
 
diff --git a/tests/test_biasanalyzer_api.py b/tests/test_biasanalyzer_api.py
index a47a3a5..a9f936b 100644
--- a/tests/test_biasanalyzer_api.py
+++ b/tests/test_biasanalyzer_api.py
@@ -1,10 +1,11 @@
-import os
 import datetime
 import logging
+import os
+
 import pytest
-from ipytree import Node
-from biasanalyzer.concept import ConceptHierarchy
 from biasanalyzer import __version__
+from biasanalyzer.concept import ConceptHierarchy
+from ipytree import Node
 
 
 def test_version():
diff --git a/tests/test_config.py b/tests/test_config.py
index 060b940..aa66c64 100644
--- a/tests/test_config.py
+++ b/tests/test_config.py
@@ -1,13 +1,10 @@
 import os
 
-from biasanalyzer.config import load_config, load_cohort_creation_config
+from biasanalyzer.config import load_cohort_creation_config, load_config
 
 
 def test_load_config():
-    try:
-        config = load_config(os.path.join(os.path.dirname(__file__), 'assets', 'config', 'test_config.yaml'))
-    except Exception as e:
-        assert False, f"load_config() raised an exception: {e}"
+    config = load_config(os.path.join(os.path.dirname(__file__), 'assets', 'config', 'test_config.yaml'))
 
     assert config.get('root_omop_cdm_database') == {
         'database_type': 'duckdb',
@@ -19,14 +16,9 @@ def test_load_config():
     }
 
 def test_load_cohort_creation_config():
-    try:
-        config = load_cohort_creation_config(
-            os.path.join(os.path.dirname(__file__), 'assets', 'cohort_creation',
-                         'test_cohort_creation_condition_occurrence_config.yaml'))
-    except Exception as e:
-        assert False, f"test_load_cohort_creation_config() raised an exception: {e}"
-
-
+    config = load_cohort_creation_config(
+        os.path.join(os.path.dirname(__file__), 'assets', 'cohort_creation',
+                     'test_cohort_creation_condition_occurrence_config.yaml'))
     assert 'inclusion_criteria' in config
     # assert 'exclusion_criteria' in config
     assert 'temporal_events' in config.get('inclusion_criteria')
diff --git a/tests/test_database.py b/tests/test_database.py
index 8fb1ed5..e08edc6 100644
--- a/tests/test_database.py
+++ b/tests/test_database.py
@@ -1,6 +1,7 @@
+from unittest.mock import Mock
+
 import duckdb
 import pytest
-from unittest.mock import Mock
 from biasanalyzer.cohort_query_builder import CohortQueryBuilder
 from biasanalyzer.database import BiasDatabase
 
@@ -43,7 +44,7 @@ def close(self):
     # Mock duckdb.connect to return our MockConn
     mock_connect = Mock(return_value=MockConn())
     monkeypatch.setattr("duckdb.connect", mock_connect)
-    db = BiasDatabase(":memory:", omop_db_url="postgresql://testuser:testpass@localhost:5432/testdb")
+    BiasDatabase(":memory:", omop_db_url="postgresql://testuser:testpass@localhost:5432/testdb")
 
     assert len(calls) >= 3
     assert any("INSTALL postgres" in call for call in calls), "INSTALL postgres must be run at BiasDatabase init"
@@ -53,7 +54,7 @@ def close(self):
 def test_bias_db_invalid_omop_db_url():
     BiasDatabase._instance = None
     with pytest.raises(ValueError, match='Unsupported OMOP database backend'):
-        db = BiasDatabase(":memory:", omop_db_url='dummy_invalid_url')
+        BiasDatabase(":memory:", omop_db_url='dummy_invalid_url')
 
 def test_create_cohort_definition_table_error_on_sequence():
     BiasDatabase._instance = None

From 74ae0306971cbc6720bf72be37237dd9b26c7019 Mon Sep 17 00:00:00 2001
From: hyi <hongyi@renci.org>
Date: Thu, 6 Nov 2025 14:23:34 -0500
Subject: [PATCH 02/12] supressed some ruff check errors

---
 biasanalyzer/cohort_query_builder.py  | 1 +
 biasanalyzer/database.py              | 1 +
 scripts/ingest_csvs_to_omop_duckdb.py | 2 ++
 3 files changed, 4 insertions(+)

diff --git a/biasanalyzer/cohort_query_builder.py b/biasanalyzer/cohort_query_builder.py
index 755f6b0..b054357 100644
--- a/biasanalyzer/cohort_query_builder.py
+++ b/biasanalyzer/cohort_query_builder.py
@@ -1,3 +1,4 @@
+# ruff: noqa: S608
 import importlib.resources
 import os
 import sys
diff --git a/biasanalyzer/database.py b/biasanalyzer/database.py
index 6eda39c..33de5a0 100644
--- a/biasanalyzer/database.py
+++ b/biasanalyzer/database.py
@@ -1,3 +1,4 @@
+# ruff: noqa: S608
 import gc
 from datetime import datetime
 from typing import Optional
diff --git a/scripts/ingest_csvs_to_omop_duckdb.py b/scripts/ingest_csvs_to_omop_duckdb.py
index dbebe38..d1ff549 100644
--- a/scripts/ingest_csvs_to_omop_duckdb.py
+++ b/scripts/ingest_csvs_to_omop_duckdb.py
@@ -1,3 +1,5 @@
+# ruff: noqa: S608
+
 """
 This script ingests both clinical and vocabulary OMOP CSV exports into a single DckDB database for
 downstream use of the core BiasAnalyzer python library.

From ddd6312c8e2f376a810fcd840cdd588996720e95 Mon Sep 17 00:00:00 2001
From: hyi <hongyi@renci.org>
Date: Thu, 6 Nov 2025 15:19:28 -0500
Subject: [PATCH 03/12] ruff reformatting

---
 biasanalyzer/__init__.py                      |   2 +-
 biasanalyzer/api.py                           | 117 ++++---
 biasanalyzer/background/threading_utils.py    |   2 +
 biasanalyzer/cohort.py                        |  93 +++---
 biasanalyzer/cohort_query_builder.py          |  70 ++--
 biasanalyzer/concept.py                       |  36 ++-
 biasanalyzer/config.py                        |   2 +-
 biasanalyzer/database.py                      | 216 +++++++------
 biasanalyzer/models.py                        |  37 ++-
 biasanalyzer/module_test.py                   | 126 ++++----
 biasanalyzer/sql.py                           |  24 +-
 biasanalyzer/utils.py                         |  20 +-
 scripts/ingest_csvs_to_omop_duckdb.py         |  22 +-
 tests/conftest.py                             |   5 +-
 tests/query_based/test_cohort_creation.py     | 301 +++++++++++-------
 .../test_hierarchical_prevalence.py           | 241 +++++++++-----
 tests/test_biasanalyzer_api.py                | 242 ++++++++------
 tests/test_config.py                          |  50 +--
 tests/test_database.py                        |  22 +-
 19 files changed, 953 insertions(+), 675 deletions(-)

diff --git a/biasanalyzer/__init__.py b/biasanalyzer/__init__.py
index b794fd4..3dc1f76 100644
--- a/biasanalyzer/__init__.py
+++ b/biasanalyzer/__init__.py
@@ -1 +1 @@
-__version__ = '0.1.0'
+__version__ = "0.1.0"
diff --git a/biasanalyzer/api.py b/biasanalyzer/api.py
index 8af9a65..57d947c 100644
--- a/biasanalyzer/api.py
+++ b/biasanalyzer/api.py
@@ -24,48 +24,55 @@ def __init__(self, config_file_path=None):
 
     def set_config(self, config_file_path: str):
         if not config_file_path:
-            notify_users('no configuration file specified. '
-                         'Call set_config(config_file_path) next to specify configurations')
+            notify_users(
+                "no configuration file specified. Call set_config(config_file_path) next to specify configurations"
+            )
         else:
             try:
                 self.config = load_config(config_file_path)
-                notify_users(f'configuration specified in {config_file_path} loaded successfully')
+                notify_users(f"configuration specified in {config_file_path} loaded successfully")
             except FileNotFoundError:
-                notify_users('specified configuration file does not exist. '
-                             'Call set_config(config_file_path) next to specify a valid configuration file',
-                             level='error')
+                notify_users(
+                    "specified configuration file does not exist. "
+                    "Call set_config(config_file_path) next to specify a valid configuration file",
+                    level="error",
+                )
             except ValidationError as ex:
-                notify_users(f'configuration yaml file is not valid with validation error: {ex}', level='error')
+                notify_users(f"configuration yaml file is not valid with validation error: {ex}", level="error")
 
     def set_root_omop(self):
         if not self.config:
-            notify_users('no valid configuration to set root OMOP CDM data. '
-                         'Call set_config(config_file_path) to specify configurations first.')
+            notify_users(
+                "no valid configuration to set root OMOP CDM data. "
+                "Call set_config(config_file_path) to specify configurations first."
+            )
             return
 
         self.cleanup()
 
-        db_type = self.config['root_omop_cdm_database']['database_type']
-        if db_type == 'postgresql':
-            user = self.config['root_omop_cdm_database']['username']
-            password = self.config['root_omop_cdm_database']['password']
-            host = self.config['root_omop_cdm_database']['hostname']
-            port = self.config['root_omop_cdm_database']['port']
-            db = self.config['root_omop_cdm_database']['database']
+        db_type = self.config["root_omop_cdm_database"]["database_type"]
+        if db_type == "postgresql":
+            user = self.config["root_omop_cdm_database"]["username"]
+            password = self.config["root_omop_cdm_database"]["password"]
+            host = self.config["root_omop_cdm_database"]["hostname"]
+            port = self.config["root_omop_cdm_database"]["port"]
+            db = self.config["root_omop_cdm_database"]["database"]
             db_url = f"postgresql://{user}:{password}@{host}:{port}/{db}"
             self.omop_cdm_db = OMOPCDMDatabase(db_url)
-            self.bias_db = BiasDatabase(':memory:', omop_db_url=db_url)
-        elif db_type == 'duckdb':
-            db_path = self.config['root_omop_cdm_database'].get('database', ":memory:")
+            self.bias_db = BiasDatabase(":memory:", omop_db_url=db_url)
+        elif db_type == "duckdb":
+            db_path = self.config["root_omop_cdm_database"].get("database", ":memory:")
             self.omop_cdm_db = OMOPCDMDatabase(db_path)
-            self.bias_db = BiasDatabase(':memory:', omop_db_url=db_path)
+            self.bias_db = BiasDatabase(":memory:", omop_db_url=db_path)
         else:
             notify_users(f"Unsupported database type: {db_type}")
 
     def _set_cohort_action(self):
         if self.omop_cdm_db is None:
-            notify_users('A valid OMOP CDM must be set before creating a cohort. '
-                         'Call set_root_omop first to set a valid root OMOP CDM')
+            notify_users(
+                "A valid OMOP CDM must be set before creating a cohort. "
+                "Call set_root_omop first to set a valid root OMOP CDM"
+            )
             return None
         if self.cohort_action is None:
             self.cohort_action = CohortAction(self.omop_cdm_db, self.bias_db)
@@ -73,25 +80,31 @@ def _set_cohort_action(self):
 
     def get_domains_and_vocabularies(self):
         if self.omop_cdm_db is None:
-            notify_users('A valid OMOP CDM must be set before getting domains. '
-                         'Call set_root_omop first to set a valid root OMOP CDM')
+            notify_users(
+                "A valid OMOP CDM must be set before getting domains. "
+                "Call set_root_omop first to set a valid root OMOP CDM"
+            )
             return None
         return self.omop_cdm_db.get_domains_and_vocabularies()
 
     def get_concepts(self, search_term, domain=None, vocabulary=None):
         if self.omop_cdm_db is None:
-            notify_users('A valid OMOP CDM must be set before getting concepts. '
-                         'Call set_root_omop first to set a valid root OMOP CDM')
+            notify_users(
+                "A valid OMOP CDM must be set before getting concepts. "
+                "Call set_root_omop first to set a valid root OMOP CDM"
+            )
             return None
         if domain is None and vocabulary is None:
-            notify_users('either domain or vocabulary must be set to constrain the number of returned concepts')
+            notify_users("either domain or vocabulary must be set to constrain the number of returned concepts")
             return None
         return self.omop_cdm_db.get_concepts(search_term, domain, vocabulary)
 
     def get_concept_hierarchy(self, concept_id):
         if self.omop_cdm_db is None:
-            notify_users('A valid OMOP CDM must be set before getting concepts. '
-                         'Call set_root_omop first to set a valid root OMOP CDM')
+            notify_users(
+                "A valid OMOP CDM must be set before getting concepts. "
+                "Call set_root_omop first to set a valid root OMOP CDM"
+            )
             return None
         return self.omop_cdm_db.get_concept_hierarchy(concept_id)
 
@@ -100,20 +113,21 @@ def display_concept_tree(self, concept_tree: dict, level: int = 0, show_in_text_
         Recursively prints the concept hierarchy tree in an indented format for display.
         """
         details = concept_tree.get("details", {})
-        if 'parents' in concept_tree:
-            tree_type = 'parents'
-        elif 'children' in concept_tree:
-            tree_type = 'children'
+        if "parents" in concept_tree:
+            tree_type = "parents"
+        elif "children" in concept_tree:
+            tree_type = "children"
         else:
-            notify_users('The input concept tree must contain parents or children key as the type of the tree.')
-            return ''
+            notify_users("The input concept tree must contain parents or children key as the type of the tree.")
+            return ""
 
         if show_in_text_format:
             if details:
                 direction_arrow = get_direction_arrow(tree_type)
                 print(
                     "  " * level + f"{direction_arrow} {details['concept_name']} (ID: {details['concept_id']}, "
-                                   f"Code: {details['concept_code']})")
+                    f"Code: {details['concept_code']})"
+                )
 
             for child in concept_tree.get(tree_type, []):
                 if child:
@@ -130,9 +144,9 @@ def display_concept_tree(self, concept_tree: dict, level: int = 0, show_in_text_
             display(VBox([Label("Concept Hierarchy"), tree]))
             return root_node
 
-
-    def create_cohort(self, cohort_name: str, cohort_desc: str, query_or_yaml_file: str, created_by: str,
-                      delay: float=0):
+    def create_cohort(
+        self, cohort_name: str, cohort_desc: str, query_or_yaml_file: str, created_by: str, delay: float = 0
+    ):
         """
         API method that allows to create a cohort
         :param cohort_name: name of the cohort
@@ -151,17 +165,15 @@ def create_cohort(self, cohort_name: str, cohort_desc: str, query_or_yaml_file:
                 if delay > 0:
                     notify_users(f"[DEBUG] Simulating long-running task with {delay} seconds delay...")
                     time.sleep(delay)
-                notify_users('cohort created successfully')
+                notify_users("cohort created successfully")
             return created_cohort
         else:
-            notify_users('failed to create a valid cohort action object')
+            notify_users("failed to create a valid cohort action object")
             return None
 
-
-    def get_cohorts_concept_stats(self, cohorts: List[int],
-                                  concept_type: str='condition_occurrence',
-                                  filter_count: int=0,
-                                  vocab=None):
+    def get_cohorts_concept_stats(
+        self, cohorts: List[int], concept_type: str = "condition_occurrence", filter_count: int = 0, vocab=None
+    ):
         """
         compute concept statistics such as concept prevalence in a union of multiple cohorts
         :param cohorts: list of cohort ids
@@ -172,26 +184,25 @@ def get_cohorts_concept_stats(self, cohorts: List[int],
         :return: ConceptHierarchy object
         """
         if not cohorts:
-            notify_users('The input cohorts list is empty. At least one cohort id must be provided.')
+            notify_users("The input cohorts list is empty. At least one cohort id must be provided.")
             return None
         c_action = self._set_cohort_action()
         if c_action:
-            return c_action.get_cohorts_concept_stats(cohorts, concept_type=concept_type, filter_count=filter_count,
-                                              vocab=vocab)
+            return c_action.get_cohorts_concept_stats(
+                cohorts, concept_type=concept_type, filter_count=filter_count, vocab=vocab
+            )
         else:
-            notify_users('failed to get concept prevalence stats for the union of cohorts')
+            notify_users("failed to get concept prevalence stats for the union of cohorts")
             return None
 
-
     def compare_cohorts(self, cohort_id1, cohort_id2):
         c_action = self._set_cohort_action()
         if c_action:
             return c_action.compare_cohorts(cohort_id1, cohort_id2)
         else:
-            notify_users('failed to create a valid cohort action object')
+            notify_users("failed to create a valid cohort action object")
             return None
 
-
     def cleanup(self):
         if self.bias_db:
             self.bias_db.close()
diff --git a/biasanalyzer/background/threading_utils.py b/biasanalyzer/background/threading_utils.py
index a6fb9a9..de89671 100644
--- a/biasanalyzer/background/threading_utils.py
+++ b/biasanalyzer/background/threading_utils.py
@@ -13,6 +13,7 @@ def set(self, result, error=None):
         self.error = error
         self.ready = True
 
+
 def run_in_background(func, *args, result_holder=None, on_complete=None, **kwargs):
     """
     Run a time-consuming function in background
@@ -23,6 +24,7 @@ def run_in_background(func, *args, result_holder=None, on_complete=None, **kwarg
     :param kwargs: any keyword arguments of the function to be passed in as a dict
     :return: a background thread
     """
+
     def wrapper():
         try:
             print("[*] Background task started...", flush=True)
diff --git a/biasanalyzer/cohort.py b/biasanalyzer/cohort.py
index 691a112..4d5af20 100644
--- a/biasanalyzer/cohort.py
+++ b/biasanalyzer/cohort.py
@@ -19,7 +19,7 @@ def __init__(self, cohort_id: int, bias_db: BiasDatabase, omop_db: OMOPCDMDataba
         self.cohort_id = cohort_id
         self.bias_db = bias_db
         self.omop_db = omop_db
-        self._cohort_data = None # cache the cohort data
+        self._cohort_data = None  # cache the cohort data
         self._metadata = None
         self.query_builder = CohortQueryBuilder(cohort_creation=False)
 
@@ -39,7 +39,7 @@ def metadata(self):
             self._metadata = self.bias_db.get_cohort_definition(self.cohort_id)
         return self._metadata
 
-    def get_stats(self, variable=''):
+    def get_stats(self, variable=""):
         """
         Get aggregation statistics for the cohort in BiasDatabase.
         variable is optional with a default empty string. Supported variables are: age, gender,
@@ -53,23 +53,26 @@ def get_distributions(self, variable):
         """
         return self.bias_db.get_cohort_distributions(self.cohort_id, variable)
 
-    def get_concept_stats(self, concept_type='condition_occurrence', filter_count=0,
-                          vocab=None, print_concept_hierarchy=False):
+    def get_concept_stats(
+        self, concept_type="condition_occurrence", filter_count=0, vocab=None, print_concept_hierarchy=False
+    ):
         """
         Get cohort concept statistics such as concept prevalence
         """
-        cohort_stats = self.bias_db.get_cohort_concept_stats(self.cohort_id,
-                                                             self.query_builder,
-                                                             concept_type=concept_type,
-                                                             filter_count=filter_count,
-                                                             vocab=vocab,
-                                                             print_concept_hierarchy=print_concept_hierarchy)
-        return (cohort_stats,
-                ConceptHierarchy.build_concept_hierarchy_from_results(self.cohort_id, concept_type,
-                                                                      cohort_stats[concept_type],
-                                                                      filter_count=filter_count,
-                                                                      vocab=vocab))
-
+        cohort_stats = self.bias_db.get_cohort_concept_stats(
+            self.cohort_id,
+            self.query_builder,
+            concept_type=concept_type,
+            filter_count=filter_count,
+            vocab=vocab,
+            print_concept_hierarchy=print_concept_hierarchy,
+        )
+        return (
+            cohort_stats,
+            ConceptHierarchy.build_concept_hierarchy_from_results(
+                self.cohort_id, concept_type, cohort_stats[concept_type], filter_count=filter_count, vocab=vocab
+            ),
+        )
 
     def __del__(self):
         self._cohort_data = None
@@ -82,8 +85,7 @@ def __init__(self, omop_db: OMOPCDMDatabase, bias_db: BiasDatabase):
         self.bias_db = bias_db
         self._query_builder = CohortQueryBuilder()
 
-    def create_cohort(self, cohort_name: str, description: str, query_or_yaml_file: str,
-                      created_by: str):
+    def create_cohort(self, cohort_name: str, description: str, query_or_yaml_file: str, created_by: str):
         """
         Create a new cohort by executing a query on OMOP CDM database
         and storing the result in BiasDatabase. The query can be passed in directly
@@ -98,21 +100,23 @@ def create_cohort(self, cohort_name: str, description: str, query_or_yaml_file:
         stages = [
             "Built query",
             "Executed query on OMOP database to get cohort data",
-            "Inserted cohort data into DuckDB - Done"
+            "Inserted cohort data into DuckDB - Done",
         ]
         progress = tqdm(total=len(stages), desc="Cohort creation", unit="stage", dynamic_ncols=True, leave=True)
 
         progress.set_postfix_str(stages[0])
-        if query_or_yaml_file.endswith('.yaml') or query_or_yaml_file.endswith('.yml'):
+        if query_or_yaml_file.endswith(".yaml") or query_or_yaml_file.endswith(".yml"):
             try:
                 cohort_config = load_cohort_creation_config(query_or_yaml_file)
-                tqdm.write(f'configuration specified in {query_or_yaml_file} loaded successfully')
+                tqdm.write(f"configuration specified in {query_or_yaml_file} loaded successfully")
             except FileNotFoundError:
-                notify_users('specified cohort creation configuration file does not exist. Make sure '
-                             'the configuration file name with path is specified correctly.')
+                notify_users(
+                    "specified cohort creation configuration file does not exist. Make sure "
+                    "the configuration file name with path is specified correctly."
+                )
                 return None
             except ValidationError as ex:
-                notify_users(f'cohort creation configuration yaml file is not valid with validation error: {ex}')
+                notify_users(f"cohort creation configuration yaml file is not valid with validation error: {ex}")
                 return None
 
             query = self._query_builder.build_query_cohort_creation(cohort_config)
@@ -132,7 +136,7 @@ def create_cohort(self, cohort_name: str, description: str, query_or_yaml_file:
                     description=description,
                     created_date=datetime.now().date(),
                     creation_info=clean_string(query),
-                    created_by=created_by
+                    created_by=created_by,
                 )
                 cohort_def_id = self.bias_db.create_cohort_definition(cohort_def, progress_obj=tqdm)
                 progress.update(1)
@@ -140,7 +144,7 @@ def create_cohort(self, cohort_name: str, description: str, query_or_yaml_file:
                 progress.set_postfix_str(stages[2])
                 # Store cohort_definition and cohort data into BiasDatabase
                 cohort_df = pd.DataFrame(result)
-                cohort_df['cohort_definition_id'] = cohort_def_id
+                cohort_df["cohort_definition_id"] = cohort_def_id
                 cohort_df = cohort_df.rename(columns={"person_id": "subject_id"})
                 self.bias_db.create_cohort_in_bulk(cohort_df)
                 progress.update(1)
@@ -158,20 +162,21 @@ def create_cohort(self, cohort_name: str, description: str, query_or_yaml_file:
                 omop_session.close()
             return None
 
-    def get_cohorts_concept_stats(self, cohorts: List[int],
-                          concept_type: str = 'condition_occurrence',
-                          filter_count: int = 0,
-                          vocab=None):
-        cohort_concept_stats = [self.bias_db.get_cohort_concept_stats(c, self._query_builder,
-                                                                      concept_type=concept_type,
-                                                                      filter_count=filter_count,
-                                                                      vocab=vocab)
-                                for c in cohorts]
-        hierarchies = [ConceptHierarchy.build_concept_hierarchy_from_results(c, concept_type,
-                                                                             c_stats.get(concept_type, []),
-                                                                             filter_count=filter_count,
-                                                                             vocab=vocab)
-                       for c, c_stats in zip(cohorts, cohort_concept_stats)]
+    def get_cohorts_concept_stats(
+        self, cohorts: List[int], concept_type: str = "condition_occurrence", filter_count: int = 0, vocab=None
+    ):
+        cohort_concept_stats = [
+            self.bias_db.get_cohort_concept_stats(
+                c, self._query_builder, concept_type=concept_type, filter_count=filter_count, vocab=vocab
+            )
+            for c in cohorts
+        ]
+        hierarchies = [
+            ConceptHierarchy.build_concept_hierarchy_from_results(
+                c, concept_type, c_stats.get(concept_type, []), filter_count=filter_count, vocab=vocab
+            )
+            for c, c_stats in zip(cohorts, cohort_concept_stats)
+        ]
         return reduce(lambda h1, h2: h1.union(h2), hierarchies).to_dict()
 
     def compare_cohorts(self, cohort_id_1: int, cohort_id_2: int):
@@ -182,11 +187,9 @@ def compare_cohorts(self, cohort_id_1: int, cohort_id_2: int):
         for variable in self.bias_db.cohort_distribution_variables:
             cohort_1_stats = self.bias_db.get_cohort_distributions(cohort_id_1, variable=variable)
             cohort_2_stats = self.bias_db.get_cohort_distributions(cohort_id_2, variable=variable)
-            cohort_1_probs = [entry['probability'] for entry in cohort_1_stats]
-            cohort_2_probs = [entry['probability'] for entry in cohort_2_stats]
+            cohort_1_probs = [entry["probability"] for entry in cohort_1_stats]
+            cohort_2_probs = [entry["probability"] for entry in cohort_2_stats]
             dist = hellinger_distance(cohort_1_probs, cohort_2_probs)
-            results.append({
-                f'{variable}_hellinger_distance': dist
-            })
+            results.append({f"{variable}_hellinger_distance": dist})
 
         return results
diff --git a/biasanalyzer/cohort_query_builder.py b/biasanalyzer/cohort_query_builder.py
index b054357..7f93f79 100644
--- a/biasanalyzer/cohort_query_builder.py
+++ b/biasanalyzer/cohort_query_builder.py
@@ -12,22 +12,22 @@ class CohortQueryBuilder:
     def __init__(self, cohort_creation=True):
         """Get the path to SQL templates, whether running from source or installed."""
         try:
-            if sys.version_info >= (3, 9): # pragma: no cover
+            if sys.version_info >= (3, 9):  # pragma: no cover
                 # Python 3.9+: Use importlib.resources.files()
                 template_path = importlib.resources.files("biasanalyzer").joinpath("sql_templates")
-            else: # pragma: no cover
+            else:  # pragma: no cover
                 # Python 3.8: Use importlib.resources.path() (context manager)
                 with importlib.resources.path("biasanalyzer", "sql_templates") as p:
                     template_path = str(p)
-        except ModuleNotFoundError: # pragma: no cover
+        except ModuleNotFoundError:  # pragma: no cover
             template_path = os.path.join(os.path.dirname(__file__), "sql_templates")
 
-        print(f'template_path: {template_path}')
-        self.env = Environment(loader=FileSystemLoader(template_path), extensions=['jinja2.ext.do'])
+        print(f"template_path: {template_path}")
+        self.env = Environment(loader=FileSystemLoader(template_path), extensions=["jinja2.ext.do"])
         if cohort_creation:
             self.env.globals.update(
-                demographics_filter=self._load_macro('demographics_filter'),
-                temporal_event_filter=self.temporal_event_filter
+                demographics_filter=self._load_macro("demographics_filter"),
+                temporal_event_filter=self.temporal_event_filter,
             )
 
     def _extract_domains(self, events):
@@ -43,7 +43,7 @@ def _load_macro(self, macro_name):
         """
         Load a macro from macros.sql.j2 into the Jinja2 environment.
         """
-        macros_template = self.env.get_template('macros.sql.j2')
+        macros_template = self.env.get_template("macros.sql.j2")
         return macros_template.module.__dict__[macro_name]
 
     def build_query_cohort_creation(self, cohort_config: dict) -> str:
@@ -52,14 +52,14 @@ def build_query_cohort_creation(self, cohort_config: dict) -> str:
         :param cohort_config: dict object loaded from yaml file for building sql query.
         :return: The rendered SQL query.
         """
-        inclusion_criteria = cohort_config.get('inclusion_criteria')
-        exclusion_criteria = cohort_config.get('exclusion_criteria', {})
+        inclusion_criteria = cohort_config.get("inclusion_criteria")
+        exclusion_criteria = cohort_config.get("exclusion_criteria", {})
         inclusion_events = inclusion_criteria.get("temporal_events", [])
         exclusion_events = exclusion_criteria.get("temporal_events", [])
-        temporal_events = bool(inclusion_events) # Only inclusion_events matter for cohort dates
+        temporal_events = bool(inclusion_events)  # Only inclusion_events matter for cohort dates
         all_domains = self._extract_domains(inclusion_events + exclusion_events)
         # Filter DOMAIN_MAPPING to exclude domains with table: None
-        valid_domains = {k: v for k, v in DOMAIN_MAPPING.items() if v.get('table')}
+        valid_domains = {k: v for k, v in DOMAIN_MAPPING.items() if v.get("table")}
         ranked_domains = {dt: valid_domains[dt] for dt in all_domains if dt in valid_domains}
 
         if not temporal_events:
@@ -71,11 +71,12 @@ def build_query_cohort_creation(self, cohort_config: dict) -> str:
             inclusion_criteria=inclusion_criteria,
             exclusion_criteria=exclusion_criteria,
             ranked_domains=ranked_domains,
-            temporal_events=temporal_events
+            temporal_events=temporal_events,
         )
 
-    def build_concept_prevalence_query(self, db_schema: str, omop_alias: str, concept_type: str, cid: int,
-                                       filter_count: int, vocab: str) -> str:
+    def build_concept_prevalence_query(
+        self, db_schema: str, omop_alias: str, concept_type: str, cid: int, filter_count: int, vocab: str
+    ) -> str:
         """
         Build a SQL query for concept prevalence statistics for a given domain and cohort.
         :param db_schema: BiasDatabase database schema under which all tables are stored.
@@ -106,7 +107,7 @@ def build_concept_prevalence_query(self, db_schema: str, omop_alias: str, concep
             start_date_column=DOMAIN_MAPPING[concept_type]["start_date"],
             cid=cid,
             filter_count=filter_count,
-            vocab=effective_vocab
+            vocab=effective_vocab,
         )
 
     @staticmethod
@@ -152,12 +153,11 @@ def render_event(event):
                         {adjusted_start} AS adjusted_start,
                         {adjusted_end} AS adjusted_end
                     FROM {rank_table}
-                    WHERE concept_id = {event['event_concept_id']}{instance_condition}
+                    WHERE concept_id = {event["event_concept_id"]}{instance_condition}
                 """
 
         return base_sql
 
-
     @staticmethod
     def render_event_group(event_group, alias_prefix="evt"):
         """
@@ -169,7 +169,7 @@ def render_event_group(event_group, alias_prefix="evt"):
         Returns:
             str: SQL query string for the event group.
         """
-        queries = [] # accumulate SQL queries when called recursively with nested event groups
+        queries = []  # accumulate SQL queries when called recursively with nested event groups
         if "events" not in event_group:  # Single event
             return CohortQueryBuilder.render_event(event_group)
         else:
@@ -177,7 +177,7 @@ def render_event_group(event_group, alias_prefix="evt"):
                 event_sql = CohortQueryBuilder.render_event_group(event, f"{alias_prefix}_{i}")
                 if event_sql:
                     queries.append(event_sql)
-            if not queries: # pragma: no cover
+            if not queries:  # pragma: no cover
                 return ""
 
             if event_group["operator"] == "AND":
@@ -199,7 +199,7 @@ def render_event_group(event_group, alias_prefix="evt"):
                 combined_sql = f"""
                     SELECT person_id, event_start_date, event_end_date, adjusted_start, adjusted_end
                     FROM (
-                        {' UNION ALL '.join(f'({q})' for q in queries)}
+                        {" UNION ALL ".join(f"({q})" for q in queries)}
                     ) AS all_events
                     WHERE person_id IN (
                         {person_id_sql}
@@ -208,8 +208,10 @@ def render_event_group(event_group, alias_prefix="evt"):
                 return combined_sql
 
             elif event_group["operator"] == "OR":
-                return (f"SELECT person_id, event_start_date, event_end_date, adjusted_start, adjusted_end "
-                        f"FROM ({' UNION '.join(queries)}) AS {alias_prefix}_or")
+                return (
+                    f"SELECT person_id, event_start_date, event_end_date, adjusted_start, adjusted_end "
+                    f"FROM ({' UNION '.join(queries)}) AS {alias_prefix}_or"
+                )
             elif event_group["operator"] == "NOT":
                 not_query = queries[0]
                 # Return a query that selects all persons from a base table (e.g., person),
@@ -226,12 +228,12 @@ def render_event_group(event_group, alias_prefix="evt"):
                 if len(queries) == 1:
                     # the other query is the timestamp event which has to be handled here as it depends on the other
                     # event in the BEFORE operator
-                    timestamp_event = next((e for e in event_group['events'] if e["event_type"] == "date"), None)
-                    non_timestamp_event = next((e for e in event_group['events'] if e["event_type"] != "date"), None)
+                    timestamp_event = next((e for e in event_group["events"] if e["event_type"] == "date"), None)
+                    non_timestamp_event = next((e for e in event_group["events"] if e["event_type"] != "date"), None)
                     if timestamp_event and non_timestamp_event:
                         timestamp = timestamp_event["timestamp"]
-                        timestamp_event_index = event_group['events'].index(timestamp_event)
-                        non_timestamp_event_index = event_group['events'].index(non_timestamp_event)
+                        timestamp_event_index = event_group["events"].index(timestamp_event)
+                        non_timestamp_event_index = event_group["events"].index(non_timestamp_event)
                         if timestamp_event_index < non_timestamp_event_index:
                             # timestamp needs to happen before non-timestamp event
                             return f"""
@@ -273,7 +275,7 @@ def render_event_group(event_group, alias_prefix="evt"):
                             """
             return ""  # pragma: no cover
 
-    def temporal_event_filter(self, event_groups, alias='c'):
+    def temporal_event_filter(self, event_groups, alias="c"):
         """
         Generates the SQL filter for temporal event criteria.
 
@@ -289,14 +291,14 @@ def temporal_event_filter(self, event_groups, alias='c'):
         for i, event_group in enumerate(event_groups):
             group_sql = self.render_event_group(event_group)
             if group_sql:
-                if alias == 'ex':
+                if alias == "ex":
                     # exclusion criteria
                     filters.append(f"AND {alias}.person_id IN (SELECT person_id FROM ({group_sql}) AS ex_subquery_{i})")
                 else:
                     filters.append(f"({group_sql})")
         if not filters:  # pragma: no cover
             return ""
-        if alias == 'ex':
+        if alias == "ex":
             # For exclusion, combine with AND as filters
             return " ".join(filters)
         else:
@@ -316,9 +318,11 @@ def temporal_event_filter(self, event_groups, alias='c'):
                 #       events:
                 #         - event_type: drug_exposure
                 #           event_concept_id: 67890
-                return (f"SELECT person_id, event_start_date, event_end_date, "
-                        f"adjusted_start, adjusted_end FROM "
-                        f"({' UNION ALL '.join(filters)}) AS combined_events")
+                return (
+                    f"SELECT person_id, event_start_date, event_end_date, "
+                    f"adjusted_start, adjusted_end FROM "
+                    f"({' UNION ALL '.join(filters)}) AS combined_events"
+                )
 
             # Single event group case with operator defined
             return filters[0]
diff --git a/biasanalyzer/concept.py b/biasanalyzer/concept.py
index 7aa77f5..5d86989 100644
--- a/biasanalyzer/concept.py
+++ b/biasanalyzer/concept.py
@@ -62,8 +62,9 @@ def to_dict(self, include_children: bool = True, include_union_metrics: bool = F
             "parent_ids": list(self._ch.graph.predecessors(self.id)),
         }
         if include_children:
-            data["children"] = [c.to_dict(include_children=True, include_union_metrics=include_union_metrics)
-                                for c in self.children]
+            data["children"] = [
+                c.to_dict(include_children=True, include_union_metrics=include_union_metrics) for c in self.children
+            ]
 
         return data
 
@@ -87,8 +88,9 @@ def _normalize_identifier(identifier: str) -> str:
             return "+".join(parts)
 
     @classmethod
-    def build_concept_hierarchy_from_results(cls, cohort_id: int, concept_type: str, results: List[dict],
-                                             filter_count=0, vocab=None):
+    def build_concept_hierarchy_from_results(
+        cls, cohort_id: int, concept_type: str, results: List[dict], filter_count=0, vocab=None
+    ):
         """
         build concept hierarchy tree managed by networkx from list of dicts returned from the concept prevalence SQL
         with cache management. cohort_id, concept_type, and filter_count are used for caching to uniquely identify
@@ -148,7 +150,7 @@ def get_root_nodes(self, serialization: bool = False) -> List:
         roots = [n for n in self.graph.nodes if self.graph.in_degree(n) == 0]
         root_nodes = [ConceptNode(r, self) for r in roots]
         if serialization:
-            return [rn.to_dict(include_children=False)  for rn in root_nodes]
+            return [rn.to_dict(include_children=False) for rn in root_nodes]
         else:
             return root_nodes
 
@@ -160,8 +162,7 @@ def get_leaf_nodes(self, serialization: bool = False) -> List:
         else:
             return leave_nodes
 
-    def iter_nodes(self, root_id: int, order: str = "bfs",
-                   serialization: bool = False):
+    def iter_nodes(self, root_id: int, order: str = "bfs", serialization: bool = False):
         """Iterate nodes in BFS or DFS order from a given root."""
         if root_id not in self.graph.nodes:
             raise ValueError(f"Root node {root_id} not found in graph.")
@@ -188,9 +189,7 @@ def iter_nodes(self, root_id: int, order: str = "bfs",
             raise ValueError("order must be 'bfs' or 'dfs'")
 
     def union(self, other: "ConceptHierarchy") -> "ConceptHierarchy":
-        new_ident = ConceptHierarchy._normalize_identifier(
-            f"{self.identifier}+{other.identifier}"
-        )
+        new_ident = ConceptHierarchy._normalize_identifier(f"{self.identifier}+{other.identifier}")
         if new_ident in ConceptHierarchy._graph_cache:
             return ConceptHierarchy._graph_cache[new_ident]
 
@@ -218,8 +217,17 @@ def to_dict(self, root_id: Optional[int] = None, include_union_metrics: bool = F
         if root_id is not None:
             if root_id not in self.graph:
                 raise ValueError(f"Input concept id {root_id} not found in the concept hierarchy graph")
-            return {"hierarchy": [ConceptNode(root_id, self).to_dict(include_children=True,
-                                                                     include_union_metrics=include_union_metrics)]}
+            return {
+                "hierarchy": [
+                    ConceptNode(root_id, self).to_dict(
+                        include_children=True, include_union_metrics=include_union_metrics
+                    )
+                ]
+            }
 
-        return {"hierarchy": [r.to_dict(include_children=True, include_union_metrics=include_union_metrics)
-                              for r in self.get_root_nodes()]}
+        return {
+            "hierarchy": [
+                r.to_dict(include_children=True, include_union_metrics=include_union_metrics)
+                for r in self.get_root_nodes()
+            ]
+        }
diff --git a/biasanalyzer/config.py b/biasanalyzer/config.py
index 657a2ab..7acd211 100644
--- a/biasanalyzer/config.py
+++ b/biasanalyzer/config.py
@@ -11,7 +11,7 @@ def load_config(config_file):
 
 
 def load_cohort_creation_config(config_file):
-    with open(config_file, encoding='utf-8') as f:
+    with open(config_file, encoding="utf-8") as f:
         config = yaml.safe_load(f)
         CohortCreationConfig(**config)
         return config
diff --git a/biasanalyzer/database.py b/biasanalyzer/database.py
index 33de5a0..e1e8b9f 100644
--- a/biasanalyzer/database.py
+++ b/biasanalyzer/database.py
@@ -1,4 +1,3 @@
-# ruff: noqa: S608
 import gc
 from datetime import datetime
 from typing import Optional
@@ -31,9 +30,10 @@ class BiasDatabase:
         "age": AGE_STATS_QUERY,
         "gender": GENDER_STATS_QUERY,
         "race": RACE_STATS_QUERY,
-        "ethnicity": ETHNICITY_STATS_QUERY
+        "ethnicity": ETHNICITY_STATS_QUERY,
     }
     _instance = None  # indicating a singleton with only one instance of the class ever created
+
     def __new__(cls, *args, **kwargs):
         if cls._instance is None:
             cls._instance = super().__new__(cls)
@@ -44,17 +44,17 @@ def _initialize(self, db_url, omop_db_url=None):
         # by default, duckdb uses in memory database
         self.conn = duckdb.connect(db_url)
         self.schema = "biasanalyzer"
-        self.omop_alias = 'omop'
+        self.omop_alias = "omop"
         self.conn.execute(f"CREATE SCHEMA IF NOT EXISTS {self.schema}")
         self.omop_cdm_db_url = omop_db_url
         if omop_db_url is not None:
-            if omop_db_url.startswith('postgresql://'):
+            if omop_db_url.startswith("postgresql://"):
                 # omop db is postgreSQL
                 self.load_postgres_extension()
                 self.conn.execute(f"""            
                             ATTACH '{self.omop_cdm_db_url}' as {self.omop_alias} (TYPE postgres)
                             """)
-            elif omop_db_url.endswith('.duckdb'):
+            elif omop_db_url.endswith(".duckdb"):
                 self.conn.execute(f"""
                             ATTACH '{self.omop_cdm_db_url}' as {self.omop_alias}
                             """)
@@ -69,13 +69,13 @@ def _initialize(self, db_url, omop_db_url=None):
 
     def _create_cohort_definition_table(self):
         try:
-            self.conn.execute(f'CREATE SEQUENCE {self.schema}.id_sequence START 1')
+            self.conn.execute(f"CREATE SEQUENCE {self.schema}.id_sequence START 1")
         except duckdb.Error as e:
             if "already exists" in str(e).lower():
                 notify_users("Sequence already exists, skipping creation.")
             else:
                 raise
-        self.conn.execute(f'''
+        self.conn.execute(f"""
             CREATE TABLE IF NOT EXISTS {self.schema}.cohort_definition (
                       id INTEGER DEFAULT nextval('{self.schema}.id_sequence'), 
                       name VARCHAR NOT NULL, 
@@ -85,11 +85,11 @@ def _create_cohort_definition_table(self):
                       created_by VARCHAR,
                       PRIMARY KEY (id)
                       )
-                ''')
+                """)
         notify_users("Cohort Definition table created.")
 
     def _create_cohort_table(self):
-        self.conn.execute(f'''
+        self.conn.execute(f"""
             CREATE TABLE IF NOT EXISTS {self.schema}.cohort (
                 subject_id BIGINT,
                 cohort_definition_id INTEGER,
@@ -97,12 +97,12 @@ def _create_cohort_table(self):
                 cohort_end_date DATE,
                 FOREIGN KEY (cohort_definition_id) REFERENCES {self.schema}.cohort_definition(id)
             )
-        ''')
+        """)
         try:
-            self.conn.execute(f'''
+            self.conn.execute(f"""
                 CREATE INDEX idx_cohort_dates ON {self.schema}.cohort (cohort_definition_id, cohort_start_date, 
                 cohort_end_date);
-            ''')
+            """)
         except duckdb.Error as e:
             if "already exists" in str(e).lower():
                 notify_users("Index already exists, skipping creation.")
@@ -115,16 +115,19 @@ def load_postgres_extension(self):
         self.conn.execute("LOAD postgres;")
 
     def create_cohort_definition(self, cohort_definition: CohortDefinition, progress_obj=None):
-        self.conn.execute(f'''
+        self.conn.execute(
+            f"""
             INSERT INTO {self.schema}.cohort_definition (name, description, created_date, creation_info, created_by)
             VALUES (?, ?, ?, ?, ?)
-        ''', (
-            cohort_definition.name,
-            cohort_definition.description,
-            cohort_definition.created_date or datetime.now(),
-            cohort_definition.creation_info,
-            cohort_definition.created_by
-        ))
+        """,
+            (
+                cohort_definition.name,
+                cohort_definition.description,
+                cohort_definition.created_date or datetime.now(),
+                cohort_definition.creation_info,
+                cohort_definition.created_by,
+            ),
+        )
         if progress_obj is None:
             notify_users("Cohort definition inserted successfully.")  # pragma: no cover
         else:
@@ -137,16 +140,16 @@ def create_cohort_definition(self, cohort_definition: CohortDefinition, progress
     def create_cohort_in_bulk(self, cohort_df: pd.DataFrame):
         # make duckdb to treat cohort_df dataframe as a virtual table named "cohort_df"
         self.conn.register("cohort_df", cohort_df)
-        self.conn.execute(f'''
+        self.conn.execute(f"""
             INSERT INTO {self.schema}.cohort (subject_id, cohort_definition_id, cohort_start_date, cohort_end_date)
             SELECT subject_id, cohort_definition_id, cohort_start_date, cohort_end_date FROM cohort_df
-        ''')
+        """)
 
     def get_cohort_definition(self, cohort_definition_id):
-        results = self.conn.execute(f'''
+        results = self.conn.execute(f"""
         SELECT id, name, description, created_date, creation_info, created_by FROM {self.schema}.cohort_definition 
         WHERE id = {cohort_definition_id} 
-        ''')
+        """)
         headers = [desc[0] for desc in results.description]
         row = results.fetchall()
         if len(row) == 0:
@@ -155,10 +158,10 @@ def get_cohort_definition(self, cohort_definition_id):
             return dict(zip(headers, row[0]))
 
     def get_cohort(self, cohort_definition_id):
-        results = self.conn.execute(f'''
+        results = self.conn.execute(f"""
         SELECT subject_id, cohort_definition_id, cohort_start_date, cohort_end_date FROM {self.schema}.cohort 
         WHERE cohort_definition_id = {cohort_definition_id}
-        ''')
+        """)
         headers = [desc[0] for desc in results.description]
         rows = results.fetchall()
         return [dict(zip(headers, row)) for row in rows]
@@ -170,7 +173,7 @@ def _execute_query(self, query_str):
         rows = results.fetchall()
         return [dict(zip(headers, row)) for row in rows]
 
-    def get_cohort_basic_stats(self, cohort_definition_id: int, variable=''):
+    def get_cohort_basic_stats(self, cohort_definition_id: int, variable=""):
         """
         Get aggregation statistics for a cohort from the cohort table.
         :param cohort_definition_id: cohort definition id representing the cohort
@@ -183,13 +186,16 @@ def get_cohort_basic_stats(self, cohort_definition_id: int, variable=''):
             if variable:
                 query_str = self.__class__.stats_queries.get(variable)
                 if query_str is None:
-                    raise ValueError(f"Statistics for variable '{variable}' is not available. "
-                                     f"Valid variables are {self.__class__.stats_queries.keys()}")
-                stats_query = query_str.format(ba_schema=self.schema, omop=self.omop_alias,
-                                               cohort_definition_id=cohort_definition_id)
+                    raise ValueError(
+                        f"Statistics for variable '{variable}' is not available. "
+                        f"Valid variables are {self.__class__.stats_queries.keys()}"
+                    )
+                stats_query = query_str.format(
+                    ba_schema=self.schema, omop=self.omop_alias, cohort_definition_id=cohort_definition_id
+                )
             else:
                 # Query the cohort data to get basic statistics
-                stats_query = f'''
+                stats_query = f"""
                     WITH cohort_Duration AS (
                         SELECT
                             subject_id,
@@ -212,11 +218,11 @@ def get_cohort_basic_stats(self, cohort_definition_id: int, variable=''):
                         CAST(PERCENTILE_CONT(0.5) WITHIN GROUP (ORDER BY duration_days) AS INT) AS median_duration,
                         ROUND(STDDEV(duration_days), 2) AS stddev_duration
                     FROM cohort_Duration                    
-                '''
+                """
             return self._execute_query(stats_query)
 
         except Exception as e:
-            notify_users(f"Error computing cohort basic statistics: {e}", level='error')
+            notify_users(f"Error computing cohort basic statistics: {e}", level="error")
             return None
 
     @property
@@ -230,18 +236,27 @@ def get_cohort_distributions(self, cohort_definition_id: int, variable: str):
         try:
             query_str = self.__class__.distribution_queries.get(variable)
             if not query_str:
-                raise ValueError(f"Distribution for variable '{variable}' is not available. "
-                                 f"Valid variables are {self.__class__.distribution_queries.keys()}")
-            query = query_str.format(ba_schema=self.schema, omop=self.omop_alias,
-                                     cohort_definition_id=cohort_definition_id)
+                raise ValueError(
+                    f"Distribution for variable '{variable}' is not available. "
+                    f"Valid variables are {self.__class__.distribution_queries.keys()}"
+                )
+            query = query_str.format(
+                ba_schema=self.schema, omop=self.omop_alias, cohort_definition_id=cohort_definition_id
+            )
             return self._execute_query(query)
         except Exception as e:
-            notify_users(f"Error computing cohort {variable} distributions: {e}", level='error')
+            notify_users(f"Error computing cohort {variable} distributions: {e}", level="error")
             return None
 
-    def get_cohort_concept_stats(self, cohort_definition_id: int, qry_builder,
-                                 concept_type='condition_occurrence', filter_count=0, vocab=None,
-                                 print_concept_hierarchy=False):
+    def get_cohort_concept_stats(
+        self,
+        cohort_definition_id: int,
+        qry_builder,
+        concept_type="condition_occurrence",
+        filter_count=0,
+        vocab=None,
+        print_concept_hierarchy=False,
+    ):
         """
         Get concept statistics for a cohort from the cohort table.
         """
@@ -251,30 +266,36 @@ def get_cohort_concept_stats(self, cohort_definition_id: int, qry_builder,
             # validate input vocab if it is not None
             if vocab is not None:
                 valid_vocabs = self._execute_query(f"SELECT distinct vocabulary_id FROM {self.omop_alias}.concept")
-                valid_vocab_ids = [row['vocabulary_id'] for row in valid_vocabs]
+                valid_vocab_ids = [row["vocabulary_id"] for row in valid_vocabs]
                 if vocab not in valid_vocab_ids:
-                    err_msg = (f"input {vocab} is not a valid vocabulary in OMOP. "
-                               f"Supported vocabulary ids are: {valid_vocab_ids}")
-                    notify_users(err_msg, level='error')
+                    err_msg = (
+                        f"input {vocab} is not a valid vocabulary in OMOP. "
+                        f"Supported vocabulary ids are: {valid_vocab_ids}"
+                    )
+                    notify_users(err_msg, level="error")
                     raise ValueError(err_msg)
 
-            query = qry_builder.build_concept_prevalence_query(self.schema, self.omop_alias, concept_type,
-                                                               cohort_definition_id, filter_count, vocab)
+            query = qry_builder.build_concept_prevalence_query(
+                self.schema, self.omop_alias, concept_type, cohort_definition_id, filter_count, vocab
+            )
             concept_stats[concept_type] = self._execute_query(query)
             cs_df = pd.DataFrame(concept_stats[concept_type])
             # Combine concept_name and prevalence into a "details" column
             cs_df["details"] = cs_df.apply(
                 lambda row: f"{row['concept_name']} (Code: {row['concept_code']}, "
-                            f"Count: {row['count_in_cohort']}, Prevalence: {row['prevalence']:.3%})", axis=1)
+                f"Count: {row['count_in_cohort']}, Prevalence: {row['prevalence']:.3%})",
+                axis=1,
+            )
 
             if print_concept_hierarchy:
-                filtered_cs_df = cs_df[cs_df['ancestor_concept_id'] != cs_df['descendant_concept_id']]
+                filtered_cs_df = cs_df[cs_df["ancestor_concept_id"] != cs_df["descendant_concept_id"]]
                 roots = find_roots(filtered_cs_df)
                 hierarchy = build_concept_hierarchy(filtered_cs_df)
-                notify_users(f'cohort concept hierarchy for {concept_type} with root concept ids {roots}:')
+                notify_users(f"cohort concept hierarchy for {concept_type} with root concept ids {roots}:")
                 for root in roots:
-                    root_detail = cs_df[(cs_df['ancestor_concept_id'] == root)
-                              & (cs_df['descendant_concept_id'] == root)]['details'].iloc[0]
+                    root_detail = cs_df[
+                        (cs_df["ancestor_concept_id"] == root) & (cs_df["descendant_concept_id"] == root)
+                    ]["details"].iloc[0]
                     print_hierarchy(hierarchy, parent=root, level=0, parent_details=root_detail)
             return concept_stats
         except Exception as e:
@@ -290,6 +311,7 @@ def close(self):
 class OMOPCDMDatabase:
     _instance = None  # indicating a singleton with only one instance of the class ever created
     _database_type = None
+
     def __new__(cls, *args, **kwargs):
         if cls._instance is None:
             cls._instance = super().__new__(cls)
@@ -297,39 +319,39 @@ def __new__(cls, *args, **kwargs):
         return cls._instance
 
     def _initialize(self, db_url):
-        if db_url.endswith('.duckdb'):
+        if db_url.endswith(".duckdb"):
             # close any potential global connections if any
-            for obj in gc.get_objects(): # pragma: no cover
+            for obj in gc.get_objects():  # pragma: no cover
                 if isinstance(obj, duckdb.DuckDBPyConnection):
                     try:
                         obj.close()
                     except Exception as e:
-                        notify_users(f'failed to close the lingering duckdb connection before opening a new one: {e}')
+                        notify_users(f"failed to close the lingering duckdb connection before opening a new one: {e}")
 
             # Handle DuckDB connection
             try:
                 self.engine = duckdb.connect(db_url)
                 notify_users(f"Connected to the DuckDB database: {db_url}.")
             except duckdb.Error as e:  # pragma: no cover
-                notify_users(f"Failed to connect to DuckDB: {e}", level='error')
+                notify_users(f"Failed to connect to DuckDB: {e}", level="error")
             self.Session = self.engine  # Use engine directly for DuckDB
-            self._database_type = 'duckdb'
+            self._database_type = "duckdb"
         else:  # pragma: no cover
             # Handle PostgreSQL connection
             try:
                 self.engine = create_engine(
                     db_url,
                     echo=False,
-                    connect_args={'options': '-c default_transaction_read_only=on'}  # Enforce read-only transactions
+                    connect_args={"options": "-c default_transaction_read_only=on"},  # Enforce read-only transactions
                 )
                 self.Session = sessionmaker(bind=self.engine)
                 notify_users("Connected to the OMOP CDM database (read-only).")
-                self._database_type = 'postgresql'
+                self._database_type = "postgresql"
             except SQLAlchemyError as e:
-                notify_users(f"Failed to connect to the database: {e}", level='error')
+                notify_users(f"Failed to connect to the database: {e}", level="error")
 
     def get_session(self):
-        if self._database_type == 'duckdb':
+        if self._database_type == "duckdb":
             return self.engine
         else:  # pragma: no cover
             # postgresql connection: provide a new session for read-only queries
@@ -337,7 +359,7 @@ def get_session(self):
 
     def execute_query(self, query, params=None):
         try:
-            if self._database_type == 'duckdb':
+            if self._database_type == "duckdb":
                 # DuckDB query execution
                 results = self.engine.execute(query, params).fetchall()
                 headers = [desc[0] for desc in self.engine.execute(query, params).description]
@@ -353,10 +375,10 @@ def execute_query(self, query, params=None):
             return [dict(zip(headers, row)) for row in results]
 
         except duckdb.Error as e:
-            notify_users(f"Error executing query: {e}", level='error')
+            notify_users(f"Error executing query: {e}", level="error")
             return []
         except SQLAlchemyError as e:  # pragma: no cover
-            notify_users(f"Error executing query: {e}", level='error')
+            notify_users(f"Error executing query: {e}", level="error")
             if omop_session:
                 omop_session.close()
             return []
@@ -370,11 +392,11 @@ def get_domains_and_vocabularies(self) -> list:
 
     def get_concepts(self, search_term: str, domain: Optional[str], vocab: Optional[str]) -> list:
         search_term_exact = search_term.lower()
-        search_term_suffix = f'{search_term_exact} '
-        search_term_prefix = f' {search_term_exact}'
-        search_term_prefix_suffix = f' {search_term_exact} '
+        search_term_suffix = f"{search_term_exact} "
+        search_term_prefix = f" {search_term_exact}"
+        search_term_prefix_suffix = f" {search_term_exact} "
 
-        if self._database_type == 'duckdb':
+        if self._database_type == "duckdb":
             # Use positional parameters and ? as placeholder to meet duckdb syntax requirement
             base_query = """
                          SELECT concept_id, concept_name, valid_start_date, valid_end_date, domain_id, vocabulary_id \
@@ -394,16 +416,20 @@ def get_concepts(self, search_term: str, domain: Optional[str], vocab: Optional[
 
             if domain is not None and vocab is not None:
                 condition_str = "domain_id = ? AND vocabulary_id = ?"
-                params = [domain, vocab, search_term_exact, search_term_prefix, search_term_suffix,
-                              search_term_prefix_suffix]
+                params = [
+                    domain,
+                    vocab,
+                    search_term_exact,
+                    search_term_prefix,
+                    search_term_suffix,
+                    search_term_prefix_suffix,
+                ]
             elif domain is None:
                 condition_str = "vocabulary_id = ?"
-                params = [vocab, search_term_exact, search_term_prefix, search_term_suffix,
-                              search_term_prefix_suffix]
+                params = [vocab, search_term_exact, search_term_prefix, search_term_suffix, search_term_prefix_suffix]
             else:
                 condition_str = "domain_id = ?"
-                params = [domain, search_term_exact, search_term_prefix, search_term_suffix,
-                              search_term_prefix_suffix]
+                params = [domain, search_term_exact, search_term_prefix, search_term_suffix, search_term_prefix_suffix]
 
         else:  # pragma: no cover
             # Use named parameters with :param_name syntax for SQLAlchemy/PostgreSQL
@@ -427,19 +453,19 @@ def get_concepts(self, search_term: str, domain: Optional[str], vocab: Optional[
                 "search_term_exact": search_term_exact,
                 "search_term_prefix": search_term_prefix,
                 "search_term_suffix": search_term_suffix,
-                "search_term_prefix_suffix": search_term_prefix_suffix
+                "search_term_prefix_suffix": search_term_prefix_suffix,
             }
 
             if domain is not None and vocab is not None:
                 condition_str = "domain_id = :domain AND vocabulary_id = :vocabulary"
-                params['domain'] = domain
-                params['vocabulary'] = vocab
+                params["domain"] = domain
+                params["vocabulary"] = vocab
             elif domain is None:
                 condition_str = "vocabulary_id = :vocabulary"
-                params['vocabulary'] = vocab
+                params["vocabulary"] = vocab
             else:
                 condition_str = "domain_id = :domain"
-                params['domain'] = domain
+                params["domain"] = domain
 
         query = base_query.format(condition_str=condition_str)
         return self.execute_query(query, params=params)
@@ -453,11 +479,7 @@ def get_concept_hierarchy(self, concept_id: int):
             # this check is important to avoid SQL injection risk
             raise ValueError("concept_id must be an integer")
 
-        stages = [
-            "Queried concept hierarchy",
-            "Fetched concept details",
-            "Built hierarchy tree"
-        ]
+        stages = ["Queried concept hierarchy", "Fetched concept details", "Built hierarchy tree"]
         progress = tqdm(total=len(stages), desc="Concept Hierarchy", unit="stage")
 
         progress.set_postfix_str(stages[0])
@@ -484,8 +506,9 @@ def get_concept_hierarchy(self, concept_id: int):
 
         progress.set_postfix_str(stages[1])
         # Collect all unique concept IDs involved in the hierarchy using set comprehension
-        concept_ids = {row['ancestor_concept_id'] for row in results} | {row['descendant_concept_id']
-                                                                         for row in results}
+        concept_ids = {row["ancestor_concept_id"] for row in results} | {
+            row["descendant_concept_id"] for row in results
+        }
         # Fetch details of each concept
         concept_details = {}
         if concept_ids:
@@ -498,7 +521,7 @@ def get_concept_hierarchy(self, concept_id: int):
                     """
 
             result = self.execute_query(query)
-            concept_details = {row['concept_id']: row for row in result}
+            concept_details = {row["concept_id"]: row for row in result}
         progress.update(1)
 
         progress.set_postfix_str(stages[2])
@@ -506,19 +529,23 @@ def get_concept_hierarchy(self, concept_id: int):
         hierarchy = {}
         reverse_hierarchy = {}
         for row in results:
-            ancestor_id = row['ancestor_concept_id']
-            descendant_id = row['descendant_concept_id']
+            ancestor_id = row["ancestor_concept_id"]
+            descendant_id = row["descendant_concept_id"]
 
             ancestor_entry = hierarchy.setdefault(
-                ancestor_id, {"details": concept_details[ancestor_id], "children": []})
+                ancestor_id, {"details": concept_details[ancestor_id], "children": []}
+            )
             descendant_entry = hierarchy.setdefault(
-                descendant_id, {"details": concept_details[descendant_id], "children": []})
+                descendant_id, {"details": concept_details[descendant_id], "children": []}
+            )
             ancestor_entry["children"].append(descendant_entry)
 
             desc_entry_rev = reverse_hierarchy.setdefault(
-                descendant_id, {"details": concept_details[descendant_id], "parents": []})
+                descendant_id, {"details": concept_details[descendant_id], "parents": []}
+            )
             ancestor_entry_rev = reverse_hierarchy.setdefault(
-                ancestor_id, {"details": concept_details[ancestor_id], "parents": []})
+                ancestor_id, {"details": concept_details[ancestor_id], "parents": []}
+            )
             desc_entry_rev["parents"].append(ancestor_entry_rev)
         progress.update(1)
         progress.close()
@@ -526,7 +553,6 @@ def get_concept_hierarchy(self, concept_id: int):
         # Return the parent hierarchy and children hierarchy of the specified concept
         return reverse_hierarchy[concept_id], hierarchy[concept_id]
 
-
     def close(self):
         if isinstance(self.engine, duckdb.DuckDBPyConnection):
             self.engine.close()
diff --git a/biasanalyzer/models.py b/biasanalyzer/models.py
index d935f73..35bbbc7 100644
--- a/biasanalyzer/models.py
+++ b/biasanalyzer/models.py
@@ -9,50 +9,50 @@
         "concept_id": "condition_concept_id",
         "start_date": "condition_start_date",
         "end_date": "condition_end_date",
-        "default_vocab": "SNOMED"  # for use by concept prevalence query
+        "default_vocab": "SNOMED",  # for use by concept prevalence query
     },
     "drug_exposure": {
         "table": "drug_exposure",
         "concept_id": "drug_concept_id",
         "start_date": "drug_exposure_start_date",
         "end_date": "drug_exposure_end_date",
-        "default_vocab": "RxNorm"  # for use by concept prevalence query
+        "default_vocab": "RxNorm",  # for use by concept prevalence query
     },
     "procedure_occurrence": {
         "table": "procedure_occurrence",
         "concept_id": "procedure_concept_id",
         "start_date": "procedure_date",
         "end_date": "procedure_date",
-        "default_vocab": "SNOMED"  # for use by concept prevalence query
+        "default_vocab": "SNOMED",  # for use by concept prevalence query
     },
     "visit_occurrence": {
         "table": "visit_occurrence",
         "concept_id": "visit_concept_id",
         "start_date": "visit_start_date",
         "end_date": "visit_end_date",
-        "default_vocab": "SNOMED"  # for use by concept prevalence query
+        "default_vocab": "SNOMED",  # for use by concept prevalence query
     },
     "measurement": {
         "table": "measurement",
         "concept_id": "measurement_concept_id",
         "start_date": "measurement_date",
         "end_date": "measurement_date",
-        "default_vocab": "LOINC"  # for use by concept prevalence query
+        "default_vocab": "LOINC",  # for use by concept prevalence query
     },
     "observation": {
         "table": "observation",
         "concept_id": "observation_concept_id",
         "start_date": "observation_date",
         "end_date": "observation_date",
-        "default_vocab": "SNOMED"  # for use by concept prevalence query
+        "default_vocab": "SNOMED",  # for use by concept prevalence query
     },
     "date": {  # Special case for static timestamps
         "table": None,
         "concept_id": None,
         "start_date": "timestamp",
-       "end_date": "timestamp",
-        "default_vocab": None
-    }
+        "end_date": "timestamp",
+        "default_vocab": None,
+    },
 }
 
 EVENT_TYPE_LITERAL = Literal[tuple(DOMAIN_MAPPING.keys())]
@@ -60,7 +60,7 @@
 
 ###===========System Configuration==============###
 class RootOMOPCDM(BaseModel):
-    model_config = ConfigDict(extra='ignore')
+    model_config = ConfigDict(extra="ignore")
     username: StrictStr
     password: StrictStr
     hostname: StrictStr
@@ -69,10 +69,13 @@ class RootOMOPCDM(BaseModel):
 
 
 class Configuration(BaseModel):
-    model_config = ConfigDict(extra='ignore')
+    model_config = ConfigDict(extra="ignore")
     root_omop_cdm_database: RootOMOPCDM
+
+
 ###===========System Configuration==============###
 
+
 ###===========CohortDefinition Model==============###
 class CohortDefinition(BaseModel):
     model_config = ConfigDict(from_attributes=True)
@@ -81,8 +84,11 @@ class CohortDefinition(BaseModel):
     created_date: date
     creation_info: str
     created_by: str
+
+
 ###===========CohortDefinition Model==============###
 
+
 ###===========Cohort Model====================###
 class Cohort(BaseModel):
     model_config = ConfigDict(from_attributes=True)
@@ -90,12 +96,15 @@ class Cohort(BaseModel):
     subject_id: int
     cohort_start_date: Optional[date]
     cohort_end_date: Optional[date]
+
+
 ###===========Cohort Model====================###
 
+
 ###=========CohortCreationConfig==================###
 class DemographicsCriteria(BaseModel):
     # Gender with "male" and "female" as valid input
-    gender: Optional[Literal['male', 'female']] = None
+    gender: Optional[Literal["male", "female"]] = None
     # Minimum birth year
     min_birth_year: Optional[int] = None
     max_birth_year: Optional[int] = None
@@ -165,7 +174,7 @@ def validate_events_list(cls, values):
 
         return values
 
-    def get_interval_sql(self, e1_alias='e1', e2_alias='e2') -> str:
+    def get_interval_sql(self, e1_alias="e1", e2_alias="e2") -> str:
         """Generate SQL for the interval."""
         if not self.interval:  # pragma: no cover
             return ""
@@ -184,4 +193,6 @@ class CohortCreationConfig(BaseModel):
     # cohort creation criteria
     inclusion_criteria: CohortCreationCriteria
     exclusion_criteria: Optional[CohortCreationCriteria] = None
+
+
 ###=========CohortCreationConfig==================###
diff --git a/biasanalyzer/module_test.py b/biasanalyzer/module_test.py
index fd1f572..b3c0093 100644
--- a/biasanalyzer/module_test.py
+++ b/biasanalyzer/module_test.py
@@ -8,55 +8,65 @@
 
 
 def cohort_creation_template_test(bias_obj):
-    cohort_data = bias_obj.create_cohort('COVID-19 patients', 'COVID-19 patients',
-                                         os.path.join(os.path.dirname(__file__), '..', 'tests', 'assets',
-                                                      'cohort_creation',
-                                                      'extras',
-                                                      'diabetes_example2',
-                                                      'cohort_creation_config_baseline_example2.yaml'),
-                                                      # 'covid_example3',
-                                                      # 'cohort_creation_config_baseline_example3.yaml'),
-                                                      # 'test_cohort_creation_condition_occurrence_config_study.yaml'),
-                                         'system')
+    cohort_data = bias_obj.create_cohort(
+        "COVID-19 patients",
+        "COVID-19 patients",
+        os.path.join(
+            os.path.dirname(__file__),
+            "..",
+            "tests",
+            "assets",
+            "cohort_creation",
+            "extras",
+            "diabetes_example2",
+            "cohort_creation_config_baseline_example2.yaml",
+        ),
+        # 'covid_example3',
+        # 'cohort_creation_config_baseline_example3.yaml'),
+        # 'test_cohort_creation_condition_occurrence_config_study.yaml'),
+        "system",
+    )
     if cohort_data:
         md = cohort_data.metadata
-        print(f'cohort_definition: {md}')
-        print(f'The first five records in the cohort {cohort_data.data[:5]}')
-        print(f'the cohort stats: {cohort_data.get_stats()}')
-        print(f'the cohort age stats: {cohort_data.get_stats("age")}')
-        print(f'the cohort gender stats: {cohort_data.get_stats("gender")}')
-        print(f'the cohort race stats: {cohort_data.get_stats("race")}')
-        print(f'the cohort ethnicity stats: {cohort_data.get_stats("ethnicity")}')
-        print(f'the cohort age distributions: {cohort_data.get_distributions("age")}')
-        print(f'the cohort gender distributions: {cohort_data.get_distributions("gender")}')
-        compare_stats = bias_obj.compare_cohorts(cohort_data.metadata['id'], cohort_data.metadata['id'])
-        print(f'compare_stats: {compare_stats}')
+        print(f"cohort_definition: {md}")
+        print(f"The first five records in the cohort {cohort_data.data[:5]}")
+        print(f"the cohort stats: {cohort_data.get_stats()}")
+        print(f"the cohort age stats: {cohort_data.get_stats('age')}")
+        print(f"the cohort gender stats: {cohort_data.get_stats('gender')}")
+        print(f"the cohort race stats: {cohort_data.get_stats('race')}")
+        print(f"the cohort ethnicity stats: {cohort_data.get_stats('ethnicity')}")
+        print(f"the cohort age distributions: {cohort_data.get_distributions('age')}")
+        print(f"the cohort gender distributions: {cohort_data.get_distributions('gender')}")
+        compare_stats = bias_obj.compare_cohorts(cohort_data.metadata["id"], cohort_data.metadata["id"])
+        print(f"compare_stats: {compare_stats}")
     return
 
 
 def condition_cohort_test(bias_obj):
-    baseline_cohort_query = ('SELECT c.person_id, MIN(c.condition_start_date) as cohort_start_date, '
-                             'MAX(c.condition_end_date) as cohort_end_date '
-                             'FROM condition_occurrence c JOIN '
-                             'person p ON c.person_id = p.person_id '
-                             'WHERE c.condition_concept_id = 201826 GROUP BY c.person_id')
-    cohort_data = bias_obj.create_cohort('Diabetics patients', 'Diabetics patients',
-                                         baseline_cohort_query, 'system')
+    baseline_cohort_query = (
+        "SELECT c.person_id, MIN(c.condition_start_date) as cohort_start_date, "
+        "MAX(c.condition_end_date) as cohort_end_date "
+        "FROM condition_occurrence c JOIN "
+        "person p ON c.person_id = p.person_id "
+        "WHERE c.condition_concept_id = 201826 GROUP BY c.person_id"
+    )
+    cohort_data = bias_obj.create_cohort("Diabetics patients", "Diabetics patients", baseline_cohort_query, "system")
     if cohort_data:
         md = cohort_data.metadata
-        print(f'cohort_definition: {md}')
-        print(f'The first five records in the cohort {cohort_data.data[:5]}')
-        print(f'the cohort stats: {cohort_data.get_stats()}')
-        print(f'the cohort age stats: {cohort_data.get_stats("age")}')
-        print(f'the cohort gender stats: {cohort_data.get_stats("gender")}')
-        print(f'the cohort race stats: {cohort_data.get_stats("race")}')
-        print(f'the cohort ethnicity stats: {cohort_data.get_stats("ethnicity")}')
-        print(f'the cohort age distributions: {cohort_data.get_distributions("age")}')
+        print(f"cohort_definition: {md}")
+        print(f"The first five records in the cohort {cohort_data.data[:5]}")
+        print(f"the cohort stats: {cohort_data.get_stats()}")
+        print(f"the cohort age stats: {cohort_data.get_stats('age')}")
+        print(f"the cohort gender stats: {cohort_data.get_stats('gender')}")
+        print(f"the cohort race stats: {cohort_data.get_stats('race')}")
+        print(f"the cohort ethnicity stats: {cohort_data.get_stats('ethnicity')}")
+        print(f"the cohort age distributions: {cohort_data.get_distributions('age')}")
         t1 = time.time()
-        _, cohort_concept_hierarchy = cohort_data.get_concept_stats(concept_type='condition_occurrence',
-                                                                    filter_count=5000)
+        _, cohort_concept_hierarchy = cohort_data.get_concept_stats(
+            concept_type="condition_occurrence", filter_count=5000
+        )
         concept_node = cohort_concept_hierarchy.get_node(concept_id=201826)
-        print(f'concept_node 201826 metric: {concept_node.get_metrics(md["id"])}')
+        print(f"concept_node 201826 metric: {concept_node.get_metrics(md['id'])}")
 
         # Print the root node
         root_nodes = cohort_concept_hierarchy.get_root_nodes()
@@ -69,53 +79,51 @@ def condition_cohort_test(bias_obj):
             print(node)
 
         hier_dict = cohort_concept_hierarchy.to_dict()
-        with open('diabetics_condition_occurrence_hierarchy_dict.txt', 'w') as cof:
+        with open("diabetics_condition_occurrence_hierarchy_dict.txt", "w") as cof:
             pprint.pprint(hier_dict, indent=2, stream=cof)
 
-
-        _, cohort_de_concept_hierarchy = cohort_data.get_concept_stats(concept_type='drug_exposure',
-                                                                       filter_count=500)
+        _, cohort_de_concept_hierarchy = cohort_data.get_concept_stats(concept_type="drug_exposure", filter_count=500)
         de_hier_dict = cohort_de_concept_hierarchy.to_dict()
-        with open('diabetics_drug_exposure_hierarchy_dict.txt', 'w') as dof:
+        with open("diabetics_drug_exposure_hierarchy_dict.txt", "w") as dof:
             pprint.pprint(de_hier_dict, indent=2, stream=dof)
         # compare_stats = bias_obj.compare_cohorts(cohort_data.metadata['id'], cohort_data.metadata['id'])
         # print(f'compare_stats: {compare_stats}')
-        print(f'times taken for computing cohort concept hierarcy: {time.time() - t1}')
+        print(f"times taken for computing cohort concept hierarcy: {time.time() - t1}")
     return
 
 
 def concept_test(bias_obj):
-    print(f'domains and vocabularies: \n{pd.DataFrame(bias_obj.get_domains_and_vocabularies())}')
+    print(f"domains and vocabularies: \n{pd.DataFrame(bias_obj.get_domains_and_vocabularies())}")
     # calling get_concepts() without passing in domain and vocabulary should raise an exception
     bias_obj.get_concepts("COVID-19")
     concepts = bias_obj.get_concepts("COVID-19", "Condition", "SNOMED")
-    print(f'concepts for COVID-19 in Condition domain with SNOMED vocabulary: \n{pd.DataFrame(concepts)}')
+    print(f"concepts for COVID-19 in Condition domain with SNOMED vocabulary: \n{pd.DataFrame(concepts)}")
     concepts = bias_obj.get_concepts("COVID-19", domain="Condition")
-    print(f'concepts for COVID-19 in Condition domain: \n{pd.DataFrame(concepts)}')
+    print(f"concepts for COVID-19 in Condition domain: \n{pd.DataFrame(concepts)}")
     concepts = bias_obj.get_concepts("COVID-19", vocabulary="SNOMED")
-    print(f'concepts for COVID-19 in SNOMED vocabulary: \n{pd.DataFrame(concepts)}')
+    print(f"concepts for COVID-19 in SNOMED vocabulary: \n{pd.DataFrame(concepts)}")
 
     parent_concept_tree, children_concept_tree = bias_obj.get_concept_hierarchy(37311061)
-    print('parent concept hierarchy for COVID-19 in text format:')
+    print("parent concept hierarchy for COVID-19 in text format:")
     print(bias_obj.display_concept_tree(parent_concept_tree))
-    print('children concept hierarchy for COVID-19 in text format:')
+    print("children concept hierarchy for COVID-19 in text format:")
     print(bias_obj.display_concept_tree(children_concept_tree))
-    print('parent concept hierarchy for COVID-19 in widget tree format:')
+    print("parent concept hierarchy for COVID-19 in widget tree format:")
     bias_obj.display_concept_tree(parent_concept_tree, show_in_text_format=False)
-    print('children concept hierarchy for COVID-19 in widget tree format:')
+    print("children concept hierarchy for COVID-19 in widget tree format:")
     bias_obj.display_concept_tree(children_concept_tree, show_in_text_format=False)
     return
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     bias = None
-    pd.set_option('display.max_rows', None)
-    pd.set_option('display.max_columns', None)
-    pd.set_option('display.width', 1000)
+    pd.set_option("display.max_rows", None)
+    pd.set_option("display.max_columns", None)
+    pd.set_option("display.width", 1000)
     try:
         bias = BIAS()
         # bias.set_config(os.path.join(os.path.dirname(__file__), '..', 'config_duckdb.yaml'))
-        bias.set_config(os.path.join(os.path.dirname(__file__), '..', 'config.yaml'))
+        bias.set_config(os.path.join(os.path.dirname(__file__), "..", "config.yaml"))
         bias.set_root_omop()
 
         cohort_creation_template_test(bias)
@@ -124,4 +132,4 @@ def concept_test(bias_obj):
     finally:
         if bias is not None:
             bias.cleanup()
-        print('done')
+        print("done")
diff --git a/biasanalyzer/sql.py b/biasanalyzer/sql.py
index a47c7c6..84c7cd8 100644
--- a/biasanalyzer/sql.py
+++ b/biasanalyzer/sql.py
@@ -1,6 +1,6 @@
 # SQL templates for querying in OMOP database
 
-AGE_DISTRIBUTION_QUERY = '''
+AGE_DISTRIBUTION_QUERY = """
     WITH Age_Cohort AS (
         SELECT p.person_id, 
                EXTRACT(YEAR FROM
@@ -42,9 +42,9 @@
         ROUND(bin_count * 1.0 / SUM(bin_count) OVER (), 2) AS probability -- Normalize to get probability
     FROM Age_Distribution
     ORDER BY age_bin                  
-'''
+"""
 
-GENDER_DISTRIBUTION_QUERY = '''
+GENDER_DISTRIBUTION_QUERY = """
     WITH Gender_Categories AS (
         SELECT 'male' AS gender, 8507 AS gender_concept_id
         UNION ALL SELECT 'female', 8532
@@ -76,9 +76,9 @@
         ROUND(COALESCE(gender_count, 0) * 1.0 / SUM(COALESCE(gender_count, 0)) OVER (), 2) AS probability
     FROM Gender_Distribution
     ORDER BY gender;
-'''
+"""
 
-AGE_STATS_QUERY = '''
+AGE_STATS_QUERY = """
     WITH Age_Cohort AS (
         SELECT p.person_id,
             EXTRACT(YEAR FROM
@@ -100,9 +100,9 @@
         CAST(PERCENTILE_CONT(0.5) WITHIN GROUP (ORDER BY age) AS INT) AS median_age,
         ROUND(STDDEV(age), 2) as stddev_age
     FROM Age_Cohort                
-'''
+"""
 
-GENDER_STATS_QUERY = '''
+GENDER_STATS_QUERY = """
     SELECT
         CASE
             WHEN p.gender_concept_id = 8507 THEN 'male'
@@ -114,9 +114,9 @@
     FROM {ba_schema}.cohort c JOIN {omop}.person p ON c.subject_id = p.person_id 
     WHERE c.cohort_definition_id = {cohort_definition_id}
     GROUP BY p.gender_concept_id
-'''
+"""
 
-RACE_STATS_QUERY = '''
+RACE_STATS_QUERY = """
         SELECT
             CASE
                 WHEN p.race_concept_id = 8516 THEN 'Black or African American'
@@ -131,9 +131,9 @@
         FROM {ba_schema}.cohort c JOIN {omop}.person p ON c.subject_id = p.person_id
         WHERE c.cohort_definition_id = {cohort_definition_id}
         GROUP BY p.race_concept_id 
-'''
+"""
 
-ETHNICITY_STATS_QUERY = '''
+ETHNICITY_STATS_QUERY = """
     SELECT
         CASE
             WHEN p.ethnicity_concept_id = 38003563 THEN 'Hispanic or Latino'
@@ -145,4 +145,4 @@
     FROM {ba_schema}.cohort c JOIN {omop}.person p ON c.subject_id = p.person_id
     WHERE c.cohort_definition_id = {cohort_definition_id}
     GROUP BY p.ethnicity_concept_id
-'''
+"""
diff --git a/biasanalyzer/utils.py b/biasanalyzer/utils.py
index 5bf257b..ad6b47d 100644
--- a/biasanalyzer/utils.py
+++ b/biasanalyzer/utils.py
@@ -29,14 +29,14 @@ def notify_users(message: str, level: str = "info"):
 
 def get_direction_arrow(tree_type):
     # the two unicodes are for up and down arrows
-    return "\U0001F53C" if tree_type == 'parents' else "\U0001F53D"
+    return "\U0001f53c" if tree_type == "parents" else "\U0001f53d"
 
 
 def clean_string(text):
     # replace newlines and tabs with a space
-    text = re.sub(r'[\n\t]', ' ', text)
+    text = re.sub(r"[\n\t]", " ", text)
     # Replace multiple spaces with a single space
-    text = re.sub(r'\s+', ' ', text)
+    text = re.sub(r"\s+", " ", text)
     # Strip leading and trailing spaces
     return text.strip()
 
@@ -55,23 +55,21 @@ def hellinger_distance(p, q):
     return np.sqrt(0.5 * np.sum((np.sqrt(p) - np.sqrt(q)) ** 2))
 
 
-def build_concept_hierarchy(df, parent_col="ancestor_concept_id", child_col="descendant_concept_id",
-                            details_col="details"):
+def build_concept_hierarchy(
+    df, parent_col="ancestor_concept_id", child_col="descendant_concept_id", details_col="details"
+):
     """
     Builds a hierarchy using only direct parent-child relationships to remove duplicate branches.
     """
     grouped = df.groupby(parent_col)
-    hierarchy = {
-        parent: list(zip(group[child_col], group[details_col]))
-        for parent, group in grouped
-    }
+    hierarchy = {parent: list(zip(group[child_col], group[details_col])) for parent, group in grouped}
     return hierarchy
 
 
 def build_concept_tree(concept_tree: dict, tree_type: str) -> Node:
     """
-        Recursively builds an ipytree Node for a given concept tree.
-        """
+    Recursively builds an ipytree Node for a given concept tree.
+    """
     # Extract concept details
     details = concept_tree.get("details", {})
     concept_name = details.get("concept_name", "Unknown Concept")
diff --git a/scripts/ingest_csvs_to_omop_duckdb.py b/scripts/ingest_csvs_to_omop_duckdb.py
index d1ff549..a96ec38 100644
--- a/scripts/ingest_csvs_to_omop_duckdb.py
+++ b/scripts/ingest_csvs_to_omop_duckdb.py
@@ -21,7 +21,7 @@
 def load_csv_to_duckdb(con, csv_path: Path, table_name: str):
     """Load a single CSV file into DuckDB."""
     t0 = time.time()
-    print(f'loading {table_name} from {csv_path}')
+    print(f"loading {table_name} from {csv_path}")
     con.execute(f"""
         CREATE OR REPLACE TABLE {table_name} AS
         SELECT * FROM read_csv_auto('{csv_path}', header=True, quote='', parallel=True)
@@ -48,12 +48,19 @@ def ingest_directory(con, csv_dir: Path):
 
 def main():
     parser = argparse.ArgumentParser(description="Ingest OMOP CSVs into DuckDB")
-    parser.add_argument("--clinical", type=Path, required=False,
-                        help="Directory containing OMOP clinical CSVs (person, condition_occurrence, etc.)")
-    parser.add_argument("--vocab", type=Path, required=False,
-                        help="Directory containing OMOP vocabulary CSVs (concept, concept_relationship, etc.)")
-    parser.add_argument("--output", type=Path, required=True,
-                        help="Output DuckDB file path")
+    parser.add_argument(
+        "--clinical",
+        type=Path,
+        required=False,
+        help="Directory containing OMOP clinical CSVs (person, condition_occurrence, etc.)",
+    )
+    parser.add_argument(
+        "--vocab",
+        type=Path,
+        required=False,
+        help="Directory containing OMOP vocabulary CSVs (concept, concept_relationship, etc.)",
+    )
+    parser.add_argument("--output", type=Path, required=True, help="Output DuckDB file path")
 
     args = parser.parse_args()
 
@@ -88,5 +95,6 @@ def main():
     print(f"Ingestion complete with {len(all_results)} tables loaded. Details shown below:")
     print(f"\n{all_results}")
 
+
 if __name__ == "__main__":
     main()
diff --git a/tests/conftest.py b/tests/conftest.py
index be1cb6b..e71d1ed 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -16,9 +16,9 @@ def fresh_bias_obj():
 
 @pytest.fixture(scope="session")
 def test_db():
-    config_file = os.path.join(os.path.dirname(__file__), 'assets', 'config', 'test_config.yaml')
+    config_file = os.path.join(os.path.dirname(__file__), "assets", "config", "test_config.yaml")
     config = load_config(config_file)
-    db_path = config['root_omop_cdm_database']['database']
+    db_path = config["root_omop_cdm_database"]["database"]
     conn = duckdb.connect(db_path)
     conn.execute("""
                 CREATE TABLE IF NOT EXISTS person (
@@ -271,7 +271,6 @@ def test_db():
                                 -- Person 5: No insulin
                         """)
 
-
     # mock configuration file
     bias = BIAS(config_file_path=config_file)
     bias.set_root_omop()
diff --git a/tests/query_based/test_cohort_creation.py b/tests/query_based/test_cohort_creation.py
index c13878e..1bc3226 100644
--- a/tests/query_based/test_cohort_creation.py
+++ b/tests/query_based/test_cohort_creation.py
@@ -12,15 +12,12 @@ def test_cohort_yaml_validation(test_db):
     invalid_data = {
         "gender": "female",
         "min_birth_year": 2000,
-        "max_birth_year": 1999  # Invalid: less than min_birth_year
+        "max_birth_year": 1999,  # Invalid: less than min_birth_year
     }
     with pytest.raises(ValueError):
         DemographicsCriteria(**invalid_data)
 
-    invalid_data = {
-        "event_type": "date",
-        "event_concept_id": "dummy"
-    }
+    invalid_data = {"event_type": "date", "event_concept_id": "dummy"}
     # validate date event_type must have a timestamp field
     with pytest.raises(ValueError):
         TemporalEvent(**invalid_data)
@@ -28,12 +25,10 @@ def test_cohort_yaml_validation(test_db):
     invalid_data = {
         "operator": "BEFORE",
         "events": [
-            {'event_type': 'condition_occurrence',
-             'event_concept_id': 201826},
-            {'event_type': 'drug_exposure',
-             'event_concept_id': 4285892},
+            {"event_type": "condition_occurrence", "event_concept_id": 201826},
+            {"event_type": "drug_exposure", "event_concept_id": 4285892},
         ],
-        "interval": [100, 50]
+        "interval": [100, 50],
     }
     # validate interval start must be smaller than interval end
     with pytest.raises(ValueError):
@@ -55,49 +50,60 @@ def test_cohort_yaml_validation(test_db):
     with pytest.raises(ValueError):
         TemporalEventGroup(**invalid_data)
 
+
 def test_cohort_creation_baseline(caplog, test_db):
     bias = test_db
     cohort = bias.create_cohort(
         "COVID-19 patient",
         "Cohort of young female patients",
-        os.path.join(os.path.dirname(__file__), '..', 'assets', 'cohort_creation',
-                     'test_cohort_creation_condition_occurrence_config_baseline.yaml'),
-        "test_user"
+        os.path.join(
+            os.path.dirname(__file__),
+            "..",
+            "assets",
+            "cohort_creation",
+            "test_cohort_creation_condition_occurrence_config_baseline.yaml",
+        ),
+        "test_user",
     )
 
     # Test cohort object and methods
     assert cohort is not None, "Cohort creation failed"
     cohort_id = cohort.cohort_id
-    assert bias.bias_db.get_cohort_definition(cohort_id)['name'] == "COVID-19 patient"
+    assert bias.bias_db.get_cohort_definition(cohort_id)["name"] == "COVID-19 patient"
     assert bias.bias_db.get_cohort_definition(cohort_id + 1) == {}
     assert cohort.metadata is not None, "Cohort creation wrongly returned None metadata"
-    assert 'creation_info' in cohort.metadata, "Cohort creation does not contain 'creation_info' key"
+    assert "creation_info" in cohort.metadata, "Cohort creation does not contain 'creation_info' key"
     assert cohort.data is not None, "Cohort creation wrongly returned None data"
     caplog.clear()
     with caplog.at_level(logging.ERROR):
-        cohort.get_distributions('ethnicity')
+        cohort.get_distributions("ethnicity")
     assert "Distribution for variable 'ethnicity' is not available" in caplog.text
 
-    assert len(cohort.get_distributions('age')) == 10, "Cohort get_distribution('age') does not return 10 age_bin items"
-    assert len(cohort.get_distributions('gender')) == 3, ("Cohort get_distribution('gender') does not return "
-                                                          "3 gender_bin items")
+    assert len(cohort.get_distributions("age")) == 10, "Cohort get_distribution('age') does not return 10 age_bin items"
+    assert len(cohort.get_distributions("gender")) == 3, (
+        "Cohort get_distribution('gender') does not return 3 gender_bin items"
+    )
 
-    patient_ids = set([item['subject_id'] for item in cohort.data])
+    patient_ids = set([item["subject_id"] for item in cohort.data])
     assert_equal(len(patient_ids), 5)
     assert_equal(patient_ids, {106, 108, 110, 111, 112})
     # select two patients to check for cohort_start_date and cohort_end_date automatically computed
-    patient_106 = next(item for item in cohort.data if item['subject_id'] == 106)
-    patient_108 = next(item for item in cohort.data if item['subject_id'] == 108)
+    patient_106 = next(item for item in cohort.data if item["subject_id"] == 106)
+    patient_108 = next(item for item in cohort.data if item["subject_id"] == 108)
 
     # Replace dates with actual values from your test data
-    assert_equal(patient_106['cohort_start_date'], datetime.date(2023, 3, 1),
-                 "Incorrect cohort_start_date for patient 106")
-    assert_equal(patient_106['cohort_end_date'], datetime.date(2023, 3, 15),
-                 "Incorrect cohort_end_date for patient 106")
-    assert_equal(patient_108['cohort_start_date'], datetime.date(2020, 4, 10),
-                 "Incorrect cohort_start_date for patient 108")
-    assert_equal(patient_108['cohort_end_date'], datetime.date(2020, 4, 27),
-                 "Incorrect cohort_end_date for patient 108")
+    assert_equal(
+        patient_106["cohort_start_date"], datetime.date(2023, 3, 1), "Incorrect cohort_start_date for patient 106"
+    )
+    assert_equal(
+        patient_106["cohort_end_date"], datetime.date(2023, 3, 15), "Incorrect cohort_end_date for patient 106"
+    )
+    assert_equal(
+        patient_108["cohort_start_date"], datetime.date(2020, 4, 10), "Incorrect cohort_start_date for patient 108"
+    )
+    assert_equal(
+        patient_108["cohort_end_date"], datetime.date(2020, 4, 27), "Incorrect cohort_end_date for patient 108"
+    )
 
 
 def test_cohort_creation_study(test_db):
@@ -105,19 +111,25 @@ def test_cohort_creation_study(test_db):
     cohort = bias.create_cohort(
         "COVID-19 patient",
         "Cohort of young female patients with COVID-19",
-        os.path.join(os.path.dirname(__file__), '..', 'assets', 'cohort_creation',
-                    'test_cohort_creation_condition_occurrence_config_study.yaml'),
-        "test_user"
+        os.path.join(
+            os.path.dirname(__file__),
+            "..",
+            "assets",
+            "cohort_creation",
+            "test_cohort_creation_condition_occurrence_config_study.yaml",
+        ),
+        "test_user",
     )
     # Test cohort object and methods
     assert cohort is not None, "Cohort creation failed"
     assert cohort.metadata is not None, "Cohort creation wrongly returned None metadata"
-    assert 'creation_info' in cohort.metadata, "Cohort creation does not contain 'creation_info' key"
+    assert "creation_info" in cohort.metadata, "Cohort creation does not contain 'creation_info' key"
     assert cohort.data is not None, "Cohort creation wrongly returned None data"
-    patient_ids = set([item['subject_id'] for item in cohort.data])
+    patient_ids = set([item["subject_id"] for item in cohort.data])
     assert_equal(len(patient_ids), 4)
     assert_equal(patient_ids, {108, 110, 111, 112})
 
+
 def test_cohort_creation_study2(caplog, test_db):
     bias = test_db
     caplog.clear()
@@ -125,21 +137,27 @@ def test_cohort_creation_study2(caplog, test_db):
         cohort = bias.create_cohort(
             "COVID-19 patient",
             "Cohort of young female patients with no COVID-19",
-            os.path.join(os.path.dirname(__file__), '..', 'assets', 'cohort_creation',
-                        'test_cohort_creation_condition_occurrence_config_study2.yaml'),
+            os.path.join(
+                os.path.dirname(__file__),
+                "..",
+                "assets",
+                "cohort_creation",
+                "test_cohort_creation_condition_occurrence_config_study2.yaml",
+            ),
             "test_user",
-            delay=1
+            delay=1,
         )
-    assert 'Simulating long-running task' in caplog.text
+    assert "Simulating long-running task" in caplog.text
     # Test cohort object and methods
     assert cohort is not None, "Cohort creation failed"
     assert cohort.metadata is not None, "Cohort creation wrongly returned None metadata"
-    assert 'creation_info' in cohort.metadata, "Cohort creation does not contain 'creation_info' key"
+    assert "creation_info" in cohort.metadata, "Cohort creation does not contain 'creation_info' key"
     assert cohort.data is not None, "Cohort creation wrongly returned None data"
-    patient_ids = set([item['subject_id'] for item in cohort.data])
+    patient_ids = set([item["subject_id"] for item in cohort.data])
     assert_equal(len(patient_ids), 1)
     assert_equal(patient_ids, {106})
 
+
 def test_cohort_creation_all(caplog, test_db):
     bias = test_db
     cohort = bias.create_cohort(
@@ -147,29 +165,35 @@ def test_cohort_creation_all(caplog, test_db):
         "Cohort of young female patients with COVID-19 who have the condition with difficulty breathing 2 to 5 days "
         "before a COVID diagnosis 3/15/20-12/11/20 AND have at least one emergency room visit or at least "
         "two inpatient visits",
-        os.path.join(os.path.dirname(__file__), '..', 'assets', 'cohort_creation',
-                     'test_cohort_creation_condition_occurrence_config.yaml'),
-        "test_user"
+        os.path.join(
+            os.path.dirname(__file__),
+            "..",
+            "assets",
+            "cohort_creation",
+            "test_cohort_creation_condition_occurrence_config.yaml",
+        ),
+        "test_user",
     )
     # Test cohort object and methods
     assert cohort is not None, "Cohort creation failed"
     assert cohort.metadata is not None, "Cohort creation wrongly returned None metadata"
-    assert 'creation_info' in cohort.metadata, "Cohort creation does not contain 'creation_info' key"
+    assert "creation_info" in cohort.metadata, "Cohort creation does not contain 'creation_info' key"
     stats = cohort.get_stats()
     assert stats is not None, "Created cohort's stats is None"
-    gender_stats = cohort.get_stats(variable='gender')
+    gender_stats = cohort.get_stats(variable="gender")
     assert gender_stats is not None, "Created cohort's gender stats is None"
     caplog.clear()
     with caplog.at_level(logging.ERROR):
-        cohort.get_stats(variable='address')
-    assert 'is not available' in caplog.text
+        cohort.get_stats(variable="address")
+    assert "is not available" in caplog.text
     assert gender_stats is not None, "Created cohort's gender stats is None"
     assert cohort.data is not None, "Cohort creation wrongly returned None data"
-    patient_ids = set([item['subject_id'] for item in cohort.data])
-    print(f'patient_ids: {patient_ids}', flush=True)
+    patient_ids = set([item["subject_id"] for item in cohort.data])
+    print(f"patient_ids: {patient_ids}", flush=True)
     assert_equal(len(patient_ids), 2)
     assert_equal(patient_ids, {108, 110})
 
+
 def test_cohort_creation_multiple_temporary_groups_with_no_operator(test_db):
     bias = test_db
     cohort = bias.create_cohort(
@@ -177,16 +201,22 @@ def test_cohort_creation_multiple_temporary_groups_with_no_operator(test_db):
         "Cohort of young female patients who either have COVID-19 with difficulty breathing 2 to 5 days "
         "before a COVID diagnosis 3/15/20-12/11/20 OR have at least one emergency room visit or at least "
         "two inpatient visits",
-        os.path.join(os.path.dirname(__file__), '..', 'assets', 'cohort_creation',
-                     'test_cohort_creation_multiple_temporal_groups_without_operator.yaml'),
-        "test_user"
+        os.path.join(
+            os.path.dirname(__file__),
+            "..",
+            "assets",
+            "cohort_creation",
+            "test_cohort_creation_multiple_temporal_groups_without_operator.yaml",
+        ),
+        "test_user",
     )
     # Test cohort object and methods
-    patient_ids = set([item['subject_id'] for item in cohort.data])
-    print(f'patient_ids: {patient_ids}', flush=True)
+    patient_ids = set([item["subject_id"] for item in cohort.data])
+    print(f"patient_ids: {patient_ids}", flush=True)
     assert_equal(len(patient_ids), 2)
     assert_equal(patient_ids, {108, 110})
 
+
 def test_cohort_creation_mixed_domains(test_db):
     """
     Test cohort creation with mixed domains (condition, drug, visit, procedure).
@@ -197,95 +227,104 @@ def test_cohort_creation_mixed_domains(test_db):
         "Cohort of female patients with diabetes who had insulin prescribed 0-30 days after diagnosis "
         "and have at least one outpatient or emergency visit and underwent a blood test before 12/31/2020, "
         "with patients born after 1995 and with cardiac surgery excluded",
-        os.path.join(os.path.dirname(__file__), '..', 'assets', 'cohort_creation',
-                     'test_cohort_creation_config.yaml'),
-        "test_user"
+        os.path.join(os.path.dirname(__file__), "..", "assets", "cohort_creation", "test_cohort_creation_config.yaml"),
+        "test_user",
     )
 
     # Test cohort object and methods
     assert cohort is not None, "Cohort creation failed"
-    print(f'metadata: {cohort.metadata}')
+    print(f"metadata: {cohort.metadata}")
     assert cohort.metadata is not None, "Cohort creation wrongly returned None metadata"
-    assert 'creation_info' in cohort.metadata, "Cohort creation does not contain 'creation_info' key"
+    assert "creation_info" in cohort.metadata, "Cohort creation does not contain 'creation_info' key"
     stats = cohort.get_stats()
     assert stats is not None, "Created cohort's stats is None"
     assert cohort.data is not None, "Cohort creation wrongly returned None data"
-    patient_ids = set([item['subject_id'] for item in cohort.data])
-    print(f'patient_ids: {patient_ids}', flush=True)
+    patient_ids = set([item["subject_id"] for item in cohort.data])
+    print(f"patient_ids: {patient_ids}", flush=True)
     assert_equal(len(patient_ids), 3)
     assert_equal(patient_ids, {1, 2, 6})
-    start_dates = [item['cohort_start_date'] for item in cohort.data]
+    start_dates = [item["cohort_start_date"] for item in cohort.data]
     assert_equal(len(start_dates), 3)
-    assert_equal(start_dates, [datetime.date(2020, 6, 1),
-                               datetime.date(2020, 6, 1),
-                               datetime.date(2018, 1, 1)])
-    end_dates = [item['cohort_end_date'] for item in cohort.data]
+    assert_equal(start_dates, [datetime.date(2020, 6, 1), datetime.date(2020, 6, 1), datetime.date(2018, 1, 1)])
+    end_dates = [item["cohort_end_date"] for item in cohort.data]
     assert_equal(len(end_dates), 3)
-    assert_equal(end_dates, [datetime.date(2020, 6, 20),
-                             datetime.date(2020, 6, 20),
-                             datetime.date(2018, 1, 20)])
+    assert_equal(end_dates, [datetime.date(2020, 6, 20), datetime.date(2020, 6, 20), datetime.date(2018, 1, 20)])
+
 
 def test_cohort_comparison(test_db):
     bias = test_db
     cohort_base = bias.create_cohort(
         "COVID-19 patient",
         "Cohort of young female patients",
-        os.path.join(os.path.dirname(__file__), '..', 'assets', 'cohort_creation',
-                     'test_cohort_creation_condition_occurrence_config_baseline.yaml'),
-        "test_user"
+        os.path.join(
+            os.path.dirname(__file__),
+            "..",
+            "assets",
+            "cohort_creation",
+            "test_cohort_creation_condition_occurrence_config_baseline.yaml",
+        ),
+        "test_user",
     )
     cohort_study = bias.create_cohort(
         "Female diabetes patients born between 1970 and 2000",
         "Cohort of female patients with diabetes who had insulin prescribed 0-30 days after diagnosis "
         "and have at least one outpatient or emergency visit and underwent a blood test before 12/31/2020, "
         "with patients born after 1995 and with cardiac surgery excluded",
-        os.path.join(os.path.dirname(__file__), '..', 'assets', 'cohort_creation',
-                     'test_cohort_creation_config.yaml'),
-        "test_user"
+        os.path.join(os.path.dirname(__file__), "..", "assets", "cohort_creation", "test_cohort_creation_config.yaml"),
+        "test_user",
     )
     results = bias.compare_cohorts(cohort_base.cohort_id, cohort_study.cohort_id)
-    assert {'gender_hellinger_distance': 0.0} in results
-    assert any('age_hellinger_distance' in r for r in results)
+    assert {"gender_hellinger_distance": 0.0} in results
+    assert any("age_hellinger_distance" in r for r in results)
+
 
 def test_cohort_invalid(caplog, test_db):
     caplog.clear()
     with caplog.at_level(logging.INFO):
-        invalid_cohort = test_db.create_cohort('invalid_cohort', 'invalid_cohort',
-                                               'invalid_yaml_file.yml',
-                                               'invalid_created_by')
-    assert 'cohort creation configuration file does not exist' in caplog.text
+        invalid_cohort = test_db.create_cohort(
+            "invalid_cohort", "invalid_cohort", "invalid_yaml_file.yml", "invalid_created_by"
+        )
+    assert "cohort creation configuration file does not exist" in caplog.text
     assert invalid_cohort is None
 
     caplog.clear()
     with caplog.at_level(logging.INFO):
-        invalid_cohort = test_db.create_cohort('invalid_cohort', 'invalid_cohort',
-                                               os.path.join(os.path.dirname(__file__), '..', 'assets', 'config',
-                                                            'test_config.yaml'), 'invalid_created_by')
-    assert 'configuration yaml file is not valid' in caplog.text
+        invalid_cohort = test_db.create_cohort(
+            "invalid_cohort",
+            "invalid_cohort",
+            os.path.join(os.path.dirname(__file__), "..", "assets", "config", "test_config.yaml"),
+            "invalid_created_by",
+        )
+    assert "configuration yaml file is not valid" in caplog.text
     assert invalid_cohort is None
 
     with caplog.at_level(logging.INFO):
-        invalid_cohort = test_db.create_cohort('invalid_cohort', 'invalid_cohort',
-                                               'INVALID SQL QUERY STRING',
-                                               'invalid_created_by')
-    assert 'Error executing query:' in caplog.text
+        invalid_cohort = test_db.create_cohort(
+            "invalid_cohort", "invalid_cohort", "INVALID SQL QUERY STRING", "invalid_created_by"
+        )
+    assert "Error executing query:" in caplog.text
     assert invalid_cohort is None
 
+
 def test_create_cohort_sqlalchemy_error(monkeypatch, fresh_bias_obj):
     # Mock omop_db methods
     class MockOmopDB:
         def get_session(self):
             return self  # not used after error
+
         def execute_query(self, query):
             raise SQLAlchemyError("Mocked SQLAlchemy error")
+
         def close(self):
             pass
 
     class MockBiasDB:
         def create_cohort_definition(self, *args, **kwargs):
             pass
+
         def create_cohort_in_bulk(self, *args, **kwargs):
             pass
+
         def close(self):
             pass
 
@@ -296,6 +335,7 @@ def close(self):
 
     assert result is None
 
+
 def test_cohort_creation_negative_instance(test_db):
     """
     Test cohort creation with negative event_instance (last occurrence of a condition).
@@ -304,25 +344,32 @@ def test_cohort_creation_negative_instance(test_db):
     cohort = bias.create_cohort(
         "Diabetes patients (last occurrence)",
         "Cohort of female patients born 1970-2000 with the last Type 2 diabetes diagnosis",
-        os.path.join(os.path.dirname(__file__), '..', 'assets', 'cohort_creation',
-                     'test_cohort_creation_negative_instance.yaml'),
-        "test_user"
+        os.path.join(
+            os.path.dirname(__file__), "..", "assets", "cohort_creation", "test_cohort_creation_negative_instance.yaml"
+        ),
+        "test_user",
     )
 
     # Test cohort object and methods
     assert cohort is not None, "Cohort creation failed"
     assert cohort.data is not None, "Cohort creation returned None data"
 
-    patient_ids = set([item['subject_id'] for item in cohort.data])
+    patient_ids = set([item["subject_id"] for item in cohort.data])
     assert_equal(len(patient_ids), 6)  # Female patients 1, 2, 3, 5
     assert_equal(patient_ids, {1, 2, 3, 5, 6, 7})
 
     # Verify dates for a specific patient (e.g., patient 1 with last diabetes diagnosis)
-    patient_1 = next(item for item in cohort.data if item['subject_id'] == 1)
-    assert_equal(patient_1['cohort_start_date'], datetime.date(2020, 6, 1),
-                 "Incorrect cohort_start_date for patient 1 (last diabetes)")
-    assert_equal(patient_1['cohort_end_date'], datetime.date(2020, 6, 1),
-                 "Incorrect cohort_end_date for patient 1 (last diabetes)")
+    patient_1 = next(item for item in cohort.data if item["subject_id"] == 1)
+    assert_equal(
+        patient_1["cohort_start_date"],
+        datetime.date(2020, 6, 1),
+        "Incorrect cohort_start_date for patient 1 (last diabetes)",
+    )
+    assert_equal(
+        patient_1["cohort_end_date"],
+        datetime.date(2020, 6, 1),
+        "Incorrect cohort_end_date for patient 1 (last diabetes)",
+    )
 
 
 def test_cohort_creation_offset(test_db):
@@ -333,28 +380,33 @@ def test_cohort_creation_offset(test_db):
     cohort = bias.create_cohort(
         "Diabetes patients with offset",
         "Cohort of female patients born 1970-2000 with Type 2 diabetes diagnosis, adjusted by +180 and -730 days",
-        os.path.join(os.path.dirname(__file__), '..', 'assets', 'cohort_creation',
-                     'test_cohort_creation_offset.yaml'),
-        "test_user"
+        os.path.join(os.path.dirname(__file__), "..", "assets", "cohort_creation", "test_cohort_creation_offset.yaml"),
+        "test_user",
     )
 
     # Test cohort object and methods
     assert cohort is not None, "Cohort creation failed"
     assert cohort.metadata is not None, "Cohort creation wrongly returned None metadata"
-    assert 'creation_info' in cohort.metadata, "Cohort creation does not contain 'creation_info' key"
+    assert "creation_info" in cohort.metadata, "Cohort creation does not contain 'creation_info' key"
     assert cohort.data is not None, "Cohort creation wrongly returned None data"
 
-    patient_ids = set([item['subject_id'] for item in cohort.data])
+    patient_ids = set([item["subject_id"] for item in cohort.data])
     assert_equal(len(patient_ids), 6)  # Female patients 1, 2, 3, 5
     assert_equal(patient_ids, {1, 2, 3, 5, 6, 7})
 
     # Verify dates for a specific patient (e.g., patient 1 with offset)
-    patient_1 = next(item for item in cohort.data if item['subject_id'] == 1)
+    patient_1 = next(item for item in cohort.data if item["subject_id"] == 1)
     # Diabetes on 2020-06-01: -730 days = 2018-06-02, +180 days = 2020-11-28
-    assert_equal(patient_1['cohort_start_date'], datetime.date(2018, 6, 2),
-                 "Incorrect cohort_start_date for patient 1 (with -730 day offset)")
-    assert_equal(patient_1['cohort_end_date'], datetime.date(2020, 11, 28),
-                 "Incorrect cohort_end_date for patient 1 (with +180 day offset)")
+    assert_equal(
+        patient_1["cohort_start_date"],
+        datetime.date(2018, 6, 2),
+        "Incorrect cohort_start_date for patient 1 (with -730 day offset)",
+    )
+    assert_equal(
+        patient_1["cohort_end_date"],
+        datetime.date(2020, 11, 28),
+        "Incorrect cohort_end_date for patient 1 (with +180 day offset)",
+    )
 
 
 def test_cohort_creation_negative_instance_offset(test_db):
@@ -365,25 +417,36 @@ def test_cohort_creation_negative_instance_offset(test_db):
     cohort = bias.create_cohort(
         "Diabetes patients (last occurrence with offset)",
         "Cohort of female patients born 1970-2000 with the last Type 2 diabetes diagnosis, adjusted by +180 days",
-        os.path.join(os.path.dirname(__file__), '..', 'assets', 'cohort_creation',
-                     'test_cohort_creation_negative_instance_offset.yaml'),
-        "test_user"
+        os.path.join(
+            os.path.dirname(__file__),
+            "..",
+            "assets",
+            "cohort_creation",
+            "test_cohort_creation_negative_instance_offset.yaml",
+        ),
+        "test_user",
     )
 
     # Test cohort object and methods
     assert cohort is not None, "Cohort creation failed"
     assert cohort.metadata is not None, "Cohort creation wrongly returned None metadata"
-    assert 'creation_info' in cohort.metadata, "Cohort creation does not contain 'creation_info' key"
+    assert "creation_info" in cohort.metadata, "Cohort creation does not contain 'creation_info' key"
     assert cohort.data is not None, "Cohort creation wrongly returned None data"
 
-    patient_ids = set([item['subject_id'] for item in cohort.data])
+    patient_ids = set([item["subject_id"] for item in cohort.data])
     assert_equal(len(patient_ids), 6)
     assert_equal(patient_ids, {1, 2, 3, 5, 6, 7})
 
     # Verify dates for a specific patient (e.g., patient 1 with last diabetes and offset)
-    patient_1 = next(item for item in cohort.data if item['subject_id'] == 1)
+    patient_1 = next(item for item in cohort.data if item["subject_id"] == 1)
     # Last diabetes on 2020-06-01: +180 days = 2020-11-28
-    assert_equal(patient_1['cohort_start_date'], datetime.date(2020, 6, 1),
-                 "Incorrect cohort_start_date for patient 1 (last diabetes)")
-    assert_equal(patient_1['cohort_end_date'], datetime.date(2020, 11, 28),
-                 "Incorrect cohort_end_date for patient 1 (last diabetes with +180 day offset)")
+    assert_equal(
+        patient_1["cohort_start_date"],
+        datetime.date(2020, 6, 1),
+        "Incorrect cohort_start_date for patient 1 (last diabetes)",
+    )
+    assert_equal(
+        patient_1["cohort_end_date"],
+        datetime.date(2020, 11, 28),
+        "Incorrect cohort_end_date for patient 1 (last diabetes with +180 day offset)",
+    )
diff --git a/tests/query_based/test_hierarchical_prevalence.py b/tests/query_based/test_hierarchical_prevalence.py
index 66893b3..41ab068 100644
--- a/tests/query_based/test_hierarchical_prevalence.py
+++ b/tests/query_based/test_hierarchical_prevalence.py
@@ -1,4 +1,3 @@
-
 import pytest
 from biasanalyzer.concept import ConceptHierarchy
 
@@ -13,47 +12,66 @@ def test_cohort_concept_hierarchical_prevalence(test_db, caplog):
     """
 
     cohort = bias.create_cohort(
-        "Diabetes Cohort",
-        "Cohort of patients with diabetes-related conditions",
-        cohort_query,
-        "test_user"
+        "Diabetes Cohort", "Cohort of patients with diabetes-related conditions", cohort_query, "test_user"
     )
     # Test cohort object and methods
     assert cohort is not None, "Cohort creation failed"
     # test concept_type must be one of the supported OMOP domain name
     with pytest.raises(ValueError):
-        cohort.get_concept_stats(concept_type='dummy_invalid')
+        cohort.get_concept_stats(concept_type="dummy_invalid")
 
     # test vocab must be None to use the default vocab or one of the supported OMOP vocabulary id
     with pytest.raises(ValueError):
-        cohort.get_concept_stats(vocab='dummy_invalid_vocab')
+        cohort.get_concept_stats(vocab="dummy_invalid_vocab")
 
     # test the cohort does not have procedure_occurrence related concepts
     with pytest.raises(ValueError):
-        cohort.get_concept_stats(concept_type='procedure_occurrence')
+        cohort.get_concept_stats(concept_type="procedure_occurrence")
 
-    concept_stats, _ = cohort.get_concept_stats(vocab='ICD10CM', print_concept_hierarchy=True)
+    concept_stats, _ = cohort.get_concept_stats(vocab="ICD10CM", print_concept_hierarchy=True)
     assert concept_stats is not None, "Failed to fetch concept stats"
     assert len(concept_stats) > 0, "No concept stats returned"
     # check returned data
-    assert not all(s['ancestor_concept_id'] == s['descendant_concept_id']
-                   for s in concept_stats['condition_occurrence']), \
-        "Some ancestor_concept_id and descendant_concept_id should differ"
+    assert not all(
+        s["ancestor_concept_id"] == s["descendant_concept_id"] for s in concept_stats["condition_occurrence"]
+    ), "Some ancestor_concept_id and descendant_concept_id should differ"
     # Check concept prevalence for overlaps
-    diabetes_prevalence = next((c for c in concept_stats['condition_occurrence']
-                                if c['ancestor_concept_id'] == 1 and c['descendant_concept_id'] == 1), None)
+    diabetes_prevalence = next(
+        (
+            c
+            for c in concept_stats["condition_occurrence"]
+            if c["ancestor_concept_id"] == 1 and c["descendant_concept_id"] == 1
+        ),
+        None,
+    )
     assert diabetes_prevalence is not None, "Parent diabetes concept prevalence missing"
-    type1_prevalence = next((c for c in concept_stats['condition_occurrence']
-                                if c['ancestor_concept_id'] == 2 and c['descendant_concept_id'] == 2), None)
+    type1_prevalence = next(
+        (
+            c
+            for c in concept_stats["condition_occurrence"]
+            if c["ancestor_concept_id"] == 2 and c["descendant_concept_id"] == 2
+        ),
+        None,
+    )
     assert type1_prevalence is not None, "Child type 1 diabetes concept prevalence missing"
-    type2_prevalence = next((c for c in concept_stats['condition_occurrence']
-                             if c['ancestor_concept_id'] == 3 and c['descendant_concept_id'] == 3), None)
+    type2_prevalence = next(
+        (
+            c
+            for c in concept_stats["condition_occurrence"]
+            if c["ancestor_concept_id"] == 3 and c["descendant_concept_id"] == 3
+        ),
+        None,
+    )
     assert type2_prevalence is not None, "Child type 2 diabetes concept prevalence missing"
-    print(f"type1_prevalence: {type1_prevalence['prevalence']}, type2_prevalence: {type2_prevalence['prevalence']}, "
-          f"diabetes_prevalence: {diabetes_prevalence['prevalence']}")
-    assert diabetes_prevalence['prevalence'] < type1_prevalence['prevalence'] + type2_prevalence['prevalence'], \
-        ("Parent diabetes concept prevalence does not reflect overlap between type 1 and type 2 diabetes "
-         "children concept prevalence")
+    print(
+        f"type1_prevalence: {type1_prevalence['prevalence']}, type2_prevalence: {type2_prevalence['prevalence']}, "
+        f"diabetes_prevalence: {diabetes_prevalence['prevalence']}"
+    )
+    assert diabetes_prevalence["prevalence"] < type1_prevalence["prevalence"] + type2_prevalence["prevalence"], (
+        "Parent diabetes concept prevalence does not reflect overlap between type 1 and type 2 diabetes "
+        "children concept prevalence"
+    )
+
 
 def test_identifier_normalization_and_cache():
     ConceptHierarchy.clear_cache()
@@ -63,39 +81,60 @@ def test_identifier_normalization_and_cache():
 
     # fake minimal results to build hierarchy
     results1 = [
-        {"ancestor_concept_id": 1, "descendant_concept_id": 1,
-         "concept_name": "Diabetes", "concept_code": "DIA",
-         "count_in_cohort": 5, "prevalence": 0.5}
+        {
+            "ancestor_concept_id": 1,
+            "descendant_concept_id": 1,
+            "concept_name": "Diabetes",
+            "concept_code": "DIA",
+            "count_in_cohort": 5,
+            "prevalence": 0.5,
+        }
     ]
     results2 = [
-        {"ancestor_concept_id": 1, "descendant_concept_id": 1,
-         "concept_name": "Diabetes2", "concept_code": "DIA",
-         "count_in_cohort": 15, "prevalence": 0.15}
+        {
+            "ancestor_concept_id": 1,
+            "descendant_concept_id": 1,
+            "concept_name": "Diabetes2",
+            "concept_code": "DIA",
+            "count_in_cohort": 15,
+            "prevalence": 0.15,
+        }
     ]
-    h1 = ConceptHierarchy.build_concept_hierarchy_from_results(1, 'condition_occurrence', results1)
-    h2 = ConceptHierarchy.build_concept_hierarchy_from_results(1, 'condition_occurrence', results2)
+    h1 = ConceptHierarchy.build_concept_hierarchy_from_results(1, "condition_occurrence", results1)
+    h2 = ConceptHierarchy.build_concept_hierarchy_from_results(1, "condition_occurrence", results2)
     assert h1 is h2  # cache reuse even though results2 is different from results1
     assert h1.identifier == "1-condition_occurrence-0-None"
-    h2 = ConceptHierarchy.build_concept_hierarchy_from_results(1, 'drug_exposure', results2)
+    h2 = ConceptHierarchy.build_concept_hierarchy_from_results(1, "drug_exposure", results2)
     assert h1 is not h2  # cache is not used since drug_exposure concept_name is different than the cached
     # condition_occurrence
     assert h2.identifier == "1-drug_exposure-0-None"
 
+
 def test_union_and_cache_behavior():
     ConceptHierarchy.clear_cache()
     results1 = [
-        {"ancestor_concept_id": 1, "descendant_concept_id": 1,
-         "concept_name": "Diabetes", "concept_code": "DIA",
-         "count_in_cohort": 5, "prevalence": 0.5}
+        {
+            "ancestor_concept_id": 1,
+            "descendant_concept_id": 1,
+            "concept_name": "Diabetes",
+            "concept_code": "DIA",
+            "count_in_cohort": 5,
+            "prevalence": 0.5,
+        }
     ]
     results2 = [
-        {"ancestor_concept_id": 2, "descendant_concept_id": 2,
-         "concept_name": "Hypertension", "concept_code": "HYP",
-         "count_in_cohort": 3, "prevalence": 0.3}
+        {
+            "ancestor_concept_id": 2,
+            "descendant_concept_id": 2,
+            "concept_name": "Hypertension",
+            "concept_code": "HYP",
+            "count_in_cohort": 3,
+            "prevalence": 0.3,
+        }
     ]
 
-    h1 = ConceptHierarchy.build_concept_hierarchy_from_results(1, 'condition_occurrence', results1)
-    h2 = ConceptHierarchy.build_concept_hierarchy_from_results(2, 'condition_occurrence', results2)
+    h1 = ConceptHierarchy.build_concept_hierarchy_from_results(1, "condition_occurrence", results1)
+    h2 = ConceptHierarchy.build_concept_hierarchy_from_results(2, "condition_occurrence", results2)
     assert "1-condition_occurrence-0-None" in ConceptHierarchy._graph_cache
     assert "2-condition_occurrence-0-None" in ConceptHierarchy._graph_cache
     h12 = h1.union(h2)
@@ -104,17 +143,28 @@ def test_union_and_cache_behavior():
     assert h21.identifier == "1-condition_occurrence-0-None+2-condition_occurrence-0-None"
     assert h12 is h21
 
+
 def test_traversal_and_serialization():
     ConceptHierarchy.clear_cache()
     results = [
-        {"ancestor_concept_id": 1, "descendant_concept_id": 1,
-         "concept_name": "Root", "concept_code": "R",
-         "count_in_cohort": 5, "prevalence": 0.5},
-        {"ancestor_concept_id": 1, "descendant_concept_id": 2,
-         "concept_name": "Child", "concept_code": "C",
-         "count_in_cohort": 2, "prevalence": 0.2}
+        {
+            "ancestor_concept_id": 1,
+            "descendant_concept_id": 1,
+            "concept_name": "Root",
+            "concept_code": "R",
+            "count_in_cohort": 5,
+            "prevalence": 0.5,
+        },
+        {
+            "ancestor_concept_id": 1,
+            "descendant_concept_id": 2,
+            "concept_name": "Child",
+            "concept_code": "C",
+            "count_in_cohort": 2,
+            "prevalence": 0.2,
+        },
     ]
-    h = ConceptHierarchy.build_concept_hierarchy_from_results(1, 'condition_occurrence', results)
+    h = ConceptHierarchy.build_concept_hierarchy_from_results(1, "condition_occurrence", results)
 
     # roots
     roots = h.get_root_nodes()
@@ -128,16 +178,12 @@ def test_traversal_and_serialization():
     leaf_nodes = h.get_leaf_nodes(serialization=True)
     assert leaf_nodes == [
         {
-            'concept_id': 2,
-            'concept_name': 'Child',
-            'concept_code': 'C',
-            'metrics': {
-                '1': {
-                    'count': 2, 'prevalence': 0.2
-                }
-            },
-            'source_cohorts': [1],
-            'parent_ids': [1]
+            "concept_id": 2,
+            "concept_name": "Child",
+            "concept_code": "C",
+            "metrics": {"1": {"count": 2, "prevalence": 0.2}},
+            "source_cohorts": [1],
+            "parent_ids": [1],
         }
     ]
 
@@ -152,14 +198,9 @@ def test_traversal_and_serialization():
         "concept_id": 1,
         "concept_name": "Root",
         "concept_code": "R",
-        "metrics": {
-            "1": {
-                "count": 5,
-                "prevalence": 0.5
-            }
-        },
-        'source_cohorts': [1],
-        "parent_ids": []
+        "metrics": {"1": {"count": 5, "prevalence": 0.5}},
+        "source_cohorts": [1],
+        "parent_ids": [],
     }
 
     # graph traversal
@@ -180,7 +221,7 @@ def test_traversal_and_serialization():
     dfs_nodes = [n.id for n in h.iter_nodes(1, order="dfs")]
     assert set(dfs_nodes) == {1, 2}
 
-    dfs_nodes = [n['concept_id'] for n in h.iter_nodes(1, order="dfs", serialization=True)]
+    dfs_nodes = [n["concept_id"] for n in h.iter_nodes(1, order="dfs", serialization=True)]
     assert set(dfs_nodes) == {1, 2}
 
     # serialization
@@ -196,27 +237,51 @@ def test_traversal_and_serialization():
         h.to_dict(111)
 
     h_dict = h.to_dict(1, include_union_metrics=True)
-    assert h_dict == {'hierarchy': [{
-        'concept_id': 1, 'concept_name': 'Root', 'concept_code': 'R',
-        'metrics': {'union': {'count': 5, 'prevalence': 0.5},
-                    '1': {'count': 5, 'prevalence': 0.5}},
-        'source_cohorts': [1],
-        'parent_ids': [],
-        'children': [{'concept_id': 2, 'concept_name': 'Child', 'concept_code': 'C',
-                      'metrics': {'union': {'count': 2, 'prevalence': 0.2},
-                                  '1': {'count': 2, 'prevalence': 0.2}},
-                      'source_cohorts': [1],
-                      'parent_ids': [1], 'children': []}]}
-    ]}
+    assert h_dict == {
+        "hierarchy": [
+            {
+                "concept_id": 1,
+                "concept_name": "Root",
+                "concept_code": "R",
+                "metrics": {"union": {"count": 5, "prevalence": 0.5}, "1": {"count": 5, "prevalence": 0.5}},
+                "source_cohorts": [1],
+                "parent_ids": [],
+                "children": [
+                    {
+                        "concept_id": 2,
+                        "concept_name": "Child",
+                        "concept_code": "C",
+                        "metrics": {"union": {"count": 2, "prevalence": 0.2}, "1": {"count": 2, "prevalence": 0.2}},
+                        "source_cohorts": [1],
+                        "parent_ids": [1],
+                        "children": [],
+                    }
+                ],
+            }
+        ]
+    }
 
     h_dict = h.to_dict()
-    assert h_dict == {'hierarchy': [{
-        'concept_id': 1, 'concept_name': 'Root', 'concept_code': 'R',
-        'metrics': {'1': {'count': 5, 'prevalence': 0.5}},
-        'source_cohorts': [1],
-        'parent_ids': [],
-        'children': [{'concept_id': 2, 'concept_name': 'Child', 'concept_code': 'C',
-                      'metrics': {'1': {'count': 2, 'prevalence': 0.2}},
-                      'source_cohorts': [1],
-                      'parent_ids': [1], 'children': []}]}
-    ]}
+    assert h_dict == {
+        "hierarchy": [
+            {
+                "concept_id": 1,
+                "concept_name": "Root",
+                "concept_code": "R",
+                "metrics": {"1": {"count": 5, "prevalence": 0.5}},
+                "source_cohorts": [1],
+                "parent_ids": [],
+                "children": [
+                    {
+                        "concept_id": 2,
+                        "concept_name": "Child",
+                        "concept_code": "C",
+                        "metrics": {"1": {"count": 2, "prevalence": 0.2}},
+                        "source_cohorts": [1],
+                        "parent_ids": [1],
+                        "children": [],
+                    }
+                ],
+            }
+        ]
+    }
diff --git a/tests/test_biasanalyzer_api.py b/tests/test_biasanalyzer_api.py
index a9f936b..6f42567 100644
--- a/tests/test_biasanalyzer_api.py
+++ b/tests/test_biasanalyzer_api.py
@@ -9,39 +9,41 @@
 
 
 def test_version():
-    assert __version__ == '0.1.0'
+    assert __version__ == "0.1.0"
+
 
 def test_set_config(caplog, fresh_bias_obj):
     caplog.clear()
     with caplog.at_level(logging.INFO):
-        fresh_bias_obj.set_config('')
-    assert 'no configuration file specified' in caplog.text
+        fresh_bias_obj.set_config("")
+    assert "no configuration file specified" in caplog.text
 
     caplog.clear()
     with caplog.at_level(logging.ERROR):
-        fresh_bias_obj.set_config('non_existent_config_file.yaml')
-    assert 'does not exist' in caplog.text
+        fresh_bias_obj.set_config("non_existent_config_file.yaml")
+    assert "does not exist" in caplog.text
 
     caplog.clear()
     with caplog.at_level(logging.ERROR):
-        invalid_config_file = os.path.join(os.path.dirname(__file__), 'assets', 'config',
-                                           'test_invalid_config.yaml')
+        invalid_config_file = os.path.join(os.path.dirname(__file__), "assets", "config", "test_invalid_config.yaml")
         fresh_bias_obj.set_config(invalid_config_file)
-    assert 'is not valid' in caplog.text
+    assert "is not valid" in caplog.text
+
 
 def test_set_root_omop(monkeypatch, caplog, fresh_bias_obj):
     caplog.clear()
     with caplog.at_level(logging.INFO):
         fresh_bias_obj.set_root_omop()
-    assert 'no valid configuration' in caplog.text
+    assert "no valid configuration" in caplog.text
 
     caplog.clear()
     with caplog.at_level(logging.INFO):
-        config_file_with_unsupported_db_type = os.path.join(os.path.dirname(__file__), 'assets', 'config',
-                                                            'test_config_unsupported_db_type.yaml')
+        config_file_with_unsupported_db_type = os.path.join(
+            os.path.dirname(__file__), "assets", "config", "test_config_unsupported_db_type.yaml"
+        )
         fresh_bias_obj.set_config(config_file_with_unsupported_db_type)
         fresh_bias_obj.set_root_omop()
-    assert 'Unsupported database type' in caplog.text
+    assert "Unsupported database type" in caplog.text
 
     # Create a fake postgresql config
     config = {
@@ -51,7 +53,7 @@ def test_set_root_omop(monkeypatch, caplog, fresh_bias_obj):
             "password": "testpass",
             "hostname": "localhost",
             "port": 5432,
-            "database": "testdb"
+            "database": "testdb",
         }
     }
 
@@ -62,6 +64,7 @@ def test_set_root_omop(monkeypatch, caplog, fresh_bias_obj):
     class MockOMOPCDMDatabase:
         def __init__(self, db_url):
             self.db_url = db_url
+
         def close(self):
             pass
 
@@ -90,35 +93,41 @@ def close(self):
     assert fresh_bias_obj.bias_db is not None
     assert fresh_bias_obj.bias_db.omop_cdm_db_url == "postgresql://testuser:testpass@localhost:5432/testdb"
 
+
 def test_set_cohort_action(caplog, fresh_bias_obj):
     caplog.clear()
     with caplog.at_level(logging.INFO):
         fresh_bias_obj._set_cohort_action()
-    assert 'valid OMOP CDM must be set' in caplog.text
+    assert "valid OMOP CDM must be set" in caplog.text
+
 
 def test_create_cohort_with_no_action(caplog, fresh_bias_obj):
     caplog.clear()
     with caplog.at_level(logging.INFO):
-        fresh_bias_obj.create_cohort('test', 'test', 'test.yaml', 'test')
-    assert 'failed to create a valid cohort action object' in caplog.text
+        fresh_bias_obj.create_cohort("test", "test", "test.yaml", "test")
+    assert "failed to create a valid cohort action object" in caplog.text
+
 
 def test_compare_cohort_with_no_action(caplog, fresh_bias_obj):
     caplog.clear()
     with caplog.at_level(logging.INFO):
         fresh_bias_obj.compare_cohorts(1, 2)
-    assert 'failed to create a valid cohort action object' in caplog.text
+    assert "failed to create a valid cohort action object" in caplog.text
+
 
 def test_cohorts_concept_stats_empty_input_cohorts(caplog, fresh_bias_obj):
     caplog.clear()
     with caplog.at_level(logging.INFO):
         fresh_bias_obj.get_cohorts_concept_stats([])
-    assert 'The input cohorts list is empty. At least one cohort id must be provided.' in caplog.text
+    assert "The input cohorts list is empty. At least one cohort id must be provided." in caplog.text
+
 
 def test_cohorts_concept_stats_no_cohort_action(caplog, fresh_bias_obj):
     caplog.clear()
     with caplog.at_level(logging.INFO):
         fresh_bias_obj.get_cohorts_concept_stats([1])
-    assert 'failed to get concept prevalence stats for the union of cohorts' in caplog.text
+    assert "failed to get concept prevalence stats for the union of cohorts" in caplog.text
+
 
 def test_cohorts_union_concept_stats(test_db):
     ConceptHierarchy.clear_cache()
@@ -147,8 +156,8 @@ def test_cohorts_union_concept_stats(test_db):
     print("Concept stats per cohort:\n", stats_df.to_string(index=False), flush=True)
 
     union_result = test_db.get_cohorts_concept_stats([1, 2])
-    print(f'union_result: {union_result}', flush=True)
-    union_result['hierarchy'] = sorted(union_result['hierarchy'], key=lambda x: x['concept_id'])
+    print(f"union_result: {union_result}", flush=True)
+    union_result["hierarchy"] = sorted(union_result["hierarchy"], key=lambda x: x["concept_id"])
     # NOTE: The union_result takes cohort_start_date and cohort_end_date into account
     # when joining cohort with condition_occurrence for inclusion/exclusion criteria.
     # That means counts may differ from the raw numbers above. For example:
@@ -159,124 +168,169 @@ def test_cohorts_union_concept_stats(test_db):
     #   - Concept 5 disappears entirely, because its single occurrence is outside
     #     the cohort date window.
     # This explains why union_result values differ from the raw stats above.
-    assert union_result == {'hierarchy': [
-        {'concept_id': 316139, 'concept_name': 'Heart failure', 'concept_code': '84114007',
-         'metrics': {'1': {'count': 2, 'prevalence': 0.4},
-                     '2': {'count': 2, 'prevalence': 0.5}},
-         'source_cohorts': [1, 2],
-         'parent_ids': [], 'children': []},
-        {'concept_id': 4041664, 'concept_name': 'Difficulty breathing', 'concept_code': '230145002',
-        'metrics': {
-            '1': {'count': 4, 'prevalence': 0.8},
-            '2': {'count': 1, 'prevalence': 0.25}
-        },
-        'source_cohorts': [1, 2],
-        'parent_ids': [], 'children': []},
-        {'concept_id': 37311061, 'concept_name': 'COVID-19', 'concept_code': '840539006',
-         'metrics': {'1': {'count': 4, 'prevalence': 0.8},
-                     '2': {'count': 4, 'prevalence': 1.0}},
-         'source_cohorts': [1, 2],
-         'parent_ids': [], 'children': []},
-    ]}
+    assert union_result == {
+        "hierarchy": [
+            {
+                "concept_id": 316139,
+                "concept_name": "Heart failure",
+                "concept_code": "84114007",
+                "metrics": {"1": {"count": 2, "prevalence": 0.4}, "2": {"count": 2, "prevalence": 0.5}},
+                "source_cohorts": [1, 2],
+                "parent_ids": [],
+                "children": [],
+            },
+            {
+                "concept_id": 4041664,
+                "concept_name": "Difficulty breathing",
+                "concept_code": "230145002",
+                "metrics": {"1": {"count": 4, "prevalence": 0.8}, "2": {"count": 1, "prevalence": 0.25}},
+                "source_cohorts": [1, 2],
+                "parent_ids": [],
+                "children": [],
+            },
+            {
+                "concept_id": 37311061,
+                "concept_name": "COVID-19",
+                "concept_code": "840539006",
+                "metrics": {"1": {"count": 4, "prevalence": 0.8}, "2": {"count": 4, "prevalence": 1.0}},
+                "source_cohorts": [1, 2],
+                "parent_ids": [],
+                "children": [],
+            },
+        ]
+    }
+
 
 def test_get_domains_and_vocabularies_invalid(caplog, fresh_bias_obj):
     caplog.clear()
     with caplog.at_level(logging.INFO):
         fresh_bias_obj.get_domains_and_vocabularies()
-    assert 'valid OMOP CDM must be set' in caplog.text
+    assert "valid OMOP CDM must be set" in caplog.text
+
 
 def test_get_domains_and_vocabularies(test_db):
     domains_and_vocabularies = test_db.get_domains_and_vocabularies()
-    expected = [{'domain_id': 'Condition', 'vocabulary_id': 'ICD10CM'},
-                {'domain_id': 'Condition', 'vocabulary_id': 'SNOMED'}]
+    expected = [
+        {"domain_id": "Condition", "vocabulary_id": "ICD10CM"},
+        {"domain_id": "Condition", "vocabulary_id": "SNOMED"},
+    ]
     assert domains_and_vocabularies == expected
 
+
 def test_get_concepts_no_omop_cdm(caplog, fresh_bias_obj):
     caplog.clear()
     with caplog.at_level(logging.INFO):
-        fresh_bias_obj.get_concepts('dummy')
-    assert 'valid OMOP CDM must be set' in caplog.text
+        fresh_bias_obj.get_concepts("dummy")
+    assert "valid OMOP CDM must be set" in caplog.text
+
 
 def test_get_concepts_no_domain_and_vocab(caplog, test_db):
     caplog.clear()
     with caplog.at_level(logging.INFO):
-        test_db.get_concepts('dummy')
-    assert 'either domain or vocabulary must be set' in caplog.text
+        test_db.get_concepts("dummy")
+    assert "either domain or vocabulary must be set" in caplog.text
+
 
 def test_get_concepts(test_db):
-    concepts = test_db.get_concepts('Heart failure', domain='Condition', vocabulary='SNOMED')
-    expected = [{'concept_id': 316139, 'concept_name': 'Heart failure',
-                 'valid_start_date': datetime.date(2012, 4, 1),
-                 'valid_end_date': datetime.date(2020, 4, 1),
-                 'domain_id': 'Condition', 'vocabulary_id': 'SNOMED'}]
+    concepts = test_db.get_concepts("Heart failure", domain="Condition", vocabulary="SNOMED")
+    expected = [
+        {
+            "concept_id": 316139,
+            "concept_name": "Heart failure",
+            "valid_start_date": datetime.date(2012, 4, 1),
+            "valid_end_date": datetime.date(2020, 4, 1),
+            "domain_id": "Condition",
+            "vocabulary_id": "SNOMED",
+        }
+    ]
     assert concepts == expected
-    concepts = test_db.get_concepts('Heart failure', vocabulary='SNOMED')
+    concepts = test_db.get_concepts("Heart failure", vocabulary="SNOMED")
     assert concepts == expected
-    concepts = test_db.get_concepts('Heart failure', domain='Condition')
-    print(f'concepts: {concepts}', flush=True)
+    concepts = test_db.get_concepts("Heart failure", domain="Condition")
+    print(f"concepts: {concepts}", flush=True)
     assert concepts == expected
 
+
 def test_get_concept_hierarchy_no_omop_cdm(caplog, fresh_bias_obj):
     caplog.clear()
     with caplog.at_level(logging.INFO):
-        fresh_bias_obj.get_concept_hierarchy('dummy')
-    assert 'valid OMOP CDM must be set' in caplog.text
+        fresh_bias_obj.get_concept_hierarchy("dummy")
+    assert "valid OMOP CDM must be set" in caplog.text
+
 
 def test_get_concept_hierarchy(test_db):
     with pytest.raises(ValueError):
-        test_db.get_concept_hierarchy('not_int_str')
+        test_db.get_concept_hierarchy("not_int_str")
 
     hierarchy = test_db.get_concept_hierarchy(2)
-    print(f'hierarchy: {hierarchy}', flush=True)
-    expected = ({'details': {'concept_id': 2, 'concept_name': 'Type 1 Diabetes Mellitus', 'vocabulary_id': 'ICD10CM',
-                             'concept_code': 'E10'}, 'parents': [{'details': {'concept_id': 1, 'concept_name':
-        'Diabetes Mellitus', 'vocabulary_id': 'ICD10CM', 'concept_code': 'E10-E14'}, 'parents': []}]},
-                {'details': {'concept_id': 2, 'concept_name': 'Type 1 Diabetes Mellitus', 'vocabulary_id': 'ICD10CM',
-                             'concept_code': 'E10'}, 'children': [{'details': {'concept_id': 4, 'concept_name':
-                    'Diabetic Retinopathy', 'vocabulary_id': 'ICD10CM', 'concept_code': 'E10.3/E11.3'},
-                                                                   'children': []}]})
+    print(f"hierarchy: {hierarchy}", flush=True)
+    expected = (
+        {
+            "details": {
+                "concept_id": 2,
+                "concept_name": "Type 1 Diabetes Mellitus",
+                "vocabulary_id": "ICD10CM",
+                "concept_code": "E10",
+            },
+            "parents": [
+                {
+                    "details": {
+                        "concept_id": 1,
+                        "concept_name": "Diabetes Mellitus",
+                        "vocabulary_id": "ICD10CM",
+                        "concept_code": "E10-E14",
+                    },
+                    "parents": [],
+                }
+            ],
+        },
+        {
+            "details": {
+                "concept_id": 2,
+                "concept_name": "Type 1 Diabetes Mellitus",
+                "vocabulary_id": "ICD10CM",
+                "concept_code": "E10",
+            },
+            "children": [
+                {
+                    "details": {
+                        "concept_id": 4,
+                        "concept_name": "Diabetic Retinopathy",
+                        "vocabulary_id": "ICD10CM",
+                        "concept_code": "E10.3/E11.3",
+                    },
+                    "children": [],
+                }
+            ],
+        },
+    )
     assert hierarchy == expected
 
+
 def test_display_concept_tree_text_format(capsys, test_db):
-    sample_tree = {
-        "details": {
-            "concept_id": 123,
-            "concept_name": "Hypertension",
-            "concept_code": "I10"
-        }
-    }
+    sample_tree = {"details": {"concept_id": 123, "concept_name": "Hypertension", "concept_code": "I10"}}
     test_db.display_concept_tree(sample_tree)
     captured = capsys.readouterr()
     assert "concept tree must contain parents or children key" in captured.out
 
-    sample_tree['children'] = [{
-        "details": {
-            "concept_id": 456,
-            "concept_name": "Essential Hypertension",
-            "concept_code": "I10.0"
-            },
-        "children": []
-        }]
+    sample_tree["children"] = [
+        {
+            "details": {"concept_id": 456, "concept_name": "Essential Hypertension", "concept_code": "I10.0"},
+            "children": [],
+        }
+    ]
     test_db.display_concept_tree(sample_tree, show_in_text_format=True)
     captured = capsys.readouterr()
     assert "Hypertension (ID: 123" in captured.out
     assert "Essential Hypertension (ID: 456" in captured.out
 
+
 def test_display_concept_tree_widget(test_db):
     sample_tree = {
-        "details": {
-            "concept_id": 456,
-            "concept_name": "Essential Hypertension",
-            "concept_code": "I10.0"
-        },
-        "parents": [{
-            "details": {
-                "concept_id": 123,
-                "concept_name": "Hypertension",
-                "concept_code": "I10"
-                },
-            "parents": []
-        }]
+        "details": {"concept_id": 456, "concept_name": "Essential Hypertension", "concept_code": "I10.0"},
+        "parents": [
+            {"details": {"concept_id": 123, "concept_name": "Hypertension", "concept_code": "I10"}, "parents": []}
+        ],
     }
 
     tree_output = test_db.display_concept_tree(sample_tree, show_in_text_format=False)
diff --git a/tests/test_config.py b/tests/test_config.py
index aa66c64..d3163d2 100644
--- a/tests/test_config.py
+++ b/tests/test_config.py
@@ -4,34 +4,40 @@
 
 
 def test_load_config():
-    config = load_config(os.path.join(os.path.dirname(__file__), 'assets', 'config', 'test_config.yaml'))
+    config = load_config(os.path.join(os.path.dirname(__file__), "assets", "config", "test_config.yaml"))
 
-    assert config.get('root_omop_cdm_database') == {
-        'database_type': 'duckdb',
-        'username': 'test_username',
-        'password': 'test_password',
-        'hostname': 'test_db_hostname',
-        'database': 'shared_test_db.duckdb',
-        'port': 5432
+    assert config.get("root_omop_cdm_database") == {
+        "database_type": "duckdb",
+        "username": "test_username",
+        "password": "test_password",
+        "hostname": "test_db_hostname",
+        "database": "shared_test_db.duckdb",
+        "port": 5432,
     }
 
+
 def test_load_cohort_creation_config():
     config = load_cohort_creation_config(
-        os.path.join(os.path.dirname(__file__), 'assets', 'cohort_creation',
-                     'test_cohort_creation_condition_occurrence_config.yaml'))
-    assert 'inclusion_criteria' in config
+        os.path.join(
+            os.path.dirname(__file__),
+            "assets",
+            "cohort_creation",
+            "test_cohort_creation_condition_occurrence_config.yaml",
+        )
+    )
+    assert "inclusion_criteria" in config
     # assert 'exclusion_criteria' in config
-    assert 'temporal_events' in config.get('inclusion_criteria')
+    assert "temporal_events" in config.get("inclusion_criteria")
     # assert 'temporal_events' in config.get('exclusion_criteria')
-    assert 'demographics' in config.get('inclusion_criteria')
+    assert "demographics" in config.get("inclusion_criteria")
     # assert 'demographics' in config.get('exclusion_criteria')
-    demographics = config.get('inclusion_criteria').get('demographics')
-    assert 'gender' in demographics
-    assert 'min_birth_year' in demographics
-    assert 'max_birth_year' in demographics
-    assert demographics['max_birth_year'] >= demographics['min_birth_year']
-    assert demographics['gender'] == 'female' or demographics['gender'] == 'male'
+    demographics = config.get("inclusion_criteria").get("demographics")
+    assert "gender" in demographics
+    assert "min_birth_year" in demographics
+    assert "max_birth_year" in demographics
+    assert demographics["max_birth_year"] >= demographics["min_birth_year"]
+    assert demographics["gender"] == "female" or demographics["gender"] == "male"
 
-    in_events = config.get('inclusion_criteria')['temporal_events']
-    assert 'operator' in in_events[0]
-    assert 'events' in in_events[0]
+    in_events = config.get("inclusion_criteria")["temporal_events"]
+    assert "operator" in in_events[0]
+    assert "events" in in_events[0]
diff --git a/tests/test_database.py b/tests/test_database.py
index e08edc6..97ab8a8 100644
--- a/tests/test_database.py
+++ b/tests/test_database.py
@@ -28,6 +28,7 @@ def execute(self, query):
     assert "INSTALL postgres" in calls[0]
     assert "LOAD postgres" in calls[1]
 
+
 def test_bias_db_postgres_omop_db_url(monkeypatch):
     # Reset singleton to get a clean instance
     BiasDatabase._instance = None
@@ -51,14 +52,17 @@ def close(self):
     assert any("LOAD postgres" in call for call in calls), "LOAD postgres must be run at BiasDatabase init"
     assert any("ATTACH" in call for call in calls), "ATTACH must be run at BiasDatabase init"
 
+
 def test_bias_db_invalid_omop_db_url():
     BiasDatabase._instance = None
-    with pytest.raises(ValueError, match='Unsupported OMOP database backend'):
-        BiasDatabase(":memory:", omop_db_url='dummy_invalid_url')
+    with pytest.raises(ValueError, match="Unsupported OMOP database backend"):
+        BiasDatabase(":memory:", omop_db_url="dummy_invalid_url")
+
 
 def test_create_cohort_definition_table_error_on_sequence():
     BiasDatabase._instance = None
     db = BiasDatabase(":memory:")
+
     class MockConn:
         def __init__(self):
             self.calls = []
@@ -77,9 +81,11 @@ def close(self):
     with pytest.raises(duckdb.Error, match="random error"):
         db._create_cohort_definition_table()
 
+
 def test_create_cohort_definition_table_sequence_exists():
     BiasDatabase._instance = None
     db = BiasDatabase(":memory:")
+
     class MockConn:
         def __init__(self):
             self.call_count = 0
@@ -104,9 +110,11 @@ def close(self):
     assert db.conn.call_count >= 2
     assert any("CREATE SEQUENCE" in sql for sql in db.conn.executed_sql)
 
+
 def test_create_cohort_index_error():
     BiasDatabase._instance = None
     db = BiasDatabase(":memory:")
+
     class MockConn:
         def __init__(self):
             self.calls = []
@@ -125,9 +133,11 @@ def close(self):
     with pytest.raises(duckdb.Error, match="random error"):
         db._create_cohort_table()
 
+
 def test_create_cohort_index_exists():
     BiasDatabase._instance = None
     db = BiasDatabase(":memory:")
+
     class MockConn:
         def __init__(self):
             self.call_count = 0
@@ -152,22 +162,24 @@ def close(self):
     assert db.conn.call_count >= 2
     assert any("CREATE INDEX" in sql for sql in db.conn.executed_sql)
 
+
 def test_get_cohort_concept_stats_handles_exception(caplog):
     BiasDatabase._instance = None
     db = BiasDatabase(":memory:")
-    db.omop_cdm_db_url = 'duckdb'
+    db.omop_cdm_db_url = "duckdb"
     qry_builder = CohortQueryBuilder(cohort_creation=False)
     with pytest.raises(ValueError):
         db.get_cohort_concept_stats(123, qry_builder)
 
+
 def test_get_cohort_attributes_handles_exception():
     BiasDatabase._instance = None
     db = BiasDatabase(":memory:")
     qry_builder = CohortQueryBuilder(cohort_creation=False)
     db.omop_cdm_db_url = None
-    result_stats = db.get_cohort_basic_stats(123, variable='age')
+    result_stats = db.get_cohort_basic_stats(123, variable="age")
     assert result_stats is None
-    result = db.get_cohort_distributions(123, 'age')
+    result = db.get_cohort_distributions(123, "age")
     assert result is None
     with pytest.raises(ValueError):
         db.get_cohort_concept_stats(123, qry_builder)

From 909ae5e31b574dfa5c23140083119730886ea8ce Mon Sep 17 00:00:00 2001
From: hyi <hongyi@renci.org>
Date: Thu, 6 Nov 2025 15:28:03 -0500
Subject: [PATCH 04/12] updated test.yml to reflect updated poetry environment

---
 .github/workflows/test.yml | 9 +++++----
 biasanalyzer/database.py   | 1 +
 2 files changed, 6 insertions(+), 4 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 24c2fc5..416e31e 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -1,4 +1,4 @@
-name: test
+name: Tests and Lint
 
 on:
   # Trigger workflow on pull requests to the main branch
@@ -11,7 +11,8 @@ on:
       - main
 
 jobs:
-  test:
+  tests:
+    name: Run Unit Tests
     runs-on: ubuntu-22.04
 
     steps:
@@ -23,12 +24,12 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v4
       with:
-        python-version: "3.8.18"  # Use your project’s Python version
+        python-version: "3.12.4"  # Use your project’s Python version
 
     # Step 3: Install Poetry
     - name: Install Poetry
       run: |
-        curl -sSL https://install.python-poetry.org | POETRY_VERSION=1.8.4 python3 -
+        curl -sSL https://install.python-poetry.org | POETRY_VERSION=2.2.1 python3 -
         echo "$HOME/.local/bin" >> $GITHUB_PATH
 
     # Step 4: Install dependencies
diff --git a/biasanalyzer/database.py b/biasanalyzer/database.py
index e1e8b9f..cb449ab 100644
--- a/biasanalyzer/database.py
+++ b/biasanalyzer/database.py
@@ -1,3 +1,4 @@
+# ruff: noqa: S608
 import gc
 from datetime import datetime
 from typing import Optional

From 942b27fdceb0f09148acd8b9ea7fe15ce3351712 Mon Sep 17 00:00:00 2001
From: hyi <hongyi@renci.org>
Date: Thu, 6 Nov 2025 15:58:30 -0500
Subject: [PATCH 05/12] add ruff check run into github workflow

---
 .github/workflows/test.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 416e31e..07b51fa 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -41,3 +41,7 @@ jobs:
     - name: Run tests
       run: |
         poetry run pytest -s --cov=biasanalyzer --cov-config=.coveragerc
+
+    # Step 6: Run Ruff check
+    - name: Run ruff
+      run: poetry run ruff check .

From ff6113e85362f421f52ac1179013e37153d61cb6 Mon Sep 17 00:00:00 2001
From: hyi <hongyi@renci.org>
Date: Thu, 6 Nov 2025 16:46:53 -0500
Subject: [PATCH 06/12] adding caching in installing dependencies in github
 workflow action

---
 .github/workflows/test.yml | 27 ++++++++++++++++++++-------
 biasanalyzer/database.py   |  1 -
 2 files changed, 20 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 07b51fa..3041361 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -12,19 +12,20 @@ on:
 
 jobs:
   tests:
-    name: Run Unit Tests
+    name: Run Unit Tests and Lint
     runs-on: ubuntu-22.04
 
     steps:
     # Step 1: Checkout the repository
     - name: Checkout code
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     # Step 2: Set up Python
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
-        python-version: "3.12.4"  # Use your project’s Python version
+        python-version: "3.12.4"  # Use project’s Python version
+        cache: "poetry"  # Built-in caching for Poetry dependencies
 
     # Step 3: Install Poetry
     - name: Install Poetry
@@ -32,16 +33,28 @@ jobs:
         curl -sSL https://install.python-poetry.org | POETRY_VERSION=2.2.1 python3 -
         echo "$HOME/.local/bin" >> $GITHUB_PATH
 
-    # Step 4: Install dependencies
+    # Step 4: Cache dependencies (additional layer, more explicit)
+    - name: Cache Poetry virtualenvs
+      uses: actions/cache@v4
+      with:
+        path: |
+          ~/.cache/pypoetry
+          ~/.cache/pip
+          ~/.local/share/pypoetry/virtualenvs
+        key: poetry-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
+        restore-keys: |
+          poetry-${{ runner.os }}-
+
+    # Step 5: Install dependencies
     - name: Install dependencies
       run: |
         poetry install --with dev
 
-    # Step 5: Run Tests
+    # Step 6: Run Tests
     - name: Run tests
       run: |
         poetry run pytest -s --cov=biasanalyzer --cov-config=.coveragerc
 
-    # Step 6: Run Ruff check
+    # Step 7: Run Ruff check
     - name: Run ruff
       run: poetry run ruff check .
diff --git a/biasanalyzer/database.py b/biasanalyzer/database.py
index cb449ab..e1e8b9f 100644
--- a/biasanalyzer/database.py
+++ b/biasanalyzer/database.py
@@ -1,4 +1,3 @@
-# ruff: noqa: S608
 import gc
 from datetime import datetime
 from typing import Optional

From 60dd89ae35a2ba5934e769c205abdea364ea990a Mon Sep 17 00:00:00 2001
From: hyi <hongyi@renci.org>
Date: Thu, 6 Nov 2025 16:59:16 -0500
Subject: [PATCH 07/12] fix workflow runner failure

---
 .github/workflows/test.yml | 18 ++++--------------
 1 file changed, 4 insertions(+), 14 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 3041361..924232b 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -29,21 +29,11 @@ jobs:
 
     # Step 3: Install Poetry
     - name: Install Poetry
-      run: |
-        curl -sSL https://install.python-poetry.org | POETRY_VERSION=2.2.1 python3 -
-        echo "$HOME/.local/bin" >> $GITHUB_PATH
-
-    # Step 4: Cache dependencies (additional layer, more explicit)
-    - name: Cache Poetry virtualenvs
-      uses: actions/cache@v4
+      uses: snok/install-poetry@v1
       with:
-        path: |
-          ~/.cache/pypoetry
-          ~/.cache/pip
-          ~/.local/share/pypoetry/virtualenvs
-        key: poetry-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
-        restore-keys: |
-          poetry-${{ runner.os }}-
+        version: 2.2.1
+        virtualenvs-create: true
+        virtualenvs-in-project: true
 
     # Step 5: Install dependencies
     - name: Install dependencies

From 4837626e5d7a7b69a61f21170dc9feebf414842b Mon Sep 17 00:00:00 2001
From: hyi <hongyi@renci.org>
Date: Thu, 6 Nov 2025 17:17:58 -0500
Subject: [PATCH 08/12] trying to fix workflow runner

---
 .github/workflows/test.yml | 18 +++++++++++++++++-
 1 file changed, 17 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 924232b..f7eb8e0 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -25,7 +25,6 @@ jobs:
       uses: actions/setup-python@v5
       with:
         python-version: "3.12.4"  # Use project’s Python version
-        cache: "poetry"  # Built-in caching for Poetry dependencies
 
     # Step 3: Install Poetry
     - name: Install Poetry
@@ -35,6 +34,23 @@ jobs:
         virtualenvs-create: true
         virtualenvs-in-project: true
 
+    - name: Verify Poetry install
+      run: |
+        echo "PATH is: $PATH"
+        which poetry
+        poetry --version
+
+    - name: Cache Poetry dependencies
+      uses: actions/cache@v4
+      with:
+        path: |
+          ~/.cache/pypoetry
+          ~/.cache/pip
+          .venv
+        key: poetry-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
+        restore-keys: |
+          poetry-${{ runner.os }}-
+
     # Step 5: Install dependencies
     - name: Install dependencies
       run: |

From 79dc993d918a1fbf7da2b389667b950ecfe47c13 Mon Sep 17 00:00:00 2001
From: hyi <hongyi@renci.org>
Date: Thu, 6 Nov 2025 17:30:10 -0500
Subject: [PATCH 09/12] suppress some strict ruff checks

---
 biasanalyzer/database.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/biasanalyzer/database.py b/biasanalyzer/database.py
index e1e8b9f..cb449ab 100644
--- a/biasanalyzer/database.py
+++ b/biasanalyzer/database.py
@@ -1,3 +1,4 @@
+# ruff: noqa: S608
 import gc
 from datetime import datetime
 from typing import Optional

From 5d4bc37a48fa4ceb36ed4f359715055b29ac7939 Mon Sep 17 00:00:00 2001
From: hyi <hongyi@renci.org>
Date: Thu, 6 Nov 2025 17:46:53 -0500
Subject: [PATCH 10/12] add poetry caching in workflow runner

---
 .github/workflows/test.yml | 22 ++++++----------------
 1 file changed, 6 insertions(+), 16 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index f7eb8e0..a85b1c3 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -20,13 +20,7 @@ jobs:
     - name: Checkout code
       uses: actions/checkout@v4
 
-    # Step 2: Set up Python
-    - name: Set up Python
-      uses: actions/setup-python@v5
-      with:
-        python-version: "3.12.4"  # Use project’s Python version
-
-    # Step 3: Install Poetry
+      # Step 3: Install Poetry
     - name: Install Poetry
       uses: snok/install-poetry@v1
       with:
@@ -40,16 +34,12 @@ jobs:
         which poetry
         poetry --version
 
-    - name: Cache Poetry dependencies
-      uses: actions/cache@v4
+      # Step 2: Set up Python
+    - name: Set up Python
+      uses: actions/setup-python@v5
       with:
-        path: |
-          ~/.cache/pypoetry
-          ~/.cache/pip
-          .venv
-        key: poetry-${{ runner.os }}-${{ hashFiles('**/poetry.lock') }}
-        restore-keys: |
-          poetry-${{ runner.os }}-
+        python-version: "3.12"  # Use project’s Python version
+        cache: "poetry"
 
     # Step 5: Install dependencies
     - name: Install dependencies

From a1e995dac4b0b04c4404edc0fb3e02f1a943ece4 Mon Sep 17 00:00:00 2001
From: hyi <hongyi@renci.org>
Date: Thu, 6 Nov 2025 17:59:16 -0500
Subject: [PATCH 11/12] remove ruff check supressor to test poetry environment
 caching in github workflow runner

---
 biasanalyzer/database.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/biasanalyzer/database.py b/biasanalyzer/database.py
index cb449ab..e1e8b9f 100644
--- a/biasanalyzer/database.py
+++ b/biasanalyzer/database.py
@@ -1,4 +1,3 @@
-# ruff: noqa: S608
 import gc
 from datetime import datetime
 from typing import Optional

From e324a3ebec69aa66f2be069e6aeccf7e60952363 Mon Sep 17 00:00:00 2001
From: hyi <hongyi@renci.org>
Date: Thu, 6 Nov 2025 18:01:07 -0500
Subject: [PATCH 12/12] add back the ruff check supressor now that the caching
 appears to work

---
 biasanalyzer/database.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/biasanalyzer/database.py b/biasanalyzer/database.py
index e1e8b9f..cb449ab 100644
--- a/biasanalyzer/database.py
+++ b/biasanalyzer/database.py
@@ -1,3 +1,4 @@
+# ruff: noqa: S608
 import gc
 from datetime import datetime
 from typing import Optional