Adding Ruff linter and formatting

.github/workflows/test.yml

@@ -1,4 +1,4 @@
-name: test
+name: Tests and Lint
 
 on:
   # Trigger workflow on pull requests to the main branch
@@ -11,32 +11,46 @@ on:
       - main
 
 jobs:
-  test:
+  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
+      # Step 3: Install Poetry
+    - name: Install Poetry
+      uses: snok/install-poetry@v1
       with:
-        python-version: "3.8.18"  # Use your project’s Python version
+        version: 2.2.1
+        virtualenvs-create: true
+        virtualenvs-in-project: true
 
-    # Step 3: Install Poetry
-    - name: Install Poetry
+    - name: Verify Poetry install
       run: |
-        curl -sSL https://install.python-poetry.org | POETRY_VERSION=1.8.4 python3 -
-        echo "$HOME/.local/bin" >> $GITHUB_PATH
+        echo "PATH is: $PATH"
+        which poetry
+        poetry --version
 
-    # Step 4: Install dependencies
+      # Step 2: Set up Python
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: "3.12"  # Use project’s Python version
+        cache: "poetry"
+
+    # 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 7: Run Ruff check
+    - name: Run ruff
+      run: poetry run ruff check .

biasanalyzer/__init__.py

@@ -1 +1 @@
-__version__ = '0.1.0'
+__version__ = "0.1.0"

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:
@@ -22,74 +24,87 @@ 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)
         return self.cohort_action
 
     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)
 
@@ -98,20 +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:
@@ -128,9 +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
@@ -149,17 +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
@@ -170,26 +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()

biasanalyzer/background/threading_utils.py

@@ -1,6 +1,7 @@
 import threading
 import traceback
 
+
 class BackgroundResult:
     def __init__(self):
         self.value = None
@@ -12,6 +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
@@ -22,6 +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)