style: Apply black, ruff, and isort formatting to Python codebase

Ran formatters and linters on the entire Python codebase.

Black formatter results:
- 102 files reformatted
- 132 files left unchanged
- 3 files failed (parse errors in example files)

Ruff linter results:
- 2219 errors found
- 1957 errors automatically fixed
- 134 errors remaining (code quality issues requiring manual review)

Isort results:
- 3 files had imports reorganized

Files with parse errors (skipped by black):
- docs/generate_word_doc.py (string formatting issue)
- examples/bug_prediction.py (syntax issue)
- examples/debugging_assistant.py (syntax issue)

Remaining ruff issues (manual review needed):
- B904: Exception handling - 84 instances need "raise ... from err"
- B007: Unused loop variables - 23 instances
- F841: Unused local variables - 12 instances
- E712: Equality comparisons to True/False - 6 instances
- UP038: isinstance type union formatting - 3 instances
- C401: Generator to comprehension - 1 instance
- B017: Blind exception assertions in tests - 2 instances

All auto-fixable formatting has been applied.
Code style is now consistent across the project.
Remaining issues are code quality improvements that require
manual review and testing.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <noreply@anthropic.com>

Author: GeneAI

agents/compliance_anticipation_agent.py

@@ -17,8 +17,9 @@
 
 import logging
 import operator
+from collections.abc import Sequence
 from datetime import datetime, timedelta
-from typing import Annotated, Dict, List, Sequence, TypedDict
+from typing import Annotated, TypedDict
 
 from langchain_core.messages import AIMessage, BaseMessage
 from langgraph.graph import END, StateGraph
@@ -49,7 +50,7 @@ class ComplianceAgentState(TypedDict):
     # Progress Tracking
     # =========================================================================
     current_step: int  # 1-5
-    completed_steps: List[int]
+    completed_steps: list[int]
     messages: Annotated[Sequence[BaseMessage], operator.add]
 
     # =========================================================================
@@ -82,20 +83,14 @@ class ComplianceAgentState(TypedDict):
     compliance_percentage: float  # 0.0-100.0
 
     # Item-Level Detail
-    compliance_categories: List[
-        str
-    ]  # ["medication_safety", "documentation", "patient_safety"]
-    category_scores: Dict[
-        str, float
-    ]  # {"medication_safety": 95.0, "documentation": 88.0}
+    compliance_categories: list[str]  # ["medication_safety", "documentation", "patient_safety"]
+    category_scores: dict[str, float]  # {"medication_safety": 95.0, "documentation": 88.0}
 
     # =========================================================================
     # Gap Identification (Step 3) - Answers: "What needs fixing?"
     # =========================================================================
-    compliance_gaps: List[Dict]  # Detailed gap information
-    gap_severity_distribution: Dict[
-        str, int
-    ]  # {"critical": 2, "high": 5, "medium": 10}
+    compliance_gaps: list[dict]  # Detailed gap information
+    gap_severity_distribution: dict[str, int]  # {"critical": 2, "high": 5, "medium": 10}
 
     # Gap Structure:
     # {
@@ -117,10 +112,10 @@ class ComplianceAgentState(TypedDict):
     # =========================================================================
     documentation_prepared: bool
     documentation_url: str  # Secure storage location
-    documentation_files: List[str]  # ["compliance_summary.pdf", "gap_analysis.xlsx"]
+    documentation_files: list[str]  # ["compliance_summary.pdf", "gap_analysis.xlsx"]
 
     # Documentation Package Contents:
-    documentation_package: Dict
+    documentation_package: dict
     # {
     #   "summary_report": {...},
     #   "evidence_files": [...],
@@ -133,11 +128,11 @@ class ComplianceAgentState(TypedDict):
     # Stakeholder Notification (Step 5) - Answers: "Who needs to act?"
     # =========================================================================
     notification_sent: bool
-    notification_recipients: List[str]  # ["charge_nurse", "nurse_manager", "cno"]
+    notification_recipients: list[str]  # ["charge_nurse", "nurse_manager", "cno"]
     notification_timestamp: str  # ISO timestamp
 
     # Action Items (Assigned Work)
-    action_items: List[Dict]
+    action_items: list[dict]
     # {
     #   "action_id": "action_001",
     #   "gap_id": "gap_001",
@@ -175,11 +170,11 @@ class ComplianceAgentState(TypedDict):
     # =========================================================================
     # Error Handling & Audit Trail
     # =========================================================================
-    errors: List[str]
-    warnings: List[str]
+    errors: list[str]
+    warnings: list[str]
 
     # Full Audit Trail
-    audit_trail: List[Dict]
+    audit_trail: list[dict]
     # {
     #   "timestamp": "2025-01-20T10:00:00Z",
     #   "step": "predict_audit",
@@ -370,9 +365,7 @@ def predict_next_audit(state: ComplianceAgentState) -> ComplianceAgentState:
     - Allows time to fix gaps without pressure
     """
 
-    logger.info(
-        f"[Step 1] Predicting {state['audit_type']} audit for {state['hospital_id']}"
-    )
+    logger.info(f"[Step 1] Predicting {state['audit_type']} audit for {state['hospital_id']}")
 
     # Add to audit trail
     state["audit_trail"].append(
@@ -478,17 +471,17 @@ def check_anticipation_window(state: ComplianceAgentState) -> ComplianceAgentSta
     - Avoids wasted effort (too early) or crisis mode (too late)
     """
 
-    logger.info(
-        f"[Step 2] Checking anticipation window ({state['days_until_audit']} days)"
-    )
+    logger.info(f"[Step 2] Checking anticipation window ({state['days_until_audit']} days)")
 
     days_until = state["days_until_audit"]
 
     if 60 <= days_until <= 120:
         state["is_within_anticipation_window"] = True
         state["time_to_act"] = "timely"
         state["anticipation_window_days"] = days_until
-        message = f"✅ Within optimal anticipation window ({days_until} days). Perfect time to prepare."
+        message = (
+            f"✅ Within optimal anticipation window ({days_until} days). Perfect time to prepare."
+        )
 
     elif days_until > 120:
         state["is_within_anticipation_window"] = False
@@ -626,9 +619,7 @@ def assess_current_compliance(state: ComplianceAgentState) -> ComplianceAgentSta
     category_pct = {}
     for cat, scores in category_scores.items():
         category_pct[cat] = (
-            (scores["compliant"] / scores["total"] * 100)
-            if scores["total"] > 0
-            else 0.0
+            (scores["compliant"] / scores["total"] * 100) if scores["total"] > 0 else 0.0
         )
 
     # Update state
@@ -650,9 +641,7 @@ def assess_current_compliance(state: ComplianceAgentState) -> ComplianceAgentSta
     state["last_updated"] = datetime.now().isoformat()
 
     # Message
-    status_emoji = (
-        "✅" if compliance_pct >= 95 else "⚠️" if compliance_pct >= 85 else "🚨"
-    )
+    status_emoji = "✅" if compliance_pct >= 95 else "⚠️" if compliance_pct >= 85 else "🚨"
     state["messages"].append(
         AIMessage(
             content=f"{status_emoji} Compliance Assessment: {compliance_pct:.1f}% "
@@ -801,9 +790,7 @@ def identify_compliance_gaps(state: ComplianceAgentState) -> ComplianceAgentStat
             "details": {
                 "gap_count": len(gaps),
                 "severity_distribution": severity_dist,
-                "gaps": [
-                    {"id": g["gap_id"], "description": g["description"]} for g in gaps
-                ],
+                "gaps": [{"id": g["gap_id"], "description": g["description"]} for g in gaps],
             },
             "user": "system",
         }
@@ -937,9 +924,7 @@ def send_anticipatory_notifications(
 
     for gap in state["compliance_gaps"]:
         assignee = determine_assignee(gap)
-        deadline = calculate_deadline(
-            gap, state["days_until_audit"], state["next_audit_date"]
-        )
+        deadline = calculate_deadline(gap, state["days_until_audit"], state["next_audit_date"])
 
         action_items.append(
             {
@@ -1075,7 +1060,7 @@ def schedule_continuous_monitoring(state: ComplianceAgentState) -> ComplianceAge
 # =============================================================================
 
 
-def get_audit_requirements(audit_type: str) -> List[Dict]:
+def get_audit_requirements(audit_type: str) -> list[dict]:
     """
     Get compliance requirements for audit type
 
@@ -1177,7 +1162,7 @@ def calculate_audit_readiness_score(state: ComplianceAgentState) -> float:
     return round(readiness_score, 1)
 
 
-def determine_assignee(gap: Dict) -> str:
+def determine_assignee(gap: dict) -> str:
     """
     Determine who should be assigned to fix this gap
 
@@ -1209,7 +1194,7 @@ def determine_assignee(gap: Dict) -> str:
         return "charge_nurse"  # Default
 
 
-def calculate_deadline(gap: Dict, days_until_audit: int, audit_date: str) -> str:
+def calculate_deadline(gap: dict, days_until_audit: int, audit_date: str) -> str:
     """
     Calculate appropriate deadline for fixing gap
 
@@ -1261,7 +1246,7 @@ def get_assignee_email(assignee: str, hospital_id: str) -> str:
     return email_map.get(assignee, f"{assignee}@{hospital_id}.hospital.com")
 
 
-def compose_notification(state: ComplianceAgentState, action_items: List[Dict]) -> Dict:
+def compose_notification(state: ComplianceAgentState, action_items: list[dict]) -> dict:
     """
     Compose notification with all relevant information
     """
@@ -1290,9 +1275,7 @@ def compose_notification(state: ComplianceAgentState, action_items: List[Dict])
 
 **Category Breakdown:**
 """
-        + "\n".join(
-            f"- {cat}: {score:.1f}%" for cat, score in state["category_scores"].items()
-        )
+        + "\n".join(f"- {cat}: {score:.1f}%" for cat, score in state["category_scores"].items())
         + f"""
 
 ---
@@ -1314,11 +1297,7 @@ def compose_notification(state: ComplianceAgentState, action_items: List[Dict])
             f"   → Time: {item['estimated_time']}"
             for i, item in enumerate(action_items[:3])
         )
-        + (
-            f"\n... and {len(action_items) - 3} more action items"
-            if len(action_items) > 3
-            else ""
-        )
+        + (f"\n... and {len(action_items) - 3} more action items" if len(action_items) > 3 else "")
         + f"""
 
 ---
@@ -1353,18 +1332,14 @@ def compose_notification(state: ComplianceAgentState, action_items: List[Dict])
         "action_items": action_items,
         "documentation_url": state["documentation_url"],
         "priority": (
-            "high"
-            if state["gap_severity_distribution"].get("critical", 0) > 0
-            else "medium"
+            "high" if state["gap_severity_distribution"].get("critical", 0) > 0 else "medium"
         ),
     }
 
     return notification
 
 
-def send_notification_to_recipients(
-    notification: Dict, recipients: List[str], hospital_id: str
-):
+def send_notification_to_recipients(notification: dict, recipients: list[str], hospital_id: str):
     """
     Send notification via configured channels
 
@@ -1407,9 +1382,7 @@ async def run_compliance_agent(
         Final agent state with all results
     """
 
-    logger.info(
-        f"Starting Compliance Anticipation Agent for {hospital_id} ({audit_type})"
-    )
+    logger.info(f"Starting Compliance Anticipation Agent for {hospital_id} ({audit_type})")
 
     # Create agent
     agent = create_compliance_agent()

agents/epic_integration_wizard.py

@@ -10,8 +10,9 @@
 
 import logging
 import operator
+from collections.abc import Sequence
 from datetime import datetime
-from typing import Annotated, Sequence, TypedDict
+from typing import Annotated, TypedDict
 
 from langchain_core.messages import AIMessage, BaseMessage
 from langgraph.graph import END, StateGraph
@@ -152,18 +153,12 @@ async def step_1_prerequisites(state: WizardState) -> WizardState:
     # Even if automated prerequisites fail, user can still configure Epic manually
     if state["prerequisites_passed"]:
         state["messages"].append(
-            AIMessage(
-                content="✅ All prerequisites met. Ready to configure Epic integration."
-            )
+            AIMessage(content="✅ All prerequisites met. Ready to configure Epic integration.")
         )
     else:
         # Don't block progression - just warn user
-        state["warnings"].append(
-            f"Some automated prerequisites missing: {', '.join(missing)}"
-        )
-        state["messages"].append(
-            AIMessage(content=f"⚠️  Manual entry mode: {', '.join(missing)}")
-        )
+        state["warnings"].append(f"Some automated prerequisites missing: {', '.join(missing)}")
+        state["messages"].append(AIMessage(content=f"⚠️  Manual entry mode: {', '.join(missing)}"))
 
     return state
 
@@ -237,9 +232,7 @@ async def step_3_connection_test(state: WizardState) -> WizardState:
             state["connection_test_error"] = str(e)
             state["connection_test_passed"] = False
             state["errors"].append(f"OAuth token request failed: {str(e)}")
-            state["messages"].append(
-                AIMessage(content=f"❌ Connection failed: {str(e)}")
-            )
+            state["messages"].append(AIMessage(content=f"❌ Connection failed: {str(e)}"))
             return state
 
         state["completed_steps"].append(3)
@@ -291,9 +284,7 @@ async def step_4_resource_permissions(state: WizardState) -> WizardState:
     state["completed_steps"].append(4)
     state["current_step"] = 5
     state["messages"].append(
-        AIMessage(
-            content=f"✅ Configured {len(scopes)} resource permissions: {', '.join(scopes)}"
-        )
+        AIMessage(content=f"✅ Configured {len(scopes)} resource permissions: {', '.join(scopes)}")
     )
 
     return state
@@ -336,9 +327,7 @@ async def step_5_test_patient_lookup(state: WizardState) -> WizardState:
 
         if search_result.get("total", 0) > 0:
             patient = search_result["entry"][0]["resource"]
-            patient_name = (
-                f"{patient['name'][0]['given'][0]} {patient['name'][0]['family']}"
-            )
+            patient_name = f"{patient['name'][0]['given'][0]} {patient['name'][0]['family']}"
 
             state["patient_data_retrieved"] = True
             state["retrieved_patient_name"] = patient_name
@@ -360,9 +349,7 @@ async def step_5_test_patient_lookup(state: WizardState) -> WizardState:
         logger.error(f"Patient lookup failed: {e}", exc_info=True)
         state["patient_test_error"] = str(e)
         state["errors"].append(f"Patient lookup error: {str(e)}")
-        state["messages"].append(
-            AIMessage(content=f"❌ Patient lookup failed: {str(e)}")
-        )
+        state["messages"].append(AIMessage(content=f"❌ Patient lookup failed: {str(e)}"))
 
     return state