fix: Fix all linting and formatting issues across codebase

- Fix E402 import order in backend/api/wizards.py
- Fix B007 loop variable in benchmark_parallelization.py
- Fix E741 ambiguous variable name in context_collector.py
- Fix F821 undefined name in test_e2e.py (add TEXT_DOCUMENT_DID_OPEN)
- Fix F841 unused variables in example files
- Run black formatter on all files
- Run ruff --fix to auto-fix issues

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

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

Author: 2 people

backend/api/wizards.py

@@ -4,6 +4,7 @@
 Provides REST endpoints for wizard data.
 """
 
+import time
 
 from fastapi import FastAPI, HTTPException
 from fastapi.middleware.cors import CORSMiddleware
@@ -18,8 +19,6 @@
     allow_headers=["*"],
 )
 
-import time
-
 # Calculate timestamps for realistic created/updated dates
 NOW = int(time.time() * 1000)
 DAY_MS = 24 * 60 * 60 * 1000

benchmark_parallelization.py

@@ -44,7 +44,7 @@ def benchmark_pipeline(iterations=100):
 
         # Benchmark
         start = time.perf_counter()
-        for i in range(iterations):
+        for _ in range(iterations):
             integration.store_pattern(
                 content=test_content,
                 pattern_type="clinical",

empathy_software_plugin/wizards/performance/profiler_parsers.py

@@ -93,9 +93,16 @@ def parse(self, data: str) -> list[FunctionProfile]:
         for line in data.split("\n"):
             match = re.match(pattern, line.strip())
             if match:
-                (ncalls, tottime, percall_tot, cumtime, percall_cum, filepath, lineno, funcname) = (
-                    match.groups()
-                )
+                (
+                    ncalls,
+                    tottime,
+                    percall_tot,
+                    cumtime,
+                    percall_cum,
+                    filepath,
+                    lineno,
+                    funcname,
+                ) = match.groups()
 
                 profiles.append(
                     FunctionProfile(

examples/coach/lsp/context_collector.py

@@ -202,7 +202,11 @@ def _get_dependencies(self, file_path: Path) -> str:
         elif (project_root / "requirements.txt").exists():
             try:
                 deps = (project_root / "requirements.txt").read_text()
-                lines = [l.strip() for l in deps.split("\n") if l.strip() and not l.startswith("#")]
+                lines = [
+                    line.strip()
+                    for line in deps.split("\n")
+                    if line.strip() and not line.startswith("#")
+                ]
                 return "Python requirements:\n" + "\n".join(lines[:15])
             except Exception:
                 return "Python project (requirements.txt found)"

examples/coach/lsp/tests/test_e2e.py

@@ -14,6 +14,9 @@
 
 from ..server import CoachLanguageServer
 
+# LSP protocol method name constant
+TEXT_DOCUMENT_DID_OPEN = "textDocument/didOpen"
+
 
 class TestEndToEnd:
     """End-to-end integration tests"""

examples/domain_wizards/tests/test_healthcare_wizard.py

@@ -49,7 +49,7 @@ def test_wizard_initialization_without_security_warns(self, caplog):
             enable_security=False,  # Not HIPAA compliant
         )
 
-        wizard = HealthcareWizard(llm)
+        HealthcareWizard(llm)
 
         # Should log warning about security not enabled
         assert any(

examples/level_5_transformative/run_full_demo.py

@@ -103,14 +103,14 @@ def analyze_healthcare_handoff(memory: PatternMemory):
     # Read healthcare code
     healthcare_file = Path(__file__).parent / "data" / "healthcare_handoff_code.py"
     with open(healthcare_file) as f:
-        healthcare_code = f.read()
+        f.read()
 
     print_info("Analyzing healthcare handoff protocol...")
     print_info(f"File: {healthcare_file.name}")
     print()
 
     # Use ComplianceWizard to analyze healthcare protocol
-    wizard = ComplianceWizard()
+    ComplianceWizard()
 
     # Create mock issues based on the healthcare code's vulnerabilities
     issues = [
@@ -190,14 +190,14 @@ def analyze_deployment_pipeline(memory: PatternMemory, healthcare_pattern: dict)
     # Read deployment code
     deployment_file = Path(__file__).parent / "data" / "deployment_pipeline.py"
     with open(deployment_file) as f:
-        deployment_code = f.read()
+        f.read()
 
     print_info("Analyzing software deployment pipeline...")
     print_info(f"File: {deployment_file.name}")
     print()
 
     # Use CICDWizard to analyze deployment
-    wizard = CICDWizard()
+    CICDWizard()
 
     print("CICDWizard Analysis:")
     print_info("Standard analysis complete")
@@ -317,7 +317,7 @@ def main():
     input("\n\nPress Enter to continue to software analysis...\n")
 
     # Step 2: Analyze software domain with cross-domain pattern matching
-    prediction = analyze_deployment_pipeline(memory, healthcare_pattern)
+    analyze_deployment_pipeline(memory, healthcare_pattern)
 
     # Summary
     print_header("SUMMARY: Level 5 Systems Empathy", "=")

tests/test_clinical_protocol_monitor.py

@@ -217,7 +217,6 @@ async def test_analyze_load_protocol_on_demand(
                 return_value=mock_trajectory_prediction,
             ),
         ):
-
             context = {
                 "patient_id": "12345",
                 "sensor_data": {"heart_rate": 105, "temperature": 38.5},
@@ -255,7 +254,6 @@ async def test_analyze_with_string_sensor_data(
                 return_value=mock_trajectory_prediction,
             ),
         ):
-
             context = {
                 "patient_id": "12345",
                 "sensor_data": '{"heart_rate": 105}',
@@ -284,7 +282,6 @@ async def test_analyze_full_workflow(
                 return_value=mock_trajectory_prediction,
             ),
         ):
-
             context = {
                 "patient_id": "12345",
                 "sensor_data": {"heart_rate": 105, "temperature": 38.5},
@@ -338,7 +335,6 @@ async def test_analyze_patient_history_storage(
                 return_value=mock_trajectory_prediction,
             ),
         ):
-
             # First reading
             context1 = {"patient_id": "12345", "sensor_data": {"heart_rate": 90}}
             await monitor.analyze(context1)
@@ -374,7 +370,6 @@ async def test_analyze_history_truncation(
                 return_value=mock_trajectory_prediction,
             ),
         ):
-
             context = {"patient_id": "12345", "sensor_data": {"heart_rate": 90}}
             await monitor.analyze(context)