chore: major linting and code style cleanup (143 fixes)

Author: somethingcoold

examples/example_ask.py

@@ -11,23 +11,25 @@
 from medkit import MedKit
 from medkit.exceptions import MedKitError
 
+
 def main():
     questions = [
         "What are new treatments for Alzheimer's?",
         "clinical trials for diabetes",
         "latest research on CRISPR",
-        "tell me about ibuprofen"
+        "tell me about ibuprofen",
     ]
-    
+
     try:
         with MedKit(debug=True) as med:
             for q in questions:
                 print(f"\n>>> Question: {q}")
                 res = med.ask(q)
                 print(f"Result type: {type(res).__name__}")
-                
+
     except MedKitError as e:
         print(f"Error: {e}")
 
+
 if __name__ == "__main__":
     main()

examples/example_async.py

@@ -2,8 +2,8 @@
 Example of using the asynchronous MedKit SDK.
 """
 
-import sys
 import asyncio
+import sys
 from pathlib import Path
 
 # Add project root to sys.path
@@ -12,24 +12,26 @@
 from medkit import AsyncMedKit
 from medkit.exceptions import MedKitError
 
+
 async def main():
     query = "diabetes"
     try:
         async with AsyncMedKit() as med:
             print(f"Async search for '{query}'...")
             results = await med.search(query)
-            
+
             print(f"\n--- Results for {query} ---")
             print(f"Drugs found: {len(results.drugs)}")
             print(f"Papers found: {len(results.papers)}")
             print(f"Trials found: {len(results.trials)}")
-            
+
             if results.papers:
                 print("\nTop Paper:")
                 print(f"- {results.papers[0].title}")
-                
+
     except MedKitError as e:
         print(f"Error: {e}")
 
+
 if __name__ == "__main__":
     asyncio.run(main())

examples/example_drugs.py

@@ -11,12 +11,13 @@
 from medkit import MedKit
 from medkit.exceptions import MedKitError
 
+
 def main():
     try:
         with MedKit() as med:
             print("Fetching info for 'ibuprofen'...")
             info = med.drug("ibuprofen")
-            
+
             print(f"Brand Name: {info.brand_name}")
             print(f"Generic Name: {info.generic_name}")
             print(f"Manufacturer: {info.manufacturer}")
@@ -26,5 +27,6 @@ def main():
     except MedKitError as e:
         print(f"Error: {e}")
 
+
 if __name__ == "__main__":
     main()

examples/example_explain.py

@@ -11,39 +11,41 @@
 from medkit import MedKit
 from medkit.exceptions import MedKitError
 
+
 def main():
     query = "diabetes"
     try:
         with MedKit() as med:
             print(f"Generating comprehensive report for '{query}'...")
             explanation = med.explain_drug(query)
-            
+
             if explanation.drug_info:
                 print("\n=== FDA Information ===")
                 print(f"Brand Name: {explanation.drug_info.brand_name}")
                 print(f"Generic Name: {explanation.drug_info.generic_name}")
             else:
                 print("\n=== FDA Information ===")
                 print(f"No FDA info found for '{query}'")
-            
+
             if explanation.papers:
                 print(f"\n=== Research Papers (Top {len(explanation.papers)}) ===")
                 for i, p in enumerate(explanation.papers, 1):
                     print(f"{i}. {p.title} ({p.year})")
             else:
                 print("\n=== Research Papers ===")
                 print("No recent papers found")
-                
+
             if explanation.trials:
-                print(f"\n=== Clinical Trials ===")
+                print("\n=== Clinical Trials ===")
                 for t in explanation.trials:
                     print(f"- {t.title} [{t.status}]")
             else:
                 print("\n=== Clinical Trials ===")
                 print("No active recruiting trials found")
-                
+
     except MedKitError as e:
         print(f"Error: {e}")
 
+
 if __name__ == "__main__":
     main()

examples/example_graph.py

@@ -11,22 +11,24 @@
 from medkit import MedKit
 from medkit.exceptions import MedKitError
 
+
 def main():
     query = "diabetes"
     try:
         with MedKit() as med:
             print(f"Building medical relationship graph for '{query}'...")
             graph = med.graph(query)
-            
+
             print(f"\nNodes found: {len(graph.nodes)}")
             print(f"Relationships found: {len(graph.edges)}")
-            
+
             print("\nRelationships:")
             for edge in graph.edges[:10]:
                 print(f"- {edge.source} --({edge.relationship})--> {edge.target}")
-                
+
     except MedKitError as e:
         print(f"Error: {e}")
 
+
 if __name__ == "__main__":
     main()

examples/example_papers.py

@@ -11,12 +11,13 @@
 from medkit import MedKit
 from medkit.exceptions import MedKitError
 
+
 def main():
     try:
         with MedKit() as med:
             print("Searching for recent papers on 'CRISPR'...")
             papers = med.papers("CRISPR", limit=5)
-            
+
             for paper in papers:
                 print(f"\nTitle: {paper.title}")
                 print(f"Journal: {paper.journal} ({paper.year})")
@@ -25,5 +26,6 @@ def main():
     except MedKitError as e:
         print(f"Error: {e}")
 
+
 if __name__ == "__main__":
     main()

examples/example_plugin.py

@@ -12,6 +12,7 @@
 from medkit import MedKit
 from medkit.providers.base import BaseProvider
 
+
 class MyHospitalProvider(BaseProvider):
     def __init__(self):
         super().__init__(name="hospital")
@@ -20,26 +21,28 @@ def search_sync(self, query: str, **kwargs) -> dict[str, Any]:
         return {
             "source": "Local Hospital Database",
             "patient_count": 120,
-            "query": query
+            "query": query,
         }
 
+
 def main():
     try:
         med = MedKit(debug=True)
-        
+
         # Register the plugin
         med.register_provider(MyHospitalProvider())
-        
+
         # Query the plugin (via some generic search or direct provider access)
         # For now, let's just see if it's in the list
         print(f"Registered providers: {list(med._providers.keys())}")
-        
+
         # Direct query test
         res = med._providers["hospital"].search_sync("diabetes")
         print(f"Plugin result: {res}")
-        
+
     except Exception as e:
         print(f"Error: {e}")
 
+
 if __name__ == "__main__":
     main()

examples/example_search.py

@@ -11,30 +11,32 @@
 from medkit import MedKit
 from medkit.exceptions import MedKitError
 
+
 def main():
     query = "insulin"
     try:
         with MedKit() as med:
             print(f"Searching for '{query}' across all sources...")
             results = med.search(query)
-            
+
             if results.drugs:
                 print("\n=== Found Drugs ===")
                 for d in results.drugs:
                     print(f"Drug: {d.brand_name} ({d.generic_name})")
-            
+
             if results.papers:
                 print(f"\n=== Research Papers (Top {len(results.papers)}) ===")
                 for i, p in enumerate(results.papers, 1):
                     print(f"{i}. {p.title} ({p.year})")
-            
+
             if results.trials:
                 print(f"\n=== Clinical Trials ({len(results.trials)}) ===")
                 for t in results.trials:
                     print(f"- {t.nct_id}: {t.status} - {t.title}")
-                
+
     except MedKitError as e:
         print(f"Error: {e}")
 
+
 if __name__ == "__main__":
     main()

examples/example_summary.py

@@ -11,37 +11,39 @@
 from medkit import MedKit
 from medkit.exceptions import MedKitError
 
+
 def main():
     query = "diabetes"
     try:
         with MedKit() as med:
             print(f"Generating medical summary for '{query}'...")
             summary = med.summary(query)
-            
+
             print(f"\nCondition: {summary.condition.capitalize()}")
-            
+
             if summary.drugs:
                 print("\nDrugs:")
                 for drug in summary.drugs:
                     print(f"- {drug}")
-            
+
             if summary.papers:
                 years = [p.year for p in summary.papers if p.year]
                 year_range = f" ({max(years)}–{min(years)})" if years else ""
                 print(f"\nLatest Research{year_range}:")
                 for p in summary.papers:
                     print(f"- {p.title} ({p.year})")
-            
+
             if summary.trials:
                 print("\nClinical Trials:")
                 for t in summary.trials:
                     print(f"- {t.nct_id}: {t.status} - {t.title}")
             else:
                 print("\nClinical Trials:")
                 print("No active recruiting trials found")
-                
+
     except MedKitError as e:
         print(f"Error: {e}")
 
+
 if __name__ == "__main__":
     main()

examples/example_trials.py

@@ -11,13 +11,14 @@
 from medkit import MedKit
 from medkit.exceptions import MedKitError
 
+
 def main():
     try:
         with MedKit() as med:
             print("Searching for recruiting clinical trials for 'breast cancer'...")
             # We specifically request recruiting trials
             trials = med.trials("breast cancer", recruiting=True, limit=5)
-            
+
             for trial in trials:
                 print(f"\nTrial: {trial.title}")
                 print(f"ID: {trial.nct_id}")
@@ -27,5 +28,6 @@ def main():
     except MedKitError as e:
         print(f"Error: {e}")
 
+
 if __name__ == "__main__":
     main()