chore: final linting and documentation sync (CI: PASSING)

interestng · interestng · commit 1103507aee15 · 2026-02-27T20:59:23.000-08:00
diff --git a/examples/example_explain.py b/examples/example_explain.py
@@ -1,5 +1,6 @@
 """
-Example of using the MedKit SDK to get a comprehensive explanation of a condition (e.g. diabetes).
+Example of using the MedKit SDK to get a comprehensive explanation of a
+condition (e.g. diabetes).
 """
 
 import sys
diff --git a/medkit/ask_engine.py b/medkit/ask_engine.py
@@ -1,9 +1,9 @@
 from __future__ import annotations
 
-from typing import TYPE_CHECKING, Any
+from typing import TYPE_CHECKING
 
 if TYPE_CHECKING:
-    from .client import AsyncMedKit, MedKit
+    pass
 
 
 class AskEngine:
diff --git a/medkit/cache.py b/medkit/cache.py
@@ -1,11 +1,9 @@
 from __future__ import annotations
 
 import hashlib
-import json
-import os
 import pickle
 from pathlib import Path
-from typing import Any, Optional
+from typing import Any
 
 
 class BaseCache:
diff --git a/medkit/cli.py b/medkit/cli.py
@@ -13,7 +13,6 @@
 from medkit import (
     ClinicalTrial,
     ConditionSummary,
-    MedicalGraph,
     MedKit,
     MedKitError,
     ResearchPaper,
@@ -62,8 +61,10 @@ def interactions(drugs: list[str]):
     with MedKit() as med:
         warns = med.interactions(drugs)
         if not warns:
+            drugs_str = ", ".join(drugs)
             console.print(
-                f"[bold green]No known interactions found for: {', '.join(drugs)}[/bold green]"
+                f"[bold green]No known interactions found for: "
+                f"{drugs_str}[/bold green]"
             )
             return
 
@@ -220,9 +221,9 @@ def search(query: str, as_json: bool = False):
                 return
 
             if results.metadata:
-                console.print(
-                    f"\n[dim italic]Latency: {results.metadata.query_time:.2f}s | Sources: {', '.join(results.metadata.sources)}[/dim italic]"
-                )
+                l_msg = f"\n[dim italic]Latency: {results.metadata.query_time:.2f}s | "
+                s_msg = f"Sources: {', '.join(results.metadata.sources)}[/dim italic]"
+                console.print(l_msg + s_msg)
 
             _render_search_results(results, query)
 
@@ -255,9 +256,11 @@ def explain(name: str):
     """
     try:
         with MedKit() as med:
-            with console.status(
-                f"[bold blue]Fetching comprehensive data for {name}...[/bold blue]"
-            ):
+            status_msg = (
+                f"[bold blue]Fetching comprehensive data for "
+                f"{name}...[/bold blue]"
+            )
+            with console.status(status_msg):
                 explanation = med.explain_drug(name)
 
             _render_explanation(explanation, name)
@@ -336,9 +339,9 @@ def _render_search_results(results: SearchResults, query: str):
         console.print("No active recruiting trials found")
 
     if results.metadata:
-        console.print(
-            f"\n[dim italic]Latency: {results.metadata.query_time:.2f}s | Sources: {', '.join(results.metadata.sources)}[/dim italic]"
-        )
+        latency_msg = f"\n[dim italic]Latency: {results.metadata.query_time:.2f}s | "
+        sources_msg = f"Sources: {', '.join(results.metadata.sources)}[/dim italic]"
+        console.print(latency_msg + sources_msg)
 
 
 def _render_summary(s: ConditionSummary):
diff --git a/medkit/client.py b/medkit/client.py
@@ -1,14 +1,14 @@
 from __future__ import annotations
 
 import time
-from typing import Any, Dict, List, Optional, Union
+from typing import Any, Dict
 
 import httpx
 
 from .ask_engine import AskEngine
 from .exceptions import MedKitError, PluginError
 from .exporter import Exporter
-from .graph import Edge, MedicalGraph, Node
+from .graph import MedicalGraph
 from .interactions import InteractionEngine
 from .models import (
     ClinicalTrial,
@@ -215,7 +215,8 @@ async def ask(self, question: str) -> Any:
 
         if self.debug:
             print(
-                f"[MedKit] Ask intent: {intent} for query: '{cleaned_q}' (from '{question}')"
+                f"[MedKit] Ask intent: {intent} for query: "
+                f"'{cleaned_q}' (from '{question}')"
             )
 
         if intent == "trials":
@@ -407,7 +408,8 @@ def ask(self, question: str) -> Any:
 
         if self.debug:
             print(
-                f"[MedKit] Ask intent: {intent} for query: '{cleaned_q}' (from '{question}')"
+                f"[MedKit] Ask intent: {intent} for query: "
+                f"'{cleaned_q}' (from '{question}')"
             )
 
         if intent == "trials":
diff --git a/medkit/exporter.py b/medkit/exporter.py
@@ -3,7 +3,7 @@
 import csv
 import json
 from pathlib import Path
-from typing import Any, List
+from typing import Any
 
 
 class Exporter:
diff --git a/medkit/graph.py b/medkit/graph.py
@@ -1,6 +1,6 @@
 from __future__ import annotations
 
-from typing import Any, Dict, List, Optional
+from typing import List
 
 from pydantic import BaseModel, Field
 
diff --git a/medkit/interactions.py b/medkit/interactions.py
@@ -1,6 +1,6 @@
 from __future__ import annotations
 
-from typing import Dict, List, Optional
+from typing import Dict, List
 
 from pydantic import BaseModel
 
@@ -22,7 +22,10 @@ class InteractionEngine:
             "ibuprofen": InteractionWarning(
                 severity="Moderate",
                 risk="Increased bleeding risk and decreased aspirin effectiveness.",
-                evidence="Multiple clinical studies (e.g., FDA labels, PubMed meta-analysis).",
+                evidence=(
+                    "Multiple clinical studies (e.g., FDA labels, "
+                    "PubMed meta-analysis)."
+                ),
             ),
             "warfarin": InteractionWarning(
                 severity="High",
diff --git a/medkit/models.py b/medkit/models.py
@@ -1,7 +1,5 @@
 from __future__ import annotations
 
-from typing import List, Optional
-
 from pydantic import BaseModel, Field
 
 
diff --git a/medkit/providers/clinicaltrials.py b/medkit/providers/clinicaltrials.py
@@ -49,8 +49,13 @@ async def get(self, item_id: str) -> ClinicalTrial:
             raise APIError(f"ClinicalTrials.gov API error: {e}") from e
 
     def _get_headers(self) -> dict[str, str]:
+        ua = (
+            "Mozilla/5.0 (Windows NT 10.0; Win64; x64) "
+            "AppleWebKit/537.36 (KHTML, like Gecko) "
+            "Chrome/120.0.0.0 Safari/537.36"
+        )
         return {
-            "User-Agent": "Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/120.0.0.0 Safari/537.36",
+            "User-Agent": ua,
             "Accept": "application/json",
         }
 
diff --git a/medkit/utils.py b/medkit/utils.py
@@ -59,7 +59,8 @@ def wait(self) -> None:
 def paginate(fetch_page: Callable[[int], List[Any]], max_pages: int = 5) -> List[Any]:
     """
     Helper function to paginate through API results.
-    `fetch_page` should be a function that takes a page index and returns a list of items.
+    `fetch_page` should be a function that takes a page index and returns a list
+    of items.
     Expects `fetch_page` to return an empty list when no more data is available.
     """
     results = []
diff --git a/pyproject.toml b/pyproject.toml
@@ -44,4 +44,4 @@ target-version = "py39"
 
 [tool.ruff.lint]
 select = ["E", "F", "I"]
-unfixable = ["F401"] # Keep unused imports in __init__.py if needed, but here we want to clean them. Actually, F401 is mostly good.
+fixable = ["ALL"]
diff --git a/tests/test_client.py b/tests/test_client.py
@@ -7,7 +7,6 @@
 import pytest
 
 from medkit.client import AsyncMedKit, MedKit
-from medkit.exceptions import NotFoundError, RateLimitError
 from medkit.models import ClinicalTrial, DrugInfo, ResearchPaper
 
 
@@ -106,7 +105,8 @@ async def test_async_search():
         med._providers["clinicaltrials"].search.return_value = []
 
         # Test search
-        # Note: we don't assert brand_name here because med.search() swallows drug errors if not found
+        # Note: we don't assert brand_name here because med.search() swallows drug
+        # errors if not found
         # but since we mocked it to return something, it should work.
         res = await med.search("aspirin")
         assert res.metadata is not None
