doc: improve code comments

app/agent.py

@@ -7,7 +7,14 @@ from google.genai import types
 
 from app.tools import dailymed, literature
 
-SYSTEM_INSTRUCTION = (Path(__file__).parent / "system_instruction.txt").read_text()
+CONFIG = types.GenerateContentConfig(
+    tools=[
+        dailymed.find_drug_set_ids,
+        dailymed.find_drug_instruction,
+        literature.search_medical_literature,
+    ],
+    system_instruction=(Path(__file__).parent / "system_instruction.txt").read_text(),
+)
 
 
 def respond(client: genai.Client, query: str) -> list[dict]:
@@ -22,7 +29,7 @@ def respond(client: genai.Client, query: str) -> list[dict]:
     resp = client.models.generate_content(
         model="gemini-2.5-flash-preview-04-17",
         contents=query,
-        config=config,
+        config=CONFIG,
     )
 
     output = ((resp.text) or "").strip()

app/tools/dailymed.py

@@ -30,7 +30,7 @@ def find_drug_instruction(set_id: str) -> str:
     """Get the instruction of a drug from the FDA database.
 
     The instruction includes dosage, contradictions, adverse
-    reactions, drung interactions, etc.
+    reactions, drug interactions, etc.
 
     Args:
         set_id: Set ID of the drug to look up.

app/tools/literature.py

@@ -25,9 +25,6 @@ def search_semantic_scholar(
 
 @retry(stop=stop_after_attempt(5), wait=wait_random_exponential(multiplier=0.5, max=10))
 def get_pubmed_abstracts(pmids: list[int]) -> dict[str, dict]:
-    """
-    Referenced `pymed` library for parsing the xml.
-    """
     resp = httpx.get(
         "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi",
         params={"db": "pubmed", "id": pmids, "retmode": "xml"},
@@ -41,6 +38,8 @@ def get_pubmed_abstracts(pmids: list[int]) -> dict[str, dict]:
         pmid = article.findtext(
             ".//PubmedData/ArticleIdList/ArticleId[@IdType='pubmed']", default=""
         )
+        # The abstract is sometimes divided into multiple
+        # sections. Concatenate into one Markdown text.
         for text in article.findall(".//AbstractText"):
             if label := text.attrib.get("Label"):
                 abstract += f"## {label}\n\n"
@@ -93,6 +92,8 @@ def search_medical_literature(query: str) -> str:
         if pubmed_abstract := pubmed_abstracts.get(
             publication["externalIds"].get("PubMed")
         ):
+            # Abstracts on PubMed are more complete than the
+            # ones returned from Semantic Scholar.
             publication["abstract"] = pubmed_abstract
 
         outputs.append(format_publication(publication))

main.py

@@ -1,11 +1,5 @@
-import json
-import os
-import re
-from pathlib import Path
-
 import streamlit as st
 from google import genai
-from google.genai import types
 
 from app import agent, config