Enable pydocstyle (D) ruff rule and add more docs (#21)

* Use pydocstyle (D) rule with google convention

Add a ruff rule to catch missing documentation. Using google convention so that undocumented-param (D417) rule is enabled to catch missing params, xref https://docs.astral.sh/ruff/rules/undocumented-param. Extended to include D213 (instead of D212) and D410 rules too.

* Fix D100 Missing docstring in public module

* Fix D101 Missing docstring in public class

* Fix D103 Missing docstring in public function

Also ignore rule D205 to allow first sentence of docstring to wrap to multiple lines.

* Fix  D417 Missing argument description in the docstring

* Update indent in pyproject.toml file

pyproject.toml

@@ -59,8 +59,22 @@ asyncio_mode = "auto"
 [tool.ruff.lint]
 select = [
     "COM",  # flake8-commas
+    "D",    # pydocstyle
     "F",    # pyflakes
     "I",    # isort
     "RUF",  # ruff-specific
     "UP",   # pyupgrade
 ]
+extend-select = [
+    "D213",     # Summary lines should be positioned on the second physical line of the docstring.
+    "D410",     # A blank line after section headings.
+]
+ignore = [
+    "D205",     # 1 blank line required between summary line and description
+    "D212",     # Multi-line docstring summary should start at the first line
+]
+
+[tool.ruff.lint.pydocstyle]
+# See https://docs.astral.sh/ruff/faq/#does-ruff-support-numpy-or-google-style-docstrings
+# for the enabled/disabled rules for the "google" convention.
+convention = "google"

src/geo_assistant/agent/graph.py

@@ -1,3 +1,5 @@
+"""Create agent graph that calls tools."""
+
 import datetime
 
 from langchain.agents import create_agent
@@ -31,6 +33,7 @@ The current date and time is {now}.
 
 
 async def create_graph():
+    """Create langchain agent graph with a list of tools."""
     checkpointer = InMemorySaver()
     graph = create_agent(
         model=llm,

src/geo_assistant/agent/llms.py

@@ -1,3 +1,5 @@
+"""Ollama chat model."""
+
 import os
 
 from dotenv import load_dotenv

src/geo_assistant/agent/state.py

@@ -1,3 +1,5 @@
+"""State schema for the geo-assistant agent."""
+
 from typing import NotRequired
 
 from geojson_pydantic import Feature, FeatureCollection
@@ -6,6 +8,8 @@ from pydantic import Field
 
 
 class GeoAssistantState(AgentState):
+    """Schema for the geo-assistant agent's state."""
+
     place: NotRequired[Feature | None] = None
     search_area: NotRequired[Feature | None] = None
     places_within_buffer: NotRequired[FeatureCollection | None] = None

src/geo_assistant/api/app.py

@@ -1,3 +1,5 @@
+"""Chat app API endpoint."""
+
 import logging
 from collections.abc import AsyncGenerator
 from contextlib import aclosing, asynccontextmanager
@@ -21,12 +23,12 @@ UI_SET_FIELDS_WHITELIST = ["point", "messages"]
 
 
 @asynccontextmanager
-async def lifespan(app: FastAPI):
+async def _lifespan(app: FastAPI):
     app.state.chatbot = await create_graph()
     yield
 
 
-app = FastAPI(title="Geo Assistant", lifespan=lifespan)
+app = FastAPI(title="Geo Assistant", lifespan=_lifespan)
 
 
 app.add_middleware(
@@ -44,6 +46,7 @@ async def stream_chat(
     chatbot: Any,
     request: Request,
 ) -> AsyncGenerator[bytes]:
+    """Agent chat stream."""
     config: dict[str, Any] = {
         "configurable": {
             "thread_id": str(thread_id),
@@ -101,6 +104,7 @@ async def stream_chat(
 
 @app.post("/chat")
 async def chat(request: ChatRequestBody, http_request: Request) -> StreamingResponse:
+    """HTTP POST endpoint at /chat."""
     generator = stream_chat(
         ui_state_update=request.agent_state_input,
         thread_id=request.thread_id,

src/geo_assistant/api/schemas/chat.py

@@ -1,13 +1,19 @@
+"""Chat API schemas."""
+
 from pydantic import BaseModel
 
 from geo_assistant.agent.state import GeoAssistantState
 
 
 class ChatRequestBody(BaseModel):
+    """Schema for the request to the Chat API."""
+
     thread_id: str
     agent_state_input: GeoAssistantState
 
 
 class ChatResponse(BaseModel):
+    """Schema for the response from the Chat API."""
+
     thread_id: str
     state: GeoAssistantState

src/geo_assistant/frontend/app.py

@@ -1,3 +1,5 @@
+"""Chat app frontend."""
+
 import base64
 import json
 import os

src/geo_assistant/tools/__init__.py

@@ -1,3 +1,5 @@
+"""List of tools available to the agent."""
+
 from geo_assistant.tools.buffer import get_search_area
 from geo_assistant.tools.naip import fetch_naip_img
 from geo_assistant.tools.overture import get_place, get_places_within_buffer

src/geo_assistant/tools/buffer.py

@@ -1,3 +1,5 @@
+"""Tool to create a buffer polygon around a geometry feature."""
+
 from typing import Annotated
 
 import geopandas as gpd
@@ -17,8 +19,14 @@ async def get_search_area(
     state: Annotated[GeoAssistantState, InjectedState],
     tool_call_id: Annotated[str, InjectedToolCallId] = "",
 ) -> Command:
-    """Get a search area buffer in km around the place defined in the agent state."""
+    """
+    Get a search area buffer in km around the place defined in the agent state.
 
+    Args:
+        buffer_size_km: Radius of the buffer in kilometres.
+        state: Pass in 'place' as state into this agent.
+        tool_call_id: Optional ID for tracking the tool call.
+    """
     place_feature = state.get("place")
 
     if not place_feature:

src/geo_assistant/tools/naip.py

@@ -1,4 +1,5 @@
-# tools/naip_mpc_tools.py
+"""Tool to query Planetary Computer STAC API for NAIP imagery."""
+
 import base64
 from concurrent.futures import ThreadPoolExecutor
 from io import BytesIO
@@ -39,7 +40,8 @@ async def fetch_naip_img(
     Args:
         start_date: Start date (YYYY-MM-DD).
         end_date: End date (YYYY-MM-DD).
-
+        state: Pass in search_area as state into this agent.
+        tool_call_id: Optional ID for tracking the tool call
     """
     if not state["search_area"]:
         return Command(

src/geo_assistant/tools/overture.py

@@ -1,3 +1,5 @@
+"""Tool to find closest matching Overture place based on user input."""
+
 import json
 import os
 from typing import Annotated
@@ -21,7 +23,8 @@ load_dotenv()
 
 
 def create_database_connection():
-    """Create and configure a DuckDB connection with necessary extensions.
+    """
+    Create and configure a DuckDB connection with necessary extensions.
 
     Args:
         database_path: Path to the DuckDB database file
@@ -43,8 +46,14 @@ async def get_place(
     place_name: str,
     tool_call_id: Annotated[str, InjectedToolCallId] = "",
 ) -> Command:
-    """Get place location from Overture Maps based on user input place name."""
+    """
+    Get place location from Overture Maps based on user input place name.
 
+    Args:
+        place_name: An address or location given as a human-readable string.
+        tool_call_id: Optional ID for tracking the tool call.
+
+    """
     db_connection = create_database_connection()
     source = os.getenv("OVERTURE_SOURCE", "local")
     if source == "s3":
@@ -162,10 +171,16 @@ async def get_places_within_buffer(
     state: Annotated[GeoAssistantState, InjectedState],
     tool_call_id: Annotated[str, InjectedToolCallId],
 ) -> Command:
-    """Get places from Overture Maps within user specified area and user specified Overture place type.
+    """
-
+    Get places from Overture Maps within user specified area and user specified Overture
-    Accepts: restaurant(s), cafe(s), coffee shop(s), bar(s), pub(s) - case insensitive."""
+    place type.
 
+    Args:
+        place: Overture place type. Accepts: restaurant(s), cafe(s), coffee shop(s),
+               bar(s), pub(s) - case insensitive.
+        state: Pass in 'search_area' as state into this agent.
+        tool_call_id: Optional ID for tracking the tool call.
+    """
     # Normalize the place type
     place = normalize_place_type(place)
 

src/geo_assistant/tools/summarize.py

@@ -17,7 +17,7 @@ dotenv.load_dotenv()
 
 
 class SatImgSummary(dspy.Signature):
-    "Describe things you see in the satellite image."
+    """Describe things you see in the satellite image."""
 
     img: dspy.Image = dspy.InputField(desc="A satellite image")
     answer: str = dspy.OutputField(desc="Description of the image")
@@ -33,7 +33,8 @@ class SatImgSummaryAgent(dspy.Module):
         temperature: float = 0.5,
         max_tokens: int = 4_096,
     ) -> None:
-        """Initialize the satellite image summary agent.
+        """
+        Initialize the satellite image summary agent.
 
         Args:
             model: The Ollama model to use for summarization
@@ -53,7 +54,8 @@ class SatImgSummaryAgent(dspy.Module):
         self.summarizer = dspy.Predict(SatImgSummary)
 
     def forward(self, img_url: str) -> dspy.Prediction:
-        """Generate a summary for the given image URL.
+        """
+        Generate a summary for the given image URL.
 
         Args:
             img_url: URL of the image to summarize
@@ -73,7 +75,12 @@ async def summarize_sat_img(
     state: Annotated[GeoAssistantState, InjectedState],
     tool_call_id: Annotated[str | None, InjectedToolCallId] = None,
 ) -> Command:
-    """Summarize the contents of a satellite image using an LLM.
+    """
+    Summarize the contents of a satellite image using an LLM.
+
+    Args:
+        state: Pass in 'naip_img_bytes' as state into this agent.
+        tool_call_id: Optional ID for tracking the tool call.
 
     Returns:
         Command containing the image summary and metadata

tests/test_api.py

@@ -1,3 +1,5 @@
+"""Tests for chat API endpoint."""
+
 from uuid import uuid4
 
 import pytest
@@ -10,7 +12,7 @@ from geo_assistant.api.app import app
 
 @pytest_asyncio.fixture
 async def initialized_app():
-    """Initialize the app's chatbot before testing"""
+    """Initialize the app's chatbot before testing."""
     # Manually initialize the chatbot as the lifespan would
     app.state.chatbot = await create_graph()
     yield app
@@ -21,6 +23,7 @@ async def initialized_app():
 
 @pytest.mark.xfail
 async def test_call_api(initialized_app):
+    """Test calling the API at the /chat HTTP POST endpoint."""
     async with AsyncClient(
         transport=ASGITransport(app=initialized_app),
         base_url="http://test",

tests/tools/test_buffer.py

@@ -1,3 +1,5 @@
+"""Tests for buffer tool."""
+
 from geojson_pydantic import Feature, Point
 from langchain_core.tools.base import ToolCall
 from pytest import fixture
@@ -8,6 +10,7 @@ from geo_assistant.tools.buffer import get_search_area
 
 @fixture
 def geo_assistant_fixture():
+    """Fixture with a GeoJSON point feature in a GeoAssistantState."""
     place_geojson = Feature(
         type="Feature",
         geometry=Point(type="Point", coordinates=[-9.1393, 38.7223]),
@@ -22,6 +25,7 @@ def geo_assistant_fixture():
 
 
 async def test_get_search_area(geo_assistant_fixture):
+    """Ensure that `get_search_area` tool returns a buffer Polygon."""
     # Call the underlying function directly to test the logic
     # This bypasses the injection framework which is better suited for integration tests
     command = await get_search_area.ainvoke(

tests/tools/test_naip.py

@@ -1,3 +1,5 @@
+"""Tests for NAIP tool."""
+
 from types import NoneType
 
 import pytest
@@ -19,7 +21,6 @@ async def test_fetch_naip():
       - Internet access (to reach Planetary Computer STAC + blobs)
       - Planetary Computer / NAIP service to be up
     """
-
     # Union Market coordinates from GeoNames: 38.90789, -76.99831
     #   N 38°54'28"  W 76°59'54"
     # We'll use a small neighborhood AOI around that point.
@@ -60,7 +61,6 @@ async def test_fetch_naip_too_large():
       - Internet access (to reach Planetary Computer STAC + blobs)
       - Planetary Computer / NAIP service to be up
     """
-
     # Union Market coordinates from GeoNames: 38.90789, -76.99831
     #   N 38°54'28"  W 76°59'54"
     # We'll use a small neighborhood AOI around that point.

tests/tools/test_overture.py

@@ -1,3 +1,5 @@
+"""Tests for Overture tool."""
+
 import os
 
 import geopandas as gpd
@@ -57,6 +59,7 @@ def geo_assistant_with_buffer_fixture():
 
 
 async def test_get_place():
+    """Ensure that `get_place` tool returns an Overture place given a place_name."""
     command = await get_place.ainvoke(
         ToolCall(
             name="get_place",
@@ -69,6 +72,10 @@ async def test_get_place():
 
 
 async def test_get_places_within_buffer(geo_assistant_with_buffer_fixture):
+    """
+    Ensure that `get_places_within_buffer` tool returns multiple Overture places that
+    fit match the category 'cafe' within a specific buffer area around a location.
+    """
     command = await get_places_within_buffer.ainvoke(
         ToolCall(
             name="get_places_within_buffer",

tests/tools/test_summarize.py

@@ -23,6 +23,10 @@ TEST_IMAGE_URL = "https://petapixel.com/assets/uploads/2022/08/French-Officials-
     ],
 )
 async def test_summarize_sat_img(img_url, summary):
+    """
+    Ensure that the `summarize_sat_img` tool can describe a satellite image in JPEG
+    format.
+    """
     # Load the image from the supplied URL and encode it in base64
     headers = {
         "User-Agent": "Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/91.0.4472.124 Safari/537.36",