ci: add ruff linting and mypy type checking

Add ruff and mypy to dev dependencies with configuration in pyproject.toml.
Add a lint CI job that runs ruff check, ruff format --check, and mypy.
Auto-fix import sorting and formatting across the codebase. Exclude
alembic/versions from linting (auto-generated migrations). Ignore B008
(FastAPI Depends pattern) and RUF001 (unicode in user-facing strings).

21 ruff lint errors and 50 mypy errors remain for manual review.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

tests/integration/test_deferred_enrichment.py

@@ -1,22 +1,24 @@
 from __future__ import annotations
 
+from datetime import UTC, datetime
+from unittest.mock import AsyncMock, MagicMock, patch
+
 import pytest
-from unittest.mock import patch, AsyncMock, MagicMock
 from sqlalchemy import select
 from sqlalchemy.ext.asyncio import AsyncSession
-from datetime import datetime, timezone
 
-from app.db.models import CrawlRun, Publication, ScholarProfile, ScholarPublication, RunStatus, RunTriggerType
+from app.db.models import CrawlRun, Publication, RunStatus, RunTriggerType, ScholarProfile, ScholarPublication
 from app.services.domains.ingestion.application import ScholarIngestionService
 from app.services.domains.openalex.types import OpenAlexWork
 from tests.integration.helpers import insert_user
 
+
 @pytest.mark.integration
 @pytest.mark.asyncio
 async def test_deferred_enrichment_sweeps_previous_runs(db_session: AsyncSession) -> None:
     # 1. Setup: Create user and scholar
     user_id = await insert_user(db_session, email="test@example.com", password="password123")
-    
+
     scholar = ScholarProfile(
         user_id=user_id,
         scholar_id="SaiiI5MAAAAJ",
@@ -25,17 +27,17 @@ async def test_deferred_enrichment_sweeps_previous_runs(db_session: AsyncSession
     )
     db_session.add(scholar)
     await db_session.flush()
-    
+
     # 2. Simulate a previous FAILED run that left an un-enriched publication
     failed_run = CrawlRun(
         user_id=user_id,
         status=RunStatus.FAILED,
         trigger_type=RunTriggerType.MANUAL,
-        start_dt=datetime.now(timezone.utc),
+        start_dt=datetime.now(UTC),
     )
     db_session.add(failed_run)
     await db_session.flush()
-    
+
     pub = Publication(
         title_raw="A fast quantum mechanical algorithm for database search",
         title_normalized="a fast quantum mechanical algorithm for database search",
@@ -45,7 +47,7 @@ async def test_deferred_enrichment_sweeps_previous_runs(db_session: AsyncSession
     )
     db_session.add(pub)
     await db_session.flush()
-    
+
     link = ScholarPublication(
         scholar_profile_id=scholar.id,
         publication_id=pub.id,
@@ -53,17 +55,17 @@ async def test_deferred_enrichment_sweeps_previous_runs(db_session: AsyncSession
     )
     db_session.add(link)
     await db_session.commit()
-    
+
     # 3. Create a NEW run
     new_run = CrawlRun(
         user_id=user_id,
         status=RunStatus.RUNNING,
         trigger_type=RunTriggerType.MANUAL,
-        start_dt=datetime.now(timezone.utc),
+        start_dt=datetime.now(UTC),
     )
     db_session.add(new_run)
     await db_session.commit()
-    
+
     # 4. Mock OpenAlex client to return enrichment data
     mock_work = OpenAlexWork(
         openalex_id="W1234567",
@@ -76,26 +78,30 @@ async def test_deferred_enrichment_sweeps_previous_runs(db_session: AsyncSession
         is_oa=True,
         oa_url="http://example.com/grover.pdf",
     )
-    
+
     mock_source = MagicMock()
     service = ScholarIngestionService(source=mock_source)
-    
+
     # We patch the client at its source, and also mock arXiv to avoid real HTTP calls
-    with patch("app.services.domains.openalex.client.OpenAlexClient") as MockClient, \
-         patch("app.services.domains.arxiv.application.discover_arxiv_id_for_publication", new=AsyncMock(return_value=None)):
+    with (
+        patch("app.services.domains.openalex.client.OpenAlexClient") as MockClient,
+        patch(
+            "app.services.domains.arxiv.application.discover_arxiv_id_for_publication", new=AsyncMock(return_value=None)
+        ),
+    ):
         mock_instance = MockClient.return_value
         mock_instance.get_works_by_filter = AsyncMock(return_value=[mock_work])
 
         # 5. Execute the enrichment pass for the NEW run
         await service._enrich_pending_publications(db_session, run_id=new_run.id)
         await db_session.commit()
-    
+
     # 6. Verification: The publication from the FAILED run should now be enriched
     await db_session.refresh(pub)
     assert pub.openalex_enriched is True
     assert pub.citation_count == 1000
     assert pub.pdf_url == "http://example.com/grover.pdf"
-    
+
     # Double check it was indeed processed
     stmt = select(Publication).where(Publication.id == pub.id)
     result = await db_session.execute(stmt)