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>

app/services/domains/portability/application.py

@@ -18,7 +18,7 @@ from app.services.domains.portability.publication_import import (
     _upsert_imported_publication,
 )
 from app.services.domains.portability.scholar_import import _upsert_imported_scholars
-from app.services.domains.portability.types import ImportExportError, ImportedPublicationInput
+from app.services.domains.portability.types import ImportedPublicationInput, ImportExportError
 
 
 async def import_user_data(
@@ -58,8 +58,8 @@ async def import_user_data(
 
 __all__ = [
     "EXPORT_SCHEMA_VERSION",
-    "MAX_IMPORT_SCHOLARS",
     "MAX_IMPORT_PUBLICATIONS",
+    "MAX_IMPORT_SCHOLARS",
     "ImportExportError",
     "ImportedPublicationInput",
     "export_user_data",

app/services/domains/portability/exporting.py

@@ -1,6 +1,6 @@
 from __future__ import annotations
 
-from datetime import datetime, timezone
+from datetime import UTC, datetime
 from typing import Any
 
 from sqlalchemy import select
@@ -11,7 +11,7 @@ from app.services.domains.portability.constants import EXPORT_SCHEMA_VERSION
 
 
 def _exported_at_iso() -> str:
-    return datetime.now(timezone.utc).replace(microsecond=0).isoformat()
+    return datetime.now(UTC).replace(microsecond=0).isoformat()
 
 
 def _serialize_export_scholar(profile: ScholarProfile) -> dict[str, Any]:
@@ -58,9 +58,7 @@ async def export_user_data(
     user_id: int,
 ) -> dict[str, Any]:
     scholars_result = await db_session.execute(
-        select(ScholarProfile)
-        .where(ScholarProfile.user_id == user_id)
-        .order_by(ScholarProfile.id.asc())
+        select(ScholarProfile).where(ScholarProfile.user_id == user_id).order_by(ScholarProfile.id.asc())
     )
     publication_result = await db_session.execute(
         select(

app/services/domains/portability/normalize.py

@@ -104,6 +104,4 @@ def _validate_import_sizes(
     if len(scholars) > MAX_IMPORT_SCHOLARS:
         raise ImportExportError(f"Import exceeds max scholars ({MAX_IMPORT_SCHOLARS}).")
     if len(publications) > MAX_IMPORT_PUBLICATIONS:
-        raise ImportExportError(
-            f"Import exceeds max publications ({MAX_IMPORT_PUBLICATIONS})."
-        )
+        raise ImportExportError(f"Import exceeds max publications ({MAX_IMPORT_PUBLICATIONS}).")

app/services/domains/portability/publication_import.py

@@ -6,8 +6,8 @@ from sqlalchemy import select
 from sqlalchemy.ext.asyncio import AsyncSession
 
 from app.db.models import Publication, ScholarProfile, ScholarPublication
-from app.services.domains.ingestion.application import build_publication_url, normalize_title
 from app.services.domains.doi.normalize import normalize_doi
+from app.services.domains.ingestion.application import build_publication_url, normalize_title
 from app.services.domains.portability.normalize import (
     _normalize_citation_count,
     _normalize_optional_text,
@@ -22,9 +22,7 @@ async def _find_publication_by_cluster(
     *,
     cluster_id: str,
 ) -> Publication | None:
-    result = await db_session.execute(
-        select(Publication).where(Publication.cluster_id == cluster_id)
-    )
+    result = await db_session.execute(select(Publication).where(Publication.cluster_id == cluster_id))
     return result.scalar_one_or_none()
 
 
@@ -33,9 +31,7 @@ async def _find_publication_by_fingerprint(
     *,
     fingerprint_sha256: str,
 ) -> Publication | None:
-    result = await db_session.execute(
-        select(Publication).where(Publication.fingerprint_sha256 == fingerprint_sha256)
-    )
+    result = await db_session.execute(select(Publication).where(Publication.fingerprint_sha256 == fingerprint_sha256))
     return result.scalar_one_or_none()
 
 

app/services/domains/portability/scholar_import.py

@@ -15,9 +15,7 @@ async def _load_user_scholar_map(
     *,
     user_id: int,
 ) -> dict[str, ScholarProfile]:
-    result = await db_session.execute(
-        select(ScholarProfile).where(ScholarProfile.user_id == user_id)
-    )
+    result = await db_session.execute(select(ScholarProfile).where(ScholarProfile.user_id == user_id))
     profiles = list(result.scalars().all())
     return {profile.scholar_id: profile for profile in profiles}
 
@@ -70,9 +68,7 @@ async def _upsert_imported_scholars(
     for item in scholars:
         try:
             scholar_id = scholar_service.validate_scholar_id(str(item["scholar_id"]))
-            display_name = scholar_service.normalize_display_name(
-                str(item.get("display_name") or "")
-            )
+            display_name = scholar_service.normalize_display_name(str(item.get("display_name") or ""))
             override_url = scholar_service.normalize_profile_image_url(
                 _normalize_optional_text(item.get("profile_image_override_url"))
             )