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ci: add ruff linting and mypy type checking

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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>
This commit is contained in:
Justin Visser 2026-02-26 22:11:41 +01:00
parent 399276ea69
commit bf04c77aa9
137 changed files with 3066 additions and 1900 deletions
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82
app/api/routers/admin_dbops.py
View file

@ -10,14 +10,14 @@ from app.api.errors import ApiException
from app.api.responses import success_payload
from app.api.schemas import (
AdminDbIntegrityEnvelope,
AdminPdfQueueBulkEnqueueEnvelope,
AdminPdfQueueRequeueEnvelope,
AdminPdfQueueEnvelope,
AdminDbRepairJobsEnvelope,
AdminRepairPublicationNearDuplicatesEnvelope,
AdminRepairPublicationNearDuplicatesRequest,
AdminPdfQueueBulkEnqueueEnvelope,
AdminPdfQueueEnvelope,
AdminPdfQueueRequeueEnvelope,
AdminRepairPublicationLinksEnvelope,
AdminRepairPublicationLinksRequest,
AdminRepairPublicationNearDuplicatesEnvelope,
AdminRepairPublicationNearDuplicatesRequest,
)
from app.db.models import DataRepairJob, User
from app.db.session import get_db_session
@ -25,8 +25,8 @@ from app.logging_utils import structured_log
from app.services.domains.dbops import (
collect_integrity_report,
list_repair_jobs,
run_publication_near_duplicate_repair,
run_publication_link_repair,
run_publication_near_duplicate_repair,
)
from app.services.domains.publications import application as publication_service
@ -136,7 +136,15 @@ async def get_integrity_report(
admin_user: User = Depends(get_api_admin_user),
):
report = await collect_integrity_report(db_session)
structured_log(logger, "info", "api.admin.db.integrity_checked", admin_user_id=int(admin_user.id), status=report.get("status"), failure_count=len(report.get("failures", [])), warning_count=len(report.get("warnings", [])))
structured_log(
logger,
"info",
"api.admin.db.integrity_checked",
admin_user_id=int(admin_user.id),
status=report.get("status"),
failure_count=len(report.get("failures", [])),
warning_count=len(report.get("warnings", [])),
)
return success_payload(request, data=report)
@ -151,7 +159,14 @@ async def get_repair_jobs(
admin_user: User = Depends(get_api_admin_user),
):
jobs = await list_repair_jobs(db_session, limit=limit)
structured_log(logger, "info", "api.admin.db.repair_jobs_listed", admin_user_id=int(admin_user.id), limit=int(limit), job_count=len(jobs))
structured_log(
logger,
"info",
"api.admin.db.repair_jobs_listed",
admin_user_id=int(admin_user.id),
limit=int(limit),
job_count=len(jobs),
)
return success_payload(
request,
data={"jobs": [_serialize_repair_job(job) for job in jobs]},
@ -186,7 +201,9 @@ async def get_pdf_queue(
status=normalized_status,
)
structured_log(
logger, "info", "api.admin.db.pdf_queue_listed",
logger,
"info",
"api.admin.db.pdf_queue_listed",
admin_user_id=int(admin_user.id),
page=int(resolved_page),
page_size=int(resolved_limit),
@ -232,7 +249,14 @@ async def requeue_pdf_lookup(
message="Publication not found.",
)
status, message = _requeue_response_state(queued=result.queued)
structured_log(logger, "info", "api.admin.db.pdf_requeued", admin_user_id=int(admin_user.id), publication_id=int(publication_id), queued=bool(result.queued))
structured_log(
logger,
"info",
"api.admin.db.pdf_requeued",
admin_user_id=int(admin_user.id),
publication_id=int(publication_id),
queued=bool(result.queued),
)
return success_payload(
request,
data={
@ -260,7 +284,15 @@ async def requeue_all_missing_pdfs(
request_email=admin_user.email,
limit=limit,
)
structured_log(logger, "info", "api.admin.db.pdf_queue_requeue_all", admin_user_id=int(admin_user.id), limit=int(limit), requested_count=int(result.requested_count), queued_count=int(result.queued_count))
structured_log(
logger,
"info",
"api.admin.db.pdf_queue_requeue_all",
admin_user_id=int(admin_user.id),
limit=int(limit),
requested_count=int(result.requested_count),
queued_count=int(result.queued_count),
)
return success_payload(
request,
data={
@ -301,7 +333,9 @@ async def trigger_publication_link_repair(
message=str(exc),
) from exc
structured_log(
logger, "info", "api.admin.db.publication_link_repair_triggered",
logger,
"info",
"api.admin.db.publication_link_repair_triggered",
admin_user_id=int(admin_user.id),
scope_mode=payload.scope_mode,
target_user_id=int(payload.user_id) if payload.user_id is not None else None,
@ -340,7 +374,16 @@ async def trigger_publication_near_duplicate_repair(
code="invalid_near_duplicate_repair_request",
message=str(exc),
) from exc
structured_log(logger, "info", "api.admin.db.dedup_repair_triggered", admin_user_id=int(admin_user.id), dry_run=bool(payload.dry_run), selected_cluster_count=len(payload.selected_cluster_keys), job_id=int(result["job_id"]), status=result["status"])
structured_log(
logger,
"info",
"api.admin.db.dedup_repair_triggered",
admin_user_id=int(admin_user.id),
dry_run=bool(payload.dry_run),
selected_cluster_count=len(payload.selected_cluster_keys),
job_id=int(result["job_id"]),
status=result["status"],
)
return success_payload(request, data=result)
@ -381,12 +424,17 @@ async def drop_all_publications(
await db_session.execute(delete(PublicationPdfJobEvent))
await db_session.execute(delete(PublicationPdfJob))
await db_session.execute(delete(Publication))
await db_session.execute(
update(ScholarProfile).values(baseline_completed=False)
)
await db_session.execute(update(ScholarProfile).values(baseline_completed=False))
await db_session.commit()
structured_log(logger, "warning", "api.admin.db.all_publications_dropped", admin_user_id=int(admin_user.id), admin_email=admin_user.email, deleted_count=int(total_publications))
structured_log(
logger,
"warning",
"api.admin.db.all_publications_dropped",
admin_user_id=int(admin_user.id),
admin_email=admin_user.email,
deleted_count=int(total_publications),
)
return success_payload(
request,
data={