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Remove flat api/services/*_*.py compatibility shims

Motivation

Phase A of the service-layer SRP refactor left 51 flat re-export modules under api/services/ (e.g. blast_task_config.py, storage_data.py) that simply forwarded to the canonical subpackage path (api.services.blast.task_config, api.services.storage.data, …). Of those 51, 44 had zero remaining callers and the other 7 had a small handful of imports plus three monkeypatch string targets in tests. The shims existed only because the test_services_facade_contract.py guard test enforced their continued presence, which in turn discouraged removing them. This change cuts the dead weight in one pass.

User-facing change

None. Pure refactor; runtime behaviour is unchanged.

API / IaC diff summary

  • Deleted 51 compatibility shim files under api/services/:
  • blast_*.py (17), db_*.py (3), k8s_*.py (10), openapi_*.py (3), storage_*.py (15), warmup_*.py (4).
  • Deleted api/tests/test_services_facade_contract.py (its sole purpose was to guard the shims that no longer exist).
  • Migrated 14 callers to the canonical subpackage path (api.services.<prefix>.<name>):
  • api/_http_utils.py, api/routes/blast/preflight.py, api/services/__init__.py (reset_credential lazy import tuple), api/services/storage/usage_cache.py (docstring reference), api/tasks/blast/__init__.py, api/tasks/blast/config_shims.py (docstring + imports), api/tasks/blast/submit_task.py, api/tasks/storage/__init__.py, api/tests/test_blast_config_sharding.py (docstring), api/tests/test_blast_database_availability.py (import + monkeypatch string), api/tests/test_blast_results_parser.py (docstring), api/tests/test_response_contracts.py (two monkeypatch strings), api/tests/test_security_audit_bundle.py (sys.modules.pop calls), api/tests/test_storage_public_access.py (docstring).
  • No production code path or HTTP contract changed.
  • Historical change notes under docs/features_change/ and the planning doc docs/research/web-blast-compatibility-plan.md keep their original flat-path references — they are a historical record, not live documentation, so they were not rewritten.
  • Live agent-facing surfaces had stale comment/link references to the removed flat paths and were updated to the canonical subpackage paths in a second pass: .github/copilot-instructions.md §9, AGENTS.md, docs/copilot/codebase-map.md (rows + dropped "Compatibility wrapper:" suffixes), plus inline comments in api/routes/storage/prepare_db.py, api/services/k8s/timestamps.py, api/services/ncbi_catalogue.py, api/services/warmup/scripts.py, web/src/api/blast.ts, web/src/api/storage.ts, web/src/utils/dbSharding.ts, web/src/pages/blastSubmit/ComputeSection.tsx, web/src/pages/blastResults/analytics/helpers.ts, scripts/dev/README.md, scripts/dev/grant-local-rbac.sh.

Validation evidence

  • uv run pytest -q api/tests → 1491 passed in 34.52s.
  • uv run ruff check api → All checks passed!
  • cd web && npx tsc --noEmit → clean.
  • uv run mkdocs build --clean --strict → success.
  • grep -rn 'api[/.]services[/.](blast|db|k8s|openapi|storage|warmup)_' across the repo (excluding .venv, node_modules, site/, .pytest_cache/, .logs/, test-results/, dist/, the docs/features_change/ historical archive, docs/research/web-blast-compatibility-plan.md, and built mock-app source maps) returns zero matches.
  • uv run python -c "import api.services; import api.services.storage.data as sd; api.services.reset_credential()" → confirmed reset_blob_service_pool resolves at the canonical api.services.storage.data path (it is in that module's __all__, forwarded from api.services.storage.client_pool).