refactor(predict): T-CONTEXTS partial — _predict_batch takes ctx#87
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refactor(predict): T-CONTEXTS partial — _predict_batch takes ctx#87
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Seventh incremental Parameter Object slice. Tackles the 11-arg offender in PredictGOTermsBatchOperation, the last named target in master plan v3.2 §24 #6. Changes: - protea/core/operations/predict_go_terms.py: - New BatchPredictContext frozen dataclass bundling the 5 required + 5 optional per-call inputs (queries, references, prediction-set handle, payload, optional enrichment maps). - _predict_batch signature collapses 11 args to 1 (ctx). - Single production call site (execute branch) builds the context inline. dataclass field defaults remove the manual None-guard block that used to reset optional dicts on entry. - tests/test_predict_go_terms.py: 6 call sites in TestPredictBatch and TestPredictBatchRerankerFeatures updated to pass BatchPredictContext. Smell budget: 74 -> 73 offenders. params>6: 19 -> 18 (_predict_batch retired). File LOC and execute method LOC tick up by 31 / 2 respectively (dataclass + multi-line ctor); both pre-existing offenders, baseline refreshed via --write-baseline. Local-first 5 verde: ruff, flake8, mypy (predict_go_terms clean; 13 pre-existing test errors on develop unchanged), pytest tests/ (1163 passed, 11 skipped), check_smells.py.
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…#94) ## Acceptance criteria (master plan §24 Fase 1 — T-CONTEXTS partial) Tenth incremental Parameter Object slice. Tackles the 8-arg KNN helper for the aspect-separated path in ``PredictGOTermsBatchOperation``, the largest remaining unnamed params offender in ``predict_go_terms`` after ``_predict_batch`` (#87). Satisfies AC \"ninguna firma productiva >6 args\". ## Changes - `protea/core/operations/predict_go_terms.py`: - New ``AspectSeparatedKnnContext`` frozen dataclass alongside ``BatchPredictContext`` (6 fields: ``valid_accessions``, ``query_embeddings``, ``ref_data_by_aspect``, ``annotation_set_id``, ``prediction_set_id``, ``payload``). - ``_run_aspect_separated_knn`` signature collapses 8 args to 3 (``self``, ``session``, ``ctx``). Body unpacks ctx fields onto locals at entry to keep the ~200-LOC function body diff-free below the signature change. - Single production call site (``execute`` branch) builds the context inline. No tests reference ``_run_aspect_separated_knn`` directly (the path is exercised via the ``execute()`` integration suite). ## Smell budget **params>6: 16 -> 15** (``_run_aspect_separated_knn`` retired). File LOC ticks up 1952 -> 1978 (+26 dataclass) and ``execute`` method 338 -> 340 (+2 multi-line ctor); both pre-existing offenders, baseline refreshed via ``--write-baseline``. ## Test plan - [x] `poetry run ruff check protea scripts` - [x] `poetry run flake8 protea/` - [x] `poetry run mypy protea/core/operations/predict_go_terms.py` (Success: no issues found) - [x] `poetry run pytest tests/ --ignore=tests/test_jobs_pg.py` (1163 passed, 11 skipped) - [x] `poetry run python scripts/check_smells.py`
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Acceptance criteria (master plan §24 Fase 1 — T-CONTEXTS partial)
Seventh incremental Parameter Object slice. Tackles the 11-arg offender
_predict_batchinPredictGOTermsBatchOperation— the last named target in master plan v3.2 §24 #6 alongside_knn_transfer_and_label(#80),export_reranker_parquets(#83), and_dump_frozen_dataset(#83).Changes
protea/core/operations/predict_go_terms.py:BatchPredictContextfrozen dataclass bundling the 5 required + 5 optional per-call inputs (queries, references, prediction-set handle, payload, optional enrichment maps)._predict_batchsignature collapses 11 args to 1 (ctx).executebranch) builds the context inline;field(default_factory=dict)removes the manualref_sequences = ref_sequences or {}reset block.tests/test_predict_go_terms.py: 6 call sites inTestPredictBatchandTestPredictBatchRerankerFeaturesretargeted to pass aBatchPredictContextinstance.Smell budget
74 -> 73 offenders. params>6: 19 -> 18 (
_predict_batchretired). File LOC ticks up 1921 -> 1952 (+31 dataclass) andexecutemethod 336 -> 338 (+2 multi-line ctor); both pre-existing offenders, baseline refreshed via--write-baseline.Test plan
poetry run ruff check protea scriptspoetry run flake8 protea/poetry run mypy protea/core/operations/predict_go_terms.py(Success: no issues found)poetry run pytest tests/ --ignore=tests/test_jobs_pg.py(1163 passed, 11 skipped)poetry run python scripts/check_smells.py(73 known, none new)