Fix NameError: import Optional in ankh_transformer_utils#36
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ankh_transformer_utils.py annotates `checkpoint_dir: Optional[str]` in get_model_and_tokenizer() but never imports Optional, so the module raises `NameError: name 'Optional' is not defined` at import time. This breaks the PLM detection path (tps_predict_fasta.py imports it), so sequence-only prediction produces no detections and downstream gather_detections_to_csv fails with `detections_plm does not exist`. Add `from typing import Optional`. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Problem
enzymeexplorer/src/embeddings_extraction/ankh_transformer_utils.pyannotatescheckpoint_dir: Optional[str]inget_model_and_tokenizer()(line 9) but neverimports
Optional. Python evaluates that annotation at function-definition time,so importing the module raises:
tps_predict_fasta.pyimports this module, so the sequence-only predictionpath crashes on import — the PLM detection step produces nothing, and the
downstream
gather_detections_to_csv.pythen fails withAssertionError: ... detections_plm does not exist.Fix
Add
from typing import Optional. One line.Verification
With the fix,
easy_predict_sequence_only.pyruns end-to-end on a 2-sequenceFASTA and produces the expected CSV (substrate-class probabilities +
isTPS+ID). Without it, the run fails as above.🤖 Generated with Claude Code