fix: remove deprecated code_mapping, dev, refresh_cache from examples and README#935
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haoyu-haoyu wants to merge 1 commit intosunlabuiuc:masterfrom
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fix: remove deprecated code_mapping, dev, refresh_cache from examples and README#935haoyu-haoyu wants to merge 1 commit intosunlabuiuc:masterfrom
haoyu-haoyu wants to merge 1 commit intosunlabuiuc:masterfrom
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The v2.0 MIMIC3Dataset/MIMIC4Dataset (based on BaseDataset) no longer accepts code_mapping, dev, or refresh_cache parameters. These were part of the legacy BaseEHRDataset API. Update README.rst, example scripts, and leaderboard utilities to use the current v2.0 API. Note: task file docstrings and pyhealth/datasets/mimicextract.py still reference code_mapping but are left for separate PRs since mimicextract.py has not yet been migrated to v2.0. Fixes sunlabuiuc#535
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Summary
Remove references to deprecated
code_mapping,dev, andrefresh_cacheparameters from example scripts and README. These parameters belonged to the legacyBaseEHRDatasetAPI and are no longer accepted by the v2.0MIMIC3Dataset/MIMIC4Dataset(based onBaseDataset).Files updated
README.rstcode_mapping={"NDC": "CCSCM"}from quickstart exampleexamples/mortality_prediction/mortality_mimic3_grasp.pycode_mapping,dev,refresh_cacheexamples/drug_recommendation/drug_recommendation_mimic4_gamenet.pycode_mapping,dev,refresh_cacheexamples/patient_linkage_mimic3_medlink.pycode_mapping,dev,refresh_cacheleaderboard/utils.pycode_mapping,dev,refresh_cachefrom MIMIC3/MIMIC4 loadersOut of scope (for follow-up PRs)
pyhealth/tasks/*.py) — these containcode_mappingin>>>doctest examples that also need updatingpyhealth/datasets/mimicextract.py— still uses the legacy API (not yet migrated to v2.0)chat-assistant/corpus/— auto-generated text corpus, will update when source docs are fixedFixes #535