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gene retrieval via API#7

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Vincent-Ustach wants to merge 49 commits intomims-harvard:mainmims-harvard/ProCyon:mainfrom GeneDx:mainGeneDx/ProCyon:mainCopy head branch name to clipboard

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Commits on Jan 16, 2025

• initial commit

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• store false for inference_bool

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• require task_desc_infile

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• task_desc_infile pathlib path

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• inference_bool default True

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• inference_bool typo

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• import DataArgs

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• set model device data_args to None

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Commits on Jan 17, 2025

• Merge pull request #2 from mims-harvard/main

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• read disease desc

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• Merge branch 'refs/heads/main' into retrieval_script

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• reduce precision of model before loading to device

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• copy retrieval script

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• rename files

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• if no model load no create_input_retrieval

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• remove unused imports

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• if no model no create_input_retrieval

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• remove unused imports

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• black formatting

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• refactor with startup and do methods for later api

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• docstrings

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• bug in calling startup_retrieval

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• fastapi app

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• add more required env vars

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• move utils to inference/retrieval_utils.py

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• fix imports for retrieval_utils

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• typo

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• update comment

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Commits on Jan 18, 2025

• instruction_source_dataset passed as argument

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• update docstring for app

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Commits on Jan 19, 2025

• bug w repeated model.to_device() commands

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• return top k

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• by default return all records

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• fillna

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Commits on Jan 22, 2025

• remove disease from input description. remove unused imports in app.

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• remove disease from input description. remove unused imports in app.

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• delete drug script

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• update docstrings

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• remove exception catch

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• move args in script

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• move args in call to do_retrieval

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• move args in app call to do_retrieval

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• try again w args in script

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• default of omim

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• declare all_protein_embeddings as global in retrieve_proteins

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• remove exceptions from highest level of app

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• duplicate loguru removed from pyproject.toml

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• black formatting

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Commits on Jan 27, 2025

• Merge pull request #1 from GeneDx/retrieval_script

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