Test cases and (eventually) fixes for #114

[mmcdermott]

STILL IN PROGRESS. We just have failing test cases for now.

[coderabbitai]

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Walkthrough

The recent updates across multiple files primarily focus on enhancing the project's functionalities and readability. Key changes include upgrading the Python setup in the workflow to version 3.11, incorporating the loguru logging library for better logging, refining several data handling functionalities, updating various import and method calls for better consistency, and improving documentation. These modifications collectively aim to boost performance, streamline data processes, and enhance logging and error handling throughout the project.

Changes

File/Directory	Change Summary
.github/workflows/tests.yml	Updated Python version from 3.10 to 3.11.
EventStream/baseline/FT_task_baseline.py	Replaced print statements with loguru.logger.info, updated string cache setting, and added Parquet file handling for specific columns.
EventStream/data/README.md	Updated representation of missing data values from np.NaN to float('nan').
EventStream/data/config.py	Enhanced PytorchDatasetConfig class to support subsampling, added caching and new properties.
EventStream/data/dataset_base.py	Refined method signatures, removed abstract methods, enhanced logging, and improved data processing logic.
EventStream/data/time_dependent_functor.py	Adjusted pl_expr method and handling of metadata keys in AgeFunctor class.
EventStream/data/types.py	Modified list structure by changing null to nul in convert_to_DL_DF method.
EventStream/data/visualize.py	Removed age distribution plotting method and attribute, updated group method calls.
EventStream/logger.py	Introduced hydra_loguru_init() function for logging initialization in Hydra applications.
EventStream/tasks/profile.py	Updated string cache setting and various data type specifications, replaced groupby with group_by.
EventStream/transformer/config.py	Enhanced logging by replacing print statements with loguru.logger.warning.
EventStream/transformer/lightning_modules/embedding.py	Replaced print statements with loguru.logger.info.
EventStream/transformer/lightning_modules/fine_tuning.py	Added loguru logging for various message types.
EventStream/transformer/lightning_modules/generative_modeling.py	Incorporated loguru logging and updated configuration logging messages.
EventStream/transformer/lightning_modules/zero_shot_evaluator.py	Added loguru logging for errors and info messages.
EventStream/transformer/model_output.py	Enhanced exception handling and replaced print statements with loguru.logger.warning.
EventStream/transformer/transformer.py	Updated attn_dropout handling and method signatures, enhanced logging and computation logic.
EventStream/utils.py	Removed unnecessary sys import, added loguru for error logging in the wrap function.
README.md	Clarified polars version dependency and updated function name changes post-version 0.19.
configs/README.md	Removed normalizer_config: standard_scaler from YAML configuration.
docs/MIMIC_IV_tutorial/data_extraction_processing.md	Updated configuration file paths and commands from EFGPT to ESGPT.
scripts/prepare_pretrain_subsets.py	Introduced new changes and enhancements (specific changes not detailed).

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