Release 0.0.3 -- ensures MIMIC-IV ETL can be run without `rootutils` and that it works with unzipped files.

mmcdermott commented 3 months ago

Summary by CodeRabbit

New Features
- Added support for ignoring additional spelling errors in spell-checking.
- Introduced an optional argument for unzipping CSV files before processing.
- Added a new transformation capability for reordering measurements based on regex patterns.
Bug Fixes
- Improved error handling for file loading processes and command-line argument validation.
Documentation
- Updated documentation for various functions to reflect parameter name changes and improved clarity.
Tests
- Introduced comprehensive tests for the new measurement reordering functionality.
- Enhanced testing framework to include new transformation-related testing scenarios.
Chores
- Removed unnecessary dependencies and cleaned up import statements across files.

coderabbitai[bot] commented 3 months ago

Walkthrough

The changes enhance the functionality and flexibility of several scripts within the project. Notable updates include expanded spell-checking options, improved data loading processes, and the introduction of new transformation capabilities for reordering measurements. Configuration files have been refined to align with these updates, ensuring clarity and consistency. Overall, these modifications streamline workflows and enrich the project's capabilities.

Changes

Files/Paths	Change Summary
`.pre-commit-config.yaml`	Expanded `codespell` ignore words list to include "crate" alongside "ehr".
`MIMIC-IV_Example/joint_script.sh`	Added optional argument `do_unzip` to enhance file processing flexibility.
`MIMIC-IV_Example/pre_MEDS.py`	Removed `load_raw_mimic_file`, replaced with dynamic file reading using `get_supported_fp`, and improved error handling.
`eICU_Example/pre_MEDS.py`	Removed `rootutils` import and initialization, simplifying directory management.
`pyproject.toml`	Removed `rootutils` from dependencies; added support for `MEDS_transform-reorder_measurements`.
`src/MEDS_transforms/...`	Various parameter renames (e.g., `code_modifier_columns` to `code_modifiers`), improved function signatures, and streamlined logic.
`src/MEDS_transforms/configs/preprocess.yaml`	Renamed configuration parameter from `code_modifier_columns` to `code_modifiers`.
`src/MEDS_transforms/configs/...`	Introduced `reorder_measurements.yaml` file to define measurement reordering rules.
`src/MEDS_transforms/utils.py`	Added `get_smallest_valid_uint_type` function for determining optimal unsigned integer types.
`tests/...`	Added tests for `reorder_measurements` functionality and enhanced utility functions for testing.

Sequence Diagram(s)

sequenceDiagram
    participant User
    participant JointScript
    participant PreMEDS
    participant Config
    participant Transform

    User->>JointScript: Run script with do_unzip argument
    JointScript->>PreMEDS: Process files based on configuration
    PreMEDS->>Config: Read dynamic file format
    Config->>Transform: Apply transformations
    Transform->>User: Return processed data

🐇 In a world of code and lines,
A rabbit hops through changing times.
With spells corrected, files in sync,
New paths appear, and stars now blink.
So let us cheer for every mod,
For coding's joy is truly broad! 🌟

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codecov-commenter commented 3 months ago

:warning: Please install the 'codecov app svg image' to ensure uploads and comments are reliably processed by Codecov.

Codecov Report

Attention: Patch coverage is 97.26027% with 4 lines in your changes missing coverage. Please review.

Project coverage is 92.48%. Comparing base (e1e6260) to head (9a5de23). Report is 415 commits behind head on main.

Files with missing lines	Patch %	Lines
src/MEDS_transforms/mapreduce/mapper.py	95.16%	3 Missing :warning:
...MEDS_transforms/transforms/reorder_measurements.py	97.56%	1 Missing :warning:

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #115 +/- ## ========================================== + Coverage 92.20% 92.48% +0.28% ========================================== Files 12 24 +12 Lines 539 1664 +1125 ========================================== + Hits 497 1539 +1042 - Misses 42 125 +83 ```

:umbrella: View full report in Codecov by Sentry.
:loudspeaker: Have feedback on the report? Share it here.

mmcdermott / MEDS_transforms