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Files that changed from the base of the PR and between 63b9705308b8b17ccf9b305cb3625355b5516399 and e5a2935ad4c206129ad2ece19781dea3493bf3e7.
Walkthrough
The changes include updates to GitHub Actions workflows, configuration files for documentation, and enhancements to data processing scripts. Key modifications involve broadening pre-commit checks, restructuring documentation, and refining YAML configurations for model training and evaluation. New utility scripts for data extraction and normalization were introduced, while existing functions were improved for clarity and functionality. Additionally, a workflow for publishing Python packages to PyPI and TestPyPI was established.
Changes
| File(s) | Change Summary |
|---|---|
.github/workflows/code-quality-pr.yaml |
Changed extra_args from --files ${{ steps.file_changes.outputs.files}} to --all-files for broader pre-commit checks. |
.pre-commit-config.yaml |
Updated exclude pattern from "sample_data|docs/MIMIC_IV_tutorial/wandb_reports" to "tests/test_data". |
.readthedocs.yaml |
New configuration file for Read the Docs, specifying build settings and linking to mkdocs.yml. |
MIMICIV_TUTORIAL/README.MD |
Added README file with setup instructions for converting MIMIC IV data into MEDS format. |
README.md |
Updated project description and key features, emphasizing flexibility and machine learning applications. |
pyproject.toml |
Updated build system requirements and project configuration, including dynamic versioning. |
src/meds_torch/data/components/pytorch_dataset.py |
Added new functions and modified existing ones for improved data handling. |
src/meds_torch/models/components/mamba.py |
Enhanced error handling for positional encoding configurations. |
src/meds_torch/models/components/transformer_decoder.py |
Improved handling of positional embeddings and added error checks. |
src/meds_torch/models/components/transformer_encoder.py |
Enhanced initialization logic for model parameters based on configuration settings. |
tests/helpers/extract_test_data.py |
New file providing a testing framework for the extraction process of patient data. |
.github/workflows/publish-to-pypi.yml |
New workflow configuration for publishing Python distributions to PyPI and TestPyPI, including build, publish, and sign jobs. |
Sequence Diagram(s)
sequenceDiagram
participant User
participant Script
participant Data
participant Model
User->>Script: Start extraction process
Script->>Data: Generate synthetic patient data
Data-->>Script: Return patient data
Script->>Model: Process data
Model-->>Script: Return processed data
Script-->>User: Extraction completeš In the code and the data,
Changes hop and play,
New scripts and paths,
A brighter way!
With models and methods,
We leap and bound,
In the world of MEDS,
Joyfully found! š
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codecov-commenter
MEDS v0.3 compatible
Summary by CodeRabbit
New Features
Bug Fixes
Documentation
Chores