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Merge pull request #169 from rvandewater/development#190

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rvandewater merged 5 commits into
developmentfrom
master
Jun 8, 2026
Merged

Merge pull request #169 from rvandewater/development#190
rvandewater merged 5 commits into
developmentfrom
master

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@rvandewater

@rvandewater rvandewater commented Jun 8, 2026

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Minor publishing changes

Summary by CodeRabbit

  • Documentation

    • Updated project description to clarify support for Intensive Care Unit (ICU) and Electronic Health Record (EHR) data.
    • Updated Python version requirement indicator to 3.12.
    • Updated CI workflow badge reference.
  • Chores

    • Updated workflow trigger configuration to explicitly enumerate supported branches.

Modernization, speed, memory usage, and flexibility improvements



New Features

    Added automated CI/CD workflows for code quality checks and E2E integration testing.
    Introduced icu-benchmarks CLI entry point for streamlined command execution.
    Added new SLURM cluster job submission scripts for batch processing.

Build & Installation

    Migrated project to modern pyproject.toml-based build system with uv package manager.
    Explicit Python 3.10+ support with improved dependency management.
    Removed legacy setup.py and environment configuration files.

Documentation

    Updated README with refreshed installation and usage guidance.
    Added comprehensive CONTRIBUTING.md with development setup instructions.
    Updated PAPER.md with new experiment framework and training workflows.

Infrastructure

    Added pre-commit hooks for automated code quality and formatting checks.
    Enhanced data processing with Polars as primary backend for improved performance.
    Improved type annotations throughout codebase for better code reliability.
@rvandewater rvandewater merged commit 34d0011 into development Jun 8, 2026
12 of 13 checks passed
@coderabbitai

coderabbitai Bot commented Jun 8, 2026

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Review Change Stack

Caution

Review failed

The pull request is closed.

ℹ️ Recent review info
⚙️ Run configuration

Configuration used: Repository UI

Review profile: CHILL

Plan: Pro

Run ID: 5f26eb3e-15a9-4883-81a7-b04000e64adc

📥 Commits

Reviewing files that changed from the base of the PR and between ad55cd8 and af52c96.

📒 Files selected for processing (2)
  • .github/workflows/python-build.yml
  • README.md

Walkthrough

This PR updates repository configuration and documentation. The GitHub Actions workflow branch trigger is refactored to explicitly enumerate branches (main, master, development, release/*), and the README is updated with a new CI badge reference, Python version downgrade from 3.13 to 3.12, and clarified project description mentioning ICU and EHR data.

Changes

Configuration and Documentation Updates

Layer / File(s) Summary
Workflow branch trigger configuration
.github/workflows/python-build.yml
Push trigger branches changed from inline list to explicit multi-line enumeration, clarifying main, master, development, and release/* branches.
README documentation and badge updates
README.md
CI badge updated to reference code-quality.yml workflow, Python version badge changed from 3.13 to 3.12, and introductory description reworded to explicitly mention Intensive Care Unit (ICU) and Electronic Health Record (EHR) data.

Estimated code review effort

🎯 1 (Trivial) | ⏱️ ~3 minutes

Possibly related PRs

  • rvandewater/YAIB#189: Both PRs modify the on: push branch trigger configuration in .github/workflows/python-build.yml, with related but distinct branch enumeration changes.

Poem

🐰 The CI paths now crystal clear,
With branches enumerated near,
And badges shining fresh and bright,
The README gleams with clearer light,
EHR hearts beat strong and right!

✨ Finishing Touches
🧪 Generate unit tests (beta)
  • Create PR with unit tests
  • Commit unit tests in branch master

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