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justin13601 / ACES

ACES: Automatic Cohort Extraction System for Event-Streams
https://eventstreamaces.readthedocs.io/en/latest/
MIT License
13 stars 0 forks source link

Doc changes #32

Closed justin13601 closed 1 month ago

justin13601 commented 1 month ago

Summary by CodeRabbit

coderabbitai[bot] commented 1 month ago

Walkthrough

The recent updates focus on refining configuration files and enhancing the functionality of the Event Stream Automatic Cohort Extraction System (ACES). Key changes include renaming trigger_event to trigger, adding index_timestamp fields, updating dependencies, and improving data handling processes. These modifications ensure better configuration management, improved data extraction, and enhanced compatibility with newer Python versions.

Changes

File/Path Change Summary
sample_configs/... Renamed trigger_event to trigger, added index_timestamp fields, and adjusted window configurations.
README.md Updated to reflect transition from ESGPT to ACES and added specific version dependencies.
scripts/run_extraction.py Main script for end-to-end task querying, loading configuration, and saving results to Parquet files.
src/aces/__main__.py Refactored data loading, updated variable names, and modified result saving mechanism.
src/aces/config.py Renamed trigger_event to trigger, added index_timestamp fields, and updated constraint checks.
src/aces/constraints.py Modified docstring by removing a TODO comment.
src/aces/extract_subtree.py Changed data types from u16 to i64 for specific fields.
src/aces/predicates.py Simplified data loading process and added example usage in the docstring.
src/aces/query.py Added a log message for identifying possible trigger nodes.
src/aces/utils.py Added a print("\n") statement within the log_tree function.
tests/test_e2e.py End-to-end tests for the full extraction process, setting up test data, and comparing output results.
.gitignore Added *.parquet and modified result.csv to results/ in the list of ignored files.
pyproject.toml Updated Python version requirement to >=3.12 and changed dependency from pandas to pyarrow.
.github/workflows/tests.yml Changed Python version for setup from 3.10 to 3.12.
src/aces/config.yaml Introduced configuration settings for the "inhospital-mortality" task.

Poem

In the world of code, a change so bright,
Triggers renamed, now set to ignite.
Index timestamps mark the way,
For data streams to never stray.
Python's new, dependencies too,
ACES shines with a clearer view.
πŸ‡βœ¨

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codecov[bot] commented 1 month ago

Codecov Report

Attention: Patch coverage is 84.68468% with 17 lines in your changes are missing coverage. Please review.

Files Coverage Ξ”
src/aces/aggregate.py 95.18% <ΓΈ> (+1.20%) :arrow_up:
src/aces/constraints.py 100.00% <ΓΈ> (ΓΈ)
src/aces/extract_subtree.py 94.59% <ΓΈ> (+2.70%) :arrow_up:
src/aces/types.py 98.64% <100.00%> (+2.70%) :arrow_up:
src/aces/utils.py 95.83% <100.00%> (+39.31%) :arrow_up:
src/aces/__main__.py 91.66% <94.11%> (+91.66%) :arrow_up:
src/aces/config.py 86.68% <85.18%> (+4.51%) :arrow_up:
src/aces/predicates.py 68.13% <87.80%> (+19.60%) :arrow_up:
src/aces/query.py 77.77% <70.83%> (+47.34%) :arrow_up: