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Create derived predicates with static variables #154

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wants to merge 19 commits into from
Closed

Create derived predicates with static variables #154

wants to merge 19 commits into from

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justin13601
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@justin13601 justin13601 commented Dec 10, 2024 •
edited by coderabbitai bot
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Summary by CodeRabbit

  • New Features

    • Predicates can now be defined in a separate configuration file.
    • Enhanced support for various versions of dependencies, including MEDS and Polars.
    • Expanded predicates configuration language to support regular expressions and multi-value constraints.

  • Bug Fixes

    • Improved error handling and logging in various functions related to predicates and query processing.

  • Documentation

    • Updated README and configuration documents to clarify usage and installation instructions.

  • Chores

    • Updated workflow configurations and dependencies for code quality and testing processes.

justin13601 and others added 19 commits October 25, 2024 02:02
@justin13601
Test config for derived predicates based on static predicates
f36821f
@justin13601
Pass in static predicates to DerivedPredicateConfig
4f8dc20
@justin13601
Logic for derived predicate between plain and static by propagating d…
6495d3c 
…own static variable values
@justin13601
Revert back to original config
6b2ec02
@justin13601
Revert DerivedPredicateConfig static attribute due to parquet issues
12e9694
@justin13601
Explicitly get list of static predicates from config plain predicates
2c8304c
@justin13601
Freeze pre-commit version and update workflows
76cbe91
@justin13601
Sort first to guarantee null timestamp rows are first per subject_id
c56e60b
@justin13601
Warnings and error messages per #141 #142 #146 (#147)
2c57b85 
* #141 note about memory in README

* #141 warning about memory in the docs

* #142 add warning messages if labels are all the same

* Add error message when predicates are specified using only strings (includes ??? case)

Closes #141, #142, and #146
@justin13601
Add percentage for printing label distribution (code rabbit suggestion)
495f2c0
@justin13601
Remove label distribution printing (can be done post-hoc)
ec07a94
@justin13601
Code quality PR workflow not on all files
ca85310
@justin13601
Exclude test coverage for logging statements
0cb8b1a
@justin13601
Update docs to clarify supported code fields
7121127
@justin13601
Polish error message
220c99a
@justin13601
Switch to warning when no rows returned
13eb15d
@justin13601
#94 nested derived predicates (ex: needed when creating different ref…
f5b0dbc 
…erence ranges for male/female)
@justin13601
Added tests for derived predicates between static and plain as well a…
8902365 
…s nested derived predicates
@justin13601
Update polars dependency requirements
10d36ac
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coderabbitai bot commented Dec 10, 2024 •
edited
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Caution

Review failed

The pull request is closed.

Walkthrough

The pull request includes updates to several workflow files and configurations to enhance the functionality and maintainability of the project. Key changes involve upgrading GitHub Actions versions for code quality checks and testing workflows, specifying Python version 3.10, and introducing a new step for installing development packages. Additionally, the pre-commit hooks version has been updated, and the README.md and configuration documentation have been enhanced to reflect new features and improved usability. The core codebase has also seen modifications to improve error handling and the configuration of predicates.

Changes

File Path Change Summary
.github/workflows/code-quality-main.yaml Updated actions: checkout to v4, setup-python to v5 with Python version 3.10, added pip install .[dev], and updated pre-commit to v3.0.1.
.github/workflows/code-quality-pr.yaml Similar updates as code-quality-main.yaml.
.github/workflows/tests.yml Updated actions: checkout to v4, setup-python to v5, and changed package install command from pip install -e .[dev] to pip install .[dev].
.pre-commit-config.yaml Updated pre-commit-hooks version from v4.4.0 to v5.0.0.
README.md Updated documentation for new features, support for MEDS v0.3.3 and Polars v1.5.*, and clarified installation instructions.
docs/source/configuration.md Added notes on memory optimization and expanded explanations for configuration fields.
pyproject.toml Updated polars version constraint to >= 1.0.0, <= 1.17.1 and restricted pre-commit to <4.
src/aces/config.py Enhanced TaskExtractorConfig class for better predicate handling and validation.
src/aces/predicates.py Improved error handling and logic in direct_load_plain_predicates function.
src/aces/query.py Adjusted logging levels and refined handling of empty results in the query function.

Possibly related issues

🐰 "In the code, we hop and play,
New features bloom, bright as day.
With Python set to three point ten,
Our workflows dance, again and again.
From predicates to hooks, we cheer,
A rabbit's joy is truly here!" 🐇✨

📜 Recent review details

Configuration used: CodeRabbit UI
Review profile: CHILL

📥 Commits

Reviewing files that changed from the base of the PR and between f822119 and 10d36ac.

📒 Files selected for processing (10)
  • .github/workflows/code-quality-main.yaml (1 hunks)
  • .github/workflows/code-quality-pr.yaml (2 hunks)
  • .github/workflows/tests.yml (1 hunks)
  • .pre-commit-config.yaml (1 hunks)
  • README.md (1 hunks)
  • docs/source/configuration.md (1 hunks)
  • pyproject.toml (2 hunks)
  • src/aces/config.py (6 hunks)
  • src/aces/predicates.py (4 hunks)
  • src/aces/query.py (3 hunks)

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@codecov Codecov
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codecov bot commented Dec 10, 2024 •
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Codecov Report

Attention: Patch coverage is 95.45455% with 1 line in your changes missing coverage. Please review.

Files with missing lines Patch % Lines
src/aces/config.py 93.75% 1 Missing ⚠️
Files with missing lines Coverage Δ
src/aces/predicates.py 83.72% <100.00%> (-0.28%) ⬇️
src/aces/query.py 72.09% <ø> (-23.66%) ⬇️
src/aces/config.py 97.22% <93.75%> (-0.41%) ⬇️

... and 4 files with indirect coverage changes

@justin13601 justin13601 deleted the 25_medsdev_static_derived_predicates branch December 10, 2024 18:19
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