Release Candidate 0.0.7

mmcdermott commented 2 weeks ago

Significant improvements to usability through the runner interface, upgrade to newer versions of MEDS and pandas, fixes to MIMIC-IV ETL, and more.

Summary by CodeRabbit

New Features
- Enhanced installation and setup instructions for the MEDS ETL process in the README.
- Introduced a new configuration file for extracting MIMIC-IV dataset in a longitudinal format.
- Added a new script to streamline the execution of the MEDS data processing pipeline.
- Implemented parallel processing configurations for both local and SLURM environments.
- Introduced a foundational helper for integration tests related to various data transformation processes.
Bug Fixes
- Simplified commands for running the MEDS ETL process, improving usability.
Documentation
- Updated terminology from "patient" to "subject" across all documentation for clarity and consistency.
- Enhanced README files with clearer instructions and examples.
Refactor
- Renamed variables and functions to reflect the shift from patient-centric to subject-centric terminology throughout the codebase.
Chores
- Updated dependency versions in the project configuration for improved functionality and performance.

coderabbitai[bot] commented 2 weeks ago

Walkthrough

The recent changes involve a comprehensive update across various files in the MIMIC-IV Example and eICU Example projects. Key modifications include the renaming of identifiers from "patient" to "subject," adjustments to installation instructions, the introduction of new configuration files, and enhancements to existing scripts and functions to improve clarity and consistency in data processing workflows.

Changes

Files	Change Summary
`MIMIC-IV_Example/README.md`, `eICU_Example/README.md`	Shifted terminology from "patient" to "subject" throughout the documentation.
`MIMIC-IV_Example/configs/.yaml`, `eICU_Example/configs/.yaml`	Renamed keys from "patient_id" to "subject_id" and updated related configuration parameters.
`MIMIC-IV_Example/pre_MEDS.py`, `eICU_Example/joint_script.sh`	Updated functions and scripts to reflect new terminology and improved handling of data processing.
`MIMIC-IV_Example/run.sh`, `MIMIC-IV_Example/slurm_runner.yaml`	Introduced a new script for running the ETL process and updated configurations for parallel processing.
`src/MEDS_transforms/.py`, `src/MEDS_transforms/configs/.yaml`	Refactored code to replace "patient" with "subject," updated function signatures, and modified configuration files to enhance clarity and functionality.
`pyproject.toml`	Updated dependencies and renamed script entries to reflect changes in terminology from "patients" to "subjects."
`src/MEDS_transforms/runner.py`	Introduced a new utility script for executing processing pipelines, including functions for dynamic module imports and parallel execution management.
`tests/MEDS_Transforms/transform_tester_base.py`	Added a new testing utility to facilitate integration tests for data transformation processes, defining essential data inputs and helper functions.

Sequence Diagram(s)

sequenceDiagram
    participant User
    participant Script
    participant Config
    participant Data

    User->>Script: Execute processing
    Script->>Config: Load configurations
    Config->>Data: Retrieve subject data
    Data-->>Script: Return subject data
    Script->>Data: Process data
    Data-->>Script: Return processed data
    Script->>User: Output results

🐇 In fields so wide and bright,
I hop with joy, what a sight!
Subjects now take the stage,
In every script, a new page.
With changes fresh and clear,
Let's celebrate, give a cheer!
🌼✨

Thank you for using CodeRabbit. We offer it for free to the OSS community and would appreciate your support in helping us grow. If you find it useful, would you consider giving us a shout-out on your favorite social media?

Share

- [X](https://twitter.com/intent/tweet?text=I%20just%20used%20%40coderabbitai%20for%20my%20code%20review%2C%20and%20it%27s%20fantastic%21%20It%27s%20free%20for%20OSS%20and%20offers%20a%20free%20trial%20for%20the%20proprietary%20code.%20Check%20it%20out%3A&url=https%3A//coderabbit.ai) - [Mastodon](https://mastodon.social/share?text=I%20just%20used%20%40coderabbitai%20for%20my%20code%20review%2C%20and%20it%27s%20fantastic%21%20It%27s%20free%20for%20OSS%20and%20offers%20a%20free%20trial%20for%20the%20proprietary%20code.%20Check%20it%20out%3A%20https%3A%2F%2Fcoderabbit.ai) - [Reddit](https://www.reddit.com/submit?title=Great%20tool%20for%20code%20review%20-%20CodeRabbit&text=I%20just%20used%20CodeRabbit%20for%20my%20code%20review%2C%20and%20it%27s%20fantastic%21%20It%27s%20free%20for%20OSS%20and%20offers%20a%20free%20trial%20for%20proprietary%20code.%20Check%20it%20out%3A%20https%3A//coderabbit.ai) - [LinkedIn](https://www.linkedin.com/sharing/share-offsite/?url=https%3A%2F%2Fcoderabbit.ai&mini=true&title=Great%20tool%20for%20code%20review%20-%20CodeRabbit&summary=I%20just%20used%20CodeRabbit%20for%20my%20code%20review%2C%20and%20it%27s%20fantastic%21%20It%27s%20free%20for%20OSS%20and%20offers%20a%20free%20trial%20for%20proprietary%20code)

Tips

### Chat There are 3 ways to chat with [CodeRabbit](https://coderabbit.ai): - Review comments: Directly reply to a review comment made by CodeRabbit. Example: - `I pushed a fix in commit .` - `Generate unit testing code for this file.` - `Open a follow-up GitHub issue for this discussion.` - Files and specific lines of code (under the "Files changed" tab): Tag `@coderabbitai` in a new review comment at the desired location with your query. Examples: - `@coderabbitai generate unit testing code for this file.` - `@coderabbitai modularize this function.` - PR comments: Tag `@coderabbitai` in a new PR comment to ask questions about the PR branch. For the best results, please provide a very specific query, as very limited context is provided in this mode. Examples: - `@coderabbitai generate interesting stats about this repository and render them as a table.` - `@coderabbitai show all the console.log statements in this repository.` - `@coderabbitai read src/utils.ts and generate unit testing code.` - `@coderabbitai read the files in the src/scheduler package and generate a class diagram using mermaid and a README in the markdown format.` - `@coderabbitai help me debug CodeRabbit configuration file.` Note: Be mindful of the bot's finite context window. It's strongly recommended to break down tasks such as reading entire modules into smaller chunks. For a focused discussion, use review comments to chat about specific files and their changes, instead of using the PR comments. ### CodeRabbit Commands (Invoked using PR comments) - `@coderabbitai pause` to pause the reviews on a PR. - `@coderabbitai resume` to resume the paused reviews. - `@coderabbitai review` to trigger an incremental review. This is useful when automatic reviews are disabled for the repository. - `@coderabbitai full review` to do a full review from scratch and review all the files again. - `@coderabbitai summary` to regenerate the summary of the PR. - `@coderabbitai resolve` resolve all the CodeRabbit review comments. - `@coderabbitai configuration` to show the current CodeRabbit configuration for the repository. - `@coderabbitai help` to get help. ### Other keywords and placeholders - Add `@coderabbitai ignore` anywhere in the PR description to prevent this PR from being reviewed. - Add `@coderabbitai summary` to generate the high-level summary at a specific location in the PR description. - Add `@coderabbitai` anywhere in the PR title to generate the title automatically. ### CodeRabbit Configuration File (`.coderabbit.yaml`) - You can programmatically configure CodeRabbit by adding a `.coderabbit.yaml` file to the root of your repository. - Please see the [configuration documentation](https://docs.coderabbit.ai/guides/configure-coderabbit) for more information. - If your editor has YAML language server enabled, you can add the path at the top of this file to enable auto-completion and validation: `# yaml-language-server: $schema=https://coderabbit.ai/integrations/schema.v2.json` ### Documentation and Community - Visit our [Documentation](https://coderabbit.ai/docs) for detailed information on how to use CodeRabbit. - Join our [Discord Community](https://discord.com/invite/GsXnASn26c) to get help, request features, and share feedback. - Follow us on [X/Twitter](https://twitter.com/coderabbitai) for updates and announcements.

codecov-commenter commented 2 weeks 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 86.19403% with 37 lines in your changes missing coverage. Please review.

Project coverage is 94.23%. Comparing base (3f73a35) to head (3519769). Report is 1 commits behind head on main.

:white_check_mark: All tests successful. No failed tests found.

Files with missing lines	Patch %	Lines
src/MEDS_transforms/runner.py	76.92%	30 Missing :warning:
src/MEDS_transforms/mapreduce/mapper.py	60.00%	2 Missing :warning:
.../MEDS_transforms/extract/finalize_MEDS_metadata.py	93.75%	1 Missing :warning:
src/MEDS_transforms/reshard_to_split.py	90.90%	1 Missing :warning:
src/MEDS_transforms/transforms/extract_values.py	75.00%	1 Missing :warning:
src/MEDS_transforms/transforms/tokenization.py	83.33%	1 Missing :warning:
src/MEDS_transforms/utils.py	80.00%	1 Missing :warning:

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #193 +/- ## ========================================== + Coverage 93.51% 94.23% +0.72% ========================================== Files 26 27 +1 Lines 1988 2100 +112 ========================================== + Hits 1859 1979 +120 + Misses 129 121 -8 ```

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

mmcdermott / MEDS_transforms