coderabbitai[bot]
commented
1 month ago Walkthrough
The changes in the README.md file for the MIMIC-IV Example include updates to installation instructions, environment variable settings, and script execution commands. The installation command for the MEDS_transforms package has been revised to dynamically fetch the latest version from PyPI. Specific directory paths for raw data have replaced placeholders, and the default behavior for the do_unzip parameter has been changed. Additionally, the number of workers has been increased from 5 to 8, along with a shift from a distributed to a local processing approach.
Changes
| File | Change Summary |
|---|---|
| MIMIC-IV_Example/README.md | - Updated installation instructions and environment variable settings. |
- Modified installation command for MEDS_transforms to fetch the latest version dynamically. |
|
| - Replaced placeholder paths with actual directory paths for MIMIC-IV data. | |
- Changed do_unzip parameter from true to false. |
|
| - Increased number of workers from 5 to 8. | |
- Changed stage runner file from slurm_runner.yaml to local_parallelism_runner.yaml. |
Possibly related PRs
-
224: The changes in
pre_MEDS.pyregarding file retrieval methods and function call adjustments may relate to the overall data handling improvements in the MIMIC-IV Example, which is also reflected in the updates to theREADME.mdfor clearer instructions and configurations.
Suggested reviewers
- mmcdermott
Poem
🐇 In the garden where data blooms,
The README now clears all the glooms.
With paths set right and workers galore,
The MEDS transform opens the door!
So hop along, let’s code and play,
For MIMIC-IV shines brighter today! 🌼
📜 Recent review details
**Configuration used: CodeRabbit UI** **Review profile: CHILL**📥 Commits
Reviewing files that changed from the base of the PR and between ca56037821ea7a033c001e5e6162dee26ee2b0f1 and e3046f798d7d9e938fa64fd1dac3ef921a3cbc88.📒 Files selected for processing (1)
* `MIMIC-IV_Example/README.md` (2 hunks)🔇 Additional comments (2)
MIMIC-IV_Example/README.md (2)
`11-14`: **Enhance version fetching mechanism with better error handling** The current implementation could fail silently if PyPI is unreachable. The previous review comment suggesting improvements to version handling is still valid and should be implemented. --- `26-26`: _:warning: Potential issue_ **Add URL validation before downloads** The URL construction depends on the fetched version, but there's no validation to ensure the URL is accessible before attempting downloads. Add URL validation before proceeding with downloads: ```diff export URL="https://raw.githubusercontent.com/mmcdermott/MEDS_transforms/$VERSION/MIMIC-IV_Example" + +# Validate URL before proceeding +if ! curl --output /dev/null --silent --head --fail "$URL/run.sh"; then + echo "Error: Invalid URL or repository path: $URL" + echo "Please check if version $VERSION exists in the repository" + exit 1 +fi ``` The previous review comment about validating downloaded files is also still valid and should be implemented.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?
codecov[bot]
Oufattole
mmcdermott
Now the tutorial will always use the latest version of meds-transform by default (by checking pypi for the latest version), and I included downloads all necessary config files as some were missing which broke the tutorial.
Summary by CodeRabbit
New Features
MEDS_transformspackage.Bug Fixes
Documentation