Feaurization walkthrough #40
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* inital commit * update paths * preprocessing * run on alpine * change pathing * HPC * local update * addressing comments
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Pull Request Overview
This PR provides a walkthrough of the featurization process for organoids by updating notebook configurations and refining the file structure and pre-commit configuration.
- Updates kernel specifications and Python versions in Jupyter notebooks.
- Refactors argument parsing and formatting in the file structure update notebook.
- Updates pre-commit hook revisions for consistency and compatibility.
Reviewed Changes
Copilot reviewed 6 out of 6 changed files in this pull request and generated 2 comments.
| File | Description |
|---|---|
| 0.preprocessing_data/notebooks/1.make_z-stack_images.ipynb | Updated kernel display name and adjusted the Python version. |
| 0.preprocessing_data/notebooks/0.update_file_structure.ipynb | Reformatted argument parsing and function definitions; adjusted notebook metadata version. |
| .pre-commit-config.yaml | Upgraded revision numbers for pre-commit hooks to the latest tags. |
Comments suppressed due to low confidence (2)
.pre-commit-config.yaml:3
- Verify that updating the revision to v0.7.0 does not introduce any breaking changes in the pre-commit hook behavior, and document if necessary.
rev: v0.7.0
.pre-commit-config.yaml:18
- Confirm and document that the ruff version update to v0.11.8 is compatible with the current codebase and pre-commit configuration.
rev: v0.11.8
| @@ -2190,7 +2190,7 @@ | |||
| "name": "python", | |||
| "nbconvert_exporter": "python", | |||
| "pygments_lexer": "ipython3", | |||
| "version": "3.11.11" | |||
| "version": "3.10.15" | |||
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Document the rationale behind downgrading the Python version from 3.11.11 to 3.10.15 to assist reviewers and future maintainers.
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| "name": "python", | ||
| "nbconvert_exporter": "python", | ||
| "pygments_lexer": "ipython3", | ||
| "version": "3.10.15" |
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Include a brief explanation for the Python version change from 3.10.16 to 3.10.15 to improve clarity for future updates.
| "version": "3.10.15" | |
| "version": "3.10.15", # Python version 3.10.15 was chosen for compatibility with project dependencies and to ensure stability during development. |
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This PR is a walk through of the featurization of the organoids.
The notebook describes the feature space and how many features are extracted for each organoid.
I recommend using ReviewNB for this PR.