Bug fix pre release #54
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…efactoring Sample dataset and gnn models refactoring, preparing for beta release version 2
Solve merge conflicts before release
BioInformatics - Stable release 1.0 Pre-commit failed because of an issue during R installation. I think I will be removing this from the pre-commit workflow since it is an optional component and not core of the package. Everything else passed. I tested all the tests/ locally as well and got no errors. Green light to merge
Removed import from jupiternotebook
…commit, locally It runs no issues all tests pass
…mmit Fixed precommit errors
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Pull Request Overview
This PR addresses a bug fix pre release while also introducing several enhancements and refactors across multiple modules and documentation. Key changes include improvements in subject representation error handling and messaging, updates to clustering modules with GPU seeding support, and updates to dataset loading logic, documentation, and CI workflows.
Reviewed Changes
Copilot reviewed 150 out of 156 changed files in this pull request and generated 3 comments.
Show a summary per file
| File | Description |
|---|---|
| bioneuralnet/downstream_task/subject_representation.py | Added GraphEmbedding implementation and improved error messages. |
| bioneuralnet/downstream_task/dpmon.py | Updated import usage and streamlined module structure. |
| bioneuralnet/downstream_task/init.py | Updated public API to include GraphEmbedding. |
| bioneuralnet/datasets/tcga_brca/README.md | Added detailed data preprocessing and file structure summary. |
| bioneuralnet/datasets/dataset_loader.py | Updated file loading logic using pathlib and multi-file support. |
| bioneuralnet/clustering/hybrid_louvain.py | Integrated GPU seed handling and enhanced logging. |
| bioneuralnet/clustering/correlated_pagerank.py | Enhanced tuning, GPU seeding, and error retry for PageRank. |
| bioneuralnet/clustering/correlated_louvain.py | Added GPU and seed support in tuning routines. |
| bioneuralnet/init.py | Updated version and expanded public API. |
| README.md | Revised project overview, structure, and installation instructions. |
| Cancer_example.ipynb | Added a new example notebook for demonstration. |
| CHANGELOG.md | Updated release notes with latest version details and fixes. |
| .readthedocs.yaml | Minor documentation configuration update. |
| .github/workflows/pre-commit.yml | Updated CI workflow with pre-commit upgrade and installation steps. |
Files not reviewed (6)
- .gitattributes: Language not supported
- .pre-commit-config.yaml: Language not supported
- MANIFEST.in: Language not supported
- bioneuralnet/datasets/monet/clinical_data.csv: Language not supported
- bioneuralnet/datasets/monet/phenotype.csv: Language not supported
- bioneuralnet/external_tools/SmCCNet.R: Language not supported
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[nitpick] Duplicate import of 'session' from 'ray.air' detected. Removing the redundant import can clean up the code.
Suggested change
| from ray.air import session |
SundousHussein
approved these changes
Apr 24, 2025
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Bug fix pre release