Release v1.0.5 #57
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Release v1.0.5 #57
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Pull Request Overview
This release bumps the package version to 1.0.5, reorganizes dataset loading for the BRCA cohort, and cleans up deprecated tools and data artifacts.
- Version and import updates for downstream tasks and utilities
- Migration of
tcga_brcaloader to a consolidated “brca” loader with CSV part concatenation - Removal of the WGCNA R script, network loader module, and bundled CSV cluster files
Reviewed Changes
Copilot reviewed 116 out of 116 changed files in this pull request and generated 2 comments.
Show a summary per file
| File | Description |
|---|---|
| bioneuralnet/external_tools/WGCNA.R | Removed legacy WGCNA R script |
| bioneuralnet/downstream_task/init.py | Switched GraphEmbedding to SubjectRepresentation export |
| bioneuralnet/datasets/network_loader.py | Deleted the now–unused NetworkLoader |
| bioneuralnet/datasets/init.py | Removed NetworkLoader from package exports |
| bioneuralnet/datasets/dataset_loader.py | Reworked loader to “brca” naming and concatenation of parts |
| bioneuralnet/init.py | Version bump to 1.0.5 and bulk import reorganization |
| MANIFEST.in | Added inclusion of new brca dataset files |
| CHANGELOG.md | Updated changelog version header |
Comments suppressed due to low confidence (3)
CHANGELOG.md:71
- Typo in 'realease'; it should be spelled 'release'.
- **New realease**: A new release will include documentation for the other updates. (1.1.0)
bioneuralnet/init.py:79
- The
WGCNAR script was removed fromexternal_tools, but it's still imported here. Please remove or replace this import.
from .external_tools import WGCNA
bioneuralnet/init.py:125
- The
NetworkLoaderclass is listed in__all__, but the modulebioneuralnet/datasets/network_loader.pywas removed. Please remove this export or reintroduce the loader.
"NetworkLoader",
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| rna_part3 = pd.read_csv(folder / "rna_1.csv", index_col=0) | ||
| rna_part4 = pd.read_csv(folder / "rna_2.csv", index_col=0) |
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It looks like rna_part3 and rna_part4 are both loading the same files (rna_1.csv and rna_2.csv again). They should reference rna_3.csv and rna_4.csv respectively.
Suggested change
| rna_part3 = pd.read_csv(folder / "rna_1.csv", index_col=0) | |
| rna_part4 = pd.read_csv(folder / "rna_2.csv", index_col=0) | |
| rna_part3 = pd.read_csv(folder / "rna_3.csv", index_col=0) | |
| rna_part4 = pd.read_csv(folder / "rna_4.csv", index_col=0) |
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| recursive-include bioneuralnet/datasets/monet *.csv | ||
| recursive-include bioneuralnet/datasets/example1 *.csv | ||
| recursive-include bioneuralnet/datasets/brca *.csv |
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The brca dataset folder does not exist (the directory is named tcga_brca). Update this path to match the actual folder name or rename the folder.
Suggested change
| recursive-include bioneuralnet/datasets/brca *.csv | |
| recursive-include bioneuralnet/datasets/tcga_brca *.csv |
Selected top 10k features by variance to reduce file size
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I will be stacking another branch on top of this one. It can be reviewed for now but not merged