Conversation
There was a problem hiding this comment.
Pull Request Overview
This PR addresses a missing statsmodels dependency in the documentation build by mocking and adding it, bumps the package version to 1.0.7, and refactors import error handling and dataset loading logic.
- Bump version to 1.0.7 across setup, init, README, and changelog
- Add
statsmodelsto install_requires and Sphinx config/mock imports - Update
preprocess_clinicalreturn logic and comment out legacy dataset splitting - Introduce
ImportErrorwith instructions for missing PyTorch/PyG modules
Reviewed Changes
Copilot reviewed 22 out of 22 changed files in this pull request and generated 2 comments.
Show a summary per file
| File | Description |
|---|---|
| setup.cfg | Version bump to 1.0.7 and add statsmodels |
| docs/source/conf.py | Update Sphinx styles, execution settings, and mock statsmodels |
| docs/source/_autosummary/...preprocess.rst | Remove multipletests from autosummary |
| bioneuralnet/utils/preprocess.py | Change concat to include df_ignore and modify return |
| bioneuralnet/network_embedding/gnn_models.py | Wrap PyTorch imports in try/except and reformat init signatures |
| bioneuralnet/network_embedding/gnn_embedding.py | Reorder imports, wrap imports in try/except |
| bioneuralnet/downstream_task/subject_representation.py | Add error handling for missing torch and unused tempfile import |
| bioneuralnet/downstream_task/dpmon.py | Add error handling for missing torch-geometric |
| bioneuralnet/datasets/dataset_loader.py | Comment out legacy CSV part-loading logic |
| bioneuralnet/init.py | Version bump to 1.0.7 |
| README.md | Update welcome header to 1.0.7 |
| CHANGELOG.md | Update changelog header to 1.0.7 and fix version range |
Comments suppressed due to low confidence (3)
docs/source/_autosummary/bioneuralnet.utils.preprocess.rst:12
- The
multipletestsfunction was removed from the autosummary, which will omit it from generated docs. If this deletion was unintentional, please re-add it or adjust the RST accordingly.
- multipletests
CHANGELOG.md:72
- Typo in 'realease'; it should be spelled 'release'.
- **New realease**: A new release will include documentation for the other updates. (1.1.0)
bioneuralnet/utils/preprocess.py:96
- Previously
df_ignorecolumns were preserved in the final output but are now dropped. Confirm ifdf_ignoreshould be included in the return or removed from the concatenation step.
return df_features[selected_columns]
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
The following issue was presented on the docs build
* ModuleNotFoundError: No module named 'statsmodels'I mocked package. We will see if it works after merging