Beta Release Clean Up #11
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…n and network visualization tools
…n and network visualization tools. README was also updated but needs review
…string for sphinx doc generation
Many of our components were dependent on the output_dir parameter, which was not necessary. This commit removes the dependency on output_dir from many of our components. - Components now return a datastructure, either a pandas dataframe or a numpy array. - This gives the user more flexibility in how they want to save the output of the component. - User can easy save the output to a csv file or pass the output to another component. - This follows common practices in popular machine learning frameworks such as scikit-learn, PyTorch, and TensorFlow. - By increasing flexibility and separation of concerns, we make our codebase more modular and easier to maintain. - Therefore adhering to the single-responsibility principle.
ramosv
requested review from
SundousHussein,
abdelhafizm and
arunangshu-github
This was referenced Dec 21, 2024
Closed
Beta release pagerank fixes
One of the largest updates include moving several components under a new component called external tools. We also updated the documentation to reflect this information. gnn_embedding code is now working as intended. Updates all the tests to reflect the changes. We will no longer be suporting a install script. we will just let using isntall pytorch and R on their own while providing documentation on where to install it from. After this commit I will remove all the sentive data from any previous commit Any .csv or .RData file will get removed from the repo I am also adding contingencies to prevent future upload of sensitive files. Other updates include: - updated the .gitignore file - updated the .pre-commit-config.yml file - updated the ArunTest.py file: almost working - updated the README.md file - updated the bioneuralnet/__init__.py file
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I used git-filter-repo to remove sensitive data from the git history. I used the following command to remove the sensitive data from the git history:
I ran the following command:
git filter-repo --path example_data/COPDGeneCounts.csv \
--path example_data/COPDGeneMetadata.csv \
--path example_data/metabolites_blood_count_adjusted_2019-08-26.csv \
--path example_data/proteins_blood_count_adjusted_protein_names.csv \
--path example_data/Y_finalgold_coarse.csv \
--invert-paths --force
then I ran to remove it from the history of every branch:
git push --force --all
git push --force --tags
This can cause conflict with your local branch.
I recommend deleting your local branch and pulling the remote branch again.
- fix page rank type errors
Modifed logo to mohamed liking.
abdelhafizm
approved these changes
Jan 20, 2025
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abdelhafizm
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abdelhafizm
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- Separating external tools from the main pipeline is a good idea.
- The HIPAA overlords thank you for removing sensitive data.
- Pre-commit looks good but it fails the test. You need to ignore the auto summary.
- GNNs need hyper parameter tuning.
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Beta Release Clean Up