Version 1.1.4: See CHANGELOG.md for changes

[ramosv]

Once this branch goes into main it will update:

• The package version including the new datasets
• New functions fill be available after installing via pip

[Copilot]

Pull Request Overview

This PR updates the package version to 1.1.4, incorporating new datasets and utility functions. The changes include:

• Adding TCGA-KIPAN and TCGA-GBMLGG datasets to the DatasetLoader
• Implementing new utility functions for data preprocessing (imputation, normalization, methylation conversion, and seed setting)
• Adding comprehensive demonstration notebooks for the new datasets
• Updating documentation to reference the new notebook structure

Reviewed Changes

Copilot reviewed 24 out of 41 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
setup.cfg	Version bump from 1.1.3 to 1.1.4
docs/source/notebooks/index.rst	New index page for notebooks section
docs/source/notebooks/TCGA-KIPAN.ipynb	Complete KIPAN dataset analysis notebook
docs/source/notebooks/TCGA-GBMLGG.ipynb	Complete GBMLGG dataset analysis notebook
docs/source/notebooks/TCGA-BRCA.ipynb	Complete BRCA dataset analysis notebook
docs/source/installation.rst	Updated Python version compatibility and navigation links
docs/source/index.rst	Updated documentation structure references
docs/source/faq.rst	Updated notebook references
docs/source/external_tools/index.rst	Updated external tool references
docs/source/examples/index.rst	Fixed typo in heading and adjusted maxdepth
docs/source/downstream_tasks.rst	Updated navigation links
docs/source/conf.py	Version update to 1.1.4
docs/source/_autosummary/bioneuralnet.utils.rst	Added new utility function references
docs/source/_autosummary/bioneuralnet.utils.data.rst	Added new data utility references
bioneuralnet/downstream_task/dpmon.py	Removed commented-out code
bioneuralnet/datasets/kipan/target.csv	New KIPAN target labels dataset
bioneuralnet/datasets/dataset_loader.py	Added KIPAN and GBMLGG dataset loading
bioneuralnet/init.py	Added new utility function exports
README.md	Version update in welcome message
MANIFEST.in	Added new dataset directories
CHANGELOG.md	Documented version 1.1.4 changes

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[ElyasYassin]

no major logic changes other than uncommenting of dataset cases, LGTM.