Documentation update to match readme

[ramosv]

• reinstanciated the pre-commit hooks
• cleaned up documention based on recent changes
• readme now matches the documentation

[Copilot]

Pull Request Overview

This PR realigns the documentation with the README, reinstates pre-commit hooks, and updates CI matrices to support Python 3.12.

• Reinstantiates and configures pre-commit hooks and GitHub Actions for Python 3.12 across platforms
• Cleans up and synchronizes .rst docs and README.md, adding examples and reference sections
• Adds autosummary stubs for external_tools.smccnet and refactors FAQ formatting

Reviewed Changes

Copilot reviewed 29 out of 29 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
docs/source/index.rst	Updated installation, examples, core features, and added interoperability note
docs/source/faq.rst	Refactored FAQ section layout and added new dependencies
docs/source/conf.py	Removed bioneuralnet.external_tools from autodoc_mock_imports
docs/source/_autosummary/bioneuralnet.metrics.evaluation.rst	Removed outdated XGB entries from autosummary
docs/source/_autosummary/bioneuralnet.external_tools.smccnet.rst	Added autosummary for smccnet module
docs/source/_autosummary/bioneuralnet.external_tools.rst	Expanded autosummary to include SmCCNet class and submodule
README.md	Synced feature descriptions, added Python 3.12 support, and references section
.pre-commit-config.yaml	Added and configured hooks with docs excluded
.github/workflows/python-app.yml	Expanded Python matrix to include 3.12 and commented out R steps
.github/workflows/pre-commit.yml	Introduced OS/python matrix for pre-commit checks

Comments suppressed due to low confidence (2)

docs/source/index.rst:114

• [nitpick] Variable names should be lowercase and descriptive; consider renaming "Example" to something like "dataset_loader" or "example_loader".

Example = DatasetLoader("example1")

docs/source/conf.py:60

• Removing this mock import may cause documentation builds to fail if external_tools isn't installed; consider keeping it in autodoc_mock_imports or ensuring the module is available.

bioneuralnet.external_tools

[Copilot]

Pull Request Overview

This PR updates the project documentation and pre-commit configuration to match the README while also reinstituting pre-commit hooks and updating CI workflows.

• Reinstantiates and updates pre-commit hooks for code quality.
• Cleans up and aligns documentation in the README with updated project information.
• Updates CI workflow files to include Python 3.12 support and comments out R-related steps.

Reviewed Changes

Copilot reviewed 60 out of 60 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
bioneuralnet/clustering/hybrid_louvain.py	Removed an extraneous whitespace line to improve code style.
README.md	Revised language and updated Python version support; refined docs.
.pre-commit-config.yaml	Added and updated hooks to support consistent pre-commit behavior.
.github/workflows/python-app.yml	Updated Python version matrix and commented out R installation steps.
.github/workflows/pre-commit.yml	Adjusted Python version setup and commented out R installation steps.

[Copilot]

Pull Request Overview

This PR aligns code signatures and documentation with the README, reinstates pre-commit hooks, and updates CI workflows to support Python 3.12.

• Updated type hints and function signatures across modules (e.g., added Path support, removed deprecated parameters)
• Cleaned up and expanded README to match current features and docs
• Reinstated and expanded pre-commit configuration; updated GitHub Actions to Python 3.12 and commented out R and test steps

Reviewed Changes

Copilot reviewed 61 out of 61 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
bioneuralnet/network_embedding/gnn_embedding.py	Expanded output_dir type to accept Path
bioneuralnet/metrics/evaluation.py	Added Union/Optional imports; removed return_all param; updated plotting signatures
bioneuralnet/external_tools/smccnet.py	Changed output_dir default to Optional[Path]
bioneuralnet/downstream_task/subject_representation.py	Streamlined logging; added phenotype‐column existence check
bioneuralnet/clustering/hybrid_louvain.py	Removed trailing whitespace
bioneuralnet/clustering/correlated_pagerank.py	Removed docstring param; added default empty‐list/dict args
README.md	Overhauled feature sections, links, code examples, and references
.pre-commit-config.yaml	Added hooks for whitespace, YAML, large files, mypy, cleanup
.github/workflows/python-app.yml	Added Python 3.12 to matrix; commented out R and test steps
.github/workflows/pre-commit.yml	Unified matrix for OS and Python; re-enabled pre-commit check

Comments suppressed due to low confidence (3)

bioneuralnet/clustering/correlated_pagerank.py:123

• Using a mutable default argument ([]) can lead to shared state across calls. Use None as the default and initialize an empty list inside the method.

def phen_omics_corr(self, nodes: List[Any] = []) -> Tuple[float, str]:

.github/workflows/python-app.yml:58

• Commenting out the pytest step disables automated testing in CI, which may allow regressions. Re-enable or replace with an equivalent test step.

# - name: Run tests with pytest

README.md:37

• [nitpick] To keep metadata in sync, update the supported Python versions in setup.py or pyproject.toml as well as in the README.

BioNeuralNet supports Python `3.10`, `3.11` and `3.12`.

[abdelhafizm]

good to go