Updated docs and code examples.

[ramosv]

Several updates were implemented in preparation for the v1.0.8
Documentation now reflects relevant examples and .ipynb workflows.
Changed theme to improve code readability.
Removed outdated documentation and non relevant information.

[Copilot]

Pull Request Overview

This PR updates documentation and code examples while also introducing various improvements in code functionality and hyperparameter settings. Key changes include updates to autosummary documentation for multiple modules, modifications in hyperparameter spaces and training configurations in the GNN embedding and evaluation routines, and minor API adjustments in clustering and external tools.

Reviewed Changes

Copilot reviewed 69 out of 69 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
docs/source/_autosummary/*.rst	Added new autosummary entries and removed outdated ones to reflect current API and examples.
bioneuralnet/network_embedding/gnn_models.py	Updated GCN, GAT, SAGE, and GIN constructors with a new optional parameter to control self-loops and normalization.
bioneuralnet/network_embedding/gnn_embedding.py	Adjusted error checking and hyperparameter tuning configurations; refined edge weight normalization in PyG data construction.
bioneuralnet/metrics/*	Revised evaluation and plotting functions, including parameter adjustments to improve performance and clarity.
bioneuralnet/clustering/hybrid_louvain.py	Reduced max_iter iterations to speed up clustering; ensure convergence criteria are met.
README.md and docs/requirements.txt	Updated badge links and dependency listings to reflect current project status.

Comments suppressed due to low confidence (2)

bioneuralnet/metrics/evaluation.py:13

• Verify that reducing the default number of runs to 10 in 'evaluate_model' still yields statistically reliable performance metrics.

def evaluate_model(X: np.ndarray, y: np.ndarray, model_type: str = "rf_classif", n_estimators: int = 150, runs: int = 10, seed: int = 119) -> Tuple[ ... ]:

bioneuralnet/clustering/hybrid_louvain.py:36

• Ensure that reducing 'max_iter' from 10 to 3 does not adversely affect the convergence and overall clustering performance.

max_iter: int = 3,

[abdelhafizm]

👍

[ramosv]

fixed pre-commit issues. We need to added it back into the dev documentation so that it runs prior to allowing commit to take place.

[ramosv]

Passed all checks + approval from @abdelhafizm
merging