Fixed #85 from issues/task tab. Added a network construction guide.

[ramosv]

This PR directly addresses #85

[Copilot]

Pull Request Overview

This PR addresses issue #85 by adding a network construction guide to the documentation and making related improvements to the network construction functionality. The changes enhance the documentation structure and improve the graph construction functions.

Key Changes

• Added a network construction guide to the documentation structure
• Updated graph construction functions with improved parameter defaults and enhanced documentation
• Modified existing notebooks to improve clarity and remove redundant content

Reviewed Changes

Copilot reviewed 5 out of 8 changed files in this pull request and generated 10 comments.

Show a summary per file

File	Description
docs/source/index.rst	Added network construction guide to documentation toctree
docs/source/datasets.ipynb	Cleaned up output format and removed redundant network generation section
docs/source/Quick_Start.ipynb	Enhanced network construction section with detailed examples and updated formatting
bioneuralnet/utils/graph.py	Major refactor of all graph construction functions with improved documentation, parameter changes, and validation
bioneuralnet/metrics/plot.py	Added layout parameter to plot_network function with multiple layout options

[ramosv]

This is a "rushed" PR to address issue #85.
Still need to update a few other things so that everything lines up properly.
This includes updating the tests, which I am almost done with. gen_lasso_graph keeps diverging, I will comment out this function until I have more time over the weekend to look into it.

[ramosv]

Merging PR without review to update docs and package. All tests are passing.

Will need to be reviewed over the weekend. @abdelhafizm