Enhance and Fix Graph Implementation for Conformity and Functionality

[TusharNaugain]

Description:

The Graph class in our repository (DevoGraph/Growing-GNN/graph.py) requires several enhancements and fixes to ensure better functionality, robustness, and API conformity. The current implementation has issues with type handling, error checking, and edge dictionary updates, which can lead to inconsistencies and potential bugs.

Expected Behavior:

1. All methods should include type annotations and detailed docstrings for better readability and maintenance.
2. Methods should have proper error handling to ensure robustness.
3. The edge dictionary should be updated accurately after adding/removing nodes to maintain graph structure.
4. Node embeddings should be handled correctly, avoiding dimension mismatches.
5. The plot method should provide better visualization and usability.

Proposed Solution:

• Add type annotations and detailed docstrings.
• Improve error handling in methods like add_daughter_cells.
• Correct the logic for updating the edge dictionary after adding/removing nodes.
• Ensure proper handling of single-dimensional new_nodes and efficient concatenation of tensors.
• Enhance the plot method for better visualization and clarity in the graph representation.

Additional Information:

• This change will break the existing API for the Graph class. Please update your codebase accordingly.
• Detailed documentation will be provided to help with the transition.