Implement visualizations and fix mypy errors

[codegen-sh]

This PR implements visualization capabilities for call graphs and dead code analysis, and fixes mypy errors in the codebase.

Features Added

• Call graph visualization with three visualizers:
  • CallGraphFromNode: Creates a directed call graph from a specified function
  • CallGraphFilter: Filters call graphs to show only specific methods (e.g., HTTP methods)
  • CallPathsBetweenNodes: Visualizes all paths between two specified functions
• Dead code visualization with DeadCodeVisualizer
• Example script showing how to use the visualizers
• Updated README with documentation for the visualization features

Fixes

• Added type annotation for graph in __init__.py
• Fixed the path parameter in DiffLite.from_git_diff() to ensure it's never None
• Added proper type annotations in issues.py for all variables flagged by mypy
• Fixed category parameter handling in create_issue()

This PR replaces PR #111 with all the fixes for the mypy errors.

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💻 View my work • About Codegen

Summary by Sourcery

Implement visualization capabilities for codebases and resolve mypy errors

New Features:

• Add call graph visualizers (CallGraphFromNode, CallGraphFilter, CallPathsBetweenNodes)
• Introduce DeadCodeVisualizer for dead code analysis
• Provide an examples script showcasing visualization usage

Bug Fixes:

• Resolve mypy errors by adding explicit type annotations and ignores in issues.py
• Ensure non-null paths and add type annotations in diff_lite.py and graph initializer

Enhancements:

• Introduce CodebaseVisualizer abstract base class to unify visualization interface

Documentation:

• Revise README with installation instructions, usage examples for new visualizers, and licensing details

[sourcery-ai]

Reviewer's Guide

This PR adds complete visualization support for call graphs and dead code analysis, updates documentation with examples, and fixes various mypy errors by adding type annotations and tightening parameter handling.

File-Level Changes

Change	Details	Files
Introduce call graph visualizers	Add base CodebaseVisualizer abstract class Implement CallGraphFromNode with recursive downstream call tracing Implement CallGraphFilter to filter by class, methods, and skip tests Implement CallPathsBetweenNodes to compute and subgraph all simple paths	codegen_on_oss/visualizers/call_graph_from_node.py codegen_on_oss/visualizers/codebase_visualizer.py codegen_on_oss/visualizers/__init__.py
Implement dead code visualization	Add DeadCodeVisualizer to identify and graph first- and second-order dead functions Exclude test files and decorated functions based on flags	codegen_on_oss/visualizers/dead_code.py
Provide examples and update documentation	Revise README with new visualization feature descriptions and usage snippets Add examples/visualization_examples.py demonstrating all visualizers	README.md examples/visualization_examples.py
Fix mypy errors via type annotations	Annotate graph as nx.DiGraph in context graph init Ensure path is never None in DiffLite.from_git_diff Add explicit type annotations and # type: ignore in issues.py Tighten dictionary initializations with typed generics and handle empty category	codegen_on_oss/analyzers/context/graph/__init__.py codegen_on_oss/analyzers/diff_lite.py codegen_on_oss/analyzers/issues.py

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