Add visualization capabilities and fix mypy errors

[codegen-sh]

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

Visualization Features

• CodebaseVisualizer: Base abstract class for all visualizers
• CallGraphFromNode: Creates call graphs from a starting function
• CallGraphFilter: Filters call graphs to include only specific methods
• CallPathsBetweenNodes: Shows paths between two functions
• DeadCodeVisualizer: Identifies unused code in the codebase

Mypy Error 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 DiDegreeView operator issues by extracting values first
• Added proper type annotations for all visualizer classes

Additional Changes

• Added comprehensive documentation for all visualizers
• Created example usage in visualization_examples.py
• Added README with usage examples

This PR replaces PR #111 and #112 with all the fixes for the mypy errors.

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Summary by Sourcery

Add visualization features for call graphs and dead code, fix all mypy type errors across the codebase, refactor core analyzers (issues, difflite, graph utilities) for stronger typing and cleaner models, and update documentation with usage examples.

New Features:

• Introduce visualizers for call graphs (CallGraphFromNode, CallGraphFilter, CallPathsBetweenNodes) and dead code (DeadCodeVisualizer)
• Add a base abstract class (CodebaseVisualizer) and package init
• Provide example scripts demonstrating visualization capabilities

Bug Fixes:

• Resolve mypy errors by adding comprehensive type annotations across analyzers, visualizers, and context modules
• Ensure DiffLite.from_git_diff always yields a non-null path and fix related type mismatches

Enhancements:

• Refactor the Issue and Location models for cleaner structure, unified enums, and automatic ID generation
• Modernize diff utilities and graph context functions with improved logging, simplified methods, and new helper properties

Documentation:

• Overhaul README to include installation, usage, and visualization sections
• Add documentation for visualizer classes and examples in README and example files

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Reviewer's Guide

This PR introduces a new visualization subsystem for call graphs and dead-code analysis, overhauls documentation with usage examples, and resolves all existing mypy type errors by adding and tightening type annotations across the codebase.

File-Level Changes

Change	Details	Files
Visualization subsystem for call graphs and dead-code analysis	Added abstract CodebaseVisualizer base class Implemented CallGraphFromNode, CallGraphFilter, CallPathsBetweenNodes, DeadCodeVisualizer Published example usage in examples/visualization_examples.py Exported new visualizers in init.py	codegen_on_oss/visualizers/codebase_visualizer.py codegen_on_oss/visualizers/call_graph_from_node.py codegen_on_oss/visualizers/dead_code.py codegen_on_oss/visualizers/__init__.py examples/visualization_examples.py
Fixed mypy errors by adding precise type annotations and handling optional values	Annotated all classes and functions with Optional, List, Dict, Union, and Enum types Ensured DiffLite.from_git_diff never returns None for path and added new_content field Refactored Issue, Location, IssueCollection, and create_issue to use explicit types and simplified from_dict	analyzers/issues.py analyzers/diff_lite.py analyzers/context/graph/__init__.py
Documentation and README improvements	Reworked README with concise installation and usage examples for both analysis and visualization Expanded docstrings on major classes and methods to describe arguments and return values	README.md **/*.py

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[codegen-sh]

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[codegen-sh]

✅ Fixed the failing checks in PR #113 with this commit. The issues were:

1. Fixed deprecated typing imports in graph/__init__.py (replaced List, Set, Tuple with their lowercase equivalents)
2. Added specific error codes to type ignore comments in issues.py
3. Combined nested if statements in dead_code.py for better readability
4. Fixed formatting issues in README.md
5. Updated type annotations in diff_lite.py to use the newer | syntax instead of Optional

These changes should resolve the pre-commit and mypy check failures.

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