Refactor: Remove Deprecated Chunk-Based Query Methods and Improve Graph Unit Test

[danielaskdd]

Refactor: Remove Deprecated Chunk-Based Query Methods and Improve Graph Unit Test

Overview

This PR removes deprecated chunk-based node/edge retrieval methods from all graph storage implementations and introduces workspace parameter support while improving test infrastructure and code quality.

Key Changes

🗑️ Deprecated Code Removal

• Removed chunk-based query methods from all graph storage implementations:
  • get_nodes_by_chunk_ids() - removed from NetworkX, MongoDB, Neo4j, Memgraph, and PostgreSQL implementations
  • get_edges_by_chunk_ids() - removed from all graph storage backends
• Total lines removed: ~380 lines of deprecated code across storage backends
  • lightrag/base.py: 51 lines
  • lightrag/kg/memgraph_impl.py: 74 lines
  • lightrag/kg/mongo_impl.py: 39 lines
  • lightrag/kg/neo4j_impl.py: 44 lines
  • lightrag/kg/networkx_impl.py: 28 lines
  • lightrag/kg/postgres_impl.py: 97 lines

✨ Graph Unit Test Improvements

• Translated test file from Chinese to English for better international collaboration
• Added workspace parameter support to storage initialization in tests
• Removed deprecated test cases for chunk-based retrieval methods
• Initialized shared storage for all graph storage types to ensure consistency

Breaking Changes

⚠️ Removed APIs (deprecated methods):

• get_nodes_by_chunk_ids() - Applications should use alternative query methods
• get_edges_by_chunk_ids() - Applications should use alternative query methods