Remove graph embedding and UMAP

[natoverse]

These workflow steps are used to provide x/y coordinates for visualization. However, the reliance on downstream dependencies from graspologic is limiting our ability to upgrade various libraries. Given that the core intent of GraphRAG is answer generation rather than vis, we have decided to remove this. As a helpful aside, there are several community examples of graph visualization for the outputs, as well as a vis guide in the docs that do not depend on these generated x/y coordinates.

[Copilot]

Pull Request Overview

This PR removes graph embedding and UMAP functionality from GraphRAG to eliminate dependencies on graspologic that were limiting library upgrades. The core indexing pipeline is preserved while removing visualization-specific x/y coordinate generation.

• Removes graph embedding (node2vec) and UMAP dimensionality reduction workflows
• Updates configuration to remove embed_graph and umap settings
• Modifies UI to focus on community exploration rather than graph visualization
• Updates documentation to reflect the removal of these features

Reviewed Changes

Copilot reviewed 32 out of 33 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
unified-search-app/pyproject.toml	Updates graphrag dependency version from 2.0.0 to 2.5.0
unified-search-app/app/ui/report_list.py	Changes column order from "id" to "human_readable_id" for consistency
unified-search-app/app/home_page.py	Removes full graph UI import and changes tab name from "Graph Explorer" to "Community Explorer"
tests/verbs/test_finalize_graph.py	Removes UMAP-related test and x/y coordinate assertions
tests/unit/config/utils.py	Removes embed_graph and umap configuration assertion functions
graphrag/index/workflows/finalize_graph.py	Removes embed_graph and layout parameters from finalize_graph workflow
graphrag/index/update/entities.py	Removes x/y coordinate fields from entity aggregation
graphrag/index/operations/finalize_entities.py	Removes graph embedding and layout operations from entity finalization
graphrag/index/operations/cluster_graph.py	Updates module docstring to remove layout reference
graphrag/data_model/schemas.py	Removes NODE_X and NODE_Y from final entity schema
graphrag/config/models/graph_rag_config.py	Removes embed_graph and umap configuration fields
graphrag/config/init_content.py	Removes embed_graph and umap sections from default configuration template
graphrag/config/defaults.py	Removes EmbedGraphDefaults and UmapDefaults classes
docs/visualization_guide.md	Removes references to embed_graph and umap requirements for visualization
docs/index/outputs.md	Removes x/y coordinate fields from entities table documentation
docs/index/methods.md	Fixes typo "expensive that" to "expensive than"
docs/index/default_dataflow.md	Removes UMAP step from network visualization phase workflow
docs/index/architecture.md	Removes EmbedGraph from sample workflow DAG
docs/config/yaml.md	Removes embed_graph and umap configuration documentation

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