Remove NetworkX from cognee core. (#1241)

<!-- .github/pull_request_template.md -->

## Description
<!-- Provide a clear description of the changes in this PR -->
Remove NetworkX from cognee core.

## DCO Affirmation
I affirm that all code in every commit of this pull request conforms to
the terms of the Topoteretes Developer Certificate of Origin.

.github/actions/setup_neo4j/action.yml

@@ -0,0 +1,67 @@
+name: 'Setup Neo4j with Graph Data Science'
+description: 'Sets up a Neo4j instance with APOC and Graph Data Science plugins for testing'
+inputs:
+  neo4j-version:
+    description: 'Neo4j version to use'
+    required: false
+    default: '5.21'
+  neo4j-password:
+    description: 'Password for Neo4j'
+    required: false
+    default: 'cognee_test_password'
+outputs:
+  neo4j-url:
+    description: 'Neo4j connection URL'
+    value: 'bolt://localhost:7687'
+  neo4j-username:
+    description: 'Neo4j username'
+    value: 'neo4j'
+  neo4j-password:
+    description: 'Neo4j password'
+    value: ${{ inputs.neo4j-password }}
+runs:
+  using: 'composite'
+  steps:
+    - name: Start Neo4j with GDS
+      shell: bash
+      run: |
+        docker run -d \
+          --name neo4j-test \
+          -p 7474:7474 -p 7687:7687 \
+          -e NEO4J_AUTH="neo4j/${{ inputs.neo4j-password }}" \
+          -e NEO4J_PLUGINS='["apoc", "graph-data-science"]' \
+          -e NEO4J_dbms_security_procedures_unrestricted="apoc.*,gds.*" \
+          -e NEO4J_apoc_export_file_enabled=true \
+          -e NEO4J_apoc_import_file_enabled=true \
+          neo4j:${{ inputs.neo4j-version }}
+    
+    - name: Wait for Neo4j to be ready
+      shell: bash
+      run: |
+        echo "Waiting for Neo4j to start..."
+        timeout=60
+        counter=0
+        
+        while [ $counter -lt $timeout ]; do
+          if docker exec neo4j-test cypher-shell -u neo4j -p "${{ inputs.neo4j-password }}" "RETURN 1" > /dev/null 2>&1; then
+            echo "Neo4j is ready!"
+            break
+          fi
+          echo "Waiting... ($counter/$timeout)"
+          sleep 2
+          counter=$((counter + 2))
+        done
+        
+        if [ $counter -ge $timeout ]; then
+          echo "Neo4j failed to start within $timeout seconds"
+          docker logs neo4j-test
+          exit 1
+        fi
+    
+    - name: Verify GDS is available
+      shell: bash
+      run: |
+        echo "Verifying Graph Data Science library is available..."
+        docker exec neo4j-test cypher-shell -u neo4j -p "${{ inputs.neo4j-password }}" \
+          "CALL gds.version() YIELD gdsVersion RETURN gdsVersion"
+        echo "GDS verification complete!"

.github/workflows/examples_tests.yml

@@ -60,6 +60,10 @@ jobs:
         with:
           python-version: '3.11.x'
 
+      - name: Setup Neo4j with GDS
+        uses: ./.github/actions/setup_neo4j
+        id: neo4j
+
       - name: Run Descriptive Graph Metrics Example
         env:
           LLM_MODEL: ${{ secrets.LLM_MODEL }}
@@ -71,7 +75,11 @@ jobs:
           EMBEDDING_ENDPOINT: ${{ secrets.EMBEDDING_ENDPOINT }}
           EMBEDDING_API_KEY: ${{ secrets.EMBEDDING_API_KEY }}
           EMBEDDING_API_VERSION: ${{ secrets.EMBEDDING_API_VERSION }}
-        run: uv run python ./cognee/tests/tasks/descriptive_metrics/networkx_metrics_test.py
+          GRAPH_DATABASE_PROVIDER: "neo4j"
+          GRAPH_DATABASE_URL: ${{ steps.neo4j.outputs.neo4j-url }}
+          GRAPH_DATABASE_USERNAME: ${{ steps.neo4j.outputs.neo4j-username }}
+          GRAPH_DATABASE_PASSWORD: ${{ steps.neo4j.outputs.neo4j-password }}
+        run: uv run python ./cognee/tests/tasks/descriptive_metrics/neo4j_metrics_test.py
 
 
   test-dynamic-steps-metrics:

cognee/api/v1/add/add.py

@@ -132,7 +132,7 @@ async def add(
         - DEFAULT_USER_EMAIL: Custom default user email
         - DEFAULT_USER_PASSWORD: Custom default user password
         - VECTOR_DB_PROVIDER: "lancedb" (default), "chromadb", "pgvector"
-        - GRAPH_DATABASE_PROVIDER: "kuzu" (default), "neo4j", "networkx"
+        - GRAPH_DATABASE_PROVIDER: "kuzu" (default), "neo4j"
 
     """
     tasks = [

cognee/infrastructure/databases/graph/get_graph_engine.py

@@ -21,10 +21,6 @@ async def get_graph_engine() -> GraphDBInterface:
     if hasattr(graph_client, "initialize"):
         await graph_client.initialize()
 
-    # Handle loading of graph for NetworkX
-    if config["graph_database_provider"].lower() == "networkx" and graph_client.graph is None:
-        await graph_client.load_graph_from_file()
-
     return graph_client
 
 
@@ -181,8 +177,7 @@ def create_graph_engine(
             graph_id=graph_identifier,
         )
 
-    from .networkx.adapter import NetworkXAdapter
-
-    graph_client = NetworkXAdapter(filename=graph_file_path)
-
-    return graph_client
+    raise EnvironmentError(
+        f"Unsupported graph database provider: {graph_database_provider}. "
+        f"Supported providers are: {', '.join(list(supported_databases.keys()) + ['neo4j', 'falkordb', 'kuzu', 'kuzu-remote', 'memgraph', 'neptune', 'neptune_analytics'])}"
+    )

cognee/modules/retrieval/cypher_search_retriever.py

@@ -1,6 +1,5 @@
 from typing import Any, Optional
 from cognee.infrastructure.databases.graph import get_graph_engine
-from cognee.infrastructure.databases.graph.networkx.adapter import NetworkXAdapter
 from cognee.modules.retrieval.base_retriever import BaseRetriever
 from cognee.modules.retrieval.utils.completion import generate_completion
 from cognee.modules.retrieval.exceptions import SearchTypeNotSupported, CypherSearchError
@@ -31,8 +30,7 @@ class CypherSearchRetriever(BaseRetriever):
         """
         Retrieves relevant context using a cypher query.
 
-        If the graph engine is an instance of NetworkXAdapter, raises SearchTypeNotSupported. If
-        any error occurs during execution, logs the error and raises CypherSearchError.
+        If any error occurs during execution, logs the error and raises CypherSearchError.
 
         Parameters:
         -----------
@@ -46,12 +44,6 @@ class CypherSearchRetriever(BaseRetriever):
         """
         try:
             graph_engine = await get_graph_engine()
-
-            if isinstance(graph_engine, NetworkXAdapter):
-                raise SearchTypeNotSupported(
-                    "CYPHER search type not supported for NetworkXAdapter."
-                )
-
             result = await graph_engine.query(query)
         except Exception as e:
             logger.error("Failed to execture cypher search retrieval: %s", str(e))

cognee/modules/retrieval/natural_language_retriever.py

@@ -1,7 +1,6 @@
 from typing import Any, Optional
 from cognee.shared.logging_utils import get_logger
 from cognee.infrastructure.databases.graph import get_graph_engine
-from cognee.infrastructure.databases.graph.networkx.adapter import NetworkXAdapter
 from cognee.infrastructure.llm.LLMGateway import LLMGateway
 from cognee.modules.retrieval.base_retriever import BaseRetriever
 from cognee.modules.retrieval.exceptions import SearchTypeNotSupported
@@ -123,9 +122,6 @@ class NaturalLanguageRetriever(BaseRetriever):
         """
         graph_engine = await get_graph_engine()
 
-        if isinstance(graph_engine, (NetworkXAdapter)):
-            raise SearchTypeNotSupported("Natural language search type not supported.")
-
         return await self._execute_cypher_query(query, graph_engine)
 
     async def get_completion(self, query: str, context: Optional[Any] = None) -> Any:

cognee/shared/utils.py

@@ -3,7 +3,6 @@
 import os
 import requests
 from datetime import datetime, timezone
-import networkx as nx
 import matplotlib.pyplot as plt
 import http.server
 import socketserver

cognee/tests/tasks/descriptive_metrics/networkx_metrics_test.py

@@ -1,7 +0,0 @@
-from cognee.tests.tasks.descriptive_metrics.metrics_test_utils import assert_metrics
-import asyncio
-
-
-if __name__ == "__main__":
-    asyncio.run(assert_metrics(provider="networkx", include_optional=False))
-    asyncio.run(assert_metrics(provider="networkx", include_optional=True))