Enhance README with Cognee description

Added a brief description of Cognee's features and capabilities.

.coderabbit.yaml

@@ -3,7 +3,7 @@
 language: en
 early_access: false
 enable_free_tier: true
-reviews:
+reviews:  
   profile: chill
   instructions: >-
     # Code Review Instructions
@@ -118,10 +118,10 @@ reviews:
           - E117
           - D208
         line_length: 100
-        dummy_variable_rgx: '^(_.*|junk|extra)$'  # Variables starting with '_' or named 'junk' or 'extras', are considered dummy variables
+        dummy_variable_rgx: '^(_.*|junk|extra)$'  # Variables starting with '_' or named 'junk' or 'extras', are considered dummy variables        
     markdownlint:
       enabled: true
     yamllint:
       enabled: true
 chat:
-  auto_reply: true
+  auto_reply: true

.env.template

@@ -91,15 +91,6 @@ DB_NAME=cognee_db
 #DB_USERNAME=cognee
 #DB_PASSWORD=cognee
 
-# -- Advanced: Custom database connection arguments (optional) ---------------
-# Pass additional connection parameters as JSON. Useful for SSL, timeouts, etc.
-# Examples:
-#   For PostgreSQL with SSL:
-#     DATABASE_CONNECT_ARGS='{"sslmode": "require", "connect_timeout": 10}'
-#   For SQLite with custom timeout:
-#     DATABASE_CONNECT_ARGS='{"timeout": 60}'
-#DATABASE_CONNECT_ARGS='{}'
-
 ################################################################################
 # 🕸️ Graph Database settings
 ################################################################################

.gitguardian.yml

@@ -28,4 +28,4 @@ secret-scan:
     - path: 'docker-compose.yml'
       comment: 'Development docker compose with test credentials (neo4j/pleaseletmein, postgres cognee/cognee)'
     - path: 'deployment/helm/docker-compose-helm.yml'
-      comment: 'Helm deployment docker compose with test postgres credentials (cognee/cognee)'
+      comment: 'Helm deployment docker compose with test postgres credentials (cognee/cognee)'

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -8,7 +8,7 @@ body:
     attributes:
       value: |
         Thanks for taking the time to fill out this bug report! Please provide a clear and detailed description.
-
+        
   - type: textarea
     id: description
     attributes:
@@ -17,7 +17,7 @@ body:
       placeholder: Describe the bug in detail...
     validations:
       required: true
-
+      
   - type: textarea
     id: reproduction
     attributes:
@@ -29,7 +29,7 @@ body:
         3. See error...
     validations:
       required: true
-
+      
   - type: textarea
     id: expected
     attributes:
@@ -38,7 +38,7 @@ body:
       placeholder: Describe what you expected...
     validations:
       required: true
-
+      
   - type: textarea
     id: actual
     attributes:
@@ -47,7 +47,7 @@ body:
       placeholder: Describe what actually happened...
     validations:
       required: true
-
+      
   - type: textarea
     id: environment
     attributes:
@@ -61,7 +61,7 @@ body:
         - Database: [e.g. Neo4j]
     validations:
       required: true
-
+      
   - type: textarea
     id: logs
     attributes:
@@ -71,7 +71,7 @@ body:
       render: shell
     validations:
       required: false
-
+      
   - type: textarea
     id: additional
     attributes:
@@ -80,7 +80,7 @@ body:
       placeholder: Any additional information...
     validations:
       required: false
-
+      
   - type: checkboxes
     id: checklist
     attributes:

.github/ISSUE_TEMPLATE/documentation.yml

@@ -8,7 +8,7 @@ body:
     attributes:
       value: |
         Thanks for helping improve our documentation! Please provide details about the documentation issue or improvement.
-
+        
   - type: dropdown
     id: doc-type
     attributes:
@@ -22,7 +22,7 @@ body:
         - New documentation request
     validations:
       required: true
-
+      
   - type: textarea
     id: location
     attributes:
@@ -31,7 +31,7 @@ body:
       placeholder: https://cognee.ai/docs/... or specific file/section
     validations:
       required: true
-
+      
   - type: textarea
     id: issue
     attributes:
@@ -40,7 +40,7 @@ body:
       placeholder: The documentation is unclear about...
     validations:
       required: true
-
+      
   - type: textarea
     id: suggestion
     attributes:
@@ -49,7 +49,7 @@ body:
       placeholder: I suggest changing this to...
     validations:
       required: false
-
+      
   - type: textarea
     id: additional
     attributes:
@@ -58,7 +58,7 @@ body:
       placeholder: Additional context...
     validations:
       required: false
-
+      
   - type: checkboxes
     id: checklist
     attributes:
@@ -71,3 +71,4 @@ body:
           required: true
         - label: I have specified the location of the documentation issue
           required: true
+

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -8,7 +8,7 @@ body:
     attributes:
       value: |
         Thanks for suggesting a new feature! Please provide a clear and detailed description of your idea.
-
+        
   - type: textarea
     id: problem
     attributes:
@@ -17,7 +17,7 @@ body:
       placeholder: I'm always frustrated when...
     validations:
       required: true
-
+      
   - type: textarea
     id: solution
     attributes:
@@ -26,7 +26,7 @@ body:
       placeholder: I would like to see...
     validations:
       required: true
-
+      
   - type: textarea
     id: alternatives
     attributes:
@@ -35,7 +35,7 @@ body:
       placeholder: I have also considered...
     validations:
       required: false
-
+      
   - type: textarea
     id: use-case
     attributes:
@@ -44,7 +44,7 @@ body:
       placeholder: This feature would help me...
     validations:
       required: true
-
+      
   - type: textarea
     id: implementation
     attributes:
@@ -53,7 +53,7 @@ body:
       placeholder: This could be implemented by...
     validations:
       required: false
-
+      
   - type: textarea
     id: additional
     attributes:
@@ -62,7 +62,7 @@ body:
       placeholder: Additional context...
     validations:
       required: false
-
+      
   - type: checkboxes
     id: checklist
     attributes:
@@ -75,3 +75,4 @@ body:
           required: true
         - label: I have described my specific use case
           required: true
+

.github/actions/setup_neo4j/action.yml

@@ -34,14 +34,14 @@ runs:
           -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!"
@@ -51,13 +51,13 @@ runs:
           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: |

.github/core-team.txt

@@ -8,3 +8,5 @@ lxobr
 pazone
 siillee
 vasilije1990
+
+

.github/pull_request_template.md

@@ -10,21 +10,26 @@ DO NOT use AI-generated descriptions. We want to understand your thought process
 <!--
 * Key requirements to the new feature or modification;
 * Proof that the changes work and meet the requirements;
+* Include instructions on how to verify the changes. Describe how to test it locally;
+* Proof that it's sufficiently tested.
 -->
 
 ## Type of Change
 <!-- Please check the relevant option -->
 - [ ] Bug fix (non-breaking change that fixes an issue)
 - [ ] New feature (non-breaking change that adds functionality)
+- [ ] Breaking change (fix or feature that would cause existing functionality to change)
+- [ ] Documentation update
 - [ ] Code refactoring
+- [ ] Performance improvement
 - [ ] Other (please specify):
 
-## Screenshots
-<!-- ADD SCREENSHOT OF LOCAL TESTS PASSING-->
+## Screenshots/Videos (if applicable)
+<!-- Add screenshots or videos to help explain your changes -->
 
 ## Pre-submission Checklist
 <!-- Please check all boxes that apply before submitting your PR -->
-- [ ] **I have tested my changes thoroughly before submitting this PR** (See `CONTRIBUTING.md`)
+- [ ] **I have tested my changes thoroughly before submitting this PR**
 - [ ] **This PR contains minimal changes necessary to address the issue/feature**
 - [ ] My code follows the project's coding standards and style guidelines
 - [ ] I have added tests that prove my fix is effective or that my feature works

.github/release-drafter.yml

@@ -3,7 +3,7 @@ tag-template: 'v$NEXT_PATCH_VERSION'
 
 categories:
   - title: 'Features'
-    labels: ['feature', 'enhancement']
+    labels: ['feature', 'enhancement']    
   - title: 'Bug Fixes'
     labels: ['bug', 'fix']
   - title: 'Maintenance'

.github/workflows/basic_tests.yml

@@ -34,6 +34,43 @@ env:
   ENV: 'dev'
 
 jobs:
+
+  lint:
+    name: Run Linting
+    runs-on: ubuntu-22.04
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Cognee Setup
+        uses: ./.github/actions/cognee_setup
+        with:
+          python-version: ${{ inputs.python-version }}
+
+      - name: Run Linting
+        uses: astral-sh/ruff-action@v2
+
+  format-check:
+    name: Run Formatting Check
+    runs-on: ubuntu-22.04
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Cognee Setup
+        uses: ./.github/actions/cognee_setup
+        with:
+          python-version: ${{ inputs.python-version }}
+
+      - name: Run Formatting Check
+        uses: astral-sh/ruff-action@v2
+        with:
+          args: "format --check"
+
   unit-tests:
     name: Run Unit Tests
     runs-on: ubuntu-22.04

.github/workflows/disable_independent_workflows.sh

@@ -31,54 +31,54 @@ WORKFLOWS=(
 for workflow in "${WORKFLOWS[@]}"; do
   if [ -f "$workflow" ]; then
     echo "Processing $workflow..."
-
+    
     # Create a backup
     cp "$workflow" "${workflow}.bak"
-
+    
     # Check if the file begins with a workflow_call trigger
     if grep -q "workflow_call:" "$workflow"; then
       echo "$workflow already has workflow_call trigger, skipping..."
       continue
     fi
-
+    
     # Get the content after the 'on:' section
     on_line=$(grep -n "^on:" "$workflow" | cut -d ':' -f1)
-
+    
     if [ -z "$on_line" ]; then
       echo "Warning: No 'on:' section found in $workflow, skipping..."
       continue
     fi
-
+    
     # Create a new file with the modified content
     {
       # Copy the part before 'on:'
       head -n $((on_line-1)) "$workflow"
-
+      
       # Add the new on: section that only includes workflow_call
       echo "on:"
       echo "  workflow_call:"
       echo "    secrets:"
       echo "      inherit: true"
-
+      
       # Find where to continue after the original 'on:' section
       next_section=$(awk "NR > $on_line && /^[a-z]/ {print NR; exit}" "$workflow")
-
+      
       if [ -z "$next_section" ]; then
         next_section=$(wc -l < "$workflow")
         next_section=$((next_section+1))
       fi
-
+      
       # Copy the rest of the file starting from the next section
       tail -n +$next_section "$workflow"
     } > "${workflow}.new"
-
+    
     # Replace the original with the new version
     mv "${workflow}.new" "$workflow"
-
+    
     echo "Modified $workflow to only run when called from test-suites.yml"
   else
     echo "Warning: $workflow not found, skipping..."
   fi
 done
 
-echo "Finished modifying workflows!"
+echo "Finished modifying workflows!" 

.github/workflows/dockerhub.yml

@@ -45,4 +45,4 @@ jobs:
           cache-to: type=registry,ref=cognee/cognee:buildcache,mode=max
 
       - name: Image digest
-        run: echo ${{ steps.build.outputs.digest }}
+        run: echo ${{ steps.build.outputs.digest }}

.github/workflows/e2e_tests.yml

@@ -288,7 +288,7 @@ jobs:
           EMBEDDING_ENDPOINT: ${{ secrets.EMBEDDING_ENDPOINT }}
           EMBEDDING_API_KEY: ${{ secrets.EMBEDDING_API_KEY }}
           EMBEDDING_API_VERSION: ${{ secrets.EMBEDDING_API_VERSION }}
-        run: uv run pytest cognee/tests/test_permissions.py -v --log-level=INFO
+        run: uv run python ./cognee/tests/test_permissions.py
 
   test-multi-tenancy:
     name: Test multi tenancy with different situations in Cognee
@@ -315,31 +315,6 @@ jobs:
           EMBEDDING_API_VERSION: ${{ secrets.EMBEDDING_API_VERSION }}
         run: uv run python ./cognee/tests/test_multi_tenancy.py
 
-  test-data-label:
-    name: Test adding of label for data in Cognee
-    runs-on: ubuntu-22.04
-    steps:
-      - name: Check out repository
-        uses: actions/checkout@v4
-
-      - name: Cognee Setup
-        uses: ./.github/actions/cognee_setup
-        with:
-          python-version: '3.11.x'
-
-      - name: Run custom data label test
-        env:
-          ENV: 'dev'
-          LLM_MODEL: ${{ secrets.LLM_MODEL }}
-          LLM_ENDPOINT: ${{ secrets.LLM_ENDPOINT }}
-          LLM_API_KEY: ${{ secrets.LLM_API_KEY }}
-          LLM_API_VERSION: ${{ secrets.LLM_API_VERSION }}
-          EMBEDDING_MODEL: ${{ secrets.EMBEDDING_MODEL }}
-          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/test_custom_data_label.py
-
   test-graph-edges:
     name: Test graph edge ingestion
     runs-on: ubuntu-22.04
@@ -659,51 +634,3 @@ jobs:
           EMBEDDING_API_KEY: ${{ secrets.EMBEDDING_API_KEY }}
           EMBEDDING_API_VERSION: ${{ secrets.EMBEDDING_API_VERSION }}
         run: uv run python ./cognee/tests/test_pipeline_cache.py
-
-  run_usage_logger_test:
-    name: Usage logger test (API/MCP)
-    runs-on: ubuntu-latest
-    defaults:
-      run:
-        shell: bash
-    services:
-      redis:
-        image: redis:7
-        ports:
-          - 6379:6379
-        options: >-
-          --health-cmd "redis-cli ping"
-          --health-interval 5s
-          --health-timeout 3s
-          --health-retries 5
-
-    steps:
-      - name: Checkout repository
-        uses: actions/checkout@v4
-
-      - name: Cognee Setup
-        uses: ./.github/actions/cognee_setup
-        with:
-          python-version: '3.11.x'
-          extra-dependencies: "redis"
-
-      - name: Install cognee-mcp (local version)
-        shell: bash
-        run: |
-          uv pip install -e ./cognee-mcp
-
-      - name: Run api/tool usage logger
-        env:
-          ENV: dev
-          LLM_MODEL: ${{ secrets.LLM_MODEL }}
-          LLM_ENDPOINT: ${{ secrets.LLM_ENDPOINT }}
-          LLM_API_KEY: ${{ secrets.LLM_API_KEY }}
-          LLM_API_VERSION: ${{ secrets.LLM_API_VERSION }}
-          EMBEDDING_MODEL: ${{ secrets.EMBEDDING_MODEL }}
-          EMBEDDING_ENDPOINT: ${{ secrets.EMBEDDING_ENDPOINT }}
-          EMBEDDING_API_KEY: ${{ secrets.EMBEDDING_API_KEY }}
-          EMBEDDING_API_VERSION: ${{ secrets.EMBEDDING_API_VERSION }}
-          GRAPH_DATABASE_PROVIDER: 'kuzu'
-          USAGE_LOGGING: true
-          CACHE_BACKEND: 'redis'
-        run: uv run pytest cognee/tests/test_usage_logger_e2e.py -v --log-level=INFO

.github/workflows/examples_tests.yml

@@ -257,7 +257,7 @@ jobs:
         with:
           python-version: '3.11.x'
 
-      - name: Run Permissions Example
+      - name: Run Memify Tests
         env:
           ENV: 'dev'
           OPENAI_API_KEY: ${{ secrets.OPENAI_API_KEY }}
@@ -270,65 +270,6 @@ jobs:
           EMBEDDING_API_KEY: ${{ secrets.EMBEDDING_API_KEY }}
           EMBEDDING_API_VERSION: ${{ secrets.EMBEDDING_API_VERSION }}
         run: uv run python ./examples/python/permissions_example.py
-
-  test-s3-permissions-example: # Make sure permission and multi-user mode work with S3 file system
-    name: Run Permissions Example
-    runs-on: ubuntu-22.04
-    defaults:
-      run:
-        shell: bash
-    services:
-      postgres: # Using postgres to avoid storing and using SQLite from S3
-        image: pgvector/pgvector:pg17
-        env:
-          POSTGRES_USER: cognee
-          POSTGRES_PASSWORD: cognee
-          POSTGRES_DB: cognee_db
-        options: >-
-          --health-cmd pg_isready
-          --health-interval 10s
-          --health-timeout 5s
-          --health-retries 5
-        ports:
-          - 5432:5432
-    steps:
-      - name: Check out repository
-        uses: actions/checkout@v4
-
-      - name: Cognee Setup
-        uses: ./.github/actions/cognee_setup
-        with:
-          python-version: '3.11.x'
-          extra-dependencies: "postgres aws"
-
-      - name: Run S3 Permissions Example
-        env:
-          ENV: 'dev'
-          OPENAI_API_KEY: ${{ secrets.OPENAI_API_KEY }}
-          LLM_MODEL: ${{ secrets.LLM_MODEL }}
-          LLM_ENDPOINT: ${{ secrets.LLM_ENDPOINT }}
-          LLM_API_KEY: ${{ secrets.LLM_API_KEY }}
-          LLM_API_VERSION: ${{ secrets.LLM_API_VERSION }}
-          EMBEDDING_MODEL: ${{ secrets.EMBEDDING_MODEL }}
-          EMBEDDING_ENDPOINT: ${{ secrets.EMBEDDING_ENDPOINT }}
-          EMBEDDING_API_KEY: ${{ secrets.EMBEDDING_API_KEY }}
-          EMBEDDING_API_VERSION: ${{ secrets.EMBEDDING_API_VERSION }}
-          STORAGE_BACKEND: 's3'
-          AWS_REGION: eu-west-1
-          AWS_ENDPOINT_URL: https://s3-eu-west-1.amazonaws.com
-          AWS_ACCESS_KEY_ID: ${{ secrets.AWS_S3_DEV_USER_KEY_ID }}
-          AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_S3_DEV_USER_SECRET_KEY }}
-          STORAGE_BUCKET_NAME: github-runner-cognee-tests
-          DATA_ROOT_DIRECTORY: "s3://github-runner-cognee-tests/cognee/data"
-          SYSTEM_ROOT_DIRECTORY: "s3://github-runner-cognee-tests/cognee/system"
-          DB_PROVIDER: 'postgres'
-          DB_NAME: 'cognee_db'
-          DB_HOST: '127.0.0.1'
-          DB_PORT: 5432
-          DB_USERNAME: cognee
-          DB_PASSWORD: cognee
-        run: uv run python ./examples/python/permissions_example.py
-
   test_docling_add:
     name: Run Add with Docling Test
     runs-on: macos-15

.github/workflows/label-core-team.yml

@@ -72,3 +72,5 @@ jobs:
             } catch (error) {
               core.warning(`Failed to add label: ${error.message}`);
             }
+
+

.github/workflows/load_tests.yml

@@ -66,3 +66,5 @@ jobs:
           AWS_ACCESS_KEY_ID: ${{ secrets.AWS_S3_DEV_USER_KEY_ID }}
           AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_S3_DEV_USER_SECRET_KEY }}
         run: uv run python ./cognee/tests/test_load.py
+  
+    

.github/workflows/pre_test.yml

@@ -5,7 +5,7 @@ permissions:
   contents: read
 jobs:
   check-uv-lock:
-    name: Lockfile and Pre-commit Hooks
+    name: Validate uv lockfile and project metadata
     runs-on: ubuntu-22.04
     steps:
       - name: Check out repository
@@ -17,9 +17,6 @@ jobs:
         uses: astral-sh/setup-uv@v4
         with:
           enable-cache: true
-
+      
       - name: Validate uv lockfile and project metadata
         run: uv lock --check || { echo "'uv lock --check' failed."; echo "Run 'uv lock' and push your changes."; exit 1; }
-
-      - name: Run pre-commit hooks
-        uses: pre-commit/action@v3.0.1

.github/workflows/release.yml

@@ -42,10 +42,10 @@ jobs:
 
           echo "tag=${TAG}" >> "$GITHUB_OUTPUT"
           echo "version=${VERSION}" >> "$GITHUB_OUTPUT"
-
+          
           git tag "${TAG}"
           git push origin "${TAG}"
-
+          
 
       - name: Create GitHub Release
         uses: softprops/action-gh-release@v2
@@ -54,8 +54,8 @@ jobs:
           generate_release_notes: true
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-
-  release-pypi-package:
+  
+  release-pypi-package:    
     needs: release-github
     name: Release PyPI Package from ${{ inputs.flavour }}
     permissions:
@@ -67,25 +67,25 @@ jobs:
         uses: actions/checkout@v4
         with:
           ref: ${{ inputs.flavour }}
-
+      
       - name: Install uv
         uses: astral-sh/setup-uv@v7
-
+      
       - name: Install Python
         run: uv python install
-
+      
       - name: Install dependencies
         run: uv sync --locked --all-extras
-
+      
       - name: Build distributions
         run: uv build
-
+      
       - name: Publish ${{ inputs.flavour }} release to PyPI
         env:
           UV_PUBLISH_TOKEN: ${{ secrets.PYPI_TOKEN }}
         run: uv publish
-
-  release-docker-image:
+  
+  release-docker-image:    
     needs: release-github
     name: Release Docker Image from ${{ inputs.flavour }}
     permissions:
@@ -128,7 +128,7 @@ jobs:
           context: .
           platforms: linux/amd64,linux/arm64
           push: true
-          tags: |
+          tags: | 
             cognee/cognee:${{ needs.release-github.outputs.version }}
             cognee/cognee:latest
           labels: |
@@ -136,31 +136,3 @@ jobs:
             flavour=${{ inputs.flavour }}
           cache-from: type=registry,ref=cognee/cognee:buildcache
           cache-to: type=registry,ref=cognee/cognee:buildcache,mode=max
-
-  trigger-docs-test-suite:
-    needs: release-pypi-package
-    if: ${{ inputs.flavour == 'main' }}
-    runs-on: ubuntu-22.04
-    steps:
-      - name: Trigger docs tests
-        run: |
-          curl -L -X POST \
-            -H "Accept: application/vnd.github+json" \
-            -H "Authorization: Bearer ${{ secrets.REPO_DISPATCH_PAT_TOKEN }}" \
-            -H "X-GitHub-Api-Version: 2022-11-28" \
-            https://api.github.com/repos/topoteretes/cognee-docs/dispatches \
-            -d '{"event_type":"new-main-release","client_payload":{"caller_repo":"'"${GITHUB_REPOSITORY}"'"}}'
-
-  trigger-community-test-suite:
-    needs: release-pypi-package
-    if: ${{ inputs.flavour == 'main' }}
-    runs-on: ubuntu-22.04
-    steps:
-      - name: Trigger community tests
-        run: |
-          curl -L -X POST \
-            -H "Accept: application/vnd.github+json" \
-            -H "Authorization: Bearer ${{ secrets.REPO_DISPATCH_PAT_TOKEN }}" \
-            -H "X-GitHub-Api-Version: 2022-11-28" \
-            https://api.github.com/repos/topoteretes/cognee-community/dispatches \
-            -d '{"event_type":"new-main-release","client_payload":{"caller_repo":"'"${GITHUB_REPOSITORY}"'"}}'

.github/workflows/release_test.yml

@@ -14,4 +14,4 @@ jobs:
   load-tests:
     name: Load Tests
     uses: ./.github/workflows/load_tests.yml
-    secrets: inherit
+    secrets: inherit

.github/workflows/search_db_tests.yml

@@ -11,21 +11,12 @@ on:
         type: string
         default: "all"
         description: "Which vector databases to test (comma-separated list or 'all')"
-      python-versions:
-        required: false
-        type: string
-        default: '["3.10", "3.11", "3.12", "3.13"]'
-        description: "Python versions to test (JSON array)"
 
 jobs:
   run-kuzu-lance-sqlite-search-tests:
-    name: Search test for Kuzu/LanceDB/Sqlite (Python ${{ matrix.python-version }})
+    name: Search test for Kuzu/LanceDB/Sqlite
     runs-on: ubuntu-22.04
     if: ${{ inputs.databases == 'all' || contains(inputs.databases, 'kuzu/lance/sqlite') }}
-    strategy:
-      matrix:
-        python-version: ${{ fromJSON(inputs.python-versions) }}
-      fail-fast: false
     steps:
       - name: Check out
         uses: actions/checkout@v4
@@ -35,7 +26,7 @@ jobs:
       - name: Cognee Setup
         uses: ./.github/actions/cognee_setup
         with:
-          python-version: ${{ matrix.python-version }}
+          python-version: ${{ inputs.python-version }}
 
       - name: Dependencies already installed
         run: echo "Dependencies already installed in setup"
@@ -54,16 +45,13 @@ jobs:
           GRAPH_DATABASE_PROVIDER: 'kuzu'
           VECTOR_DB_PROVIDER: 'lancedb'
           DB_PROVIDER: 'sqlite'
-        run: uv run pytest cognee/tests/test_search_db.py -v --log-level=INFO
+        run: uv run python ./cognee/tests/test_search_db.py
 
   run-neo4j-lance-sqlite-search-tests:
-    name: Search test for Neo4j/LanceDB/Sqlite (Python ${{ matrix.python-version }})
+    name: Search test for Neo4j/LanceDB/Sqlite
     runs-on: ubuntu-22.04
     if: ${{ inputs.databases == 'all' || contains(inputs.databases, 'neo4j/lance/sqlite') }}
-    strategy:
-      matrix:
-        python-version: ${{ fromJSON(inputs.python-versions) }}
-      fail-fast: false
+
     steps:
       - name: Check out
         uses: actions/checkout@v4
@@ -73,7 +61,7 @@ jobs:
       - name: Cognee Setup
         uses: ./.github/actions/cognee_setup
         with:
-          python-version: ${{ matrix.python-version }}
+          python-version: ${{ inputs.python-version }}
 
       - name: Setup Neo4j with GDS
         uses: ./.github/actions/setup_neo4j
@@ -100,16 +88,12 @@ jobs:
           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 pytest cognee/tests/test_search_db.py -v --log-level=INFO
+        run: uv run python ./cognee/tests/test_search_db.py
 
   run-kuzu-pgvector-postgres-search-tests:
-      name: Search test for Kuzu/PGVector/Postgres (Python ${{ matrix.python-version }})
+      name: Search test for Kuzu/PGVector/Postgres
       runs-on: ubuntu-22.04
       if: ${{ inputs.databases == 'all' || contains(inputs.databases, 'kuzu/pgvector/postgres') }}
-      strategy:
-        matrix:
-          python-version: ${{ fromJSON(inputs.python-versions) }}
-        fail-fast: false
       services:
         postgres:
           image: pgvector/pgvector:pg17
@@ -133,7 +117,7 @@ jobs:
         - name: Cognee Setup
           uses: ./.github/actions/cognee_setup
           with:
-            python-version: ${{ matrix.python-version }}
+            python-version: ${{ inputs.python-version }}
             extra-dependencies: "postgres"
 
         - name: Dependencies already installed
@@ -159,16 +143,12 @@ jobs:
             DB_PORT: 5432
             DB_USERNAME: cognee
             DB_PASSWORD: cognee
-          run: uv run pytest cognee/tests/test_search_db.py -v --log-level=INFO
+          run: uv run python ./cognee/tests/test_search_db.py
 
   run-neo4j-pgvector-postgres-search-tests:
-    name: Search test for Neo4j/PGVector/Postgres (Python ${{ matrix.python-version }})
+    name: Search test for Neo4j/PGVector/Postgres
     runs-on: ubuntu-22.04
     if: ${{ inputs.databases == 'all' || contains(inputs.databases, 'neo4j/pgvector/postgres') }}
-    strategy:
-      matrix:
-        python-version: ${{ fromJSON(inputs.python-versions) }}
-      fail-fast: false
     services:
       postgres:
         image: pgvector/pgvector:pg17
@@ -192,7 +172,7 @@ jobs:
       - name: Cognee Setup
         uses: ./.github/actions/cognee_setup
         with:
-          python-version: ${{ matrix.python-version }}
+          python-version: ${{ inputs.python-version }}
           extra-dependencies: "postgres"
 
       - name: Setup Neo4j with GDS
@@ -225,4 +205,4 @@ jobs:
           DB_PORT: 5432
           DB_USERNAME: cognee
           DB_PASSWORD: cognee
-        run: uv run pytest cognee/tests/test_search_db.py -v --log-level=INFO
+        run: uv run python ./cognee/tests/test_search_db.py

.github/workflows/test_different_operating_systems.yml

@@ -10,7 +10,7 @@ on:
         required: false
         type: string
         default: '["3.10.x", "3.12.x", "3.13.x"]'
-      os:
+      os: 
         required: false
         type: string
         default: '["ubuntu-22.04", "macos-15", "windows-latest"]'

.github/workflows/test_llms.yml

@@ -173,4 +173,4 @@ jobs:
           EMBEDDING_MODEL: "amazon.titan-embed-text-v2:0"
           EMBEDDING_DIMENSIONS: "1024"
           EMBEDDING_MAX_TOKENS: "8191"
-        run: uv run python ./examples/python/simple_example.py
+        run: uv run python ./examples/python/simple_example.py

.github/workflows/test_suites.yml

@@ -18,11 +18,11 @@ env:
   RUNTIME__LOG_LEVEL: ERROR
   ENV: 'dev'
 
-jobs:
+jobs: 
   pre-test:
     name: basic checks
     uses: ./.github/workflows/pre_test.yml
-
+    
   basic-tests:
     name: Basic Tests
     uses: ./.github/workflows/basic_tests.yml

.github/workflows/vector_db_tests.yml

@@ -103,55 +103,6 @@ jobs:
           EMBEDDING_API_VERSION: ${{ secrets.EMBEDDING_API_VERSION }}
         run: uv run python ./cognee/tests/test_pgvector.py
 
-  run-pgvector-multi-user-tests:
-    name: PGVector Multi-User Tests
-    runs-on: ubuntu-22.04
-    if: ${{ inputs.databases == 'all' || contains(inputs.databases, 'postgres') }}
-    services:
-      postgres:
-        image: pgvector/pgvector:pg17
-        env:
-          POSTGRES_USER: cognee
-          POSTGRES_PASSWORD: ${{ secrets.POSTGRES_PASSWORD }}
-          POSTGRES_DB: cognee_db
-        options: >-
-          --health-cmd pg_isready
-          --health-interval 10s
-          --health-timeout 5s
-          --health-retries 5
-        ports:
-          - 5432:5432
-    steps:
-      - name: Check out
-        uses: actions/checkout@v4
-        with:
-          fetch-depth: 0
-
-      - name: Cognee Setup
-        uses: ./.github/actions/cognee_setup
-        with:
-          python-version: ${{ inputs.python-version }}
-          extra-dependencies: "postgres"
-
-      - name: Run PGVector Permissions Tests
-        env:
-          ENV: 'dev'
-          ENABLE_BACKEND_ACCESS_CONTROL: 'true'
-          LLM_MODEL: ${{ secrets.LLM_MODEL }}
-          LLM_ENDPOINT: ${{ secrets.LLM_ENDPOINT }}
-          LLM_API_KEY: ${{ secrets.LLM_API_KEY }}
-          LLM_API_VERSION: ${{ secrets.LLM_API_VERSION }}
-          EMBEDDING_MODEL: ${{ secrets.EMBEDDING_MODEL }}
-          EMBEDDING_ENDPOINT: ${{ secrets.EMBEDDING_ENDPOINT }}
-          EMBEDDING_API_KEY: ${{ secrets.EMBEDDING_API_KEY }}
-          EMBEDDING_API_VERSION: ${{ secrets.EMBEDDING_API_VERSION }}
-          VECTOR_DB_URL: 127.0.0.1
-          VECTOR_DB_PORT: 5432
-          VECTOR_DB_USERNAME: cognee
-          VECTOR_DB_PASSWORD: ${{ secrets.POSTGRES_PASSWORD }}
-          VECTOR_DATASET_DATABASE_HANDLER: pgvector
-        run: uv run python ./cognee/tests/test_permissions.py
-
   run-lancedb-tests:
     name: LanceDB Tests
     runs-on: ubuntu-22.04

.gitignore

@@ -147,8 +147,6 @@ venv/
 ENV/
 env.bak/
 venv.bak/
-mise.toml
-deployment/helm/values-local.yml
 
 # Spyder project settings
 .spyderproject

.mergify.yml

@@ -6,4 +6,4 @@ pull_request_rules:
     actions:
       backport:
         branches:
-          - main
+          - main

.pre-commit-config.yaml

@@ -7,7 +7,6 @@ repos:
     -   id: trailing-whitespace
     -   id: end-of-file-fixer
     -   id: check-yaml
-        exclude: ^deployment/helm/templates/
     -   id: check-added-large-files
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.

AGENTS.md

@@ -128,3 +128,5 @@ MCP server and Frontend:
 ## CI Mirrors Local Commands
 
 Our GitHub Actions run the same ruff checks and pytest suites shown above (`.github/workflows/basic_tests.yml` and related workflows). Use the commands in this document locally to minimize CI surprises.
+
+

CLAUDE.md

@@ -1,590 +0,0 @@
-# CLAUDE.md
-
-This file provides guidance to Claude Code (claude.ai/code) when working with code in this repository.
-
-## Project Overview
-
-Cognee is an open-source AI memory platform that transforms raw data into persistent knowledge graphs for AI agents. It replaces traditional RAG (Retrieval-Augmented Generation) with an ECL (Extract, Cognify, Load) pipeline combining vector search, graph databases, and LLM-powered entity extraction.
-
-**Requirements**: Python 3.9 - 3.12
-
-## Development Commands
-
-### Setup
-```bash
-# Create virtual environment (recommended: uv)
-uv venv && source .venv/bin/activate
-
-# Install with pip, poetry, or uv
-uv pip install -e .
-
-# Install with dev dependencies
-uv pip install -e ".[dev]"
-
-# Install with specific extras
-uv pip install -e ".[postgres,neo4j,docs,chromadb]"
-
-# Set up pre-commit hooks
-pre-commit install
-```
-
-### Available Installation Extras
-- **postgres** / **postgres-binary** - PostgreSQL + PGVector support
-- **neo4j** - Neo4j graph database support
-- **neptune** - AWS Neptune support
-- **chromadb** - ChromaDB vector database
-- **docs** - Document processing (unstructured library)
-- **scraping** - Web scraping (Tavily, BeautifulSoup, Playwright)
-- **langchain** - LangChain integration
-- **llama-index** - LlamaIndex integration
-- **anthropic** - Anthropic Claude models
-- **gemini** - Google Gemini models
-- **ollama** - Ollama local models
-- **mistral** - Mistral AI models
-- **groq** - Groq API support
-- **llama-cpp** - Llama.cpp local inference
-- **huggingface** - HuggingFace transformers
-- **aws** - S3 storage backend
-- **redis** - Redis caching
-- **graphiti** - Graphiti-core integration
-- **baml** - BAML structured output
-- **dlt** - Data load tool (dlt) integration
-- **docling** - Docling document processing
-- **codegraph** - Code graph extraction
-- **evals** - Evaluation tools
-- **deepeval** - DeepEval testing framework
-- **posthog** - PostHog analytics
-- **monitoring** - Sentry + Langfuse observability
-- **distributed** - Modal distributed execution
-- **dev** - All development tools (pytest, mypy, ruff, etc.)
-- **debug** - Debugpy for debugging
-
-### Testing
-```bash
-# Run all tests
-pytest
-
-# Run with coverage
-pytest --cov=cognee --cov-report=html
-
-# Run specific test file
-pytest cognee/tests/test_custom_model.py
-
-# Run specific test function
-pytest cognee/tests/test_custom_model.py::test_function_name
-
-# Run async tests
-pytest -v cognee/tests/integration/
-
-# Run unit tests only
-pytest cognee/tests/unit/
-
-# Run integration tests only
-pytest cognee/tests/integration/
-```
-
-### Code Quality
-```bash
-# Run ruff linter
-ruff check .
-
-# Run ruff formatter
-ruff format .
-
-# Run both linting and formatting (pre-commit)
-pre-commit run --all-files
-
-# Type checking with mypy
-mypy cognee/
-
-# Run pylint
-pylint cognee/
-```
-
-### Running Cognee
-```bash
-# Using Python SDK
-python examples/python/simple_example.py
-
-# Using CLI
-cognee-cli add "Your text here"
-cognee-cli cognify
-cognee-cli search "Your query"
-cognee-cli delete --all
-
-# Launch full stack with UI
-cognee-cli -ui
-```
-
-## Architecture Overview
-
-### Core Workflow: add → cognify → search/memify
-
-1. **add()** - Ingest data (files, URLs, text) into datasets
-2. **cognify()** - Extract entities/relationships and build knowledge graph
-3. **search()** - Query knowledge using various retrieval strategies
-4. **memify()** - Enrich graph with additional context and rules
-
-### Key Architectural Patterns
-
-#### 1. Pipeline-Based Processing
-All data flows through task-based pipelines (`cognee/modules/pipelines/`). Tasks are composable units that can run sequentially or in parallel. Example pipeline tasks: `classify_documents`, `extract_graph_from_data`, `add_data_points`.
-
-#### 2. Interface-Based Database Adapters
-Multiple backends are supported through adapter interfaces:
-- **Graph**: Kuzu (default), Neo4j, Neptune via `GraphDBInterface`
-- **Vector**: LanceDB (default), ChromaDB, PGVector via `VectorDBInterface`
-- **Relational**: SQLite (default), PostgreSQL
-
-Key files:
-- `cognee/infrastructure/databases/graph/graph_db_interface.py`
-- `cognee/infrastructure/databases/vector/vector_db_interface.py`
-
-#### 3. Multi-Tenant Access Control
-User → Dataset → Data hierarchy with permission-based filtering. Enable with `ENABLE_BACKEND_ACCESS_CONTROL=True`. Each user+dataset combination can have isolated graph/vector databases (when using supported backends: Kuzu, LanceDB, SQLite, Postgres).
-
-### Layer Structure
-
-```
-API Layer (cognee/api/v1/)
-    ↓
-Main Functions (add, cognify, search, memify)
-    ↓
-Pipeline Orchestrator (cognee/modules/pipelines/)
-    ↓
-Task Execution Layer (cognee/tasks/)
-    ↓
-Domain Modules (graph, retrieval, ingestion, etc.)
-    ↓
-Infrastructure Adapters (LLM, databases)
-    ↓
-External Services (OpenAI, Kuzu, LanceDB, etc.)
-```
-
-### Critical Data Flow Paths
-
-#### ADD: Data Ingestion
-`add()` → `resolve_data_directories` → `ingest_data` → `save_data_item_to_storage` → Create Dataset + Data records in relational DB
-
-Key files: `cognee/api/v1/add/add.py`, `cognee/tasks/ingestion/ingest_data.py`
-
-#### COGNIFY: Knowledge Graph Construction
-`cognify()` → `classify_documents` → `extract_chunks_from_documents` → `extract_graph_from_data` (LLM extracts entities/relationships using Instructor) → `summarize_text` → `add_data_points` (store in graph + vector DBs)
-
-Key files:
-- `cognee/api/v1/cognify/cognify.py`
-- `cognee/tasks/graph/extract_graph_from_data.py`
-- `cognee/tasks/storage/add_data_points.py`
-
-#### SEARCH: Retrieval
-`search(query_text, query_type)` → route to retriever type → filter by permissions → return results
-
-Available search types (from `cognee/modules/search/types/SearchType.py`):
-- **GRAPH_COMPLETION** (default) - Graph traversal + LLM completion
-- **GRAPH_SUMMARY_COMPLETION** - Uses pre-computed summaries with graph context
-- **GRAPH_COMPLETION_COT** - Chain-of-thought reasoning over graph
-- **GRAPH_COMPLETION_CONTEXT_EXTENSION** - Extended context graph retrieval
-- **TRIPLET_COMPLETION** - Triplet-based (subject-predicate-object) search
-- **RAG_COMPLETION** - Traditional RAG with chunks
-- **CHUNKS** - Vector similarity search over chunks
-- **CHUNKS_LEXICAL** - Lexical (keyword) search over chunks
-- **SUMMARIES** - Search pre-computed document summaries
-- **CYPHER** - Direct Cypher query execution (requires `ALLOW_CYPHER_QUERY=True`)
-- **NATURAL_LANGUAGE** - Natural language to structured query
-- **TEMPORAL** - Time-aware graph search
-- **FEELING_LUCKY** - Automatic search type selection
-- **FEEDBACK** - User feedback-based refinement
-- **CODING_RULES** - Code-specific search rules
-
-Key files:
-- `cognee/api/v1/search/search.py`
-- `cognee/modules/retrieval/context_providers/TripletSearchContextProvider.py`
-- `cognee/modules/search/types/SearchType.py`
-
-### Core Data Models
-
-#### Engine Models (`cognee/infrastructure/engine/models/`)
-- **DataPoint** - Base class for all graph nodes (versioned, with metadata)
-- **Edge** - Graph relationships (source, target, relationship type)
-- **Triplet** - (Subject, Predicate, Object) representation
-
-#### Graph Models (`cognee/shared/data_models.py`)
-- **KnowledgeGraph** - Container for nodes and edges
-- **Node** - Entity (id, name, type, description)
-- **Edge** - Relationship (source_node_id, target_node_id, relationship_name)
-
-### Key Infrastructure Components
-
-#### LLM Gateway (`cognee/infrastructure/llm/LLMGateway.py`)
-Unified interface for multiple LLM providers: OpenAI, Anthropic, Gemini, Ollama, Mistral, Bedrock. Uses Instructor for structured output extraction.
-
-#### Embedding Engines
-Factory pattern for embeddings: `cognee/infrastructure/databases/vector/embeddings/get_embedding_engine.py`
-
-#### Document Loaders
-Support for PDF, DOCX, CSV, images, audio, code files in `cognee/infrastructure/files/`
-
-## Important Configuration
-
-### Environment Setup
-Copy `.env.template` to `.env` and configure:
-
-```bash
-# Minimal setup (defaults to OpenAI + local file-based databases)
-LLM_API_KEY="your_openai_api_key"
-LLM_MODEL="openai/gpt-4o-mini"  # Default model
-```
-
-**Important**: If you configure only LLM or only embeddings, the other defaults to OpenAI. Ensure you have a working OpenAI API key, or configure both to avoid unexpected defaults.
-
-Default databases (no extra setup needed):
-- **Relational**: SQLite (metadata and state storage)
-- **Vector**: LanceDB (embeddings for semantic search)
-- **Graph**: Kuzu (knowledge graph and relationships)
-
-All stored in `.venv` by default. Override with `DATA_ROOT_DIRECTORY` and `SYSTEM_ROOT_DIRECTORY`.
-
-### Switching Databases
-
-#### Relational Databases
-```bash
-# PostgreSQL (requires postgres extra: pip install cognee[postgres])
-DB_PROVIDER=postgres
-DB_HOST=localhost
-DB_PORT=5432
-DB_USERNAME=cognee
-DB_PASSWORD=cognee
-DB_NAME=cognee_db
-```
-
-#### Vector Databases
-Supported: lancedb (default), pgvector, chromadb, qdrant, weaviate, milvus
-```bash
-# ChromaDB (requires chromadb extra)
-VECTOR_DB_PROVIDER=chromadb
-
-# PGVector (requires postgres extra)
-VECTOR_DB_PROVIDER=pgvector
-VECTOR_DB_URL=postgresql://cognee:cognee@localhost:5432/cognee_db
-```
-
-#### Graph Databases
-Supported: kuzu (default), neo4j, neptune, kuzu-remote
-```bash
-# Neo4j (requires neo4j extra: pip install cognee[neo4j])
-GRAPH_DATABASE_PROVIDER=neo4j
-GRAPH_DATABASE_URL=bolt://localhost:7687
-GRAPH_DATABASE_NAME=neo4j
-GRAPH_DATABASE_USERNAME=neo4j
-GRAPH_DATABASE_PASSWORD=yourpassword
-
-# Remote Kuzu
-GRAPH_DATABASE_PROVIDER=kuzu-remote
-GRAPH_DATABASE_URL=http://localhost:8000
-GRAPH_DATABASE_USERNAME=your_username
-GRAPH_DATABASE_PASSWORD=your_password
-```
-
-### LLM Provider Configuration
-
-Supported providers: OpenAI (default), Azure OpenAI, Google Gemini, Anthropic, AWS Bedrock, Ollama, LM Studio, Custom (OpenAI-compatible APIs)
-
-#### OpenAI (Recommended - Minimal Setup)
-```bash
-LLM_API_KEY="your_openai_api_key"
-LLM_MODEL="openai/gpt-4o-mini"  # or gpt-4o, gpt-4-turbo, etc.
-LLM_PROVIDER="openai"
-```
-
-#### Azure OpenAI
-```bash
-LLM_PROVIDER="azure"
-LLM_MODEL="azure/gpt-4o-mini"
-LLM_ENDPOINT="https://YOUR-RESOURCE.openai.azure.com/openai/deployments/gpt-4o-mini"
-LLM_API_KEY="your_azure_api_key"
-LLM_API_VERSION="2024-12-01-preview"
-```
-
-#### Google Gemini (requires gemini extra)
-```bash
-LLM_PROVIDER="gemini"
-LLM_MODEL="gemini/gemini-2.0-flash-exp"
-LLM_API_KEY="your_gemini_api_key"
-```
-
-#### Anthropic Claude (requires anthropic extra)
-```bash
-LLM_PROVIDER="anthropic"
-LLM_MODEL="claude-3-5-sonnet-20241022"
-LLM_API_KEY="your_anthropic_api_key"
-```
-
-#### Ollama (Local - requires ollama extra)
-```bash
-LLM_PROVIDER="ollama"
-LLM_MODEL="llama3.1:8b"
-LLM_ENDPOINT="http://localhost:11434/v1"
-LLM_API_KEY="ollama"
-EMBEDDING_PROVIDER="ollama"
-EMBEDDING_MODEL="nomic-embed-text:latest"
-EMBEDDING_ENDPOINT="http://localhost:11434/api/embed"
-HUGGINGFACE_TOKENIZER="nomic-ai/nomic-embed-text-v1.5"
-```
-
-#### Custom / OpenRouter / vLLM
-```bash
-LLM_PROVIDER="custom"
-LLM_MODEL="openrouter/google/gemini-2.0-flash-lite-preview-02-05:free"
-LLM_ENDPOINT="https://openrouter.ai/api/v1"
-LLM_API_KEY="your_api_key"
-```
-
-#### AWS Bedrock (requires aws extra)
-```bash
-LLM_PROVIDER="bedrock"
-LLM_MODEL="anthropic.claude-3-sonnet-20240229-v1:0"
-AWS_REGION="us-east-1"
-AWS_ACCESS_KEY_ID="your_access_key"
-AWS_SECRET_ACCESS_KEY="your_secret_key"
-# Optional for temporary credentials:
-# AWS_SESSION_TOKEN="your_session_token"
-```
-
-#### LLM Rate Limiting
-```bash
-LLM_RATE_LIMIT_ENABLED=true
-LLM_RATE_LIMIT_REQUESTS=60  # Requests per interval
-LLM_RATE_LIMIT_INTERVAL=60  # Interval in seconds
-```
-
-#### Instructor Mode (Structured Output)
-```bash
-# LLM_INSTRUCTOR_MODE controls how structured data is extracted
-# Each LLM has its own default (e.g., gpt-4o models use "json_schema_mode")
-# Override if needed:
-LLM_INSTRUCTOR_MODE="json_schema_mode"  # or "tool_call", "md_json", etc.
-```
-
-### Structured Output Framework
-```bash
-# Use Instructor (default, via litellm)
-STRUCTURED_OUTPUT_FRAMEWORK="instructor"
-
-# Or use BAML (requires baml extra: pip install cognee[baml])
-STRUCTURED_OUTPUT_FRAMEWORK="baml"
-BAML_LLM_PROVIDER=openai
-BAML_LLM_MODEL="gpt-4o-mini"
-BAML_LLM_API_KEY="your_api_key"
-```
-
-### Storage Backend
-```bash
-# Local filesystem (default)
-STORAGE_BACKEND="local"
-
-# S3 (requires aws extra: pip install cognee[aws])
-STORAGE_BACKEND="s3"
-STORAGE_BUCKET_NAME="your-bucket-name"
-AWS_REGION="us-east-1"
-AWS_ACCESS_KEY_ID="your_access_key"
-AWS_SECRET_ACCESS_KEY="your_secret_key"
-DATA_ROOT_DIRECTORY="s3://your-bucket/cognee/data"
-SYSTEM_ROOT_DIRECTORY="s3://your-bucket/cognee/system"
-```
-
-## Extension Points
-
-### Adding New Functionality
-
-1. **New Task Type**: Create task function in `cognee/tasks/`, return Task object, register in pipeline
-2. **New Database Backend**: Implement `GraphDBInterface` or `VectorDBInterface` in `cognee/infrastructure/databases/`
-3. **New LLM Provider**: Add configuration in LLM config (uses litellm)
-4. **New Document Processor**: Extend loaders in `cognee/modules/data/processing/`
-5. **New Search Type**: Add to `SearchType` enum and implement retriever in `cognee/modules/retrieval/`
-6. **Custom Graph Models**: Define Pydantic models extending `DataPoint` in your code
-
-### Working with Ontologies
-Cognee supports ontology-based entity extraction to ground knowledge graphs in standardized semantic frameworks (e.g., OWL ontologies).
-
-Configuration:
-```bash
-ONTOLOGY_RESOLVER=rdflib  # Default: uses rdflib and OWL files
-MATCHING_STRATEGY=fuzzy   # Default: fuzzy matching with 80% similarity
-ONTOLOGY_FILE_PATH=/path/to/your/ontology.owl  # Full path to ontology file
-```
-
-Implementation: `cognee/modules/ontology/`
-
-## Branching Strategy
-
-**IMPORTANT**: Always branch from `dev`, not `main`. The `dev` branch is the active development branch.
-
-```bash
-git checkout dev
-git pull origin dev
-git checkout -b feature/your-feature-name
-```
-
-## Code Style
-
-- **Formatter**: Ruff (configured in `pyproject.toml`)
-- **Line length**: 100 characters
-- **String quotes**: Use double quotes `"` not single quotes `'` (enforced by ruff-format)
-- **Pre-commit hooks**: Run ruff linting and formatting automatically
-- **Type hints**: Encouraged (mypy checks enabled)
-- **Important**: Always run `pre-commit run --all-files` before committing to catch formatting issues
-
-## Testing Strategy
-
-Tests are organized in `cognee/tests/`:
-- `unit/` - Unit tests for individual modules
-- `integration/` - Full pipeline integration tests
-- `cli_tests/` - CLI command tests
-- `tasks/` - Task-specific tests
-
-When adding features, add corresponding tests. Integration tests should cover the full add → cognify → search flow.
-
-## API Structure
-
-FastAPI application with versioned routes under `cognee/api/v1/`:
-- `/add` - Data ingestion
-- `/cognify` - Knowledge graph processing
-- `/search` - Query interface
-- `/memify` - Graph enrichment
-- `/datasets` - Dataset management
-- `/users` - Authentication (if `REQUIRE_AUTHENTICATION=True`)
-- `/visualize` - Graph visualization server
-
-## Python SDK Entry Points
-
-Main functions exported from `cognee/__init__.py`:
-- `add(data, dataset_name)` - Ingest data
-- `cognify(datasets)` - Build knowledge graph
-- `search(query_text, query_type)` - Query knowledge
-- `memify(extraction_tasks, enrichment_tasks)` - Enrich graph
-- `delete(data_id)` - Remove data
-- `config()` - Configuration management
-- `datasets()` - Dataset operations
-
-All functions are async - use `await` or `asyncio.run()`.
-
-## Security Considerations
-
-Several security environment variables in `.env`:
-- `ACCEPT_LOCAL_FILE_PATH` - Allow local file paths (default: True)
-- `ALLOW_HTTP_REQUESTS` - Allow HTTP requests from Cognee (default: True)
-- `ALLOW_CYPHER_QUERY` - Allow raw Cypher queries (default: True)
-- `REQUIRE_AUTHENTICATION` - Enable API authentication (default: False)
-- `ENABLE_BACKEND_ACCESS_CONTROL` - Multi-tenant isolation (default: True)
-
-For production deployments, review and tighten these settings.
-
-## Common Patterns
-
-### Creating a Custom Pipeline Task
-```python
-from cognee.modules.pipelines.tasks.Task import Task
-
-async def my_custom_task(data):
-    # Your logic here
-    processed_data = process(data)
-    return processed_data
-
-# Use in pipeline
-task = Task(my_custom_task)
-```
-
-### Accessing Databases Directly
-```python
-from cognee.infrastructure.databases.graph import get_graph_engine
-from cognee.infrastructure.databases.vector import get_vector_engine
-
-graph_engine = await get_graph_engine()
-vector_engine = await get_vector_engine()
-```
-
-### Using LLM Gateway
-```python
-from cognee.infrastructure.llm.get_llm_client import get_llm_client
-
-llm_client = get_llm_client()
-response = await llm_client.acreate_structured_output(
-    text_input="Your prompt",
-    system_prompt="System instructions",
-    response_model=YourPydanticModel
-)
-```
-
-## Key Concepts
-
-### Datasets
-Datasets are project-level containers that support organization, permissions, and isolated processing workflows. Each user can have multiple datasets with different access permissions.
-
-```python
-# Create/use a dataset
-await cognee.add(data, dataset_name="my_project")
-await cognee.cognify(datasets=["my_project"])
-```
-
-### DataPoints
-Atomic knowledge units that form the foundation of graph structures. All graph nodes extend the `DataPoint` base class with versioning and metadata support.
-
-### Permissions System
-Multi-tenant architecture with users, roles, and Access Control Lists (ACLs):
-- Read, write, delete, and share permissions per dataset
-- Enable with `ENABLE_BACKEND_ACCESS_CONTROL=True`
-- Supports isolated databases per user+dataset (Kuzu, LanceDB, SQLite, Postgres)
-
-### Graph Visualization
-Launch visualization server:
-```bash
-# Via CLI
-cognee-cli -ui  # Launches full stack with UI at http://localhost:3000
-
-# Via Python
-from cognee.api.v1.visualize import start_visualization_server
-await start_visualization_server(port=8080)
-```
-
-## Debugging & Troubleshooting
-
-### Debug Configuration
-- Set `LITELLM_LOG="DEBUG"` for verbose LLM logs (default: "ERROR")
-- Enable debug mode: `ENV="development"` or `ENV="debug"`
-- Disable telemetry: `TELEMETRY_DISABLED=1`
-- Check logs in structured format (uses structlog)
-- Use `debugpy` optional dependency for debugging: `pip install cognee[debug]`
-
-### Common Issues
-
-**Ollama + OpenAI Embeddings NoDataError**
-- Issue: Mixing Ollama with OpenAI embeddings can cause errors
-- Solution: Configure both LLM and embeddings to use the same provider, or ensure `HUGGINGFACE_TOKENIZER` is set when using Ollama
-
-**LM Studio Structured Output**
-- Issue: LM Studio requires explicit instructor mode
-- Solution: Set `LLM_INSTRUCTOR_MODE="json_schema_mode"` (or appropriate mode)
-
-**Default Provider Fallback**
-- Issue: Configuring only LLM or only embeddings defaults the other to OpenAI
-- Solution: Always configure both LLM and embedding providers, or ensure valid OpenAI API key
-
-**Permission Denied on Search**
-- Behavior: Returns empty list rather than error (prevents information leakage)
-- Solution: Check dataset permissions and user access rights
-
-**Database Connection Issues**
-- Check: Verify database URLs, credentials, and that services are running
-- Docker users: Use `DB_HOST=host.docker.internal` for local databases
-
-**Rate Limiting Errors**
-- Enable client-side rate limiting: `LLM_RATE_LIMIT_ENABLED=true`
-- Adjust limits: `LLM_RATE_LIMIT_REQUESTS` and `LLM_RATE_LIMIT_INTERVAL`
-
-## Resources
-
-- [Documentation](https://docs.cognee.ai/)
-- [Discord Community](https://discord.gg/NQPKmU5CCg)
-- [GitHub Issues](https://github.com/topoteretes/cognee/issues)
-- [Example Notebooks](examples/python/)
-- [Research Paper](https://arxiv.org/abs/2505.24478) - Optimizing knowledge graphs for LLM reasoning

CONTRIBUTING.md

@@ -1,16 +1,16 @@
 > [!IMPORTANT]
 > **Note for contributors:** When branching out, create a new branch from the `dev` branch.
 
-# 🎉 Welcome to **cognee**!
+# 🎉 Welcome to **cognee**! 
 
-We're excited that you're interested in contributing to our project!
-We want to ensure that every user and contributor feels welcome, included and supported to participate in cognee community.
+We're excited that you're interested in contributing to our project! 
+We want to ensure that every user and contributor feels welcome, included and supported to participate in cognee community. 
 This guide will help you get started and ensure your contributions can be efficiently integrated into the project.
 
 ## 🌟 Quick Links
 
 - [Code of Conduct](CODE_OF_CONDUCT.md)
-- [Discord Community](https://discord.gg/bcy8xFAtfd)
+- [Discord Community](https://discord.gg/bcy8xFAtfd)  
 - [Issue Tracker](https://github.com/topoteretes/cognee/issues)
 - [Cognee Docs](https://docs.cognee.ai)
 
@@ -62,11 +62,6 @@ Looking for a place to start? Try filtering for [good first issues](https://gith
 
 ## 2. 🛠️ Development Setup
 
-### Required tools
-* [Python](https://www.python.org/downloads/)
-* [uv](https://docs.astral.sh/uv/getting-started/installation/)
-* pre-commit: `uv run pip install pre-commit && pre-commit install`
-
 ### Fork and Clone
 
 1. Fork the [**cognee**](https://github.com/topoteretes/cognee) repository
@@ -98,26 +93,8 @@ git checkout -b feature/your-feature-name
 4. **Commits**: Write clear commit messages
 
 ### Running Tests
-
-Rename `.env.example` into `.env` and provide your OPENAI_API_KEY as LLM_API_KEY
-
 ```shell
-uv run python cognee/tests/test_library.py
-```
-
-### Running Simple Example
-
-Rename `.env.example` into `.env` and provide your OPENAI_API_KEY as LLM_API_KEY
-
-Make sure to run ```shell uv sync ``` in the root cloned folder or set up a virtual environment to run cognee
-
-```shell
-python examples/python/simple_example.py
-```
-or
-
-```shell
-uv run python examples/python/simple_example.py
+python cognee/cognee/tests/test_library.py
 ```
 
 ### Running Simple Example
@@ -129,7 +106,7 @@ Make sure to run ```shell uv sync ``` in the root cloned folder or set up a virt
 ```shell
 python cognee/cognee/examples/python/simple_example.py
 ```
-or
+or 
 
 ```shell
 uv run python cognee/cognee/examples/python/simple_example.py
@@ -137,7 +114,8 @@ uv run python cognee/cognee/examples/python/simple_example.py
 
 ## 4. 📤 Submitting Changes
 
-1. Make sure that `pre-commit` and hooks are installed. See `Required tools` section for more information. Try executing `pre-commit run` if you are not sure.
+1. Install ruff on your system
+2. Run ```ruff format .``` and ``` ruff check ``` and fix the issues
 3. Push your changes:
 ```shell
 git add .

Dockerfile

@@ -32,14 +32,18 @@ COPY README.md pyproject.toml uv.lock entrypoint.sh ./
 
 # Install the project's dependencies using the lockfile and settings
 RUN --mount=type=cache,target=/root/.cache/uv \
-    uv sync --extra debug --extra api --extra postgres --extra neo4j --extra llama-index --extra ollama --extra mistral --extra groq --extra anthropic --extra chromadb --frozen --no-install-project --no-dev --no-editable
+    uv sync --extra debug --extra api --extra postgres --extra neo4j --extra llama-index --extra ollama --extra mistral --extra groq --extra anthropic --frozen --no-install-project --no-dev --no-editable
+
+# Copy Alembic configuration
+COPY alembic.ini /app/alembic.ini
+COPY alembic/ /app/alembic
 
 # Then, add the rest of the project source code and install it
 # Installing separately from its dependencies allows optimal layer caching
 COPY ./cognee /app/cognee
 COPY ./distributed /app/distributed
 RUN --mount=type=cache,target=/root/.cache/uv \
-uv sync --extra debug --extra api --extra postgres --extra neo4j --extra llama-index --extra ollama --extra mistral --extra groq --extra anthropic --extra chromadb --frozen --no-dev --no-editable
+uv sync --extra debug --extra api --extra postgres --extra neo4j --extra llama-index --extra ollama --extra mistral --extra groq --extra anthropic --frozen --no-dev --no-editable
 
 FROM python:3.12-slim-bookworm
 

README.md

@@ -65,14 +65,11 @@ Use your data to build personalized and dynamic memory for AI Agents. Cognee let
 
 ## About Cognee
 
-Cognee is an open-source tool and platform that transforms your raw data into persistent and dynamic AI memory for Agents. It combines vector search with graph databases to make your documents both searchable by meaning and connected by relationships.
+Cognee is an open-source tool and platform that transforms your raw data into persistent and dynamic AI memory for Agents. It combines vector search with graph databases to make your documents both searchable by meaning and connected by relationships. 
+Cognee offers default memory creation and search which we describe bellow. But with Cognee you can build your own!
 
-You can use Cognee in two ways:
 
-1. [Self-host Cognee Open Source](https://docs.cognee.ai/getting-started/installation), which stores all data locally by default.
-2. [Connect to Cognee Cloud](https://platform.cognee.ai/), and get the same OSS stack on managed infrastructure for easier development and productionization.
-
-### Cognee Open Source (self-hosted):
+### Cognee Open Source:
 
 - Interconnects any type of data — including past conversations, files, images, and audio transcriptions
 - Replaces traditional RAG systems with a unified memory layer built on graphs and vectors
@@ -80,11 +77,6 @@ You can use Cognee in two ways:
 - Provides Pythonic data pipelines for ingestion from 30+ data sources
 - Offers high customizability through user-defined tasks, modular pipelines, and built-in search endpoints
 
-### Cognee Cloud (managed):
-- Hosted web UI dashboard
-- Automatic version updates
-- Resource usage analytics
-- GDPR compliant, enterprise-grade security
 
 ## Basic Usage & Feature Guide
 
@@ -119,7 +111,7 @@ To integrate other LLM providers, see our [LLM Provider Documentation](https://d
 
 ### Step 3: Run the Pipeline
 
-Cognee will take your documents, generate a knowledge graph from them and then query the graph based on combined relationships.
+Cognee will take your documents, generate a knowledge graph from them and then query the graph based on combined relationships. 
 
 Now, run a minimal pipeline:
 
@@ -158,7 +150,7 @@ As you can see, the output is generated from the document we previously stored i
   Cognee turns documents into AI memory.
 ```
 
-### Use the Cognee CLI
+### Use the Cognee CLI 
 
 As an alternative, you can get started with these essential commands:
 

alembic/README

@@ -0,0 +1 @@
+Generic single-database configuration with an async dbapi.

assets/community/README.pt.md

@@ -43,10 +43,10 @@ Saiba mais sobre os [casos de uso](https://docs.cognee.ai/use-cases) e [avaliaç
 
 ## Funcionalidades
 
-- Conecte e recupere suas conversas passadas, documentos, imagens e transcrições de áudio
-- Reduza alucinações, esforço de desenvolvimento e custos
-- Carregue dados em bancos de dados de grafos e vetores usando apenas Pydantic
-- Transforme e organize seus dados enquanto os coleta de mais de 30 fontes diferentes
+- Conecte e recupere suas conversas passadas, documentos, imagens e transcrições de áudio  
+- Reduza alucinações, esforço de desenvolvimento e custos  
+- Carregue dados em bancos de dados de grafos e vetores usando apenas Pydantic  
+- Transforme e organize seus dados enquanto os coleta de mais de 30 fontes diferentes  
 
 ## Primeiros Passos
 
@@ -108,7 +108,7 @@ if __name__ == '__main__':
 Exemplo do output:
 ```
   O Processamento de Linguagem Natural (NLP) é um campo interdisciplinar e transdisciplinar que envolve ciência da computação e recuperação de informações. Ele se concentra na interação entre computadores e a linguagem humana, permitindo que as máquinas compreendam e processem a linguagem natural.
-
+  
 ```
 
 Visualização do grafo:

assets/community/README.ru.md

@@ -141,7 +141,7 @@ if __name__ == '__main__':
 2. Простая демонстрация GraphRAG
 [Видео](https://github.com/user-attachments/assets/d80b0776-4eb9-4b8e-aa22-3691e2d44b8f)
 
-3. Cognee с Ollama
+3. Cognee с Ollama 
 [Видео](https://github.com/user-attachments/assets/8621d3e8-ecb8-4860-afb2-5594f2ee17db)
 
 ## Правила поведения

assets/community/README.zh.md

@@ -114,7 +114,7 @@ if __name__ == '__main__':
 示例输出：
 ```
   自然语言处理（NLP）是计算机科学和信息检索的跨学科领域。它关注计算机和人类语言之间的交互，使机器能够理解和处理自然语言。
-
+  
 ```
 图形可视化：
 <a href="https://rawcdn.githack.com/topoteretes/cognee/refs/heads/main/assets/graph_visualization.html"><img src="https://rawcdn.githack.com/topoteretes/cognee/refs/heads/main/assets/graph_visualization.png" width="100%" alt="图形可视化"></a>

cognee-frontend/package.json

@@ -9,15 +9,14 @@
     "lint": "next lint"
   },
   "dependencies": {
-    "@auth0/nextjs-auth0": "^4.14.0",
+    "@auth0/nextjs-auth0": "^4.13.1",
     "classnames": "^2.5.1",
     "culori": "^4.0.1",
     "d3-force-3d": "^3.0.6",
-    "next": "^16.1.1",
-    "react": "^19.2.3",
-    "react-dom": "^19.2.3",
+    "next": "16.1.1",
+    "react": "^19.2.0",
+    "react-dom": "^19.2.0",
     "react-force-graph-2d": "^1.27.1",
-    "react-markdown": "^10.1.0",
     "uuid": "^9.0.1"
   },
   "devDependencies": {

cognee-frontend/src/app/(graph)/CogneeAddWidget.tsx

@@ -55,7 +55,7 @@ export default function CogneeAddWidget({ onData, useCloud = false }: CogneeAddW
     setTrue: setProcessingFilesInProgress,
     setFalse: setProcessingFilesDone,
   } = useBoolean(false);
-
+  
   const handleAddFiles = (dataset: Dataset, event: ChangeEvent<HTMLInputElement>) => {
     event.stopPropagation();
 

cognee-frontend/src/app/(graph)/GraphControls.tsx

@@ -111,7 +111,7 @@ export default function GraphControls({ data, isAddNodeFormOpen, onGraphShapeCha
 
   const [isAuthShapeChangeEnabled, setIsAuthShapeChangeEnabled] = useState(true);
   const shapeChangeTimeout = useRef<number | null>(null);
-
+  
   useEffect(() => {
     onGraphShapeChange(DEFAULT_GRAPH_SHAPE);
 

cognee-frontend/src/app/(graph)/GraphVisualization.tsx

@@ -57,7 +57,7 @@ export default function GraphVisualization({ ref, data, graphControls, className
     // Initial size calculation
     handleResize();
 
-    // ResizeObserver
+    // ResizeObserver 
     const resizeObserver = new ResizeObserver(() => {
       handleResize();
     });
@@ -216,7 +216,7 @@ export default function GraphVisualization({ ref, data, graphControls, className
   }, [data, graphRef]);
 
   const [graphShape, setGraphShape] = useState<string>();
-
+  
   const zoomToFit: ForceGraphMethods["zoomToFit"] = (
     durationMs?: number,
     padding?: number,
@@ -227,15 +227,15 @@ export default function GraphVisualization({ ref, data, graphControls, className
       // eslint-disable-next-line @typescript-eslint/no-explicit-any
       return undefined as any;
     }
-
+  
     return graphRef.current.zoomToFit?.(durationMs, padding, nodeFilter);
   };
-
+  
   useImperativeHandle(ref, () => ({
     zoomToFit,
     setGraphShape,
   }));
-
+  
 
   return (
     <div ref={containerRef} className={classNames("w-full h-full", className)} id="graph-container">

cognee-frontend/src/app/(graph)/example_data.json

@@ -1373,4 +1373,4 @@
       "padding": 20
     }
   }
-}
+} 

cognee-frontend/src/app/dashboard/Dashboard.tsx

@@ -15,8 +15,6 @@ import AddDataToCognee from "./AddDataToCognee";
 import NotebooksAccordion from "./NotebooksAccordion";
 import CogneeInstancesAccordion from "./CogneeInstancesAccordion";
 import InstanceDatasetsAccordion from "./InstanceDatasetsAccordion";
-import cloudFetch from "@/modules/instances/cloudFetch";
-import localFetch from "@/modules/instances/localFetch";
 
 interface DashboardProps {
   user?: {
@@ -28,17 +26,6 @@ interface DashboardProps {
   accessToken: string;
 }
 
-const cogneeInstances = {
-  cloudCognee: {
-    name: "CloudCognee",
-    fetch: cloudFetch,
-  },
-  localCognee: {
-    name: "LocalCognee",
-    fetch: localFetch,
-  }
-};
-
 export default function Dashboard({ accessToken }: DashboardProps) {
   fetch.setAccessToken(accessToken);
   const { user } = useAuthenticatedUser();
@@ -51,7 +38,7 @@ export default function Dashboard({ accessToken }: DashboardProps) {
     updateNotebook,
     saveNotebook,
     removeNotebook,
-  } = useNotebooks(cogneeInstances.localCognee);
+  } = useNotebooks();
 
   useEffect(() => {
     if (!notebooks.length) {

cognee-frontend/src/app/dashboard/DatasetsAccordion.tsx

@@ -134,7 +134,7 @@ export default function DatasetsAccordion({
   } = useBoolean(false);
 
   const [datasetToRemove, setDatasetToRemove] = useState<Dataset | null>(null);
-
+  
   const handleDatasetRemove = (dataset: Dataset) => {
     setDatasetToRemove(dataset);
     openRemoveDatasetModal();

cognee-frontend/src/app/dashboard/InstanceDatasetsAccordion.tsx

@@ -3,7 +3,6 @@ import { useCallback, useEffect } from "react";
 
 import { fetch, isCloudEnvironment, useBoolean } from "@/utils";
 import { checkCloudConnection } from "@/modules/cloud";
-import { setApiKey } from "@/modules/instances/cloudFetch";
 import { CaretIcon, CloseIcon, CloudIcon, LocalCogneeIcon } from "@/ui/Icons";
 import { CTAButton, GhostButton, IconButton, Input, Modal } from "@/ui/elements";
 
@@ -25,7 +24,6 @@ export default function InstanceDatasetsAccordion({ onDatasetsChange }: Instance
   const checkConnectionToCloudCognee = useCallback((apiKey?: string) => {
       if (apiKey) {
         fetch.setApiKey(apiKey);
-        setApiKey(apiKey);
       }
       return checkCloudConnection()
         .then(setCloudCogneeConnected)

cognee-frontend/src/app/plan/Plan.tsx

@@ -45,7 +45,7 @@ export default function Plan() {
           <div className="bg-white rounded-xl px-5 py-5 mb-2">
             Affordable and transparent pricing
           </div>
-
+        
           <div className="grid grid-cols-3 gap-x-2.5">
             <div className="pt-13 py-4 px-5 mb-2.5 rounded-tl-xl rounded-tr-xl bg-white h-full">
               <div>Basic</div>

cognee-frontend/src/modules/chat/hooks/useChat.ts

@@ -40,7 +40,7 @@ export default function useChat(dataset: Dataset) {
     setTrue: disableSearchRun,
     setFalse: enableSearchRun,
   } = useBoolean(false);
-
+  
   const refreshChat = useCallback(async () => {
     const data = await fetchMessages();
     return setMessages(data);

cognee-frontend/src/modules/ingestion/useDatasets.ts

@@ -46,7 +46,7 @@ function useDatasets(useCloud = false) {
   //     checkDatasetStatuses(datasets);
   //   }, 50000);
   // }, [fetchDatasetStatuses]);
-
+  
   // useEffect(() => {
   //   return () => {
   //     if (statusTimeout.current !== null) {
@@ -95,7 +95,6 @@ function useDatasets(useCloud = false) {
       })
       .catch((error) => {
         console.error('Error fetching datasets:', error);
-        throw error;
       });
   }, [useCloud]);
 

cognee-frontend/src/modules/instances/cloudFetch.ts

@@ -1,59 +0,0 @@
-import handleServerErrors from "@/utils/handleServerErrors";
-
-// let numberOfRetries = 0;
-
-const cloudApiUrl = process.env.NEXT_PUBLIC_CLOUD_API_URL || "http://localhost:8001";
-
-let apiKey: string | null = process.env.NEXT_PUBLIC_COGWIT_API_KEY || null;
-
-export function setApiKey(newApiKey: string) {
-  apiKey = newApiKey;
-};
-
-export default async function cloudFetch(url: URL | RequestInfo, options: RequestInit = {}): Promise<Response> {
-  // function retry(lastError: Response) {
-  //   if (numberOfRetries >= 1) {
-  //     return Promise.reject(lastError);
-  //   }
-
-  //   numberOfRetries += 1;
-
-  //   return global.fetch("/auth/token")
-  //     .then(() => {
-  //       return fetch(url, options);
-  //     });
-  // }
-
-  const authHeaders = {
-    "Authorization": `X-Api-Key ${apiKey}`,
-  };
-
-  return global.fetch(
-    cloudApiUrl + "/api" + (typeof url === "string" ? url : url.toString()).replace("/v1", ""),
-    {
-      ...options,
-      headers: {
-        ...options.headers,
-        ...authHeaders,
-      } as HeadersInit,
-      credentials: "include",
-    },
-  )
-    .then((response) => handleServerErrors(response, null, true))
-    .catch((error) => {
-      if (error.message === "NEXT_REDIRECT") {
-        throw error;
-      }
-
-      if (error.detail === undefined) {
-        return Promise.reject(
-          new Error("No connection to the server.")
-        );
-      }
-
-      return Promise.reject(error);
-    });
-    // .finally(() => {
-    //   numberOfRetries = 0;
-    // });
-}

cognee-frontend/src/modules/instances/localFetch.ts

@@ -1,27 +0,0 @@
-import handleServerErrors from "@/utils/handleServerErrors";
-
-const localApiUrl = process.env.NEXT_PUBLIC_LOCAL_API_URL || "http://localhost:8000";
-
-export default async function localFetch(url: URL | RequestInfo, options: RequestInit = {}): Promise<Response> {
-  return global.fetch(
-    localApiUrl + "/api" + (typeof url === "string" ? url : url.toString()),
-    {
-      ...options,
-      credentials: "include",
-    },
-  )
-    .then((response) => handleServerErrors(response, null, false))
-    .catch((error) => {
-      if (error.message === "NEXT_REDIRECT") {
-        throw error;
-      }
-
-      if (error.detail === undefined) {
-        return Promise.reject(
-          new Error("No connection to the server.")
-        );
-      }
-
-      return Promise.reject(error);
-    });
-}

cognee-frontend/src/modules/instances/types.ts

@@ -1,4 +0,0 @@
-export interface CogneeInstance {
-  name: string;
-  fetch: typeof global.fetch;
-}

cognee-frontend/src/modules/notebooks/createNotebook.ts

@@ -1,13 +0,0 @@
-import { CogneeInstance } from "@/modules/instances/types";
-
-export default function createNotebook(notebookName: string, instance: CogneeInstance) {
-  return instance.fetch("/v1/notebooks/", {
-    body: JSON.stringify({ name: notebookName }),
-    method: "POST",
-    headers: {
-      "Content-Type": "application/json",
-    },
-  }).then((response: Response) =>
-    response.ok ? response.json() : Promise.reject(response)
-  );
-}

cognee-frontend/src/modules/notebooks/deleteNotebook.ts

@@ -1,7 +0,0 @@
-import { CogneeInstance } from "@/modules/instances/types";
-
-export default function deleteNotebook(notebookId: string, instance: CogneeInstance) {
-  return instance.fetch(`/v1/notebooks/${notebookId}`, {
-    method: "DELETE",
-  });
-}

cognee-frontend/src/modules/notebooks/getNotebooks.ts

@@ -1,12 +0,0 @@
-import { CogneeInstance } from "@/modules/instances/types";
-
-export default function getNotebooks(instance: CogneeInstance) {
-  return instance.fetch("/v1/notebooks/", {
-    method: "GET",
-    headers: {
-      "Content-Type": "application/json",
-    },
-  }).then((response: Response) =>
-    response.ok ? response.json() : Promise.reject(response)
-  );
-}

cognee-frontend/src/modules/notebooks/runNotebookCell.ts

@@ -1,14 +0,0 @@
-import { Cell } from "@/ui/elements/Notebook/types";
-import { CogneeInstance } from "@/modules/instances/types";
-
-export default function runNotebookCell(notebookId: string, cell: Cell, instance: CogneeInstance) {
-  return instance.fetch(`/v1/notebooks/${notebookId}/${cell.id}/run`, {
-    body: JSON.stringify({
-      content: cell.content,
-    }),
-    method: "POST",
-    headers: {
-      "Content-Type": "application/json",
-    },
-  }).then((response: Response) => response.json());
-}

cognee-frontend/src/modules/notebooks/saveNotebook.ts

@@ -1,13 +0,0 @@
-import { CogneeInstance } from "@/modules/instances/types";
-
-export default function saveNotebook(notebookId: string, notebookData: object, instance: CogneeInstance) {
-  return instance.fetch(`/v1/notebooks/${notebookId}`, {
-    body: JSON.stringify(notebookData),
-    method: "PUT",
-    headers: {
-      "Content-Type": "application/json",
-    },
-  }).then((response: Response) =>
-    response.ok ? response.json() : Promise.reject(response)
-  );
-}

cognee-frontend/src/modules/notebooks/useNotebooks.ts

@@ -1,18 +1,20 @@
 import { useCallback, useState } from "react";
+import { fetch, isCloudEnvironment } from "@/utils";
 import { Cell, Notebook } from "@/ui/elements/Notebook/types";
-import { CogneeInstance } from "@/modules/instances/types";
-import createNotebook from "./createNotebook";
-import deleteNotebook from "./deleteNotebook";
-import getNotebooks from "./getNotebooks";
-import runNotebookCell from "./runNotebookCell";
-import { default as persistNotebook } from "./saveNotebook";
 
-function useNotebooks(instance: CogneeInstance) {
+function useNotebooks() {
   const [notebooks, setNotebooks] = useState<Notebook[]>([]);
 
   const addNotebook = useCallback((notebookName: string) => {
-    return createNotebook(notebookName, instance)
-      .then((notebook: Notebook) => {
+    return fetch("/v1/notebooks", {
+        body: JSON.stringify({ name: notebookName }),
+        method: "POST",
+        headers: {
+          "Content-Type": "application/json",
+        },
+      }, isCloudEnvironment())
+      .then((response) => response.json())
+      .then((notebook) => {
         setNotebooks((notebooks) => [
           ...notebooks,
           notebook,
@@ -20,29 +22,36 @@ function useNotebooks(instance: CogneeInstance) {
 
         return notebook;
       });
-  }, [instance]);
+  }, []);
 
   const removeNotebook = useCallback((notebookId: string) => {
-    return deleteNotebook(notebookId, instance)
+    return fetch(`/v1/notebooks/${notebookId}`, {
+      method: "DELETE",
+    }, isCloudEnvironment())
     .then(() => {
       setNotebooks((notebooks) =>
         notebooks.filter((notebook) => notebook.id !== notebookId)
       );
     });
-  }, [instance]);
+  }, []);
 
   const fetchNotebooks = useCallback(() => {
-    return getNotebooks(instance)
+    return fetch("/v1/notebooks", {
+      headers: {
+        "Content-Type": "application/json",
+      },
+    }, isCloudEnvironment())
+    .then((response) => response.json())
     .then((notebooks) => {
       setNotebooks(notebooks);
 
       return notebooks;
     })
     .catch((error) => {
-      console.error("Error fetching notebooks:", error.detail);
+      console.error("Error fetching notebooks:", error);
       throw error
     });
-  }, [instance]);
+  }, []);
 
   const updateNotebook = useCallback((updatedNotebook: Notebook) => {
     setNotebooks((existingNotebooks) =>
@@ -55,13 +64,20 @@ function useNotebooks(instance: CogneeInstance) {
   }, []);
 
   const saveNotebook = useCallback((notebook: Notebook) => {
-    return persistNotebook(notebook.id, {
-      name: notebook.name,
-      cells: notebook.cells,
-    }, instance);
-  }, [instance]);
+    return fetch(`/v1/notebooks/${notebook.id}`, {
+      body: JSON.stringify({
+        name: notebook.name,
+        cells: notebook.cells,
+      }),
+      method: "PUT",
+      headers: {
+        "Content-Type": "application/json",
+      },
+    }, isCloudEnvironment())
+    .then((response) => response.json())
+  }, []);
 
-  const runCell = useCallback((notebook: Notebook, cell: Cell) => {
+  const runCell = useCallback((notebook: Notebook, cell: Cell, cogneeInstance: string) => {
     setNotebooks((existingNotebooks) =>
       existingNotebooks.map((existingNotebook) =>
         existingNotebook.id === notebook.id ? {
@@ -73,11 +89,20 @@ function useNotebooks(instance: CogneeInstance) {
               error: undefined,
             } : existingCell
           ),
-        } : existingNotebook
+        } : notebook
       )
     );
 
-    return runNotebookCell(notebook.id, cell, instance)
+    return fetch(`/v1/notebooks/${notebook.id}/${cell.id}/run`, {
+        body: JSON.stringify({
+          content: cell.content,
+        }),
+        method: "POST",
+        headers: {
+          "Content-Type": "application/json",
+        },
+      }, cogneeInstance === "cloud")
+      .then((response) => response.json())
       .then((response) => {
         setNotebooks((existingNotebooks) =>
           existingNotebooks.map((existingNotebook) =>
@@ -90,11 +115,11 @@ function useNotebooks(instance: CogneeInstance) {
                   error: response.error,
                 } : existingCell
               ),
-            } : existingNotebook
+            } : notebook
           )
         );
       });
-  }, [instance]);
+  }, []);
 
   return {
     notebooks,

cognee-frontend/src/ui/Icons/GitHubIcon.tsx

@@ -7,4 +7,4 @@ export default function GitHubIcon({ width = 24, height = 24, color = 'currentCo
       </g>
     </svg>
   );
-}
+}

cognee-frontend/src/ui/Layout/Header.tsx

@@ -46,7 +46,7 @@ export default function Header({ user }: HeaderProps) {
 
     checkMCPConnection();
     const interval = setInterval(checkMCPConnection, 30000);
-
+    
     return () => clearInterval(interval);
   }, [setMCPConnected, setMCPDisconnected]);
 

cognee-frontend/src/ui/Partials/SearchView/SearchView.tsx

@@ -90,7 +90,7 @@ export default function SearchView() {
     scrollToBottom();
 
     setSearchInputValue("");
-
+    
     // Pass topK to sendMessage
     sendMessage(chatInput, searchType, topK)
       .then(scrollToBottom)
@@ -171,4 +171,4 @@ export default function SearchView() {
       </form>
     </div>
   );
-}
+}

cognee-frontend/src/ui/elements/Modal/index.ts

@@ -1,2 +1,3 @@
 export { default as Modal } from "./Modal";
 export { default as useModal } from "./useModal";
+

cognee-frontend/src/ui/elements/Notebook/MarkdownPreview.tsx

@@ -1,76 +0,0 @@
-import { memo } from "react";
-import ReactMarkdown from "react-markdown";
-
-interface MarkdownPreviewProps {
-  content: string;
-  className?: string;
-}
-
-function MarkdownPreview({ content, className = "" }: MarkdownPreviewProps) {
-  return (
-    <div className={`min-h-24 max-h-96 overflow-y-auto p-4 prose prose-sm max-w-none ${className}`}>
-      <ReactMarkdown
-        components={{
-          h1: ({ children }) => <h1 className="text-2xl font-bold mt-4 mb-2">{children}</h1>,
-          h2: ({ children }) => <h2 className="text-xl font-bold mt-3 mb-2">{children}</h2>,
-          h3: ({ children }) => <h3 className="text-lg font-bold mt-3 mb-2">{children}</h3>,
-          h4: ({ children }) => <h4 className="text-base font-bold mt-2 mb-1">{children}</h4>,
-          h5: ({ children }) => <h5 className="text-sm font-bold mt-2 mb-1">{children}</h5>,
-          h6: ({ children }) => <h6 className="text-xs font-bold mt-2 mb-1">{children}</h6>,
-          p: ({ children }) => <p className="mb-2">{children}</p>,
-          ul: ({ children }) => <ul className="list-disc list-inside mb-2 ml-4">{children}</ul>,
-          ol: ({ children }) => <ol className="list-decimal list-inside mb-2 ml-4">{children}</ol>,
-          li: ({ children }) => <li className="mb-1">{children}</li>,
-          blockquote: ({ children }) => (
-            <blockquote className="border-l-4 border-gray-300 pl-4 italic my-2">{children}</blockquote>
-          ),
-          code: ({ className, children, ...props }) => {
-            const isInline = !className;
-            return isInline ? (
-              <code className="bg-gray-100 px-1 py-0.5 rounded text-sm font-mono" {...props}>
-                {children}
-              </code>
-            ) : (
-              <code className="block bg-gray-100 p-2 rounded text-sm font-mono overflow-x-auto" {...props}>
-                {children}
-              </code>
-            );
-          },
-          pre: ({ children }) => (
-            <pre className="bg-gray-100 p-2 rounded text-sm font-mono overflow-x-auto mb-2">
-              {children}
-            </pre>
-          ),
-          a: ({ href, children }) => (
-            <a href={href} className="text-blue-600 hover:underline" target="_blank" rel="noopener noreferrer">
-              {children}
-            </a>
-          ),
-          strong: ({ children }) => <strong className="font-bold">{children}</strong>,
-          em: ({ children }) => <em className="italic">{children}</em>,
-          hr: () => <hr className="my-4 border-gray-300" />,
-          table: ({ children }) => (
-            <div className="overflow-x-auto my-2">
-              <table className="min-w-full border border-gray-300">{children}</table>
-            </div>
-          ),
-          thead: ({ children }) => <thead className="bg-gray-100">{children}</thead>,
-          tbody: ({ children }) => <tbody>{children}</tbody>,
-          tr: ({ children }) => <tr className="border-b border-gray-300">{children}</tr>,
-          th: ({ children }) => (
-            <th className="border border-gray-300 px-4 py-2 text-left font-bold">
-              {children}
-            </th>
-          ),
-          td: ({ children }) => (
-            <td className="border border-gray-300 px-4 py-2">{children}</td>
-          ),
-        }}
-      >
-        {content}
-      </ReactMarkdown>
-    </div>
-  );
-}
-
-export default memo(MarkdownPreview);

cognee-frontend/src/ui/elements/Notebook/Notebook.tsx

@@ -2,17 +2,15 @@
 
 import { v4 as uuid4 } from "uuid";
 import classNames from "classnames";
-import { Fragment, MouseEvent, MutableRefObject, useCallback, useEffect, useRef, useState, memo } from "react";
+import { Fragment, MouseEvent, RefObject, useCallback, useEffect, useRef, useState } from "react";
 
 import { useModal } from "@/ui/elements/Modal";
 import { CaretIcon, CloseIcon, PlusIcon } from "@/ui/Icons";
-import PopupMenu from "@/ui/elements/PopupMenu";
-import { IconButton, TextArea, Modal, GhostButton, CTAButton } from "@/ui/elements";
+import { IconButton, PopupMenu, TextArea, Modal, GhostButton, CTAButton } from "@/ui/elements";
 import { GraphControlsAPI } from "@/app/(graph)/GraphControls";
 import GraphVisualization, { GraphVisualizationAPI } from "@/app/(graph)/GraphVisualization";
 
 import NotebookCellHeader from "./NotebookCellHeader";
-import MarkdownPreview from "./MarkdownPreview";
 import { Cell, Notebook as NotebookType } from "./types";
 
 interface NotebookProps {
@@ -21,186 +19,7 @@ interface NotebookProps {
   updateNotebook: (updatedNotebook: NotebookType) => void;
 }
 
-interface NotebookCellProps {
-  cell: Cell;
-  index: number;
-  isOpen: boolean;
-  isMarkdownEditMode: boolean;
-  onToggleOpen: () => void;
-  onToggleMarkdownEdit: () => void;
-  onContentChange: (value: string) => void;
-  onCellRun: (cell: Cell, cogneeInstance: string) => Promise<void>;
-  onCellRename: (cell: Cell) => void;
-  onCellRemove: (cell: Cell) => void;
-  onCellUp: (cell: Cell) => void;
-  onCellDown: (cell: Cell) => void;
-  onCellAdd: (afterCellIndex: number, cellType: "markdown" | "code") => void;
-}
-
-const NotebookCell = memo(function NotebookCell({
-  cell,
-  index,
-  isOpen,
-  isMarkdownEditMode,
-  onToggleOpen,
-  onToggleMarkdownEdit,
-  onContentChange,
-  onCellRun,
-  onCellRename,
-  onCellRemove,
-  onCellUp,
-  onCellDown,
-  onCellAdd,
-}: NotebookCellProps) {
-  return (
-    <Fragment>
-      <div className="flex flex-row rounded-xl border-1 border-gray-100">
-        <div className="flex flex-col flex-1 relative">
-          {cell.type === "code" ? (
-            <>
-              <div className="absolute left-[-1.35rem] top-2.5">
-                <IconButton className="p-[0.25rem] m-[-0.25rem]" onClick={onToggleOpen}>
-                  <CaretIcon className={classNames("transition-transform", isOpen ? "rotate-0" : "rotate-180")} />
-                </IconButton>
-              </div>
-
-              <NotebookCellHeader
-                cell={cell}
-                runCell={onCellRun}
-                renameCell={onCellRename}
-                removeCell={onCellRemove}
-                moveCellUp={onCellUp}
-                moveCellDown={onCellDown}
-                className="rounded-tl-xl rounded-tr-xl"
-              />
-
-              {isOpen && (
-                <>
-                  <TextArea
-                    value={cell.content}
-                    onChange={onContentChange}
-                    isAutoExpanding
-                    name="cellInput"
-                    placeholder="Type your code here..."
-                    className="resize-none min-h-36 max-h-96 overflow-y-auto rounded-tl-none rounded-tr-none rounded-bl-xl rounded-br-xl border-0 !outline-0"
-                  />
-
-                  <div className="flex flex-col bg-gray-100 overflow-x-auto max-w-full">
-                    {cell.result && (
-                      <div className="px-2 py-2">
-                        output: <CellResult content={cell.result} />
-                      </div>
-                    )}
-                    {!!cell.error?.length && (
-                      <div className="px-2 py-2">
-                        error: {cell.error}
-                      </div>
-                    )}
-                  </div>
-                </>
-              )}
-            </>
-          ) : (
-            <>
-              <div className="absolute left-[-1.35rem] top-2.5">
-                <IconButton className="p-[0.25rem] m-[-0.25rem]" onClick={onToggleOpen}>
-                  <CaretIcon className={classNames("transition-transform", isOpen ? "rotate-0" : "rotate-180")} />
-                </IconButton>
-              </div>
-
-              <NotebookCellHeader
-                cell={cell}
-                renameCell={onCellRename}
-                removeCell={onCellRemove}
-                moveCellUp={onCellUp}
-                moveCellDown={onCellDown}
-                className="rounded-tl-xl rounded-tr-xl"
-              />
-
-              {isOpen && (
-                <div className="relative rounded-tl-none rounded-tr-none rounded-bl-xl rounded-br-xl border-0 overflow-hidden">
-                  <GhostButton
-                    onClick={onToggleMarkdownEdit}
-                    className="absolute top-2 right-2.5 text-xs leading-[1] !px-2 !py-1 !h-auto"
-                  >
-                    {isMarkdownEditMode ? "Preview" : "Edit"}
-                  </GhostButton>
-                  {isMarkdownEditMode ? (
-                    <TextArea
-                      value={cell.content}
-                      onChange={onContentChange}
-                      isAutoExpanding
-                      name="markdownInput"
-                      placeholder="Type your markdown here..."
-                      className="resize-none min-h-24 max-h-96 overflow-y-auto rounded-tl-none rounded-tr-none rounded-bl-xl rounded-br-xl border-0 !outline-0 !bg-gray-50"
-                    />
-                  ) : (
-                    <MarkdownPreview content={cell.content} className="!bg-gray-50" />
-                  )}
-                </div>
-              )}
-            </>
-          )}
-        </div>
-      </div>
-      <div className="ml-[-1.35rem]">
-        <PopupMenu
-          openToRight={true}
-          triggerElement={<PlusIcon />}
-          triggerClassName="p-[0.25rem] m-[-0.25rem]"
-        >
-          <div className="flex flex-col gap-0.5">
-            <button
-              onClick={() => onCellAdd(index, "markdown")}
-              className="hover:bg-gray-100 w-full text-left px-2 cursor-pointer"
-            >
-              <span>text</span>
-            </button>
-          </div>
-          <div
-            onClick={() => onCellAdd(index, "code")}
-            className="hover:bg-gray-100 w-full text-left px-2 cursor-pointer"
-          >
-            <span>code</span>
-          </div>
-        </PopupMenu>
-      </div>
-    </Fragment>
-  );
-});
-
 export default function Notebook({ notebook, updateNotebook, runCell }: NotebookProps) {
-  const [openCells, setOpenCells] = useState(new Set(notebook.cells.map((c: Cell) => c.id)));
-  const [markdownEditMode, setMarkdownEditMode] = useState<Set<string>>(new Set());
-
-  const toggleCellOpen = useCallback((id: string) => {
-    setOpenCells((prev) => {
-      const newState = new Set(prev);
-
-      if (newState.has(id)) {
-        newState.delete(id)
-      } else {
-        newState.add(id);
-      }
-
-      return newState;
-    });
-  }, []);
-
-  const toggleMarkdownEditMode = useCallback((id: string) => {
-    setMarkdownEditMode((prev) => {
-      const newState = new Set(prev);
-
-      if (newState.has(id)) {
-        newState.delete(id);
-      } else {
-        newState.add(id);
-      }
-
-      return newState;
-    });
-  }, []);
-
   useEffect(() => {
     if (notebook.cells.length === 0) {
       const newCell: Cell = {
@@ -215,7 +34,7 @@ export default function Notebook({ notebook, updateNotebook, runCell }: Notebook
       });
       toggleCellOpen(newCell.id)
     }
-  }, [notebook, updateNotebook, toggleCellOpen]);
+  }, [notebook, updateNotebook]);
 
   const handleCellRun = useCallback((cell: Cell, cogneeInstance: string) => {
     return runCell(notebook, cell, cogneeInstance);
@@ -224,7 +43,7 @@ export default function Notebook({ notebook, updateNotebook, runCell }: Notebook
   const handleCellAdd = useCallback((afterCellIndex: number, cellType: "markdown" | "code") => {
     const newCell: Cell = {
       id: uuid4(),
-      name: cellType === "markdown" ? "Markdown Cell" : "Code Cell",
+      name: "new cell",
       type: cellType,
       content: "",
     };
@@ -240,7 +59,7 @@ export default function Notebook({ notebook, updateNotebook, runCell }: Notebook
 
     toggleCellOpen(newCell.id);
     updateNotebook(newNotebook);
-  }, [notebook, updateNotebook, toggleCellOpen]);
+  }, [notebook, updateNotebook]);
 
   const removeCell = useCallback((cell: Cell, event?: MouseEvent) => {
     event?.preventDefault();
@@ -262,12 +81,14 @@ export default function Notebook({ notebook, updateNotebook, runCell }: Notebook
     openCellRemoveConfirmModal(cell);
   }, [openCellRemoveConfirmModal]);
 
-  const handleCellInputChange = useCallback((cellId: string, value: string) => {
+  const handleCellInputChange = useCallback((notebook: NotebookType, cell: Cell, value: string) => {
+    const newCell = {...cell, content: value };
+
     updateNotebook({
       ...notebook,
-      cells: notebook.cells.map((cell: Cell) => (cell.id === cellId ? {...cell, content: value} : cell)),
+      cells: notebook.cells.map((cell: Cell) => (cell.id === newCell.id ? newCell : cell)),
     });
-  }, [notebook, updateNotebook]);
+  }, [updateNotebook]);
 
   const handleCellUp = useCallback((cell: Cell) => {
     const index = notebook.cells.indexOf(cell);
@@ -310,28 +131,133 @@ export default function Notebook({ notebook, updateNotebook, runCell }: Notebook
     }
   }, [notebook, updateNotebook]);
 
+  const [openCells, setOpenCells] = useState(new Set(notebook.cells.map((c: Cell) => c.id)));
+
+  const toggleCellOpen = (id: string) => {
+    setOpenCells((prev) => {
+      const newState = new Set(prev);
+
+      if (newState.has(id)) {
+        newState.delete(id)
+      } else {
+        newState.add(id);
+      }
+
+      return newState;
+    });
+  };
+
   return (
     <>
       <div className="bg-white rounded-xl flex flex-col gap-0.5 px-7 py-5 flex-1">
         <div className="mb-5">{notebook.name}</div>
 
         {notebook.cells.map((cell: Cell, index) => (
-          <NotebookCell
-            key={cell.id}
-            cell={cell}
-            index={index}
-            isOpen={openCells.has(cell.id)}
-            isMarkdownEditMode={markdownEditMode.has(cell.id)}
-            onToggleOpen={() => toggleCellOpen(cell.id)}
-            onToggleMarkdownEdit={() => toggleMarkdownEditMode(cell.id)}
-            onContentChange={(value) => handleCellInputChange(cell.id, value)}
-            onCellRun={handleCellRun}
-            onCellRename={handleCellRename}
-            onCellRemove={handleCellRemove}
-            onCellUp={handleCellUp}
-            onCellDown={handleCellDown}
-            onCellAdd={handleCellAdd}
-          />
+          <Fragment key={cell.id}>
+            <div key={cell.id} className="flex flex-row rounded-xl border-1 border-gray-100">
+              <div className="flex flex-col flex-1 relative">
+                {cell.type === "code" ? (
+                  <>
+                    <div className="absolute left-[-1.35rem] top-2.5">
+                      <IconButton className="p-[0.25rem] m-[-0.25rem]" onClick={toggleCellOpen.bind(null, cell.id)}>
+                        <CaretIcon className={classNames("transition-transform", openCells.has(cell.id) ? "rotate-0" : "rotate-180")} />
+                      </IconButton>
+                    </div>
+
+                    <NotebookCellHeader
+                      cell={cell}
+                      runCell={handleCellRun}
+                      renameCell={handleCellRename}
+                      removeCell={handleCellRemove}
+                      moveCellUp={handleCellUp}
+                      moveCellDown={handleCellDown}
+                      className="rounded-tl-xl rounded-tr-xl"
+                    />
+
+                    {openCells.has(cell.id) && (
+                      <>
+                        <TextArea
+                          value={cell.content}
+                          onChange={handleCellInputChange.bind(null, notebook, cell)}
+                          // onKeyUp={handleCellRunOnEnter}
+                          isAutoExpanding
+                          name="cellInput"
+                          placeholder="Type your code here..."
+                          contentEditable={true}
+                          className="resize-none min-h-36 max-h-96 overflow-y-auto rounded-tl-none rounded-tr-none rounded-bl-xl rounded-br-xl border-0 !outline-0"
+                        />
+
+                        <div className="flex flex-col bg-gray-100 overflow-x-auto max-w-full">
+                          {cell.result && (
+                            <div className="px-2 py-2">
+                              output: <CellResult content={cell.result} />
+                            </div>
+                          )}
+                          {!!cell.error?.length && (
+                            <div className="px-2 py-2">
+                              error: {cell.error}
+                            </div>
+                          )}
+                        </div>
+                      </>
+                    )}
+                  </>
+                ) : (
+                  <>
+                    <div className="absolute left-[-1.35rem] top-2.5">
+                      <IconButton className="p-[0.25rem] m-[-0.25rem]" onClick={toggleCellOpen.bind(null, cell.id)}>
+                        <CaretIcon className={classNames("transition-transform", openCells.has(cell.id) ? "rotate-0" : "rotate-180")} />
+                      </IconButton>
+                    </div>
+
+                    <NotebookCellHeader
+                      cell={cell}
+                      renameCell={handleCellRename}
+                      removeCell={handleCellRemove}
+                      moveCellUp={handleCellUp}
+                      moveCellDown={handleCellDown}
+                      className="rounded-tl-xl rounded-tr-xl"
+                    />
+
+                    {openCells.has(cell.id) && (
+                      <TextArea
+                        value={cell.content}
+                        onChange={handleCellInputChange.bind(null, notebook, cell)}
+                        // onKeyUp={handleCellRunOnEnter}
+                        isAutoExpanding
+                        name="cellInput"
+                        placeholder="Type your text here..."
+                        contentEditable={true}
+                        className="resize-none min-h-24 max-h-96 overflow-y-auto rounded-tl-none rounded-tr-none rounded-bl-xl rounded-br-xl border-0 !outline-0"
+                      />
+                    )}
+                  </>
+                )}
+              </div>
+            </div>
+            <div className="ml-[-1.35rem]">
+              <PopupMenu
+                openToRight={true}
+                triggerElement={<PlusIcon />}
+                triggerClassName="p-[0.25rem] m-[-0.25rem]"
+              >
+                <div className="flex flex-col gap-0.5">
+                  <button
+                    onClick={() => handleCellAdd(index, "markdown")}
+                    className="hover:bg-gray-100 w-full text-left px-2 cursor-pointer"
+                  >
+                    <span>text</span>
+                  </button>
+                </div>
+                <div
+                  onClick={() => handleCellAdd(index, "code")}
+                  className="hover:bg-gray-100 w-full text-left px-2 cursor-pointer"
+                >
+                  <span>code</span>
+                </div>
+              </PopupMenu>
+            </div>
+          </Fragment>
         ))}
       </div>
 
@@ -362,10 +288,6 @@ function CellResult({ content }: { content: [] }) {
     getSelectedNode: () => null,
   });
 
-  if (content.length === 0) {
-    return <span>OK</span>;
-  }
-
   for (const line of content) {
     try {
       if (Array.isArray(line)) {
@@ -376,7 +298,7 @@ function CellResult({ content }: { content: [] }) {
               <span className="text-sm pl-2 mb-4">reasoning graph</span>
               <GraphVisualization
                 data={transformInsightsGraphData(line)}
-                ref={graphRef as MutableRefObject<GraphVisualizationAPI>}
+                ref={graphRef as RefObject<GraphVisualizationAPI>}
                 graphControls={graphControls}
                 className="min-h-80"
               />
@@ -424,7 +346,7 @@ function CellResult({ content }: { content: [] }) {
                   <span className="text-sm pl-2 mb-4">reasoning graph (datasets: {datasetName})</span>
                   <GraphVisualization
                     data={transformToVisualizationData(graph)}
-                    ref={graphRef as MutableRefObject<GraphVisualizationAPI>}
+                    ref={graphRef as RefObject<GraphVisualizationAPI>}
                     graphControls={graphControls}
                     className="min-h-80"
                   />
@@ -434,7 +356,8 @@ function CellResult({ content }: { content: [] }) {
           }
         }
       }
-      else if (typeof(line) === "object" && line["result"] && typeof(line["result"]) === "string") {
+
+      if (typeof(line) === "object" && line["result"] && typeof(line["result"]) === "string") {
         const datasets = Array.from(
           // eslint-disable-next-line @typescript-eslint/no-explicit-any
           new Set(Object.values(line["datasets"]).map((dataset: any) => dataset.name))
@@ -446,46 +369,39 @@ function CellResult({ content }: { content: [] }) {
             <span className="block px-2 py-2 whitespace-normal">{line["result"]}</span>
           </div>
         );
-
-        if (line["graphs"]) {
-          Object.entries<{ nodes: []; edges: []; }>(line["graphs"]).forEach(([datasetName, graph]) => {
-            parsedContent.push(
-              <div key={datasetName} className="w-full h-full bg-white">
-                <span className="text-sm pl-2 mb-4">reasoning graph (datasets: {datasetName})</span>
-                <GraphVisualization
-                  data={transformToVisualizationData(graph)}
-                  ref={graphRef as MutableRefObject<GraphVisualizationAPI>}
-                  graphControls={graphControls}
-                  className="min-h-80"
-                />
-              </div>
-            );
-          });
-        }
       }
-      else if (typeof(line) === "object" && line["result"] && typeof(line["result"]) === "object") {
+      if (typeof(line) === "object" && line["graphs"]) {
+        Object.entries<{ nodes: []; edges: []; }>(line["graphs"]).forEach(([datasetName, graph]) => {
+          parsedContent.push(
+            <div key={datasetName} className="w-full h-full bg-white">
+              <span className="text-sm pl-2 mb-4">reasoning graph (datasets: {datasetName})</span>
+              <GraphVisualization
+                data={transformToVisualizationData(graph)}
+                ref={graphRef as RefObject<GraphVisualizationAPI>}
+                graphControls={graphControls}
+                className="min-h-80"
+              />
+            </div>
+          );
+        });
+      }
+
+      if (typeof(line) === "object" && line["result"] && typeof(line["result"]) === "object") {
         parsedContent.push(
           <pre className="px-2 w-full h-full bg-white text-sm" key={String(line).slice(0, -10)}>
             {JSON.stringify(line["result"], null, 2)}
           </pre>
         )
       }
-      else if (typeof(line) === "object") {
-        parsedContent.push(
-          <pre className="px-2 w-full h-full bg-white text-sm" key={String(line).slice(0, -10)}>
-            {JSON.stringify(line, null, 2)}
-          </pre>
-        )
-      }
-      else if (typeof(line) === "string") {
+      if (typeof(line) === "string") {
         parsedContent.push(
           <pre className="px-2 w-full h-full bg-white text-sm whitespace-normal" key={String(line).slice(0, -10)}>
             {line}
           </pre>
         )
       }
-    } catch {
-      // It is fine if we don't manage to parse the output line, we show it as it is.
+    } catch (error) {
+      console.error(error);
       parsedContent.push(
         <pre className="px-2 w-full h-full bg-white text-sm whitespace-normal" key={String(line).slice(0, -10)}>
           {line}
@@ -499,6 +415,7 @@ function CellResult({ content }: { content: [] }) {
       {item}
     </div>
   ));
+
 };
 
 function transformToVisualizationData(graph: { nodes: [], edges: [] }) {
@@ -534,7 +451,7 @@ function transformInsightsGraphData(triplets: Triplet[]) {
       target: string,
       label: string,
     }
-  } = {};
+  } = {};          
 
   for (const triplet of triplets) {
     nodes[triplet[0].id] = {
@@ -554,7 +471,7 @@ function transformInsightsGraphData(triplets: Triplet[]) {
       label: triplet[1]["relationship_name"],
     };
   }
-
+  
   return {
     nodes: Object.values(nodes),
     links: Object.values(links),

cognee-frontend/src/ui/elements/Notebook/NotebookCellHeader.tsx

@@ -1,12 +1,9 @@
-"use client";
-
 import { useState } from "react";
 import classNames from "classnames";
 
 import { isCloudEnvironment, useBoolean } from "@/utils";
 import { PlayIcon } from "@/ui/Icons";
-import PopupMenu from "@/ui/elements/PopupMenu";
-import { IconButton } from "@/ui/elements";
+import { PopupMenu, IconButton } from "@/ui/elements";
 import { LoadingIndicator } from "@/ui/App";
 
 import { Cell } from "./types";
@@ -42,7 +39,7 @@ export default function NotebookCellHeader({
     if (runCell) {
       setIsRunningCell();
       runCell(cell, runInstance)
-        .finally(() => {
+        .then(() => {
           setIsNotRunningCell();
         });
     }
@@ -56,7 +53,7 @@ export default function NotebookCellHeader({
             {isRunningCell ? <LoadingIndicator /> : <IconButton onClick={handleCellRun}><PlayIcon /></IconButton>}
           </>
         )}
-        <span className="ml-4">{cell.type === "markdown" ? "Markdown Cell" : cell.name}</span>
+        <span className="ml-4">{cell.name}</span>
       </div>
       <div className="pr-4 flex flex-row items-center gap-8">
           {runCell && (

cognee-frontend/src/ui/elements/TextArea.tsx

@@ -1,12 +1,12 @@
 "use client";
 
 import classNames from "classnames";
-import { InputHTMLAttributes, useCallback, useEffect, useRef } from "react"
+import { InputHTMLAttributes, useCallback, useEffect, useLayoutEffect, useRef } from "react"
 
 interface TextAreaProps extends Omit<InputHTMLAttributes<HTMLTextAreaElement>, "onChange"> {
   isAutoExpanding?: boolean; // Set to true to enable auto-expanding text area behavior. Default is false.
-  value?: string;
-  onChange?: (value: string) => void;
+  value: string;
+  onChange: (value: string) => void;
 }
 
 export default function TextArea({
@@ -19,81 +19,95 @@ export default function TextArea({
   placeholder = "",
   onKeyUp,
   ...props
-}: TextAreaProps) {
-  const textareaRef = useRef<HTMLTextAreaElement>(null);
-  const maxHeightRef = useRef<number | null>(null);
-  const throttleTimeoutRef = useRef<number | null>(null);
-  const lastAdjustTimeRef = useRef<number>(0);
-  const THROTTLE_MS = 250; // 4 calculations per second
+ }: TextAreaProps) {
+  const handleTextChange = useCallback((event: Event) => {
+    const fakeTextAreaElement = event.target as HTMLDivElement;
+    const newValue = fakeTextAreaElement.innerText;
 
-  const adjustHeight = useCallback(() => {
-    if (!isAutoExpanding || !textareaRef.current) return;
-
-    const textarea = textareaRef.current;
-
-    // Cache maxHeight on first calculation
-    if (maxHeightRef.current === null) {
-      const computedStyle = getComputedStyle(textarea);
-      maxHeightRef.current = computedStyle.maxHeight === "none"
-        ? Infinity
-        : parseInt(computedStyle.maxHeight) || Infinity;
-    }
-
-    // Reset height to auto to get the correct scrollHeight
-    textarea.style.height = "auto";
-    // Set height to scrollHeight, but respect max-height
-    const scrollHeight = textarea.scrollHeight;
-    textarea.style.height = `${Math.min(scrollHeight, maxHeightRef.current)}px`;
-    lastAdjustTimeRef.current = Date.now();
-  }, [isAutoExpanding]);
-
-  const handleChange = useCallback((event: React.ChangeEvent<HTMLTextAreaElement>) => {
-    const newValue = event.target.value;
     onChange?.(newValue);
+  }, [onChange]);
 
-    // Throttle height adjustments to avoid blocking typing
-    if (isAutoExpanding) {
-      const now = Date.now();
-      const timeSinceLastAdjust = now - lastAdjustTimeRef.current;
-
-      if (timeSinceLastAdjust >= THROTTLE_MS) {
-        adjustHeight();
-      } else {
-        if (throttleTimeoutRef.current !== null) {
-          clearTimeout(throttleTimeoutRef.current);
-        }
-        throttleTimeoutRef.current = window.setTimeout(() => {
-          adjustHeight();
-          throttleTimeoutRef.current = null;
-        }, THROTTLE_MS - timeSinceLastAdjust);
-      }
+  const handleKeyUp = useCallback((event: Event) => {
+    if (onKeyUp) {
+      onKeyUp(event as unknown as React.KeyboardEvent<HTMLTextAreaElement>);
     }
-  }, [onChange, isAutoExpanding, adjustHeight]);
+  }, [onKeyUp]);
 
-  useEffect(() => {
-    if (isAutoExpanding && textareaRef.current) {
-      adjustHeight();
+  const handleTextAreaFocus = (event: React.FocusEvent<HTMLDivElement>) => {
+    if (event.target.innerText.trim() === placeholder) {
+      event.target.innerText = "";
+    }
+  };
+  const handleTextAreaBlur = (event: React.FocusEvent<HTMLDivElement>) => {
+    if (value === "") {
+      event.target.innerText = placeholder;
+    }
+  };
+
+  const handleChange = (event: React.ChangeEvent<HTMLTextAreaElement>) => {
+    onChange(event.target.value);
+  };
+
+  const fakeTextAreaRef = useRef<HTMLDivElement>(null);
+
+  useLayoutEffect(() => {
+    const fakeTextAreaElement = fakeTextAreaRef.current;
+
+    if (fakeTextAreaElement && fakeTextAreaElement.innerText.trim() !== "") {
+      fakeTextAreaElement.innerText = placeholder;
+    }
+  }, [placeholder]);
+
+  useLayoutEffect(() => {
+    const fakeTextAreaElement = fakeTextAreaRef.current;
+
+    if (fakeTextAreaElement) {
+      fakeTextAreaElement.addEventListener("input", handleTextChange);
+      fakeTextAreaElement.addEventListener("keyup", handleKeyUp);
     }
-  }, [value, isAutoExpanding, adjustHeight]);
 
-  useEffect(() => {
     return () => {
-      if (throttleTimeoutRef.current !== null) {
-        clearTimeout(throttleTimeoutRef.current);
+      if (fakeTextAreaElement) {
+        fakeTextAreaElement.removeEventListener("input", handleTextChange);
+        fakeTextAreaElement.removeEventListener("keyup", handleKeyUp);
       }
     };
-  }, []);
+  }, [handleKeyUp, handleTextChange]);
 
-  return (
+  useEffect(() => {
+    const fakeTextAreaElement = fakeTextAreaRef.current;
+    const textAreaText = fakeTextAreaElement?.innerText;
+
+    if (fakeTextAreaElement && (value === "" || value === "\n")) {
+      fakeTextAreaElement.innerText = placeholder;
+      return;
+    }
+
+    if (fakeTextAreaElement && textAreaText !== value) {
+      fakeTextAreaElement.innerText = value;
+    }
+  }, [placeholder, value]);
+
+  return isAutoExpanding ? (
+    <>
+      <div
+        ref={fakeTextAreaRef}
+        contentEditable="true"
+        role="textbox"
+        aria-multiline="true"
+        className={classNames("block w-full rounded-md bg-white px-4 py-4 text-base text-gray-900 outline-1 -outline-offset-1 outline-gray-300 placeholder:text-gray-400 focus:outline-2 focus:-outline-offset-2 focus:outline-indigo-600", className)}
+        onFocus={handleTextAreaFocus}
+        onBlur={handleTextAreaBlur}
+      />
+    </>
+  ) : (
     <textarea
-      ref={isAutoExpanding ? textareaRef : undefined}
       name={name}
       style={style}
       value={value}
       placeholder={placeholder}
       className={classNames("block w-full rounded-md bg-white px-4 py-4 text-base text-gray-900 outline-1 -outline-offset-1 outline-gray-300 placeholder:text-gray-400 focus:outline-2 focus:-outline-offset-2 focus:outline-indigo-600", className)}
       onChange={handleChange}
-      onKeyUp={onKeyUp}
       {...props}
     />
   )

cognee-frontend/src/ui/elements/index.ts

@@ -10,4 +10,4 @@ export { default as NeutralButton } from "./NeutralButton";
 export { default as StatusIndicator } from "./StatusIndicator";
 export { default as StatusDot } from "./StatusDot";
 export { default as Accordion } from "./Accordion";
-export { default as Notebook } from "./Notebook";
+export { default as Notebook } from "./Notebook"; 

cognee-frontend/src/utils/fetch.ts

@@ -57,7 +57,7 @@ export default async function fetch(url: string, options: RequestInit = {}, useC
           new Error("Backend server is not responding. Please check if the server is running.")
         );
       }
-
+      
       if (error.detail === undefined) {
         return Promise.reject(
           new Error("No connection to the server.")
@@ -74,7 +74,7 @@ export default async function fetch(url: string, options: RequestInit = {}, useC
 fetch.checkHealth = async () => {
   const maxRetries = 5;
   const retryDelay = 1000; // 1 second
-
+  
   for (let i = 0; i < maxRetries; i++) {
     try {
       const response = await global.fetch(`${backendApiUrl.replace("/api", "")}/health`);
@@ -90,7 +90,7 @@ fetch.checkHealth = async () => {
       await new Promise(resolve => setTimeout(resolve, retryDelay));
     }
   }
-
+  
   throw new Error("Backend server is not responding after multiple attempts");
 };
 

cognee-frontend/src/utils/handleServerErrors.ts

@@ -1,12 +1,8 @@
 import { redirect } from "next/navigation";
 
-export default function handleServerErrors(
-  response: Response,
-  retry: ((response: Response) => Promise<Response>) | null = null,
-  useCloud: boolean = false,
-): Promise<Response> {
+export default function handleServerErrors(response: Response, retry?: (response: Response) => Promise<Response>, useCloud?: boolean): Promise<Response> {
   return new Promise((resolve, reject) => {
-    if ((response.status === 401 || response.status === 403) && !useCloud) {
+    if (response.status === 401 && !useCloud) {
       if (retry) {
         return retry(response)
           .catch(() => {

cognee-mcp/Dockerfile

@@ -34,8 +34,8 @@ RUN --mount=type=cache,target=/root/.cache/uv \
     uv sync --frozen --no-install-project --no-dev --no-editable
 
 # Copy Alembic configuration
-COPY cognee/alembic.ini /app/cognee/alembic.ini
-COPY cognee/alembic/ /app/cognee/alembic
+COPY alembic.ini /app/alembic.ini
+COPY alembic/ /app/alembic
 
 # Then, add the rest of the project source code and install it
 # Installing separately from its dependencies allows optimal layer caching

cognee-mcp/README.md

@@ -105,14 +105,14 @@ If you'd rather run cognee-mcp in a container, you have two options:
       ```bash
       # For HTTP transport (recommended for web deployments)
       docker run -e TRANSPORT_MODE=http --env-file ./.env -p 8000:8000 --rm -it cognee/cognee-mcp:main
-      # For SSE transport
+      # For SSE transport  
       docker run -e TRANSPORT_MODE=sse --env-file ./.env -p 8000:8000 --rm -it cognee/cognee-mcp:main
       # For stdio transport (default)
       docker run -e TRANSPORT_MODE=stdio --env-file ./.env --rm -it cognee/cognee-mcp:main
       ```
-
+      
       **Installing optional dependencies at runtime:**
-
+      
       You can install optional dependencies when running the container by setting the `EXTRAS` environment variable:
       ```bash
       # Install a single optional dependency group at runtime
@@ -122,7 +122,7 @@ If you'd rather run cognee-mcp in a container, you have two options:
         --env-file ./.env \
         -p 8000:8000 \
         --rm -it cognee/cognee-mcp:main
-
+      
       # Install multiple optional dependency groups at runtime (comma-separated)
       docker run \
         -e TRANSPORT_MODE=sse \
@@ -131,7 +131,7 @@ If you'd rather run cognee-mcp in a container, you have two options:
         -p 8000:8000 \
         --rm -it cognee/cognee-mcp:main
       ```
-
+      
       **Available optional dependency groups:**
       - `aws` - S3 storage support
       - `postgres` / `postgres-binary` - PostgreSQL database support
@@ -160,7 +160,7 @@ If you'd rather run cognee-mcp in a container, you have two options:
    # With stdio transport (default)
    docker run -e TRANSPORT_MODE=stdio --env-file ./.env --rm -it cognee/cognee-mcp:main
    ```
-
+   
    **With runtime installation of optional dependencies:**
    ```bash
    # Install optional dependencies from Docker Hub image
@@ -357,7 +357,7 @@ You can configure both transports simultaneously for testing:
       "url": "http://localhost:8000/sse"
     },
     "cognee-http": {
-      "type": "http",
+      "type": "http", 
       "url": "http://localhost:8000/mcp"
     }
   }

cognee-mcp/entrypoint.sh

@@ -7,11 +7,11 @@ echo "Environment: $ENVIRONMENT"
 # Install optional dependencies if EXTRAS is set
 if [ -n "$EXTRAS" ]; then
     echo "Installing optional dependencies: $EXTRAS"
-
+    
     # Get the cognee version that's currently installed
     COGNEE_VERSION=$(uv pip show cognee | grep "Version:" | awk '{print $2}')
     echo "Current cognee version: $COGNEE_VERSION"
-
+    
     # Build the extras list for cognee
     IFS=',' read -ra EXTRA_ARRAY <<< "$EXTRAS"
     # Combine base extras from pyproject.toml with requested extras
@@ -28,11 +28,11 @@ if [ -n "$EXTRAS" ]; then
             fi
         fi
     done
-
+    
     echo "Installing cognee with extras: $ALL_EXTRAS"
     echo "Running: uv pip install 'cognee[$ALL_EXTRAS]==$COGNEE_VERSION'"
     uv pip install "cognee[$ALL_EXTRAS]==$COGNEE_VERSION"
-
+    
     # Verify installation
     echo ""
     echo "✓ Optional dependencies installation completed"
@@ -56,22 +56,24 @@ if [ -n "$API_URL" ]; then
     echo "Skipping database migrations (API server handles its own database)"
 else
     echo "Direct mode: Using local cognee instance"
+    # Run Alembic migrations with proper error handling.
+    # Note on UserAlreadyExists error handling:
+    # During database migrations, we attempt to create a default user. If this user
+    # already exists (e.g., from a previous deployment or migration), it's not a
+    # critical error and shouldn't prevent the application from starting. This is
+    # different from other migration errors which could indicate database schema
+    # inconsistencies and should cause the startup to fail. This check allows for
+    # smooth redeployments and container restarts while maintaining data integrity.
     echo "Running database migrations..."
 
-    set +e # Disable exit on error to handle specific migration errors
-    MIGRATION_OUTPUT=$(cd cognee && alembic upgrade head)
+    MIGRATION_OUTPUT=$(alembic upgrade head)
     MIGRATION_EXIT_CODE=$?
-    set -e
 
     if [[ $MIGRATION_EXIT_CODE -ne 0 ]]; then
-
-        echo "Migration failed with unexpected error. Trying to run Cognee without migrations."
-        echo "Initializing database tables..."
-        python /app/src/run_cognee_database_setup.py
-        INIT_EXIT_CODE=$?
-
-        if [[ $INIT_EXIT_CODE -ne 0 ]]; then
-            echo "Database initialization failed!"
+        if [[ "$MIGRATION_OUTPUT" == *"UserAlreadyExists"* ]] || [[ "$MIGRATION_OUTPUT" == *"User default_user@example.com already exists"* ]]; then
+            echo "Warning: Default user already exists, continuing startup..."
+        else
+            echo "Migration failed with unexpected error."
             exit 1
         fi
     fi
@@ -91,19 +93,19 @@ if [ -n "$API_URL" ]; then
     if echo "$API_URL" | grep -q "localhost" || echo "$API_URL" | grep -q "127.0.0.1"; then
         echo "⚠️  Warning: API_URL contains localhost/127.0.0.1"
         echo "   Original: $API_URL"
-
+        
         # Try to use host.docker.internal (works on Mac/Windows and recent Linux with Docker Desktop)
         FIXED_API_URL=$(echo "$API_URL" | sed 's/localhost/host.docker.internal/g' | sed 's/127\.0\.0\.1/host.docker.internal/g')
-
+        
         echo "   Converted to: $FIXED_API_URL"
         echo "   This will work on Mac/Windows/Docker Desktop."
         echo "   On Linux without Docker Desktop, you may need to:"
         echo "     - Use --network host, OR"
         echo "     - Set API_URL=http://172.17.0.1:8000 (Docker bridge IP)"
-
+        
         API_URL="$FIXED_API_URL"
     fi
-
+    
     API_ARGS="--api-url $API_URL"
     if [ -n "$API_TOKEN" ]; then
         API_ARGS="$API_ARGS --api-token $API_TOKEN"

cognee-mcp/pyproject.toml

@@ -8,6 +8,7 @@ requires-python = ">=3.10"
 dependencies = [
     # For local cognee repo usage remove comment bellow and add absolute path to cognee. Then run `uv sync --reinstall` in the mcp folder on local cognee changes.
     #"cognee[postgres,codegraph,gemini,huggingface,docs,neo4j] @ file:/Users/igorilic/Desktop/cognee",
+    # TODO: Remove gemini from optional dependecnies for new Cognee version after 0.3.4
     "cognee[postgres,docs,neo4j]==0.5.0",
     "fastmcp>=2.10.0,<3.0.0",
     "mcp>=1.12.0,<2.0.0",

cognee-mcp/src/cognee_client.py

@@ -151,7 +151,7 @@ class CogneeClient:
         query_type: str,
         datasets: Optional[List[str]] = None,
         system_prompt: Optional[str] = None,
-        top_k: int = 10,
+        top_k: int = 5,
     ) -> Any:
         """
         Search the knowledge graph.

cognee-mcp/src/run_cognee_database_setup.py

@@ -1,5 +0,0 @@
-from cognee.modules.engine.operations.setup import setup
-import asyncio
-
-if __name__ == "__main__":
-    asyncio.run(setup())

cognee-mcp/src/server.py

@@ -8,7 +8,6 @@ from pathlib import Path
 from typing import Optional
 
 from cognee.shared.logging_utils import get_logger, setup_logging, get_log_file_location
-from cognee.shared.usage_logger import log_usage
 import importlib.util
 from contextlib import redirect_stdout
 import mcp.types as types
@@ -92,7 +91,6 @@ async def health_check(request):
 
 
 @mcp.tool()
-@log_usage(function_name="MCP cognify", log_type="mcp_tool")
 async def cognify(
     data: str, graph_model_file: str = None, graph_model_name: str = None, custom_prompt: str = None
 ) -> list:
@@ -259,7 +257,6 @@ async def cognify(
 @mcp.tool(
     name="save_interaction", description="Logs user-agent interactions and query-answer pairs"
 )
-@log_usage(function_name="MCP save_interaction", log_type="mcp_tool")
 async def save_interaction(data: str) -> list:
     """
     Transform and save a user-agent interaction into structured knowledge.
@@ -319,7 +316,6 @@ async def save_interaction(data: str) -> list:
 
 
 @mcp.tool()
-@log_usage(function_name="MCP search", log_type="mcp_tool")
 async def search(search_query: str, search_type: str, top_k: int = 10) -> list:
     """
     Search and query the knowledge graph for insights, information, and connections.
@@ -500,7 +496,6 @@ async def search(search_query: str, search_type: str, top_k: int = 10) -> list:
 
 
 @mcp.tool()
-@log_usage(function_name="MCP list_data", log_type="mcp_tool")
 async def list_data(dataset_id: str = None) -> list:
     """
     List all datasets and their data items with IDs for deletion operations.
@@ -629,7 +624,6 @@ async def list_data(dataset_id: str = None) -> list:
 
 
 @mcp.tool()
-@log_usage(function_name="MCP delete", log_type="mcp_tool")
 async def delete(data_id: str, dataset_id: str, mode: str = "soft") -> list:
     """
     Delete specific data from a dataset in the Cognee knowledge graph.
@@ -709,7 +703,6 @@ async def delete(data_id: str, dataset_id: str, mode: str = "soft") -> list:
 
 
 @mcp.tool()
-@log_usage(function_name="MCP prune", log_type="mcp_tool")
 async def prune():
     """
     Reset the Cognee knowledge graph by removing all stored information.
@@ -746,7 +739,6 @@ async def prune():
 
 
 @mcp.tool()
-@log_usage(function_name="MCP cognify_status", log_type="mcp_tool")
 async def cognify_status():
     """
     Get the current status of the cognify pipeline.
@@ -892,11 +884,26 @@ async def main():
 
         await setup()
 
-        # Run Cognee migrations
+        # Run Alembic migrations from the main cognee directory where alembic.ini is located
         logger.info("Running database migrations...")
-        from cognee.run_migrations import run_migrations
+        migration_result = subprocess.run(
+            ["python", "-m", "alembic", "upgrade", "head"],
+            capture_output=True,
+            text=True,
+            cwd=Path(__file__).resolve().parent.parent.parent,
+        )
 
-        await run_migrations()
+        if migration_result.returncode != 0:
+            migration_output = migration_result.stderr + migration_result.stdout
+            # Check for the expected UserAlreadyExists error (which is not critical)
+            if (
+                "UserAlreadyExists" in migration_output
+                or "User default_user@example.com already exists" in migration_output
+            ):
+                logger.warning("Warning: Default user already exists, continuing startup...")
+            else:
+                logger.error(f"Migration failed with unexpected error: {migration_output}")
+                sys.exit(1)
 
         logger.info("Database migrations done.")
     elif args.api_url:

cognee-mcp/src/test_client.py

@@ -627,7 +627,8 @@ class TestModel:
         print(f"Failed: {failed}")
         print(f"Success Rate: {(passed / total_tests * 100):.1f}%")
 
-        assert failed == 0, f"\n ⚠️ {failed} test(s) failed - review results above for details"
+        if failed > 0:
+            print(f"\n ⚠️ {failed} test(s) failed - review results above for details")
 
 
 async def main():

cognee-starter-kit/.env.template

@@ -16,4 +16,4 @@ EMBEDDING_API_VERSION=""
 
 
 GRAPHISTRY_USERNAME=""
-GRAPHISTRY_PASSWORD=""
+GRAPHISTRY_PASSWORD=""

cognee-starter-kit/README.md

@@ -1,20 +1,8 @@
-# ⚠️ DEPRECATED - Go to `new-examples/` Instead
-
-This starter kit is deprecated. Its examples have been integrated into the `/new-examples/` folder.
-
-| Old Location | New Location |
-|--------------|--------------|
-| `src/pipelines/default.py` | none |
-| `src/pipelines/low_level.py` | `new-examples/custom_pipelines/organizational_hierarchy/` |
-| `src/pipelines/custom-model.py` | `new-examples/demos/custom_graph_model_entity_schema_definition.py` |
-| `src/data/` | Included in `new-examples/custom_pipelines/organizational_hierarchy/data/` |
-
-----------
 
 # Cognee Starter Kit
 Welcome to the <a href="https://github.com/topoteretes/cognee">cognee</a> Starter Repo! This repository is designed to help you get started quickly by providing a structured dataset and pre-built data pipelines using cognee to build powerful knowledge graphs.
 
-You can use this repo to ingest, process, and visualize data in minutes.
+You can use this repo to ingest, process, and visualize data in minutes. 
 
 By following this guide, you will:
 
@@ -80,7 +68,7 @@ Custom model uses custom pydantic model for graph extraction. This script catego
 python src/pipelines/custom-model.py
 ```
 
-## Graph preview
+## Graph preview 
 
 cognee provides a visualize_graph function that will render the graph for you.
 

cognee/__init__.py

@@ -33,5 +33,3 @@ from .api.v1.ui import start_ui
 
 # Pipelines
 from .modules import pipelines
-
-from cognee.run_migrations import run_migrations

cognee/alembic/README

@@ -1 +0,0 @@
-Generic single-database configuration with an async dbapi.

cognee/alembic/versions/1a58b986e6e1_enable_delete_for_old_tutorial_notebooks.py

@@ -1,52 +0,0 @@
-"""Enable delete for old tutorial notebooks
-
-Revision ID: 1a58b986e6e1
-Revises: 46a6ce2bd2b2
-Create Date: 2025-12-17 11:04:44.414259
-
-"""
-
-from typing import Sequence, Union
-
-from alembic import op
-import sqlalchemy as sa
-
-
-# revision identifiers, used by Alembic.
-revision: str = "1a58b986e6e1"
-down_revision: Union[str, None] = "e1ec1dcb50b6"
-branch_labels: Union[str, Sequence[str], None] = None
-depends_on: Union[str, Sequence[str], None] = None
-
-
-def change_tutorial_deletable_flag(deletable: bool) -> None:
-    bind = op.get_bind()
-    inspector = sa.inspect(bind)
-
-    if "notebooks" not in inspector.get_table_names():
-        return
-
-    columns = {col["name"] for col in inspector.get_columns("notebooks")}
-    required_columns = {"name", "deletable"}
-    if not required_columns.issubset(columns):
-        return
-
-    notebooks = sa.table(
-        "notebooks",
-        sa.Column("name", sa.String()),
-        sa.Column("deletable", sa.Boolean()),
-    )
-
-    tutorial_name = "Python Development with Cognee Tutorial 🧠"
-
-    bind.execute(
-        notebooks.update().where(notebooks.c.name == tutorial_name).values(deletable=deletable)
-    )
-
-
-def upgrade() -> None:
-    change_tutorial_deletable_flag(True)
-
-
-def downgrade() -> None:
-    change_tutorial_deletable_flag(False)

cognee/alembic/versions/a1b2c3d4e5f6_add_label_column_to_data.py

@@ -1,38 +0,0 @@
-"""Add label column to data table
-
-Revision ID: a1b2c3d4e5f6
-Revises: 211ab850ef3d
-Create Date: 2025-11-17 17:54:32.123456
-
-"""
-
-from typing import Sequence, Union
-
-from alembic import op
-import sqlalchemy as sa
-
-# revision identifiers, used by Alembic.
-revision: str = "a1b2c3d4e5f6"
-down_revision: Union[str, None] = "46a6ce2bd2b2"
-branch_labels: Union[str, Sequence[str], None] = None
-depends_on: Union[str, Sequence[str], None] = None
-
-
-def _get_column(inspector, table, name, schema=None):
-    for col in inspector.get_columns(table, schema=schema):
-        if col["name"] == name:
-            return col
-    return None
-
-
-def upgrade() -> None:
-    conn = op.get_bind()
-    insp = sa.inspect(conn)
-
-    label_column = _get_column(insp, "data", "label")
-    if not label_column:
-        op.add_column("data", sa.Column("label", sa.String(), nullable=True))
-
-
-def downgrade() -> None:
-    op.drop_column("data", "label")