Merge branch 'dev' into fix_security_issue

.env.example

@@ -3,3 +3,7 @@
 # CORS_ALLOWED_ORIGINS="https://yourdomain.com,https://another.com"
 # For local development, you might use:
 # CORS_ALLOWED_ORIGINS="http://localhost:3000"
+
+LLM_API_KEY="your-openai-api-key"
+LLM_MODEL="openai/gpt-4o-mini"
+LLM_PROVIDER="openai"

.github/ISSUE_TEMPLATE/documentation.yml

@@ -71,4 +71,3 @@ body:
           required: true
         - label: I have specified the location of the documentation issue
           required: true
-

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -75,4 +75,3 @@ body:
           required: true
         - label: I have described my specific use case
           required: true
-

.github/core-team.txt

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

.github/pull_request_template.md

@@ -24,7 +24,7 @@ DO NOT use AI-generated descriptions. We want to understand your thought process
 
 ## Pre-submission Checklist
 <!-- Please check all boxes that apply before submitting your PR -->
-- [ ] **I have tested my changes thoroughly before submitting this PR**
+- [ ] **I have tested my changes thoroughly before submitting this PR** (See `CONTRIBUTING.md`)
 - [ ] **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/workflows/label-core-team.yml

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

.github/workflows/load_tests.yml

@@ -66,5 +66,3 @@ 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: Validate uv lockfile and project metadata
+    name: Lockfile and Pre-commit Hooks
     runs-on: ubuntu-22.04
     steps:
       - name: Check out repository
@@ -20,3 +20,6 @@ jobs:
 
       - 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_test.yml

@@ -15,4 +15,3 @@ jobs:
     name: Load Tests
     uses: ./.github/workflows/load_tests.yml
     secrets: inherit
-

.gitignore

@@ -147,6 +147,7 @@ venv/
 ENV/
 env.bak/
 venv.bak/
+mise.toml
 
 # Spyder project settings
 .spyderproject

.pre-commit-config.yaml

@@ -7,6 +7,7 @@ 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

@@ -128,5 +128,3 @@ 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.
-
-

CONTRIBUTING.md

@@ -62,6 +62,11 @@ 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
@@ -93,29 +98,31 @@ 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
-python cognee/cognee/tests/test_library.py
+uv run python cognee/tests/test_library.py
 ```
 
 ### Running Simple Example
 
-Change .env.example into .env and provide your OPENAI_API_KEY as LLM_API_KEY
+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 cognee/cognee/examples/python/simple_example.py
+python examples/python/simple_example.py
 ```
 or
 
 ```shell
-uv run python cognee/cognee/examples/python/simple_example.py
+uv run python examples/python/simple_example.py
 ```
 
 ## 4. 📤 Submitting Changes
 
-1. Install ruff on your system
-2. Run ```ruff format .``` and ``` ruff check ``` and fix the issues
+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.
 3. Push your changes:
 ```shell
 git add .

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

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

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

@@ -74,4 +74,3 @@ function MarkdownPreview({ content, className = "" }: MarkdownPreviewProps) {
 }
 
 export default memo(MarkdownPreview);
-

cognee/modules/notebooks/tutorials/python-development-with-cognee/data/copilot_conversations.json

@@ -105,4 +105,3 @@
     }
   }
 }
-

cognee/modules/notebooks/tutorials/python-development-with-cognee/data/pep_style_guide.md

@@ -72,4 +72,3 @@ profile = "black"
 - E501: line too long -> break with parentheses
 - E225: missing whitespace around operator
 - E402: module import not at top of file
-

cognee/modules/notebooks/tutorials/python-development-with-cognee/data/zen_principles.md

@@ -72,4 +72,3 @@ Use modules/packages to separate concerns; avoid wildcard imports.
 - Is this the simplest working solution?
 - Are errors explicit and logged?
 - Are modules/namespaces used appropriately?
-

cognee/modules/retrieval/__init__.py

@@ -1 +0,0 @@
-

cognee/tasks/temporal_graph/__init__.py

@@ -1 +0,0 @@
-

deployment/helm/docker-compose-helm.yml

@@ -43,4 +43,3 @@ networks:
 
 volumes:
   postgres_data:
-

deployment/helm/templates/postgres_service.yaml

@@ -11,4 +11,3 @@ spec:
       targetPort: {{ .Values.postgres.port }}
   selector:
     app: {{ .Release.Name }}-postgres
-

examples/python/weighted_graph_visualization.html

@@ -209,4 +209,3 @@
         </svg>
     </body>
     </html>
-    

mise.toml

@@ -0,0 +1,2 @@
+[tools]
+python = "latest"

new-examples/custom_pipelines/organizational_hierarchy/data/companies.json

@@ -36,4 +36,3 @@
     ]
   }
 ]
-

new-examples/custom_pipelines/organizational_hierarchy/data/people.json

@@ -50,4 +50,3 @@
     "department": "HR"
   }
 ]
-

new-examples/custom_pipelines/product_recommendation/data/customers.json

@@ -106,4 +106,3 @@
     "action": "purchased"
   }]
 }]
-

tools/check-package.sh

@@ -58,4 +58,3 @@ fi
 
 # error in package
 exit 1
-