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Merge dev and main (#1699)

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

## Description
<!--
Please provide a clear, human-generated description of the changes in
this PR.
DO NOT use AI-generated descriptions. We want to understand your thought
process and reasoning.
-->

## 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/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**
- [ ] **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
- [ ] I have added necessary documentation (if applicable)
- [ ] All new and existing tests pass
- [ ] I have searched existing PRs to ensure this change hasn't been
submitted already
- [ ] I have linked any relevant issues in the description
- [ ] My commits have clear and descriptive messages

## DCO Affirmation
I affirm that all code in every commit of this pull request conforms to
the terms of the Topoteretes Developer Certificate of Origin.
This commit is contained in:
Vasilije 2025-10-29 20:35:34 +01:00 • committed by GitHub
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3
.env.template
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@ -242,13 +242,14 @@ LITELLM_LOG="ERROR"
########## Local LLM via Ollama ###############################################
#LLM_API_KEY ="ollama"
#LLM_MODEL="llama3.1:8b"
#LLM_PROVIDER="ollama"
#LLM_ENDPOINT="http://localhost:11434/v1"
#EMBEDDING_PROVIDER="ollama"
#EMBEDDING_MODEL="nomic-embed-text:latest"
#EMBEDDING_ENDPOINT="http://localhost:11434/api/embeddings"
#EMBEDDING_ENDPOINT="http://localhost:11434/api/embed"
#EMBEDDING_DIMENSIONS=768
#HUGGINGFACE_TOKENIZER="nomic-ai/nomic-embed-text-v1.5"

20
.github/workflows/dockerhub-mcp.yml vendored
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@ -7,14 +7,29 @@ on:
jobs:
docker-build-and-push:
runs-on: ubuntu-latest
runs-on:
group: Default
labels:
- docker_build_runner
steps:
- name: Check and free disk space before build
run: |
echo "=== Before cleanup ==="
df -h
echo "Removing unused preinstalled SDKs to free space..."
sudo rm -rf /usr/share/dotnet /usr/local/lib/android /opt/ghc || true
docker system prune -af || true
echo "=== After cleanup ==="
df -h
- name: Checkout repository
uses: actions/checkout@v4
- name: Set up Docker Buildx
uses: docker/setup-buildx-action@v3
with:
buildkitd-flags: --root /tmp/buildkit
- name: Log in to Docker Hub
uses: docker/login-action@v3
@ -34,7 +49,7 @@ jobs:
- name: Build and push
id: build
uses: docker/build-push-action@v5
uses: docker/build-push-action@v6
with:
context: .
platforms: linux/amd64,linux/arm64
@ -45,5 +60,6 @@ jobs:
cache-from: type=registry,ref=cognee/cognee-mcp:buildcache
cache-to: type=registry,ref=cognee/cognee-mcp:buildcache,mode=max
- name: Image digest
run: echo ${{ steps.build.outputs.digest }}

132
AGENTS.md Normal file
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@ -0,0 +1,132 @@
## Repository Guidelines
This document summarizes how to work with the cognee repository: how it’s organized, how to build, test, lint, and contribute. It mirrors our actual tooling and CI while providing quick commands for local development.
## Project Structure & Module Organization
- `cognee/`: Core Python library and API.
- `api/`: FastAPI application and versioned routers (add, cognify, memify, search, delete, users, datasets, responses, visualize, settings, sync, update, checks).
- `cli/`: CLI entry points and subcommands invoked via `cognee` / `cognee-cli`.
- `infrastructure/`: Databases, LLM providers, embeddings, loaders, and storage adapters.
- `modules/`: Domain logic (graph, retrieval, ontology, users, processing, observability, etc.).
- `tasks/`: Reusable tasks (e.g., code graph, web scraping, storage). Extend with new tasks here.
- `eval_framework/`: Evaluation utilities and adapters.
- `shared/`: Cross-cutting helpers (logging, settings, utils).
- `tests/`: Unit, integration, CLI, and end-to-end tests organized by feature.
- `__main__.py`: Entrypoint to route to CLI.
- `cognee-mcp/`: Model Context Protocol server exposing cognee as MCP tools (SSE/HTTP/stdio). Contains its own README and Dockerfile.
- `cognee-frontend/`: Next.js UI for local development and demos.
- `distributed/`: Utilities for distributed execution (Modal, workers, queues).
- `examples/`: Example scripts demonstrating the public APIs and features (graph, code graph, multimodal, permissions, etc.).
- `notebooks/`: Jupyter notebooks for demos and tutorials.
- `alembic/`: Database migrations for relational backends.
Notes:
- Co-locate feature-specific helpers under their respective package (`modules/`, `infrastructure/`, or `tasks/`).
- Extend the system by adding new tasks, loaders, or retrievers rather than modifying core pipeline mechanisms.
## Build, Test, and Development Commands
Python (root) – requires Python >= 3.10 and < 3.14. We recommend `uv` for speed and reproducibility.
- Create/refresh env and install dev deps:
```bash
uv sync --dev --all-extras --reinstall
```
- Run the CLI (examples):
```bash
uv run cognee-cli add "Cognee turns documents into AI memory."
uv run cognee-cli cognify
uv run cognee-cli search "What does cognee do?"
uv run cognee-cli -ui # Launches UI, backend API, and MCP server together
```
- Start the FastAPI server directly:
```bash
uv run python -m cognee.api.client
```
- Run tests (CI mirrors these commands):
```bash
uv run pytest cognee/tests/unit/ -v
uv run pytest cognee/tests/integration/ -v
```
- Lint and format (ruff):
```bash
uv run ruff check .
uv run ruff format .
```
- Optional static type checks (mypy):
```bash
uv run mypy cognee/
```
MCP Server (`cognee-mcp/`):
- Install and run locally:
```bash
cd cognee-mcp
uv sync --dev --all-extras --reinstall
uv run python src/server.py # stdio (default)
uv run python src/server.py --transport sse
uv run python src/server.py --transport http --host 127.0.0.1 --port 8000 --path /mcp
```
- API Mode (connect to a running Cognee API):
```bash
uv run python src/server.py --transport sse --api-url http://localhost:8000 --api-token YOUR_TOKEN
```
- Docker quickstart (examples): see `cognee-mcp/README.md` for full details
```bash
docker run -e TRANSPORT_MODE=http --env-file ./.env -p 8000:8000 --rm -it cognee/cognee-mcp:main
```
Frontend (`cognee-frontend/`):
```bash
cd cognee-frontend
npm install
npm run dev # Next.js dev server
npm run lint # ESLint
npm run build && npm start
```
## Coding Style & Naming Conventions
Python:
- 4-space indentation, modules and functions in `snake_case`, classes in `PascalCase`.
- Public APIs should be type-annotated where practical.
- Use `ruff format` before committing; `ruff check` enforces import hygiene and style (line-length 100 configured in `pyproject.toml`).
- Prefer explicit, structured error handling. Use shared logging utilities in `cognee.shared.logging_utils`.
MCP server and Frontend:
- Follow the local `README.md` and ESLint/TypeScript configuration in `cognee-frontend/`.
## Testing Guidelines
- Place Python tests under `cognee/tests/`.
- Unit tests: `cognee/tests/unit/`
- Integration tests: `cognee/tests/integration/`
- CLI tests: `cognee/tests/cli_tests/`
- Name test files `test_*.py`. Use `pytest.mark.asyncio` for async tests.
- Avoid external state; rely on test fixtures and the CI-provided env vars when LLM/embedding providers are required. See CI workflows under `.github/workflows/` for expected environment variables.
- When adding public APIs, provide/update targeted examples under `examples/python/`.
## Commit & Pull Request Guidelines
- Use clear, imperative subjects (≤ 72 chars) and conventional commit styling in PR titles. Our CI validates semantic PR titles (see `.github/workflows/pr_lint`). Examples:
- `feat(graph): add temporal edge weighting`
- `fix(api): handle missing auth cookie`
- `docs: update installation instructions`
- Reference related issues/discussions in the PR body and provide brief context.
- PRs should describe scope, list local test commands run, and mention any impacts on MCP server or UI if applicable.
- Sign commits and affirm the DCO (see `CONTRIBUTING.md`).
## 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.

2
README.md
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@ -97,7 +97,7 @@ Hosted platform:
### 📦 Installation
You can install Cognee using either **pip**, **poetry**, **uv** or any other python package manager.
You can install Cognee using either **pip**, **poetry**, **uv** or any other python package manager..
Cognee supports Python 3.10 to 3.12

2
cognee-mcp/pyproject.toml
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@ -9,7 +9,7 @@ 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,codegraph,huggingface,docs,neo4j]==0.3.7",
"cognee[postgres,docs,neo4j]==0.3.7",
"fastmcp>=2.10.0,<3.0.0",
"mcp>=1.12.0,<2.0.0",
"uv>=0.6.3,<1.0.0",

6
cognee-mcp/src/client.py
View file

@ -37,12 +37,10 @@ async def run():
toolResult = await session.call_tool("prune", arguments={})
toolResult = await session.call_tool(
"codify", arguments={"repo_path": "SOME_REPO_PATH"}
)
toolResult = await session.call_tool("cognify", arguments={})
toolResult = await session.call_tool(
"search", arguments={"search_type": "CODE", "search_query": "exceptions"}
"search", arguments={"search_type": "GRAPH_COMPLETION"}
)
print(f"Cognify result: {toolResult.content}")

64
cognee-mcp/uv.lock generated
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@ -718,19 +718,10 @@ wheels = [
]
[package.optional-dependencies]
codegraph = [
{ name = "fastembed", marker = "python_full_version < '3.13'" },
{ name = "transformers" },
{ name = "tree-sitter" },
{ name = "tree-sitter-python" },
]
docs = [
{ name = "lxml" },
{ name = "unstructured", extra = ["csv", "doc", "docx", "epub", "md", "odt", "org", "pdf", "ppt", "pptx", "rst", "rtf", "tsv", "xlsx"] },
]
huggingface = [
{ name = "transformers" },
]
neo4j = [
{ name = "neo4j" },
]
@ -745,7 +736,7 @@ name = "cognee-mcp"
version = "0.4.0"
source = { editable = "." }
dependencies = [
{ name = "cognee", extra = ["codegraph", "docs", "huggingface", "neo4j", "postgres"] },
{ name = "cognee", extra = ["docs", "neo4j", "postgres"] },
{ name = "fastmcp" },
{ name = "httpx" },
{ name = "mcp" },
@ -759,7 +750,7 @@ dev = [
[package.metadata]
requires-dist = [
{ name = "cognee", extras = ["postgres", "codegraph", "huggingface", "docs", "neo4j"], specifier = "==0.3.7" },
{ name = "cognee", extras = ["postgres", "docs", "neo4j"], specifier = "==0.3.7" },
{ name = "fastmcp", specifier = ">=2.10.0,<3.0.0" },
{ name = "httpx", specifier = ">=0.27.0,<1.0.0" },
{ name = "mcp", specifier = ">=1.12.0,<2.0.0" },
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version = "0.24.0"
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