chore: migrate from Poetry to uv for dependency management

.github/workflows/ci.yml

@@ -3,36 +3,65 @@ name: Backend CI
 on:
   push:
     branches:
-      - main  # Runs on every push to the main branch
+      - main
   pull_request:
     branches:
-      - main  # Runs on PR to the main branch
+      - main
 
 jobs:
-  test:
+  lint:
+    name: Lint and Format Check
     runs-on: ubuntu-latest
 
     steps:
     - name: Checkout Repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v2
+      with:
+        version: "latest"
 
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: '3.12'
+        cache: 'uv'
 
-    - name: Install Poetry
-      run: |
-        curl -sSL https://install.python-poetry.org | python3 -
-        export PATH="$HOME/.poetry/bin:$PATH"  # Ensure Poetry is in the PATH
+    - name: Sync dependencies
+      working-directory: ./backend
+      run: uv sync --frozen --no-install-project --group dev
 
-    - name: Change to Backend Directory
-      run: cd backend  # Change to the backend folder
+    - name: Lint with Ruff
+      working-directory: ./backend
+      run: uv run --no-sync ruff check app/
 
-    - name: Install dependencies with Poetry
-      run: |
-        cd backend  # Change to the backend folder again if needed
-        poetry install --no-root # Install the dependencies using Poetry
+    - name: Format check with Ruff
+      working-directory: ./backend
+      run: uv run --no-sync ruff format app/ --check
+
+  test:
+    name: Test Suite
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout Repository
+      uses: actions/checkout@v4
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v2
+      with:
+        version: "latest"
+
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.12'
+        cache: 'uv'
+
+    - name: Sync dependencies
+      working-directory: ./backend
+      run: uv sync --frozen --no-install-project --group dev
 
     - name: Create .env file with GitHub Secrets
       run: |
@@ -56,7 +85,7 @@ jobs:
         echo "LANGFUSE_SECRET_KEY=${{ secrets.LANGFUSE_SECRET_KEY }}" >> backend/app/.env
         echo "LANGFUSE_PUBLIC_KEY=${{ secrets.LANGFUSE_PUBLIC_KEY }}" >> backend/app/.env
         echo "LANGFUSE_HOST=${{ secrets.LANGFUSE_HOST }}" >> backend/app/.env
-    - name: Run Tests with Poetry
-      run: |
-        cd backend/app
-        poetry run pytest tests/ --maxfail=1 --disable-warnings -q
+
+    - name: Run Tests
+      working-directory: ./backend
+      run: uv run --no-sync pytest app/tests/ --maxfail=1 --disable-warnings -v

README.md

@@ -12,7 +12,7 @@ An AI-powered platform for discovering, analyzing, and exploring biomodels from
 ## Architecture
 This is a monolithic repository containing both frontend and backend services:
 - **Frontend**: Next.js 15 with TypeScript, Tailwind CSS, and Radix UI components
-- **Backend**: FastAPI with Python 3.12+, Poetry for dependency management
+- **Backend**: FastAPI with Python 3.12+, uv for dependency management
 - **Vector Database**: Qdrant for knowledge base storage and retrieval
 - **Containerization**: Docker and Docker Compose
 
@@ -45,7 +45,7 @@ VCell-GSoC/
 ### Backend
 - **Framework**: FastAPI
 - **Language**: Python 3.12+
-- **Dependency Management**: Poetry
+- **Dependency Management**: uv
 - **Database**: Qdrant Vector Database
 - **AI/ML**: OpenAI API, LangChain
 - **File Processing**: PyPDF, Markitdown
@@ -95,9 +95,9 @@ VCell-GSoC/
 #### Backend Setup
 ```bash
 cd backend
-poetry install --no-root
-poetry run uvicorn app.main:app --port 8000
-# poetry run uvicorn app.main:app --reload
+uv sync
+uv run uvicorn app.main:app --port 8000
+# uv run uvicorn app.main:app --reload
 ```
 
 #### Frontend Setup

SETUP.md

@@ -11,7 +11,7 @@ Before you begin, ensure you have the following installed:
 - **Node.js 18+** - For frontend development
 - **Python 3.12+** - For backend development
 - **Git** - For version control
-- **Poetry** - For Python dependency management (install via `pip install poetry`)
+- **[uv](https://docs.astral.sh/uv/)** - For Python dependency management (install via `curl -LsSf https://astral.sh/uv/install.sh | sh`)
 
 ## Initial Setup
 
@@ -205,8 +205,8 @@ docker run -d \
 
 ```bash
 cd backend
-poetry install --no-root
-poetry run uvicorn app.main:app --reload --host 0.0.0.0 --port 8000
+uv sync
+uv run uvicorn app.main:app --reload --host 0.0.0.0 --port 8000
 ```
 
 ### 5.3 Start Frontend

backend/Dockerfile

@@ -3,26 +3,25 @@ FROM python:3.12-slim
 
 # 2. Set environment vars
 ENV PYTHONDONTWRITEBYTECODE=1 \
-    PYTHONUNBUFFERED=1 \
-    POETRY_VIRTUALENVS_CREATE=false
+    PYTHONUNBUFFERED=1
 
-# 3. Install Poetry
-RUN pip install --no-cache-dir poetry
+# 3. Install uv
+COPY --from=ghcr.io/astral-sh/uv:latest /uv /uvx /bin/
 
 # 4. Set work directory
 WORKDIR /app
 
 # 5. Copy only pyproject + lock first for caching
-COPY pyproject.toml poetry.lock* ./
+COPY pyproject.toml uv.lock ./
 
-# 6. Install dependencies (without virtualenvs, no-root to skip package install)
-RUN poetry install --no-interaction --no-ansi --no-root
+# 6. Install dependencies without installing the local project package.
+RUN uv sync --frozen --no-install-project
 
 # 8. Now copy the full project
 COPY . .
 
 # 9. Expose the FastAPI dev port
 EXPOSE 8000
 
-# 10. Run uvicorn in dev mode with reload
-CMD ["sh", "-c", "poetry run uvicorn app.main:app --host 0.0.0.0 --port 8000"]
+# 10. Run uvicorn without re-syncing on each container start.
+CMD ["uv", "run", "--no-sync", "uvicorn", "app.main:app", "--host", "0.0.0.0", "--port", "8000"]

backend/README.md

@@ -20,7 +20,7 @@ backend/
 │   ├── schemas/               # Pydantic data models
 │   └── utils/                 # Utility functions
 ├── tests/                     # Test suite
-├── pyproject.toml            # Poetry configuration
+├── pyproject.toml            # Project configuration
 └── Dockerfile                # Container configuration
 ```
 
@@ -65,7 +65,7 @@ backend/
 ## Tech Stack
 - **Framework**: FastAPI 0.115+
 - **Language**: Python 3.12+
-- **Dependency Management**: Poetry
+- **Dependency Management**: uv
 - **Database**: Qdrant Vector Database
 - **AI/ML**: OpenAI API, LangChain
 - **File Processing**: PyPDF, Markitdown
@@ -77,7 +77,7 @@ backend/
 
 ### Prerequisites
 - Python 3.12+
-- Poetry
+- [uv](https://docs.astral.sh/uv/)
 - Docker (for Qdrant)
 
 ### Installation
@@ -89,7 +89,7 @@ backend/
 
 2. **Install dependencies**
    ```bash
-   poetry install
+   uv sync
    ```
 
 3. **Set up environment variables**
@@ -100,7 +100,7 @@ backend/
 
 4. **Start the development server**
    ```bash
-   poetry run uvicorn app.main:app --reload
+   uv run uvicorn app.main:app --reload
    ```
 
 ### Using Docker

backend/app/__init__.py

@@ -0,0 +1 @@
+"""VCell Backend Application"""

backend/app/schemas/__init__.py

@@ -0,0 +1 @@
+"""Pydantic schemas for VCell Backend"""

backend/app/utils/__init__.py

@@ -0,0 +1 @@
+"""Utility functions for VCell Backend"""

backend/pyproject.toml

@@ -1,36 +1,76 @@
-[tool.poetry]
+[project]
 name = "vcell-backend"
 version = "0.1.0"
 description = ""
-authors = ["Kacem Mathlouthi <[email protected]>"]
+authors = [{name = "Kacem Mathlouthi", email = "[email protected]"}]
 readme = "README.md"
+requires-python = ">=3.12,<3.14"
+dependencies = [
+    "fastapi>=0.115.12,<0.116.0",
+    "uvicorn[standard]>=0.34.3,<0.35.0",
+    "pydantic-settings>=2.9.1,<3.0.0",
+    "httpx>=0.28.1,<0.29.0",
+    "openai>=1.84.0,<2.0.0",
+    "qdrant-client>=1.15.0,<2.0.0",
+    "langchain>=0.3.27,<0.4.0",
+    "langchain-text-splitters>=0.3.8,<0.4.0",
+    "langfuse>=3.2.4,<4.0.0",
+    "pypdf>=5.8.0,<6.0.0",
+    "pypdf2>=3.0.1,<4.0.0",
+    "python-multipart>=0.0.20,<0.1.0",
+    "markitdown[all]>=0.1.2,<0.2.0",
+    "notebook>=7.4.4,<8.0.0",
+    "ipykernel>=6.30.0,<7.0.0",
+]
 
-[tool.poetry.dependencies]
-python = ">=3.12,<3.14"
-fastapi = "^0.115.12"
-uvicorn = {extras = ["standard"], version = "^0.34.3"}
-pydantic-settings = "^2.9.1"
-httpx = "^0.28.1"
-black = "^25.1.0"
-openai = "^1.84.0"
-qdrant-client = "^1.15.0"
-langchain = "^0.3.27"
-pypdf = "^5.8.0"
-pypdf2 = "^3.0.1"
-python-multipart = "^0.0.20"
-markitdown = {extras = ["all"], version = "^0.1.2"}
-notebook = "^7.4.4"
-ipykernel = "^6.30.0"
-langfuse = "^3.2.4"
-pytest = "^8.4.1"
-pytest-asyncio = "^1.1.0"
+[dependency-groups]
+dev = [
+    "pytest>=8.4.1,<9.0.0",
+    "pytest-asyncio>=1.1.0,<2.0.0",
+    "ruff>=0.3.0,<1.0.0",
+]
 
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
 
-[tool.poetry.group.dev.dependencies]
-pytest = "^8.4.0"
-httpx = "^0.28.1"
-pytest-asyncio = "^1.0.0"
+[tool.uv]
+managed = true
 
-[build-system]
-requires = ["poetry-core"]
-build-backend = "poetry.core.masonry.api"
+[tool.ruff]
+line-length = 100
+target-version = "py312"
+exclude = [
+    ".git",
+    ".venv",
+    "__pycache__",
+    "*.egg-info",
+    ".pytest_cache",
+]
+
+[tool.ruff.lint]
+select = [
+    "E",      # pycodestyle errors
+    "W",      # pycodestyle warnings
+    "F",      # Pyflakes
+    "I",      # isort
+    "C",      # flake8-comprehensions
+    "B",      # flake8-bugbear
+    "UP",     # pyupgrade
+    "ARG",    # flake8-unused-arguments
+    "SIM",    # flake8-simplify
+]
+ignore = [
+    "E501",   # line too long (handled by formatter)
+    "W503",   # line break before binary operator
+    "E203",   # whitespace before ':'
+]
+
+[tool.ruff.lint.isort]
+known-first-party = ["app"]
+multi-line-string-mode = "multi"
+
+[tool.pytest.ini_options]
+asyncio_mode = "auto"
+testpaths = ["app/tests"]
+python_files = ["test_*.py"]