chore: migrate from Poetry to uv for dependency management

.github/workflows/ci.yml

@@ -14,25 +14,22 @@ jobs:
 
     steps:
     - name: Checkout Repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v4
+
+    - name: Install uv
+      uses: astral-sh/setup-uv@v5
+      with:
+        enable-cache: true
+        cache-dependency-glob: "backend/uv.lock"
 
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: '3.12'
 
-    - 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: Change to Backend Directory
-      run: cd backend  # Change to the backend folder
-
-    - 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: Install dependencies
+      working-directory: backend
+      run: uv sync --frozen
 
     - name: Create .env file with GitHub Secrets
       run: |
@@ -56,7 +53,7 @@ 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 pytest app/tests/ --maxfail=1 --disable-warnings -q

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
+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
+CMD ["uv", "run", "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/pyproject.toml

@@ -1,36 +1,38 @@
-[tool.poetry]
+[project]
 name = "vcell-backend"
 version = "0.1.0"
 description = ""
-authors = ["Kacem Mathlouthi <kacem.mathlouthi@insat.ucar.tn>"]
+authors = [{name = "Kacem Mathlouthi", email = "kacem.mathlouthi@insat.ucar.tn"}]
 readme = "README.md"
+requires-python = ">=3.12,<3.14"
+dependencies = [
+    "fastapi>=0.115.12",
+    "uvicorn[standard]>=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[all]>=0.1.2",
+    "notebook>=7.4.4",
+    "ipykernel>=6.30.0",
+    "langfuse>=3.2.4",
+]
 
-[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"
-
-
-[tool.poetry.group.dev.dependencies]
-pytest = "^8.4.0"
-httpx = "^0.28.1"
-pytest-asyncio = "^1.0.0"
+[dependency-groups]
+dev = [
+    "pytest>=8.4.0",
+    "httpx>=0.28.1",
+    "pytest-asyncio>=1.0.0",
+]
 
 [build-system]
-requires = ["poetry-core"]
-build-backend = "poetry.core.masonry.api"
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[tool.hatch.build.targets.wheel]
+packages = ["app"]