docs: update documentation for uv package management

Update developer documentation to use uv as primary package manager:
- Add uv installation instructions to for-developers.md
- Update REPO-GUIDELINES.md with uv sync/run commands
- Add uv run prefixes to tool commands in tools.md

Author: vredchenko

claude-code/smartem-decisions/REPO-GUIDELINES.md

@@ -2,8 +2,8 @@
 
 ## Development Environment
 - **Python Version**: 3.12+ (strict requirement - utilize modern typing features)
-- **venv**: Use `source .venv/bin/activate` for tools such as pip, ruff or tox
-- **Package Management**: Use `pip install -e .[all]` for full development setup
+- **Package Manager**: uv (https://docs.astral.sh/uv/)
+- **Package Management**: Use `uv sync --extra all` for full development setup
 - **Code Style**: Ruff (120 char line length) with pyright type checking
 
 ## Code Standards
@@ -41,17 +41,17 @@ This applies to ALL files: Python code, Markdown documentation, configuration fi
 ## Common Commands
 ```bash
 # Development setup
-pip install -e .[all]
+uv sync --extra all
 
 # Testing
-pytest
+uv run pytest
 
-# Type checking  
-pyright src tests
+# Type checking
+uv run pyright src tests
 
 # Linting and formatting
-ruff check
-ruff format
+uv run ruff check
+uv run ruff format
 
 # Pre-commit checks
 pre-commit run --all-files
@@ -60,8 +60,8 @@ pre-commit run --all-files
 cd ../smartem-devtools/webui && npm run dev
 
 # Database migrations
-python -m alembic upgrade head
-python -m alembic revision --autogenerate -m "Description"
+uv run alembic upgrade head
+uv run alembic revision --autogenerate -m "Description"
 ```
 
 ## Project Architecture
@@ -88,7 +88,6 @@ python -m alembic revision --autogenerate -m "Description"
 ## Testing & Quality
 - **Coverage**: Tests run with coverage reporting
 - **Doctests**: Documentation examples are executable
-- **Multiple environments**: tox for cross-environment testing
 - **CI/CD**: GitHub Actions with pre-commit hooks
 
 ## Documentation

docs/development/tools.md

@@ -10,16 +10,16 @@ Transform single-line XML and .dm files into human-readable format with proper i
 
 ```bash
 # Reformat all .xml and .dm files in a directory recursively
-python tools/format_xml.py <directory_path> -r
+uv run python tools/format_xml.py <directory_path> -r
 
 # Process multiple directories
-python tools/format_xml.py -r \
+uv run python tools/format_xml.py -r \
   ../smartem-decisions-test-datasets/metadata_Supervisor_20250114_220855_23_epuBSAd20_GrOxDDM \
   ../smartem-decisions-test-datasets/metadata_Supervisor_20241220_140307_72_et2_gangshun \
   ../smartem-decisions-test-datasets/metadata_Supervisor_20250108_101446_62_cm40593-1_EPU
 
 # Display all available options
-python tools/format_xml.py --help
+uv run python tools/format_xml.py --help
 ```
 
 ## Data Analysis and Debugging Tools
@@ -30,10 +30,10 @@ Identify duplicate foil hole manifests within directory structures to detect dat
 
 ```bash
 # Display help and usage information
-tools/find_foilhole_duplicates.py --help
+uv run tools/find_foilhole_duplicates.py --help
 
 # Example: Search for duplicates in test data
-tools/find_foilhole_duplicates.py ./tests/testdata/bi37708-28
+uv run tools/find_foilhole_duplicates.py ./tests/testdata/bi37708-28
 ```
 
 ### File Size Analysis
@@ -94,21 +94,21 @@ Comprehensive CLI tool for simulating external data processing messages that wou
 
 ```bash
 # List all available message types
-python tools/external_message_simulator.py list-messages
+uv run python tools/external_message_simulator.py list-messages
 
 # Individual message simulation examples
-python tools/external_message_simulator.py motion-correction --foilhole-id "FH_001_001_001" --quality-score 0.85
-python tools/external_message_simulator.py ctf-complete --foilhole-id "FH_001_001_001" --resolution 3.2
-python tools/external_message_simulator.py gridsquare-prediction --gridsquare-id "GS_001_001" --prediction-score 0.85
-python tools/external_message_simulator.py model-update --model-name "ResNet-50"
+uv run python tools/external_message_simulator.py motion-correction --foilhole-id "FH_001_001_001" --quality-score 0.85
+uv run python tools/external_message_simulator.py ctf-complete --foilhole-id "FH_001_001_001" --resolution 3.2
+uv run python tools/external_message_simulator.py gridsquare-prediction --gridsquare-id "GS_001_001" --prediction-score 0.85
+uv run python tools/external_message_simulator.py model-update --model-name "ResNet-50"
 
 # Complete workflow simulation for a single grid square
-python tools/external_message_simulator.py workflow-simulation --gridsquare-id "DEV_001"
+uv run python tools/external_message_simulator.py workflow-simulation --gridsquare-id "DEV_001"
 
 # Batch simulation with different quality scenarios
-python tools/external_message_simulator.py batch-simulation --gridsquare-count 5 --scenario mixed
-python tools/external_message_simulator.py batch-simulation --gridsquare-count 3 --scenario good
-python tools/external_message_simulator.py batch-simulation --gridsquare-count 2 --scenario poor
+uv run python tools/external_message_simulator.py batch-simulation --gridsquare-count 5 --scenario mixed
+uv run python tools/external_message_simulator.py batch-simulation --gridsquare-count 3 --scenario good
+uv run python tools/external_message_simulator.py batch-simulation --gridsquare-count 2 --scenario poor
 ```
 
 **Available Message Types:**
@@ -126,7 +126,7 @@ Example client for testing agent-backend communication via Server-Sent Events:
 
 ```bash
 # Start the SSE client to receive instructions from backend
-python tools/sse_client_example.py
+uv run python tools/sse_client_example.py
 
 # The client will:
 # 1. Auto-create a new session with the backend
@@ -161,12 +161,12 @@ pre-commit run --all-files
 
 ```bash
 # Run comprehensive test suite
-pytest
+uv run pytest
 
 # Type checking with pyright
-pyright src tests
+uv run pyright src tests
 
 # Code formatting and linting
-ruff check
-ruff format
+uv run ruff check
+uv run ruff format
 ```

docs/getting-started/for-developers.md

@@ -10,53 +10,75 @@ python3 --version
 
 **Note:** The project specifically requires Python 3.12+ to utilise advanced typing features and maintain compatibility with the latest scientific computing libraries.
 
-## Create a Virtual Environment
+## Install uv (Recommended)
 
-It is strongly recommended that you install SmartEM Decisions within a virtual environment to prevent conflicts with existing Python installations and maintain a clean development environment:
+We recommend using [uv](https://docs.astral.sh/uv/) for Python package management. uv is a fast Python package manager that handles virtual environments and dependencies efficiently.
+
+### Install uv
 
 ```bash
-python3 -m venv /path/to/venv
-source /path/to/venv/bin/activate
+# On macOS and Linux
+curl -LsSf https://astral.sh/uv/install.sh | sh
+
+# Or with pip
+pip install uv
+
+# Or with Homebrew (macOS)
+brew install uv
 ```
 
-For development work, consider creating the virtual environment within the project directory:
+## Installing the Library
+
+### Development Installation (Recommended)
+
+For development work, clone the repository and install using uv:
 
 ```bash
-python3 -m venv .venv
-source .venv/bin/activate
+# Clone the repository
+git clone https://github.com/DiamondLightSource/smartem-decisions.git
+cd smartem-decisions
+
+# Install all dependencies (creates virtual environment automatically)
+uv sync --extra all
 ```
 
-## Installing the Library
+This will create a `.venv` directory and install all dependencies including development tools.
 
-### Standard Installation
+### Running Commands
 
-You can install the library and its core dependencies using `pip`:
+With uv, prefix commands with `uv run` to execute them in the virtual environment:
 
 ```bash
-python3 -m pip install smartem-decisions
+# Run tests
+uv run pytest
+
+# Type checking
+uv run pyright src tests
+
+# Linting
+uv run ruff check
 ```
 
-### Development Installation
+### Standard Installation (pip)
 
-For development work or if you require the latest features, install directly from the source repository:
+You can also install the library using pip:
 
 ```bash
-# Clone and install in development mode
-git clone https://github.com/DiamondLightSource/smartem-decisions.git
-cd smartem-decisions
-pip install -e .[all]
+python3 -m pip install smartem-decisions
 ```
 
 ### Installation with Optional Dependencies
 
 Install with specific feature sets:
 
 ```bash
-# Install with MCP (Model Context Protocol) support
-pip install -e .[mcp]
+# Using uv (recommended)
+uv sync --extra mcp      # Install with MCP support
+uv sync --extra all      # Install with all dependencies
 
-# Install with all optional dependencies (recommended for development)
-pip install -e .[all]
+# Using pip
+pip install -e .[mcp]    # Install with MCP support
+pip install -e .[all]    # Install with all dependencies
 ```
 
 ## Verify Installation
@@ -65,17 +87,17 @@ Verify that all components are correctly installed by running:
 
 ```bash
 # Test core functionality
-python -c "import smartem_backend, smartem_agent, smartem_common; print('Core components imported successfully')"
+uv run python -c "import smartem_backend, smartem_agent, smartem_common; print('Core components imported successfully')"
 
 # Test MCP functionality (if installed with MCP support)
-python -c "import smartem_mcp; print('MCP components available')"
+uv run python -c "import smartem_mcp; print('MCP components available')"
 ```
 
 You can also verify the CLI tools are available:
 
 ```bash
 # Check agent CLI is accessible
-python -m smartem_agent --help
+uv run python -m smartem_agent --help
 ```
 
 ## Next Steps