mett 0.0.1a1

Python client and CLI for the METT Data Portal API

METT Data Portal Client

Python client library and command-line interface (CLI) for the METT Data Portal API. Access genomic data, experimental results, and protein interactions for gut microbiome research.

Features

• 🚀 High-level Python API - Clean, intuitive interface for programmatic access
• 💻 Command-line Interface - Powerful CLI with tab completion and rich output
• 📊 Multiple Output Formats - JSON, TSV, and formatted tables
• 🔒 Flexible Authentication - Environment variables or config file support
• 📚 Comprehensive Documentation - Auto-generated API reference with examples
• 🔄 Auto-generated SDK - Stays in sync with the API schema

Quick Start

Installation

pip install mett

CLI Usage

# List all species
mett species list

# Search genomes
mett genomes search --query "Bacteroides" --per-page 5

# Get gene information
mett genes get BU_ATCC8492_00001

Python API

from mett_dataportal import DataPortalClient

# Initialize client
client = DataPortalClient()

# List species
species = client.list_species()
print(f"Found {len(species)} species")

# Search genomes
result = client.search_genomes(query="Bacteroides", per_page=5)
print(f"Found {len(result.items)} genomes")

Documentation

Quick Links

• 📖 API Reference - Complete API documentation with tabbed examples (Quarto format)
• 📘 Usage Guide - Detailed usage examples for CLI and Python API
• ⚙️ Configuration Guide - Authentication and configuration options
• 🔧 Development Guide - Setup, testing, and contributing
• 📦 Architecture Guide - Package architecture and design decisions

Viewing API Documentation

The API reference is in Quarto format (.qmd). To view it:

# Generate from OpenAPI spec (if needed)
python3 scripts/generate-api-docs.py

# Render to HTML
quarto render docs/reference/api-reference.qmd

# Open in browser
open docs/reference/api-reference.html

Or use preview mode (auto-reloads on changes):

quarto preview docs/reference/api-reference.qmd

The rendered HTML includes interactive tabs showing examples in three formats:

• Friendly CLI - High-level mett commands
• Generic CLI - mett api request commands
• cURL - Raw HTTP requests

For more information, see the Documentation README.

Installation

From PyPI

pip install mett

From Source

Recommended (with uv)

git clone https://github.com/your-org/mett-dataportal-client.git
cd mett-dataportal-client

# Create a virtual environment and install all dependencies from pyproject.toml
uv sync --all-extras --dev

# Run the CLI via uv (no manual activation needed)
uv run mett --help

Running tests and linting

With uv (recommended):

# Install all dev dependencies (if not already done)
uv sync --all-extras --dev

# Run tests
uv run pytest -v

# Run Ruff lint and formatting checks
uv run ruff check mett_dataportal/ scripts/ tests/
uv run ruff format --check mett_dataportal/ scripts/ tests/

# (Optional) Run pre-commit hooks on all files
uv run pre-commit run --all-files

Alternative (classic pip workflow)

If you prefer not to use uv, you can still work with a standard virtual environment:

python -m venv .venv
source .venv/bin/activate

pip install --upgrade pip
pip install -e ".[dev]"

# CLI is now on PATH inside the venv
mett --help

Requirements

• Python 3.10+
• See pyproject.toml for full dependency list

Project Structure

mett-dataportal-client/
├── mett_dataportal/          # Main package
│   ├── cli/                  # CLI commands (organized by API type)
│   │   ├── core/             # Core APIs (system, species, genomes, genes)
│   │   ├── experimental/    # Experimental APIs (drugs, proteomics, etc.)
│   │   └── interactions/    # Interaction APIs (PPI, TTP)
│   ├── client.py             # High-level API client
│   ├── config.py             # Configuration management
│   └── utils.py              # Utility functions
├── mett_dataportal_sdk/      # Auto-generated SDK
├── docs/                      # Documentation
│   ├── guides/                # User guides
│   │   ├── USAGE.md          # Usage examples
│   │   └── CONFIGURATION.md  # Configuration guide
│   ├── developers/            # Developer documentation
│   │   └── DEVELOPMENT.md    # Development guide
│   ├── reference/             # API reference
│   │   ├── api-reference.qmd # Main API reference (Quarto)
│   │   └── cli-examples*.md  # Example files
│   └── assets/                # Static assets (CSS, etc.)
├── scripts/                   # Utility scripts
└── tests/                     # Test suite

Contributing

We welcome contributions! Please see CONTRIBUTING.md for guidelines.

1. Fork the repository
2. Create a feature branch (git checkout -b feature/amazing-feature)
3. Make your changes
4. Run tests and linting (see Running tests and linting above)
5. Commit your changes (git commit -m 'Add amazing feature')
6. Push to the branch (git push origin feature/feature/amazing-feature)
7. Open a Pull Request

License

MIT License - see LICENSE file for details.

Support

• Issues: GitHub Issues
• Documentation: See docs/ directory
• Email: [e-mail]

Acknowledgments

Built for the METT Data Portal project. Special thanks to all contributors.

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Note: For development environments without SSL certificates, you may need to set:

export METT_VERIFY_SSL=false