mett 0.0.1a5

Python client and CLI for the METT Data Portal API

METT Data Portal Client

Python client library and command-line interface (CLI) for the Microbial Ecosystems Transversal Themes (METT) Data Portal.

• Portal: http://www.gut-microbes.org/
• Install from PyPI: pip install mett
• Python import package: mett_client

Features

• 🚀 High-level Python API - Clean, intuitive interface for programmatic access
• 💻 Command-line Interface - CLI with rich output and shell completion
• 📊 Multiple Output Formats - JSON, TSV, and formatted tables
• 🔒 Flexible Configuration - Environment variables and config file support
• 📚 Documentation - Usage examples and API details
• 🔄 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_client import DataPortalClient

# Initialize client
client = DataPortalClient()

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

# List genomes (paginated)
result = client.list_genomes(per_page=5)
print(f"Found {len(result.items)} genomes")

# Search genomes by species
result = client.species_genomes("BU", per_page=5)
print(f"Found {len(result.items)} BU genomes")

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

# Search genomes - check first genome
if result.items:
    print(f"First genome: {result.items[0].isolate_name}")

Configuration

The client/CLI can be configured using environment variables (recommended for CI and local dev) or a config file (if supported by your implementation).

Common environment variables

# Base URL for the METT Data Portal API (if your client supports overriding it)
export METT_BASE_URL="https://www.gut-microbes.org/"

# If the API requires authentication (token / key), set it here (adjust name to match your implementation)
# export METT_API_TOKEN="..."

# SSL verification (useful for dev environments without certificates)
export METT_VERIFY_SSL=false

Documentation

Complete documentation is available in the docs/ directory:

• Getting Started - Overview and quick start
• CLI Guide - Command-line interface
• Python API - Python client library
• Configuration - Setup and authentication
• Troubleshooting - Common issues and solutions

Source & Support

• Source repository: https://github.com/EBI-Metagenomics/mett-dataportal-client
• Issues / feature requests: https://github.com/EBI-Metagenomics/mett-dataportal-client/issues

Development

From Source (with uv) — recommended

git clone https://github.com/EBI-Metagenomics/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)

# 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_client/ scripts/ tests/
uv run ruff format --check mett_client/ 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

License

Apache-2.0 License - see LICENSE file for details.

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

export METT_VERIFY_SSL=false