mett 0.0.1a3

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_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}")

Documentation

For complete documentation including usage guides, API reference, and configuration options, please visit the GitHub repository.

Installation

From PyPI

pip install mett

From Source

Recommended (with uv)

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 (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_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