code repository
license

Common package for integrating with Mass Dynamics workflows

Installation

This project uses uv to manage its environment and dependencies. Install it first if you don't have it:

curl -LsSf https://astral.sh/uv/install.sh | sh

To install md_dataset from GitHub repository, do:

git clone git@github.com:MassDynamics/md_dataset.git
cd md_dataset
uv sync

To develop the package:

uv sync --extra dev
uv run ruff check
uv run pytest

The CI helpers wrap these commands:

./scripts/test   # uv run pytest -n auto
./scripts/lint   # uv run ruff check
./scripts/audit  # uv run pip-audit

Documentation

R implementation

To run a dataset locally, you can using localstack:

USE_LOCALSTACK=true

To use an AWS source buckets:

RESULTS_BUCKET=bucket-name
BOTO3_PROFILE=your-profile

These will both use a local prefect installation.

Credits

This initial package was created with Copier and the NLeSC/python-template.