nova-galaxy

=======================

Introduction

This is the repository for the nova-galaxy project. This project creates a python package that makes it easier to work with the ORNL Galaxy instance.

Documentation

A user guide, examples, and a full API for this package can be found at https://nova-galaxy.readthedocs.io/en/stable/.

Installation

You can install this package directly with

pip install nova-galaxy

or with Pixi:

pixi add --pypi nova-galaxy

Formatting

pixi run ruff format

Linting

pixi run ruff check
pixi run mypy .

Testing

You can run the tests for this package with the following command from the base directory:

NOVA_GALAXY_TEST_GALAXY_URL=galaxy-url NOVA_GALAXY_TEST_GALAXY_KEY=key pixi run pytest tests/

with NOVA_GALAXY_TEST_GALAXY_URL being the url of your Galaxy instance and NOVA_GALAXY_TEST_GALAXY_KEY being your Galaxy API Key.

To run tests with coverage (include the above environment variables):

pixi run coverage run
pixi run coverage report

CI/CD in GitHub

Take a look at the .github/workflows folder. Actions to lint and test your code will run automatically on each commit. The action for building and releasing this package needs to be triggered manually.

Publishing docs to readthedocs.io

This repo has a webhook that automatically triggers documentation builds on readthedocs.