nova-galaxy 0.11.3

Utilties for accessing the ORNL Galaxy instance

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 Poetry by placing the following in your pyproject.toml file (you can version lock with typical Semantic Versioning syntax)

[tool.poetry.dependencies]
nova-galaxy = "*"

Formatting

poetry run ruff format

Linting

poetry run ruff check
poetry 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 poetry 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):

poetry run coverage run
poetry 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.