nova-galaxy 0.8.1

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 GitLab

Take a look at the .gitlab-ci.yml file. It configures pipelines to run in GitLab. Some jobs will run automatically on each commit, jobs to build packages and Docker images need to be trigerred manually. Don't forget to set versions properly: in pyproject.toml for python package and in .gitlab-ci.yml for Docker tag.