Ensembl Python general-purpose utils

Centralise generic Python utils used by other projects within Ensembl design to facilitate frequent tasks such as input file path checks, archive files IO manipulation or logging setup, among others.

For more information, please consult this repository’s GitHub pages.

Getting Started

Basic installation

This library is publicly available in PyPI so it can be easily installed with your favourite Python dependency and packaging management tool, e.g.

pip install ensembl-utils

Quick usage

Besides the standard import ensembl.utils, this library also provides some useful command line scripts:

• extract_file - to easily extract archive files in different formats

Furthermore, ensembl-utils also has a pytest plugin with some useful functionalities to ease your unit testing. You can enable it by adding it explicitly when running pytest:

pytest -p ensembl.utils.plugin ...

Or adding the following line to your conftest.py:

pytest_plugins = ("ensembl.utils.plugin",)

Dependencies

This repository has been developed to support SQLAlchemy version 1.4 (1.4.45 or later, to ensure “future-compatibility”) as well as version 2.0+.