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.
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-utilsBesides 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",)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+.