Using these utils

You can easily take advantage of the provided functionalities by importing this library in your code as usual:

import ensembl.utils

This library also provides some scripts that can help you via the command line:

• extract_file - to easily extract archive files in different formats

Note: All of them include the --help option to provide further information about their purpose and how to use them.

pytest plugin

This repository provides a pytest plugin with some useful functionalities to do unit testing. In particular, there is one fixture to access the test files in a folder with the same name as the test being run (data_dir) and a fixture to build and provide unit test databases (test_dbs).

To use these elements you need to enable the plugin once you have installed the repository. There are two main ways to do this:

1. Explicitly indicating it when running pytest:

   pytest -p ensembl.utils.plugin ...
   

2. Adding the following line to your conftest.py file at the root of where the unit tests are located:

   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+.