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
:
bash
pytest -p ensembl.utils.plugin ...
- Adding the following line to your
conftest.py
file at the root of where the unit tests are located:python 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+.