Ensembl Python Base Library

Centralise generic Python code use across all other project within Ensembl, more particularly database access layers and ORMs, reusable eHive components, etc.

Getting Started

Installing the development environment with venv

python -m venv <VIRTUAL_ENVIRONMENT_NAME>
source <VIRTUAL_ENVIRONMENT_NAME>/bin/activate
git clone https://github.com/Ensembl/ensembl-py.git
cd ensembl-py
pip install -e .[cicd,dev,docs]

Testing with pytest

Run test suite from the root of the repository is as simple as to run:

pytest

To run tests, calculate and display testing coverage stats:

coverage run -m pytest
coverage report -m

Generate documentation via mkdocs

mkdocs build

Open automatically generated documentation page at site/index.html.

Automatic formatting (PEP8 compliance)

black --check .

Use --diff to print a diff of what Black would change, without actually changing the files.

To actually reformat all files in the repository:

black .

Linting and type checking

pylint src/python/ensembl
pylint --recursive=y src/python/tests
mypy src/python/ensembl
mypy src/python/tests

pylint will check the code for syntax, name errors and formatting style. mypy will use type hints to statically type check the code.

It should be relatively easy (and definitely useful) to integrate both pylint and mypy in your IDE/Text editor.

Useful resources

Python Documentation

• Official Python Docs

Python virtual environments management

• Python venv

Auto-generating documentation

• mkdocs

Linting, type checking and formatting

• Pylint
• Mypy
• Black
• Google Python Style Guide

Testing

• pytest
• Coverage

CI/CD

• GitLab CI/CD

Development tools

• IPython

Distributing

• Packaging Python
• Apache 2.0 License
• Semantic Versioning