Contributing Guide

This document outlines the baseline contribution guidelines for all packages in the geneweaver-* ecosystem. These guidelines are intended to concretely define what processes and practices a developer should follow when contributing to the project for their contribution to be accepted.

Tests

GeneWeaver is a community driven project with a variety of contributors. The project relies on automated tests to allow developers to be confident that their changes do not break existing functionality.

All contributed code should be tested. Test code coverage is calculated using the pytest-cov module. The minimum code coverage threshold varies per module. Code should be well tested through a variety of tests, not just a high code coverage percentage.

The geneweaver-testing module provides baseline automated tests and fixtures, as do the other geneweaver-* modules. The testing tools in these modules can be utilized to make writing tests for your code as straightforward as possible.

Code Style

In order to make the code in the geneweaver-* ecosystem consistent, and to make it as easy as possible to contribute to the codebase, we have adopted a set of code style standards and auto-formatting tools.

Docstrings

All PyTest Tests and PyTest Fixtures should have docstrings. The docstrings should follow the Google Style for docstrings.

Type Annotations

All PyTest Tests and PyTest Fixtures should have type annotations. MyPy will be used to check type annotations.

Code Linting - Ruff and MyPy

All code in the geneweaver-* ecosystem is linted using ruff and mypy.

GeneWeaver strives to use the most comprehensive set of linting rules reasonably available, to both ensure that the code is as clean as possible, and to provide as much feedback as possible to the developer.

Ruleset Configuration for ruff:

[tool.ruff]
select = [
# Pyflakes Ruleset
    "E", 
# Pycodestyle Ruleset (E - Error, W - Warning)
    "F", "W", 
# McCabe Complexity
    "C90",
# pep8-naming
    "N",
# flake8-builtins
    "A",
# flake8-bugbear
    "B", 
# flake8-annotations
    "ANN",
# flake8-pytest-stlye    
    "PT",
# pydocstyle
    "D", 
# Isort
    "I", 
# eradicate
    "ERA", 
# pandas-vet
    "PD", 
# NumPy-specific rules
    "NPY", 
]

You can find comprehensive documentation on theses rulesets in the ruff documentation

Code Formatting - Black and Ruff

All code in the geneweaver-* ecosystem is formatted using black and isort.

Development Process

Before submitting a pull request, please run the following commands to check your code:

ruff check src/geneweaver tests --fix
black src/geneweaver tests
pytest tests