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Contributing Guide

Thanks for your interest in contributing to biahub!

Getting started

Please read the Home page for an overview of the project, and how you can install and use the package.

Making changes

Any change made to the main branch or release maintenance branches need to be proposed in a pull request (PR).

Follow these instructions to fork the repository.

Setting up a development environment

  1. Install the package in development mode:
pip install -e ".[dev]"
  1. Install pre-commit hooks:
pre-commit install

The pre-commit hooks automatically run style checks (e.g. flake8, black, isort) when staged changes are committed. Resolve any violations before committing your changes. You can manually run the pre-commit hooks at any time using the make pre-commit command.

Makefile

A makefile is included to help with a few basic development commands. Currently, the following commands are available:

make setup-develop # setup the package in development mode
make uninstall # uninstall the package
make check-format # run black and isort format check
make format # run black and isort formatting
make lint # run flake8 linting
make pre-commit # run pre-commit hooks on all files
make test # run pytest

Building documentation locally

The documentation is built using Zensical. To preview the docs locally:

  1. Install Zensical:
pip install zensical
  1. Serve the documentation locally:
zensical serve

This will start a local server at http://localhost:8000 with live reload enabled.

  1. To build the static site:
zensical build

The built site will be in the site/ directory.