bioutils

Package Description

This project is a product of the biocommons community.

• Github repository: https://github.com/biocommons/bioutils/
• Documentation https://biocommons.github.io/bioutils/

Python Package Installation

Install from PyPI with pip install bioutils or uv pip install bioutils, then try it:

Developer Setup

Install Prerequisites

These tools are required to get started:

• git: Version control system
• GNU make: Current mechanism for consistent invocation of developer tools.
• uv: An extremely fast Python package and project manager, written in Rust.

MacOS or Linux Systems

• Install brew
• brew install git make uv

Linux (Debian-based systems)

You may also install using distribution packages:

sudo apt install git make

Then install uv using the uv installation instructions.

One-time developer setup

Create a Python virtual environment, install dependencies, install pre-commit hooks, and install an editable package:

make devready

Development

N.B. Developers are strongly encouraged to use make to invoke tools to ensure consistency with the CI/CD pipelines. Type make to see a list of supported targets. A subset are listed here:

» make
🌟🌟 biocommons conventional make targets 🌟🌟

Using these targets promots consistency between local development and ci/cd commands.

usage: make [target ...]

BASIC USAGE
help                Display help message

SETUP, INSTALLATION, PACKAGING
devready            Prepare local dev env: Create virtual env, install the pre-commit hooks
build               Build package
publish             publish package to PyPI

FORMATTING, TESTING, AND CODE QUALITY
cqa                 Run code quality assessments
test                Test the code with pytest

DOCUMENTATION
docs-serve          Build and serve the documentation
docs-test           Test if documentation can be built without warnings or errors

CLEANUP
clean               Remove temporary and backup files
cleaner             Remove files and directories that are easily rebuilt
cleanest            Remove all files that can be rebuilt
distclean           Remove untracked files and other detritus