Package Description
This project is a product of the biocommons community.
- Github repository: https://github.com/biocommons/bioutils/
- Documentation https://biocommons.github.io/bioutils/
Install from PyPI with pip install bioutils or uv pip install bioutils, then try it:
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.
- Install brew
brew install git make uv
You may also install using distribution packages:
sudo apt install git make
Then install uv using the uv installation instructions.
Create a Python virtual environment, install dependencies, install pre-commit hooks, and install an editable package:
make devready
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