Cookiecutter BioIO Reader

A cookiecutter template for creating a new BioIO file format reader plugin.

About

Cookiecutter is a Python package to generate templated projects. This repository is a template for cookiecutter to generate a new BioIO File Format Reader Plugin. This cookiecutter generates:

• A directory structure for your project
• Prebuilt pyproject.toml file to help you develop and install your reader plugin package
  • Preconfigured to additionally label your reader plugin package as a bioio reader plugin
• Includes basic examples of modules, tests, etc.
• Continuous integration
  • Preconfigured to generate project documentation
  • Preconfigured to automatically run tests every time you push to GitHub
  • Preconfigured to help you release your reader plugin package publicly (PyPI)

Quickstart

To use this template use the following commands.

1. pip install cookiecutter
2. cookiecutter gh:bioio-devs/cookiecutter-bioio-reader

Once the project is generated, move to the newly created project directory and follow the instructions in SETUP.md.

Notes

1. Requires setuptools>=64.0 to install library locally in editable mode
   • Most environment managers pull in the latest setuptools automatically when creating a new environment anyway.
2. Must initialize the project as a git repository prior to installing locally.
   • This is due to the dynamic version management with setuptools-scm.
   • After running the cookiecutter, you should push code to a remote host (GitHub, GitLab, etc.) or at the very least, run git init prior to install.

Features

• Uses pytest for local testing, simply run just build from a terminal.
• Runs tests on Windows, Mac, and Ubuntu on every commit to main and every commit to branches with an open pull request to main using GitHub Actions.
• Releases your Python Package to PyPI when you push to main after pushing a new git tag with just tag-for-release and just release.
• Automatically builds documentation using Sphinx on every push to main and deploys to GitHub Pages.
• Includes very minimal example code to get started.

List of available just commands:

just

Available recipes:
    build                    # run lint and then run tests
    clean                    # clean all build, python, and lint files
    default                  # list all available commands
    install                  # install with all deps
    lint                     # lint, format, and check all files
    release                  # release a new version
    tag-for-release version  # tag a new version
    test                     # run tests
    update-from-cookiecutter # update this repo using latest cookiecutter-bioio-reader