biocommons.example Test Package

This repo provides a template for biocommons Python packages. Here's how to use it:

1. Click the Use this template button. Name the new repo like "biocommons.something".
2. Clone your repo locally.
3. In the repo, type make rename. The new name will be chosen based on the repo name.
4. Remove this header.
5. Commit and push.

Installation

To install from pypi: pip install biocommons.example

Developer Setup

Developers must install zsh, which is required by the Makefile. zsh is included by default in MacOS, and is readily available on all modern Linux distributions.

Setup like this:

make devready
source venv/bin/activate

Code reformatting:

make reformat

Install pre-commit hook:

# included in `make devready`, not necessary for new installations
pre-commit install

Test:

make test   # for current environment
make tox    # for all supported versions

Build:

git tag 0.0.0
make build

Try it:

$ python3 -m biocommons.example
Marvin says:
There's only one life-form as intelligent as me within thirty parsecs...

$ marvin-quote
Marvin says:
You think you've got problems? What are you supposed to do if you...

$ ipython
>>> from biocommons.example import __version__, get_quote_from_marvin
>>> __version__
'0.1.dev8+gd5519a8.d20211123'
>>> get_quote()
"The first ten million years were the worst, ...

Features

Code structure and features

• Modern pyproject.toml with setuptools
• Versioning based on git tag (only)
• Easy development setup
• Support for namespaces
• Testing with coverage using pytest; tests may be in tests/, embedded in the package, and in doc strings
• Examples for logging and package data
• Command-line with argument parsing with argparse

DevOps

• Quality tools: Code linting and reformatting with Ruff
• GitHub Actions for testing and packaging

ToDo

• Add devcontainer support