Python Package Skeleton Template

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Summary

This repository is a skeleton template for a Python application/library compliant with the latest team-development and software deployment practices within a continuous integration (CI) framework. You can use this repository as a source of information and a resource to study CI. Also, you can use this repository as a direct template for your repositories.

Note that this repository reflects the setup I like the most and that covers the CI needs for my Python projects, which include:

• A robust Python library/application file hierarchy with packages, modules, clients, and documentation:
  • detailed, yet simple, setup.py
  • retrievable README and CHANGELOG
  • documentation deployed in ReadTheDocs_
  • the unusual adoption of the src directory layer (love it)
  • examples of packages and modules hierarchy
  • examples of Python command-line interfaces
• A unique testing framework for developers with tox_ and pytest_
  • guarantees tests are reproducible for all developers
  • ensures same lint rules are always applied (local and remotely)
  • ensures all desired Python versions are covered
  • adopts hypothesis_
• Fully automated continuous integration services with GitHub Actions_
  • automatic testing on Linux, MacOS, and Windows
  • automatic testing simulated upon deployment with tox
  • test coverage report to Codecov
  • automated version bump with bump2version_, git tagging, and Python packaging to PyPI on Pull Request merge

Motivation

I developed this repository to understand how to implement the best practices for team-based development and automatic deployment of a scientific software written in Python. Nonetheless, I believe the strategy reviewed here can be applied to most general-purpose Python libraries.

This repository does not intend to be a cookiecutter-like repository. There are very well documented cookiecutters, even for scientific software, if you are looking for one of those. However, when I started developing Python libraries, I decided that blindly using a cookiecutter would not provide me the learning insights from configuring CI services because I would miss the details of what was actually being implemented. Hence, assembling this template from scratch as a full working repository was my best approach to obtain a useful understanding of CI. Now, this repository serves as a reference guide for all my projects and hopefully will serve you, too. I keep constantly updating this repository, expect one to two updates/reviews per year.

Acknowledgments

I want to acknowledge ionel_ discussions about Packaging a python library. They are a pillar in my understanding and decisions on this matter, and I really recommend reading his blog post_ and references herein.

I configured the CI pipeline to my needs by taking bits and pieces from many places. Kudos to python-nameless_ and cookiecutter-pylibrary_; two primary sources of information for the python-project-skeleton repository, especially in the first versions using Travis and Appveyor.

When migrating to GitHub Actions, I based my choices on the version bump and deploying workflows @JoaoRodrigues <https://github.com/JoaoRodrigues>_ assembled for pdb-tools; on the tox-gh-actions package; and on structlog_. Implementation details have evolved with newest versions.

I refer to other important sources of information as comments in the specific files. Thanks, everyone, for keeping open discussions on internet.

How to use this repository

The documentation_ pages explain how to use this template for your projects and the implementation details adopted here. The documentation pages also serve to demonstrate how to compile documentation with Sphinx and deploy it online with ReadTheDocs_.

Issues and Discussions

As usual for any GitHub-based project, raise an issue_ if you find any bug or want to suggest an improvement, or open a discussion_ if you want to discuss or chat :wink:

Projects using this skeleton

Below, a list of the projects using this repository as template or as base for their CI implementations:

• julie-forman-kay-lab/IDPConformerGenerator <https://github.com/julie-forman-kay-lab/IDPConformerGenerator>_
• haddocking/HADDOCK3 <https://github.com/haddocking/haddock3>_
• THGLab/MCSCE <https://github.com/THGLab/MCSCE>_
• joaomcteixeira/taurenmd <https://github.com/joaomcteixeira/taurenmd>_
• MDAnalysis/mdacli <https://github.com/MDAnalysis/mdacli>_

If you use this repository as a reference for your works, let me know, so I list your work above, as well.

Version

v0.11.3

.. _GitHub Actions: https://github.com/features/actions .. _PyPI: https://pypi.org .. _blog post: https://blog.ionelmc.ro/2014/05/25/python-packaging/ .. _bump2version: https://github.com/c4urself/bump2version .. _cookiecutter-pylibrary: https://github.com/ionelmc/cookiecutter-pylibrary .. _cookiecutter: https://cookiecutter.readthedocs.io/en/latest/index.html .. _discussion: https://github.com/joaomcteixeira/python-project-skeleton/discussions .. _documentation: https://python-project-skeleton.readthedocs.io/ .. _even for scientific software: https://github.com/MolSSI/cookiecutter-cms .. _hypothesis: https://hypothesis.readthedocs.io/en/latest/ .. _ionel: https://github.com/ionelmc .. _issue: https://github.com/joaomcteixeira/python-project-skeleton/issues .. _latest branch: https://github.com/joaomcteixeira/python-project-skeleton/tree/latest .. _master branch: https://github.com/joaomcteixeira/python-project-skeleton/tree/master .. _pdb-tools: https://github.com/haddocking/pdb-tools/blob/2a070bbacee9d6608b44bb6d2f749beefd6a7690/.github/workflows/bump-version-on-push.yml .. _project's documentation: https://python-project-skeleton.readthedocs.io/en/latest/index.html .. _pytest: https://docs.pytest.org/en/stable/ .. _python-nameless: https://github.com/ionelmc/python-nameless .. _structlog: https://github.com/hynek/structlog .. _test.pypi.org: https://test.pypi.org .. _tox-gh-actions: https://github.com/ymyzk/tox-gh-actions .. _tox: https://tox.readthedocs.io/en/latest/ .. _ReadTheDocs: https://readthedocs.org/