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Scientific Python Library Development Guide and Cookiecutter
https://learn.scientific-python.org/development
BSD 3-Clause "New" or "Revised" License
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cookiecutter cookiecutter-python cookiecutter-python3 pypi-package python scikit-hep

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Scientific Python: guide, cookie, & sp-repo-review

Cookie

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PyPI version PyPI platforms

A copier/cookiecutter template for new Python projects based on the Scientific Python Developer Guide. What makes this different from other templates for Python packages?

Be sure you have read the Scientific-Python Development Guide first, and possibly used them on a project or two. This is not a minimal example or tutorial. It is a collection of useful tooling for starting a new project using cookiecutter, or for copying in individual files for an existing project (by hand, from {{cookiecutter.project_name}}/).

During generation you can select from the following backends for your package:

  1. hatch: This uses hatchling, a modern builder with nice file inclusion, extendable via plugins, and good error messages. (Recommended for pure Python projects)
  2. flit: A modern, lightweight PEP 621 build system for pure Python projects. Replaces setuptools, no MANIFEST.in, setup.py, or setup.cfg. Low learning curve. Easy to bootstrap into new distributions. Difficult to get the right files included, little dynamic metadata support.
  3. pdm: A modern, less opinionated all-in-one solution to pure Python projects supporting standards. Replaces setuptools, venv/pipenv, pip, wheel, and twine. Supports PEP 621.
  4. poetry: An all-in-one solution to pure Python projects. Replaces setuptools, venv/pipenv, pip, wheel, and twine. Higher learning curve, but is all-in-one. Makes some bad default assumptions for libraries. The only one with a non-standard pyproject.toml config.
  5. setuptools: The classic build system, but with the new standardized configuration.
  6. pybind11: This is setuptools but with an C++ extension written in pybind11 and wheels generated by cibuildwheel.
  7. scikit-build: A scikit-build (CMake) project also using pybind11, using scikit-build-core. (Recommended for C++ projects)
  8. meson-python: A Meson project also using pybind11. (No VCS versioning)
  9. maturin: A PEP 621 builder for Rust binary extensions. (No VCS versioning) (Recommended for Rust projects)

Currently, the best choice is probably hatch for pure Python projects, and scikit-build (such as the scikit-build-core + pybind11 choice) for binary projects.

To use (modern copier version)

Install copier and copier-templates-extensions. Using pipx, that's:

pipx install copier
pipx inject copier copier-templates-extensions

Now, run copier to generate your project:

copier copy gh:scientific-python/cookie <pkg> --trust

(<pkg> is the path to put the new project. If copier is old, use --UNSAFE instead of --trust)

You will get a nicer CLI experience with answer validation. You will also get a .copier-answers.yml file, which will allow you to perform updates in the future.

Note: Add --vcs-ref=HEAD to get the latest version instead of the last tagged version; HEAD always passes tests (and is what cookiecutter uses).

To use (classic cookiecutter version)

Install cookiecutter, ideally with brew install cookiecutter if you use brew, otherwise with pipx install cookiecutter (or prepend pipx run to the command below, and skip installation). Then run:

cookiecutter gh:scientific-python/cookie

If you are using cookiecutter 2.2.3+, you will get nice descriptions for the options like copier!

To use (classic cruft version)

You can also use cruft, which adds the ability update to cookiecutter projects. Install with pipx install cruft (or prepend pipx run to the command below, and skip installation). Then run:

cruft create gh:scientific-python/cookie

Post generation

Check the key setup files, pyproject.toml, and possibly setup.cfg and setup.py (pybind11 example). Update README.md. Also update and add docs to docs/.

There are a few example dependencies and a minimum Python version of 3.9, feel free to change it to whatever you actually need/want. There is also a basic backports structure with a small typing example.

Contained components:

For developers:

You can test locally with nox:

# See all commands
nox -l

# Run a specific check
nox -s "lint(scikit-build)"

# Run a noxfile command on the project noxfile
nox -s "nox(hatch)" -- docs

If you don't have nox locally, you can use pipx, such as pipx run nox instead.

Other similar projects

Hypermodern-Python is another project worth checking out with many similarities, like great documentation for each feature and many of the same tools used. It has a slightly different set of features, and has a stronger focus on GitHub Actions - most our guide could be adapted to a different CI system fairly easily if you don't want to use GHA. It also forces the use of Poetry (instead of having a backend selection), and doesn't support compiled projects. It currently dumps all development dependencies into a shared environment, causing long solve times and high chance of conflicts. It also does not use pre-commit the way it was intended to be used. It also has quite a bit of custom code.

History

A lot of the guide, cookiecutter, and repo-review started out as part of Scikit-HEP. These projects were merged, generalized, and combined with the NSLS-II guide during the 2023 Scientific-Python Developers Summit.

sp-repo-review

sp-repo-review provides checks based on the [Scientific-Python Development Guide][] at scientific-python/cookie for repo-review.

This tool can check the style of a repository. Use like this:

pipx run 'sp-repo-review[cli]' <path to repository>

This will produce a list of results - green checkmarks mean this rule is followed, red x’s mean the rule is not. A yellow warning sign means that the check was skipped because a previous required check failed. Some checks will fail, that’s okay - the goal is bring all possible issues to your attention, not to force compliance with arbitrary checks. Eventually there might be a way to mark checks as ignored.

For example, GH101 expects all your action files to have a nice name: field. If you are happy with the file-based names you see in CI, you should feel free to simply ignore this check (just visually ignore it for the moment, a way to specify ignored checks will likely be added eventually).

All checks are mentioned at least in some way in the [Scientific-Python Development Guide][]. You should read that first - if you are not attempting to follow them, some of the checks might not work. For example, the guidelines specify pytest configuration be placed in pyproject.toml. If you place it somewhere else, then all the pytest checks will be skipped.

This was originally developed for Scikit-HEP before moving to Scientific Python.

Other ways to use

You can also use GitHub Actions:

- uses: scientific-python/cookie@<version>

Or pre-commit:

- repo: https://github.com/scientific-python/cookie
  rev: <version>
  hooks:
    - id: sp-repo-review

If you use additional_dependencies to add more plugins, like validate-pyproject, you should also include "repo-review[cli]" to ensure the CLI requirements are included.

List of checks

General

PyProject

Documentation

GitHub Actions

MyPy

Pre-commit

Ruff