scientific-python/cookie — Gitpedia

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?

Lives with the Scientific-Python Development Guide: Every decision is
clearly documented and every tool described, and everything is kept in sync.
Ten different backends to choose from for building packages.
Optional VCS versioning for most backends.
Selection for your preferred documentation engine (Sphinx, MkDocs, or
Zensical).
Template generation tested in GitHub Actions using nox.
Supports generation with copier, cookiecutter, and cruft.
Supports GitHub Actions if targeting a github.com url (the default), and
adds experimental GitLab CI support otherwise.
Includes several compiled backends using pybind11, with wheels produced
for all platforms using cibuildwheel.
Provides sp-repo-review to evaluate existing repos against the
guidelines, with a WebAssembly version integrated with the guide. Checks are
hyperlinked back to the guide.
Follows PyPA best practices and regularly updated. Recent additions:
- PEP 639: SPDX licenses
- PEP 735: Dependency groups
Uses uv for high performance CI and task running.

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:

hatch: This uses hatchling, a modern builder with nice file inclusion,
extendable via plugins, and good error messages. (Recommended for pure
Python projects)
uv: The uv_build backend is written in Rust and is integrated into'
uv, meaning it can build without downloading anything extra and can even
avoid running Python at all when building, making it the fastest backend for
simple packages. No dynamic metadata support.
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.
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.
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.
setuptools: The classic build system, but with the new standardized
configuration.
pybind11: This is setuptools but with an C++ extension written in
pybind11 and wheels generated by cibuildwheel.
scikit-build: A scikit-build (CMake) project also using pybind11, using
scikit-build-core. (Recommended for C++ projects)
meson-python: A Meson project also using pybind11. (No VCS versioning)
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 (copier version)

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

bash
uv tool install --with copier-templates-extensions copier

Now, run copier to generate your project:

bash
copier copy gh:scientific-python/cookie <pkg> --trust --vcs-ref=HEAD

(<pkg> is the path to put the new project. --vcs-ref=HEAD gets the current
version instead of the last tag, matching cookiecutter's behavior. Note you can
combine these two lines into one with uvx, just remember to pass --with
before the program name in that case.)

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 (cookiecutter version)

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

bash
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 (cruft version)

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

bash
cruft create https://github.com/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 3.10, 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

GitHub Actions runs testing for the generation itself
- Uses nox so cookie development can be checked locally
- Uses uv for high performance CI
GitHub actions deployment
- C++ backends include cibuildwheel for wheel builds
- Uses PyPI trusted publisher deployment
A GitHub release configuration that skips common bot commits when
auto-generating release notes
Dependabot keeps actions up to date periodically, through useful pull requests
A contributing guide
Formatting handled by pre-commit or prek
- No reason not to be strict on a new project; remove what you don't want.
- Includes MyPy - static typing
- Includes Ruff - standard formatting, linting and autofixes
  - Replaces Flake8, isort, pyupgrade, yesqa, pycln, and dozens of plugins
- Includes spell checking
One of several popular licenses
A pylint nox target can be used to run pylint, which integrated GHA
annotations
A ReadTheDocs-ready docs/ folder and docs dependency-group
A tests/ folder and pytest test dependency-group
A dev group for uv run integration
A noxfile is included with a few common targets
A README
Code coverage reporting with automatic uploads to Codecov after tests run

For developers

You can test locally with nox:

console
# 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 uv, such as uvx 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:

bash
uvx 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 (you can specify ignored checks in pyproject.toml or
by passing args to repo-review, see the repo-review
docs).

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.

Extras

cli: Dependencies to run the CLI (not needed for programmatic access, like
on Web Assembly)
pyproject: Include validate pyproject with schema store.
all: All extras

Helper utility

There's also a script, accessible as sp-ruff-checks, that will compare your
ruff checks to the known values. It's a little more elegant on the command line
than the Ruff family description, which will only print out a basic list.

Other ways to use

You can also use GitHub Actions:

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

Or pre-commit:

yaml
- 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