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

Cookie

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.
• Eleven different backends to choose from for building packages.
• Optional VCS versioning for most backends.
• 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. All checks cross-linked.
• Follows PyPA best practices and regularly updated.

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. whey: A modern PEP 621 builder with some automation options for Trove classifiers. Development seems to be stalled, possibly. (No VCS versioning)
5. 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.
6. setuptools621: The classic build system, but with the new standardized configuration.
7. setuptools: The classic build system. Most powerful, but high learning curve and lots of configuration required.
8. pybind11: This is setuptools but with an C++ extension written in pybind11 and wheels generated by cibuildwheel.
9. scikit-build: A scikit-build (CMake) project also using pybind11, using scikit-build-core. (Recommended for C++ projects)
10. meson-python: A Meson project also using pybind11. (No VCS versioning)
11. 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 3.8, 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
• GitHub actions deploy
  • C++ backends include cibuildwheel for wheel builds
  • Uses PyPI trusted publisher deployment
• Dependabot keeps actions up to date periodically, through useful pull requests
• Formatting handled by pre-commit
  • 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
• An pylint nox target can be used to run pylint, which integrated GHA annotations
• A ReadTheDocs-ready Sphinx docs folder and [docs] extra
• A test folder and pytest [test] extra
• A noxfile is included with a few common targets

Setuptools only:

• Setuptools controlled by setup.cfg and a nominal setup.py.
  • Using declarative syntax avoids needless boilerplate that is often wrong (like incorrectly handling the encoding when opening a README).
  • Easier to adapt to PEP 621 eventually.
  • Any actual logic can sit in setup.py and be clearly separate from simple metadata.
• Versioning handled by setuptools_scm
  • You can easily switch to manual versioning, but this avoids duplicating the version as git tags and in the source, and versions every commit uniquely, sidestepping some caching problems.
• MANIFEST.in checked with check-manifest
• setup.cfg checked by setup-cfg-fmt

For developers:

You can test locally with nox:

# See all commands
nox -l

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

# Run a noxfile command on the project noxfile
nox -s "nox(whey)" -- 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.

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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

• PY001: Has a pyproject.toml
• PY002: Has a README.(md|rst) file
• PY003: Has a LICENSE* file
• PY004: Has docs folder
• PY005: Has tests folder
• PY006: Has pre-commit config
• PY007: Supports an easy task runner (nox or tox)

PyProject

• PP002: Has a proper build-system table
• PP003: Does not list wheel as a build-dep
• PP301: Has pytest in pyproject
• PP302: Sets a minimum pytest to at least 6
• PP303: Sets the test paths
• PP304: Sets the log level in pytest
• PP305: Specifies xfail_strict
• PP306: Specifies strict config
• PP307: Specifies strict markers
• PP308: Specifies useful pytest summary
• PP309: Filter warnings specified

Documentation

• RTD100: Uses ReadTheDocs (pyproject config)
• RTD101: You have to set the RTD version number to 2
• RTD102: You have to set the RTD build image
• RTD103: You have to set the RTD python version

GitHub Actions

• GH100: Has GitHub Actions config
• GH101: Has nice names
• GH102: Auto-cancel on repeated PRs
• GH103: At least one workflow with manual dispatch trigger
• GH104: Use unique names for upload-artifact
• GH200: Maintained by Dependabot
• GH210: Maintains the GitHub action versions with Dependabot
• GH211: Do not pin core actions as major versions
• GH212: Require GHA update grouping

MyPy

• MY100: Uses MyPy (pyproject config)
• MY101: MyPy strict mode
• MY102: MyPy show_error_codes deprecated
• MY103: MyPy warn unreachable
• MY104: MyPy enables ignore-without-code
• MY105: MyPy enables redundant-expr
• MY106: MyPy enables truthy-bool

Pre-commit

• PC100: Has pre-commit-hooks
• PC110: Uses black or ruff-format
• PC111: Uses blacken-docs
• PC140: Uses mypy
• PC160: Uses codespell
• PC170: Uses PyGrep hooks (only needed if RST present)
• PC180: Uses prettier
• PC190: Uses Ruff
• PC191: Ruff show fixes if fixes enabled
• PC901: Custom pre-commit CI message

Ruff

• RF001: Has Ruff config
• RF002: Target version must be set
• RF003: src directory specified if used
• RF101: Bugbear must be selected
• RF102: isort must be selected
• RF103: pyupgrade must be selected
• RF201: Avoid using deprecated config settings
• RF202: Use (new) lint config section