Project scaffolding from templates

Starting from a maintained community template gives a research software project the whole quality baseline - packaging, tests, CI, linting, citation files, docs - in one step, encoded the way its community actually practices it. The skill here is threefold: pick the right generator, generate (or retrofit) honestly, and keep the project in sync as the template evolves.

Choosing a generator

• Copier: templates are versioned; copier update can replay template improvements into an already-generated project later. Prefer it when the template supports it - staying current is the hard part of template use, and Copier is built for it.
• cookiecutter: widest ecosystem of templates; generation is one-shot (no built-in update path), so treat the result as a starting point you own from day one.

Prefer a template maintained by a research software community over a generic one: it will encode citation files, FAIR practices and research-specific CI that generic templates omit.

The NLeSC python-template (reference implementation)

The Netherlands eScience Center's Copier template (https://github.com/NLeSC/python-template, Apache-2.0, actively maintained) is a strong default for research Python packages:

pipx install copier
copier copy https://github.com/nlesc/python-template.git path/to/project
copier update                    # later: pull template improvements

• Three profiles: Minimum (essentials), Recommended (curated defaults), or fully custom - match the profile to the software tier (analysis code -> Minimum; shared tools -> Recommended).
• It can also retrofit structure onto EXISTING code: run copier copy into the existing directory and reconcile.
• What it encodes (Recommended): src/ layout, setuptools + setuptools-scm build backend, pytest with branch coverage, tox matrix following the SPEC 0 version policy (three most recent Python minors), ruff as single linter/formatter/import-sorter, type checking (Pyright default, Mypy optional), pre-commit, EditorConfig, CITATION.cff plus a cffconvert CI check, Zenodo DOI instructions, Sphinx docs with Read the Docs, SonarCloud analysis, changelog, community files, and a next_steps.yml workflow that opens onboarding issues for the manual setup steps (Zenodo, SonarCloud, Read the Docs).
• Expect opinionated defaults (line length 79, SonarCloud rather than other coverage services); accept them unless the project has a reason not to - fighting a template forfeits copier update.

Choosing a build backend

When scaffolding by hand or answering template questions:

• setuptools + setuptools-scm: the template's default; version derived from git tags; battle-tested.
• hatchling: modern, minimal configuration; good default for new hand-rolled packages.
• poetry / PDM: bring their own dependency workflow; choose them only when the team wants that workflow, not just a build backend.

Whatever the choice, keep all tool configuration in pyproject.toml sections rather than scattered dotfiles where the tools support it.

After scaffolding

Generation is the start, not the finish:

• Work through the template's onboarding steps (the NLeSC template opens them as GitHub issues) instead of leaving badges broken.
• Delete generated options the project will not use rather than letting them rot; record the answers file (.copier-answers.yml) in git so copier update works.
• Route the per-practice follow-ups to the sibling skills: tests (rseng-testing), CI (rseng-ci-cd), docs (rseng-documentation), citation (rseng-citation-metadata), releases (rseng-publishing-releasing), FAIR posture (rseng-fair-software, rseng-fairguard).

Working with this skill

This skill is source-independent: its authority is the template and generator documentation linked below, not a bundled content source.

Learn more (verified):

• https://github.com/NLeSC/python-template - the template
• https://research-software-directory.org/software/nlesc-python-template - its Research Software Directory entry
• https://copier.readthedocs.io/en/stable/ - Copier documentation

Related skills

Check whether any of these applies before moving on:

• rseng-ci-cd - generated workflow files need understanding
• rseng-citation-metadata - template ships CITATION.cff and cffconvert check
• rseng-dependency-management - keeping generated tooling current
• rseng-fair-software - templates encode the FAIR baseline
• rseng-project-kickoff - management-side project start
• rseng-publishing-releasing - packaging and release setup follow-up