🧬 analysis_template

A cruft template for notebook-first single-cell and spatial analysis repos, managed with pixi. Humans work in notebooks; coding agents follow the analysis-workflow plugin, which every generated repo enables.

Building a reusable Python library? Use the scverse cookiecutter instead.

Create a project

uvx cruft create https://github.com/quadbio/analysis_template
cd my-analysis
git init -b main               # before pixi install: the package takes its version from git
pixi install
pixi run install-hooks
pixi run test
git add -A && git commit -m "Create from analysis_template"

You're prompted for the repository name, the package name (derived from it), a description, and your name and e-mail. Then push it, e.g. gh repo create <owner>/my-analysis --private --source . --push. The generated README.md takes it from there.

Update a project

uvx cruft check                # is this project behind the template?
uvx cruft update               # apply the template's changes since the last update

Resolve conflicts and any *.rej files by hand; pre-commit refuses to commit either. README.md, analysis/, data/, src/ and tests/ belong to the project once created, and updates leave them alone ([tool.cruft] skip in its pyproject.toml).

A repo created before this template used cruft starts receiving updates with uvx cruft link https://github.com/quadbio/analysis_template.

Develop the template

Everything a project gets lives under {{cookiecutter.project_name}}/; cookiecutter.json holds the prompts. uvx cookiecutter . --no-input -o <dir> renders your working tree (cruft create renders the last commit). CI creates a project on every pull request and runs its tests and pre-commit.

License

BSD 3-Clause.