Lab software standards, software project templates

[jsstevenson]

This is highly aspirational, but I'd be interested in defining some common code and project standards where possible. All of this would be domain and/or language specific, but I'm thinking of stuff like (taking Python as an example)

• Linting/formatting (Black? Flake8? And any custom settings therein. Plus Isort, Darglint)
• Testing (We're more or less settled on Pytest, but what kind of coverage tools and settings? Use Tox for encapsulated testing? Run mypy checks as well?)
• Common pre-commit hooks for as much of the above as possible
• Build tool -- pyproject.toml?
• Environment management - stick with Pipenv or move to Poetry?
• CI driven checks on conventional commit messages? Auto generate release notes and versioning?

In particular, if we could identify consistent elements from the above that could structure a Cookie Cutter template, that might be useful for ensuring that new projects start on the right foot, and with minimal labor to tack on necessary boilerplate.

[jsstevenson]

Relevant: https://github.com/cancervariants/variation-normalization/issues/475

[korikuzma]

@jsstevenson You did it! https://github.com/GenomicMedLab/software-templates 🚀 . I'm going to close this issue