Workflow checklist

Overview

Teaching: 5 min
Exercises: 20 min
Duration: 0 min

How to use this checklist

Copy the checklist to a new document.
For each item, think about what it involves, and when you will do it.
Consider how you might remind yourself to do it, or persuade yourself to make time for it.
As you come up with your answers, write them in the space provided, or tick one of the existing suggestions.
- The suggestions are roughly in the order of recommended best practice.
When you’ve answered all the points in a section, tick it off.

I will find out who will be the rights holder for the software
- When I apply for funding
- At the beginning of the project
- When I put the code on a repository
- When I make the repository public
- When _____ gets back to me, and I’ll chase them if they haven’t by ______.
- ___________________________.
I will decide on what license to apply to the software
- When I’ve found out who the rights holder is
- When I make the repository public
- ___________________________.
I will review the license applied to the software
- When I add new dependencies
- ___________________________.

I will write instructions for using the code
- When I start to write code
- When I put my code on a repository
- ___________________________.
I will document the code using
- Recognised standard tools (e.g. Doxygen)
- Separate documents
- Inline comments
- ___________________________.
I will update the documentation
- As I make changes to the code
- At a set time each day/week/month/_____
- Before I publish a new version
- ___________________________.
I will publish the documentation
- Automatically using continuous integration
- Whenever I publish a new version of the software
- ___________________________.

I will make the code readable
- As I write it
- Once things are working like they should
- Before I publish a new version
- ___________________________.
I will organise my files
- Using a well-planned and clear directory structure
- ___________________________.

I will make sure my dependencies are listed
- Using a full environment management system (e.g. Docker, Apptainer)
- Using automated dependency management tools (e.g. conda, renv)
- By automatically documenting them when the code runs
- By including them in the documentation
- ___________________________.
I will review my dependency list
- Automatically using dependency management tools
- When I add or remove a dependency
- Before I publish a new version
- ___________________________.

I will test my software
- Using a testing framework (e.g. Cypress, pytest, testthat)
- By having a set of things I do every time
- ___________________________.
I will run my software tests
- Automatically using continuous integration
- Before I push to the repository
- Before I publish a new version
- ___________________________.

I will upload my code to
- A dedicated code repository (e.g. GitHub)
- A well-resourced repository (e.g. OSF, FigShare, Zenodo, university repositories)
- A personal website
- ___________________________.
I will make the code publicly accessible
- By enabling the approriate permissions in the repository
- By publishing specific versions
- ___________________________.

I will publish my code by
- Issuing releases on a code repository
- Ensuring the code repository is publicly accessible
- ___________________________.
I will do this
- Whenever milestones are reached
- Whenever I publish a related output (e.g. research paper)
- Automatically whenever I push to the repository
- ___________________________.

I will make my code citable by
- Publishing specific releases with a DOI (e.g. via Zenodo)
- Writing a technical/methods paper and submitting it to a journal
- Citing specific releases directly
- Citing the repository with a time/version stamp
- Citing the repository only
- ___________________________.
I will do this
- When I publish the code
- When I publish a related output
- ___________________________.