Resources

General resources

• CodeRefinery lessons: https://coderefinery.github.io/

• Software Carpentry lessons: https://software-carpentry.org/lessons/

• The Turing Way: https://the-turing-way.netlify.app/

• FAIR software: https://fair-software.nl/

• TU Delft DCC Guides: https://tu-delft-dcc.github.io/

Resources per topics

FAIR research software

• Introducing the FAIR principles for research software

• https://fair-software.nl

• Publishing data and code at TU Delft

• Blog Anton Akhmerov (Applied Sciences)

Software Management Plans

• eScience Center - Practical Guide to Software Management Plans

• Software Sustainability Institute - Checklist for an SMP

Version control with git

• Code Refinery Git lesson

• Code Refinery lesson

• Pro Git book

• DCC Guides - Branch management

• The Turing Way - Version control for data

• Templates for .gitignore

Project planning and management

• GitHub boards

• Build Better Scientific Software - Better Planning blogs

• GitFlow original blog post by Vincent Driessen

• Gitflow process

Licenses

• TU Delft - Research Software Policy

• TU Delft - Guidelines on Research Software

• The Turing Way - Software Licenses

Reproducible environments

• Code Refinery lesson

• The Turing Way - Reproducible environments

Conda

• Conda cheat sheet

• Faster conda alternative: Mamba

• Pin exact versions with conda-lock

Matlab

• Find your Matlab dependencies

• Matlab Dependency Analyzer

Containers

• Introduction to Docker containers

• The Turing Way - containerized workflow

• Ditching Docker Hub: serve research software with GHCR + Zenodo

Documentation

• Code Refinery lesson - Documentation

• Quarto

• Myst parser

• CITATION.cff reference

Sphinx

• Theme gallery

• Jupyerbook

• Code Refinery lesson - Deploying documentation

Examples of contributing guidelines

• Contributing guide

• eScience Center - matchms

Code quality

• The Turing Way - code quality

• Code Refinery lesson on modular code

• EOSC documentation

• OpenSSF Best Practices Badge

• Utrecht University - Code quality

• Clean code by Uncle Bob

• SonarCloud - Getting started

• Repository Badges

Testing

• Code Refinery lesson - Testing

• The Turing Way - Testing

• Code Refinery - Automated testing

Reviewing code

• The Turing Way - Code reviewing process

• Example of a review process

Refactoring

• Best practices for refactoring code for Python

• What is refactoring?