Checklist

[pescini]

General checks

• Repository
  • Software code available on a public repository
• License
  • A plain-text LICENSE file with the contents of an OSI approved software license . Choices
• Installation
  • List of dependencies
  • Provide the software via a package manager
    • Conda via Bioconda
    • Language specific package manager: Pypi, Bioconductor, etc
  • Installation proceeding as outlined in the documentation

• Code structure

• Automated tests
  • Continuous integration with automated tests verifying the functionality of the software
• Versioning & DOI
  • Connect repository to archiving tool like Zenodo
  • Generate releases often

Documentation

• README.md
• Documentation together with the code: GitHub page, ReadTheDoc
• A statement of need: Section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is
• Installation instructions: Clearly-stated list of dependencies, installation guideline
• Example usage: Examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Documentation of the core functionality of the software documented to a satisfactory level (e.g., API method documentation)
• Performance
• Community guidelines: Clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support
  • Code of Conduct
  • CONTRIBUTING.md file
  • Roadmap
• API documentation inside the functions

Credits to Bérénice Batut @bebatut