ELIXIR Europe

ELIXIR is a distributed European infrastructure that helps life scientists find, analyse, and share data, software, standards, and expertise. This GitHub organisation supports work undertaken within the ELIXIR network, mainly Platforms, Communities, Projects, and other collaborative activities.

The recommendations below help keep ELIXIR repositories understandable, reusable, maintainable, and easy to hand over.

Choose a descriptive name and add a short repository description. Use GitHub topics to identify the relevant ELIXIR activity, subject area, and technology.

See GitHub’s guidance on repository READMEs. Please also consider:

• what the repository contains and why it exists;
• which ELIXIR Platform, Community, Project, Work Package, or other group is responsible for it;
• how to install, build, or use it;
• where users can ask questions or report problems; and
• whether it is active, in maintenance mode, or retained as a stable reference.

Repositories intended for reuse should contain a licence file such as LICENSE, LICENSE.md, or LICENSE.txt. A public repository without a licence can be viewed and forked on GitHub, but that does not give others general permission to reuse, modify, or redistribute its contents. Read more about this on GitHub: Licensing a repository and the guidance on how to Choose a License.

Every actively maintained repository should have at least one accountable administrator beyond the Hub’s default organisation administrators. Where possible:

• provide access through an appropriately scoped GitHub team;
• avoid single-person teams;
• review teams that have unnecessarily broad access; and
• use a CODEOWNERS file to identify the people or teams responsible for reviewing changes. CODEOWNERS helps route reviews, but it does not replace accountable repository administrators.

Repositories producing citable research software should include a CITATION.cff file and use versioned GitHub releases. Please see the guidance here Connecting a GitHub repository to Zenodo and here Archiving a GitHub release in Zenodo.

ELIXIR periodically reviews repositories that may no longer be maintained.

A repository may be proposed for archival when all three of these indicators apply:

1. it has no licence file;
2. it has had no commits to its main branch in the past two years, with discretion to extend this to three years; and
3. it has no repository-level administrators beyond the organisation’s default administrators.

Archiving does not delete a repository: it makes it read-only and can be reversed. As the archiving process is in principle lossless (see documentation), we will do not aim to circulate the candidate list. Should you need to take corrective actions, or revert the archiving, please contact one of the GitHub admins.

If you are unsure how to name, license, administer, publish, transfer, or archive a repository, contact the responsible ELIXIR group or the organisation’s GitHub administrators before making the change.