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Project completion

Once you have completed your project in OpenSAFELY, there are a number of tasks to complete to align with our open working principles.

Please read and complete the tasks below.

Update all READMEs🔗

As of the 24th October 2022 we have changed how we managed repo READMEs. You can ignore this section if you created your repo after that date.

If you created your repo before this date then you will have the older README format, which expected you to update the file as your project progressed. We have now moved to keeping that information in your project on the Jobs site.

The current README template has the updated version for new repos.

To update your repository's README to match this new README:

  1. Copy the content from the template repository's latest README (typically just the first section).
  2. Manually edit those changed sections into your research repository's README.

  3. You will need to replace the placeholder string in the README's "View on OpenSAFELY" URL to point to your repository:

  4. ${GITHUB_REPOSITORY_NAME} is the name of your repo.

Warning

Each branch in your repository has a separate README, each of which will need updating.

Tidy up your repo🔗

You should ensure your repo is as tidy as possible once you have completed your project. Consider the following:

License🔗

  • Check the LICENSE file exists, and that it allows modification and distribution without cost. We recommend the MIT Licence (example).

Tests🔗

Try to ensure your automated tests (on the repo's Actions tab) are green. It's not essential, but it is a better look to be able to demonstrate your code is minimally runnable.

Contents🔗

Review your GitHub repository to make it simpler for people to explore:

  • Merge or close all open Pull Requests (unless they are ongoing work in progress).
  • Ensure that all branches are merged or deleted apart from the main or master branch. Old branches may contain draft work or previous ideas that are no longer needed. Note that deleting them does not delete the files permanently, they will still be in the repository history if you need to revisit them later. You may need to leave one or two branches open if they are ongoing work in progress (try to make sure they are named clearly).
  • Delete any files that were not used/experimental and not used in final analysis, e.g. old versions of study definitions. Again they will still be in the repository history if you need them later.
  • Are there old issues that can be closed? Some issues may have been fixed, or may be no longer relevant.

GitHub Release🔗

Consider making a GitHub Release, and linking to that (instructions here). A Release is a coherent snapshot of the code as it existed at a given point in time, along with a title and a description. By default, releases are displayed on your repo home page. For example, you might make separate releases of the code to accompany a preprint and the final versions of the paper.

Consider obtaining a DOI for your releases, and using that for referencing your code.

Update project status🔗

Update the status of the project on the Jobs site if relevant.

Update project workspaces🔗

Update the purposes of your project workspaces on the Jobs site.

Request the repo is made public🔗

If your repository is private, you can request it is made public via the jobs site. Click the "Change repo visibility" button on the workspace page of any workspace connected to it. You will be prompted to check various bits of metadata associated with the repository, its branches, connected workspaces, and the project. Once you have completed this page it will be checked by the OpenSAFELY team before being made public.

Info

You will be prompted to make it public sooner, if you first ran the code against an OpenSAFELY database more than 12 months ago.

Make your outputs on the jobs site public🔗

Consider making all outputs released to the project workspace on the jobs site "published". You can publish outputs from the "latest" release in the Released Outputs section of your workspace. When you click publish, all of the latest outputs will be made public. If you do not want to publish all of the latest outputs, you should discuss this with your co-pilot.

Add your publication to the OpenSAFELY website🔗

See here for instructions on how to do this.