Contributing

To start contributing to the codebase, request Anthony or Jesse to be added as a collaborator in the github repo.

What we should incorporate

  • Bug fixes

  • New features

  • Code improvements

What we shouldn’t incorporate

  • Experimental code

  • User specific configs (e.g my version of biosamples.tsv`)

  • Reference files not used in the generic version of the code

Process

  1. Start from the dev branch: git checkout dev

  2. Create a new branch: git checkout -b update_dev_docs

  3. Make the appropriate changes to the files you care about

    • Update the docs if applicable

    • Run/Add/Update tests. See Testing

    • If you made significant changes, do a full ABC run. Run CRISPRi benchmarking to ensure no regressions

  4. Git add, commit, and push your changes to Github (You may have to rebase on top of the latest changes to dev)

  5. Create a PR (Pull Request) to merge your branch into dev

  6. Add atancoder (Anthony) as a reviewer

  7. Merge PR after approval and all checks pass