The question of whether to create a separate anonymous GitHub account for conference submissions is one that many researchers face, and the answer is straightforward: yes, this is a common and practical approach. The real challenge is not whether to do it, but how to do it thoroughly. A quick rename of your repository or a new account with a fresh email address is not enough. Reviewers are trained to spot inconsistencies, and a single overlooked detail can compromise the entire anonymization process.
The practical steps are simple but require discipline. Create a new account with no identifying information, use a neutral username that does not hint at your identity, and ensure the email associated with it is not linked to your personal or institutional accounts. Then, carefully audit your code. This means checking for embedded author names in comments, hardcoded paths that reveal your local machine's username, and any metadata in files like Jupyter notebooks or PDFs that might contain your name or affiliation. Even the commit history matters. If you have been committing under your real name, that history will carry over to the anonymous repository. You can either squash the history into a single commit or use tools to rewrite it, but do not ignore it.
Once the paper is accepted, the transition back to your official account is straightforward. Move the repository, update the remote URLs, and ensure that any links in the paper point to the new location. The anonymous account can be deleted or left dormant. The key is to treat the anonymized version as a separate artifact, not a quick clone of your main work. This is not about hiding your identity; it is about giving reviewers the chance to evaluate your work on its merits, without the noise of your personal brand.
For those concerned about the effort, consider this: the cost of a mistake is high. A broken anonymization can lead to desk rejection, which wastes your time and the reviewers's. The process is not glamorous, but it is a professional necessity. Treat it as part of the submission workflow, like formatting the PDF or writing the abstract. The sooner you build this into your routine, the less stressful it becomes. And when you move the code to your official account after acceptance, you can do so with confidence, knowing that your work stands on its own.