Chapter 2 Publish Your First Archive

Time required: 2-3 minutes

2.1 Step 1: Start from Zenodo

2.1.1 Prepare Your Repository

Make sure your code is ready:

  • ✅ All important files are committed and pushed
  • ✅ README.md explains what the code does
  • ✅ Any necessary documentation is included

2.2 Step 2: Create the GitHub Release

You should now be on GitHub’s “Draft a new release” page.

2.2.1 Fill in Release Details

Tag version: Use semantic versioning (e.g., v1.0.0):

  • v1.0.0 for first major release
  • v1.1.0 for feature updates
  • v1.0.1 for bug fixes

Release title: Descriptive name (e.g., “Initial analysis code release”)

Description (fully optional): Brief summary of what’s in this version

## Analysis code for [Your Project Name]

This release contains the complete analysis code for reproducing 
the results in [paper/project name].

### Contents
- Data processing scripts
- Statistical analysis code  
- Visualization functions
- Documentation and examples

2.2.2 Publish the Release

  1. Click “Publish release”
  2. GitHub creates the release
  3. Zenodo will automatically detect it! 🎉

2.3 Step 3: Get Your DOI from Zenodo

2.3.1 Go Back to Zenodo

Now that you’ve created the GitHub release:

  1. Go back to zenodo.org
  2. Navigate to “GitHub” → “Enabled Repositories”
  3. Reload the page - your repository should now show the new release!
  4. If needed, you can also click the “Sync now” button

2.3.2 Review and Publish

  1. Click on your draft repository
  2. Review the metadata (auto-filled from GitHub)
  3. Add any missing information:
    • Authors and affiliations
    • Keywords
    • Description
  4. Click “Publish”

2.3.3 Get Your DOI!

🎉 Success! Zenodo assigns a permanent DOI to your code.

2.4 Step 4: Use Your Citation

2.4.1 DOI Badge for GitHub

Zenodo provides a DOI badge for your README:

[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1234567.svg)](https://doi.org/10.5281/zenodo.1234567)

Add this to your repository’s README.md file.

2.4.2 Citation Format

Zenodo generates citations in multiple formats:

APA:

Smith, J. (2024). Analysis code for awesome research project (v1.0.0) 
[Computer software]. Zenodo. https://doi.org/10.5281/zenodo.1234567

BibTeX:

@software{smith2024analysis,
  author = {Smith, John},
  title = {Analysis code for awesome research project},
  version = {v1.0.0},
  year = {2024},
  publisher = {Zenodo},
  doi = {10.5281/zenodo.1234567}
}

2.5 Future Releases = Automatic Updates

The best part: Every future GitHub release automatically creates a new Zenodo version!

  1. Create new GitHub release → Zenodo automatically archives it
  2. Each gets its own version DOI
  3. Plus one “concept DOI” that always points to the latest version

2.6 Troubleshooting

Release not appearing in Zenodo?

  • Wait 5-10 minutes (can take time to sync)
  • Check if repository is still “enabled” in Zenodo
  • Verify the release is public on GitHub

Want to remove your submission from Zenodo?

  • Contact and request removal
  • Important: You have only a 30-day grace period after publication for deletion
  • Include your DOI and reason for removal in the email
  • After 30 days, deletion requests will be declined

Discovered a mistake after the 30-day grace period?

  • Create a new version of your record with the corrections
  • Set the old record’s visibility to “restricted”
  • Use the “Notes” field to explain the errors and recommend using the newer version
  • This way you can fix mistakes even when deletion is no longer possible

🎉 Congratulations!

Your code now has a permanent DOI and is properly archived for long-term access. You can cite it in papers, share it with confidence, and ensure it’s preserved beyond GitHub’s lifespan.

Your 5-minute investment just made your research more professional and citable!