6. After Acceptance

Lock your version permanently with two clicks

3 min read

Your paper has been accepted. Now it is time to permanently lock your code and data, publish your Zenodo record, and update your data availability statement.

This is the payoff for all the setup you did on Day 1.

The acceptance checklist

Step 1: Make all final changes

Incorporate all final reviewer and editor revisions:

Update analysis.qmd if any analysis changed
Update index.qmd for all text changes
Re-render analysis.qmd to update figures
Re-render index.qmd to generate the final manuscript PDF
Update your renv snapshot if you installed any new packages:

renv::snapshot()

Step 2: Final commit and push

In Positron Source Control:

Stage all changed files
Write a clear final commit message:

"final version — accepted by Aquatic Conservation July 2026"

Commit and Sync to GitHub

Step 3: Create a GitHub release

This is the trigger that tells Zenodo to archive your code.

Step 1

Go to your GitHub repository in your browser

Step 2

Click Releases (right sidebar) → Create a new release

Step 3

Set the tag to v1.0 and the title to something like: "Final accepted version — Aquatic Conservation"

Step 4

Click Publish release

Zenodo automatically detects this release, archives a permanent snapshot of your entire repository at that exact point, and assigns your reserved DOI to it.

Step 4: Publish your Zenodo record

Step 1

Go to zenodo.org and find your draft record

Step 2

Check and update the metadata if needed — title, authors, description

Step 3

Add the published paper DOI in the “Related identifiers” field once you have it

Step 4

Set license: CC BY 4.0 for data, MIT for code

Step 5

Click Publish — the record is now permanently locked and publicly available

Once published, a Zenodo record cannot be deleted

This is intentional — permanent archiving means permanent. You can upload a new version (which gets a new DOI), but the original record stays. Make sure your metadata is correct before clicking Publish.

Step 5: Update your data availability statement

Replace the “upon acceptance” note in your final manuscript:

Before:

Data and code are available on Zenodo at 
https://doi.org/10.5281/zenodo.1234567 
(will be made publicly available upon acceptance).

After:

Data and code supporting this study are available on 
Zenodo at https://doi.org/10.5281/zenodo.1234567 
and on GitHub at 
https://github.com/yourusername/koura-habitat-mesocosm.

The complete timeline

When	Action	Where
Day 1	Create project, init Git, push to GitHub	Positron
Day 1	Connect GitHub to Zenodo	Zenodo
Day 1	Set up renv	Positron terminal
Throughout	Commit and sync regularly	Positron
Submission	Reserve Zenodo DOI (draft)	Zenodo
Submission	Add DOI + GitHub link to manuscript	index.qmd
During review	Continue committing revisions	Positron
Acceptance	Final commit and push	Positron
Acceptance	Create GitHub release v1.0	GitHub website
Acceptance	Publish Zenodo record	Zenodo website
Acceptance	Update data availability statement	index.qmd
Published	Cite DOI in future work	Everywhere

What you have now

After following this workflow, you have:

A complete version history of every decision made during the research
A publicly accessible code repository that reviewers and readers can explore
A permanent, citable archive with a DOI that will work forever
A fully reproducible analysis — anyone can clone your repository, run renv::restore(), render analysis.qmd, and reproduce every figure and result
A manuscript that was produced directly from the same code, eliminating copy-paste errors

This guide itself follows this workflow

This guide was written in Quarto and version controlled on GitHub. A permanent Zenodo DOI will be added once it is archived. The source code is available at github.com/OlivierRaven/Open_Research_Workflow.

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