Joss submission

[lmoresi]

Reviewer / editor feedback for JOSS review from today:

(See openjournals/joss-reviews#7831 (comment) )

Updated paper, fixed bugs, checked doi's and orcid id

[Copilot]

Pull Request Overview

This PR addresses reviewer/editor feedback for a JOSS (Journal of Open Source Software) submission by updating the paper, fixing bugs, and verifying DOIs and ORCID IDs.

• Fixed bibliography references and DOI citations
• Updated acknowledgments section with additional funding sources
• Corrected formatting for C++ notation in the text

Reviewed Changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 1 comment.

File	Description
docs/joss-paper/paper.md	Updated bibliography citations, improved C++ formatting, and enhanced acknowledgments
docs/joss-paper/paper.crossref	Updated timestamp/batch ID and corrected DOI references
docs/joss-paper/paper.bib	Removed file path annotation and corrected DOI for Zienkiewicz reference

[lmoresi]

We'll need to do this:

• merge this branch into main
• bring any bug fixes from dev into main
• check the CI works correctly / tests passing etc (fix as required)
• check binder (main) launches, runs correctly (fix as required)
• make a test release to check Zenodo linking
• check zenodo authorship for this release matches JOSS authorship
• bump the version number (1.0 ?)
• signal JOSS that we are done

L

[lmoresi]

• updated zenodo author list to match JOSS paper
• checked zenodo linking is active
• do a test release to validate this, get the badge/doi, update the README

[lmoresi]

• Checked that the releases are working & automatically publishing to zenodo
• Updated doi / badge in the README

[lmoresi]

Just going to push this to main. Changes are entirely within the joss-paper directory.

(and the zenodo.json file)

[lmoresi]

Do not delete the joss-submission branch. We can also make this a tag / release but we should keep the branch for now.