[REVIEW]: DuneCopasi: A multi-compartment reaction-diffusion simulator for systems biology

[editorialbot]

Submitting author: !--author-handle-->@SoilRos<!--end-author-handle-- (Santiago Ospina De Los Ríos) Repository: https://gitlab.dune-project.org/copasi/dune-copasi Branch with paper.md (empty if default branch): master Version: v2.1.0 Editor: !--editor-->@prashjha<!--end-editor-- Reviewers: @ayush9pandey, @ajbaird Archive: 10.5281/zenodo.10855069

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Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@ayush9pandey & @ajbaird, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @prashjha know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @ayush9pandey

📝 Checklist for @ajbaird

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[prashjha]

Hi @SoilRos, article looks good! Please respond to my comments above to proceed.

[SoilRos]

@ayush9pandey thank you! Using the web CLI makes sense, it has almost everything as the other versions.

@prashjha I am preparing a release (v2.1.0) so that the paper can be associated with the latest version that incorporates the feedback from the reviewers. It should take me one day or two until all checks are done and binaries, containers, packages, docs, etc. are rolled out and are online. Then, I can archive the new version with zenodo and associate it in the paper asked. I hope that this timeline sounds fine. If not please let me know and I associate version 2.0.1 right away.

BTW: while making the release, our CI found a typo by the end of the last sentence of the first figure: "dervied biventricular geometry" -> "derivied from biventricular geometry". I already incorporated this in the latest commit of the joss/review branch.

[prashjha]

Hi @SoilRos, that sounds good to me. Ping me when this is done!

[SoilRos]

@editorialbot set v2.1.0 as version

[editorialbot]

I'm sorry @SoilRos, I'm afraid I can't do that. That's something only editors are allowed to do.

[SoilRos]

@editorialbot set master as branch

[editorialbot]

Done! branch is now master

[SoilRos]

Hi @prashjha, the release v2.1.0 and its derivatives are now ready. In particular, this includes the numerous documentation improvements made through this review (thank you @ajbaird & @ayush9pandey!). Could you please update the version number? Additionally, all the changes are now incorporated into the master and releases/2.1 branches of the repository (no changes made since last comment). Finally, the Zenodo archive is ready and available through its DOI, https://doi.org/10.5281/zenodo.14231120, and with a matching title and description as with the paper.

[prashjha]

@editorialbot set v2.1.0 as version

[editorialbot]

Done! version is now v2.1.0

[prashjha]

@editorialbot set 10.5281/zenodo.10855069 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.10855069

[prashjha]

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

• Double check authors and affiliations (including ORCIDs)
• Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
• Archive the release on Zenodo/figshare/etc and post the DOI here.
• Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
• Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

• [x] Read the text of the paper and offer comments/corrections (as either a list or a pull request)
• [x] Check that the archive title, author list, version tag, and the license are correct
• [x] Set archive DOI with @editorialbot set <DOI here> as archive
• [x] Set version with @editorialbot set <version here> as version
• [x] Double check rendering of paper with @editorialbot generate pdf
• [x] Specifically check the references with @editorialbot check references and ask author(s) to update as needed
• [ ] Recommend acceptance with @editorialbot recommend-accept

[prashjha]

@SoilRos, I see that the Zenodo archive and paper author lists are different. Have you and the authors discussed this and are all okay with it?