[REVIEW]: flowerMD: Flexible Library of Organic Workflows and Extensible Recipes for Molecular Dynamics

editorialbot commented 10 months ago

Submitting author: !--author-handle-->@marjanalbouye@lucydot<!--end-editor-- Reviewers: @LIVazquezS, @abhishektiwari Archive: 10.5281/zenodo.10215501

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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

@csadorf & @LIVazquezS & @abhishektiwari, 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 @lucydot 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 @abhishektiwari

📝 Checklist for @LIVazquezS

Kevin-Mattheus-Moerman commented 8 months ago

@editorialbot set 1.1.1 as version

editorialbot commented 8 months ago

Done! version is now 1.1.1

Kevin-Mattheus-Moerman commented 8 months ago

@marjanAlbouye as AEiC I will now help to process final steps. I have check the paper, this review, the archive link, and your repository. Most seems in order, however, I do have the below point that requires your attention.

On the paper:

[x] It looks like this should be added as the DOI for the below reference: 10.1371/journal.pcbi.1005659

Eastman, P., Swails, J., Chodera, J. D., McGibbon, R. T., Zhao, Y., Beauchamp, K. A., Wang,
L.-P., Simmonett, A. C., Harrigan, M. P., Stern, C. D., & others. (2017). OpenMM
7: Rapid development of high performance algorithms for molecular dynamics. PLoS
Computational Biology, 13(7), e1005659.

marjanalbooyeh commented 8 months ago

@editorialbot generate pdf

editorialbot commented 8 months ago

:warning: An error happened when generating the pdf.

marjanalbooyeh commented 8 months ago

@editorialbot generate pdf

editorialbot commented 8 months ago

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

marjanalbooyeh commented 8 months ago

@Kevin-Mattheus-Moerman Thanks for noticing the missing DOI. We fixed it, it should be good now.

Kevin-Mattheus-Moerman commented 8 months ago

@editorialbot accept

editorialbot commented 8 months ago

Doing it live! Attempting automated processing of paper acceptance...

editorialbot commented 8 months ago

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

``` cff-version: "1.2.0" authors: - family-names: Albooyeh given-names: Marjan orcid: "https://orcid.org/0009-0001-9565-3076" - family-names: Jones given-names: Chris orcid: "https://orcid.org/0000-0002-6196-5274" - family-names: Barrett given-names: Rainier orcid: "https://orcid.org/0000-0002-5728-9074" - family-names: Jankowski given-names: Eric orcid: "https://orcid.org/0000-0002-3267-1410" contact: - family-names: Jankowski given-names: Eric orcid: "https://orcid.org/0000-0002-3267-1410" doi: 10.5281/zenodo.10215501 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Albooyeh given-names: Marjan orcid: "https://orcid.org/0009-0001-9565-3076" - family-names: Jones given-names: Chris orcid: "https://orcid.org/0000-0002-6196-5274" - family-names: Barrett given-names: Rainier orcid: "https://orcid.org/0000-0002-5728-9074" - family-names: Jankowski given-names: Eric orcid: "https://orcid.org/0000-0002-3267-1410" date-published: 2023-12-15 doi: 10.21105/joss.05989 issn: 2475-9066 issue: 92 journal: Journal of Open Source Software publisher: name: Open Journals start: 5989 title: "FlowerMD: Flexible Library of Organic Workflows and Extensible Recipes for Molecular Dynamics" type: article url: "https://joss.theoj.org/papers/10.21105/joss.05989" volume: 8 title: "FlowerMD: Flexible Library of Organic Workflows and Extensible Recipes for Molecular Dynamics" ```

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

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editorialbot commented 8 months ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot commented 8 months ago

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/4844
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05989
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

marjanalbooyeh commented 8 months ago

On behalf of the authors of flowerMD, I would like to thank the reviewers and editors for all the helpful comments and suggestions. This was a great learning experience for us. Thank you!

Kevin-Mattheus-Moerman commented 8 months ago

@editorialbot remove @csadorf as reviewer

editorialbot commented 8 months ago

@csadorf removed from the reviewers list!

Kevin-Mattheus-Moerman commented 8 months ago

@editorialbot re-accept

editorialbot commented 8 months ago

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

Kevin-Mattheus-Moerman commented 8 months ago

@editorialbot reaccept

editorialbot commented 8 months ago

Rebuilding paper!

editorialbot commented 8 months ago

🌈 Paper updated!

New PDF and metadata files :point_right: https://github.com/openjournals/joss-papers/pull/4846

Kevin-Mattheus-Moerman commented 8 months ago

@marjanAlbouye congratulations on this JOSS publication! :christmas_tree: :gift:

Thanks for editing @lucydot! And a special thanks to the reviewers: @LIVazquezS, @abhishektiwari !

editorialbot commented 8 months ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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lucydot commented 8 months ago

@csadorf removed from the reviewers list!

@Kevin-Mattheus-Moerman, a quick note to say that @csadorf had to withdraw for personal reasons. They communicated this to me before the paper was in accepted for publication; I managed to drop the ball on it. Thanks for catching.

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