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[REVIEW]: primerForge: a Python program for identifying primer pairs capable of distinguishing groups of genomes from each other #6850

Closed editorialbot closed 1 month ago

editorialbot commented 4 months ago

Submitting author: !--author-handle-->@dr-joe-wirth<!--end-author-handle-- (Joseph S. Wirth) Repository: https://github.com/dr-joe-wirth/primerForge/ Branch with paper.md (empty if default branch): Version: v1.3.5 Editor: !--editor-->@csoneson<!--end-editor-- Reviewers: @flashton2003, @mbhall88 Archive: 10.5281/zenodo.13759569

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Markdown: [![status](https://joss.theoj.org/papers/684c8541ebcea328d87fc0927ab17bbe/status.svg)](https://joss.theoj.org/papers/684c8541ebcea328d87fc0927ab17bbe)

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

@flashton2003 & @mbhall88, 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 @csoneson 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 @mbhall88

📝 Checklist for @flashton2003

csoneson commented 2 months ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance

dr-joe-wirth commented 1 month ago

@csoneson i have made changes to manuscript to address your comment.

@editorialbot generate pdf

dr-joe-wirth commented 1 month ago

@editorialbot generate pdf

editorialbot commented 1 month ago

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

csoneson commented 1 month ago

@dr-joe-wirth Thanks for this. The next steps now are outlined in the post above (https://github.com/openjournals/joss-reviews/issues/6850#issuecomment-2322781947).

dr-joe-wirth commented 1 month ago

@csoneson I have done these things.

csoneson commented 1 month ago

Thanks. A few comments:

dr-joe-wirth commented 1 month ago
  • It looks like the Zenodo archive was not generated from the GitHub release, could that be? The version in Zenodo is "v1" (not "v1.3.5"), and the files are not listed. Could you look into this (see here for instructions)?
  • Do you want to archive v1.3.5, or the current v1.3.6 (does the latter include changes resulting from the review)?

Hey @csoneson I think I misunderstood what needed to be archived. The archive I created is storing the .tar.gz file for the v1.3.5 release because that was the version used in the manuscript. I was looking at using the Zenodo integration, but it will not archive a repo until a release is created. I am preparing v1.3.7, but I was unsure what would be preferred and ultimately decided to archive the release in the paper instead of the repo itself. If you prefer, I can link the primerForge repo to Zenodo and then share a link once I create a new release.

  • The title of the Zenodo archive is not the same as that of the paper.

What should the name of the Zenodo archive be? I named it "primerForge v1.3.5" but should it match the title of the repo or the title of the manuscript?

  • The author list is almost identical, but middle initials are not indicated in the Zenodo archive.

I will fix this once I know how you prefer me to archive the software.

dr-joe-wirth commented 1 month ago

@csoneson would it be best if I reran the benchmarking using primerForge v1.3.7 and updated the manuscript with those values? That way I could archive the latest release and have it match the manuscript.

csoneson commented 1 month ago

@dr-joe-wirth Sorry for the delay. Are there major changes to version 1.3.7 compared to what was evaluated by the reviewers? I just want to make sure that the paper doesn't suddenly describe things that the reviewers didn't have the chance to comment on. I believe there are also ways of importing previous releases to Zenodo (although I have not tried them myself) - e.g. described in https://github.com/zenodo/zenodo/issues/1463.

csoneson commented 1 month ago

Regarding the name and author list of the Zenodo archive, they should be the same as those of the paper.

dr-joe-wirth commented 1 month ago

@csoneson

Regarding the name and author list of the Zenodo archive, they should be the same as those of the paper.

I will make sure to do this.

I believe there are also ways of importing previous releases to Zenodo (although I have not tried them myself) - e.g. described in https://github.com/zenodo/zenodo/issues/1463.

I will look into this so that the manuscript will not need to be changed. If this is not possible, then the only changes would be to Table 2 where the runtimes would change slightly.

Are there major changes to version v1.3.7 compared to what was evaluated by the reviewers? I just want to make sure that the paper doesn't suddenly describe things that the reviewers didn't have the chance to comment on.

Most of the changes since v1.3.5 are improvements to performance; the base functionality and workflow remains unchanged. The only new feature is the implementation of a sorting method; it does not change the results produced by primerForge but it does change the order that they are written in the output file. Here is a summary of the changes:

The full list of changes can be found here

dr-joe-wirth commented 1 month ago

@csoneson I believe that I have archived the repository the correct way this time. I used that hack to get Zenodo to archive v1.3.5. The doi is 10.5281/zenodo.13759569

csoneson commented 1 month ago

@editorialbot set 10.5281/zenodo.13759569 as archive

editorialbot commented 1 month ago

Done! archive is now 10.5281/zenodo.13759569

csoneson commented 1 month ago

@editorialbot set v1.3.5 as version

editorialbot commented 1 month ago

Done! version is now v1.3.5

csoneson commented 1 month ago

@dr-joe-wirth This looks great, thanks! I will now hand over to the topic AEiC for the last steps. Thanks for submitting to JOSS!

csoneson commented 1 month ago

@editorialbot recommend-accept

editorialbot commented 1 month ago 
Attempting dry run of processing paper acceptance...
editorialbot commented 1 month ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

✅ OK DOIs

- 10.12688/f1000research.6924.1 is OK
- 10.1093/nar/gks596 is OK
- 10.1093/bib/bbs038 is OK
- 10.1371/journal.pcbi.1010137 is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None
editorialbot commented 1 month ago

:wave: @openjournals/bcm-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/5881, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

Kevin-Mattheus-Moerman commented 1 month ago

@dr-joe-wirth as AEiC for JOSS I will now help to process this submission for acceptance in JOSS. I have checked this review, your repository, the archive link, and the paper. Everything seems to be in order, so I'll now proceed to accept this submission.

Kevin-Mattheus-Moerman commented 1 month ago

@editorialbot accept

editorialbot commented 1 month ago 
Doing it live! Attempting automated processing of paper acceptance...
editorialbot commented 1 month 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: Wirth given-names: Joseph S. orcid: "https://orcid.org/0000-0002-9750-2845" - family-names: Katz given-names: Lee S. orcid: "https://orcid.org/0000-0002-2533-9161" - family-names: Williams given-names: Grant M. orcid: "https://orcid.org/0000-0002-6033-485X" - family-names: Chen given-names: Jessica C. orcid: "https://orcid.org/0000-0002-9320-6774" doi: 10.5281/zenodo.13759569 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Wirth given-names: Joseph S. orcid: "https://orcid.org/0000-0002-9750-2845" - family-names: Katz given-names: Lee S. orcid: "https://orcid.org/0000-0002-2533-9161" - family-names: Williams given-names: Grant M. orcid: "https://orcid.org/0000-0002-6033-485X" - family-names: Chen given-names: Jessica C. orcid: "https://orcid.org/0000-0002-9320-6774" date-published: 2024-09-16 doi: 10.21105/joss.06850 issn: 2475-9066 issue: 101 journal: Journal of Open Source Software publisher: name: Open Journals start: 6850 title: "primerForge: a Python program for identifying primer pairs capable of distinguishing groups of genomes from each other" type: article url: "https://joss.theoj.org/papers/10.21105/joss.06850" volume: 9 title: "primerForge: a Python program for identifying primer pairs capable of distinguishing groups of genomes from each other" ```

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.

Find more information on .cff files here and here.

editorialbot commented 1 month ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot commented 1 month ago

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

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/5886
  2. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06850
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

Kevin-Mattheus-Moerman commented 1 month ago

@dr-joe-wirth congratulations on this JOSS publication!

Thanks for editing @csoneson !!

And a special thank you to the reviewers: @flashton2003, @mbhall88 !!!

editorialbot commented 1 month ago

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

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