[REVIEW]: biopixR: Extracting Insights from Biological Images

editorialbot commented 3 months ago

Submitting author: !--author-handle-->@Brauckhoff@fabian-s<!--end-editor-- Reviewers: @ColemanRHarris, @tijeco Archive: 10.5281/zenodo.13899162

Status

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Markdown: [![status](https://joss.theoj.org/papers/80bda20fb774fd758a14b5ff02aaed68/status.svg)](https://joss.theoj.org/papers/80bda20fb774fd758a14b5ff02aaed68)

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

@ColemanRHarris & @tijeco, 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 @fabian-s 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 @tijeco

📝 Checklist for @ColemanRHarris

Brauckhoff commented 1 month ago

@fabian-s We have made a tagged release of biopixR with version 1.2.0. The package has been successfully archived in Zenodo with the title and author list matching the information in the paper.

The DOI for the archived version is: 10.5281/zenodo.13899162 (https://doi.org/10.5281/zenodo.13899162)

fabian-s commented 1 month ago

@editorialbot set 10.5281/zenodo.13899162 as archive

editorialbot commented 1 month ago

Done! archive is now 10.5281/zenodo.13899162

fabian-s commented 1 month ago

@editorialbot set v1.2.0 as version

editorialbot commented 1 month ago

Done! version is now v1.2.0

fabian-s commented 1 month ago

@editorialbot recommend-accept

editorialbot commented 1 month ago

Attempting dry run of processing paper acceptance...

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/5975, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

editorialbot commented 1 month ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

✅ OK DOIs

- 10.21105/joss.06394 is OK
- 10.32614/CRAN.package.biopixR is OK
- 10.21037/jlpm.2019.04.05 is OK
- 10.1016/j.biosx.2024.100484 is OK
- 10.32614/rj-2011-002 is OK
- 10.32614/RJ-2012-018 is OK
- 10.32614/CRAN.package.countcolors is OK
- 10.21105/joss.01012 is OK
- 10.32614/CRAN.package.magick is OK
- 10.1201/9781138359444 is OK
- 10.1007/978-0-387-75936-4 is OK
- 10.1109/tsmc.1973.4309314 is OK
- 10.18637/jss.v021.i05 is OK
- 10.32614/CRAN.package.cluster is OK
- 10.1007/s00604-019-3449-y is OK
- 10.1080/17425247.2016.1192122 is OK
- 10.1007/s10544-018-0314-4 is OK
- 10.1007/s00604-014-1243-4 is OK
- 10.1038/76469 is OK
- 10.1007/s11356-020-08127-2 is OK
- 10.1038/s41598-019-41136-x is OK
- 10.1021/ac103277s is OK
- 10.3390/molecules201219766 is OK
- 10.1007/s00216-019-02199-x is OK
- 10.1007/10_2011_132 is OK
- 10.21037/jlpm.2018.11.01 is OK
- 10.21037/jlpm.2018.04.10 is OK
- 10.18637/jss.v049.i09 is OK
- 10.1198/106186007X178663 is OK
- 10.32614/RJ-2015-011 is OK
- 10.5281/ZENODO.12744222 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: R: A Language and Environment for Statistical Comp...
- No DOI given, and none found for title: Tcl/Tk Interface
- No DOI given, and none found for title: RStudio: Integrated Development Environment for R
- No DOI given, and none found for title: Advanced R
- No DOI given, and none found for title: ’Radiomic’ Image Processing Toolbox
- No DOI given, and none found for title: foodwebr: Visualise Function Dependencies

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

devSJR commented 1 month ago

I have checked the proof and think it is correct.

devSJR commented 1 month ago

@fabian-s is it our task to move forward with the command @editorialbot accept?

fabian-s commented 1 month ago

nah, @bcm-eics need to look this over and give their thumbs up

devSJR commented 1 month ago

Thanks for the rapid feedback.

Kevin-Mattheus-Moerman commented 1 month ago

@devSJR @Brauckhoff as AEiC for JOSS I will now help to process this submission for acceptance in JOSS. I will now process some final checks:

Checks on repository

[x] Project has OSI approved license
[x] Project features contributing guidelines

Checks on review issue

[x] Review completed
[x] Software license tag listed here matches a tagged release

Checks on archive

[x] Archive listed title and authors matches paper
[x] Archive listed license matches software license
[x] Archive listed version tag matches tagged release (and includes a potential v).

Checks on paper

[x] Checked paper formatting
[x] Check affiliations to make sure country acronyms are not used
[x] Checked reference rendering
[x] Checked if pre-print citations can be updated by published versions
[x] Checked for typos

Kevin-Mattheus-Moerman commented 1 month ago

@editorialbot set 1.2.0 as version

editorialbot commented 1 month ago

Done! version is now 1.2.0

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: Brauckhoff given-names: Tim orcid: "https://orcid.org/0009-0002-0142-7017" - family-names: Kieffer given-names: Coline - family-names: Rödiger given-names: Stefan orcid: "https://orcid.org/0000-0002-1441-6512" contact: - family-names: Rödiger given-names: Stefan orcid: "https://orcid.org/0000-0002-1441-6512" doi: 10.5281/zenodo.13899162 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Brauckhoff given-names: Tim orcid: "https://orcid.org/0009-0002-0142-7017" - family-names: Kieffer given-names: Coline - family-names: Rödiger given-names: Stefan orcid: "https://orcid.org/0000-0002-1441-6512" date-published: 2024-10-20 doi: 10.21105/joss.07074 issn: 2475-9066 issue: 102 journal: Journal of Open Source Software publisher: name: Open Journals start: 7074 title: "biopixR: Extracting Insights from Biological Images" type: article url: "https://joss.theoj.org/papers/10.21105/joss.07074" volume: 9 title: "`biopixR`: Extracting Insights from Biological Images" ```

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

🦋🦋🦋 👉 Bluesky post 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:

Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/6020
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.07074
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

Kevin-Mattheus-Moerman commented 1 month ago

@Brauckhoff congratulations on this JOSS publication.

Thanks for editing @fabian-s !!

And a special thank you to the reviewers: @ColemanRHarris, @tijeco !!!

editorialbot commented 1 month ago

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

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