editorialbot commented 1 year ago

Submitting author: !--author-handle-->@kdm9@marcosvital<!--end-editor-- Reviewers: @bricoletc, @gbouras13, @abhishektiwari Archive: 10.5281/zenodo.10795245

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/89901b387b0acb458c0efe6637fad366"><img src="https://joss.theoj.org/papers/89901b387b0acb458c0efe6637fad366/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/89901b387b0acb458c0efe6637fad366/status.svg)](https://joss.theoj.org/papers/89901b387b0acb458c0efe6637fad366)

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

@bricoletc & @gbouras13 & @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 @marcosvital 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 @bricoletc

📝 Checklist for @abhishektiwari

📝 Checklist for @gbouras13

marcosvital commented 8 months ago

@editorialbot check references

editorialbot commented 8 months ago

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

OK DOIs

- 10.1371/journal.pbio.1002311 is OK
- 10.1093/bioinformatics/bts480 is OK
- 10.1186/s13104-016-1900-2 is OK
- 10.1038/nmeth.3176 is OK
- 10.1186/s13059-016-0997-x is OK
- 10.1038/ncomms11257 is OK
- 10.1186/1756-0500-5-337 is OK
- 10.1093/bioinformatics/btr509 is OK
- 10.7717/peerj-cs.104 is OK
- 10.1371/journal.pcbi.1005727 is OK
- 10.1111/mec.15287 is OK
- 10.1101/2022.04.08.487684 is OK
- 10.1038/s41396-020-0665-8 is OK
- 10.1093/bioinformatics/btt468 is OK
- 10.1101/gr.210641.116 is OK
- 10.21105/joss.05627 is OK
- 10.1093/bioinformatics/btw354 is OK
- 10.1093/bioinformatics/bty191 is OK
- 10.1093/bioinformatics/btab705 is OK
- 10.1093/gigascience/giab008 is OK
- 10.1093/bioinformatics/btp352 is OK
- 10.5281/ZENODO.7728364 is OK
- 10.5281/ZENODO.4677629 is OK
- 10.1101/2021.08.07.455511 is OK
- 10.1186/s13059-019-1891-0 is OK
- 10.1093/bioinformatics/btx699 is OK
- 10.1093/bib/bbad375 is OK
- 10.1038/s41592-021-01101-x is OK

MISSING DOIs

- No DOI given, and none found for title: Aligning sequence reads, clone sequences and assem...

INVALID DOIs

- None

marcosvital commented 8 months ago

@kdm9 can you check the missing DOI for one reference?

kdm9 commented 8 months ago

Oops, fixed now thanks @marcosvital

kdm9 commented 8 months ago

@editorialbot generate pdf

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

kdm9 commented 8 months ago

@editorialbot generate pdf

kdm9 commented 8 months ago

@editorialbot check references

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:

editorialbot commented 8 months ago

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

OK DOIs

- 10.1101/2021.08.07.455511 is OK
- 10.21105/joss.05627 is OK
- 10.1038/nmeth.3176 is OK
- 10.1038/s41592-021-01101-x is OK
- 10.1093/gigascience/giab008 is OK
- 10.1093/bioinformatics/btw354 is OK
- 10.1101/2022.04.08.487684 is OK
- 10.1101/gr.210641.116 is OK
- 10.1093/bioinformatics/bts480 is OK
- 10.5281/ZENODO.4677629 is OK
- 10.1093/bioinformatics/btp352 is OK
- 10.1093/bioinformatics/btr509 is OK
- 10.48550/arXiv.1303.3997 is OK
- 10.1093/bioinformatics/bty191 is OK
- 10.1093/bioinformatics/btab705 is OK
- 10.1186/1756-0500-5-337 is OK
- 10.7717/peerj-cs.104 is OK
- 10.1038/ncomms11257 is OK
- 10.1371/journal.pbio.1002311 is OK
- 10.1371/journal.pcbi.1005727 is OK
- 10.1111/mec.15287 is OK
- 10.1186/s13059-016-0997-x is OK
- 10.1093/bioinformatics/btx699 is OK
- 10.1038/s41396-020-0665-8 is OK
- 10.1186/s13104-016-1900-2 is OK
- 10.1093/bioinformatics/btt468 is OK
- 10.1186/s13059-019-1891-0 is OK
- 10.5281/ZENODO.7728364 is OK
- 10.1093/bib/bbad375 is OK

MISSING DOIs

- None

INVALID DOIs

- None

kdm9 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:

marcosvital commented 8 months ago

Oops, fixed now thanks @marcosvital

Great! So let's go for our next (and probably final) steps.

marcosvital commented 8 months ago

@editorialbot recommend-accept

editorialbot commented 8 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 8 months ago

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

OK DOIs

- 10.1101/2021.08.07.455511 is OK
- 10.21105/joss.05627 is OK
- 10.1038/nmeth.3176 is OK
- 10.1038/s41592-021-01101-x is OK
- 10.1093/gigascience/giab008 is OK
- 10.1093/bioinformatics/btw354 is OK
- 10.1101/2022.04.08.487684 is OK
- 10.1101/gr.210641.116 is OK
- 10.1093/bioinformatics/bts480 is OK
- 10.5281/ZENODO.4677629 is OK
- 10.1093/bioinformatics/btp352 is OK
- 10.1093/bioinformatics/btr509 is OK
- 10.48550/arXiv.1303.3997 is OK
- 10.1093/bioinformatics/bty191 is OK
- 10.1093/bioinformatics/btab705 is OK
- 10.1186/1756-0500-5-337 is OK
- 10.7717/peerj-cs.104 is OK
- 10.1038/ncomms11257 is OK
- 10.1371/journal.pbio.1002311 is OK
- 10.1371/journal.pcbi.1005727 is OK
- 10.1111/mec.15287 is OK
- 10.1186/s13059-016-0997-x is OK
- 10.1093/bioinformatics/btx699 is OK
- 10.1038/s41396-020-0665-8 is OK
- 10.1186/s13104-016-1900-2 is OK
- 10.1093/bioinformatics/btt468 is OK
- 10.1186/s13059-019-1891-0 is OK
- 10.5281/ZENODO.7728364 is OK
- 10.1093/bib/bbad375 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 8 months 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/5127, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

kdm9 commented 8 months ago

@marcosvital, I've checked the final proof and it looks good to me. Many thanks to you all

Kevin-Mattheus-Moerman commented 8 months ago

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
[x] Recommend acceptance with @editorialbot recommend-accept

Kevin-Mattheus-Moerman commented 8 months ago

@marcosvital thanks for editing here. Just a comment, please run @editorialbot create post-review checklist in the future (sorry if you did and I missed it) and ensure all steps are checked/completed (for instance the archive title doesn't match the paper title at present, the license does not match the project license, and also the version tag listed here does not match the repository listed version tag). No worries though, I'll take it from here now.

Kevin-Mattheus-Moerman commented 8 months ago

@editorialbot set 1.0.0 as version

editorialbot commented 8 months ago

Done! version is now 1.0.0

Kevin-Mattheus-Moerman commented 8 months ago

@kdm9 as AEiC I will now help to process this work for acceptance in JOSS. I have checked this review, your repository, the paper, and the archive. Most seems in order, I only have the below point that needs your attention:

[x] Please edit the archive title to match the full paper title.
[x] Please edit the archive listed license to match your software license.

Kevin-Mattheus-Moerman commented 8 months ago

@kdm9 :wave: could you have a look at the above? Thanks

kdm9 commented 8 months ago

@Kevin-Mattheus-Moerman apologies, to confirm: I need to change the Zenodo DOI tarball name to the full paper title?

kdm9 commented 8 months ago

I've now done that, so if that wasn't what was needed please let me know what was :)

Kevin-Mattheus-Moerman commented 8 months ago

@kdm9 Not the zip/tarrball but the actual title and license listed for the archive. See the red highlighted bits in this screenshot: temp

Kevin-Mattheus-Moerman commented 8 months ago

@kdm9 okay, looks like you did it :smile: our messages crossed paths

kdm9 commented 8 months ago

brilliant, many thanks. Any remaining issues?

Kevin-Mattheus-Moerman commented 8 months ago

@kdm9 no, I think now it is all set. Thanks.

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: - email: kdmpapers@gmail.com family-names: Murray given-names: Kevin D. orcid: "https://orcid.org/0000-0002-2466-1917" - family-names: Borevitz given-names: Justin O. orcid: "https://orcid.org/0000-0001-8408-3699" - family-names: Weigel given-names: Detlef orcid: "https://orcid.org/0000-0002-2114-7963" - family-names: Warthmann given-names: Norman orcid: "https://orcid.org/0000-0002-1178-8409" contact: - email: kdmpapers@gmail.com family-names: Murray given-names: Kevin D. orcid: "https://orcid.org/0000-0002-2466-1917" - family-names: Warthmann given-names: Norman orcid: "https://orcid.org/0000-0002-1178-8409" doi: 10.5281/zenodo.10795245 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - email: kdmpapers@gmail.com family-names: Murray given-names: Kevin D. orcid: "https://orcid.org/0000-0002-2466-1917" - family-names: Borevitz given-names: Justin O. orcid: "https://orcid.org/0000-0001-8408-3699" - family-names: Weigel given-names: Detlef orcid: "https://orcid.org/0000-0002-2114-7963" - family-names: Warthmann given-names: Norman orcid: "https://orcid.org/0000-0002-1178-8409" date-published: 2024-03-25 doi: 10.21105/joss.06062 issn: 2475-9066 issue: 95 journal: Journal of Open Source Software publisher: name: Open Journals start: 6062 title: "Acanthophis: a comprehensive plant hologenomics pipeline" type: article url: "https://joss.theoj.org/papers/10.21105/joss.06062" volume: 9 title: "Acanthophis: a comprehensive plant hologenomics pipeline" ```

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 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/5169
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06062
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

kdm9 commented 8 months ago

brilliant, many thanks again to you all: @bricoletc @gbouras13 @abhishektiwari @marcosvital and @Kevin-Mattheus-Moerman

Kevin-Mattheus-Moerman commented 8 months ago

@kdm9 congratulations on this publication!

Thanks for editing @marcosvital, and a special thank you to the reviewers: @bricoletc, @gbouras13, @abhishektiwari !!

editorialbot commented 8 months ago

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

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.06062/status.svg)](https://doi.org/10.21105/joss.06062)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06062">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06062/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06062/status.svg
   :target: https://doi.org/10.21105/joss.06062

This is how it will look in your documentation:

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openjournals / joss-reviews

[REVIEW]: Acanthophis: a comprehensive plant hologenomics pipeline #6062

Status

Reviewer instructions & questions

Checklists

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance