[REVIEW]: autoStreamTree: Genomic variant data fitted to geospatial networks

editorialbot commented 9 months ago

Submitting author: !--author-handle-->@tkchafin@crvernon<!--end-editor-- Reviewers: @xin-huang, @abhishektiwari Archive: 10.5281/zenodo.10866066

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/233409855e9d2064941a4f68f6921d38"><img src="https://joss.theoj.org/papers/233409855e9d2064941a4f68f6921d38/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/233409855e9d2064941a4f68f6921d38/status.svg)](https://joss.theoj.org/papers/233409855e9d2064941a4f68f6921d38)

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

@xin-huang & @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 @crvernon 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 @xin-huang

📝 Checklist for @abhishektiwari

editorialbot commented 6 months ago

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

tkchafin commented 6 months ago

OK I think I've fixed everything that was noted in the paper.

crvernon commented 6 months ago

Thanks @tkchafin , you still need to remove the extra space in "...environmental/ spatial..." to simply make it read "...environmental/spatial..." per the following comment:

LINE 116: spacing should be consistent, either include or not, for "...environmental/ spatial..." before and after the "/"

tkchafin commented 6 months ago

Ok, fixed just now at L116 and throughout

tkchafin commented 6 months ago

@editorialbot generate pdf

editorialbot commented 6 months ago

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

crvernon commented 6 months ago

Alright @tkchafin , looking good! - we are almost there! Next is just setting up the archive for your new release.

We want to make sure the archival has the correct metadata that JOSS requires. This includes a title that matches the paper title and a correct author list.

So here is what we have left to do:

[x] Conduct a GitHub release of the current reviewed version of the software and archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
[x] Check the archival deposit (e.g., in Zenodo) to ensure it has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
[x] Please respond with the DOI of the archived version here

I can then move forward with accepting the submission.

tkchafin commented 6 months ago

Finished the Zenodo upload, here's the DOI: https://zenodo.org/doi/10.5281/zenodo.10866066

crvernon commented 5 months ago

@editorialbot set 10.5281/zenodo.10866066 as archive

editorialbot commented 5 months ago

Done! archive is now 10.5281/zenodo.10866066

crvernon commented 5 months ago

@editorialbot set v1.1.5 as version

editorialbot commented 5 months ago

Done! version is now v1.1.5

crvernon commented 5 months ago

@editorialbot check references

editorialbot commented 5 months ago

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

OK DOIs

- 10.1111/j.1461-0248.2006.01007.x is OK
- 10.1111/j.1558-5646.1967.tb03411.x is OK
- 10.1111/ddi.13160 is OK
- 10.1093/bioinformatics/btr330 is OK
- 10.1007/BF01386390 is OK
- 10.1093/bioinformatics/btn129 is OK
- 10.1139/F08-171 is OK
- 10.1038/s41597-019-0300-6 is OK
- 10.1111/ele.12084 is OK
- 10.1061/(ASCE)0733-9429(1990)116:7(946) is OK
- 10.1111/evo.12883 is OK
- 10.21105/joss.03021 is OK
- 10.2307/2408641 is OK

MISSING DOIs

- No DOI given, and none found for title: Package ‘adespatial’
- No DOI given, and none found for title: Exploring network structure, dynamics, and functio...
- No DOI given, and none found for title: Diversification across a dynamic landscape: Phylog...
- No DOI given, and none found for title: Scikit-learn: Machine learning in Python

INVALID DOIs

- None

crvernon commented 5 months ago

👋 - @tkchafin I am recommending that this submission be accepted for publication. An EiC will review shortly and if all goes well this will go live soon! Thanks to @xin-huang and @abhishektiwari for a timely and constructive review!

crvernon commented 5 months ago

@editorialbot recommend-accept

editorialbot commented 5 months ago

Attempting dry run of processing paper acceptance...

editorialbot commented 5 months ago

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

OK DOIs

- 10.1111/j.1461-0248.2006.01007.x is OK
- 10.1111/j.1558-5646.1967.tb03411.x is OK
- 10.1111/ddi.13160 is OK
- 10.1093/bioinformatics/btr330 is OK
- 10.1007/BF01386390 is OK
- 10.1093/bioinformatics/btn129 is OK
- 10.1139/F08-171 is OK
- 10.1038/s41597-019-0300-6 is OK
- 10.1111/ele.12084 is OK
- 10.1061/(ASCE)0733-9429(1990)116:7(946) is OK
- 10.1111/evo.12883 is OK
- 10.21105/joss.03021 is OK
- 10.2307/2408641 is OK

MISSING DOIs

- No DOI given, and none found for title: Package ‘adespatial’
- No DOI given, and none found for title: Exploring network structure, dynamics, and functio...
- No DOI given, and none found for title: Diversification across a dynamic landscape: Phylog...
- No DOI given, and none found for title: Scikit-learn: Machine learning in Python

INVALID DOIs

- None

editorialbot commented 5 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/5173, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

Kevin-Mattheus-Moerman commented 5 months ago

@editorialbot set 1.1.5 as version

editorialbot commented 5 months ago

Done! version is now 1.1.5

Kevin-Mattheus-Moerman commented 5 months ago

@tkchafin 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. Most seems in order, however the below are some points that require your attention:

[x] Please write out all countries in full in your affiliations, so write out United Kingdom and Unites States of America.
[x] Please edit the ZENODO archive listed license to match your software license.

Kevin-Mattheus-Moerman commented 5 months ago

@crvernon thanks for editing here. Just a tip, I recommend running @editorialbot create post-review checklist at the end of a review next time. It will help catch things like the archive license.

crvernon commented 5 months ago

Thanks for the feedback @Kevin-Mattheus-Moerman! I'll do so next time.

tkchafin commented 5 months ago

Both fixed!

Kevin-Mattheus-Moerman commented 5 months ago

@editorialbot generate pdf

editorialbot commented 5 months ago

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

Kevin-Mattheus-Moerman commented 5 months ago

@editorialbot accept

editorialbot commented 5 months ago

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

editorialbot commented 5 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: tyler.chafin@bioss.ac.uk family-names: Chafin given-names: Tyler K. orcid: "https://orcid.org/0000-0001-8687-5905" - family-names: Mussmann given-names: Steven M. orcid: "https://orcid.org/0000-0002-5237-5088" - family-names: Douglas given-names: Marlis R. orcid: "https://orcid.org/0000-0001-6234-3939" - family-names: Douglas given-names: Michael E. orcid: "https://orcid.org/0000-0001-9670-7825" contact: - email: tyler.chafin@bioss.ac.uk family-names: Chafin given-names: Tyler K. orcid: "https://orcid.org/0000-0001-8687-5905" doi: 10.5281/zenodo.10866066 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - email: tyler.chafin@bioss.ac.uk family-names: Chafin given-names: Tyler K. orcid: "https://orcid.org/0000-0001-8687-5905" - family-names: Mussmann given-names: Steven M. orcid: "https://orcid.org/0000-0002-5237-5088" - family-names: Douglas given-names: Marlis R. orcid: "https://orcid.org/0000-0001-6234-3939" - family-names: Douglas given-names: Michael E. orcid: "https://orcid.org/0000-0001-9670-7825" date-published: 2024-03-27 doi: 10.21105/joss.06160 issn: 2475-9066 issue: 95 journal: Journal of Open Source Software publisher: name: Open Journals start: 6160 title: "autoStreamTree: Genomic variant data fitted to geospatial networks" type: article url: "https://joss.theoj.org/papers/10.21105/joss.06160" volume: 9 title: "autoStreamTree: Genomic variant data fitted to geospatial networks" ```

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 5 months ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot commented 5 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/5183
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06160
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 5 months ago

@tkchafin Congratulations on this JOSS publication!

Thanks for editing @crvernon, and a special thank you to the reviewers: @xin-huang, @abhishektiwari !!!

editorialbot commented 5 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.06160/status.svg)](https://doi.org/10.21105/joss.06160)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06160">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06160/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06160/status.svg
   :target: https://doi.org/10.21105/joss.06160

This is how it will look in your documentation:

We need your help!

The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://reviewers.joss.theoj.org/join
Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss

openjournals / joss-reviews