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[REVIEW]: Eaglescope: an interactive visualization and cohort selection tool for biomedical data exploration. #6837

Closed editorialbot closed 1 week ago

editorialbot commented 5 months ago

Submitting author: !--author-handle-->@birm<!--end-author-handle-- (Ryan Birmingham) Repository: https://github.com/sharmalab/eaglescope Branch with paper.md (empty if default branch): Version: 1.1.1 Editor: !--editor-->@csoneson<!--end-editor-- Reviewers: @flekschas, @sebastian-raubach Archive: 10.5281/zenodo.14040758

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/229f0d11e01fb7316ef9da35d9e466ae"><img src="https://joss.theoj.org/papers/229f0d11e01fb7316ef9da35d9e466ae/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/229f0d11e01fb7316ef9da35d9e466ae/status.svg)](https://joss.theoj.org/papers/229f0d11e01fb7316ef9da35d9e466ae)

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

@flekschas & @sebastian-raubach, 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 @sebastian-raubach

📝 Checklist for @flekschas

csoneson commented 3 weeks ago

@editorialbot generate pdf

editorialbot commented 3 weeks ago

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

csoneson commented 3 weeks ago

@editorialbot check references

editorialbot commented 3 weeks ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

✅ OK DOIs

- 10.1126/scisignal.2004088 is OK
- 10.1109/VAHC.2017.8387496 is OK
- 10.1038/s41598-020-60981-9 is OK
- 10.1007/s10278-013-9622-7 is OK
- 10.1200/cci.20.00001 is OK
- 10.1093/jamia/ocy178 is OK
- 10.1111/aogs.13319 is OK
- 10.1055/s-0039-1687862 is OK
- 10.1177/1473871614526077 is OK
- 10.1007/978-1-4939-3578-9_5 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Bokeh: An Interactive Visualization Library for Mo...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None
csoneson commented 3 weeks ago

@editorialbot check repository

editorialbot commented 3 weeks ago

Software report:

github.com/AlDanial/cloc v 1.90  T=1.03 s (1745.7 files/s, 246024.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JavaScript                     115           7028          22506         133813
JSON                            17              3              0          26925
SVG                           1567              0             24          24921
CSS                             45           4894            551          21147
Sass                            19            519             34           4755
LESS                            18            504             55           4636
HTML                             8             69             53            673
Markdown                         6             85              0            488
CSV                              1              0              0            302
TeX                              1             10              0            117
YAML                             5             16              4             81
Dockerfile                       1              3              0             15
Bourne Shell                     1              0              0              3
-------------------------------------------------------------------------------
SUM:                          1804          13131          23227         217876
-------------------------------------------------------------------------------

Commit count by author:

   143  Ryan Birmingham
    72  Birm
    19  Yahia Zakaria
    17  Nan Li
     9  Jasox NaN
     7  Mohamed Nasser
     3  nanli-emory
     1  ArthurMor4is
     1  Pranav
     1  dependabot[bot]
editorialbot commented 3 weeks ago

Paper file info:

📄 Wordcount for paper.md is 767

✅ The paper includes a Statement of need section

editorialbot commented 3 weeks ago

License info:

✅ License found: BSD 3-Clause "New" or "Revised" License (Valid open source OSI approved license)

csoneson commented 3 weeks ago

👋🏻 @birm - I have gone through the submission and overall it looks good! Just a couple of comments regarding the paper:

Once this is fixed, you can create a new proof with @editorialbot generate pdf.

I will make another post below with the steps to take after that. Thanks!

csoneson commented 3 weeks ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance

birm commented 3 weeks ago

@editorialbot generate pdf

editorialbot commented 3 weeks ago

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

birm commented 3 weeks ago

I've put version 1.1 here: https://github.com/sharmalab/eaglescope/releases/tag/1.1 And archived here: https://zenodo.org/records/14032049

Also I've added Tony Pan's ORCID, so I'll regenerate the PDF once more:

birm commented 3 weeks ago

@editorialbot generate pdf

editorialbot commented 3 weeks ago

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

birm commented 3 weeks ago

And once more to fix the corresponding author:

birm commented 3 weeks ago

@editorialbot generate pdf

editorialbot commented 3 weeks ago

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

csoneson commented 3 weeks ago

Thank you @birm! For the Zenodo archive, could you link it directly to the GitHub repository (see here), so that all the files are visible in the archive as well (not just the compressed repo)? Also, please make sure that the title and author list of the archive agree with those of the paper. Thanks!

birm commented 3 weeks ago

Ok, it went and made a new DOI at https://zenodo.org/records/14040758

csoneson commented 3 weeks ago

@editorialbot set 10.5281/zenodo.14040758 as archive

editorialbot commented 3 weeks ago

Done! archive is now 10.5281/zenodo.14040758

csoneson commented 3 weeks ago

@editorialbot set 1.1.1 as version

editorialbot commented 3 weeks ago

Done! version is now 1.1.1

csoneson commented 3 weeks ago

Great, thanks @birm! Final detail: could you swap the order of the authors in the Zenodo archive to agree with the order in the paper? In the meanwhile I will pass the submission to the Associate EiC for the final steps.

csoneson commented 3 weeks ago

@editorialbot recommend-accept

editorialbot commented 3 weeks ago 
Attempting dry run of processing paper acceptance...
editorialbot commented 3 weeks ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

✅ OK DOIs

- 10.1126/scisignal.2004088 is OK
- 10.1109/VAHC.2017.8387496 is OK
- 10.1038/s41598-020-60981-9 is OK
- 10.1007/s10278-013-9622-7 is OK
- 10.1200/cci.20.00001 is OK
- 10.1093/jamia/ocy178 is OK
- 10.1111/aogs.13319 is OK
- 10.1055/s-0039-1687862 is OK
- 10.1177/1473871614526077 is OK
- 10.1007/978-1-4939-3578-9_5 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Bokeh: An Interactive Visualization Library for Mo...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None
editorialbot commented 3 weeks 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/6091, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

Kevin-Mattheus-Moerman commented 1 week ago

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

Checks on repository

Checks on review issue

Checks on archive

Checks on paper

Kevin-Mattheus-Moerman commented 1 week ago

@editorialbot accept

editorialbot commented 1 week ago 
Doing it live! Attempting automated processing of paper acceptance...
Kevin-Mattheus-Moerman commented 1 week ago

@birm one this I could not see is contributing guidelines. Can you point me to them or can you add them if missing? (see here for some examples: https://contributing.md/example/).

editorialbot commented 1 week 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: Birmingham given-names: Ryan orcid: "https://orcid.org/0000-0002-7943-6346" - family-names: Li given-names: Nan orcid: "https://orcid.org/0000-0002-3975-4809" - family-names: Pan given-names: Tony orcid: "https://orcid.org/0000-0001-7945-6534" - family-names: Zakaria given-names: Yahia orcid: "https://orcid.org/0009-0001-0705-4082" contact: - family-names: Birmingham given-names: Ryan orcid: "https://orcid.org/0000-0002-7943-6346" doi: 10.5281/zenodo.14040758 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Birmingham given-names: Ryan orcid: "https://orcid.org/0000-0002-7943-6346" - family-names: Li given-names: Nan orcid: "https://orcid.org/0000-0002-3975-4809" - family-names: Pan given-names: Tony orcid: "https://orcid.org/0000-0001-7945-6534" - family-names: Zakaria given-names: Yahia orcid: "https://orcid.org/0009-0001-0705-4082" date-published: 2024-11-15 doi: 10.21105/joss.06837 issn: 2475-9066 issue: 103 journal: Journal of Open Source Software publisher: name: Open Journals start: 6837 title: "Eaglescope: an interactive visualization and cohort selection tool for biomedical data exploration." type: article url: "https://joss.theoj.org/papers/10.21105/joss.06837" volume: 9 title: "Eaglescope: an interactive visualization and cohort selection tool for biomedical data exploration." ```

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 week ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot commented 1 week ago

🦋🦋🦋 👉 Bluesky post for this paper 👈 🦋🦋🦋

editorialbot commented 1 week 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/6144
  2. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06837
  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 week ago

@birm congratulations on this JOSS publication!

Thanks for editing @csoneson !

And a special thank you to the reviewers: @flekschas, @sebastian-raubach !!

editorialbot commented 1 week 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.06837/status.svg)](https://doi.org/10.21105/joss.06837) HTML: DOI badge reStructuredText: .. image:: https://joss.theoj.org/papers/10.21105/joss.06837/status.svg :target: https://doi.org/10.21105/joss.06837 ```

This is how it will look in your documentation:

DOI

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