[REVIEW]: FlowSieve: A Coarse-Graining Utility for Geophysical Flows on the Sphere

[editorialbot]

Submitting author: @bastorer (Benjamin Storer)
Repository: https://github.com/husseinaluie/FlowSieve
Branch with paper.md (empty if default branch):
Version: v3.3.0
Editor: @kthyng
Reviewers: @NoraLoose, @ashwinvis
Archive: 10.5281/zenodo.7818192

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/62a2bfe9452051063e099fa9eebbab77"><img src="https://joss.theoj.org/papers/62a2bfe9452051063e099fa9eebbab77/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/62a2bfe9452051063e099fa9eebbab77/status.svg)](https://joss.theoj.org/papers/62a2bfe9452051063e099fa9eebbab77)

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

@NoraLoose & @kris-rowe, 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 @kthyng 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 @NoraLoose

📝 Checklist for @ashwinvis

[editorialbot]

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf

[editorialbot]

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

OK DOIs

- 10.1175/JPO-D-17-0100.1 is OK
- 10.1007/s13137-019-0123-9 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=1.39 s (185.9 files/s, 291013.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C++                            174          39318          96505         204359
C/C++ Header                    23           9112          29337          20386
Python                          28            655            303           1680
Markdown                        17            409              0           1136
make                             6            106            103            230
Bourne Shell                     8             46             76            130
TeX                              1              3              0             25
YAML                             1              1              4             18
-------------------------------------------------------------------------------
SUM:                           258          49650         126328         227964
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 363

[kthyng]

@NoraLoose, @kris-rowe Here is the review issue! Please read through the instructions above for how to proceed with the review, and don't hesitate to reach out with any questions as they arise. Thank you!

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[kthyng]

/ooo April 15 until July 15

[kthyng]

@bastorer I am going to be on leave for a few months, but never fear — another editor will take over here.

[danielskatz]

While @kthyng is ooo (or ideally until we finish this review), I'll take over as editor.

It looks like everything is started:

• @NoraLoose needs to generate a checklist (with the command @editorialbot generate my checklist) and then get started
• @kris-rowe has already started their review

If you have any questions, please let me know!

[danielskatz]

@editorialbot assign me as editor

[editorialbot]

Assigned! @danielskatz is now the editor

[NoraLoose]

Review checklist for @NoraLoose

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/husseinaluie/FlowSieve?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@bastorer) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Does the paper have a section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[NoraLoose]

Hi @danielskatz, thanks for the ping - I have started the review. I will go on vacation for 2 weeks, but finishing up this review is my number 1 priority when I'm back (the week of May 2). Sorry for the delay and thanks for understanding!

[danielskatz]

👋 @kris-rowe - A couple of weeks in, I just wanted to check on how your review is coming.

[danielskatz]

@bastorer - have you been able to make any progress on any of the issues @NoraLoose created before her vacation?

[kris-rowe]

👋 @kris-rowe - A couple of weeks in, I just wanted to check on how your review is coming.

The last couple of weeks have been hectic, so this has slipped a bit. I will aim to get most of my review completed by the end of the week to keep the process moving along.

[danielskatz]

👋 @bastorer (repeating) - have you been able to make any progress on any of the issues @NoraLoose created before her vacation?

[kthyng]

@editorialbot set v3.3.0 as version

[editorialbot]

Done! version is now v3.3.0

[kthyng]

@editorialbot generate pdf

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[kthyng]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1038/s41467-022-33031-3 is OK
- 10.1175/JPO-D-17-0100.1 is OK
- 10.1007/s13137-019-0123-9 is OK
- 10.1029/2021MS002552 is OK
- 10.21105/joss.03947 is OK
- 10.1017/CBO9781139170666 is OK

MISSING DOIs

- 10.1126/sciadv.abq2566 may be a valid DOI for title: Direct observational evidence of an oceanic dual kinetic energy cascade and its seasonality

INVALID DOIs

- None

[bastorer]

@bastorer it's not required, but you might consider creating a release or tag for your software on Github to match your official version.

Good idea. I've added a release + tag pointing to the Zenodo version

[kthyng]

@editorialbot accept

[editorialbot]

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

[bastorer]

MISSING DOIs

• 10.1126/sciadv.abq2566 may be a valid DOI for title: Direct observational evidence of an oceanic dual kinetic energy cascade and its seasonality

I just updated this reference :-) I had the old arXiv reference.

[kthyng]

Oops, I didn't even look carefully at the results of my editorialbot command!!

[kthyng]

I can update after the acceptance finalizes if needed.

[editorialbot]

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: Storer
  given-names: Benjamin A.
  orcid: "https://orcid.org/0000-0001-5955-2158"
- family-names: Aluie
  given-names: Hussein
  orcid: "https://orcid.org/0000-0003-3516-3697"
contact:
- family-names: Aluie
  given-names: Hussein
  orcid: "https://orcid.org/0000-0003-3516-3697"
doi: 10.5281/zenodo.7818192
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Storer
    given-names: Benjamin A.
    orcid: "https://orcid.org/0000-0001-5955-2158"
  - family-names: Aluie
    given-names: Hussein
    orcid: "https://orcid.org/0000-0003-3516-3697"
  date-published: 2023-04-11
  doi: 10.21105/joss.04277
  issn: 2475-9066
  issue: 84
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 4277
  title: "FlowSieve: A Coarse-Graining Utility for Geophysical Flows on
    the Sphere"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.04277"
  volume: 8
title: "FlowSieve: A Coarse-Graining Utility for Geophysical Flows on
  the Sphere"

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]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[editorialbot]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

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

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.04277 joss-papers#4113
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04277
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[bastorer]

Oops, I didn't even look carefully at the results of my editorialbot command!!

Looks like timings worked out perfect, the paper at the DOI destination has the correct reference!

[kthyng]

Phew! Always better to not create extra work for myself :)

I'll write a final comment to close this issue once the DOI resolves in a few minutes!

[bastorer]

Fantastic, thank you very much for all of your help with this process :-)

[kthyng]

Congrats on your new publication @bastorer! Sorry for the extended time required for the review. Thank you to reviewers @NoraLoose and @ashwinvis for their hard work, time, and expertise!!

[editorialbot]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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.04277/status.svg)](https://doi.org/10.21105/joss.04277)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.04277">
  <img src="https://joss.theoj.org/papers/10.21105/joss.04277/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04277/status.svg
   :target: https://doi.org/10.21105/joss.04277

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
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[bastorer]

Hi @kthyng

Sorry to resurrect this issue, but my PI asked me to include some additional funding acknowledgements in the JOSS paper (similar to openjournals/joss#485). I've updated the paper.md file (relevant commit: husseinaluie/FlowSieve@00bcbe0).

Is it possible to update the JOSS version of the paper with the additional funding acknowledgements?

Thanks!
Ben

[kthyng]

@bastorer Yes! Check out the results after I run the command and let's see if it just works...

[kthyng]

@editorialbot reaccept

[editorialbot]

Rebuilding paper!

[editorialbot]

🌈 Paper updated!

New PDF and metadata files 👉 openjournals/joss-papers#4291

[bastorer]

Yes, that looks great, thanks!