[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: v3.0.0 Editor: @kthyng Reviewers: @NoraLoose, @kris-rowe Archive: Pending

Status

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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 @kris-rowe

📝 Checklist for @NoraLoose

[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:

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

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[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]

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

[kris-rowe]

Review checklist for @kris-rowe

Conflict of interest

• [x] 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

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

General checks

• [x] 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?

[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

• [x] 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

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

General checks

• [x] Repository: Is the source code for this software available at the https://github.com/husseinaluie/FlowSieve?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] 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?
• [x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [ ] Functionality: Have the functional claims of the software been confirmed?
• [x] 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

• [x] 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).
• [x] 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?
• [x] 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

• [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [x] 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?
• [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] 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?

[danielskatz]

👋 @bastorer - note in particular that https://github.com/husseinaluie/FlowSieve/issues/5 is a showstopper here. The license you have chosen is

1. not a software license but a data license
2. not OSI-approved

JOSS cannot publish papers about software that does not have an OSI-approved license.

[danielskatz]

👋 @bastorer - Please let us know your status.

I'll also try to email you, but without you as the author responding to comments and issues, we can't make progress and may need to close this submission.

[bastorer]

Hi @danielskatz

Sorry about the slow response. I'll work through the issues Nora's created tomorrow, including the license (thanks for pointing that out!).

[danielskatz]

👋 @bastorer - any updates?

[danielskatz]

👋 @bastorer - we really do need to make progress on this

[kris-rowe]

@danielskatz Should I continue to work on my review for this, or should I wait for the license issue to be resolved?

[danielskatz]

It's hard to say, given the lack of response from @bastorer over the last 5 weeks - I would have liked a response saying that this wouldn't be a problem and could be changed, or that it is a problem and that the submission needs to be withdrawn. I now wonder if we will need to reject this submission if we don't hear back soon.

I'm sorry I can't be more clear.

[danielskatz]

👋 @bastorer - I plan to reject this submission in 2 weeks if I don't hear anything from you.

[bastorer]

Hi @danielskatz

I'm very sorry about the slow responses. It also looks like my in-line email responses didn't show up like I thought they would, but I was also very slow to respond.

I've submitted commits addressing the issues posted on the FlowSieve repository, including changing the license to one on the OSI-approved list.

[danielskatz]

@bastorer - thanks. Perhaps you can add some comments in the issues that you think are now resolved, and the creators of those issues can then potentially close them and continue their reviews

[danielskatz]

@NoraLoose & @kris-rowe - I hope we can now continue your reviews.

[danielskatz]

@NoraLoose & @kris-rowe - I've been on vacation the last 2 weeks and now want to check in with you again on this. Can you update me on any more you can do on your reviews?

[kris-rowe]

@danielskatz I need to get caught up on my review. Will push on this today/tomorrow now that the license issue has been resolved.