[REVIEW]: QUPS: A MATLAB Toolbox for Rapid Prototyping of Ultrasound Beamforming and Imaging Techniques

editorialbot commented 1 month ago

Submitting author: !--author-handle-->@thorstone25@adamltyson<!--end-editor-- Reviewers: @jonbmartin, @rafaelorozco Archive: Pending

Status

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Markdown: [![status](https://joss.theoj.org/papers/3dbb3657260a79d5850d074e5ba29325/status.svg)](https://joss.theoj.org/papers/3dbb3657260a79d5850d074e5ba29325)

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

@jonbmartin & @rafaelorozco, 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 @adamltyson 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 @rafaelorozco

editorialbot commented 1 month ago

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editorialbot commented 1 month ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.26 s (1003.7 files/s, 206236.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
XML                            158              0              0          21933
MATLAB                          74           2612           9574          12264
C/C++ Header                     2            138            105           1915
C                                3            209            268            997
CUDA                             6            181            255            806
OpenCL                           7            148            260            549
Markdown                         3             91              0            359
YAML                             3              4              4             74
TeX                              1              5              0             54
-------------------------------------------------------------------------------
SUM:                           257           3388          10466          38951
-------------------------------------------------------------------------------

Commit count by author:

   618  Thurston
   277  Thurston Brevett
   140  thorstone25
     5  Anthony Podkowa
     4  Walter Simson
     1  Saachi
     1  Your Name
     1  l-l-z
     1  thurston

editorialbot commented 1 month ago

Paper file info:

📄 Wordcount for paper.md is 1095

✅ The paper includes a Statement of need section

editorialbot commented 1 month ago

License info:

✅ License found: Apache License 2.0 (Valid open source OSI approved license)

editorialbot commented 1 month ago

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

OK DOIs

- 10.1117/1.3360308 is OK
- 10.1109/IUS52206.2021.9593605 is OK
- 10.1109/ULTSYM.2017.8092389 is OK
- 10.1145/3204919.3204927 is OK

MISSING DOIs

- No DOI given, and none found for title: FIELD: A program for simulating ultrasound systems

INVALID DOIs

- None

editorialbot commented 1 month ago

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

adamltyson commented 1 month ago

@jonbmartin, @rafaelorozco, this is the review thread for the paper. All of our communications will happen here from now on.

As a reviewer, the first step is to create a checklist for your review by entering:

@editorialbot generate my checklist

as the top of a new comment in this thread.

These checklists contain the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. The first comment in this thread also contains links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#6772 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within about 2-4 weeks. Please let me know if any of you require some more time. We can also use EditorialBot (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@adamltyson) if you have any questions/concerns.

adamltyson commented 4 weeks ago

Hi @jonbmartin, @rafaelorozco 👋. Just checking in to see how the review is going. Please let me know if I can help in any way!

rafaelorozco commented 3 weeks ago

Review checklist for @rafaelorozco

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/thorstone25/qups?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@thorstone25) 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
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] 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?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] 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)?
[x] 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, who the target audience is, and its relation to other work?
[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?

rafaelorozco commented 3 weeks ago

Hello, Everything looks great. I was able to install and run tests successfully as described in the repo.

I have only left Community guidelines unchecked since I couldnt find instructions on how to contribute to the software. After this addition, I highly recommend the publication of this manuscript to JOSS. Congratulations @thorstone25 on the work for this package

adamltyson commented 3 weeks ago

Thanks for the quick turnaround @rafaelorozco!

@thorstone25 could you add community guidelines to the repository so @rafaelorozco can tick off this section:

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

thorstone25 commented 3 weeks ago

Thank you @rafaelorozco ! I appreciate you taking the time to review it!

@adamltyson and @rafaelorozco, I just added a CONTRIBUTING.md file to the main branch of the repository. Is that sufficient?

adamltyson commented 2 weeks ago

Looks good to me. As long as the reviewers are happy, I'm happy!

rafaelorozco commented 2 weeks ago

Yes, looks good from my side!

adamltyson commented 1 week ago

Hi @jonbmartin, checking in again to see how the review is going. Let me know if you have any questions.

adamltyson commented 1 week ago

Hi @jonbmartin. Sorry to chase you, but do you have an idea of when you'll be able to complete this review? Let me know if you have any questions.

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