[REVIEW]: Tide Model Driver for MATLAB #6018

editorialbot · 2023-11-03T21:40:47Z

Submitting author: @chadagreene (Chad Greene)
Repository: https://github.com/chadagreene/Tide-Model-Driver
Branch with paper.md (empty if default branch):
Version: v3.0.0
Editor: @kthyng
Reviewers: @adamdanz, @lnferris
Archive: 10.5281/zenodo.10724881

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/228e6fd7edc42dc6d443ce60feef8c6d"><img src="https://joss.theoj.org/papers/228e6fd7edc42dc6d443ce60feef8c6d/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/228e6fd7edc42dc6d443ce60feef8c6d/status.svg)](https://joss.theoj.org/papers/228e6fd7edc42dc6d443ce60feef8c6d)

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

@adamdanz & @lnferris, 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 @adamdanz

📝 Checklist for @lnferris

The text was updated successfully, but these errors were encountered:

editorialbot · 2023-11-03T21:40:49Z

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

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editorialbot · 2023-11-03T21:40:53Z

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

OK DOIs

- 10.1175/JTECH-1687.1 is OK
- 10.1175/1520-0485(1980)010<1399:TROTCO>2.0.CO;2 is OK
- 10.1016/S0967-0637(98)00070-3 is OK
- 10.1029/2003GL019003 is OK
- 10.1002/2016RG000546 is OK
- 10.18739/A21Z41V08 is OK
- 10.1007/s001900000101 is OK
- 10.1002/2014RG000450 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2023-11-03T21:40:54Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.13 s (541.0 files/s, 119999.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
MATLAB                          38           1208           3058           3884
Markdown                        17            576              0           2268
HTML                            13            636           2294           1879
TeX                              1              9              0             81
XML                              2              7             13             34
YAML                             1              1              4             18
-------------------------------------------------------------------------------
SUM:                            72           2437           5369           8164
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2023-11-03T21:40:55Z

Wordcount for paper.md is 508

kthyng · 2023-11-03T21:41:30Z

Hi @adamdanz, @lnferris! Here is the review issue. Please check out the text above and let me know if you have any questions, now or as you go.

editorialbot · 2023-11-03T21:42:21Z

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

kthyng · 2023-11-20T17:43:27Z

@adamdanz and @lnferris Any questions for getting your review started?

adamdanz · 2023-11-20T23:36:45Z

Thanks for the bump, Kristen. I’ll get started on this this week and will let you know if I have any questions. Adam From: Kristen Thyng ***@***.***> Sent: Monday, November 20, 2023 12:44 PM To: openjournals/joss-reviews ***@***.***> Cc: Adam Danz ***@***.***>; Mention ***@***.***> Subject: Re: [openjournals/joss-reviews] [REVIEW]: Tide Model Driver for MATLAB (Issue #6018) @adamdanz<https://github.com/adamdanz> and @lnferris<https://github.com/lnferris> Any questions for getting your review started? — Reply to this email directly, view it on GitHub<#6018 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AE7ETLO4BFBFNHRCYRTHR4DYFOJETAVCNFSM6AAAAAA65AO74CVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQMJZGUZTANZQGQ>. You are receiving this because you were mentioned.Message ID: ***@***.******@***.***>>

adamdanz · 2023-12-10T21:26:56Z

Review checklist for @adamdanz

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/chadagreene/Tide-Model-Driver?
License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@chadagreene) 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
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.
Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
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

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, who the target audience is, and its relation to other work?
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?

adamdanz · 2023-12-10T22:36:01Z

I've completed this review. The paper summarizes the software well; the documentation is superb and the tests are sufficient to confirm consistent and expected results.

I wasn't able to find explicit guidelines for 3rd party contributions and issue reports within this submission but I checked this box as complete since the submission is in a public GitHub repo that is commonly used for these 3rd party interactions.

kthyng · 2023-12-11T21:19:02Z

@adamdanz Excellent! Thank you for your review.

@lnferris How are things on your end?

lnferris · 2023-12-13T19:31:36Z

I am back in office and looking at this! Thanks for the bump.

…

On Dec 11, 2023, at 4:19 PM, Kristen Thyng ***@***.***> wrote: @adamdanz <https://github.com/adamdanz> Excellent! Thank you for your review. @lnferris <https://github.com/lnferris> How are things on your end? — Reply to this email directly, view it on GitHub <#6018 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AF3ORTPDIA3BB7YWCTKNHWDYI52FDAVCNFSM6AAAAAA65AO74CVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNJQHEYDINJSGE>. You are receiving this because you were mentioned.

lnferris · 2023-12-14T17:04:24Z

Review checklist for @lnferris

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/chadagreene/Tide-Model-Driver?
License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
Contribution and authorship: Has the submitting author (@chadagreene) 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
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.
Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
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

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, who the target audience is, and its relation to other work?
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?

lnferris · 2024-02-24T15:34:37Z

I am having Github 2FA issues but the remaining boxes can be checked. I have no further comments.

…

On Feb 21, 2024, at 5:32 PM, Kristen Thyng ***@***.***> wrote: Ok @lnferris <https://github.com/lnferris> has 3 remaining checkboxes. I have ended up interceding on two of them and will note here that they have been accounted for with the updates in chadagreene/Tide-Model-Driver#19 <chadagreene/Tide-Model-Driver#19>. Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)? Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)? @lnferris <https://github.com/lnferris> Did you have any further comments or questions on Functionality: Have the functional claims of the software been confirmed? — Reply to this email directly, view it on GitHub <#6018 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AF3ORTKMSX7VQ5B5GD57GCTYUZYZTAVCNFSM6AAAAAA65AO74CVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNJYGE3DENRTGI>. You are receiving this because you were mentioned.

kthyng · 2024-02-27T22:59:15Z

ok great! let's move forward

kthyng · 2024-02-27T22:59:36Z

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Double check authors and affiliations (including ORCIDs)
Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
Archive the release on Zenodo/figshare/etc and post the DOI here.
Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

Read the text of the paper and offer comments/corrections (as either a list or a pull request)
Check that the archive title, author list, version tag, and the license are correct
Set archive DOI with @editorialbot set <DOI here> as archive
Set version with @editorialbot set <version here> as version
Double check rendering of paper with @editorialbot generate pdf
Specifically check the references with @editorialbot check references and ask author(s) to update as needed
Recommend acceptance with @editorialbot recommend-accept

kthyng · 2024-02-27T23:01:09Z

@chadagreene please go through the list above (you can make a checklist for yourself if that helps) and do each item. Let me know when you're done.

chadagreene · 2024-02-28T23:59:30Z

@kthyng Done. DOI: https://doi.org/10.5281/zenodo.10724881

kthyng · 2024-03-04T22:42:03Z

@editorialbot generate pdf

kthyng · 2024-03-04T22:43:08Z

@chadagreene do you want to keep v3.0.0 associated with this JOSS paper?

editorialbot · 2024-03-04T22:43:11Z

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

kthyng · 2024-03-04T22:43:41Z

I see it is v3.0.0 on github but v1 on Zenodo

kthyng · 2024-03-04T22:44:44Z

Also can you update the metadata on Zenodo to include all of the authors from your JOSS paper?

kthyng · 2024-03-04T22:47:28Z

@editorialbot check references

editorialbot · 2024-03-04T22:47:50Z

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

OK DOIs

- 10.1175/JTECH-1687.1 is OK
- 10.1016/0309-1708(89)90017-1 is OK
- 10.1175/1520-0485(1980)010<1399:TROTCO>2.0.CO;2 is OK
- 10.1016/S0967-0637(98)00070-3 is OK
- 10.1029/2003GL019003 is OK
- 10.1002/2016RG000546 is OK
- 10.18739/A21Z41V08 is OK
- 10.1007/s001900000101 is OK
- 10.1002/2014RG000450 is OK

MISSING DOIs

- None

INVALID DOIs

- None

chadagreene · 2024-03-08T21:40:41Z

@kthyng Thanks for catching these things. I've filled in the author list on Zenodo and made the version 3.0.0 consistent throughout.

kthyng · 2024-03-12T19:10:01Z

@editorialbot set 10.5281/zenodo.10724881 as archive

editorialbot · 2024-03-12T19:10:03Z

Done! archive is now 10.5281/zenodo.10724881

kthyng · 2024-03-12T19:10:47Z

@editorialbot set v3.0.0 as version

editorialbot · 2024-03-12T19:10:49Z

Done! version is now v3.0.0

kthyng · 2024-03-12T19:11:27Z

Ok everything is done now!

kthyng · 2024-03-12T19:11:34Z

@editorialbot accept

editorialbot · 2024-03-12T19:11:35Z

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

editorialbot · 2024-03-12T19:18:11Z

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: Greene
  given-names: Chad A.
  orcid: "https://orcid.org/0000-0001-6710-6297"
- family-names: Erofeeva
  given-names: Svetlana
  orcid: "https://orcid.org/0000-0002-4489-7505"
- family-names: Padman
  given-names: Laurie
  orcid: "https://orcid.org/0000-0003-2010-642X"
- family-names: Howard
  given-names: Susan L.
  orcid: "https://orcid.org/0000-0002-9183-0178"
- family-names: Sutterley
  given-names: Tyler
  orcid: "https://orcid.org/0000-0002-6964-1194"
- family-names: Egbert
  given-names: Gary
contact:
- family-names: Greene
  given-names: Chad A.
  orcid: "https://orcid.org/0000-0001-6710-6297"
doi: 10.5281/zenodo.10724881
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Greene
    given-names: Chad A.
    orcid: "https://orcid.org/0000-0001-6710-6297"
  - family-names: Erofeeva
    given-names: Svetlana
    orcid: "https://orcid.org/0000-0002-4489-7505"
  - family-names: Padman
    given-names: Laurie
    orcid: "https://orcid.org/0000-0003-2010-642X"
  - family-names: Howard
    given-names: Susan L.
    orcid: "https://orcid.org/0000-0002-9183-0178"
  - family-names: Sutterley
    given-names: Tyler
    orcid: "https://orcid.org/0000-0002-6964-1194"
  - family-names: Egbert
    given-names: Gary
  date-published: 2024-03-12
  doi: 10.21105/joss.06018
  issn: 2475-9066
  issue: 95
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6018
  title: Tide Model Driver for MATLAB
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06018"
  volume: 9
title: Tide Model Driver for MATLAB

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 · 2024-03-12T19:18:14Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2024-03-12T19:18:15Z

🚨🚨🚨 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 👉 Creating pull request for 10.21105.joss.06018 joss-papers#5122
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06018
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

kthyng · 2024-03-12T19:23:52Z

Congrats on your new publication @chadagreene! Many thanks to reviewers @adamdanz and @lnferris for your time, hard work, and expertise!!

editorialbot · 2024-03-12T19:23:54Z

🎉🎉🎉 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.06018/status.svg)](https://doi.org/10.21105/joss.06018)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06018">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06018/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06018/status.svg
   :target: https://doi.org/10.21105/joss.06018

This is how it will look in your documentation:

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kthyng · 2024-03-12T19:24:32Z

@chadagreene If you're interested in joining the reviewers database you can sign up here: https://reviewers.joss.theoj.org/

chadagreene · 2024-03-12T20:09:46Z

🎉Many thanks everyone for sharing your time and expertise!

editorialbot added Matlab review TeX Track: 6 (ESE) Earth Sciences and Ecology labels Nov 3, 2023

editorialbot assigned kthyng Nov 3, 2023

editorialbot mentioned this issue Nov 3, 2023

[PRE REVIEW]: Tide Model Driver for MATLAB #5770

Closed

editorialbot added accepted published Papers published in JOSS labels Mar 12, 2024

kthyng closed this as completed Mar 12, 2024

[REVIEW]: Tide Model Driver for MATLAB #6018

[REVIEW]: Tide Model Driver for MATLAB #6018

Comments

editorialbot commented Nov 3, 2023 • edited

Status

Reviewer instructions & questions

Checklists

editorialbot commented Nov 3, 2023

editorialbot commented Nov 3, 2023

editorialbot commented Nov 3, 2023

editorialbot commented Nov 3, 2023

kthyng commented Nov 3, 2023

editorialbot commented Nov 3, 2023

kthyng commented Nov 20, 2023

adamdanz commented Nov 20, 2023 via email

adamdanz commented Dec 10, 2023 • edited

Review checklist for @adamdanz

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

adamdanz commented Dec 10, 2023

kthyng commented Dec 11, 2023

lnferris commented Dec 13, 2023 via email

lnferris commented Dec 14, 2023 • edited by kthyng

Review checklist for @lnferris

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

lnferris commented Feb 24, 2024 via email

kthyng commented Feb 27, 2024

kthyng commented Feb 27, 2024 • edited

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance

kthyng commented Feb 27, 2024

chadagreene commented Feb 28, 2024

kthyng commented Mar 4, 2024

kthyng commented Mar 4, 2024

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kthyng commented Mar 4, 2024

kthyng commented Mar 4, 2024

kthyng commented Mar 4, 2024

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chadagreene commented Mar 8, 2024

kthyng commented Mar 12, 2024

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kthyng commented Mar 12, 2024

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kthyng commented Mar 12, 2024

kthyng commented Mar 12, 2024

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kthyng commented Mar 12, 2024

editorialbot commented Mar 12, 2024

kthyng commented Mar 12, 2024

chadagreene commented Mar 12, 2024

editorialbot commented Nov 3, 2023 •

edited

adamdanz commented Dec 10, 2023 •

edited

lnferris commented Dec 14, 2023 •

edited by kthyng

kthyng commented Feb 27, 2024 •

edited