[REVIEW]: shipgrav: A Python package for marine gravimetry #7358

editorialbot · 2024-10-15T21:05:14Z

Submitting author: @hfmark (Hannah Mark)
Repository: https://github.com/PFPE/shipgrav
Branch with paper.md (empty if default branch):
Version: v1.0.6
Editor: @rwegener2
Reviewers: @andreww, @malmans2
Archive: 10.5281/zenodo.14199589

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/672f14b918768cf09b3a994fc3fd18d3"><img src="https://joss.theoj.org/papers/672f14b918768cf09b3a994fc3fd18d3/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/672f14b918768cf09b3a994fc3fd18d3/status.svg)](https://joss.theoj.org/papers/672f14b918768cf09b3a994fc3fd18d3)

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

@andreww & @malmans2, 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 @rwegener2 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 @andreww

📝 Checklist for @malmans2

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

editorialbot · 2024-10-15T21:05:18Z

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 · 2024-10-15T21:05:32Z

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

✅ OK DOIs

- 10.1029/2020JB021109 is OK
- 10.1016/S0012-821X(97)00194-5 is OK
- 10.1111/j.1365-246X.1973.tb06513.x is OK
- 10.1029/JZ071i002p00465 is OK
- 10.1029/JZ071i002p00487 is OK
- 10.1190/1.1440369 is OK
- 10.1190/1.1442196 is OK
- 10.1029/RG005i004p00477 is OK
- 10.1029/JZ064i012p02351 is OK
- 10.1002/andp.19193641604 is OK
- 10.1126/science.1258213 is OK
- 10.1029/2019GC008711 is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

editorialbot · 2024-10-15T21:05:33Z

Software report:

github.com/AlDanial/cloc v 1.90  T=0.03 s (1051.1 files/s, 142166.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          19            704           1159           1963
YAML                             6             26             25            344
TeX                              1             13              0            175
Markdown                         2             22              0             64
Bourne Shell                     1              8             19             52
TOML                             2              5              0             51
DOS Batch                        1              8              1             26
reStructuredText                 1             12             10             17
HTML                             1              0              0             10
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            35            802           1221           2711
-------------------------------------------------------------------------------

Commit count by author:

    56	Hannah Mark

editorialbot · 2024-10-15T21:05:37Z

Paper file info:

📄 Wordcount for paper.md is 879

✅ The paper includes a Statement of need section

editorialbot · 2024-10-15T21:05:40Z

License info:

🟡 License found: GNU General Public License v3.0 (Check here for OSI approval)

editorialbot · 2024-10-15T21:06:32Z

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

rwegener2 · 2024-10-15T21:07:22Z

👋🏼 @hfmark, @andreww, @malmans2 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#REVIEW_NUMBER 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 (@rwegener2) if you have any questions/concerns.

andreww · 2024-10-25T08:27:01Z

Review checklist for @andreww

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/PFPE/shipgrav?
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 (@hfmark) 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?

andreww · 2024-10-25T14:40:17Z

I've now had a chance to look over and try out the code, and read the manuscript. The manuscript itself looks good and is easy to read. One minor thing is that the role of the contributors could be clarified (see PFPE/shipgrav#4).

I ran into problems running the tests (see PFPE/shipgrav#1, PFPE/shipgrav#2 and PFPE/shipgrav#3) and the examples (PFPE/shipgrav#6). I expect this could all be fixed by automating the tests (and covering different python versions) and making the documentation around setting up and running the examples a bit clearer / more reproducible.

Not in an issue, but it would be useful to add some guidelines for (new) contributors, and maybe look at the paper and think about giving more explicit information on the "state of the field" (there is some info in there around line 31 and 32, but are there any comparable packages for parts of the pipe line?)

hfmark · 2024-10-25T14:53:55Z

Thanks @andreww ! Most of the issues you've raised I know I can fix easily; the thing with the example scripts running looks like it's a problem with the r2r data download. curl used to work! But trying it again on my own computer, it's failing to download most of the files, hence the empty list of BGM filenames ☹️. I'll work on all of the above and update on the issues as I go.

As for comparable packages, I can think of two that are public that cover some bits of this workflow, though not the whole thing. Not that marine gravity specialists are especially secretive, but I do think we've been a bit behind the curve in terms of open source. Fair point about expanding on that in the paper, I'll work on that as well.

hfmark · 2024-10-26T01:40:47Z

@editorialbot generate pdf

editorialbot · 2024-10-26T01:42:15Z

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

hfmark · 2024-10-26T01:44:37Z

@editorialbot generate pdf

editorialbot · 2024-10-26T01:45:58Z

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

hfmark · 2024-10-26T01:46:49Z

ok, I think I got all the issues raised so far (and a few extras that popped up along the way)! I updated the proof above for the one slight change to the paper.

rwegener2 · 2024-10-27T11:45:47Z

Hi @malmans2! How is the review going? Your first step is to comment on this review with @editorialbot generate my checklist to generate your set of steps. If you have any questions please don't hesitate to reach out!

malmans2 · 2024-10-28T07:48:25Z

Review checklist for @malmans2

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/PFPE/shipgrav?
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 (@hfmark) 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?

rwegener2 · 2024-11-21T16:34:22Z

@editorialbot check references

editorialbot · 2024-11-21T16:34:37Z

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

✅ OK DOIs

- 10.1029/2020JB021109 is OK
- 10.1016/S0012-821X(97)00194-5 is OK
- 10.1111/j.1365-246X.1973.tb06513.x is OK
- 10.1029/JZ071i002p00465 is OK
- 10.1029/JZ071i002p00487 is OK
- 10.1190/1.1440369 is OK
- 10.1190/1.1442196 is OK
- 10.1029/RG005i004p00477 is OK
- 10.1029/JZ064i012p02351 is OK
- 10.1002/andp.19193641604 is OK
- 10.1126/science.1258213 is OK
- 10.1029/2019GC008711 is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

rwegener2 · 2024-11-21T16:49:42Z

Thanks again to everyone for their contributions! @hfmark at this point I'll ask you to please complete the steps in section 2 of this previous comment including final checks and creating an archive copy of the software. Once that is complete I'll complete my final steps (Section 3) and move the submission back to the Track Editor.

hfmark · 2024-11-21T18:39:37Z

Wonderful, thank you all! @rwegener2 I've released v1.0.6 and put it on zenodo (DOI: 10.5281/zenodo.14199589) with all the authors, orcids, etc confirmed. I think that's all the steps for me for now!

rwegener2 · 2024-11-21T21:07:20Z

@editorialbot set 10.5281/zenodo.14199589 as DOI

editorialbot · 2024-11-21T21:07:23Z

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

rwegener2 · 2024-11-21T21:07:53Z

@editorialbot set v1.0.6 as version

editorialbot · 2024-11-21T21:07:55Z

Done! version is now v1.0.6

rwegener2 · 2024-11-21T21:08:09Z

@editorialbot set 10.5281/zenodo.14199589 as archive

editorialbot · 2024-11-21T21:08:13Z

Done! archive is now 10.5281/zenodo.14199589

rwegener2 · 2024-11-21T21:08:26Z

@editorialbot generate pdf

editorialbot · 2024-11-21T21:09:50Z

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

rwegener2 · 2024-11-21T21:12:23Z

@editorialbot recommend-accept

editorialbot · 2024-11-21T21:12:26Z

Attempting dry run of processing paper acceptance...

editorialbot · 2024-11-21T21:12:42Z

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

✅ OK DOIs

- 10.1029/2020JB021109 is OK
- 10.1016/S0012-821X(97)00194-5 is OK
- 10.1111/j.1365-246X.1973.tb06513.x is OK
- 10.1029/JZ071i002p00465 is OK
- 10.1029/JZ071i002p00487 is OK
- 10.1190/1.1440369 is OK
- 10.1190/1.1442196 is OK
- 10.1029/RG005i004p00477 is OK
- 10.1029/JZ064i012p02351 is OK
- 10.1002/andp.19193641604 is OK
- 10.1126/science.1258213 is OK
- 10.1029/2019GC008711 is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

editorialbot · 2024-11-21T21:14:32Z

👋 @openjournals/ese-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#6170, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

kthyng · 2024-11-22T19:57:38Z

Hi! I'll take over now as Track Associate Editor in Chief to do some final submission editing checks. After these checks are complete, I will publish your submission!

Are checklists all checked off?
Check that version was updated and make sure the version from JOSS matches github and Zenodo.
Check that software archive exists, has been input to JOSS, and title and author list match JOSS paper (or purposefully do not).
Check paper.

kthyng · 2024-11-22T20:02:45Z

@editorialbot accept

editorialbot · 2024-11-22T20:02:48Z

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

editorialbot · 2024-11-22T20:10:23Z

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: Mark
  given-names: Hannah F.
  orcid: "https://orcid.org/0000-0002-1722-3759"
- family-names: Zhu
  given-names: Jasmine
- family-names: Tominaga
  given-names: Masako
  orcid: "https://orcid.org/0000-0002-1169-4146"
- family-names: Aliod
  given-names: Daniel
- family-names: Tivey
  given-names: Maurice
contact:
- family-names: Mark
  given-names: Hannah F.
  orcid: "https://orcid.org/0000-0002-1722-3759"
doi: 10.5281/zenodo.14199589
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Mark
    given-names: Hannah F.
    orcid: "https://orcid.org/0000-0002-1722-3759"
  - family-names: Zhu
    given-names: Jasmine
  - family-names: Tominaga
    given-names: Masako
    orcid: "https://orcid.org/0000-0002-1169-4146"
  - family-names: Aliod
    given-names: Daniel
  - family-names: Tivey
    given-names: Maurice
  date-published: 2024-11-22
  doi: 10.21105/joss.07358
  issn: 2475-9066
  issue: 103
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 7358
  title: "shipgrav: A Python package for marine gravimetry"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.07358"
  volume: 9
title: "shipgrav: A Python package for marine gravimetry"

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 · 2024-11-22T20:10:27Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2024-11-22T20:10:28Z

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

editorialbot · 2024-11-22T20:10:29Z

🚨🚨🚨 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.07358 joss-papers#6174
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.07358
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

kthyng · 2024-11-22T20:14:16Z

Congratulations on your new publication @hfmark! Many thanks to editor @rwegener2 and to reviewers @andreww and @malmans2 for your time, hard work, and expertise!! JOSS wouldn't be able to function nor succeed without your efforts.

Note we have a new tool for reviewers! You can go to https://joss.theoj.org/papers/reviewed_by/@your-github-username to see the JOSS submissions you have reviewed, and you can also copy a badge there with the number of your JOSS reviews.

@hfmark You can join JOSS as a reviewer by signing up at https://reviewers.joss.theoj.org/!

editorialbot · 2024-11-22T20:14:18Z

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

If you would like to include a link to your paper from your README use the following

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[![DOI](https://joss.theoj.org/papers/10.21105/joss.07358/status.svg)](https://doi.org/10.21105/joss.07358)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.07358">
  <img src="https://joss.theoj.org/papers/10.21105/joss.07358/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.07358/status.svg
   :target: https://doi.org/10.21105/joss.07358

This is how it will look in your documentation:

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editorialbot added Python review Shell TeX Track: 6 (ESE) Earth Sciences and Ecology labels Oct 15, 2024

editorialbot assigned rwegener2 Oct 15, 2024

editorialbot mentioned this issue Oct 15, 2024

[PRE REVIEW]: shipgrav: A Python package for marine gravimetry #7180

Closed

openjournals deleted a comment from editorialbot Nov 21, 2024

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Nov 21, 2024

editorialbot added accepted published Papers published in JOSS labels Nov 22, 2024

kthyng closed this as completed Nov 22, 2024

[REVIEW]: shipgrav: A Python package for marine gravimetry #7358

[REVIEW]: shipgrav: A Python package for marine gravimetry #7358

Comments

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Reviewer instructions & questions

Checklists

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Review checklist for @andreww

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

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Review checklist for @malmans2

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

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