[REVIEW]: ocean_data_tools: A MATLAB toolbox for interacting with bulk freely-available oceanographic data

[whedon]

Submitting author: @lnferris (L. N. Ferris)
Repository: https://github.com/lnferris/ocean_data_tools
Version: v1.0.1
Editor: @kthyng
Reviewers: @kakearney, @castelao
Archive: 10.5281/zenodo.4151538

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/83f5dd842625232afa133d9636cffcfd/status.svg)](https://joss.theoj.org/papers/83f5dd842625232afa133d9636cffcfd)

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

@castelao & @kakearney, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

1. Make sure you're logged in to your GitHub account
2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

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 ✨

Review checklist for @castelao

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 repository url?
• 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 (@lnferris) 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: Do the authors clearly state 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?

Review checklist for @kakearney

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 repository url?
• 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 (@lnferris) 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: Do the authors clearly state 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?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @castelao, @kakearney it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

2. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

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

@whedon commands

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

@whedon generate pdf

[whedon]

Reference check summary:

OK DOIs

- 10.11646/zootaxa.4802.1.5 is OK
- 10.1111/ddi.13079 is OK
- 10.5281/zenodo.3928714 is OK
- 10.1126/science.277.5334.1956 is OK
- 10.5670/oceanog.2016.66 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

👉 Check article proof 📄 👈

[kthyng]

@castelao, @chadagreene, here is where the review happens.

[kthyng]

@whedon remind @Reviewer in 2 weeks

[whedon]

@Reviewer doesn't seem to be a reviewer or author for this submission.

[kthyng]

heh, oops.

[kthyng]

@whedon remind @chadagreene in 2 weeks

[whedon]

Reminder set for @chadagreene in 2 weeks

[chadagreene]

Hmm, I officially accepted the invitation to review a couple hours ago, and now my email is getting flooded by emails with the subject line starting

Re: [openjournals/joss-reviews] [PRE REVIEW]:

and they are all unrelated to the review I accepted the invitation for. I have hit "unsubscribe" on about 10 of these emails so far, yet they keep rolling in. Anybody know how I can stop receiving these emails?

[danielskatz]

see the comments further up in this issue (or your issue, if it's a different one) - there are screenshots that show how to do this

[chadagreene]

Got it, thanks @danielskatz!

[lnferris]

@chadagreene I am implementing documentation using relative links between markdown files. E.g. https://github.com/lnferris/ocean_data_tools#building-uniform-structs-from-data-sources-1 links to https://github.com/lnferris/ocean_data_tools/blob/master/docs/argo_build.md

[kthyng]

@chadagreene please see the issues I started on your behalf above, and create similar issues for future comments. Then usually there is a short summary of a review actually in this review issue that refers to the open issues. There is a bit of bookkeeping with this setup.

@lnferris Can you copy and paste your comments that have been in response to these comments from @chadagreene into the relevant issue above? This way, it is clear what work has been done on a given issue, as well as it being clear when it is finished since the issue can be closed.

[whedon]

👋 @chadagreene, please update us on how your review is going.

[lnferris]

@kthyng Just to confirm I don't need to be doing anything on my end, correct?

[kthyng]

@lnferris Looks like you've addressed the comments that have come in, so just wait for more input from the reviewers once they get going.

Friendly ping to @chadagreene and @castelao about this review.

[kthyng]

Hi @lnferris I have heard from @chadagreene that he won't be able to review your submission, unfortunately. I will remove him as a reviewer and search for another reviewer.

In the meantime, a ping to @castelao to keep this on his radar!

[kthyng]

Hi @kakearney! @chadagreene suggested that you would be a good reviewer for this package. Are you interested in reviewing this for JOSS? The review process is of the software itself and a short paper, and since this is already the review issue on github, you can see the checklist-based approach above. You can also get more information here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html
I would hope for the review in the next 3-4 weeks if possible since this review time period has already started, but I can be flexible if needed.

[lnferris]

@kthyng it looks like @castelao isn't an assignee, are they supposed to be assigned?

[kthyng]

@lnferris He might not have accepted the invitation to review yet. I'll invite again just in case.

[kthyng]

Oops, it's just the one i "fixed" — the docs weren't working for me at the time so I guessed. Can you update your paper? It should be a ";" between the two parenthetical references instead of a comma.

[lnferris]

[lnferris]

Fixed I believe.

[kthyng]

@whedon generate pdf

[whedon]

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

[kthyng]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.11646/zootaxa.4802.1.5 is OK
- 10.1111/ddi.13079 is OK
- 10.5281/zenodo.4151538 is OK
- 10.1126/science.277.5334.1956 is OK
- 10.5670/oceanog.2016.66 is OK
- 10.1029/2019GC008392 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

Check final proof 👉 openjournals/joss-papers#1884

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1884, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[kthyng]

@openjournals/dev the XML title doesn't have underscores that should be present. How should we proceed? Thanks.

[arfon]

@openjournals/dev the XML title doesn't have underscores that should be present. How should we proceed? Thanks.

Let's proceed with the submission and I'll fix this after we've published.

[kthyng]

ok thanks @arfon

[kthyng]

@whedon accept deposit=true

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

🚨🚨🚨 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.02497 joss-papers#1886
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02497
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...

[kthyng]

Congrats on your publication @lnferris!! Many thanks to reviewers @kakearney and @castelao for sharing your time and expertise. We couldn't do this process without you!!

once the DOI resolves, I'll close this issue. And @arfon will be able to fix the XML file at this point.

[kthyng]

Ok DOI resolves but I guess the issue should stay open until we hear from @arfon.

[arfon]

Ok DOI resolves but I guess the issue should stay open until we hear from @arfon.

Should all be fixed up now.

[whedon]

🎉🎉🎉 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.02497/status.svg)](https://doi.org/10.21105/joss.02497)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02497">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02497/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02497/status.svg
   :target: https://doi.org/10.21105/joss.02497

This is how it will look in your documentation:

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[lnferris]

Thank you, @kthyng @kakearney @castelao @chadagreene for sharing your time and wisdom. This has been an awesome experience.