[REVIEW]: IndividualDisplacements.jl: a Julia package to simulate and study particle displacements within the climate system

[whedon]

Submitting author: @gaelforget (Gael Forget)
Repository: https://github.com/JuliaClimate/IndividualDisplacements.jl
Version: v0.2.0
Editor: @kthyng
Reviewer: @milankl, @visr
Archive: 10.5281/zenodo.4678742

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Markdown: [![status](https://joss.theoj.org/papers/f61c861699db08f38b2512818a4862db/status.svg)](https://joss.theoj.org/papers/f61c861699db08f38b2512818a4862db)

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

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

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2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

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✨ 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 @milankl

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 (@gaelforget) 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 @visr

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 (@gaelforget) 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. @milankl, @visr 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]

PDF failed to compile for issue #2813 with the following error:

Can't find any papers to compile :-(

[kthyng]

@milankl, @visr this is where the actual review takes place. As you go through the checklist and the JOSS reviewer docs, open issues in the software repository, then link to this review issue for bookkeeping. That way, this issue stays relatively clean but has clear links out to all related review issues and they can be tracked independently in other issues. Let me know if you have any questions and otherwise I'll check in periodically.

[kthyng]

@whedon generate pdf from branch josspaper

[whedon]

Attempting PDF compilation from custom branch josspaper. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #2813 with the following error:

Can't find any papers to compile :-(

[kthyng]

@whedon generate pdf from branch josspaper

[whedon]

Attempting PDF compilation from custom branch josspaper. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #2813 with the following error:

Can't find any papers to compile :-(

[kthyng]

@whedon generate pdf from branch josspaper

[whedon]

Attempting PDF compilation from custom branch josspaper. Reticulating splines etc...

[whedon]

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

[whedon]

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

[whedon]

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

[milankl]

Hey Kristen @kthyng, the invitation expired. Could you send a new one?

[kthyng]

@whedon re-invite @milankl as reviewer

[whedon]

OK, the reviewer has been re-invited.

@milankl please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

[kthyng]

@milankl how about now?

[milankl]

Works fine. Thanks!

[whedon]

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

[kyleniemeyer]

Hi @gaelforget, looks like there were still some issues, or perhaps I made mistakes: JuliaClimate/Drifters.jl#72

[gaelforget]

@whedon generate pdf

[whedon]

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

[gaelforget]

@whedon generate pdf

[whedon]

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

[gaelforget]

Hi @gaelforget, looks like there were still some issues, or perhaps I made mistakes: JuliaClimate/IndividualDisplacements.jl#72

Just did a couple more tweaks. Although I feel unsure what the desired rendering really is in some cases, this looks good to me now.

[kyleniemeyer]

@whedon accept

@gaelforget ok, looks good to me.

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1038/s41561-019-0333-7 is OK
- 10.5281/zenodo.1211363 is OK
- 10.1175/2009JPO4043.1 is OK
- 10.7910/DVN/RNXA2A is OK
- 10.7910/DVN/NXYKDW is OK
- 10.5194/gmd-8-3071-2015 is OK
- 10.5281/zenodo.3967889 is OK
- 10.5281/zenodo.2653669 is OK
- 10.5281/zenodo.4193582 is OK
- 10.1029/2020GL089137 is OK
- 10.5194/gmd-12-4955-2019 is OK
- 10.1016/j.ocemod.2017.11.008 is OK
- 10.1029/2019GL085837 is OK
- 10.5281/zenodo.3995076 is OK
- 10.5281/zenodo.4517441 is OK
- 10.5194/gmd-2020-385 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#2263

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2263, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[kyleniemeyer]

@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.02813 joss-papers#2264
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.02813
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...

[kyleniemeyer]

Congrats @gaelforget on your article's publication in JOSS!

Many thanks to @milankl and @visr for reviewing this, and @kthyng for editing.

[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.02813/status.svg)](https://doi.org/10.21105/joss.02813)

HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.02813/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02813/status.svg
   :target: https://doi.org/10.21105/joss.02813

This is how it will look in your documentation:

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[gaelforget]

Congrats @gaelforget on your article's publication in JOSS!

Many thanks to @milankl and @visr for reviewing this, and @kthyng for editing.

Awesome news! Thank you @kyleniemeyer

Thank you @milankl and @visr -- your reviews definitely helped improve IndividualDisplacements.jl

Thank you also @kthyng and @kyleniemeyer for editing