[REVIEW]: pybeach: A Python package for extracting the location of dune toes on beach profile transects

[whedon]

Submitting author: @TomasBeuzen (Tomas Beuzen)
Repository: https://github.com/TomasBeuzen/pybeach
Version: v0.1.1
Editor: @kbarnhart
Reviewer: @csherwood-usgs, @edlazarus, @ncohn
Archive: 10.5281/zenodo.3579501

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/8b211e45c6919ea8057946484e757c28/status.svg)](https://joss.theoj.org/papers/8b211e45c6919ea8057946484e757c28)

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

@csherwood-usgs & @edlazarus & @ncohn, 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 @kbarnhart know.

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @csherwood-usgs

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 (@TomasBeuzen) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 @edlazarus

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 (@TomasBeuzen) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 @ncohn

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 (@TomasBeuzen) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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. @csherwood-usgs, @edlazarus, @ncohn it looks like you're currently assigned to review this paper 🎉.

⭐ 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]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[kbarnhart]

/ooo November 24 until November 28

[ooo]

👍 Marked @kbarnhart as OOO from Sunday, November 24th 2019 to Thursday, November 28th 2019. 📆

[csherwood-usgs]

Dear Bot and Katy, Thanks for the opportunity to review this useful contribution. I have submitted some issues to the repo and checked all of the boxes on the review, but there is no indication that my part of the process is complete, so I am sending this email into the void to let you know. Regards, Chris

…

On Sun, Nov 24, 2019 at 8:02 PM whedon ***@***.***> wrote: Assigned #1890 <#1890> to @csherwood-usgs <https://github.com/csherwood-usgs>. — You are receiving this because you were assigned. Reply to this email directly, view it on GitHub <#1890?email_source=notifications&email_token=AAMLIMZZAWLZJ2HPLTBRQ73QVMPXVA5CNFSM4JNB4S5KYY3PNVWWK3TUL52HS4DFWZEXG43VMVCXMZLOORHG65DJMZUWGYLUNFXW5KTDN5WW2ZLOORPWSZGOVB3UUTI#event-2826390093>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAMLIM3X36PAZDDKP4LLXGDQVMPXVANCNFSM4JNB4S5A> .

-- *Christopher R. Sherwood* csherwood@usgs.gov U.S. Geological Survey 384 Woods Hole Road Woods Hole MA 02543 774 269 9399 (cell) 508 457 2269 (office) 508 457 2310 (fax)

[kbarnhart]

@csherwood-usgs thanks for making your review as issues in the main repo. I've linked them here (just by including a hyperlink). This helps create the record of what issues and/or changes in the main repo were made as part of this review.

@ncohn @edlazarus let me know if you have any questions as you proceed with your reviews. If you make any issues in the main repo, just link them with this issue using a markdown hyperlink

[display this](url_goes_here)

Once you've all finished your reviews and @TomasBeuzen has finished addressing them, I'll ask each of you to affirm your recommendation to accept the package for publication in JOSS.

I'll be OOO Dec 1st-4th with no internet (GMT+12).

[kbarnhart]

/ooo December 1 until December 4

[ooo]

👍 Marked @kbarnhart as OOO from Sunday, December 1st 2019 to Wednesday, December 4th 2019. 📆

[edlazarus]

My checklist is checked – the write-up is very clean & clear – I think this is a great py-tool contribution.

[ncohn]

Echoing much of what Chris and Eli have said - this is a nice contribution that is likely to benefit many in the coastal process field. I personally expect to use this for my work since having a rapid approach for characterizing the dune toe via multiple approaches is incredibly useful.

As part of this review, I tested against profiles from the U.S. Pacific Northwest (PNW) which the commonly used maximum curvature approach rarely does a good job of for estimating a realistic dune toe position. Unsurprisingly, the relative relief and maximum curvature approaches coded into “pybeach” often give drastically different estimates for the dune toe for PNW dunes – just as you would expect from those methods. I was quite impressed with the new ML approach that was included, which generally matched the “eye estimated” dune toe well. I did not do an extensive assessment of the tool for all types of dune morphologies, but on my first assessment I am quite impressed. Nice job Tom!

Overall, the python code is well written and is easy to use for a relatively novice python user. The JOSS paper is also well written, concise, and gives an appropriate overview of the tool. Chris noted some dependency issues that I also ran into on my first attempt with the tool, but seem to have been fixed with updates to the repo. As I continue to use the code I will add issues on the git-hub repo, but at this stage I don’t see any need major issues that require attention before publication.

[kbarnhart]

Thanks to @csherwood-usgs @ncohn @edlazarus for your reviews.

@TomasBeuzen, please ping me here when you've finished addressing reviewer comments.

[kbarnhart]

@edlazarus can you assess the license file and either check that box or request a change?

[edlazarus]

@edlazarus can you assess the license file and either check that box or request a change?

Done! Dunno how I missed that box. Apologies!

[TomasBeuzen]

@kbarnhart - I believe I've addressed all reviewer comments.

@csherwood-usgs @ncohn @edlazarus - thank you so much for your time and effort in reviewing pybeach, it's very much appreciated!

[kbarnhart]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[kbarnhart]

@whedon check references

[whedon]

Attempting to check references...

[whedon]

OK DOIs

- 10.1016/j.margeo.2006.11.004 is OK
- 10.1016/j.geomorph.2016.02.024 is OK
- 10.2112/JCOASTRES-D-17-00082.1 is OK
- https://doi.org/10.5066/F7GF0S0Z is OK
- https://doi.org/10.1038/s41598-017-05792-1 is OK
- https://doi.org/10.1016/j.envsoft.2019.104528 is OK
- http://doi.org/10.5281/zenodo.2697004 is OK
- https://doi.org/10.1016/j.envsoft.2019.01.018 is OK
- https://doi.org/10.1111/sed.12049 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

👉 Check article proof 📄 👈

[kbarnhart]

@whedon set 10.5281/zenodo.3579501 as archive

[whedon]

OK. 10.5281/zenodo.3579501 is the archive.

[kbarnhart]

@TomasBeuzen I noticed a small typo in your comment, but found the correct DOI in the badge you provided.

[kbarnhart]

@openjournals/joss-eics this is ready for final processing.

[arfon]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

OK DOIs

- 10.1016/j.margeo.2006.11.004 is OK
- 10.1016/j.geomorph.2016.02.024 is OK
- 10.2112/JCOASTRES-D-17-00082.1 is OK
- https://doi.org/10.5066/F7GF0S0Z is OK
- https://doi.org/10.1038/s41598-017-05792-1 is OK
- https://doi.org/10.1016/j.envsoft.2019.104528 is OK
- http://doi.org/10.5281/zenodo.2697004 is OK
- https://doi.org/10.1016/j.envsoft.2019.01.018 is OK
- https://doi.org/10.1111/sed.12049 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

Check final proof 👉 openjournals/joss-papers#1193

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1193, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[arfon]

@TomasBeuzen - I spotted a typo in your paper here: TomasBeuzen/pybeach#8 . Also, I think you mention scikit-learn in the paper - perhaps a citation would be appropriate?

[TomasBeuzen]

@arfon - thanks for the typo fix and yes definitely agree a scikit-learn citation is necessary, sorry I missed that!

Paper has now been updated.

[arfon]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

OK DOIs

- 10.1016/j.margeo.2006.11.004 is OK
- 10.1016/j.geomorph.2016.02.024 is OK
- 10.2112/JCOASTRES-D-17-00082.1 is OK
- https://doi.org/10.5066/F7GF0S0Z is OK
- https://doi.org/10.1038/s41598-017-05792-1 is OK
- https://doi.org/10.1016/j.envsoft.2019.104528 is OK
- http://doi.org/10.5281/zenodo.2697004 is OK
- https://doi.org/10.1016/j.envsoft.2019.01.018 is OK
- https://doi.org/10.1111/sed.12049 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

Check final proof 👉 openjournals/joss-papers#1194

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1194, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[arfon]

@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.01890 joss-papers#1195
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01890
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...

[arfon]

@csherwood-usgs, @edlazarus, @ncohn - many thanks for your reviews here and to @kbarnhart for editing this submission ✨

@TomasBeuzen - your paper is now accepted into JOSS ⚡🚀💥

[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.01890/status.svg)](https://doi.org/10.21105/joss.01890)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01890">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01890/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01890/status.svg
   :target: https://doi.org/10.21105/joss.01890

This is how it will look in your documentation:

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