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[REVIEW]: pybeach: A Python package for extracting the location of dune toes on beach profile transects #1890

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whedon opened this issue Nov 13, 2019 · 60 comments
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@whedon whedon commented Nov 13, 2019

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

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/8b211e45c6919ea8057946484e757c28"><img src="https://joss.theoj.org/papers/8b211e45c6919ea8057946484e757c28/status.svg"></a>
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

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

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

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?
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@whedon whedon commented Nov 13, 2019

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:

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

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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
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@whedon whedon commented Nov 13, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Nov 13, 2019

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@kbarnhart kbarnhart commented Nov 24, 2019

/ooo November 24 until November 28

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@ooo ooo bot commented Nov 24, 2019

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@csherwood-usgs csherwood-usgs commented Nov 25, 2019

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@kbarnhart kbarnhart commented Nov 28, 2019

@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).

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@kbarnhart kbarnhart commented Nov 28, 2019

/ooo December 1 until December 4

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@ooo ooo bot commented Nov 28, 2019

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@edlazarus edlazarus commented Nov 29, 2019

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

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@ncohn ncohn commented Dec 2, 2019

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.

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@kbarnhart kbarnhart commented Dec 5, 2019

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

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

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@kbarnhart kbarnhart commented Dec 5, 2019

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

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@edlazarus edlazarus commented Dec 6, 2019

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

Done! Dunno how I missed that box. Apologies!

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@TomasBeuzen TomasBeuzen commented Dec 6, 2019

@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!

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@kbarnhart kbarnhart commented Dec 16, 2019

@TomasBeuzen great! Thanks for the ping (I was sucked into the AGUniverse last week).

Can you

  • Fix the [Harley2017] citation (sorry I missed these two citation related commenst in my earlier issue).
  • Add a date to Leaman (n.d.)
  • Make a tagged release and archive. Ensure that the title and author list are the same as the paper.
  • Report the current version number and archive DOI in the here.

At that point I will be able to update the version and archive DOI. I will then be able to hand the publication over for final processing by the Editors in Chief.

Nice work! 🎉

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@TomasBeuzen TomasBeuzen commented Dec 16, 2019

Hi @kbarnhart - no problem! I unfortunately missed AGU this year but it looked great!

  • Harley2017 and Leaman2019 citations have been corrected.
  • Have made a tagged release and archived with Zenodo.
  • Version number: v0.1.1
  • DOI: 10.5281/zenodo.3579501 DOI
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@kbarnhart kbarnhart commented Dec 16, 2019

@whedon generate pdf

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@whedon whedon commented Dec 16, 2019

Attempting PDF compilation. Reticulating splines etc...
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@kbarnhart kbarnhart commented Dec 16, 2019

@whedon check references

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@whedon whedon commented Dec 16, 2019

Attempting to check references...
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@whedon whedon commented Dec 16, 2019


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
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@whedon whedon commented Dec 16, 2019

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@kbarnhart kbarnhart commented Dec 16, 2019

@whedon set 10.5281/zenodo.3579501 as archive

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@whedon whedon commented Dec 16, 2019

OK. 10.5281/zenodo.3579501 is the archive.

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@kbarnhart kbarnhart commented Dec 16, 2019

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

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@kbarnhart kbarnhart commented Dec 16, 2019

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

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@arfon arfon commented Dec 20, 2019

@whedon accept

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@whedon whedon commented Dec 20, 2019

Attempting dry run of processing paper acceptance...
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@whedon whedon commented Dec 20, 2019


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
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@whedon whedon commented Dec 20, 2019

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
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@arfon arfon commented Dec 20, 2019

@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?

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@TomasBeuzen TomasBeuzen commented Dec 20, 2019

@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.

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@arfon arfon commented Dec 20, 2019

@whedon accept

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@whedon whedon commented Dec 20, 2019

Attempting dry run of processing paper acceptance...
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@whedon whedon commented Dec 20, 2019


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
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@whedon whedon commented Dec 20, 2019

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
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@arfon arfon commented Dec 20, 2019

@whedon accept deposit=true

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@whedon whedon commented Dec 20, 2019

Doing it live! Attempting automated processing of paper acceptance...
@whedon whedon added the accepted label Dec 20, 2019
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@whedon whedon commented Dec 20, 2019

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

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@whedon whedon commented Dec 20, 2019

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited 👉 openjournals/joss-papers#1195
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01890
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

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@arfon arfon commented Dec 20, 2019

@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 ⚡️🚀💥

@arfon arfon closed this Dec 20, 2019
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@whedon whedon commented Dec 20, 2019

🎉🎉🎉 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:

DOI

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