[REVIEW]: WDPM: the Wetland DEM Ponding Model

[whedon]

Submitting author: @KevinShook (Kevin Shook) Repository: https://github.com/CentreForHydrology/WDPM Version: v2.0b Editor: @kbarnhart Reviewer: @r-barnes, @awickert, @KCallaghan Archive: 10.5281/zenodo.5165172

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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

@r-barnes & @awickert & @KCallaghan, 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 six weeks ✨

Review checklist for @r-barnes

Conflict of interest

• [x] 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

• [x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• [x] Repository: Is the source code for this software available at the repository url?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Contribution and authorship: Has the submitting author (@KevinShook) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] 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

• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• [x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• [x] 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

• [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] 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 @awickert

Conflict of interest

• [x] 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

• [x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• [x] Repository: Is the source code for this software available at the repository url?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Contribution and authorship: Has the submitting author (@KevinShook) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] 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

• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• [x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• [x] 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

• [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] 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 @KCallaghan

Conflict of interest

• [x] 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

• [x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• [x] Repository: Is the source code for this software available at the repository url?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Contribution and authorship: Has the submitting author (@KevinShook) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] 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

• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• [x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• [x] 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

• [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] 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. @r-barnes, @awickert, @KCallaghan it looks like you're currently assigned to review this paper :tada:.

:warning: JOSS reduced service mode :warning:

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.

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[whedon]

Reference check summary:

OK DOIs

- 10.1002/hyp.6787 is OK
- 10.1002/hyp.8381 is OK
- 10.1002/hyp.9867 is OK
- 10.1016/j.jhydrol.2014.12.014 is OK
- 10.1016/S0022-1694(03)00175-6 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[kbarnhart]

@KevinShook, @r-barnes, @awickert, @KCallaghan

I wanted to check in and see how things were going with this review, and to answer any questions if you have them. As mentioned above, JOSS is presently requesting reviewers complete their reviews in six weeks (a bit more than three weeks from now).

@KCallaghan thanks for linking all of your issues to this one 👍 🎉

[KevinShook]

There are still some outstanding issues with the program, particularly in terms of the installation. This may be because the code has not been looked at for over 6 years. We are attempting to fix the issues.

[awickert]

@kbarnhart The review is in the schedule! It should reach the top of the queue in 1.5 weeks.

[kbarnhart]

All- Thanks for the updates. Please let me know if I can do anything to support the review process.

[KevinShook]

Thanks very much - will do

[r-barnes]

That's it for me this morning; I'll circle back to inspecting the C and OpenCL code later.

[kbarnhart]

Thanks everyone for linking issues and keeping everyone updated on this issue thread. As always, authors and reviewers, please feel free to reach out to me for support in this review process.

[awickert]

@kbarnhart - I didn't accept the invite in time and it expired, so I cannot update the checklist. Can you re-send? (With apologies!)

I finished a first pass through, and will be able to add more material once I am able to compile the source code.

[danielskatz]

@whedon re-invite @awickert as reviewer

[whedon]

OK, the reviewer has been re-invited.

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

[kbarnhart]

Thanks @danielskatz !

[kbarnhart]

@KevinShook and @r-barnes @awickert @KCallaghan

I wanted to write a quick message to check in and provide some guidance regarding the JOSS process. As best as I can tell the reviewers have been quite thorough and have opened many issues in the source repository as part of their reviews.

At this point, the next step is for the authors to address these issues and close them when completed. If the authors have clarifying questions for the reviewers or for me (e.g., does this pull request address your concern), please tag us into the conversation. If the authors think that an issue that was opened is out of scope, the issue itself is the place to discuss. As always, please consider me a resource throughout this process.

Once the authors feel like they have addressed the reviewers issues such that the reviewers are able to complete the review checklist, they should comment here indicating this.

Know that I'll check into this thread and the main repository to keep track of progress/status changes at a frequency of about every 1-2 weeks.

Questions, comments, or concerns always welcome.

[KevinShook]

Thanks very much, this is very helpful for understanding the process. We'll work on addressing the issues raised.

[kbarnhart]

@KevinShook I wanted to check in and see how things were going with addressing the issues raised by reviewers. Know that JOSS doesn't have a required timeline for revisions, but it would be helpful for me to know an approximate time frame.

[KevinShook]

Thanks very much for keeping in touch. We have almost completed the conversion of the GUI from Python 2 to 3. Once the tested is complete then the rest of the issues should be fairly simple to address. I have started editing the paper itself, and the requested clarifications seem to be relatively easily addressed. Barring unforeseen issues, I would anticipate completion sometime this month.

[kbarnhart]

@KevinShook Thanks for the update. If issues come up that I can assist with, please let me know.

[kbarnhart]

@whedon remind kbarnhart in 2 weeks

@KevinShook just setting a reminder for myself to check in on this in a few weeks.

[whedon]

Reminder set for kbarnhart in 2 weeks

[kbarnhart]

@KevinShook I wanted to check in and see how things were going with addressing reviewer comments.

[KevinShook]

Thanks for getting in touch. I just merged a pull request today which should have all of the fixes to date. The GUI has been converted from Python 2 to 3, and no-longer crashes. I believe that the style issues have also been addressed. The main outstanding issues are a) there's still one warning left to fix, and b) although we have a makefile, it's not included as it needs a bit of work. The paper has been updated, but still needs to be gone over, and the manual is being updated as well.

[r-barnes]

@KevinShook: I'd recommend cmake as a better option than a makefile (example here): they're relatively simple to write and provide better cross-system compatibility. If you'd like help getting one setup, I'm happy to help.

[KevinShook]

Thanks very much. We are planning on going with cmake as was recommended by one of the developers.

[kbarnhart]

Thanks for the update @KevinShook 👍

[kbarnhart]

@KevinShook another quick check in from me. No rush if you and your co-authors are still addressing issues raised by the reviewers.

[KevinShook]

Thanks for checking in. We are still finishing a few issues. We are replacing the makefile with cmake as was suggested by r-barnes (thanks!). We are also working on having the program work with a single executable. Previously, the GUI called a separate executable, from the command line version, which is obviously not desireable. One these are done, the manual will need to be updated. I'm going away for 3 weeks, so will probably not be able to work on it much in the interim.

[kbarnhart]

@KevinShook Sounds good, thanks for the update.

[kbarnhart]

@KevinShook another quick check in from me. No rush if you and your co-authors are still addressing issues raised by the reviewers.

[KevinShook]

Thanks. We have finally solved a problem which was responsible for there being 2 different executables. There is now a single executable, but we are working on making it more efficient. When this last hurdle is cleared, we can finally cross off all of the technical issues, and finish the documentation.

[kbarnhart]

@KevinShook another quick check in from me (I'm trying to do this about once a month). Of course no rush if you and co-authors are still working to address the remaining technical and documentation issues.

[KevinShook]

Thanks very much. We're nearly finished. The revised code has been pushed to our GitHub repo, as has the revised paper. I believe that we have addressed all of the concerns with the program, and I'm just waiting for the approval of two the co-authors on the paper and the program manual, to reply to all of the issues.

[kbarnhart]

@KevinShook thanks for that update. I'll stay tuned for your response to the in-repo issues.

[kbarnhart]

@KevinShook I wanted to touch base again on how finishing addressing the reviewer issues was going.

[KevinShook]

Thanks for keeping in touch. I have replied to all but 3 issues, and I believe that all but these last 3 have been solved. I didn't close the issues, as I assumed that this would be up to the person creating them.

The program now runs (much better thanks to the reviewers), and the GUI has also been greatly improved. The last 3 issues (#18, #14, and #13) are concerned with programming style and are being addressed right now. They should be finished in the next few days.

[kbarnhart]

@KevinShook Thanks for this update. Glad to know that the review comments have improved the software. I concur with you that the reviewers who created the issues should be the people who close them.

Once you have finished addressing the final issues, please ping me and the reviewers here to let them know that it is time for them to complete their reviews.

[kbarnhart]

@KevinShook another quick check in from me to see how things are going in finishing addressing the reviewer's comments.

[KevinShook]

I think that we have addressed all of the comments. I'm just waiting for the final sign-off from the last co-author before contacting you and the other reviewers. I did see that some of the comments have already been closed.

[kbarnhart]

@KevinShook thanks for the update!

[KevinShook]

The paper is finally complete and has been pushed to the repo. Thanks for your patience! What would be the best way for me to contact all the reviewers to tell them that we have finished?

[kbarnhart]

@whedon generate pdf

[kbarnhart]

@whedon check references

[whedon]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[whedon]

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

OK DOIs

- 10.1029/2020WR027984 is OK
- 10.1002/hyp.10567 is OK
- 10.1007/s10669-018-9684-7 is OK
- 10.1111/j.1745-6584.1988.tb00794.x is OK
- 10.1002/esp.3888 is OK
- 10.1002/hyp.6787 is OK
- 10.1002/hyp.8381 is OK
- 10.1002/hyp.9867 is OK
- 10.1016/j.jhydrol.2014.12.014 is OK
- 10.1016/S0022-1694(03)00175-6 is OK

MISSING DOIs

- 10.1016/s0022-1694(98)00098-5 may be a valid DOI for title: Water and Solute Transfer between a Prairie Wetland and Adjacent Uplands, 1. Water Balance
- 10.3390/w11122486 may be a valid DOI for title: “Garbage in, Garbage Out” Does Not Hold True for Indigenous Community Flood Extent Modeling in the Prairie Pothole Region
- 10.1016/0022-1694(93)90275-e may be a valid DOI for title: Hydrology of a Prairie Slough

INVALID DOIs

- None

[kbarnhart]

@KevinShook thanks for the update.

@r-barnes @awickert @KCallaghan as you are able, please revisit your review at this point. If you think @KevinShook has addressed all of your concerns, please close in-repo issues and check off remaining checkboxes above.

As always, if you have questions for me ask them here or email krbarnhart@usgs.gov

[KevinShook]

@whedon check references

[whedon]

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

OK DOIs

- 10.1029/2020WR027984 is OK
- 10.1002/hyp.10567 is OK
- 10.1007/s10669-018-9684-7 is OK
- /10.1016/S0022-1694(98)00098-5 is OK
- 10.1111/j.1745-6584.1988.tb00794.x is OK
- 10.1002/esp.3888 is OK
- 10.1002/hyp.6787 is OK
- 10.1002/hyp.8381 is OK
- 10.1002/hyp.9867 is OK
- 10.1016/j.jhydrol.2014.12.014 is OK
- 10.1016/S0022-1694(03)00175-6 is OK
- 10.3390/w11122486 is OK
- 10.1016/0022-1694(93)90275-E is OK

MISSING DOIs

- None

INVALID DOIs

- None

[KevinShook]

I added the missing DOIs

[KevinShook]

A strange (but welcome) thing just happened. Out of the blue, Oluwaseun Sharomi contacted us! It turns out he had moved from Abu Dhabi to the USA, which was why we were unable to contact him. He has given his consent to be a co-author, so I have added him to the paper.