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[REVIEW]: GroundwaterDupuitPercolator: A Landlab component for groundwater flow #1935

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whedon opened this issue Dec 4, 2019 · 59 comments
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@whedon whedon commented Dec 4, 2019

Submitting author: @DavidLitwin (David Litwin)
Repository: https://github.com/landlab/landlab
Version: v2.0.0b5
Editor: @kthyng
Reviewers: @dvalters, @rreinecke
Archive: 10.5281/zenodo.3660698

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/6936ca6851c622de48b2c5f6cf45a7bd"><img src="https://joss.theoj.org/papers/6936ca6851c622de48b2c5f6cf45a7bd/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/6936ca6851c622de48b2c5f6cf45a7bd/status.svg)](https://joss.theoj.org/papers/6936ca6851c622de48b2c5f6cf45a7bd)

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

@dvalters & @rreinecke, 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 try and complete your review in the next two weeks

Review checklist for @dvalters

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 (@DavidLitwin) 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 @rreinecke

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 (@DavidLitwin) 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 Dec 4, 2019

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @dvalters, @rreinecke 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:

watching

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

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
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@whedon whedon commented Dec 4, 2019

Attempting to check references...
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@whedon whedon commented Dec 4, 2019

Attempting PDF compilation. Reticulating splines etc...
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@whedon whedon commented Dec 4, 2019


OK DOIs

- 10.1029/WR006i005p01296 is OK
- 10.1016/S0167-5648(09)70009-7 is OK
- 10.1029/2002WR001728 is OK
- 10.1016/j.advwatres.2017.09.008 is OK
- 10.1002/esp.1369 is OK
- 10.1016/j.jhydrol.2003.12.043 is OK
- 10.1002/2014WR015809 is OK
- 10.1002/2013WR013918 is OK
- 10.1029/WR007i005p01256 is OK
- 10.1126/science.aaf7891 is OK
- 10.1016/j.jhydrol.2008.11.002 is OK
- 10.1029/92WR00802 is OK
- 10.5194/esurf-5-21-2017 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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@whedon whedon commented Dec 4, 2019

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@kthyng kthyng commented Dec 12, 2019

Just a quick note to reviewers @dvalters, @nicgaspar that this is where the review is to take place. Thanks!

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@kthyng kthyng commented Dec 31, 2019

Happy New Year @dvalters and @nicgaspar! Here is a friendly reminder for your review, maybe in a few days after you have celebrated the new year coming in. Thanks!

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@nicgaspar nicgaspar commented Jan 9, 2020

Hi @kthyng! I'm behind as always. I just realized that I have a COI. I am still willing to go ahead with the review if you think it is OK. But I actively collaborate with Katy Barnhart and Greg Tucker, both of whom are co-authors. As in we are working on papers together now, and have published together in the last year.

I feel I can be unbiased, but I should let you know. Sorry this took so long.

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@kthyng kthyng commented Jan 13, 2020

@nicgaspar Hm I think that is too close. I will search for a new reviewer. Thank you for pointing this out.

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@kthyng kthyng commented Jan 13, 2020

Hi @rreinecke! You were interested in this JOSS submission before — any chance you still are and are available to review it? It turns out we had a conflict of interest with another reviewer.

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@kthyng kthyng commented Jan 13, 2020

@dvalters What is your timeline for working on this review? Thanks.

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@rreinecke rreinecke commented Jan 13, 2020

@kthyng Sure.

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@kthyng kthyng commented Jan 13, 2020

@rreinecke Awesome! Thanks. I will add you on.

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@kthyng kthyng commented Jan 13, 2020

@whedon add @rreinecke as reviewer

@whedon whedon assigned dvalters, kthyng and nicgaspar and unassigned kthyng, nicgaspar and dvalters Jan 13, 2020
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@whedon whedon commented Jan 13, 2020

OK, @rreinecke is now a reviewer

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@kthyng kthyng commented Jan 13, 2020

@whedon remove @nicgaspar as reviewer

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@dvalters dvalters commented Feb 6, 2020

Yep, sorry forgot to say after checking the boxes - all good from my side as far as a I can see!

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@kthyng kthyng commented Feb 6, 2020

@whedon generate pdf

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@whedon whedon commented Feb 6, 2020

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@kthyng kthyng commented Feb 6, 2020

@DavidLitwin Just read through your paper and have one small typo in the paper #1144 and a few in the bib file #1145. See what you think.

After that, let me know: what is the appropriate version number to use?

Also, can you set up an archive of your code at, for example, Zenodo, and report back here with the doi?

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@DavidLitwin DavidLitwin commented Feb 6, 2020

@kthyng thank you for the typo corrections.

@kbarnhart I want to make sure the version and doi are handled correctly.. If we do it similarly to the JOSS paper for lithology, the landlab release where the component was introduced is referenced, along with the current landlab release and associated DOI. The component first appears in v.1.10 I believe, and current release is v2.0.0b5. @kbarnhart can you confirm this?

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@DavidLitwin DavidLitwin commented Feb 6, 2020

Just fixed one other typo in landlab/landlab#1146.

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@kbarnhart kbarnhart commented Feb 6, 2020

@DavidLitwin you are correct. the typo you just fixed isn't in v2.0.0b5, but I'm not sure if that is important. if it is, we can make a new release.

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@DavidLitwin DavidLitwin commented Feb 7, 2020

@kbarnhart I think that should be fine, right? @kthyng zenodo seems to be having some trouble right now, but the DOI is 10.5281/zenodo.154179.

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@kbarnhart kbarnhart commented Feb 7, 2020

@DavidLitwin I don't think that is the correct DOI.

That looks like the DOI for v1.0.1.

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@DavidLitwin DavidLitwin commented Feb 7, 2020

@kbarnhart do you have the correct one? That's the one that appears in the readme for landlab on github, and I can't find anything past 1.5.4 with a DOI on zenodo.

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@kbarnhart kbarnhart commented Feb 7, 2020

@DavidLitwin I would manually make a Zenodo archive rather than use the auto-created Zenodo archive that sometimes get made when a new tag is created.

I also say this because I know in the JOSS docs there is a statement that the title and authors of the zenodo archive should match. The docs say:

Check the archive deposit has the correct metadata (title and author list), and request the author edit it if it doesn’t match the paper.

So I think you'll need to download a .zip of the current version of Landlab and archive it with the name and authors of this contribution. I'll let @kthyng chime in if she thinks this is not correct.

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@kthyng kthyng commented Feb 8, 2020

@kbarnhart Yes this sounds correct to me. I haven't gone through the process myself but we do want the relevant version of the code archived at something like Zenodo, and we want the authors/title to match the paper exactly. Having the whole Landlab in the archive does make sense, given this is a submodule.

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@DavidLitwin DavidLitwin commented Feb 9, 2020

@kthyng and @kbarnhart I have created an archive of the latest landlab release (2.0.0b5) here:

http://doi.org/10.5281/zenodo.3660698

Please let me know if there are any issues with this and I will try to resolve them.

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@kthyng kthyng commented Feb 10, 2020

@whedon set v2.0.0b5 as version

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@whedon whedon commented Feb 10, 2020

OK. v2.0.0b5 is the version.

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@kthyng kthyng commented Feb 10, 2020

@whedon set 10.5281/zenodo.3660698 as archive

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@whedon whedon commented Feb 10, 2020

OK. 10.5281/zenodo.3660698 is the archive.

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@kthyng kthyng commented Feb 10, 2020

@whedon accept

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@whedon whedon commented Feb 10, 2020

Attempting dry run of processing paper acceptance...
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@whedon whedon commented Feb 10, 2020

Reference check summary:

OK DOIs

- 10.1029/WR006i005p01296 is OK
- 10.1016/S0167-5648(09)70009-7 is OK
- 10.1029/2002WR001728 is OK
- 10.1016/j.advwatres.2017.09.008 is OK
- 10.1002/esp.1369 is OK
- 10.1016/j.jhydrol.2003.12.043 is OK
- 10.1002/2014WR015809 is OK
- 10.1002/2013WR013918 is OK
- 10.1029/WR007i005p01256 is OK
- 10.1126/science.aaf7891 is OK
- 10.1016/j.jhydrol.2008.11.002 is OK
- 10.1029/92WR00802 is OK
- 10.5194/esurf-5-21-2017 is OK
- 10.1002/hyp.8319 is OK
- 10.1029/2008WR007536 is OK
- 10.1029/2006WR005752 is OK
- 10.1016/j.advwatres.2005.08.006 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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@whedon whedon commented Feb 10, 2020

Check final proof 👉 openjournals/joss-papers#1290

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1290, 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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@kthyng kthyng commented Feb 10, 2020

@whedon accept deposit=true

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@whedon whedon commented Feb 10, 2020

Doing it live! Attempting automated processing of paper acceptance...
@whedon whedon added the accepted label Feb 10, 2020
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@whedon whedon commented Feb 10, 2020

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

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@whedon whedon commented Feb 10, 2020

🚨🚨🚨 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#1291
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01935
  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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@kthyng kthyng commented Feb 10, 2020

Congratulations to @DavidLitwin on your new publication! Thanks to reviewers @dvalters and @rreinecke for your time and expertise.

@kthyng kthyng closed this Feb 10, 2020
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@whedon whedon commented Feb 10, 2020

🎉🎉🎉 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.01935/status.svg)](https://doi.org/10.21105/joss.01935)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01935">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01935/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01935/status.svg
   :target: https://doi.org/10.21105/joss.01935

This is how it will look in your documentation:

DOI

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