[REVIEW]: FullSWOF: Full Shallow-Water equations for Overland Flow

[whedon]

Submitting author: @mlep (Frédéric Darboux), on behalf of (Carine Lucas)
Repository: https://www.idpoisson.fr/fullswof/
Version: v1.07.00
Editor: @kyleniemeyer
Reviewer: @wkearn
Archive: 10.5281/zenodo.1095748

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Reviewer questions

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Conflict of interest

• As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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?
• Version: Does the release version given match the GitHub release (v1.07.00)?
• Authorship: Has the submitting author (@) 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 function 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

• Authors: Does the paper.md file include a list of authors with their affiliations?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

[whedon]

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[wkearn]

@kyleniemeyer I can't seem to find a paper.md file for this submission.

[kyleniemeyer]

Hi Carine, can you point to where the paper is in the repository?

Also, could you clarify which version was submitted? I notice that there are three—is it all of them?

[kyleniemeyer]

Hi @wkearn, just FYI—I am currently trying to contact the authors of this submission, since it somehow made it through without having a GitHub account associated with the submitter.

[kyleniemeyer]

Hi @mlep, tagging you in this issue

[kyleniemeyer]

@wkearn regarding the paper location, I have this from the authors:

The paper (paper.md) is located as the guidelines indicated at:
http://www.univ-orleans.fr/mapmo/soft/FullSWOF/paper.md
You will also find the bibliography file:
http://www.univ-orleans.fr/mapmo/soft/FullSWOF/paper.bib
and the metadata file:
http://www.univ-orleans.fr/mapmo/soft/FullSWOF/codemeta.json

[wkearn]

Great! I'll finish this up shortly. Thanks!

[wkearn]

FullSWOF is an excellent, mature piece of software. Everything works as advertised, and the documentation is comprehensive.

I have one minor concern to be addressed before I can recommend acceptance, and a few suggestions that would be nice to see, but aren't critical.

Minor concern: community guidelines

There doesn't appear to be explicitly stated information on how someone might go about contributing to the software, what kinds of features the developers are most interested in adding, what kinds of improvements are likely to be accepted to the main code base, etc. This creates a relatively high barrier to entry for someone who wants to get involved with development but who doesn't really know where to start.

I call this a minor concern because the contact information for the developers is available on the website, and the documentation contains information on testing/benchmarking for outside contributors. I'd be satisfied with a statement along the lines of "If you are interested in contributing to FullSWOF, contact the developers at ..." in the "How to contact us?" part of the website or in the Introduction to the documentation, though a comprehensive set of contributor guidelines and a list of desired features would be ideal.

Suggestions

1. It would be nice to have a real-world example walked through in the documentation. The tests shown are classical shallow water benchmarks, but aren't all that helpful in showing how you might go about modeling a flood event with FullSWOF, for instance. Many examples are available in the various published papers that use FullSWOF, so it might be just a matter of finding a good one, linking to the appropriate data, and walking through the steps required to reproduce the findings in the paper. I would recommend the Thies example.

2. The authors could be a bit more explicit in their statement of need about the target audience of FullSWOF. Is this meant to be used primarily by numerical modelers, surface water hydrologists, or stakeholders interested in flood risks?

[kyleniemeyer]

Thanks @wkearn!

Hi @mlep, could you and your coauthors take a look at this feedback?

[mlep]

Thank you @wkearn for your review and constructive comments. Please, find below our replies.

Minor concern: community guidelines

There doesn't appear to be explicitly stated information on how someone might go about contributing to the software, what kinds of features the developers are most interested in adding, what kinds of improvements are likely to be accepted to the main code base, etc. This creates a relatively high barrier to entry for someone who wants to get involved with development but who doesn't really know where to start.

I call this a minor concern because the contact information for the developers is available on the website, and the documentation contains information on testing/benchmarking for outside contributors. I'd be satisfied with a statement along the lines of "If you are interested in contributing to FullSWOF, contact the developers at ..." in the "How to contact us?" part of the website or in the Introduction to the documentation, though a comprehensive set of contributor guidelines and a list of desired features would be ideal.

Indeed, we have overlooked this issue. In fact, we already have a short to-do list at the beginning of the changelog.txt file (https://sourcesup.renater.fr/scm/viewvc.php/trunk/changelog.txt?view=markup&root=fullswof-2d), but this list is hidden to new comers.
We have now added a paragraph in the main webpage (http://www.univ-orleans.fr/mapmo/soft/FullSWOF/), in the section "How to contact us?".
We will think how to improve this, perhaps with a todo.txt file at the root of the repository.

Suggestions

• It would be nice to have a real-world example walked through in the documentation. The tests shown are classical shallow water benchmarks, but aren't all that helpful in showing how you might go about modeling a flood event with FullSWOF, for instance. Many examples are available in the various published papers that use FullSWOF, so it might be just a matter of finding a good one, linking to the appropriate data, and walking through the steps required to reproduce the findings in the paper. I would recommend the Thies example.

Thanks again for your suggestion. We are going to add the Thies case into the directory Examples in the next few days.
Additionally, we are in the process of making data input easier for users: we are developing routines to convert GIS data (AscGrid format) into the FullSWOF format (and vice-versa). We are testing them internally at the moment.

• The authors could be a bit more explicit in their statement of need about the target audience of FullSWOF. Is this meant to be used primarily by numerical modelers, surface water hydrologists, or stakeholders interested in flood risks?

FullSWOF's primary target are surface water hydrologists. Numerical modelers are the secondary target. We have altered the text (in the file http://www.univ-orleans.fr/mapmo/soft/FullSWOF/paper.md) to state this point explicitly, in the first paragraph : "Several features make FullSWOF particularly suitable for surface water hydrologists:[...]" and "The modular structure of FullSWOF is also useful to numerical modelers willing to test new schemes or boundary conditions."

[wkearn]

Looks good!

I'm happy to recommend acceptance at this point.

[mlep]

@wkearn: Thank you for your recommendation (and sorry for the delay).
@kyleniemeyer: What is the next stage? Do we have something to do?

[kyleniemeyer]

@mlep I'm going to look over the paper from an editorial perspective, but once that is finalized we will need you to archive the accepted version of the software and provide us the DOI (using, e.g., Zenodo or Figshare).

[kyleniemeyer]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #448 with the following error: 

 /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/find.rb:43:in `block in find': No such file or directory (Errno::ENOENT)
	from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/find.rb:43:in `collect!'
	from /app/vendor/ruby-2.3.4/lib/ruby/2.3.0/find.rb:43:in `find'
	from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-33e05183aa0d/lib/whedon/processor.rb:49:in `find_paper_paths'
	from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-33e05183aa0d/bin/whedon:32:in `prepare'
	from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/command.rb:27:in `run'
	from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/invocation.rb:126:in `invoke_command'
	from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor.rb:387:in `dispatch'
	from /app/vendor/bundle/ruby/2.3.0/gems/thor-0.20.0/lib/thor/base.rb:466:in `start'
	from /app/vendor/bundle/ruby/2.3.0/bundler/gems/whedon-33e05183aa0d/bin/whedon:75:in `<top (required)>'
	from /app/vendor/bundle/ruby/2.3.0/bin/whedon:22:in `load'
	from /app/vendor/bundle/ruby/2.3.0/bin/whedon:22:in `<main>'

[arfon]

@kyleniemeyer - @whedon won't know how to compile this automatically as the software isn't in a Git repository.

[kyleniemeyer]

@arfon hmm, so what do we do?

[arfon]

@arfon hmm, so what do we do?

I usually process submissions like this myself locally with the Whedon gem. @mlep - could you please explain how I can download the source code for this repository (together with the paper.md and paper.bib files)?

[mlep]

Dear @arfon,

The files related to the manuscript are here:

• http://www.univ-orleans.fr/mapmo/soft/FullSWOF/paper.md
• http://www.univ-orleans.fr/mapmo/soft/FullSWOF/paper.bib
• http://www.univ-orleans.fr/mapmo/soft/FullSWOF/codemeta.json

For the source codes of the software, they are here:

• https://sourcesup.renater.fr/scm/viewvc.php?root=fullswof-2d
• https://sourcesup.renater.fr/scm/viewvc.php?root=fullswof-1d
• https://sourcesup.renater.fr/scm/viewvc.php?root=fullswof-ui

Thank you for your time.

[arfon]

@kyleniemeyer - here's the compiled PDF: 10.21105.joss.00448.pdf

[kyleniemeyer]

@mlep it looks like the URLs included in the text of the paper were not handled properly; rather than the single quotation marks, could you instead wrap all the links with < >?

Also, minor wording fix: FullSWOF is solving these -> FullSWOF solves these

[mlep]

@kyleniemeyer We have modified the syntax for the URLs and fixed the wording. Thank you for your comments!

[kyleniemeyer]

@mlep thanks! Could you now archive the software (all elements of it—essentially the entire contents of the repository) and provide us the DOI, using something like Zenodo?

[kyleniemeyer]

@arfon could you regenerate the PDF for this one, please?

[arfon]

Here you go: 10.21105.joss.00448.pdf

[mlep]

@kyleniemeyer Files are now archived on Zenodo. The doi is 10.5281/zenodo.1095748

[kyleniemeyer]

@whedon set 10.5281/zenodo.1095748 as archive

[whedon]

OK. 10.5281/zenodo.1095748 is the archive.

[kyleniemeyer]

@arfon this paper is accepted and ready to be published.

[mlep]

@kyleniemeyer How fast!

[arfon]

@wkearn - many thanks for your review here and to @kyleniemeyer for editing this submission ✨

@mlep - your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00448 ⚡️ 🚀 💥

[whedon]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippet:

[![DOI](http://joss.theoj.org/papers/10.21105/joss.00448/status.svg)](https://doi.org/10.21105/joss.00448)

This is how it will look in your documentation:

We need your help!

Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider volunteering to review for us sometime in the future. You can add your name to the reviewer list here: http://joss.theoj.org/reviewer-signup.html

[mlep]

@kyleniemeyer @arfon @wkearn: Thank you for managing JOSS editorial process.

[mlep]

@kyleniemeyer @arfon @wkearn: Because of the merging of two laboratories, the URL of the repository has changed from http://www.univ-orleans.fr/mapmo/soft/FullSWOF/ to https://www.idpoisson.fr/fullswof/ .
Could the URL be updated on the page of the article (http://joss.theoj.org/papers/10.21105/joss.00448)?
Cheers.

Note: currently there is an automatic redirection, but we do not know for how long it will last.

[kyleniemeyer]

@mlep could you update the address in the Markdown paper? that will make this easier, if possible.

[mlep]

@kyleniemeyer The updated md file is here: https://www.univ-orleans.fr/mapmo/membres/lucas/paper.md

[kyleniemeyer]

@arfon is it possible to update the paper?

[arfon]

@arfon is it possible to update the paper?

Yep. I've updated the paper with the new address. The PDF might take a few hours to update because of caching.

[mlep]

@arfon Thank you for the update.
Just a point of attention: the year, volume and number written at the bottom of the pdf file have changed. It is intended?
Before, it was:

Delestre et al., (2017). FullSWOF: Full Shallow-Water equations for Overland Flow. Journal of Open Source Software, 2(20), 448, doi:10.21105/joss.00448

Now it is:

Delestre et al., (2018). FullSWOF: Full Shallow-Water equations for Overland Flow. Journal of Open Source Software, 3(22), 448. https://doi.org/10.21105/joss.00448

[arfon]

@mlep - good catch. Thanks for spotting that. (It should now be fixed)

[mlep]

Thank you for the update. We enjoyed the review process and support given by your journal.