[REVIEW]: Water Systems Integrated Modelling framework, WSIMOD: A Python package for integrated modelling of water quality and quantity across the water cycle

[editorialbot]

Submitting author: @barneydobson (Barnaby Dobson)
Repository: https://github.com/barneydobson/wsi
Branch with paper.md (empty if default branch):
Version: 0.3_joss_reviewed
Editor: @crvernon
Reviewers: @cheginit, @jlarsen-usgs
Archive: 10.5281/zenodo.7662569

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/9df09dbd84388e336f911bb1d55c7a87"><img src="https://joss.theoj.org/papers/9df09dbd84388e336f911bb1d55c7a87/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/9df09dbd84388e336f911bb1d55c7a87/status.svg)](https://joss.theoj.org/papers/9df09dbd84388e336f911bb1d55c7a87)

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

@cheginit & @jlarsen-usgs, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @crvernon know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @cheginit

📝 Checklist for @jlarsen-usgs

[editorialbot]

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For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

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[editorialbot]

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

OK DOIs

- 10.1088/1748-9326/abb050 is OK
- 10.1016/j.scitotenv.2021.150642 is OK
- 10.1016/j.watres.2017.09.039 is OK
- 10.3389/frwa.2021.641462 is OK
- 10.1029/2021WR030778 is OK
- 10.3389/frwa.2021.773974 is OK
- 10.1002/essoar.10511984.1 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.30 s (198.5 files/s, 59203.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          34           2504           4000           6902
SVG                              2              0              1           2355
XML                              1              0             52           1534
Markdown                        16             91              0            212
JSON                             3              0              0             76
TeX                              1              6              0             75
YAML                             2              7              4             47
CSS                              1              4              3             20
-------------------------------------------------------------------------------
SUM:                            60           2612           4060          11221
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 448

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[crvernon]

👋 @barneydobson @cheginit @jlarsen-usgs This is the review thread for the paper. All of our communications will happen here from now on.

Please read the "Reviewer instructions & questions" in the first comment above.

Both reviewers have checklists at the top of this thread (in that first comment) with the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention #4996 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for the review process to be completed within about 4-6 weeks but please make a start well ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.

[crvernon]

👋 @cheginit and @jlarsen-usgs could you provide an update to how things are going? Also please let me know if you have any questions.

[jlarsen-usgs]

@crvernon I've blocked out time this week to complete my review. Thanks for the nudge

[cheginit]

Review checklist for @cheginit

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 https://github.com/barneydobson/wsi?
• 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 (@barneydobson) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
• 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?

[jlarsen-usgs]

Review checklist for @jlarsen-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 https://github.com/barneydobson/wsi?
• 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 (@barneydobson) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
• 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?

[crvernon]

👋 @cheginit and @jlarsen-usgs looks like you are making great progress! @barneydobson let me know if you have any questions!

[barneydobson]

Thanks @crvernon I have replied to tasks for the two review issues, to check - there's nothing else waiting for me? (Not rushing the reviewers, just want to make sure I'm not holding anything up)

[crvernon]

Great @barneydobson ! @cheginit and @jlarsen-usgs how are we doing on your end? Great work everyone!

[cheginit]

@barneydobson Thanks for taking the time to address my concerns. @crvernon In my opinion, the submission is ready for publication.

[crvernon]

Thanks @cheginit !

[jlarsen-usgs]

@crvernon, All of my review comments have been addressed. I think the submission is ready to move ahead with publication

[crvernon]

Thanks @jlarsen-usgs !

[crvernon]

@editorialbot generate pdf

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[crvernon]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1088/1748-9326/abb050 is OK
- 10.1016/j.scitotenv.2021.150642 is OK
- 10.1016/j.watres.2017.09.039 is OK
- 10.3389/frwa.2021.641462 is OK
- 10.1029/2021WR030778 is OK
- 10.3389/frwa.2021.773974 is OK
- 10.1016/j.jenvman.2022.117045 is OK
- 10.1016/j.envsoft.2013.05.004 is OK
- 10.13031/2013.42259 is OK
- j.envsoft.2009.11.009 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[crvernon]

@barneydobson - we are almost there! Next is just addressing the following few comments that I had for your paper and setting up the archive for your new release.

• THROUGHOUT: please put a space in between the phrase and the reference. For example, "...integration framework [@rauch:2017]." instead of "...integration framework[@rauch:2017]."
• LINE 47: missing examples "(e.g., )"
• LINE 68: need to remove \bibliography from your paper.md

We want to make sure the archival has the correct metadata that JOSS requires. This includes a title that matches the paper title and a correct author list.

So here is what we have left to do:

• Conduct a GitHub release of the current reviewed version of the software you now have on the main and archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)

• Check the archival deposit (e.g., in Zenodo) to ensure it has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.

• Please list the DOI of the archived version here

I can then move forward with accepting the submission.

[barneydobson]

Thanks @crvernon , those paper changes now corrected.

I've made a release, created an archive with the correct metadata.

With DOI: 10.5281/zenodo.7662569

[kthyng]

Hi! I see the archive and version are set ✅

[kthyng]

Please check the capitalization in your references. You can preserve capitalization by placing {} around characters/words in your .bib file.

Also the acknowledgements for "The design of ..." look a little strange — please make sure they are coming through as you intend.

[barneydobson]

@kthyng Thanks for your comments there. I have updated the acknowledgements to include them as references, which I should have done from the start - hopefully you'll agree they are clearer now.

RE capitalizations, they seem OK to me (and are in curly braces in the .bib file) - is there any specific that seem wrong?

[kthyng]

@editorialbot generate pdf

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[kthyng]

@barneydobson References comments:

• Shrestha et al has "belgium" and the river not capitalized
• Also Gironas needs a space before the acronym in the title

[barneydobson]

Got it - both now corrected, apologies for missing those!

[kthyng]

@editorialbot generate pdf

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[kthyng]

Looks great!

[kthyng]

@editorialbot accept

[editorialbot]

Doing it live! Attempting automated processing of paper acceptance...

[editorialbot]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[editorialbot]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

🚨🚨🚨 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.04996 joss-papers#4025
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04996
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...

[kthyng]

Congrats on your new publication @barneydobson! Many thanks to editor @crvernon and reviewers @cheginit and @jlarsen-usgs for your time, hard work, and expertise!!

[editorialbot]

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

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HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.04996/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04996/status.svg
   :target: https://doi.org/10.21105/joss.04996

This is how it will look in your documentation:

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