[REVIEW]: Tethys: a Spatiotemporal Downscaling Model for Global Water Demand

[editorialbot]

Submitting author: @ifthompson (Isaac Thompson)
Repository: https://github.com/JGCRI/tethys
Branch with paper.md (empty if default branch): main
Version: v2.1.0
Editor: @kthyng
Reviewers: @Mariosmsk, @nickrsan
Archive: 10.5281/zenodo.10966693

Status

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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

@Mariosmsk & @nickrsan, 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 @jsta 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 @nickrsan

📝 Checklist for @Mariosmsk

[editorialbot]

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[editorialbot]

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

OK DOIs

- 10.5194/hess-22-2117-2018 is OK
- 10.5334/jors.197 is OK
- 10.1038/s41597-023-02086-2 is OK
- 10.5194/hess-17-4555-2013 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.03 s (1471.6 files/s, 104552.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          19            380            269            769
SVG                              4              4              4            298
CSS                              2             54             11            244
reStructuredText                 8            227            235            220
YAML                             4             24             14            109
TeX                              1              0              0             52
Markdown                         2             18              0             48
DOS Batch                        1              8              1             26
JSON                             1              0              0             20
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            43            719            541           1795
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 561

[editorialbot]

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

[jsta]

Hello @nickrsan and @Mariosmsk! Thanks so much for agreeing to review. Links to reviewing information are in the top message. You can generate your checklist with @editorialbot generate my checklist. Please let me know if you have questions.

[nickrsan]

Review checklist for @nickrsan

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/JGCRI/tethys?
• 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 (@ifthompson) 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?

[nickrsan]

@jsta Thank you! I'll work through this when I have time, but likely not for a few weeks as mentioned before (but on my last review found it helpful to make the checklist early so I could knock out small parts when I have time). Looking forward to taking a look at the package

[Mariosmsk]

Review checklist for @Mariosmsk

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/JGCRI/tethys?
• 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 (@ifthompson) 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?

[nickrsan]

Hi all, just checking in to say I'm finally at a point where I can schedule some time to conduct this review and start filling in my checklist. Thanks for your patience.

[Mariosmsk]

Hi @ifthompson,

Some comments so far.

License: Does the repository contain a plain-text LICENSE file with the contents of an [OSI approved]
(https://opensource.org/licenses/alphabetical) software license?

I recommend updating the License file to include an OSI-approved software license. Additionally, please ensure that the setup.py file correctly references the chosen license. This will help ensure compliance with open-source licensing standards.

Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.

I checked the usage example, I have the image after spatial downscaling but not the image before. It's essential to also provide the original image before downscaling.

Installation: Does installation proceed as outlined in the documentation?

Installation proceeded as outlined in the documentation. However, I recommend adding matplotlib to the requirements.txt file to ensure all dependencies are clearly documented and can be easily installed. Regarding the Dask example, I encountered Java-related errors, even though I believe I have added Java to the path. For better reproducibility, consider including code in the example that automatically configures the Java path. This will improve the user experience and minimize potential issues during execution.

[kthyng]

Hi @nickrsan and @Mariosmsk! How are your reviews coming along?

@ifthompson Have you been able to respond to all of the reviewer comments?

[nickrsan]

Hi there - I apologize for my slowness, but it hasn't fallen off my radar. I'll schedule time for this next week. Thanks for your patience!

[kthyng]

@nickrsan Great!

@Mariosmsk @ifthompson How are things on your end?

[nickrsan]

Just making a note for the license checkbox since GitHub isn't picking up the license from its format and advertising it by name - it appears to be a 2-clause BSD license - not anything the authors need to respond to, just to mark this for the review.

[nickrsan]

Hi all,

As a progress update, I've filed a few issues - mostly minor, but blocking further review, on the tethys repository (see cross-references above from GitHub). Also, I'll note that two unit tests are currently failing on my machine (Win 11, Python 3.10) - though I think one is that I probably need to set the JAVA path (test_regional_query) and the other I'll dig into and file an issue if appropriate (test_easy_query not producing expected output).

[kthyng]

Hi @ifthompson — we haven't heard from you for awhile. Still with us?

[jsta]

@crvernon Do you have any insight into Issac's availability that might inform this review?

[crvernon]

@jsta Let me see if I can reach him. If not, I will handle any reviewer comments. Thanks!

[kthyng]

I'm going to take over as editor here!

@crvernon Have you been able to get in contact with the author? If not can you take over? If progress can't be made on this soon, I'd like to pause it for now, or withdraw if it looks like the submission won't be able to be finished.

[kthyng]

@editorialbot assign me as editor

[editorialbot]

Done! version is now v2.1.0

[crvernon]

@editorialbot set 10.5281/zenodo.10966693 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.10966693

[crvernon]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.5194/hess-22-2117-2018 is OK
- 10.5334/jors.197 is OK
- 10.1038/s41597-023-02086-2 is OK
- 10.5194/hess-17-4555-2013 is OK
- 10.5194/gmd-12-677-2019 is OK
- 10.5194/gmd-15-2533-2022 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[crvernon]

@editorialbot generate pdf

[editorialbot]

⚠️ An error happened when generating the pdf. Problem with affiliations for Chris Vernon, perhaps the affiliations index need quoting?.

[crvernon]

@editorialbot generate pdf

[editorialbot]

⚠️ An error happened when generating the pdf. Problem with affiliations for Chris Vernon, perhaps the affiliations index need quoting?.

[crvernon]

@editorialbot generate pdf

[editorialbot]

⚠️ An error happened when generating the pdf. Problem with affiliations for Chris Vernon, perhaps the affiliations index need quoting?.

[crvernon]

@xuanxu could you help me out with the above error? The format in the paper.md file seems consistent with what I have always done.

Thanks in advance!

[xuanxu]

@crvernon it seems you fixed the file in the main branch, but the branch set for the submission is dev

[crvernon]

@xuanxu ahh, missed that. Thank you!

[crvernon]

@editorialbot set main as branch

[editorialbot]

Done! branch is now main

[crvernon]

@editorialbot generate pdf

[editorialbot]

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

[crvernon]

Alright @kthyng this one is ready for you. Thanks!

[kthyng]

Ok looks good!

[kthyng]

@editorialbot accept

[editorialbot]

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

[editorialbot]

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Thompson
  given-names: Isaac
  orcid: "https://orcid.org/0000-0001-9594-0043"
- family-names: Vernon
  given-names: Chris R.
  orcid: "https://orcid.org/0000-0002-3406-6214"
- family-names: Khan
  given-names: Zarrar
  orcid: "https://orcid.org/0000-0002-8147-8553"
contact:
- family-names: Vernon
  given-names: Chris R.
  orcid: "https://orcid.org/0000-0002-3406-6214"
doi: 10.5281/zenodo.10966693
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Thompson
    given-names: Isaac
    orcid: "https://orcid.org/0000-0001-9594-0043"
  - family-names: Vernon
    given-names: Chris R.
    orcid: "https://orcid.org/0000-0002-3406-6214"
  - family-names: Khan
    given-names: Zarrar
    orcid: "https://orcid.org/0000-0002-8147-8553"
  date-published: 2024-05-29
  doi: 10.21105/joss.05855
  issn: 2475-9066
  issue: 97
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5855
  title: "Tethys: A Spatiotemporal Downscaling Model for Global Water
    Demand"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05855"
  volume: 9
title: "Tethys: A Spatiotemporal Downscaling Model for Global Water
  Demand"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

[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.05855 joss-papers#5408
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05855
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]

Congratulations on your new publication @ifthompson and @crvernon! Many thanks to reviewers @Mariosmsk and @nickrsan for your time, hard work, and expertise!! JOSS wouldn't be able to function nor succeed without your efforts.

[editorialbot]

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

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