[REVIEW]: hf_hydrodata: A Python package for accessing hydrologic simulations and observations across the United States

[editorialbot]

Submitting author: @amy-defnet (Amy Defnet)
Repository: https://github.com/hydroframe/hf_hydrodata
Branch with paper.md (empty if default branch):
Version: v1.1.12
Editor: @rwegener2
Reviewers: @thodson-usgs, @alessandroamaranto
Archive: 10.5281/zenodo.12700800

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/0f71e8275dbff415d2f76e1089c34dc8"><img src="https://joss.theoj.org/papers/0f71e8275dbff415d2f76e1089c34dc8/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/0f71e8275dbff415d2f76e1089c34dc8/status.svg)](https://joss.theoj.org/papers/0f71e8275dbff415d2f76e1089c34dc8)

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

@thodson-usgs & @alessandroamaranto, 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 @rwegener2 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 @thodson-usgs

📝 Checklist for @alessandroamaranto

[editorialbot]

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

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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

- 10.1126/science.aaf7891 is OK
- 10.5194/gmd-14-7223-2021 is OK
- 10.1016/j.jhydrol.2023.130294 is OK
- 10.1109/MCSE.2011.37 is OK
- 10.5281/zenodo.3509134 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.09 s (829.1 files/s, 233366.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          19           1630           2462           7049
CSV                             16              0              0            633
reStructuredText                24            256            426            416
Jupyter Notebook                 6              0           8203            256
Markdown                         2             72              0            163
YAML                             2             56             12            119
TeX                              1              4              0             53
TOML                             1              6              2             33
Bourne Shell                     3              1              5             28
DOS Batch                        1              8              1             27
make                             1              4              5             11
HTML                             1              0              0              7
CSS                              1              0              0              6
-------------------------------------------------------------------------------
SUM:                            78           2037          11116           8801
-------------------------------------------------------------------------------

Commit count by author:

    68	wh3248
    53	Bill Hasling
    37	Amy Defnet
    13	amymjohnson4000
     9	Will Lytle
     8	Amy Johnson
     4	George Artavanis
     4	reedmaxwell
     2	Laura Condon
     1	gartavanis

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 986

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🟡 License found: Other (Check here for OSI approval)

[editorialbot]

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

[rwegener2]

👋🏼 @amy-defnet @thodson-usgs @alessandroamaranto this is the review thread for the paper. All of our communications will happen here from now on.

As a reviewer, the first step is to create a checklist for your review by entering

@editorialbot generate my checklist

as the top of a new comment in this thread.

These checklists contain the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. The first comment in this thread also contains 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 openjournals/joss-reviews#6623 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 reviews to be completed within about 2-4 weeks. Please let me know if any of you require some more time. We can also use EditorialBot (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@rwegener2) if you have any questions/concerns.

[thodson-usgs]

Review checklist for @thodson-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/hydroframe/hf_hydrodata?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@amy-defnet) 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?

[rwegener2]

Hey @alessandroamaranto 👋🏻. If you have any questions about where to begin please don't hesitate to reach out! The first step is to create your checklist by commenting in this issue with @editorialbot generate my checklist. You can ping me right on this issue for questions.

[alessandroamaranto]

Review checklist for @alessandroamaranto

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/hydroframe/hf_hydrodata?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@amy-defnet) 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?

[thodson-usgs]

@rwegener2, I've completed my review. The package is functional and documented. However, it mainly provides an API to another database, which I had to register to use, as well as maintain a temporary 2-day PIN. Some question whether it meets the bar of scholarly effort, because a lot of this data is publicly available from other endpoints and Python packages. To that end, it might be good to request either a "state of the field" to better explain its niche, or else a usage example that does something more than query a database or project spatial coordinates.

[alessandroamaranto]

@rwegener2 My review is still in process. However, I already agree with @thodson-usgs in the state of the field paragraph. It would be beneficial for the authors to elaborate on similar applications, (for example https://cran.r-project.org/web/packages/dataRetrieval/index.html), and highlight how hf_hydrodata offers distinct advantages in these areas.

[amy-defnet]

Thank you both for your reviews and feedback! @thodson-usgs @alessandroamaranto While it is true that our API is providing access to datasets that are publicly accessible, the value of our database and tool is that we are pulling together data across many different datasets and processing it so that it can be easily accessed with a single API call. For example, users can easily grab both groundwater, surface water, and ET observations from a basin and get data that is in a consistent and easy to use format. Without our tool, this would have required interacting with three different APIs and conducting significant post-processing on data to get it into a usable format. We agree that this point was not made clearly enough in our original manuscript. Our team has updated our paper draft on the main branch with a "State of the Field" section to address these comments.

[rwegener2]

Thanks @amy-defnet for the explanation and for clarifying that information in the manuscript. Please also include a similar description somewhere in your documentation and comment here to let the team know when you've added that.

@thodson-usgs and @alessandroamaranto This seems to be a sufficient statement of scholarly effort. Are you both satisfied?
@alessandroamaranto anything else you need to continue your review?

[thodson-usgs]

For JOSS, I'm satisfied.
But I'll pick on this point a little more, b/c it isn't the only package in this space.
I don't think you need to list them, but if this package is primarily a preprocessor targeting a particular model (i.e. Parflow) then say so. If it's more general, I would list some of the specific models that it's helpful for. Your readers will appreciate that.

[amy-defnet]

Thanks @rwegener2: I've updated our README to also include the "state of the field" description that we had added to our manuscript.

[rwegener2]

@alessandroamaranto Do you have any questions to finish your review?

[alessandroamaranto]

Sorry for the delay but..my daughter was born! If I remember correctly, I was basically ok with the idea of the state of the field section for giving the green light. I will just have a look at the final version in the afternoon (but just to cross all the t's), and then proceed.

…

On Sat, Jun 15, 2024 at 5:34 PM Rachel Wegener ***@***.***> wrote: @alessandroamaranto <https://github.com/alessandroamaranto> Do you have any questions to finish your review? — Reply to this email directly, view it on GitHub <#6623 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADJOC4LLB56D6KCM77HUCCLZHRNHFAVCNFSM6AAAAABGH5TTBKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNRZHEYTOMJQGI> . You are receiving this because you were mentioned.Message ID: ***@***.***>

-- Alessandro Amaranto. Postdoctoral research fellow Dept. of Electronics, Information, and Bioengineering Politecnico di Milano, Italy

[alessandroamaranto]

for me it's a go

[amy-defnet]

Congratulations, @alessandroamaranto! Thanks for the review.

@rwegener2 can you advise on what the next steps are? Let me know if you need anything from our end. Thanks!

[rwegener2]

Sorry for the delay but..my daughter was born!'

Congratulations @alessandroamaranto!!!

[rwegener2]

@amy-defnet at this point could you please:

• Make a tagged release of your software, and list the version tag of the archived version here.
• Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
• Check the archival deposit (e.g., in Zenodo) 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 recommending acceptance of the submission.

[rwegener2]

Hi @amy-defnet 👋🏻

Just a few minor requests for the text:

• line 14: The second comma caused me to stumble. I suggest removing it "in situ observations such as streamflow rate and depth to groundwater , can be used to ...". Or, alternately, add a comma between "observations" and "such as"
• line 63-65: I was a little confused here - is this sentence is talking about the gridded data products still, or all of the aforementioned data products? Maybe: "Many of these gridded data products, such as inputs and outputs from the national ParFlow model and multiple gridded atmospheric forcing datasets, are not publicly available by other means."
• line 73-75: Is this a complete sentence? Maybe: "However the API is structured to take in compatible input parameters (where applicable) and to make the data querying process as seamless as possible across the different data types." or "However the API is structured to take in compatible input parameters (where applicable) in order to make the data querying process as seamless as possible across the different data types."

Cross through is the existing text to be deleted. Bolded text is text to be added. Thanks!

[amy-defnet]

Thanks, @rwegener2! I've adjusted the text given your suggestions.

I created a tagged release, which is version 1.1.12. I archived this with Zenodo and confirmed that the metadata there aligns with the paper title and authors. The DOI is: 10.5281/zenodo.12700800.

Let me know if you need anything else!

[rwegener2]

@editorialbot generate pdf

[editorialbot]

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

[rwegener2]

@editorialbot set https://doi.org/10.5281/zenodo.12700800 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.12700800

[rwegener2]

@editorialbot set v1.1.12 as version

[editorialbot]

Done! version is now v1.1.12

[rwegener2]

@editorialbot generate pdf

[editorialbot]

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

[rwegener2]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1126/science.aaf7891 is OK
- 10.5194/gmd-14-7223-2021 is OK
- 10.1016/j.jhydrol.2023.130294 is OK
- 10.1109/MCSE.2011.37 is OK
- 10.5281/zenodo.3509134 is OK
- 10.5066/P9X4L3GE is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/ese-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#5678, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[kthyng]

Hi! I'll take over now as Track Associate Editor in Chief to do some final submission editing checks. After these checks are complete, I will publish your submission!

• Are checklists all checked off?
• Check that version was updated and make sure the version from JOSS matches github and Zenodo.
• Check that software archive exists, has been input to JOSS, and title and author list match JOSS paper (or purposefully do not).
• Check paper.

[kthyng]

I see that two boxes are not checked off for @thodson-usgs but I also read through the discussion that implied their subsequent checking ✅

[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: Defnet
  given-names: Amy
  orcid: "https://orcid.org/0000-0003-2261-708X"
- family-names: Hasling
  given-names: William
- family-names: Condon
  given-names: Laura
  orcid: "https://orcid.org/0000-0003-3639-8076"
- family-names: Johnson
  given-names: Amy
- family-names: Artavanis
  given-names: Georgios
- family-names: Triplett
  given-names: Amanda
  orcid: "https://orcid.org/0009-0009-8085-3938"
- family-names: Lytle
  given-names: William
- family-names: Maxwell
  given-names: Reed
  orcid: "https://orcid.org/0000-0002-1364-4441"
doi: 10.5281/zenodo.12700800
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Defnet
    given-names: Amy
    orcid: "https://orcid.org/0000-0003-2261-708X"
  - family-names: Hasling
    given-names: William
  - family-names: Condon
    given-names: Laura
    orcid: "https://orcid.org/0000-0003-3639-8076"
  - family-names: Johnson
    given-names: Amy
  - family-names: Artavanis
    given-names: Georgios
  - family-names: Triplett
    given-names: Amanda
    orcid: "https://orcid.org/0009-0009-8085-3938"
  - family-names: Lytle
    given-names: William
  - family-names: Maxwell
    given-names: Reed
    orcid: "https://orcid.org/0000-0002-1364-4441"
  date-published: 2024-07-26
  doi: 10.21105/joss.06623
  issn: 2475-9066
  issue: 99
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6623
  title: "hf_hydrodata: A Python package for accessing hydrologic
    simulations and observations across the United States"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06623"
  volume: 9
title: "hf_hydrodata: A Python package for accessing hydrologic
  simulations and observations across the United States"

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.06623 joss-papers#5685
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06623
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 @amy-defnet! Many thanks to @rwegener2 and to reviewers @thodson-usgs and @alessandroamaranto 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! 🎉🎉🎉

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.06623/status.svg)](https://doi.org/10.21105/joss.06623)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06623">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06623/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06623/status.svg
   :target: https://doi.org/10.21105/joss.06623

This is how it will look in your documentation:

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The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

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[kthyng]

@amy-defnet Please register at https://reviewers.joss.theoj.org/ if you'd like to review for JOSS in the future!

[amy-defnet]

Thanks, @kthyng! Thank you so much @rwegener2 and @thodson-usgs and @alessandroamaranto for taking the time to review and provide your feedback!