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[REVIEW]: hf_hydrodata: A Python package for accessing hydrologic simulations and observations across the United States #6623

Closed editorialbot closed 2 months ago

editorialbot commented 5 months ago

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

Status

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 commented 5 months ago

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:

@editorialbot commands

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

@editorialbot generate pdf
editorialbot commented 5 months ago 
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 commented 5 months ago

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 commented 5 months ago

Paper file info:

📄 Wordcount for paper.md is 986

✅ The paper includes a Statement of need section

editorialbot commented 5 months ago

License info:

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

editorialbot commented 5 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

rwegener2 commented 5 months ago

👋🏼 @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 commented 5 months ago

Review checklist for @thodson-usgs

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

rwegener2 commented 4 months ago

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 commented 4 months ago

Review checklist for @alessandroamaranto

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

thodson-usgs commented 4 months ago

@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 commented 4 months ago

@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 commented 4 months ago

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 commented 3 months ago

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 commented 3 months ago

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 commented 3 months ago

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

rwegener2 commented 3 months ago

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

alessandroamaranto commented 3 months ago

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 https://github.com/openjournals/joss-reviews/issues/6623#issuecomment-2169917102, 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 commented 3 months ago

for me it's a go

amy-defnet commented 2 months ago

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 commented 2 months ago

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

Congratulations @alessandroamaranto!!!

rwegener2 commented 2 months ago

@rwegener2 can you advise on what the next steps are?

Yes, thanks for checking in @amy-defnet . The next step is for me to perform the post-review checks. I'll start that process now. There will be a few steps for you, which I'll post below. Once you and I both finish our steps we will be ready for the final set of checks by the Track Editor-in-Chief, who will then, upon recommendation, publish the article.

rwegener2 commented 2 months ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance

Editor checks paper proof:

Editor checks archive generated by author:

Editor double checks paper and recommends submission:

rwegener2 commented 2 months ago

@editorialbot generate pdf

editorialbot commented 2 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

rwegener2 commented 2 months ago

@editorialbot check references

editorialbot commented 2 months ago 
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
rwegener2 commented 2 months ago

@amy-defnet at this point could you please:

I can then move forward with recommending acceptance of the submission.

rwegener2 commented 2 months ago

Hi @amy-defnet 👋🏻

Just a few minor requests for the text:

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

amy-defnet commented 2 months ago

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 commented 2 months ago

@editorialbot generate pdf

editorialbot commented 2 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

rwegener2 commented 2 months ago

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

editorialbot commented 2 months ago

Done! archive is now 10.5281/zenodo.12700800

rwegener2 commented 2 months ago

@editorialbot set v1.1.12 as version

editorialbot commented 2 months ago

Done! version is now v1.1.12

rwegener2 commented 2 months ago

@editorialbot generate pdf

editorialbot commented 2 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

rwegener2 commented 2 months ago

@editorialbot recommend-accept

editorialbot commented 2 months ago 
Attempting dry run of processing paper acceptance...
editorialbot commented 2 months ago 
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 commented 2 months ago

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

Check final proof :point_right::page_facing_up: Download article

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

kthyng commented 2 months ago

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!

kthyng commented 2 months ago

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 commented 2 months ago

@editorialbot accept

editorialbot commented 2 months ago 
Doing it live! Attempting automated processing of paper acceptance...
editorialbot commented 2 months ago

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 commented 2 months ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot commented 2 months ago

🚨🚨🚨 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 :point_right: https://github.com/openjournals/joss-papers/pull/5685
  2. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06623
  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...

kthyng commented 2 months ago

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.