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[REVIEW]: SubsetTools: A Python package to subset data to build and run ParFlow hydrologic models #6752

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editorialbot opened this issue May 14, 2024 · 79 comments
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accepted published Papers published in JOSS Python recommend-accept Papers recommended for acceptance in JOSS. review TeX Track: 6 (ESE) Earth Sciences and Ecology

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editorialbot commented May 14, 2024

Submitting author: @gartavanis (Georgios Artavanis)
Repository: https://github.com/hydroframe/subsettools
Branch with paper.md (empty if default branch): joss-paper
Version: v2.0.1
Editor: @cheginit
Reviewers: @JannisHoch, @dvalters
Archive: 10.5281/zenodo.12707059

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/295484053df46efd1ab01743c62385af"><img src="https://joss.theoj.org/papers/295484053df46efd1ab01743c62385af/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/295484053df46efd1ab01743c62385af/status.svg)](https://joss.theoj.org/papers/295484053df46efd1ab01743c62385af)

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

@JannisHoch & @dvalters, 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 @cheginit 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 @dvalters

📝 Checklist for @JannisHoch

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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

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

OK DOIs

- 10.13182/NSE96-A24230 is OK
- 10.1016/j.advwatres.2005.08.006 is OK
- 10.1029/2007wr006004 is OK
- 10.1016/j.advwatres.2012.10.001 is OK
- 10.1126/science.aaf7891 is OK
- 10.5194/gmd-8-923-2015 is OK
- 10.5194/gmd-14-7223-2021 is OK
- 10.1111/gwat.13357 is OK
- 10.1016/j.jhydrol.2023.130294 is OK
- 10.5194/essd-13-3263-2021 is OK

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.1016/S0309-1708(00)00075-0 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1175/JHM422.1 is INVALID because of 'https://doi.org/' prefix

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Software report:

github.com/AlDanial/cloc v 1.90  T=0.04 s (1153.6 files/s, 255214.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
YAML                            10              3              7           4965
Python                          14            333            490           1298
Jupyter Notebook                 8              0           2843            482
Markdown                        13            146              0            357
TeX                              1             11              0            140
reStructuredText                 2             30             14             76
TOML                             1              4              0             29
DOS Batch                        1              8              1             27
make                             1              4              5             10
-------------------------------------------------------------------------------
SUM:                            51            539           3360           7384
-------------------------------------------------------------------------------

Commit count by author:

   228	George Artavanis
   113	gartavanis
    50	aktriplett
     2	arbennett

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Paper file info:

📄 Wordcount for paper.md is 1364

✅ The paper includes a Statement of need section

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License info:

✅ License found: MIT License (Valid open source OSI approved license)

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

@cheginit
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👋🏼 @gartavanis, @JannisHoch & @dvalters, this is the review thread for the paper. All of our communications will happen here from now on.

As a reviewer, the first step, as mentioned in the first comment of this issue, 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#6752 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 notify me 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 don't hesitate to ping me (@cheginit) if you have any questions/concerns.

@cheginit
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Hi @JannisHoch and @dvalters, a friendly reminder for reviewing this submission.

@dvalters
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dvalters commented Jun 6, 2024

Review checklist for @dvalters

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

General checks

  • Repository: Is the source code for this software available at the https://github.com/hydroframe/subsettools?
  • 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 (@gartavanis) 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?

@dvalters
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dvalters commented Jun 6, 2024

I'm part way through the review and just waiting for a PIN/registration process to complete so I can access the ParFlow data for testing. Will continue once this is received

@cheginit
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cheginit commented Jun 8, 2024

@dvalters Thank you for the update. Also, please let me know about your experience with the process of getting the PIN.

@JannisHoch
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JannisHoch commented Jun 10, 2024

Review checklist for @JannisHoch

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

General checks

  • Repository: Is the source code for this software available at the https://github.com/hydroframe/subsettools?
  • 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 (@gartavanis) 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?

@dvalters
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dvalters commented Jun 14, 2024

Hi @cheginit The software meets all the requirements to be accepted by JOSS and I suggest it be accepted as is. Getting the PIN and registering it to access the sample data was fairly straightforward.

I could not get every single test to run on my machine, however I suspect that is down to requiring extra data sources for certain tests that I don't have. The software clearly has a fairly comprehensive suite of tests and I'm happy for it to pass that criteria without me needing to verify every single unit test. (which I would not have time to do)

[...] if the submitting authors have followed best practices (have documentation, tests, continuous integration, and a license) then their review should be rapid.

A nice piece of software @gartavanis 👍

@JannisHoch
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sorry for being slow with the review, will work on it next week

@cheginit
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@dvalters Thanks for taking the time to review the package. Usually, pytest tests can be run with a single pytest command invocation. @gartavanis, I noticed that in your contribution file, there's no explicit guidance on running the tests. Also, there's no contribution instruction on the website. Please make sure to add them.

@JannisHoch Thanks for the update.

@dvalters
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@cheginit yes I was able to invoke the test suite using pytest - I just meant that some of the tests failed, but it looked like an input data issue (so specific tests failed as presumably they rely on an external data source?)

@cheginit
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@dvalters I see. In that case, I'd appreciate it if you open an issue in their repo and report the failing tests, i.e., the log of running pytest, so the authors can address the issue or justify them.

@cheginit
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:wave @JannisHoch, just a friendly reminder about this review.

@JannisHoch
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@cheginit what's the definition of "original data" and "original results"?

@cheginit
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@JannisHoch In this context, original means that the data and results are produced for/by the software. For example, original data means that new data has been prepared for running the software and original results mean that the software produced new results that must be verifiable by following the instructions provided by the authors.

@JannisHoch
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Great thanks.

I created two issues. Once satisfactorily adressed, I will proceed with the review.

@cheginit
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@JannisHoch Awesome, thanks for the update!

@gartavanis
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Thanks for your review @dvalters! I'm happy to look at your pytest log, and address any issues there.

@cheginit Thanks for your suggestions. I've added instructions for running tests on the contributing file. Also, I fixed the link to the contributing instructions on the README.

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cheginit commented Jul 3, 2024

@JannisHoch A friendly reminder for this revidw.

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

@cheginit
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cheginit commented Jul 10, 2024

@gartavanis We're almost there! Please check the "Additional Author Tasks" in the previous comment and do those tasks, so I can move on to recommending acceptance!

@gartavanis
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@cheginit, I have created a new release of subsettools (https://github.com/hydroframe/subsettools/releases/tag/2.0.1). It's also on PyPI. This is version 2.0.1. The Zenodo archive is here: https://zenodo.org/records/12707059. (DOI: 10.5281/zenodo.12707059). Please let me know if there's anything else that remains to be done on our end. Thanks again for your time!

@cheginit
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@editorialbot set v2.0.1 as version

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Done! version is now v2.0.1

@cheginit
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@editorialbot set 10.5281/zenodo.12707059 as archive

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Done! archive is now 10.5281/zenodo.12707059

@cheginit
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@editorialbot recommend-accept

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Attempting dry run of processing paper acceptance...

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

OK DOIs

- 10.13182/NSE96-A24230 is OK
- 10.1016/S0309-1708(00)00075-0 is OK
- 10.1016/j.advwatres.2005.08.006 is OK
- 10.1029/2007wr006004 is OK
- 10.1016/j.advwatres.2012.10.001 is OK
- 10.1126/science.aaf7891 is OK
- 10.5194/gmd-8-923-2015 is OK
- 10.1175/JHM422.1 is OK
- 10.5194/gmd-14-7223-2021 is OK
- 10.1111/gwat.13357 is OK
- 10.1016/j.jhydrol.2023.130294 is OK
- 10.5194/essd-13-3263-2021 is OK

MISSING DOIs

- None

INVALID DOIs

- None

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👋 @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#5600, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

@editorialbot editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Jul 10, 2024
@cheginit
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@gartavanis Thanks for working on addressing the issues diligently and congrats on making it this far! The EiC will take over the submission for the final publication, in the meanwhile, please check the final proof of the paper in the previous comment, just to make sure everything looks good such as authors' names.

@gartavanis
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The final proof looks good. Thank you @cheginit, @dvalters and @JannisHoch for your time, suggestions and the smooth review process!

@kthyng
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kthyng commented Jul 17, 2024

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.

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kthyng commented Jul 17, 2024

Hi @gartavanis, I see that the version is v2.0.1 here and the repo itself, but in Zenodo it is v1. Can you update that? While you're at it, I see that your title and author list in Zenodo already match the JOSS paper (thanks!), though the authors with middle initials included might appreciate them being in Zenodo also.

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kthyng commented Jul 17, 2024

Paper:

  • page 2 paragraph before "Functionality" section: typo "Subset tools... hydrology students,researchers" (no space)

@gartavanis
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Hi @kthyng, thanks for the comments! I added the version number on Zenodo and the middle initials.

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kthyng commented Jul 17, 2024

@editorialbot generate pdf

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

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kthyng commented Jul 17, 2024

@editorialbot accept

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

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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: Triplett
  given-names: Amanda K.
  orcid: "https://orcid.org/0009-0009-8085-3938"
- family-names: Artavanis
  given-names: Georgios
  orcid: "https://orcid.org/0009-0007-6015-7746"
- family-names: Hasling
  given-names: William M.
- family-names: Maxwell
  given-names: Reed M.
  orcid: "https://orcid.org/0000-0002-1364-4441"
- family-names: Defnet
  given-names: Amy
  orcid: "https://orcid.org/0000-0003-2261-708X"
- family-names: Johnson
  given-names: Amy M.
- family-names: Lytle
  given-names: William
- family-names: Bennett
  given-names: Andrew
- family-names: Leonarduzzi
  given-names: Elena
- family-names: Gallagher
  given-names: Lisa K.
- family-names: Condon
  given-names: Laura E.
  orcid: "https://orcid.org/0000-0003-3639-8076"
contact:
- family-names: Triplett
  given-names: Amanda K.
  orcid: "https://orcid.org/0009-0009-8085-3938"
- family-names: Artavanis
  given-names: Georgios
  orcid: "https://orcid.org/0009-0007-6015-7746"
- family-names: Maxwell
  given-names: Reed M.
  orcid: "https://orcid.org/0000-0002-1364-4441"
- family-names: Condon
  given-names: Laura E.
  orcid: "https://orcid.org/0000-0003-3639-8076"
doi: 10.5281/zenodo.12707059
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Triplett
    given-names: Amanda K.
    orcid: "https://orcid.org/0009-0009-8085-3938"
  - family-names: Artavanis
    given-names: Georgios
    orcid: "https://orcid.org/0009-0007-6015-7746"
  - family-names: Hasling
    given-names: William M.
  - family-names: Maxwell
    given-names: Reed M.
    orcid: "https://orcid.org/0000-0002-1364-4441"
  - family-names: Defnet
    given-names: Amy
    orcid: "https://orcid.org/0000-0003-2261-708X"
  - family-names: Johnson
    given-names: Amy M.
  - family-names: Lytle
    given-names: William
  - family-names: Bennett
    given-names: Andrew
  - family-names: Leonarduzzi
    given-names: Elena
  - family-names: Gallagher
    given-names: Lisa K.
  - family-names: Condon
    given-names: Laura E.
    orcid: "https://orcid.org/0000-0003-3639-8076"
  date-published: 2024-07-17
  doi: 10.21105/joss.06752
  issn: 2475-9066
  issue: 99
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6752
  title: "SubsetTools: A Python package to subset data to build and run
    ParFlow hydrologic models"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06752"
  volume: 9
title: "SubsetTools: A Python package to subset data to build and run
  ParFlow hydrologic models"

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.

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🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

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🚨🚨🚨 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 👉 Creating pull request for 10.21105.joss.06752 joss-papers#5639
  2. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06752
  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...

@editorialbot editorialbot added accepted published Papers published in JOSS labels Jul 17, 2024
@kthyng
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kthyng commented Jul 17, 2024

Congratulations on your new publication @gartavanis! Many thanks to @cheginit and to reviewers @JannisHoch and @dvalters for your time, hard work, and expertise!! JOSS wouldn't be able to function nor succeed without your efforts.

@kthyng kthyng closed this as completed Jul 17, 2024
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🎉🎉🎉 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.06752/status.svg)](https://doi.org/10.21105/joss.06752)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06752">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06752/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06752/status.svg
   :target: https://doi.org/10.21105/joss.06752

This is how it will look in your documentation:

DOI

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