[REVIEW]: xagg: A Python package to aggregate gridded data onto polygons

editorialbot commented 1 month ago

Submitting author: !--author-handle-->@ks905383@crvernon<!--end-editor-- Reviewers: @thurber, @hariharanragothaman Archive: Pending

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

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

@editorialbot generate my checklist

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

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

Checklists

📝 Checklist for @hariharanragothaman

📝 Checklist for @thurber

editorialbot commented 1 month ago

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editorialbot commented 1 month ago

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

✅ OK DOIs

- 10.1002/qj.3803 is OK
- 10.1093/reep/ret016 is OK
- 10.1073/pnas.0906865106 is OK
- 10.1126/science.aal4369 is OK
- 10.21105/jose.00090 is OK
- 10.1073/pnas.2208095119 is OK
- 10.1093/qje/qjac020 is OK
- 10.5281/zenodo.8370810 is OK
- 10.48690/1523377 is OK
- 10.3390/rs15092247 is OK
- 10.20944/preprints202406.0149.v1 is OK
- 10.48550/arXiv.2311.18521 is OK
- 10.1002/met.2101 is OK
- 10.5334/jors.148 is OK
- 10.5281/zenodo.12625316 is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

editorialbot commented 1 month ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.04 s (1060.6 files/s, 234742.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
XML                              1             72              1           2934
Python                          17            732           1280           1656
YAML                            15             12             44            283
TeX                              1             14              0            233
reStructuredText                 6             91             43            132
Markdown                         2             47              0            105
Jupyter Notebook                 2              0           2409             38
DOS Batch                        1              8              1             26
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            46            980           3785           5416
-------------------------------------------------------------------------------

Commit count by author:

   123  Kevin Schwarzwald
    13  kerriegeil
    10  ks905383
     6  dependabot[bot]
     3  Ray Bell
     3  jsadler2

editorialbot commented 1 month ago

Paper file info:

📄 Wordcount for paper.md is 1022

✅ The paper includes a Statement of need section

editorialbot commented 1 month ago

License info:

🟡 License found: GNU General Public License v3.0 (Check here for OSI approval)

editorialbot commented 1 month ago

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

crvernon commented 1 month ago

👋 @ks905383 , @thurber, and @hariharanragothaman - This is the review thread for the paper. All of our communications will happen here from now on.

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

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

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention https://github.com/openjournals/joss-reviews/issues/7239 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

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

hariharanragothaman commented 1 month ago

Thanks @crvernon for all the detailed context. Will definitely follow the guidelines and suggestions! ✅

hariharanragothaman commented 1 month ago

Review checklist for @hariharanragothaman

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/ks905383/xagg/?
[x] 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 (@ks905383) 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?

thurber commented 1 month ago

Review checklist for @thurber

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/ks905383/xagg/?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@ks905383) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

crvernon commented 2 weeks ago

👋 @ks905383 , @thurber, and @hariharanragothaman - could you each provide a short update here in this thread? Thanks!

thurber commented 2 weeks ago

hi @crvernon, my review is in process, i logged a couple minor issues today; once those are resolved i can wrap up.

@ks905383, the review checklist includes confirming that a community/contribution guideline exists as part of your documentation. Can you add something like that, or point me toward it if i've missed it?

ks905383 commented 1 week ago

@ks905383, the review checklist includes confirming that a community/contribution guideline exists as part of your documentation. Can you add something like that, or point me toward it if i've missed it?

Ah yes, that's definitely missing right now, thanks for pointing that out. Do you have any favorite templates? Otherwise I'll look around for a good example to work off of.

thurber commented 1 week ago

Ah yes, that's definitely missing right now, thanks for pointing that out. Do you have any favorite templates? Otherwise I'll look around for a good example to work off of.

The GitHub guidelines are pretty good and point to some examples: https://docs.github.com/en/communities/setting-up-your-project-for-healthy-contributions/setting-guidelines-for-repository-contributors

ks905383 commented 1 week ago

Thanks @thurber for the raised issues and suggestions! I've fixed the bugs that you ran into (the fixes are in the main branch; I'll include them in the next update with any other fixes from this review, unless you'd like to check them earlier) and added contribution guidelines to the README and the docs.

thurber commented 1 week ago

Thanks @ks905383; I'll try to wrap up my review today or early next week!

thurber commented 4 days ago

@ks905383, I've tested the updates you made to address my issues, and all looks good! I have a couple final thoughts below, but otherwise feel the publication is ready. Thanks for this useful software!

[ ] In your updates last week, a couple files got added to the root of the repo that probably don't belong: one file just named = and another named =0.7.1.
[ ] I think it is important to make it more obvious in both the paper and the docs that the software is currently only designed to work with data and shapes defined on an equirectangular projection, and additionally that the data must be defined on a rectangular grid. It would be amazing to eventually support other projections and non-rectangular grids, but I recognize that as being difficult and out of scope.

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