[REVIEW]: W2W: A Python package that injects WUDAPT’s Local Climate Zone information in WRF

[editorialbot]

Submitting author: @matthiasdemuzere (Matthias Demuzere) Repository: https://github.com/matthiasdemuzere/w2w Branch with paper.md (empty if default branch): Version: v0.2.0 Editor: @crvernon Reviewers: @thurber, @erexer 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 & @erexer, 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 @thurber

📝 Checklist for @erexer

[editorialbot]

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.05 s (188.2 files/s, 75251.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                           3            509            254           2096
TeX                              1             39              0            351
Markdown                         2             83              0            192
YAML                             2              3              0             56
INI                              1              3              0             13
-------------------------------------------------------------------------------
SUM:                             9            637            254           2708
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1971

[editorialbot]

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

OK DOIs

- 10.5194/essd-2022-92 is OK
- 10.1002/joc.3746 is OK
- 10.1175/BAMS-D-11-00019.1 is OK
- 10.1029/2020GL088758 is OK
- 10.1023/A:1019207923078 is OK
- 10.1007/s00704-009-0142-9 is OK
- 10.1023/A:1016099921195 is OK
- 10.1016/j.uclim.2020.100584 is OK
- 10.3390/atmos11121349 is OK
- 10.1371/journal.pone.0214474 is OK
- 10.1038/s41597-020-00605-z is OK
- 10.3389/fenvs.2021.637455 is OK
- 10.5065/1dfh-6p97 is OK
- 10.1029/2021JD035002 is OK
- 10.1175/BAMS-D-16-0236.1 is OK
- 10.1016/j.uclim.2016.04.001 is OK
- 10.1002/joc.5447 is OK
- 10.1007/s00704-019-02881-1 is OK
- 10.1016/j.uclim.2019.100460 is OK
- 10.1016/j.uclim.2020.100616 is OK
- 10.1016/j.atmosres.2020.105220 is OK
- 10.1088/1748-9326/ac0377 is OK
- 10.1186/s40562-018-0126-7 is OK
- 10.1175/JAMC-D-17-0328.1 is OK

MISSING DOIs

- 10.1029/2021jd035316 may be a valid DOI for title: Modelling Large-Scale Heatwave by Incorporating Enhanced Urban Representation

INVALID DOIs

- None

[editorialbot]

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

[crvernon]

:wave: @matthiasdemuzere , @thurber , @erexer - 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/4432 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.

[thurber]

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/matthiasdemuzere/w2w?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Contribution and authorship: Has the submitting author (@matthiasdemuzere) 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

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 and who the target audience is?
• [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?

[erexer]

Review checklist for @erexer

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/matthiasdemuzere/w2w?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Contribution and authorship: Has the submitting author (@matthiasdemuzere) 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

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 and who the target audience is?
• [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?

[kyleniemeyer]

Hi @erexer, just checking in on the status of your review. Are you able to complete it soon, or do you have feedback for the authors based on the unchecked items?

[crvernon]

@kyleniemeyer ... @erexer notified me that they will be back from vacation next week. Thanks!

[erexer]

@kyleniemeyer As Chris said I was out the past couple of weeks but I'll be reviewing w2w this week. Thanks for your patience!

[crvernon]

@matthiasdemuzere and @erexer how are things going on satisfying that last checkbox? Can you give me a progress report here on any outstanding issues? Thanks!

[jkittner]

Matthias should be back from vaccation in the next days. Then we can finally address the last point.

[matthiasdemuzere]

@crvernon I just addressed the last point (see here), and I am awaiting approval from my colleagues.

Once in, I hope this sufficiently addresses all helpful feedback provided by @erexer!

[matthiasdemuzere]

Ok, all checks by @erexer are addressed now. I am looking forward to the next steps!

[crvernon]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.5194/essd-2022-92 is OK
- 10.1002/joc.3746 is OK
- 10.1175/BAMS-D-11-00019.1 is OK
- 10.1029/2020GL088758 is OK
- 10.1023/A:1019207923078 is OK
- 10.1007/s00704-009-0142-9 is OK
- 10.1023/A:1016099921195 is OK
- 10.1016/j.uclim.2020.100584 is OK
- 10.3390/atmos11121349 is OK
- 10.1371/journal.pone.0214474 is OK
- 10.1038/s41597-020-00605-z is OK
- 10.3389/fenvs.2021.637455 is OK
- 10.5065/1dfh-6p97 is OK
- 10.1029/2021JD035002 is OK
- 10.1175/BAMS-D-16-0236.1 is OK
- 10.1016/j.uclim.2016.04.001 is OK
- 10.1002/joc.5447 is OK
- 10.1007/s00704-019-02881-1 is OK
- 10.1016/j.uclim.2019.100460 is OK
- 10.1016/j.uclim.2020.100616 is OK
- 10.1016/j.atmosres.2020.105220 is OK
- 10.1088/1748-9326/ac0377 is OK
- 10.1186/s40562-018-0126-7 is OK
- 10.1175/JAMC-D-17-0328.1 is OK

MISSING DOIs

- 10.1029/2021jd035316 may be a valid DOI for title: Modelling Large-Scale Heatwave by Incorporating Enhanced Urban Representation

INVALID DOIs

- None

[crvernon]

@editorialbot generate pdf

[editorialbot]

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

[crvernon]

Editor's note: The missing DOI warning above does not seem to be an issue and is represented correctly in the paper.

MISSING DOIs

• 10.1029/2021jd035316 may be a valid DOI for title: Modelling Large-Scale Heatwave by Incorporating Enhanced Urban Representation

[crvernon]

@matthiasdemuzere here are a few outstanding things you need to address:

In paper.md:

• [x] [LINE 73] need an actual citation for "the chord length formula" and not a link to a wikipedia page, which can change often.

Once the above change has been made:

• [ ] Conduct a GitHub release of the current reviewed version of the software you now have on the main and archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository) - you can link your GitHub repository to automatically generate your DOI on release. Zenodo will recognize your CITATION.cff file and populate the metadata of your release with that information.
• [ ] Check the archival deposit (e.g., in Zenodo) to ensure it 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 accepting the submission!

[matthiasdemuzere]

@dargueso will follow up on the reference.

When fixed, I'll look into the remaining three check boxes!

[dargueso]

@matthiasdemuzere here are a few outstanding things you need to address:

In paper.md:

• [ ] [LINE 73] need an actual citation for "the chord length formula" and not a link to a wikipedia page, which can change often.

We have clarified the method and added references for the KDtree algorithm. We used the Euclidean distance as a metric of proximity over the 3D space by converting geographical coordinates (R, lat, lon) to cartesian coordinates (x, y ,z). The resulting length is the chord of the great circle arc. We added a definition of the great circle arc to the text, but we think the chord is a well established term and does not need a reference.

Hope this make the method clearer.

[crvernon]

@dargueso fine for me. Thanks.

[dargueso]

@crvernon, Thanks to you for your time reviewing the manuscript!

[crvernon]

No problem @matthiasdemuzere and @dargueso

Once you get the following knocked out, we will move forward. Thanks!

• [ ] Conduct a GitHub release of the current reviewed version of the software you now have on the main and archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository) - you can link your GitHub repository to automatically generate your DOI on release. Zenodo will recognize your CITATION.cff file and populate the metadata of your release with that information.
• [ ] Check the archival deposit (e.g., in Zenodo) to ensure it 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

[matthiasdemuzere]

• [x] Conduct a GitHub release of the current reviewed version of the software you now have on the main and archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository) - you can link your GitHub repository to automatically generate your DOI on release. Zenodo will recognize your CITATION.cff file and populate the metadata of your release with that information.

I have released a new version 0.4.1, and created a Zenodo repo for this: 10.5281/zenodo.7016607

• [x] Check the archival deposit (e.g., in Zenodo) to ensure it 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.

I checked these things, looks fine to me.

• [x] Please list the DOI of the archived version here

10.5281/zenodo.7016607

I hope all of the above is as expected?

[crvernon]

@editorialbot set v0.4.1 as version

[editorialbot]

Done! version is now v0.4.1

[crvernon]

@editorialbot set 10.5281/zenodo.7016607 as archive