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[REVIEW]: naturf: a package for generating urban parameters for numerical weather modeling #6712

Closed editorialbot closed 6 months ago

editorialbot commented 7 months ago

Submitting author: !--author-handle-->@levisweetbreu<!--end-author-handle-- (Levi Sweet-Breu) Repository: https://github.com/IMMM-SFA/naturf.git Branch with paper.md (empty if default branch): Version: v1.0.3 Editor: !--editor-->@cheginit<!--end-editor-- Reviewers: @praneethd7, @caimeng2 Archive: 10.5281/zenodo.11454159

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Markdown: [![status](https://joss.theoj.org/papers/e52937327089a970773a331a5cf643fd/status.svg)](https://joss.theoj.org/papers/e52937327089a970773a331a5cf643fd)

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

@praneethd7 & @caimeng2, 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 @praneethd7

📝 Checklist for @caimeng2

editorialbot commented 7 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 7 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.04 s (999.0 files/s, 198340.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                           8            612            505           2383
YAML                             5             42             28            355
reStructuredText                12            262            162            299
SVG                              4              4              4            298
CSS                              2             53             11            244
TeX                              1              3              0            104
Markdown                         2             32              0             79
TOML                             2              6              2             61
DOS Batch                        1              8              1             26
Jupyter Notebook                 1              0           2113             26
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            39           1026           2833           3884
-------------------------------------------------------------------------------

Commit count by author:

   103  erexer
    72  levisweet
    54  Chris Vernon
    39  em rexer
    39  levisweetbreu
    15  lg6
    14  crvernon
    13  Levi Sweet-Breu
    12  Sweet, Levi
     7  Stefan Krawczyk
     5  Dumas, Melissa
     4  emily rexer
     2  kurte
     1  Allen, Melissa R
     1  Melissa Allen-Dumas
     1  Sweet L T
editorialbot commented 7 months ago

Paper file info:

📄 Wordcount for paper.md is 830

✅ The paper includes a Statement of need section

editorialbot commented 7 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1016/j.rser.2020.110030 is OK
- 10.1175/2009BAMS2675.1 is OK
- 10.1175/BAMS-D-16-0236.1 is OK
- 10.21105/joss.03541 is OK
- 10.5281/zenodo.3946761 is OK

MISSING DOIs

- No DOI given, and none found for title: An Introduction to the WUDAPT project
- No DOI given, and none found for title: Hamilton: a modular open source declarative paradi...

INVALID DOIs

- None
editorialbot commented 7 months ago

License info:

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

editorialbot commented 7 months ago

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

cheginit commented 7 months ago

👋🏼 @levisweetbreu @praneethd7 & @caimeng2 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#6712 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.

praneethd7 commented 7 months ago

Review checklist for @praneethd7

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

praneethd7 commented 7 months ago

Hello @levisweetbreu👋! I am glad to review this work. I wanted to get a clarification on this item in the checklist:

Contribution and authorship: Has the submitting author (@levisweetbreu) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

I have made sure you have made the major contributions to the repository. I noticed there are commits from 5 people on the repository but only 4 authors are listed. I wanted to make sure you have listed out to all authors and have the authorship order correct. Thank you!

levisweetbreu commented 7 months ago

@praneethd7 thank you for your comment, we have added another author and the paper has been updated!

praneethd7 commented 7 months ago

@editorialbot commands

editorialbot commented 7 months ago

Hello @praneethd7, here are the things you can ask me to do:


# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Run checks and provide information on the repository and the paper file
@editorialbot check repository

# Check the references of the paper for missing DOIs
@editorialbot check references

# Generates the pdf paper
@editorialbot generate pdf

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers
praneethd7 commented 7 months ago

@editorialbot generate pdf

editorialbot commented 7 months ago

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

praneethd7 commented 7 months ago

@levisweetbreu The manuscript has the following statement:

NATURF was used to demonstrate that simulated new developments in the Chicago Loop neighborhood in Chicago Illinois, USA affect temperature and energy use both in the new developments and the preexisting neighborhoods (Allen-Dumas et al., 2020).

However, I did not find any mention of the package or the word NATURF in the manuscript @allen2020impacts. The way it is currently written sounds like the package existed before the publication.

cheginit commented 7 months ago

@praneethd7 Thanks for starting the review!

I just have one note. It'd be better to create issues in naturf's repo for each comment that you have, so the authors can address them, and you can close them whenever they address it. This makes it much easier to keep track of issues. Whenever you open an issue, please make sure to reference openjournals/joss-reviews#6712 so it shows up here, and I can follow the progress.

Thank you!

cheginit commented 6 months ago

Hi @praneethd7, @caimeng2, just a friendly reminder for the review.

caimeng2 commented 6 months ago

Review checklist for @caimeng2

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

caimeng2 commented 6 months ago

Hi,

This is great software. I can see it being useful. And the documentation is sufficient. I have two more suggestions for improvement:

  1. The description of the functionality in the paper could be made clearer. Something similar to the "Purpose" section in README would be nice. Currently, the "Design and Functionality" section focuses more on the design aspects rather than explaining the functionality.

  2. I noticed a minor issue where the version number in the user guide is listed as 1.0.1, while the latest version is 1.0.2. Please ensure that the use guide is up-to-date.

Aside from these, and the three open issues already noted, I am satisfied with the package and would recommend acceptance.

cheginit commented 6 months ago

👋🏼 @caimeng2 Thanks for spending time or the review and providing comments to improve the package. Please make sure to check the one remaining checkbox once you're satisfied with the authors' response.

levisweetbreu commented 6 months ago

@caimeng2 Thank you for your thoughtful review and comments! To your first suggestion above, I have added a new paragraph to the "Design and Functionality" section to better describe the functionality of our software.

praneethd7 commented 6 months ago

@editorialbot generate pdf

editorialbot commented 6 months ago

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

praneethd7 commented 6 months ago

@levisweetbreu @cheginit Hello. I have completed the review from my end and I am pleased to accept this submission for publication😄. The authors have patiently addressed all of my comments🤗. This is a great package that will be helpful to researchers trying to compute these urban parameters and model built environments. The package does exactly what it promises and installation (and usage) was straightforward. The documentation, code formatting, installation instructions, and automated tests are all in place and well-written, thereby encouraging community contributions. Happy to have reviewed this work!

I do have a set of minor suggestions but I leave it to the author's discretion to address them

cheginit commented 6 months ago

@praneethd7, thanks for your time and effort that you put into this review and proving comments for the authors to improve their submission.

@levisweetbreu, please address the remaining comments provided by @praneethd7 and @caimeng2 and ping me whenever you did so, so I can start my final checks before recommending acceptance.

levisweetbreu commented 6 months ago

@cheginit I believe all comments have been addressed. All remaining open issues are slated for future improvements on the software.

cheginit commented 6 months ago

@levisweetbreu Thanks for letting me know. I will work on the final checks.

@caimeng2 Can you please check if the authors have addressed your concerns about your last remaining checkbox, and if so, mark it as checked?

caimeng2 commented 6 months ago

@cheginit done. All the issues I raised have been closed

cheginit commented 6 months ago

@caimeng2 Thanks for your prompt response, apprecaite it.

cheginit commented 6 months ago

@editorialbot generate pdf

editorialbot commented 6 months ago

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

cheginit commented 6 months ago

@editorialbot check references

editorialbot commented 6 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1016/j.rser.2020.110030 is OK
- 10.1175/2009BAMS2675.1 is OK
- 10.1175/BAMS-D-16-0236.1 is OK
- 10.21105/joss.03541 is OK
- 10.5281/zenodo.3946761 is OK
- 10.1007/s00704-005-0143-2 is OK
- 10.1016/j.uclim.2019.100460 is OK
- 10.15485/2283980 is OK
- 10.57931/2349436 is OK

MISSING DOIs

- No DOI given, and none found for title: An Introduction to the WUDAPT project
- No DOI given, and none found for title: Hamilton: a modular open source declarative paradi...

INVALID DOIs

- None
cheginit commented 6 months ago

@levisweetbreu There are two references without DOI, and it appears that they don't have one. Please confirm the missing DOIs.

Once confirmed, please do the following, so I can then move forward with recommending acceptance of the submission:

levisweetbreu commented 6 months ago

@cheginit I confirm that there are not DOIs for those two references.

Our version is: v1.0.3 Our archive DOI is: 10.5281/zenodo.11454159

cheginit commented 6 months ago

@editorialbot set v1.0.3 as version

editorialbot commented 6 months ago

Done! version is now v1.0.3

cheginit commented 6 months ago

@editorialbot set 10.5281/zenodo.11454159 as archive

editorialbot commented 6 months ago

Done! archive is now 10.5281/zenodo.11454159

cheginit commented 6 months ago

@editorialbot recommend-accept

editorialbot commented 6 months ago 
Attempting dry run of processing paper acceptance...
editorialbot commented 6 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1016/j.rser.2020.110030 is OK
- 10.1175/2009BAMS2675.1 is OK
- 10.1175/BAMS-D-16-0236.1 is OK
- 10.21105/joss.03541 is OK
- 10.5281/zenodo.3946761 is OK
- 10.1007/s00704-005-0143-2 is OK
- 10.1016/j.uclim.2019.100460 is OK
- 10.15485/2283980 is OK
- 10.57931/2349436 is OK

MISSING DOIs

- No DOI given, and none found for title: An Introduction to the WUDAPT project
- No DOI given, and none found for title: Hamilton: a modular open source declarative paradi...

INVALID DOIs

- None
editorialbot commented 6 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/5455, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

cheginit commented 6 months ago

@levisweetbreu Congrats on your publication! Great work on addressing the comments and thanks to the reviewers, @praneethd7 and @caimeng2, for their time and effort to improve the submission.

EiC will take over this submission for the final publication. In the meanwhile, please check the final proof of the paper in the previous comment, to ensure everything looks good.

levisweetbreu commented 6 months ago

@cheginit @praneethd7 @caimeng2 Thank you all for your comments and advice! I greatly appreciate your time and work on this!

kthyng commented 6 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 6 months ago

Paper comments:

levisweetbreu commented 6 months ago

@kthyng Those comments have now been addressed!

kthyng commented 6 months ago

@editorialbot generate pdf

editorialbot commented 6 months ago

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