[REVIEW]: superblockify: A Python Package for Automated Generation, Visualization, and Analysis of Potential Superblocks in Cities

editorialbot commented 4 months ago

Submitting author: !--author-handle-->@cbueth@crvernon<!--end-editor-- Reviewers: @erexer, @caimeng2 Archive: 10.5281/zenodo.13300611

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

@erexer & @dinacmistry, 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 @erexer

📝 Checklist for @caimeng2

editorialbot commented 4 months ago

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editorialbot commented 4 months ago

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

crvernon commented 4 months ago

👋 @cbueth, @erexer, and @dinacmistry - 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/6798 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.

erexer commented 4 months ago

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/NERDSITU/superblockify?
[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 (@cbueth) 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?

erexer commented 4 months ago

@editorialbot generate pdf

editorialbot commented 4 months ago

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

crvernon commented 4 months ago

:wave: @cbueth, @erexer, and @dinacmistry - looks like we have some good activity going here! Can each of you give a short update of how things are going? Thanks!

cbueth commented 4 months ago

Thank you all for the activity and she short reminder!

We are happy to see the many filled check marks and have just replied with the asked for changes in issues https://github.com/NERDSITU/superblockify/issues/86 and https://github.com/NERDSITU/superblockify/issues/87. The new release candidate 1.0.0rc9 is up on PyPI.

Please let us know if there are any further questions!

crvernon commented 4 months ago

FYI @dinacmistry - you can generate your review checklist by commenting: @editorialbot generate my checklist in this review thread. Thanks!

erexer commented 4 months ago

@crvernon things are going well, I'm working through the checklist, going over functionality now.

crvernon commented 3 months ago

:wave: @dinacmistry - do you need help getting your checklist set up? Thanks!

crvernon commented 3 months ago

👋 @dinacmistry - will you provide a timeline of when you may be able to complete your review? Thanks!

crvernon commented 3 months ago

👋 @caimeng2 - Would you be willing to review this submission to JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

caimeng2 commented 3 months ago

👋 @caimeng2 - Would you be willing to review this submission to JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

Thanks for the invite! I can review the package in the week of July 22. Will that work?

crvernon commented 3 months ago

@editorialbot add @caimeng2 as reviewer

@caimeng2 yes, thank you! You can add your checklist by commenting the following here in this thread:

@editorialbot generate my checklist

editorialbot commented 3 months ago

@caimeng2 added to the reviewers list!

erexer commented 2 months ago

@cbueth have you had a chance to look at https://github.com/NERDSITU/superblockify/issues/88?

cbueth commented 2 months ago

Thank you for the reminder @erexer, for some reason I missed the issue, but will get into the feedback and improvements these days.

caimeng2 commented 2 months ago

Review checklist for @caimeng2

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/NERDSITU/superblockify?
[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 (@cbueth) 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?

cbueth commented 2 months ago

Hey @caimeng2 :wave:, thank you for taking the time to review our submission. We are looking forward to your feedback.

Just to note, there have been minor changes addressed regarding the minimum working example script @erexer noticed in https://github.com/NERDSITU/superblockify/issues/88, but they have not been integrated into the latest release candidate, yet.

caimeng2 commented 2 months ago

Hey @caimeng2 👋, thank you for taking the time to review our submission. We are looking forward to your feedback.

Just to note, there have been minor changes addressed regarding the minimum working example script @erexer noticed in NERDSITU/superblockify#88, but they have not been integrated into the latest release candidate, yet.

Good to know. Thanks!

cbueth commented 2 months ago

We just merged the feedback from https://github.com/NERDSITU/superblockify/issues/88 by @erexer in PR https://github.com/NERDSITU/superblockify/pull/89 and released a 1.0.0rc10 with the changes to PyPI.

Coming week we'll get into the comments on the paper noted by @caimeng2 in https://github.com/NERDSITU/superblockify/issues/90.

Thanks everyone for the collaboration on the review! :raised_hands:

erexer commented 2 months ago

superblockify is looking good to me and I approve for publication 🎉

cbueth 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:

cbueth 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:

caimeng2 commented 2 months ago

@crvernon I'm done with the review as well. The author has addressed all my comments and improved the paper and documentation greatly. I think the package is good to go.

crvernon commented 2 months ago

Great, thanks @caimeng2!

crvernon 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

- 10.1136/bmj.n443 is OK
- 10.1016/j.jtrangeo.2024.103817 is OK
- 10.1016/j.erss.2020.101486 is OK
- 10.5281/zenodo.10476253 is OK
- 10.1016/j.landusepol.2022.106111 is OK
- 10.3390/app13042095 is OK
- 10.1038/s41893-022-00855-2 is OK
- 10.1177/23998083221098739 is OK
- 10.1016/j.envres.2024.118550 is OK
- 10.1016/j.compenvurbsys.2017.05.004 is OK
- 10.1007/s41109-019-0189-1 is OK
- 10.1007/978-3-030-12381-9_12 is OK
- 10.1016/j.socnet.2007.11.001 is OK
- 10.13140/RG.2.2.26204.36481 is OK
- 10.5281/zenodo.8009629 is OK
- 10.1038/s41467-018-04978-z is OK
- 10.1103/PhysRevLett.87.198701 is OK
- 10.54337/aau451017237 is OK
- 10.1016/j.envint.2019.105132 is OK
- 10.1007/978-3-319-74983-9_11 is OK
- 10.2905/9F06F36F-4B11-47EC-ABB0-4F8B7B1D72EA is OK
- 10.1177/0956247809344361 is OK
- 10.5281/zenodo.8087361 is OK
- 10.1016/j.apgeog.2023.103116 is OK
- 10.1038/s41598-022-10783-y is OK

MISSING DOIs

- No DOI given, and none found for title: TuneOurBlock
- No DOI given, and none found for title: QGIS Geographic Information System
- No DOI given, and none found for title: Potenziale von Superblock-Konzepten als Beitrag zu...
- No DOI given, and none found for title: Walking and cycling: latest evidence to support po...
- No DOI given, and none found for title: BCNecologia: 20 años de la Agencia de Ecología Urb...
- No DOI given, and none found for title: Exploring Network Structure, Dynamics, and Functio...
- No DOI given, and none found for title: OpenStreetMap
- No DOI given, and none found for title: Urbanization
- No DOI given, and none found for title: Pilotstudie Supergrätzl - Ergebnisbericht Am Beisp...
- No DOI given, and none found for title: Streetspace Guidance: Appendix Six (a): Supplement...

INVALID DOIs

- None

crvernon 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:

cbueth commented 2 months ago

To me the draft is looking good! Just on the reviewer list shouldn't there just be the two active reviewers? What other steps are there for our side?

crvernon commented 2 months ago

:wave: @cbueth - I just need to do my pass at this point and then I will advise. I'll follow up with additional instructions. Thanks!

crvernon commented 2 months ago

@cbueth - wow, this submission is very clean! Thank you for making my job easy! I have only one needed edit at this point:

[x] In the caption for Figure 1, you simply state the city names. Could you also place these into their global context? E.g., Baltimore, MD, USA.

Next is just setting up the archive for your new release.

We want to make sure the archival has the correct metadata that JOSS requires. This includes a title that matches the paper title and a correct author list.

So here is what we have left to do:

[x] Conduct a GitHub release of the current reviewed version of the software if you haven't already and archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository). Please ensure that the software archive uses the same license as the license you have posted on GitHub.
[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 exactly) and author list (should match the paper exactly and the order in which they are listed; 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.
[x] Please respond with the 1) DOI of the archived version and the 2) version here.

I can then move forward with accepting the submission.

cbueth commented 2 months ago

@crvernon Thank you for checking and editing our submission. We are delighted to hear for you that our submission is clean!

https://github.com/NERDSITU/superblockify/commit/01892f179872d77f2884f875ee62609c970d3748: The caption has been updated with the more specific location strings: "Athens, GR (top row) and Baltimore, MD, USA (bottom row) [...]"
We have tagged and released 1.0.0. The same release has been published on Zenodo with the filled in metadata, same title and license.
1. DOI for 1.0.0: 10.5281/zenodo.13300611 (for all versions 10.5281/zenodo.13300610)
2. The version number for the release is as planned version 1.0.0.

This should be all.

crvernon 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:

crvernon commented 2 months ago

@editorialbot set 10.5281/zenodo.13300611 as archive

editorialbot commented 2 months ago

Done! archive is now 10.5281/zenodo.13300611

crvernon commented 2 months ago

@editorialbot set 1.0.0 as version

editorialbot commented 2 months ago

Done! version is now 1.0.0

crvernon commented 2 months ago

@editorialbot remove @dinacmistry from reviewers

editorialbot commented 2 months ago

@dinacmistry removed from the reviewers list!

crvernon 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

- 10.1136/bmj.n443 is OK
- 10.1016/j.jtrangeo.2024.103817 is OK
- 10.1016/j.erss.2020.101486 is OK
- 10.5281/zenodo.10476253 is OK
- 10.1016/j.landusepol.2022.106111 is OK
- 10.3390/app13042095 is OK
- 10.1038/s41893-022-00855-2 is OK
- 10.1177/23998083221098739 is OK
- 10.1016/j.envres.2024.118550 is OK
- 10.1016/j.compenvurbsys.2017.05.004 is OK
- 10.1007/s41109-019-0189-1 is OK
- 10.1007/978-3-030-12381-9_12 is OK
- 10.1016/j.socnet.2007.11.001 is OK
- 10.13140/RG.2.2.26204.36481 is OK
- 10.5281/zenodo.8009629 is OK
- 10.1038/s41467-018-04978-z is OK
- 10.1103/PhysRevLett.87.198701 is OK
- 10.54337/aau451017237 is OK
- 10.1016/j.envint.2019.105132 is OK
- 10.1007/978-3-319-74983-9_11 is OK
- 10.2905/9F06F36F-4B11-47EC-ABB0-4F8B7B1D72EA is OK
- 10.1177/0956247809344361 is OK
- 10.5281/zenodo.8087361 is OK
- 10.1016/j.apgeog.2023.103116 is OK
- 10.1038/s41598-022-10783-y is OK

MISSING DOIs

- No DOI given, and none found for title: TuneOurBlock
- No DOI given, and none found for title: QGIS Geographic Information System
- No DOI given, and none found for title: Potenziale von Superblock-Konzepten als Beitrag zu...
- No DOI given, and none found for title: Walking and cycling: latest evidence to support po...
- No DOI given, and none found for title: BCNecologia: 20 años de la Agencia de Ecología Urb...
- No DOI given, and none found for title: Exploring Network Structure, Dynamics, and Functio...
- No DOI given, and none found for title: OpenStreetMap
- No DOI given, and none found for title: Urbanization
- No DOI given, and none found for title: Pilotstudie Supergrätzl - Ergebnisbericht Am Beisp...
- No DOI given, and none found for title: Streetspace Guidance: Appendix Six (a): Supplement...

INVALID DOIs

- None

editorialbot commented 2 months ago

:wave: @openjournals/sbcs-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/5765, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

crvernon commented 2 months ago

@editorialbot accept

openjournals / joss-reviews