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

[editorialbot]

Submitting author: @cbueth (Carlson Büth)
Repository: https://github.com/NERDSITU/superblockify
Branch with paper.md (empty if default branch): submission
Version: 1.0.0
Editor: @crvernon
Reviewers: @erexer, @caimeng2
Archive: 10.5281/zenodo.13300611

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/87426e988ebd0a6d7f592eb16d1fd209"><img src="https://joss.theoj.org/papers/87426e988ebd0a6d7f592eb16d1fd209/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/87426e988ebd0a6d7f592eb16d1fd209/status.svg)](https://joss.theoj.org/papers/87426e988ebd0a6d7f592eb16d1fd209)

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]

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]

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

[crvernon]

👋 @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 #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]

Review checklist for @erexer

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

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/NERDSITU/superblockify?
• 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 (@cbueth) 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?

[erexer]

@editorialbot generate pdf

[editorialbot]

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

[crvernon]

👋 @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]

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 NERDSITU/superblockify#86 and NERDSITU/superblockify#87. The new release candidate 1.0.0rc9 is up on PyPI.

Please let us know if there are any further questions!

[crvernon]

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

[erexer]

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

[crvernon]

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

[crvernon]

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

[crvernon]

👋 @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]

👋 @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]

@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]

@caimeng2 added to the reviewers list!

[erexer]

@cbueth have you had a chance to look at NERDSITU/superblockify#88?

[cbueth]

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

[caimeng2]

Review checklist for @caimeng2

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

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/NERDSITU/superblockify?
• 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 (@cbueth) 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?

[cbueth]

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.

[crvernon]

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

• 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:

• 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.

• 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.

• 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]

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

• NERDSITU/superblockify@01892f1: 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]

@editorialbot generate pdf

[editorialbot]

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

[crvernon]

@editorialbot set 10.5281/zenodo.13300611 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.13300611

[crvernon]

@editorialbot set 1.0.0 as version

[editorialbot]

Done! version is now 1.0.0

[crvernon]

@editorialbot remove @dinacmistry from reviewers

[editorialbot]

@dinacmistry removed from the reviewers list!

[crvernon]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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]

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

[crvernon]

@editorialbot accept

[editorialbot]

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

[editorialbot]

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: Büth
  given-names: Carlson M.
  orcid: "https://orcid.org/0000-0003-2298-8438"
- family-names: Vybornova
  given-names: Anastassia
  orcid: "https://orcid.org/0000-0001-6915-2561"
- family-names: Szell
  given-names: Michael
  orcid: "https://orcid.org/0000-0003-3022-2483"
doi: 10.5281/zenodo.13300611
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Büth
    given-names: Carlson M.
    orcid: "https://orcid.org/0000-0003-2298-8438"
  - family-names: Vybornova
    given-names: Anastassia
    orcid: "https://orcid.org/0000-0001-6915-2561"
  - family-names: Szell
    given-names: Michael
    orcid: "https://orcid.org/0000-0003-3022-2483"
  date-published: 2024-08-14
  doi: 10.21105/joss.06798
  issn: 2475-9066
  issue: 100
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6798
  title: "superblockify: A Python Package for Automated Generation,
    Visualization, and Analysis of Potential Superblocks in Cities"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06798"
  volume: 9
title: "`superblockify`: A Python Package for Automated Generation,
  Visualization, and Analysis of Potential Superblocks in Cities"

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.

[editorialbot]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.06798 joss-papers#5766
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06798
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[crvernon]

@cbueth I noticed that you have backticks around the title in your paper. This causes formatting issues in the way our site formats your publication. Could you remove these? No need to conduct a new release or anything.

Let me know when this is done and I'll finalize this one.

Thanks.

[cbueth]

First, thank you for the editorial and review work, and accepting our submission! 👏

@crvernon Sure, they were just removed in the paper.md on the submission branch, see NERDSITU/superblockify@64730fb.

[crvernon]

@editorialbot reaccept

[editorialbot]

Rebuilding paper!

[editorialbot]

🌈 Paper updated!

New PDF and metadata files 👉 openjournals/joss-papers#5768

[crvernon]

🥳 Congratulations on your new publication @cbueth! Many thanks to @erexer and @caimeng2 for your time, hard work, and expertise!! JOSS wouldn't be able to function nor succeed without your efforts.

Please consider becoming a reviewer for JOSS if you are not already: https://reviewers.joss.theoj.org/join

[editorialbot]

🎉🎉🎉 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.06798/status.svg)](https://doi.org/10.21105/joss.06798)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06798">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06798/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06798/status.svg
   :target: https://doi.org/10.21105/joss.06798

This is how it will look in your documentation:

We need your help!

The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

• Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://reviewers.joss.theoj.org/join
• Making a small donation to support our running costs here: https://numfocus.org/donate-to-joss