[REVIEW]: Mobilkit: A Python Toolkit for Urban Resilience and Disaster Risk Management Analytics using High Frequency Human Mobility Data

[editorialbot]

Submitting author: @takayabe0505 (Takahiro Yabe)
Repository: https://github.com/mindearth/mobilkit
Branch with paper.md (empty if default branch):
Version: v0.2.8
Editor: @crvernon
Reviewers: @ifthompson, @levisweetbreu
Archive: 10.6084/m9.figshare.24707115

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/aee7d69db418d0e47105ce41c91a096d"><img src="https://joss.theoj.org/papers/aee7d69db418d0e47105ce41c91a096d/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/aee7d69db418d0e47105ce41c91a096d/status.svg)](https://joss.theoj.org/papers/aee7d69db418d0e47105ce41c91a096d)

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

@ssujit & @jlevente, 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 @levisweetbreu

📝 Checklist for @ifthompson

[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

[crvernon]

👋 @takayabe0505 @ssujit @jlevente 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 #5201 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.

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=1.54 s (27.8 files/s, 20969.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Jupyter Notebook                11              0          20418           3844
Python                          10            849           2334           2972
XML                              9              0              0           1401
Markdown                         4             61              0            187
reStructuredText                 4             84             54             84
YAML                             2              5             11             29
TeX                              1              0              0             24
make                             1              4              7              9
TOML                             1              0              0              6
-------------------------------------------------------------------------------
SUM:                            43           1003          22824           8556
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 728

[editorialbot]

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

OK DOIs

- None

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[jlevente]

Review checklist for @jlevente

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/mindearth/mobilkit?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@takayabe0505) 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?

[crvernon]

👋 @ssujit, @jlevente could you give me a short update as to how things are going with your reviews? Thanks!

[crvernon]

📣 Mid-week Rally! 📣

@ssujit and @jlevente could you give me a short update as to how things are going with your reviews?

Thanks!

[crvernon]

👋 @ssujit and @jlevente could you give me a short update as to how things are going with your reviews?

@ssujit let me know if you are having trouble creating your reviewer checklist.

[crvernon]

Please update 🙏 ...

👋 @ssujit and @jlevente could you give me a short update as to how things are going with your reviews?

@ssujit let me know if you are having trouble creating your reviewer checklist.

[crvernon]

🚨 MIDWEEK RALLY 🚨

@ssujit and @jlevente - Could you please provide an update to how things are going here? Please do let me know if you are unable to review this article so I may move it forward. As always, let me know if you have any questions!

Have a great day!

[crvernon]

❗ Last call for a response before I have to assign different reviewers @ssujit and @jlevente! Please respond in this thread if you are able to conduct this review within the very near future. Thanks!

[crvernon]

@takayabe0505 I am removing your current reviewers due to no response. I will find you two more to keep this review going. Apologies.

[crvernon]

@editorialbot remove @ssujit as reviewer

[editorialbot]

@ssujit removed from the reviewers list!

[crvernon]

@editorialbot remove @jlevente as reviewer

[editorialbot]

@jlevente removed from the reviewers list!

[crvernon]

👋 @ifthompson can you help out with this one?

[crvernon]

👋 @levisweetbreu let me know if you are able to help out with this one. Thanks!

[ifthompson]

@crvernon Yes, I can review this in the near future.

[crvernon]

@editorialbot assign @ifthompson as reviewer

[editorialbot]

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

[crvernon]

@editorialbot add @ifthompson as reviewer

[editorialbot]

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

OK DOIs

- None

MISSING DOIs

- None

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#4984, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[oliviaguest]

@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

- None

MISSING DOIs

- None

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#5003, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[oliviaguest]

@takayabe0505 can you fix the double parentheses for the citations please? So make it for example:

(e.g., De Montjoye et al., 2016 or Pappalardo et al., 2019)

Otherwise, it's looking good. Just tag me when you're done. :)

[ubi15]

@oliviaguest we substituted the parentheses with an em dash (as the inner parenthesis is due to the citation style).

Let us know if you need any other edit.

[oliviaguest]

@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

- None

MISSING DOIs

- None

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#5045, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[oliviaguest]

@ubi15 no, sorry, this still isn't right. Please change to not use parentheses. I think you haven't seen the command yet, I'll tag it in a PR for you, no problem. 😊

Take a look at this and feel free to merge or make your own edits as needed: mindearth/mobilkit#18

[ubi15]

Thanks a lot @oliviaguest , I completely missed the square brackets. We merged your suggestions, many many thanks for your help on this!

[oliviaguest]

@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

- None

MISSING DOIs

- None

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#5081, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[oliviaguest]

@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: Ubaldi
  given-names: Enrico
  orcid: "https://orcid.org/0000-0003-1685-9939"
- family-names: Yabe
  given-names: Takahiro
  orcid: "https://orcid.org/0000-0001-8967-1967"
- family-names: Jones
  given-names: Nicholas
- family-names: Khan
  given-names: Maham Faisal
- family-names: Feliciotti
  given-names: Alessandra
  orcid: "https://orcid.org/0000-0002-1471-5360"
- family-names: Clemente
  given-names: Riccardo Di
  orcid: "https://orcid.org/0000-0001-8005-6351"
- family-names: Ukkusuri
  given-names: Satish V.
- family-names: Strano
  given-names: Emanuele
  orcid: "https://orcid.org/0000-0002-2339-6824"
contact:
- family-names: Yabe
  given-names: Takahiro
  orcid: "https://orcid.org/0000-0001-8967-1967"
doi: 10.6084/m9.figshare.24707115
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Ubaldi
    given-names: Enrico
    orcid: "https://orcid.org/0000-0003-1685-9939"
  - family-names: Yabe
    given-names: Takahiro
    orcid: "https://orcid.org/0000-0001-8967-1967"
  - family-names: Jones
    given-names: Nicholas
  - family-names: Khan
    given-names: Maham Faisal
  - family-names: Feliciotti
    given-names: Alessandra
    orcid: "https://orcid.org/0000-0002-1471-5360"
  - family-names: Clemente
    given-names: Riccardo Di
    orcid: "https://orcid.org/0000-0001-8005-6351"
  - family-names: Ukkusuri
    given-names: Satish V.
  - family-names: Strano
    given-names: Emanuele
    orcid: "https://orcid.org/0000-0002-2339-6824"
  date-published: 2024-03-01
  doi: 10.21105/joss.05201
  issn: 2475-9066
  issue: 95
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5201
  title: "Mobilkit: A Python Toolkit for Urban Resilience and Disaster
    Risk Management Analytics"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05201"
  volume: 9
title: "Mobilkit: A Python Toolkit for Urban Resilience and Disaster
  Risk Management Analytics"

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.05201 joss-papers#5082
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05201
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...

[oliviaguest]

@arfon do you know why the version of the paper that editorialbot published is not the latest?

[oliviaguest]

Huge thanks to the editor: @crvernon reviewers: @ifthompson, @levisweetbreu! ✨ JOSS appreciates your work and effort. ✨ Also, big congratulations to the author @takayabe0505! 🥳 🍾

[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.05201/status.svg)](https://doi.org/10.21105/joss.05201)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05201">
  <img src="https://joss.theoj.org/papers/10.21105/joss.05201/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05201/status.svg
   :target: https://doi.org/10.21105/joss.05201

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