[REVIEW]: DTCC Builder: A mesh generator for automatic, efficient, and robust mesh generation for large-scale city modeling and simulation

[editorialbot]

Submitting author: @alogg (Anders Logg)
Repository: https://github.com/dtcc-platform/dtcc-builder
Branch with paper.md (empty if default branch): joss-2022
Version: v0.9
Editor: @crvernon
Reviewers: @ifthompson, @ipadjen
Archive: 10.5281/zenodo.7988751

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/ea3e547804d0e1b730751428da2184a1"><img src="https://joss.theoj.org/papers/ea3e547804d0e1b730751428da2184a1/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/ea3e547804d0e1b730751428da2184a1/status.svg)](https://joss.theoj.org/papers/ea3e547804d0e1b730751428da2184a1)

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

@pralitp & @ifthompson, 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 @ifthompson

📝 Checklist for @ipadjen

[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]

👋 @alogg, @pralitp, @ifthompson - 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 #4928 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.

[ifthompson]

Review checklist for @ifthompson

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://gitlab.com/dtcc-platform/dtcc-builder.git?
• 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 (@alogg) 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]

📣 Mid-week rally!

👋 @pralitp and @ifthompson could you provide an update to how things are going? Also please let me know if you have any questions.

Keep up the good work!

[ifthompson]

I've worked my way through the checklist. Documentation is very nice and I was able to install and run successfully. Only thing I did not find was clear Community Guidelines for how users can contribute, report issues, and get support (I assume this is just raise an issue on the repository, so include a sentence saying that, or point to broader guidelines if they are elsewhere in the DTCC project).

A few other notes:

It might be helpful to include that tip for Windows users about the Unix-style line endings in the Installation section, in addition (or instead) of the Development section. Also, there may be a .gitattributes setting that tells Git not to convert line endings.

There is a typo in paper.md, "algorihtms" is misspelled in the Method and implementation first paragraph last sentence https://gitlab.com/dtcc-platform/dtcc-builder/-/blob/joss-2022/doc/paper-joss-2022/paper.md#method-and-implementation

[alogg]

@ifthompson Thanks, I have fixed these issues and pushed to the joss-2022 branch on GitLab:

1. Typo in paper.md fixed

2. Added .gitattributes with recommended configuration for Unix-style line endings

3. Added documentation on how to contribute in contributing.md:

Contributing

Contributions to DTCC Builder are welcome and may come in the form of
bug reports, feature requests, documentation, or code.

To contribute, register a GitLab account and post an issue detailing
your bug report, feature request or idea for writing documentation or
code on the project page for
DTCC Builder.

Make sure to also check out the developer notes and
note that any source code contributions need to be made open-source
under the MIT License.

[ifthompson]

@alogg Great! I think that completes my checklist. @crvernon let me know if anything else is required on my end.

[crvernon]

👋 @pralitp could you provide an update to how things are going? Also please let me know if you have any questions.

Thanks @ifthompson you are all good for now!

[crvernon]

👋 @pralitp could you provide an update to how things are going? Also please let me know if you have any questions.

[alogg]

@crvernon Are we waiting for something? Anything we need to do on our end?

[crvernon]

@alogg no, you are all good. I'll check with our second reviewer again and get you some feedback ASAP. Thanks!

[vbassn]

@crvernon Sorry to bother you again, but I have finished reviewing for JoSS and I remember reading the soft "deadline" for reviewers is 6 weeks. I think we are way past that, think we could have it assigned to someone else if the second reviewer is unresponsive?
PS: For some reason I cannot mention "pralitp"

[crvernon]

@vbassn I'll work on getting us a review that can turn this around quickly. Best.

[crvernon]

👋 Hello @ipadjen - are you able to help with reviewing this for JOSS? Thanks!

[ipadjen]

Hello! Sure, I'll try to be swift

[crvernon]

Thanks @ipadjen!

[crvernon]

@editorialbot add @ipadjen as reviewer

[editorialbot]

@ipadjen added to the reviewers list!

[crvernon]

@editorialbot remove @pralitp as reviewer

[editorialbot]

@pralitp removed from the reviewers list!

[crvernon]

@ipadjen you can generate your checklist by commenting the following

@editorialbot generate my checklist

[crvernon]

@editorialbot set v0.9 as version

[editorialbot]

Done! version is now v0.9

[crvernon]

@editorialbot set 10.5281/zenodo.7988751 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.7988751

[crvernon]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.2148/benv.46.4.547 is OK
- 10.21105/joss.02866 is OK
- 10.1186/s40965-019-0064-0 is OK
- 10.3389/fbuil.2022.899332 is OK
- 10.1007/bfb0014497 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[crvernon]

@editorialbot generate pdf

[editorialbot]

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

[crvernon]

👋 - @anderslogg and @vbassn I am recommending that this submission be accepted for publication. An EiC will review shortly and if all goes well this will go live soon! Thanks to @ifthompson and @ipadjen for a constructive review!

[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

- 10.2148/benv.46.4.547 is OK
- 10.21105/joss.02866 is OK
- 10.1186/s40965-019-0064-0 is OK
- 10.3389/fbuil.2022.899332 is OK
- 10.1007/bfb0014497 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/csism-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#4277, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[danielskatz]

@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: Logg
  given-names: Anders
  orcid: "https://orcid.org/0000-0002-1547-4773"
- family-names: Naserentin
  given-names: Vasilis
  orcid: "https://orcid.org/0000-0002-3485-9329"
- family-names: Wästberg
  given-names: Dag
  orcid: "https://orcid.org/0000-0002-8630-8262"
doi: 10.5281/zenodo.7988751
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Logg
    given-names: Anders
    orcid: "https://orcid.org/0000-0002-1547-4773"
  - family-names: Naserentin
    given-names: Vasilis
    orcid: "https://orcid.org/0000-0002-3485-9329"
  - family-names: Wästberg
    given-names: Dag
    orcid: "https://orcid.org/0000-0002-8630-8262"
  date-published: 2023-06-01
  doi: 10.21105/joss.04928
  issn: 2475-9066
  issue: 86
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 4928
  title: "DTCC Builder: A mesh generator for automatic, efficient, and
    robust mesh generation for large-scale city modeling and simulation"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.04928"
  volume: 8
title: "DTCC Builder: A mesh generator for automatic, efficient, and
  robust mesh generation for large-scale city modeling and simulation"

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]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[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.04928 joss-papers#4284
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04928
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...

[danielskatz]

Congratulations to @alogg (Anders Logg) and co-authors!!

And thanks to @ifthompson and @ipadjen for reviewing, and to @crvernon for editing!
We couldn't do this without your voluntary efforts

[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:

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HTML:
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reStructuredText:
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