[REVIEW]: DelaunayTriangulation.jl: A Julia package for Delaunay triangulations and Voronoi tessellations in the plane #7174

editorialbot · 2024-09-04T09:06:21Z

Submitting author: @DanielVandH (Daniel VandenHeuvel)
Repository: https://github.com/JuliaGeometry/DelaunayTriangulation.jl
Branch with paper.md (empty if default branch): paper
Version: v1.4.2
Editor: @vissarion
Reviewers: @PieterjanRobbe, @mtsch
Archive: 10.5281/zenodo.13847646

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/9f806b9bc4dd2f31f5e7ca67b64448bd/status.svg)](https://joss.theoj.org/papers/9f806b9bc4dd2f31f5e7ca67b64448bd)

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@PieterjanRobbe & @mtsch, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
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Checklists

📝 Checklist for @PieterjanRobbe

📝 Checklist for @mtsch

The text was updated successfully, but these errors were encountered:

editorialbot · 2024-09-04T09:06:24Z

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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editorialbot · 2024-09-04T09:06:46Z

Software report:

github.com/AlDanial/cloc v 1.90  T=0.45 s (619.8 files/s, 167654.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                          187           5186          11288          41961
Markdown                        75           2053              0           9646
TOML                             6            705              2           3323
TeX                              1             25              0            246
YAML                             6              9             11            175
JSON                             1              0              0             22
-------------------------------------------------------------------------------
SUM:                           276           7978          11301          55373
-------------------------------------------------------------------------------

Commit count by author:

   534	DanielVandH
    49	Daniel VandenHeuvel
     3	dependabot[bot]
     2	Júlio Hoffimann
     1	CompatHelper Julia
     1	Simon
     1	himcraft

editorialbot · 2024-09-04T09:06:50Z

Paper file info:

📄 Wordcount for paper.md is 973

✅ The paper includes a Statement of need section

editorialbot · 2024-09-04T09:06:54Z

License info:

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

editorialbot · 2024-09-04T09:07:53Z

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

✅ OK DOIs

- 10.1142/8685 is OK
- 10.1016/S0925-7721(98)00035-2 is OK
- 10.14288/1.0067778 is OK
- 10.1137/141000671 is OK
- 10.1016/S0168-874X(96)00054-6 is OK
- 10.1137/050643568 is OK
- 10.1016/S0070-2153(07)81013-1 is OK
- 10.1137/S0036144599352836 is OK
- 10.1007/s00285-024-02045-4 is OK
- 10.1007/BFb0014497 is OK
- 10.1109/WCICA.2008.4593771 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1002/nme.2579 is OK
- 10.1016/j.cej.2023.145776 is OK
- 10.21105/joss.03349 is OK
- 10.5281/zenodo.11178646 is OK
- 10.5281/zenodo.11176971 is OK
- 10.1017/CBO9780511606014 is OK
- 10.1088/1751-8121/ac4a1d is OK
- 10.1007/PL00009321 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Delaunay Mesh Generation
- No DOI given, and none found for title: Natural neighbor interpolation - critical assessme...
- No DOI given, and none found for title: ExactPredicates.jl: Fast and exact geometrical pre...
- No DOI given, and none found for title: AdaptivePredicates.jl: Port of Shewchuk’s robust p...
- No DOI given, and none found for title: MATLAB version: R2024a
- No DOI given, and none found for title: CGAL User and Reference Manual

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

editorialbot · 2024-09-04T09:08:27Z

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

PieterjanRobbe · 2024-09-04T16:11:58Z

Review checklist for @PieterjanRobbe

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/JuliaGeometry/DelaunayTriangulation.jl?
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 (@DanielVandH) 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?

mtsch · 2024-09-04T22:04:03Z

Review checklist for @mtsch

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/JuliaGeometry/DelaunayTriangulation.jl?
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 (@DanielVandH) 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?

DanielVandH · 2024-09-10T11:19:53Z

@editorialbot generate pdf

editorialbot · 2024-09-10T11:21:28Z

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

DanielVandH · 2024-09-10T11:26:09Z

I've made some changes in response to @PieterjanRobbe's comments over at JuliaGeometry/DelaunayTriangulation.jl#181, and made some other minor changes. The pdf has been regenerated, see above. To summarise:

Since I just finished implementing weighted triangulations and power diagrams this weekend, I've mentioned them in the summary as a feature that the package supports.
I changed the language of "The most feature-rich" in comparing my package to other software. I now just claim to support features that most of the other packages don't support, which I think should be appropriate. I also now mention that there are other Julia packages that support triangulations, and link to where I discuss that in my package's README since it would be a bit cluttered to also do a full comparison in the paper.
The summary paragraphs have been reordered. I now mention the package first and then, in the second paragraph, define triangulations and tessellations.
Since random power diagrams often look bad, I changed the README example to use a rng object for reproducibility. I also made the example use a bit less text width.

Thanks again to @PieterjanRobbe for the comments, I appreciate it.

DanielVandH · 2024-09-25T08:23:10Z

@editorialbot generate pdf

editorialbot · 2024-09-25T08:24:52Z

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

DanielVandH · 2024-09-25T08:32:18Z

I've made some changes in response to @mtsch's comments over at JuliaGeometry/DelaunayTriangulation.jl#189. The pdf has been regenerated, see above. To summarise:

I've added a sentence at the end of the summary pointing the reader to the mathematical details section of DelaunayTriangulation.jl's document, allowing them to easily know where to find more information about these methods.
To help make the mean exit time example clearer, I have mentioned some applications where it arises, mentioning diffusive transport, economics, and a specific example in finance. I also introduce the notation $T(x, y)$ prior to showing the equations describing the model, to avoid the need to have to read ahead and then look back up to the equations.

Thanks again @mtsch, I appreciate your feedback.

DanielVandH · 2024-09-25T08:36:24Z

@editorialbot generate pdf

editorialbot · 2024-09-25T08:38:30Z

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

DanielVandH · 2024-09-25T08:38:58Z

(Just fixed a minor reference issue)

DanielVandH · 2024-09-26T06:28:43Z

@editorialbot generate pdf

editorialbot · 2024-09-26T06:30:47Z

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

vissarion · 2024-09-26T06:48:36Z

@mtsch, @PieterjanRobbe thanks a lot for your efforts! It seems that your checklists are completed.

Are your finished with your reviews and recommend acceptance?

vissarion · 2024-09-26T12:20:34Z

@DanielVandH I opened an issue in the repository with some editing suggestions.

PieterjanRobbe · 2024-09-26T15:55:24Z

Looks good to me!

editorialbot · 2024-09-26T19:13:32Z

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

DanielVandH · 2024-09-26T19:14:46Z

To address @vissarion's comments at JuliaGeometry/DelaunayTriangulation.jl#190, I've:

Clarified the difference between unconstrained and constrained Delaunay triangulations by defining them separately. The Delaunay criterion is also explicitly mentioned.
Mentioned the programming languages used in the other software mentioned. I've also now extended my README to include a more detailed comparison with other software packages, including this table

to give more detail. This isn't in the paper itself due to space reasons, but I do refer back to it.

Fixed some typos.

Thanks again for the feedback.

mtsch · 2024-09-26T22:48:31Z

@vissarion I'm finished with my review and I think this paper will make a great addition to JOSS! The package, its documentation, and paper are all top notch in my opinion.

vissarion · 2024-09-27T09:17:25Z

@DanielVandH thanks for addressing my comments.

In particular, the table of related software and the comparisons looks great! However I think it would be good to double-check the table data once more especially the licenses part (e.g. I think that CGAL has multiple open source licenses for several parts and the option for commercial, but in your case only the triangulations package should be considered). Although, I am not an expert in licensing so this is just an advice and can be done independently from the submission.

vissarion · 2024-09-27T09:17:51Z

Continuing on the review part when a submission is ready to be accepted, we ask that the authors issue a new tagged release of the software (if changed), and archive it (see this guide). Please do this and post the version number and archive DOI here.
Please make sure that the author names, affiliations as well as the title of the archive (e.g. zenodo) is exactly the same with the submission.

DanielVandH · 2024-09-27T10:24:45Z

Thanks for pointing out that issue with CGAL's licenses. Indeed there is also a triangulation package there with a GNU GPL license. I mention now that it has GPL/GNU GPL/Commerical licenses.

I've tagged a new version (v1.4.2) of the package. I already had a Zenodo setup at https://zenodo.org/records/13847646 which has been updated accordingly; the DOI is https://doi.org/10.5281/zenodo.13847646. Is that all correct?

vissarion · 2024-09-27T11:18:13Z

@editorialbot set 10.5281/zenodo.13847646 as archive

editorialbot · 2024-09-27T11:18:16Z

Done! archive is now 10.5281/zenodo.13847646

vissarion · 2024-09-27T11:18:33Z

@editorialbot set v1.4.2 as version

editorialbot · 2024-09-27T11:18:35Z

Done! version is now v1.4.2

vissarion · 2024-09-27T11:19:09Z

@editorialbot recommend-accept

editorialbot · 2024-09-27T11:19:11Z

Attempting dry run of processing paper acceptance...

editorialbot · 2024-09-27T11:19:47Z

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

✅ OK DOIs

- 10.1142/8685 is OK
- 10.1016/S0925-7721(98)00035-2 is OK
- 10.14288/1.0067778 is OK
- 10.1137/141000671 is OK
- 10.1016/S0168-874X(96)00054-6 is OK
- 10.1137/050643568 is OK
- 10.1016/S0070-2153(07)81013-1 is OK
- 10.1137/S0036144599352836 is OK
- 10.1007/s00285-024-02045-4 is OK
- 10.1007/BFb0014497 is OK
- 10.1109/WCICA.2008.4593771 is OK
- 10.1038/s41592-019-0686-2 is OK
- 10.1002/nme.2579 is OK
- 10.1016/j.cej.2023.145776 is OK
- 10.21105/joss.03349 is OK
- 10.5281/zenodo.11178646 is OK
- 10.5281/zenodo.11176971 is OK
- 10.1017/CBO9780511606014 is OK
- 10.1088/1751-8121/ac4a1d is OK
- 10.1007/PL00009321 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Delaunay Mesh Generation
- No DOI given, and none found for title: Natural neighbor interpolation - critical assessme...
- No DOI given, and none found for title: First passage times of diffusion processes and the...
- No DOI given, and none found for title: ExactPredicates.jl: Fast and exact geometrical pre...
- No DOI given, and none found for title: AdaptivePredicates.jl: Port of Shewchuk’s robust p...
- No DOI given, and none found for title: MATLAB version: R2024a
- No DOI given, and none found for title: CGAL User and Reference Manual

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

editorialbot · 2024-09-27T11:21:13Z

👋 @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#5925, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

danielskatz · 2024-09-27T13:04:06Z

👋 @DanielVandH - As the track editor, I'm now reviewing this for final publication. It looks very good, though I have one question. There's no acknowledgment section, so I want to check to make sure this is intentional and that you don't want to mention any funding or other acknowledgements. Is this correct?

DanielVandH · 2024-09-27T13:05:08Z

That's correct

danielskatz · 2024-09-27T13:18:22Z

@editorialbot accept

editorialbot · 2024-09-27T13:18:24Z

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

danielskatz · 2024-09-27T13:24:17Z

I'll check on this, and close it if it's done, in about 30 minutes...

editorialbot · 2024-09-27T13:25:30Z

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: VandenHeuvel
  given-names: Daniel J.
  orcid: "https://orcid.org/0000-0001-6462-0135"
contact:
- family-names: VandenHeuvel
  given-names: Daniel J.
  orcid: "https://orcid.org/0000-0001-6462-0135"
doi: 10.5281/zenodo.13847646
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: VandenHeuvel
    given-names: Daniel J.
    orcid: "https://orcid.org/0000-0001-6462-0135"
  date-published: 2024-09-27
  doi: 10.21105/joss.07174
  issn: 2475-9066
  issue: 101
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 7174
  title: "DelaunayTriangulation.jl: A Julia package for Delaunay
    triangulations and Voronoi tessellations in the plane"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.07174"
  volume: 9
title: "DelaunayTriangulation.jl: A Julia package for Delaunay
  triangulations and Voronoi tessellations in the plane"

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 · 2024-09-27T13:25:34Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2024-09-27T13:25:35Z

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

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.07174 joss-papers#5926
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.07174
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

danielskatz · 2024-09-27T13:55:22Z

Congratulations to @DanielVandH (Daniel VandenHeuvel) on your publication!!

And thanks to @PieterjanRobbe and @mtsch for reviewing, and to @vissarion for editing!
JOSS depends on volunteers and couldn't be successful without you

editorialbot · 2024-09-27T13:55:24Z

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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  <img src="https://joss.theoj.org/papers/10.21105/joss.07174/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.07174/status.svg
   :target: https://doi.org/10.21105/joss.07174

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mtsch · 2024-09-27T13:56:35Z

Congratulations!

DanielVandH · 2024-09-27T13:56:35Z

Thanks all!

editorialbot added Julia review TeX Track: 7 (CSISM) Computer science, Information Science, and Mathematics labels Sep 4, 2024

editorialbot assigned vissarion Sep 4, 2024

editorialbot mentioned this issue Sep 4, 2024

[PRE REVIEW]: DelaunayTriangulation.jl: A Julia package for Delaunay triangulations and Voronoi tessellations in the plane #6937

Closed

PieterjanRobbe mentioned this issue Sep 9, 2024

[JOSS] Review comments JuliaGeometry/DelaunayTriangulation.jl#181

Closed

DanielVandH mentioned this issue Sep 25, 2024

[JOSS] Review comments JuliaGeometry/DelaunayTriangulation.jl#189

Closed

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Sep 27, 2024

editorialbot added accepted published Papers published in JOSS labels Sep 27, 2024

danielskatz closed this as completed Sep 27, 2024

[REVIEW]: DelaunayTriangulation.jl: A Julia package for Delaunay triangulations and Voronoi tessellations in the plane #7174

[REVIEW]: DelaunayTriangulation.jl: A Julia package for Delaunay triangulations and Voronoi tessellations in the plane #7174

Comments

editorialbot commented Sep 4, 2024 • edited Loading

Status

Reviewer instructions & questions

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PieterjanRobbe commented Sep 4, 2024 • edited Loading

Review checklist for @PieterjanRobbe

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

mtsch commented Sep 4, 2024 • edited Loading

Review checklist for @mtsch

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

DanielVandH commented Sep 10, 2024

editorialbot commented Sep 10, 2024

DanielVandH commented Sep 10, 2024 • edited Loading

DanielVandH commented Sep 25, 2024

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editorialbot commented Sep 4, 2024 •

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DanielVandH commented Sep 26, 2024 •

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