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

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editorialbot opened this issue Jun 27, 2024 · 50 comments
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[PRE REVIEW]: DelaunayTriangulation.jl: A Julia package for Delaunay triangulations and Voronoi tessellations in the plane #6937

editorialbot opened this issue Jun 27, 2024 · 50 comments
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@vissarion @mtsch @PieterjanRobbe
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Julia pre-review TeX Track: 7 (CSISM) Computer science, Information Science, and Mathematics

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editorialbot commented Jun 27, 2024 •
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Submitting author: @DanielVandH (Daniel VandenHeuvel)
Repository: https://github.com/JuliaGeometry/DelaunayTriangulation.jl
Branch with paper.md (empty if default branch): paper
Version: v1.0.3
Editor: @vissarion
Reviewers: @PieterjanRobbe, @mtsch
Managing EiC: Daniel S. Katz

Status

status

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HTML: <a href="https://joss.theoj.org/papers/9f806b9bc4dd2f31f5e7ca67b64448bd"><img src="https://joss.theoj.org/papers/9f806b9bc4dd2f31f5e7ca67b64448bd/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/9f806b9bc4dd2f31f5e7ca67b64448bd/status.svg)](https://joss.theoj.org/papers/9f806b9bc4dd2f31f5e7ca67b64448bd)

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Thanks for submitting your paper to JOSS @DanielVandH. Currently, there isn't a JOSS editor assigned to your paper.

@DanielVandH if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

Editor instructions

The JOSS submission bot @editorialbot is here to help you find and assign reviewers and start the main review. To find out what @editorialbot can do for you type:

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@editorialbot editorialbot added pre-review Track: 7 (CSISM) Computer science, Information Science, and Mathematics labels Jun 27, 2024
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Hello human, 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

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Software report:

github.com/AlDanial/cloc v 1.90  T=0.45 s (616.6 files/s, 166696.1 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            212
YAML                             6              9             11            175
JSON                             1              0              0             22
-------------------------------------------------------------------------------
SUM:                           276           7978          11301          55339
-------------------------------------------------------------------------------

Commit count by author:

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

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Paper file info:

📄 Wordcount for paper.md is 969

✅ The paper includes a Statement of need section

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License info:

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

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⚠️ An error happened when generating the pdf. Problem with ORCID (https://orcid.org/0000-0001-6462-0135) for Daniel VandenHeuvel. ORCID looks to be the wrong length.

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

OK DOIs

- 10.1016/S0925-7721(98)00035-2 is OK
- 10.5281/zenodo.11178646 is OK
- 10.5281/zenodo.11176971 is OK

MISSING DOIs

- No DOI given, and none found for title: Delaunay Mesh Generation
- No DOI given, and none found for title: Voronoi Diagrams and Delaunay Triangulations
- No DOI given, and none found for title: Natural neighbor interpolation - critical assessme...
- No DOI given, and none found for title: Delaunay refinement mesh generation of curve-bound...
- 10.1137/141000671 may be a valid DOI for title: Julia: A fresh approach to numerical computing
- 10.1016/s0168-874x(96)00054-6 may be a valid DOI for title: Delaunay triangulation and 3D adaptive mesh genera...
- 10.1137/050643568 may be a valid DOI for title: Adaptive finite element methods for elliptic PDEs ...
- No DOI given, and none found for title: ExactPredicates.jl: Fast and exact geometrical pre...
- 10.1016/s0070-2153(07)81013-1 may be a valid DOI for title: Delaunay-object-dynamics: Cell mechanics with a 3D...
- No DOI given, and none found for title: Centroidal Voronoi tessellations: Applications and...
- 10.1101/2022.09.13.507714 may be a valid DOI for title: Calibration of agent based models for monophasic a...
- 10.1007/bfb0014497 may be a valid DOI for title: Triangle:  Engineering a 2D quality mesh generator...
- No DOI given, and none found for title: MATLAB version: R2024a
- 10.1109/wcica.2008.4593771 may be a valid DOI for title: Path planning based on constrained Delaunay triang...
- No DOI given, and none found for title: SciPy 1.0: Fundamental Algorithms for Scientific C...
- No DOI given, and none found for title: CGAL User and Reference Manual
- No DOI given, and none found for title: Gmsh: a three-dimensional finite element mesh gene...
- 10.31224/3017 may be a valid DOI for title: New computational tools and experiments reveal how...
- 10.21105/joss.03349 may be a valid DOI for title: Makie.jl: Flexible high-performance data visualiza...
- No DOI given, and none found for title: A Guide to First Passage Processes
- 10.1088/1751-8121/ac4a1d may be a valid DOI for title: Mean exit time in irregularly-shaped annular and c...

INVALID DOIs

- None

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👋 @DanielVandH - Thanks for your submission.

Note that your paper does not compile. Please follow the example paper and note that you can click on the error above to find out more about it. In addition, you could work on the possibly missing DOIs that editorialbot suggests, but note that some may be incorrect. Please feel free to make changes to your .bib file, then use the command @editorialbot check references to check again, and the command @editorialbot generate pdf after making changes to the .md file or when the references are right to make a new PDF. editorialbot commands need to be the first entry in a new comment.

@DanielVandH
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Thanks @danielskatz. I'll check out the compiling issues - it worked when I did it in https://github.com/JuliaGeometry/DelaunayTriangulation.jl/actions/runs/9697066359, did I configure the workflow file incorrectly?

I'll get all the DOIs fixed up. I'll get them manually incase some of them are incorrect as you suggest, thanks.

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@DanielVandH if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

Of those that I can see in that list, Kevin Moerman and juliohm are probably suitable.

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@editorialbot check references

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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
- 10.21105/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

MISSING 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: MATLAB version: R2024a
- No DOI given, and none found for title: CGAL User and Reference Manual

INVALID DOIs

- https://doi.org/10.1016/j.cej.2023.145776 is INVALID because of 'https://doi.org/' prefix

@DanielVandH
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@editorialbot check references

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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

MISSING 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: MATLAB version: R2024a
- No DOI given, and none found for title: CGAL User and Reference Manual

INVALID DOIs

- None

@DanielVandH
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@editorialbot generate pdf

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

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Five most similar historical JOSS papers:

Gridap: An extensible Finite Element toolbox in Julia
Submitting author: @fverdugo
Handling editor: @Kevin-Mattheus-Moerman (Active)
Reviewers: @PetrKryslUCSD, @TeroFrondelius, @KristofferC
Similarity score: 0.7475

Makie.jl: Flexible high-performance data visualization for Julia
Submitting author: @jkrumbiegel
Handling editor: @Kevin-Mattheus-Moerman (Active)
Reviewers: @fverdugo, @gaelforget
Similarity score: 0.7306

GaussianRandomFields.jl: A Julia package to generate and sample from Gaussian random fields
Submitting author: @PieterjanRobbe
Handling editor: @jbytecode (Active)
Reviewers: @ziyiyin97, @shahmoradi
Similarity score: 0.7302

DynamicalBilliards.jl: An easy-to-use, modular and extendable Julia package for Dynamical Billiard systems in two dimensions.
Submitting author: @Datseris
Handling editor: @kyleniemeyer (Active)
Reviewers: @ahwillia
Similarity score: 0.7222

GridapDistributed: a massively parallel finite element toolbox in Julia
Submitting author: @amartinhuertas
Handling editor: @Kevin-Mattheus-Moerman (Active)
Reviewers: @PetrKryslUCSD, @Leticia-maria, @jedbrown
Similarity score: 0.7170

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

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- 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: MATLAB version: R2024a
- No DOI given, and none found for title: CGAL User and Reference Manual

As far as I can tell, none of these titles have a DOI assigned to them, and https://www.crossref.org/guestquery also seems to show no DOIs for them.

@danielskatz
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Thanks @danielskatz. I'll check out the compiling issues - it worked when I did it in https://github.com/JuliaGeometry/DelaunayTriangulation.jl/actions/runs/9697066359, did I configure the workflow file incorrectly?

I'll get all the DOIs fixed up. I'll get them manually incase some of them are incorrect as you suggest, thanks.

Sometimes there can be difference between the action and what we do. I'm unsure why, but I'm pinging @openjournals/dev in case this is something they can fix.

@danielskatz
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Thanks for your fixes @DanielVandH

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@editorialbot assign @Kevin-Mattheus-Moerman as editor

thanks Kevin!

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Assigned! @Kevin-Mattheus-Moerman is now the editor

@danielskatz
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@Kevin-Mattheus-Moerman - will you be able to get started on this soon?

@danielskatz
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👋 @vissarion & @hugoledoux - I know you are both at your limits currently, but there is at least an appearance of a COI with @Kevin-Mattheus-Moerman and this submission, so I wonder if either of you would be able to take it, even if you can't start on it immediately?

@vissarion
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@danielskatz I can take it.

@danielskatz
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@editorialbot assign @vissarion as editor

Thanks!

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Assigned! @vissarion is now the editor

@vissarion
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Hi @fverdugo @PieterjanRobbe @Datseris @amartinhuertas would any of you be willing to review this submission for 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

@Datseris
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Sorry, I don't have any time to spare at the moment I'm fully booked.

@PieterjanRobbe
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Sure, I'm available!

@DanielVandH
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@editorialbot generate pdf

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

@editorialbot
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Five most similar historical JOSS papers:

Makie.jl: Flexible high-performance data visualization for Julia
Submitting author: @jkrumbiegel
Handling editor: @Kevin-Mattheus-Moerman (Active)
Reviewers: @fverdugo, @gaelforget
Similarity score: 0.7483

Gridap: An extensible Finite Element toolbox in Julia
Submitting author: @fverdugo
Handling editor: @Kevin-Mattheus-Moerman (Active)
Reviewers: @PetrKryslUCSD, @TeroFrondelius, @KristofferC
Similarity score: 0.7394

Ripserer.jl: flexible and efficient persistent homology computation in Julia
Submitting author: @mtsch
Handling editor: @VivianePons (Retired)
Reviewers: @juliohm, @sauln
Similarity score: 0.7282

DynamicalBilliards.jl: An easy-to-use, modular and extendable Julia package for Dynamical Billiard systems in two dimensions.
Submitting author: @Datseris
Handling editor: @kyleniemeyer (Active)
Reviewers: @ahwillia
Similarity score: 0.7278

AeroAcoustics.jl: A Julia package for aeroacoustics
Submitting author: @1oly
Handling editor: @faroit (Active)
Reviewers: @nantonel, @thejasvibr
Similarity score: 0.7217

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

@DanielVandH
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Just had to make a quick update to the summary (specifically "making use of AdaptivePredicates.jl and ExactPredicates.jl for computing predicates with robust arithmetic", AdaptivePredicates.jl is the new default rather than only ExactPredicates.jl) after I upgraded DelaunayTriangulation.jl to v1.1.0

@fverdugo
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Hi, I cannot review a paper this time. I will happy to help again in the future.

@vissarion
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@editorialbot add @PieterjanRobbe as reviewer

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@PieterjanRobbe added to the reviewers list!

@evetion evetion mentioned this issue Aug 20, 2024
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@danielskatz
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👋 @vissarion - how are you doing on finding a second reviewer? This seems a bit stalled

@DanielVandH
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Any updates on this so far / things I should do to help progress?

@vissarion
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Sorry for the delays here, I was on vacation.

@vissarion
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Hi @mtsch @atzberg @yossibokor @evetion @HaoZeke would any of you be willing to review this submission for 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

@fverdugo
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fverdugo commented Sep 3, 2024

@vissarion Which is the timeline for reviewing this paper?

@mtsch
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mtsch commented Sep 3, 2024

I'd be happy to review this!

@yossibokor
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yossibokor commented Sep 3, 2024 via email

@atzberg
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atzberg commented Sep 3, 2024 via email

@evetion
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evetion commented Sep 4, 2024

Happy to review, but note that I'm close to the domain/language and have used the package incidentally.

@vissarion
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@fverdugo typically we request a review in (at most) six weeks.

Thank you all for your availability! Since after @mtsch's positive reply we have two reviewers, we will proceed that way and let you know if there is a need of extra help.

@vissarion
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@editorialbot add @mtsch as reviewer

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@mtsch added to the reviewers list!

@vissarion
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@editorialbot start review

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OK, I've started the review over in #7174.

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