[REVIEW]: votess: A multi-target, GPU-capable, parallel Voronoi tessellator

[editorialbot]

Submitting author: @samridh-dev (Samridh Dev Singh)
Repository: https://github.com/samridh-dev/votess.git
Branch with paper.md (empty if default branch):
Version: v1.0.0
Editor: @Kevin-Mattheus-Moerman
Reviewers: @BrunoLevy, @DanielVandH, @pmocz
Archive: Pending

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/6ec6dde5a3af204839779715b3d644ea/status.svg)](https://joss.theoj.org/papers/6ec6dde5a3af204839779715b3d644ea)

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

@BrunoLevy & @DanielVandH & @pmocz, 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 @Kevin-Mattheus-Moerman 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 @BrunoLevy

📝 Checklist for @DanielVandH

📝 Checklist for @pmocz

[editorialbot]

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

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[editorialbot]

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

✅ OK DOIs

- 10.1017/S1743921311000378 is OK
- 10.1145/3272127.3275092 is OK
- 10.1145/235815.235821 is OK
- 10.2172/946741 is OK
- 10.1016/j.parco.2023.102995 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: CGAL User and Reference Manual
- No DOI given, and none found for title: Geogram: a programming library of geometric algori...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.98  T=0.75 s (78.9 files/s, 420197.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C++                             25           1538            169         309445
Python                           3            136             56           1118
C/C++ Header                    14            200            170            525
Markdown                         3            112              2            390
CMake                            9             51             12            176
YAML                             2             20             42            117
TeX                              1              6              0             67
Bourne Shell                     2              5              2             54
-------------------------------------------------------------------------------
SUM:                            59           2068            453         311892
-------------------------------------------------------------------------------

Commit count by author:

   289	samridh-dev
     2	Samridh D. Singh

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 705

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🟡 License found: GNU General Public License v3.0 (Check here for OSI approval)

[editorialbot]

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

[DanielVandH]

Review checklist for @DanielVandH

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/samridh-dev/votess.git?
• 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 (@samridh-dev) 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?

[BrunoLevy]

Review checklist for @BrunoLevy

Summary: It is an interesting package. Efficient parallel Voronoi on the GPU for numerical cosmology is important. In its current form, the article lacks some comparison data, and a couple of references are missing.

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/samridh-dev/votess.git?
• 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 (@samridh-dev) 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?
  • (I did not test build/run on GPU, build scripts seem reasonable)
  • it installs many dependencies, for instance voro++ is not really needed, it is just there for comparision
• 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.)
  Performance evaluation is not complete, see JOSS: evaluation / comparison samridh-dev/votess#13

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?
  A section explaining the difference between Bowyer-Watson based methods (geogram, CGAL, hextreme) and clipping-based methods (Voro++, Ray et.al) is missing.
• 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?
  see JOSS reviewing / references samridh-dev/votess#14

[BrunoLevy]

@editorialbot commands

[editorialbot]

Hello @BrunoLevy, here are the things you can ask me to do:

# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Run checks and provide information on the repository and the paper file
@editorialbot check repository

# Check the references of the paper for missing DOIs
@editorialbot check references

# Generates the pdf paper
@editorialbot generate pdf

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers

[pmocz]

Review checklist for @pmocz

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/samridh-dev/votess.git?
• 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 (@samridh-dev) 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?
• The instructions look clear, but I am unable to verify because I do not have hardware that can use SYCL
• Functionality: Have the functional claims of the software been confirmed?
• see above notes
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)
• see above notes

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).
• would be great to have some standalone docs, but for now the README is clear and contains all info to install and use the code
• 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?
• nice set of benchmarks against other codes included. There are more packages out there to test, but the authors should not be over-burdened. The discussion writeup should highlight the main differences, at a high-level, between the algorithms of each package tested
• 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?
• of possible interest to the authors: https://github.com/kazewong/Voronoids
• possible reference to cite.