[REVIEW]: HOHQMesh: An All Quadrilateral/Hexahedral Unstructured Mesh Generator for High Order Elements

[editorialbot]

Submitting author: @andrewwinters5000 (Andrew Winters)
Repository: https://github.com/trixi-framework/HOHQMesh
Branch with paper.md (empty if default branch): paper-2024-joss
Version: v1.5.2
Editor: @xuanxu
Reviewers: @fhindenlang, @anderslogg
Archive: Pending

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/bb9bb324fccf69238a2d690c9125044b"><img src="https://joss.theoj.org/papers/bb9bb324fccf69238a2d690c9125044b/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/bb9bb324fccf69238a2d690c9125044b/status.svg)](https://joss.theoj.org/papers/bb9bb324fccf69238a2d690c9125044b)

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

@fhindenlang & @anderslogg, 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 @xuanxu 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 @fhindenlang

[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]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.10 s (1133.6 files/s, 394615.5 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
Fortran 90                       70           2863          14514          18379
Markdown                         25            539              0           1824
make                              1             92             14            637
TeX                               1             41              4            419
YAML                              7             17             24            325
Bourne Again Shell                6             37             29            167
JSON                              1              0              0             34
CMake                             2             17              3             33
JavaScript                        1              1              0             15
TOML                              1              0              0              3
--------------------------------------------------------------------------------
SUM:                            115           3607          14588          21836
--------------------------------------------------------------------------------

Commit count by author:

   236	David Kopriva
    51	Andrew Winters
    43	Michael Schlottke-Lakemper
    24	dependabot[bot]
    18	DavidAKopriva
    13	Joe Schoonover
     6	Hendrik Ranocha
     1	Arpit Babbar
     1	Joseph Schoonover

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1225

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🟡 License found: Other (Check here for OSI approval)

[editorialbot]

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

✅ OK DOIs

- 10.5281/zenodo.13959058 is OK
- 10.5281/zenodo.13959071 is OK
- 10.1093/gji/ggab308 is OK
- 10.1002/nme.397 is OK
- 10.1007/978-3-319-12886-3_8 is OK
- 10.1080/00221689909498511 is OK
- 10.1111/cgf.12014 is OK
- 10.1016/j.cpc.2015.02.008 is OK
- 10.1016/j.cpc.2019.05.015 is OK
- 10.1016/j.camwa.2020.05.004 is OK
- 10.1016/j.jcp.2021.110467 is OK
- 10.21105/jcon.00077 is OK
- 10.1016/j.cpc.2023.108700 is OK
- 10.1137/120876034 is OK
- 10.1093/acprof:oso/9780198528692.001.0001 is OK
- 10.1007/978-0-387-72067-8 is OK
- 10.1007/978-90-481-2261-5 is OK
- 10.1016/j.jcp.2004.01.004 is OK
- 10.1137/141000671 is OK
- 10.1088/1742-6596/1671/1/012015 is OK
- 10.1007/s10915-024-02451-2 is OK
- 10.1016/j.jcp.2024.113471 is OK
- 10.1007/s10915-013-9730-z is OK
- 10.1016/j.amc.2015.08.047 is OK
- 10.1016/j.jcp.2020.109363 is OK
- 10.48550/arXiv.2404.09050 is OK
- 10.1103/PhysRevFluids.9.053901 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: NEK fast high-order scalable CFD NEK: Fast high-or...
- No DOI given, and none found for title: A Spectral Element Method tool for 2D wave propaga...
- No DOI given, and none found for title: Algorithms for quadrilateral and hexahedral mesh g...
- No DOI given, and none found for title: The Malpasset dam failure. An overview and test ca...
- No DOI given, and none found for title: Spectral-element and adjoint methods in seismology
- No DOI given, and none found for title: DGSEM for General Advection-Diffusion Equations
- No DOI given, and none found for title: High Order Methods for Incompressible Fluid Flow
- No DOI given, and none found for title: Shallow water simulations with Trixi.jl
- No DOI given, and none found for title: A novel entropy stable discontinuous Galerkin spec...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

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

[xuanxu]

@fhindenlang, @anderslogg – 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. Please create your checklist typing:

@editorialbot generate my checklist

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 https://github.com/openjournals/joss-reviews/issues/7476 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.

[fhindenlang]

Review checklist for @fhindenlang

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/trixi-framework/HOHQMesh?
• 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 (@andrewwinters5000) 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?