Skip to content

/ joss-reviews

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

[REVIEW]: DVRlib: A C++ library for geometric mesh improvement using Directional Vertex Relaxation #2372

Open
whedon opened this issue Jun 20, 2020 · 13 comments
Open

[REVIEW]: DVRlib: A C++ library for geometric mesh improvement using Directional Vertex Relaxation #2372

whedon opened this issue Jun 20, 2020 · 13 comments
Assignees
@hugoledoux @jhale @Kevin-Mattheus-Moerman @jonwong12
Labels
review

Comments

@whedon
Copy link
Collaborator

@whedon whedon commented Jun 20, 2020 •
edited by hugoledoux

Submitting author: @rram84 (Ramsharan Rangarajan)
Repository: https://bitbucket.org/rram/dvrlib/src/joss/
Version: v1.0
Editor: @Kevin-Mattheus-Moerman
Reviewer: @hugoledoux, @jhale, @jonwong12
Archive: Pending

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/9b16f05d126e812c783e4b34061160a3"><img src="https://joss.theoj.org/papers/9b16f05d126e812c783e4b34061160a3/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/9b16f05d126e812c783e4b34061160a3/status.svg)](https://joss.theoj.org/papers/9b16f05d126e812c783e4b34061160a3)

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

@hugoledoux & @jhale & @jonwong12, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

  1. Make sure you're logged in to your GitHub account
  2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

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 try and complete your review in the next six weeks ✨

Review checklist for @hugoledoux

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

General checks

  • Repository: Is the source code for this software available at the repository url?
  • 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 (@rram84) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • 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?

Review checklist for @jhale

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

General checks

  • Repository: Is the source code for this software available at the repository url?
  • 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 (@rram84) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • 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?

Review checklist for @jonwong12

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

General checks

  • Repository: Is the source code for this software available at the repository url?
  • 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 (@rram84) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • 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?
@whedon whedon added the review label Jun 20, 2020
@whedon whedon mentioned this issue Jun 20, 2020
Closed
@whedon
Copy link
Collaborator Author

@whedon whedon commented Jun 20, 2020

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @hugoledoux, @jhale, @jonwong12 it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

  1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

watching

  1. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

notifications

For a list of things I can do to help you, just type:

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf
@whedon
Copy link
Collaborator Author

@whedon whedon commented Jun 20, 2020

👉 Check article proof 📄 👈

@hugoledoux
Copy link
Collaborator

@hugoledoux hugoledoux commented Jun 23, 2020 •
edited

@rram84 I am working on the review and I opened a few issues in your repository for the cmake dependencies (https://bitbucket.org/rram/dvrlib/issues/1/), and the fact that the unit tests are not compiling for me (https://bitbucket.org/rram/dvrlib/issues/2/).

Also, I spotted a few typos and things that could be improved in the paper, simpler to just give you my handwritten notes: https://hugoledoux.stackstorage.com/s/2b4KXD6ZqeqfEHJ
and btw, in JOSS all the DOIs for papers should be given, you have none. Better to add them now.
@hugoledoux
Copy link
Collaborator

@hugoledoux hugoledoux commented Jun 23, 2020

Community guidelines

While there is a section about contribution deep inside the docs (https://rram.bitbucket.io/dvr-docs/html/contributing.html), maybe better to add a file CONTRIBUTING.md to the root of the repository? This is more standard in my opinion.
@hugoledoux
Copy link
Collaborator

@hugoledoux hugoledoux commented Jun 23, 2020

State of the field

In the paper, there is not really links to other similar software. Also, in the docs there is a nice summary of what your software is not, and that should be added I reckon.

It is also important to note what DVRlib is not:
DVRlib is not a mesh generator, but can be coupled to one.
DVRlib is not a tool for adaptive mesh refinement, but can improve an adaptively refined mesh.
DVRlib is not a mesh untangling tool, but can improve an untangled mesh.
DVRlib is not a mesh simplification tool.

A large number of software libraries provide a variety of tools for generating, improving and manipulating unstructured meshes. In this context, it is important to note that DVRlib is neither intended to be, nor is it a comprehensive mesh improvement toolbox. DVRlib performs a very specific type of mesh improvement, commonly termed as geometric mesh optimization, to improve mesh quality. It can be coupled with a broader suite of operations, including topological operations such as face swapping and vertex insertion/removal.
@rram84
Copy link

@rram84 rram84 commented Jun 24, 2020 •
edited

Community guidelines

While there is a section about contribution deep inside the docs (https://rram.bitbucket.io/dvr-docs/html/contributing.html), maybe better to add a file CONTRIBUTING.md to the root of the repository? This is more standard in my opinion.

@hugoledoux Thank you for taking up the review for this submission.
I added CONTRIBUTING.md to the root directory, and linked to it in README.md.
@rram84
Copy link

@rram84 rram84 commented Jun 25, 2020

@whedon generate pdf
@whedon
Copy link
Collaborator Author

@whedon whedon commented Jun 25, 2020

👉 Check article proof 📄 👈

@rram84
Copy link

@rram84 rram84 commented Jun 25, 2020

State of the field

In the paper, there is not really links to other similar software. Also, in the docs there is a nice summary of what your software is not, and that should be added I reckon.

It is also important to note what DVRlib is not:
DVRlib is not a mesh generator, but can be coupled to one.
DVRlib is not a tool for adaptive mesh refinement, but can improve an adaptively refined mesh.
DVRlib is not a mesh untangling tool, but can improve an untangled mesh.
DVRlib is not a mesh simplification tool.

A large number of software libraries provide a variety of tools for generating, improving and manipulating unstructured meshes. In this context, it is important to note that DVRlib is neither intended to be, nor is it a comprehensive mesh improvement toolbox. DVRlib performs a very specific type of mesh improvement, commonly termed as geometric mesh optimization, to improve mesh quality. It can be coupled with a broader suite of operations, including topological operations such as face swapping and vertex insertion/removal.

@hugoledoux
The paper now includes a section on what DVRlib does and doesn't, as you suggested. I made a number of other small revisions to improve the paper.

The paper now cites the following softwares:
Mesh generators (which use relaxation libraries under the hood): Hypermesh, CGAL, TetGen, Gmsh. The documentation pages include examples using DVRlib to improve meshes generated by these softwares.
Dedicated mesh relaxation libraries: Optimesh, Mesquite and GETMe.

I also cite:

  • Netgen, which is much broader in scope, but has popular mesh generation/improvement routines.
  • Budd et al (2009) on mesh motion for r-adaptivity.
@rram84
Copy link

@rram84 rram84 commented Jun 27, 2020

@rram84 I am working on the review and I opened a few issues in your repository for the cmake dependencies (https://bitbucket.org/rram/dvrlib/issues/1/), and the fact that the unit tests are not compiling for me (https://bitbucket.org/rram/dvrlib/issues/2/).

I addressed these issues with changes to CMakeLists.txt and a more detailed set of instructions in README.md. Please see the comments under each issue.

Also, I spotted a few typos and things that could be improved in the paper, simpler to just give you my handwritten notes: https://hugoledoux.stackstorage.com/s/2b4KXD6ZqeqfEHJ
and btw, in JOSS all the DOIs for papers should be given, you have none. Better to add them now.

Thank you for the notes. The paper and references have been revised.
@jonwong12
Copy link
Collaborator

@jonwong12 jonwong12 commented Jun 29, 2020

Sorry. I've just gotten around to do a review, but the invitation expired. Can you please re-invite and I'll accept it on time this time.

@rram84 Not sure if you're aware of this work, but I believe it does some "random" mesh relaxation.
@danielskatz
Copy link

@danielskatz danielskatz commented Jun 29, 2020

@whedon re-invite @jonwong12 as reviewer
@whedon
Copy link
Collaborator Author

@whedon whedon commented Jun 29, 2020

OK, the reviewer has been re-invited.

@jonwong12 please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@hugoledoux hugoledoux

@jhale jhale

@Kevin-Mattheus-Moerman Kevin-Mattheus-Moerman

@jonwong12 jonwong12

Labels
review
Projects
None yet
Milestone
No milestone
Linked pull requests

Successfully merging a pull request may close this issue.

None yet
7 participants
@hugoledoux @jhale @danielskatz @Kevin-Mattheus-Moerman @whedon @jonwong12 @rram84
You can’t perform that action at this time.