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]: TBFMM: A C++ generic and parallel fast multipole method library #2444

Open
whedon opened this issue Jul 6, 2020 · 8 comments
Open

[REVIEW]: TBFMM: A C++ generic and parallel fast multipole method library #2444

whedon opened this issue Jul 6, 2020 · 8 comments
Assignees
@poulson @pitsianis @sarats @Himscipy
Labels
review

Comments

@whedon
Copy link
Collaborator

@whedon whedon commented Jul 6, 2020 •
edited by sarats

Submitting author: @berenger-eu (Bérenger Bramas)
Repository: https://gitlab.inria.fr/bramas/tbfmm
Version: v1.0
Editor: @poulson
Reviewer: @pitsianis, @Himscipy, @sarats
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/63718bbb2e660a1715587e8f037fc546"><img src="https://joss.theoj.org/papers/63718bbb2e660a1715587e8f037fc546/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/63718bbb2e660a1715587e8f037fc546/status.svg)](https://joss.theoj.org/papers/63718bbb2e660a1715587e8f037fc546)

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

@pitsianis & @Himscipy & @sarats, 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 @poulson know.

✨ Please try and complete your review in the next six weeks ✨

Review checklist for @pitsianis

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 (@berenger-eu) 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 @Himscipy

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 (@berenger-eu) 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 @sarats

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 (@berenger-eu) 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 Jul 6, 2020
@whedon whedon mentioned this issue Jul 6, 2020
Closed
@whedon
Copy link
Collaborator Author

@whedon whedon commented Jul 6, 2020

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @pitsianis, @Himscipy, @sarats 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 Jul 6, 2020 

Reference check summary:

OK DOIs

- 10.7717/peerj-cs.183 is OK
- 10.1002/cpe.3723 is OK
- 10.1137/130915662 is OK
- 10.1063/1.472369 is OK
- 10.1063/1.468354 is OK
- 10.1063/1.2194548 is OK

MISSING DOIs

- https://doi.org/10.1109/aps.1994.407723 may be missing for title: The fast multipole method for periodic structures
- https://doi.org/10.1109/tpds.2017.2697857 may be missing for title: Bridging the Gap Between OpenMP and Task-Based Runtime Systems for the Fast Multipole Method
- https://doi.org/10.1155/2017/5482468 may be missing for title: Inastemp: A Novel Intrinsics-as-Template Library for Portable SIMD-Vectorization
- https://doi.org/10.4208/cicp.020215.150515sw may be missing for title: PVFMM: A parallel kernel independent FMM for particle and volume potentials
- https://doi.org/10.1016/j.enganabound.2012.07.004 may be missing for title: Fast multipole method applied to Symmetric Galerkin boundary element method for 3D elasticity and fracture problems

INVALID DOIs

- https://doi.org/10.1016/0021-9991(87)90140-9 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.cam.2003.12.011 is INVALID because of 'https://doi.org/' prefix
@whedon
Copy link
Collaborator Author

@whedon whedon commented Jul 6, 2020

👉 Check article proof 📄 👈

@sarats
Copy link
Collaborator

@sarats sarats commented Jul 10, 2020

I have been unable to edit/complete checklist above. Whedon has been forgetful and didn't assign me.
@danielskatz
Copy link

@danielskatz danielskatz commented Jul 10, 2020

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

@whedon whedon commented Jul 10, 2020

The reviewer already has a pending invite.

@sarats please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations
@danielskatz
Copy link

@danielskatz danielskatz commented Jul 10, 2020

Actually, you have to accept the invitation. See the instructions in the first comment in this issue.
@sarats
Copy link
Collaborator

@sarats sarats commented Jul 10, 2020

Done. Thought I did this only once when I first reviewed for JOSS. Didn't realize it's required for every review.
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@poulson poulson

@pitsianis pitsianis

@sarats sarats

@Himscipy Himscipy

Labels
review
Projects
None yet
Milestone
No milestone
Linked pull requests

Successfully merging a pull request may close this issue.

None yet
6 participants
@poulson @pitsianis @danielskatz @sarats @Himscipy @whedon
You can’t perform that action at this time.