Joss-reviews: [REVIEW]: FLAM: Fast Linear Algebra in MATLAB

Created on 21 Nov 2019  ·  85Comments  ·  Source: openjournals/joss-reviews

Submitting author: @klho (Kenneth L. Ho)
Repository: https://github.com/klho/FLAM
Version: v1.1.0 (will update on completion)
Editor: @melissawm
Reviewers: @sivaramambikasaran, @pitsianis, @vijaysm
Archive: 10.5281/zenodo.3930385

Status

status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/b2835e0005748f954fdf0b1baef017f7/status.svg)](https://joss.theoj.org/papers/b2835e0005748f954fdf0b1baef017f7)

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

@sivaramambikasaran & @pitsianis & @vijaysm, 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 @melissawm know.

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

Review checklist for @sivaramambikasaran

Conflict of interest

  • [x] 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

  • [x] Repository: Is the source code for this software available at the repository url?
  • [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • [x] Contribution and authorship: Has the submitting author (@klho) 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 @pitsianis

Conflict of interest

  • [x] 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

  • [x] Repository: Is the source code for this software available at the repository url?
  • [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • [x] Contribution and authorship: Has the submitting author (@klho) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

  • [x] Installation: Does installation proceed as outlined in the documentation?
  • [x] Functionality: Have the functional claims of the software been confirmed?
  • [x] 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

  • [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
  • [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
  • [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
  • [x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
  • [x] 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

  • [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
  • [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
  • [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
  • [x] 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 @vijaysm

Conflict of interest

  • [x] 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

  • [x] Repository: Is the source code for this software available at the repository url?
  • [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • [x] Contribution and authorship: Has the submitting author (@klho) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

  • [x] Installation: Does installation proceed as outlined in the documentation?
  • [x] Functionality: Have the functional claims of the software been confirmed?
  • [x] 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

  • [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
  • [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
  • [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
  • [x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
  • [x] 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

  • [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
  • [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
  • [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
  • [x] 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?
accepted published recommend-accept review
Source
picture whedon

All 85 comments

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @sivaramambikasaran, @pitsianis it looks like you're currently assigned to review this paper :tada:.

:star: Important :star:

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 😿

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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 picture whedon on 21 Nov 2019 
Attempting to check references...
whedon picture whedon on 21 Nov 2019 
Attempting PDF compilation. Reticulating splines etc...
whedon picture whedon on 21 Nov 2019

```Reference check summary:

OK DOIs

  • 10.1007/s10915-013-9714-z is OK
  • 10.21105/joss.01167 is OK
  • 10.1016/j.jcp.2016.12.051 is OK
  • 10.1016/j.jcp.2018.12.014 is OK
  • 10.1017/jfm.2017.150 is OK
  • 10.1137/15M1010117 is OK
  • 10.1007/s11464-012-0188-3 is OK
  • 10.4208/cicp.150215.260615sw is OK
  • 10.1016/0021-9991(87)90140-9 is OK
  • 10.1007/s006070050015 is OK
  • 10.1137/120866683 is OK
  • 10.1137/120902677 is OK
  • 10.1002/cpa.21577 is OK
  • 10.1002/cpa.21582 is OK
  • 10.1137/16M1081920 is OK
  • 10.1016/j.enganabound.2019.06.020 is OK
  • 10.1186/s40687-017-0100-6 is OK
  • 10.1349/ddlp.2447 is OK
  • 10.1137/060662253 is OK
  • 10.1137/15M1024500 is OK
  • 10.1137/16M1095949 is OK
  • 10.1137/17M1116477 is OK
  • 10.1145/2930660 is OK
  • 10.1007/s10915-018-0872-x is OK
  • 10.1002/nla.691 is OK

MISSING DOIs

  • None

INVALID DOIs

  • None
    ```
whedon picture whedon on 21 Nov 2019

:point_right: Check article proof :page_facing_up: :point_left:

whedon picture whedon on 21 Nov 2019

@melissawm @kyleniemeyer Wanted to check if MATLAB code is okay under JOSS guidelines given that the underlying ecosystem for the code is neither free nor open source? (My MATLAB license expired today and prompted this question).

sivaramambikasaran picture sivaramambikasaran on 29 Nov 2019

@sivaramambikasaran this is ok (especially since, in this case, the code is octave-compatible according to the authors)

melissawm picture melissawm on 29 Nov 2019
👍1

I also agree that there is no issue with the use of MATLAB, even if it were not compatible with Octave (I did not verify such a claim).

The issue I have is with the name of the project, because the title/acronym refers to a much more general subject and as an acronym it is very close to this project

https://www.cs.utexas.edu/~flame

The submitter should select a title and acronym that reflects more accurately the capabilities of this software.

pitsianis picture pitsianis on 29 Nov 2019

Hi all, just checking in on this review. Is there anything I can help with?

melissawm picture melissawm on 12 Dec 2019

@whedon generate pdf

klho picture klho on 27 Dec 2019 
Attempting PDF compilation. Reticulating splines etc...
whedon picture whedon on 27 Dec 2019

:point_right: Check article proof :page_facing_up: :point_left:

whedon picture whedon on 27 Dec 2019

@whedon check references

klho picture klho on 27 Dec 2019 
Attempting to check references...
whedon picture whedon on 27 Dec 2019

```Reference check summary:

OK DOIs

  • 10.1007/s10915-013-9714-z is OK
  • 10.21105/joss.01167 is OK
  • 10.1016/j.jcp.2016.12.051 is OK
  • 10.1016/j.jcp.2018.12.014 is OK
  • 10.1017/jfm.2017.150 is OK
  • 10.1137/15M1010117 is OK
  • 10.1007/s11464-012-0188-3 is OK
  • 10.4208/cicp.150215.260615sw is OK
  • 10.1016/0021-9991(87)90140-9 is OK
  • 10.1007/s006070050015 is OK
  • 10.1137/120866683 is OK
  • 10.1137/120902677 is OK
  • 10.1002/cpa.21577 is OK
  • 10.1002/cpa.21582 is OK
  • 10.1137/16M1081920 is OK
  • 10.1016/j.enganabound.2019.06.020 is OK
  • 10.1186/s40687-017-0100-6 is OK
  • 10.1349/ddlp.2447 is OK
  • 10.1137/060662253 is OK
  • 10.1137/15M1024500 is OK
  • 10.1137/16M1095949 is OK
  • 10.1137/17M1116477 is OK
  • 10.1145/2930660 is OK
  • 10.4310/CMS.2019.v17.n6.a7 is OK
  • 10.1007/s10915-018-0872-x is OK
  • 10.1002/nla.691 is OK

MISSING DOIs

  • None

INVALID DOIs

  • None
    ```
whedon picture whedon on 27 Dec 2019

Hi all, just checking in on this review. Is there anything I can help with?

Sorry for the delay. I will complete the review this weekend.

pitsianis picture pitsianis on 10 Jan 2020

Hi all, just checking in on this review. Is there anything I can help with?

Sorry for the delay. Will finish it by Jan 20th.

sivaramambikasaran picture sivaramambikasaran on 11 Jan 2020

Hello @pitsianis and @sivaramambikasaran , any updates on this review?

melissawm picture melissawm on 3 Feb 2020

I have opened this issue regarding the title and acronym of this project.

pitsianis picture pitsianis on 8 Feb 2020

Thanks, @pitsianis . Are there any other concerns?

klho picture klho on 9 Feb 2020

Hello @pitsianis and @sivaramambikasaran , do you have any updates on this review? If you have any blocking concerns please let me know so we can best resolve the issue. Thanks!

melissawm picture melissawm on 27 Feb 2020

Thanks, @pitsianis . Are there any other concerns?

Do not get me wrong this is exceptional work, it solves a very complex and important problem successfully with simple and elegant code, it has been published in many good journal articles and this software deserves publishing at JOSS.

Now on my concerns. The claim is overly wide in the title. The first paragraph does put things in their right context. A better title will alleviate all my concerns on this.

The remaining issues are minor.

  1. I would prefer to see a specific simple example to be presented so that a user not familiar with this work could appreciate the capabilities of this software. A single phrase description like "This example solves the Poisson equation on the unit square with Dirichlet boundary conditions" won't say much to the great majority of a diverse, non-specialist audience, right? But if, for example, show in addition the discretized matrix, perhaps more people might link it with something they have seen before.

  2. MATLAB users expect when issuing help command to see the list of arguments that command expects and a description of what they are. You have done a great job documenting all major functions, but none of the */test functions.

  3. State in the paper the maximum number of dimensions that points belong to in $\mathbb{R}^d$, that the software supports. In several locations there are mentions like for $d > 1$, for all $d$ etc but could I try it for $d = 1000$? ;-)

  4. No explicit statement in the article whether there exists related software and how it compares to this one.

With the above fixed, I will conclude my (very delayed, sorry) review accepting this work.

pitsianis picture pitsianis on 6 Mar 2020

These seem very fair -- will get to them and let you know when I'm done.

Also, let me know what you think about modifying the paper (and README?) title as in this comment.

klho picture klho on 6 Mar 2020

Dear authors and reviewers

We wanted to notify you that in light of the current COVID-19 pandemic, JOSS has decided to suspend submission of new manuscripts and to handle existing manuscripts (such as this one) on a "best efforts basis". We understand that you may need to attend to more pressing issues than completing a review or updating a repository in response to a review. If this is the case, a quick note indicating that you need to put a "pause" on your involvement with a review would be appreciated but is not required.

Thanks in advance for your understanding.

_Arfon Smith, Editor in Chief, on behalf of the JOSS editorial team._

arfon picture arfon on 14 Mar 2020

@whedon generate pdf

klho picture klho on 19 Mar 2020

:point_right: Check article proof :page_facing_up: :point_left:

whedon picture whedon on 19 Mar 2020

@whedon check references

klho picture klho on 19 Mar 2020 
Reference check summary:

OK DOIs

- 10.1007/s10915-013-9714-z is OK
- 10.21105/joss.01167 is OK
- 10.1016/j.jcp.2016.12.051 is OK
- 10.1016/j.jcp.2018.12.014 is OK
- 10.1017/jfm.2017.150 is OK
- 10.1137/15M1010117 is OK
- 10.1007/s11464-012-0188-3 is OK
- 10.4208/cicp.150215.260615sw is OK
- 10.1016/0021-9991(87)90140-9 is OK
- 10.1007/s006070050015 is OK
- 10.1137/120866683 is OK
- 10.1137/120902677 is OK
- 10.1002/cpa.21577 is OK
- 10.1002/cpa.21582 is OK
- 10.1137/16M1081920 is OK
- 10.1016/j.enganabound.2019.06.020 is OK
- 10.1186/s40687-017-0100-6 is OK
- 10.1349/ddlp.2447 is OK
- 10.1137/060662253 is OK
- 10.1137/15M1024500 is OK
- 10.1137/16M1095949 is OK
- 10.1137/17M1116477 is OK
- 10.1145/2930660 is OK
- 10.4310/CMS.2019.v17.n6.a7 is OK
- 10.1007/s10915-018-0872-x is OK
- 10.1002/nla.691 is OK

MISSING DOIs

- https://doi.org/10.1007/s10444-020-09774-2 may be missing for title: A boundary integral equation approach to computing eigenvalues of the Stokes operator

INVALID DOIs

- None
whedon picture whedon on 19 Mar 2020

@whedon generate pdf

klho picture klho on 19 Mar 2020

:point_right: Check article proof :page_facing_up: :point_left:

whedon picture whedon on 19 Mar 2020

@whedon check references

klho picture klho on 19 Mar 2020 
Reference check summary:

OK DOIs

- 10.1007/s10915-013-9714-z is OK
- 10.21105/joss.01167 is OK
- 10.1007/s10444-020-09774-2 is OK
- 10.1016/j.jcp.2016.12.051 is OK
- 10.1016/j.jcp.2018.12.014 is OK
- 10.1017/jfm.2017.150 is OK
- 10.1137/15M1010117 is OK
- 10.1007/s11464-012-0188-3 is OK
- 10.4208/cicp.150215.260615sw is OK
- 10.1016/0021-9991(87)90140-9 is OK
- 10.1007/s006070050015 is OK
- 10.1137/120866683 is OK
- 10.1137/120902677 is OK
- 10.1002/cpa.21577 is OK
- 10.1002/cpa.21582 is OK
- 10.1137/16M1081920 is OK
- 10.1016/j.enganabound.2019.06.020 is OK
- 10.1186/s40687-017-0100-6 is OK
- 10.1349/ddlp.2447 is OK
- 10.1137/060662253 is OK
- 10.1137/15M1024500 is OK
- 10.1137/16M1095949 is OK
- 10.1137/17M1116477 is OK
- 10.1145/2930660 is OK
- 10.4310/CMS.2019.v17.n6.a7 is OK
- 10.1007/s10915-018-0872-x is OK
- 10.1002/nla.691 is OK

MISSING DOIs

- None

INVALID DOIs

- None
whedon picture whedon on 19 Mar 2020

Please see the following changes:

  1. I've added a subtitle to the paper so that it now reads "FLAM: Fast Linear Algebra in MATLAB - Algorithms for Hierarchical Matrices". A similar addition has been made to the README.

  2. I've elaborated on the example in the README and tried to emphasize why the example is impressive. However, I'm a little at a loss on how to make it much more approachable: showing the discretized IE matrix would require a lot more background and notation, which I would really like to avoid; and even switching to a more "standard" PDE example would require some discussion of nested dissection, etc., which is arguably similarly specialized (at least for an introductory example). At any rate, let me know your thoughts on the current revision.

  3. All test code arguments have now been documented.

  4. Strictly speaking, there is no dimensional limitation in the code itself, but I have added statements to both the paper and the README.

  5. Related software is cited in the opening paragraph. I've now also added another paragraph near the end summarizing some perhaps key distinctions.

klho picture klho on 19 Mar 2020

I approve the publication of this paper with the latest changes.

pitsianis picture pitsianis on 19 Mar 2020

Thank you, @pitsianis !

melissawm picture melissawm on 19 Mar 2020

Hello @sivaramambikasaran, I know this is a busy time, but I'm concerned about this review as we haven't had any responses from you in a while. Would you please let us know if you are unable to complete the review, so we can find another reviewer and finish this so that @klho can have this paper published as soon as possible? Thank you in advance!

melissawm picture melissawm on 19 Mar 2020

Hi, just pinging since it's been two weeks without any response.

klho picture klho on 3 Apr 2020

@melissawm - it might be worth trying to contact @sivaramambikasaran over email if you've not tried that already?

arfon picture arfon on 3 Apr 2020

@arfon unfortunately I have, and have had no response for a long time. I think it may be time to look for another reviewer. I was trying to avoid that since it probably means more delays because a new reviewer will have to start from scratch, but I see no other solution at this point. Thanks for your patience, @klho

melissawm picture melissawm on 3 Apr 2020
👍1

Thanks -- that might be for the best.

klho picture klho on 3 Apr 2020

@whedon generate pdf

klho picture klho on 3 Apr 2020

:point_right: Check article proof :page_facing_up: :point_left:

whedon picture whedon on 3 Apr 2020

@whedon check references

klho picture klho on 3 Apr 2020 
Reference check summary:

OK DOIs

- 10.1007/s10915-013-9714-z is OK
- 10.21105/joss.01167 is OK
- 10.1007/s10444-020-09774-2 is OK
- 10.1016/j.jcp.2016.12.051 is OK
- 10.1016/j.jcp.2018.12.014 is OK
- 10.1017/jfm.2017.150 is OK
- 10.4310/CMS.2020.v18.n1.a4 is OK
- 10.1137/15M1010117 is OK
- 10.1007/s11464-012-0188-3 is OK
- 10.4208/cicp.150215.260615sw is OK
- 10.1016/0021-9991(87)90140-9 is OK
- 10.1007/s006070050015 is OK
- 10.1137/120866683 is OK
- 10.1137/120902677 is OK
- 10.1002/cpa.21577 is OK
- 10.1002/cpa.21582 is OK
- 10.1137/16M1081920 is OK
- 10.1016/j.enganabound.2019.06.020 is OK
- 10.1186/s40687-017-0100-6 is OK
- 10.1349/ddlp.2447 is OK
- 10.1137/060662253 is OK
- 10.1137/15M1024500 is OK
- 10.1137/16M1095949 is OK
- 10.1137/17M1116477 is OK
- 10.1145/2930660 is OK
- 10.4310/CMS.2019.v17.n6.a7 is OK
- 10.1007/s10915-018-0872-x is OK
- 10.1002/nla.691 is OK

MISSING DOIs

- None

INVALID DOIs

- None
whedon picture whedon on 3 Apr 2020

Hello @vijaysm, would you be willing/available to review this software paper for JOSS? We do realize this may be a complicated time for all (you can read Arfon's message above about our current paused status). However, if you can let us know if you think you could spare some time to review this some time in the future (or not), please just mention it in this thread. Thank you in advance!

melissawm picture melissawm on 5 Apr 2020

Hi @melissawm, thanks for reaching out for the review. I should be able to find enough time to review the paper in the coming days. I'll get started on this next week.

vijaysm picture vijaysm on 6 Apr 2020

That's great, thank you so much!

melissawm picture melissawm on 6 Apr 2020

@whedon add @vijaysm as reviewer

melissawm picture melissawm on 6 Apr 2020

OK, @vijaysm is now a reviewer

whedon picture whedon on 6 Apr 2020

@melissawm I don't see a checklist with my name on it at the top of the issue page. Please let me know where to update my progress.

vijaysm picture vijaysm on 20 Apr 2020

@melissawm I don't see a checklist with my name on it at the top of the issue page. Please let me know where to update my progress.

@vijaysm - I've added a checklist for you above.

arfon picture arfon on 20 Apr 2020

Thanks @arfon, sorry @vijaysm that was my mistake!

melissawm picture melissawm on 20 Apr 2020

:wave: @vijaysm and @sivaramambikasaran - how are you getting on with your reviews?

arfon picture arfon on 20 May 2020

I should be done with the review in about a week from now. I've been
swamped with a paper deadline due this week and can finish up the review
after.

On Wed., May 20, 2020, 10:16 Arfon Smith, notifications@github.com wrote:

👋 @vijaysm https://github.com/vijaysm and @sivaramambikasaran
https://github.com/sivaramambikasaran - how are you getting on with
your reviews?

—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
https://github.com/openjournals/joss-reviews/issues/1906#issuecomment-631501519,
or unsubscribe
https://github.com/notifications/unsubscribe-auth/AACVEPPWNYEOYQQ2QZDHMYLRSPQ4VANCNFSM4JQFOEVA
.

vijaysm picture vijaysm on 20 May 2020
👍1

@whedon generate pdf

klho picture klho on 20 May 2020

:point_right: Check article proof :page_facing_up: :point_left:

whedon picture whedon on 20 May 2020

@whedon check references

klho picture klho on 20 May 2020 
Reference check summary:

OK DOIs

- 10.1007/s10915-013-9714-z is OK
- 10.21105/joss.01167 is OK
- 10.1007/s10444-020-09774-2 is OK
- 10.1016/j.jcp.2016.12.051 is OK
- 10.1016/j.jcp.2018.12.014 is OK
- 10.1017/jfm.2017.150 is OK
- 10.4310/CMS.2020.v18.n1.a4 is OK
- 10.1137/15M1010117 is OK
- 10.1007/s11464-012-0188-3 is OK
- 10.4208/cicp.150215.260615sw is OK
- 10.1016/0021-9991(87)90140-9 is OK
- 10.1007/s006070050015 is OK
- 10.1137/120866683 is OK
- 10.1137/120902677 is OK
- 10.1002/cpa.21577 is OK
- 10.1002/cpa.21582 is OK
- 10.1137/16M1081920 is OK
- 10.1016/j.enganabound.2019.06.020 is OK
- 10.1186/s40687-017-0100-6 is OK
- 10.1349/ddlp.2447 is OK
- 10.1137/060662253 is OK
- 10.1137/19M1288048 is OK
- 10.1137/15M1024500 is OK
- 10.1137/16M1095949 is OK
- 10.1137/17M1116477 is OK
- 10.1145/2930660 is OK
- 10.4310/CMS.2019.v17.n6.a7 is OK
- 10.1007/s10915-018-0872-x is OK
- 10.1002/nla.691 is OK

MISSING DOIs

- None

INVALID DOIs

- None
whedon picture whedon on 20 May 2020

@melissawm @arfon I have reviewed the software, repository, verified functionality and the accompanying article. I recommend the acceptance of the paper and publication in JOSS. I think this will be a useful toolbox for tackling matrices with a hierarchical structure as the authors have clearly pointed out applications and research areas where they are already being used.

Some suggestion and comments for @klho to improve the submission.

  • It might be interesting to have a comparative figure showcasing performance of the hierarchical solvers in FLAM against standard generalized LU solvers for dense matrices or PCG with ILU preconditioners for sparse matrices in MATLAB. This will give the readers a better sense of performance gains that can be achieved with FLAM. The README file in the repository does have some performance numbers for both time and memory complexity, and can be highlighted in the paper. I also can see that some of the references do help in this regard as well.
  • Please mention minimum required versions of MATLAB and Octave to use FLAM in the article and the README file in the repository
  • Fix the typo in the article: FMM is Fast Multipole Method and not *Multiple. Capitalize appropriately as well.
vijaysm picture vijaysm on 22 Jun 2020

👍 thanks @vijaysm! @klho - please let us know when you've had a chance to incorporate @vijaysm's feedback.

arfon picture arfon on 22 Jun 2020

@whedon generate pdf

klho picture klho on 23 Jun 2020

:point_right: Check article proof :page_facing_up: :point_left:

whedon picture whedon on 23 Jun 2020

@vijaysm Thanks for the feedback; please see my responses below:

  1. I've added a brief paragraph highlighting some numerical examples. I'm hesitant to put much more in the paper since I'd like to keep it light and avoid having to give too much background explanation. (Many) more details can be found in the cited papers.

  2. This is quite reasonable but unfortunately might not doable. I don't have access to old versions of MATLAB to test. While I can download old versions of Octave, this is very time-consuming and ultimately may not be very informative. What I can say is that only "core" features of MATLAB/Octave are used, so compatibility should be quite stable (up to harmless warnings, e.g., for broadcasting), at least since 2014 when this project was initiated (and likely much further). But I have no way of making that statement precise, which is why I'd prefer to leave it off altogether. Please let me know your thoughts and how strongly you feel about this.

  3. Thanks for catching the typo! However, I don't agree with the capitalization and so have not changed that; please see https://en.wikipedia.org/wiki/Wikipedia:Manual_of_Style/Capital_letters#Expanded_forms_of_abbreviations.

klho picture klho on 23 Jun 2020

:wave: @vijaysm - do you find @klho's response above satisfactory? If so, I believe we can move forward with accepting this paper.

arfon picture arfon on 2 Jul 2020

I apologize. I thought I had replied to @klho's comments.

@klho Thanks for updating the paper.

  1. I agree that the citations have more details but I just wanted you to highlight some clear advantages of the hierarchical solvers in FLAM to give the reader a better idea before diving deeper into using the software implementation.

  2. For the minimum version, you can go ahead and mention the MATLAB/Octave versions that you have tested so far, even if these are the latest ones. It just eliminates confusion from a user standpoint on which version would work for FLAM.

  3. This is fine. It was more of an aesthetic suggestion but as long as you are consistent throughout the paper and in README, I think we can leave it as is.

@arfon I am satisfied with the author response. After a minor update to include details for [2] in the README, you can go ahead and accept the paper. Thanks.

vijaysm picture vijaysm on 3 Jul 2020

@vijaysm There is already a statement on the last tested version in the README. Is that sufficient?

klho picture klho on 3 Jul 2020

From README.md in the repository:

FLAM is freely available under the GNU GPLv3 and was last tested on MATLAB R2019a and Octave 4.2.2.

Excellent. Yes, this will suffice.

vijaysm picture vijaysm on 3 Jul 2020

@whedon check references

arfon picture arfon on 4 Jul 2020 
Reference check summary:

OK DOIs

- 10.1007/s10915-013-9714-z is OK
- 10.21105/joss.01167 is OK
- 10.1007/s10444-020-09774-2 is OK
- 10.1016/j.jcp.2016.12.051 is OK
- 10.1016/j.jcp.2018.12.014 is OK
- 10.1017/jfm.2017.150 is OK
- 10.4310/CMS.2020.v18.n1.a4 is OK
- 10.1137/15M1010117 is OK
- 10.1007/s11464-012-0188-3 is OK
- 10.4208/cicp.150215.260615sw is OK
- 10.1016/0021-9991(87)90140-9 is OK
- 10.1007/s006070050015 is OK
- 10.1137/120866683 is OK
- 10.1137/120902677 is OK
- 10.1002/cpa.21577 is OK
- 10.1002/cpa.21582 is OK
- 10.1137/16M1081920 is OK
- 10.1016/j.enganabound.2019.06.020 is OK
- 10.1186/s40687-017-0100-6 is OK
- 10.1349/ddlp.2447 is OK
- 10.1137/060662253 is OK
- 10.1137/19M1288048 is OK
- 10.1137/15M1024500 is OK
- 10.1137/16M1095949 is OK
- 10.1137/17M1116477 is OK
- 10.1145/2930660 is OK
- 10.4310/CMS.2019.v17.n6.a7 is OK
- 10.1007/s10915-018-0872-x is OK
- 10.1002/nla.691 is OK

MISSING DOIs

- None

INVALID DOIs

- None
whedon picture whedon on 4 Jul 2020

@whedon generate pdf

arfon picture arfon on 4 Jul 2020

:point_right: Check article proof :page_facing_up: :point_left:

whedon picture whedon on 4 Jul 2020

@klho - At this point could you make a new release of this software that includes the changes that have resulted from this review. Then, please make an archive of the software in Zenodo/figshare/other service and update this thread with the DOI of the archive? For the Zenodo/figshare archive, please make sure that:

  • The title of the archive is the same as the JOSS paper title
  • That the authors of the archive are the same as the JOSS paper authors

I can then move forward with accepting the submission.

arfon picture arfon on 4 Jul 2020

@arfon - Done: the Zenodo archive is at https://zenodo.org/record/3930385. Thanks for moving quickly.

klho picture klho on 4 Jul 2020

@whedon set 10.5281/zenodo.3930385 as archive

arfon picture arfon on 4 Jul 2020

OK. 10.5281/zenodo.3930385 is the archive.

whedon picture whedon on 4 Jul 2020

@whedon accept

arfon picture arfon on 4 Jul 2020 
Attempting dry run of processing paper acceptance...
whedon picture whedon on 4 Jul 2020 
Reference check summary:

OK DOIs

- 10.1007/s10915-013-9714-z is OK
- 10.21105/joss.01167 is OK
- 10.1007/s10444-020-09774-2 is OK
- 10.1016/j.jcp.2016.12.051 is OK
- 10.1016/j.jcp.2018.12.014 is OK
- 10.1017/jfm.2017.150 is OK
- 10.4310/CMS.2020.v18.n1.a4 is OK
- 10.1137/15M1010117 is OK
- 10.1007/s11464-012-0188-3 is OK
- 10.4208/cicp.150215.260615sw is OK
- 10.1016/0021-9991(87)90140-9 is OK
- 10.1007/s006070050015 is OK
- 10.1137/120866683 is OK
- 10.1137/120902677 is OK
- 10.1002/cpa.21577 is OK
- 10.1002/cpa.21582 is OK
- 10.1137/16M1081920 is OK
- 10.1016/j.enganabound.2019.06.020 is OK
- 10.1186/s40687-017-0100-6 is OK
- 10.1349/ddlp.2447 is OK
- 10.1137/060662253 is OK
- 10.1137/19M1288048 is OK
- 10.1137/15M1024500 is OK
- 10.1137/16M1095949 is OK
- 10.1137/17M1116477 is OK
- 10.1145/2930660 is OK
- 10.4310/CMS.2019.v17.n6.a7 is OK
- 10.1007/s10915-018-0872-x is OK
- 10.1002/nla.691 is OK

MISSING DOIs

- None

INVALID DOIs

- None
whedon picture whedon on 4 Jul 2020

:wave: @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1536

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1536, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true

whedon picture whedon on 4 Jul 2020

@whedon accept deposit=true

arfon picture arfon on 4 Jul 2020 
Doing it live! Attempting automated processing of paper acceptance...
whedon picture whedon on 4 Jul 2020

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon picture whedon on 4 Jul 2020

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/1537
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01906
  3. If everything looks good, then close this review issue.

  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

    Any issues? Notify your editorial technical team...

whedon picture whedon on 4 Jul 2020

@sivaramambikasaran, @pitsianis, @vijaysm - many thanks for your reviews here and to @melissawm for editing this submission ✨

@klho - your paper is now accepted into JOSS :zap::rocket::boom:

arfon picture arfon on 4 Jul 2020

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.01906/status.svg)](https://doi.org/10.21105/joss.01906)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01906">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01906/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01906/status.svg
   :target: https://doi.org/10.21105/joss.01906

This is how it will look in your documentation:

DOI

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whedon picture whedon on 4 Jul 2020
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