[REVIEW]: ropenblas: Download, Compile and Link OpenBLAS Library with R

whedon commented 4 years ago

Submitting author: @prdm0 (Pedro Rafael Marinho) Repository: https://github.com/prdm0/ropenblas Version: v0.2.9 Editor: @timtroendle Reviewers: @pratikvn, @myousefi2016 Archive: 10.5281/zenodo.4618251

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Status

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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

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

Make sure you're logged in to your GitHub account
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 @timtroendle 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 ✨

Review checklist for @pratikvn

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

[x] I confirm that I read and will adhere to the JOSS 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 (@prdm0) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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 @myousefi2016

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

[x] I confirm that I read and will adhere to the JOSS 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 (@prdm0) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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?

whedon commented 4 years ago

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

:warning: JOSS reduced service mode :warning:

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.

: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 😿

To fix this do the following two things:

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whedon commented 4 years ago

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

OK DOIs

- None

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 4 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

prdm0 commented 4 years ago

Dear @timtroendle , Is there a maximum time limit for improvements to be implemented? When the suggestions are implemented, should I generate a new PDF using @whedon generate pdf?

Kind regards.

timtroendle commented 4 years ago

Dear @prdm0, there is no hard time limit for you to implement changes. However, if this should take you a longer time it would be great if you could let us know. At the moment we are waiting for review comments from @sahilseth.

prdm0 commented 3 years ago

Dear @timtroendle, I intend to quickly make the changes suggested by the first reviewer. When they are implemented, should I update the PDF or should I wait for suggestions from the second reviewer?

timtroendle commented 3 years ago

That should be fine as long as it doesn't disturb the second reviewer. @sahilseth, please let us know in case you prefer to see the original paper.

timtroendle commented 3 years ago

@sahilseth, can you please give us an update where you stand with your review?

prdm0 commented 3 years ago

@timtroendle, I'm waiting for some feedback from @sahilseth so that I can implement all suggestions for improvement from both reviewers.

Kind regards.

sahilseth commented 3 years ago

@timtroendle Could you please re-add me as a reviewer, I am not able to submit feedback. Sorry, we couldn't find that repository invitation.

timtroendle commented 3 years ago

Sure. Not sure why you weren't assigned, sorry about that. Did this work?

sahilseth commented 3 years ago

I was still getting the same error if you would like o re-add me as a reviewer, I will try again. If not, I can copy-paste the review as a comment here tonight.

timtroendle commented 3 years ago

@whedon add @sahilseth as reviewer

whedon commented 3 years ago

OK, @sahilseth is now a reviewer

timtroendle commented 3 years ago

I gave it another try. Please let me know if it works now.

sahilseth commented 3 years ago

Perfect, that worked

timtroendle commented 3 years ago

@sahilseth, can you please give us an update on where you stand with your review? We need to finish this first round of reviews. Can you please let me know how long this will take you?

timtroendle commented 3 years ago

@whedon add @jgoldfar as reviewer

whedon commented 3 years ago

OK, @jgoldfar is now a reviewer

timtroendle commented 3 years ago

@openjournals/dev, sorry for the trouble but Whedon did not assign the new reviewer to this issue and I am unable to assign them manually. Is there anything I can do here?

arfon commented 3 years ago

@whedon re-invite @sahilseth as reviewer

whedon commented 3 years ago

@sahilseth already has access.

arfon commented 3 years ago

@whedon re-invite @jgoldfar as reviewer

whedon commented 3 years ago

The reviewer already has a pending invite.

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

arfon commented 3 years ago

@openjournals/dev, sorry for the trouble but Whedon did not assign the new reviewer to this issue and I am unable to assign them manually. Is there anything I can do here?

@timtroendle - I'm not sure exactly who has the issue here but @sahilseth should be able to complete their review (update checkboxes etc.) fine, @jgoldfar needs to accept the invite in the message above before they will be able to update their checkboxes.

@timtroendle - just as an FYI - adding reviewers after the pre-review stage is generally a little more challenging (as you're finding out!) which is why we prefer to have the reviewers assigned in the pre-review issue if at all possible.

timtroendle commented 3 years ago

@arfon - great, thanks for the update and for letting me know.

timtroendle commented 3 years ago

@sahilseth, @jgoldfar, please can you give us an update about how much time you will need to finish the review?

prdm0 commented 3 years ago

@Pratikvn sent me suggestions. Is another reviewer missing to send the corrections?

timtroendle commented 3 years ago

Yes, we are waiting for a second review to be finished.

jgoldfar commented 3 years ago

I will complete my review (and the checklist above - unable to update on mobile) by Friday. Thanks for the reminder!

prdm0 commented 3 years ago

I received @pratikvn reviews on the "Issue" of the ropenblas project https://github.com/prdm0/ropenblas/issues/21. @jgoldfar will also send in the same way or will something here also be sent?

timtroendle commented 3 years ago

Hi @jgoldfar, did you have the time to look at this submission?

timtroendle commented 3 years ago

@sahilseth @jgoldfar We need to proceed. Please let me know whether you can finish your review within the next two weeks or whether you prefer to drop the review.

timtroendle commented 3 years ago

@whedon add @myousefi2016 as reviewer.

whedon commented 3 years ago

OK, @myousefi2016 is now a reviewer

myousefi2016 commented 3 years ago

Hi @timtroendle, thanks for giving me this opportunity to review ropenblas. One quick comment for @prdm0 to speed up the review process a bit: The software paper is great and describes very interesting and useful details. I just reflected that in my evaluation in the Software paper section. But, for Quality of writing: I suggest to double check with a native English speaker (I'm not a native English speaker either) to make sure there is no typo or grammatical error to improve the level of writing quality.

prdm0 commented 3 years ago

Dear @myousefi2016 , thanks for the suggestion. I will revise the text as suggested. I look forward to the other suggestions, if any, in issues of the package project in the Github. Kind regards.

myousefi2016 commented 3 years ago

@timtroendle I think I'm done with the review and I'm just waiting for revision of the software paper.

prdm0 commented 3 years ago

Dear, soon I will be returning the PDF with all the requested corrections. Best regards.

prdm0 commented 3 years ago

Dear @timtroendle ,

I proceeded with the changes suggested by the reviewers. I modified the documentation on GitHub and the library website as suggested by one of the reviewers, as well as made several changes to the paper. Among them I mention the inclusion of a benchmark, changes in writing and a better explanation of some concepts.

@whedon generate pdf

prdm0 commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

prdm0 commented 3 years ago

Dear, I did one more complete review of the paper's English. I believe that the article is now in a presentable format. Thank you for all the suggestions that have enriched the material.

prdm0 commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

timtroendle commented 3 years ago

@whedon remove @sahilseth as reviewer

whedon commented 3 years ago

OK, @sahilseth is no longer a reviewer

timtroendle commented 3 years ago

@whedon remove @jgoldfar as reviewer

whedon commented 3 years ago

OK, @jgoldfar is no longer a reviewer

timtroendle commented 3 years ago

Thank you for the update, @prdm0. @pratikvn and @myousefi2016, could you please have a look at the revisions and update your corresponding checklist above? Also, a review issue is still open: https://github.com/prdm0/ropenblas/issues/21. @pratikvn, can you please close the issue if the changes have been implemented sufficiently?

openjournals / joss-reviews