[REVIEW]: GENRE (GPU Elastic-Net REgression): A CUDA-Accelerated Package for Massively Parallel Linear Regression with Elastic-Net Regularization

whedon commented 4 years ago

Submitting author: @Christopher-Khan (Christopher Khan) Repository: https://github.com/VU-BEAM-Lab/GENRE Version: v1.0.2 Editor: @sjpfenninger Reviewer: @marouenbg, @krystophny Archive: 10.5281/zenodo.4076520

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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

@marouenbg & @krystophny, 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 @sjpfenninger 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 @marouenbg

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 (@Christopher-Khan) 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 @krystophny

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 (@Christopher-Khan) 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?

sjpfenninger commented 3 years ago

@Christopher-Khan Apologies for the delay. This looks good now!

sjpfenninger commented 3 years ago

@whedon accept

whedon commented 3 years ago

Attempting dry run of processing paper acceptance...

whedon commented 3 years ago

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

OK DOIs

- 10.1111/j.1467-9868.2005.00503.x is OK
- 10.18637/jss.v033.i01 is OK
- 10.1109/tuffc.2014.2928 is OK
- 10.1109/tuffc.2015.007004 is OK
- 10.1109/tuffc.2017.2729944 is OK
- 10.1186/1753-6561-6-s2-s10 is OK
- 10.3389/fgene.2013.00270 is OK
- 10.1016/j.neuroimage.2008.08.020 is OK
- 10.1109/isbi.2014.6868131 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 3 years ago

: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/1790

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1790, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

kthyng commented 3 years ago

Hi @Christopher-Khan! I see that you archive and version are set and up to date. I just looked at your paper and unfortunately it is far too long. A JOSS paper is to be between 250 and 1000 words. Can you move some of the content from the paper to your documentation?

Christopher-Khan commented 3 years ago

Hi @kthyng! Sure. I can move the section titled "Example Benchmark Comparing GENRE with glmnet" to my documentation on GitHub. That will make the paper two pages shorter. Do you want me to make a new Zenodo archive then and give the DOI for that one? I ask because I don't think Zenodo allows for files in archives to be updated if the archive is more than a week old. Thank you!

krystophny commented 3 years ago

@Christopher-Khan if you make a new release on github, Zenodo will create a new version of the same entry with a new doi. Probably that’s better than creating a new archive

Christopher-Khan 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:

Christopher-Khan commented 3 years ago

@krystophny thank you. That's what I meant actually instead of creating a new archive. @kthyng I have moved the section in the JOSS paper titled "Example Benchmark Comparing GENRE with glmnet" from the paper to the section in the README.md file titled "Comparing with Other Packages". The new DOI is below. I hope the paper is better now in terms of its length.

DOI: 10.5281/zenodo.4076520

Thank you for your time.

kthyng commented 3 years ago

@Christopher-Khan Yes looks good! We can proceed now.

kthyng commented 3 years ago

@whedon set 10.5281/zenodo.4076520 as archive

whedon commented 3 years ago

OK. 10.5281/zenodo.4076520 is the archive.

kthyng commented 3 years ago

@whedon accept

whedon commented 3 years ago

Attempting dry run of processing paper acceptance...

whedon commented 3 years ago

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

OK DOIs

- 10.1111/j.1467-9868.2005.00503.x is OK
- 10.18637/jss.v033.i01 is OK
- 10.1109/tuffc.2014.2928 is OK
- 10.1109/tuffc.2015.007004 is OK
- 10.1109/tuffc.2017.2729944 is OK
- 10.1186/1753-6561-6-s2-s10 is OK
- 10.3389/fgene.2013.00270 is OK
- 10.1016/j.neuroimage.2008.08.020 is OK
- 10.1109/isbi.2014.6868131 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 3 years ago

: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/1797

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1797, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

kthyng commented 3 years ago

@whedon accept deposit=true

whedon commented 3 years ago

Doing it live! Attempting automated processing of paper acceptance...

whedon commented 3 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 3 years ago

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

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/1798
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02644
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

kthyng commented 3 years ago

Congrats on the new publication @Christopher-Khan! Thanks to editor @sjpfenninger and reviewers @marouenbg and @krystophny for your time and expertise!!

(will close this issue once doi resolves)

whedon commented 3 years ago

: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.02644/status.svg)](https://doi.org/10.21105/joss.02644)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02644">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02644/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02644/status.svg
   :target: https://doi.org/10.21105/joss.02644

This is how it will look in your documentation:

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Christopher-Khan commented 3 years ago

Awesome! Thank you @kthyng, @sjpfenninger, @marouenbg, and @krystophny! This review process has been great!

Christopher-Khan commented 3 years ago

@whedon set v1.0.2 as version

whedon commented 3 years ago

I'm sorry @Christopher-Khan, I'm afraid I can't do that. That's something only editors are allowed to do.

Christopher-Khan commented 3 years ago

@sjpfenninger. Last thing. Do I need to set the version at the top of this review from v1.0.1 to v1.0.2 because that's the newest version that actually got accepted? If so, I believe only editors can do that. Thank you!

arfon commented 3 years ago

@whedon set v1.0.2 as version

whedon commented 3 years ago

OK. v1.0.2 is the version.

Christopher-Khan commented 3 years ago

@arfon Great! Thank you!

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