[REVIEW]: COINSTAC: Collaborative Informatics and Neuroimaging Suite Toolkit for Anonymous Computation

[whedon]

Submitting author: @hvgazula (Harshvardhan Gazula)
Repository: https://github.com/trendscenter/coinstac
Version: v5.1.3
Editor: @cMadan
Reviewer: @gkiar, @yarikoptic
Archive: 10.5281/zenodo.4111006

Status

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Markdown: [![status](https://joss.theoj.org/papers/c51a4a8f4aec5d8af4c8c31d2a37b0ad/status.svg)](https://joss.theoj.org/papers/c51a4a8f4aec5d8af4c8c31d2a37b0ad)

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

@gkiar & @yarikoptic, 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 @cMadan know.

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

Review checklist for @gkiar

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

• I confirm that I read and will adhere to the JOSS 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 (@hvgazula) 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 @yarikoptic

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

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the repository url? (correction: moved and being redirected to https://github.com/trendscenter/coinstac now)
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license? (needs work: Please provide LICENSE file trendscenter/coinstac#879, "Copyright (c) 2013-2018 GitHub Inc." of the downloaded releases trendscenter/coinstac#876)
• Contribution and authorship: Has the submitting author (@hvgazula) 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]

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

⭐ 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:

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

PDF failed to compile for issue #2166 with the following error:

Can't find any papers to compile :-(

[gkiar]

@whedon generate pdf from branch paper-branch

[whedon]

Attempting PDF compilation from custom branch paper-branch. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[gkiar]

@cMadan I have left my initial review at trendscenter/coinstac#849 and checked off the already-met requirements in my form above.

[gkiar]

@whedon generate pdf from branch paper-branch

[whedon]

Attempting PDF compilation from custom branch paper-branch. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[arfon]

👋 @yarikoptic - just a friendly check-in to see how things are going with your review?

[yarikoptic]

@arfon sorry for the delay... will do today/tomorrow

[yarikoptic]

Sorry for the delay again, an update: my feedback to authors and here is starting to flow! ;-)

[yarikoptic]

FTR: my review of the manuscript with some additional references -- trendscenter/coinstac#881

[kthyng]

Hi @hvgazula! Looks like you have a review in as noted immediately above. How are things going on your end to address the comments?

[hvgazula]

Hello @kthyng Thanks for checking. I shall be pasting my comments sometime tonight.

[hvgazula]

Hello @kthyng Thanks for checking. I shall be pasting my comments sometime tonight.

Hi @kthyng and @cMadan FYI, I submitted my responses to the second reviewer as well last week and will now wait to hear from both the reviewers if they have any comments. Thanks!

[hvgazula]

Tagging @gkiar and @yarikoptic just in case as a reminder 👍

[cMadan]

@gkiar @yarikoptic, do you know when you might be able to look over these changes? Thanks!

[cMadan]

Fyi. I just sent an email to remind @gkiar and @yarikoptic about this review.

[hvgazula]

Fyi. I just sent an email to remind @gkiar and @yarikoptic about this review.

Thank you very much.

[gkiar]

I have updated my review. The only remaining piece from my perspective is the addition of issue guidelines and PR templates for contributors and users, fitting the description provided in the review template above.

[cMadan]

Great, thank you, @gkiar!

[cMadan]

@whedon generate pdf

[whedon]

PDF failed to compile for issue #2166 with the following error:

Can't find any papers to compile :-(

[cMadan]

@whedon generate pdf from branch paper-branch

[whedon]

Attempting PDF compilation from custom branch paper-branch. Reticulating splines etc...

[whedon]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[cMadan]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

PDF failed to compile for issue #2166 with the following error:

Can't find any papers to compile :-(

[cMadan]

@whedon accept from branch paper-branch

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.3389/fnins.2016.00365 is OK
- 10.12688/f1000research.12353.1 is OK
- 10.3389/fninf.2018.00055 is OK
- 10.3389/fninf.2014.00054 is OK
- 10.3389/fninf.2011.00037 is OK
- 10.1016/j.neuroimage.2015.06.076 is OK
- 10.7490/f1000research.1114354.1 is OK
- 10.1561/9781601988195 is OK
- 10.1007/s11682-013-9269-5 is OK
- 10.1093/ije/dyv193 is OK
- 10.1101/846386 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

Check final proof 👉 openjournals/joss-papers#1849

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1849, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true from branch paper-branch 

[kyleniemeyer]

Hi @hvgazula, I'm the EIC on duty this week, doing some final checks before publishing your article.

The only thing I noticed is that your article is missing an explicit Statement of Need section, which we have begun requiring for all articles. Can you add this? You might be able to just rename an existing section, or move some of your text into the new one.

[hvgazula]

Hi @hvgazula, I'm the EIC on duty this week, doing some final checks before publishing your article.

The only thing I noticed is that your article is missing an explicit Statement of Need section, which we have begun requiring for all articles. Can you add this? You might be able to just rename an existing section, or move some of your text into the new one.

@kyleniemeyer Done. Thanks for letting me know about it. Really appreciate it. Please let me know if there's anything else I need to do.

[kyleniemeyer]

@whedon generate pdf

[whedon]

PDF failed to compile for issue #2166 with the following error:

Can't find any papers to compile :-(

[kyleniemeyer]

@whedon generate pdf from branch paper-branch

[whedon]

Attempting PDF compilation from custom branch paper-branch. Reticulating splines etc...

[whedon]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[kyleniemeyer]

@whedon accept deposit=true from branch paper-branch

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

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

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.02166 joss-papers#1856
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02166
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[kyleniemeyer]

Congrats @hvgazula on your article's publication in JOSS!

Many thanks to @gkiar and @yarikoptic for reviewing this, and @cMadan for editing.

[whedon]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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.02166/status.svg)](https://doi.org/10.21105/joss.02166)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02166">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02166/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02166/status.svg
   :target: https://doi.org/10.21105/joss.02166

This is how it will look in your documentation:

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