[REVIEW]: Parcellating the parcellation issue - a proof of concept for reproducible analyses using Neurolibre

[roboneuro]

Submitting author: @pbellec (Pierre Bellec)
Repository: https://github.com/pbellec/editorial_parcellation
Branch with paper.md (empty if default branch): main
Version: v1.0.0
Editor: @agahkarakuzu
Reviewers: @agahkarakuzu
Reproducible preprint: https://preprint.neurolibre.org/10.55458/neurolibre.00010
Repository archive: 10.5281/zenodo.10031956
Data archive: 10.5281/zenodo.10031958
Book archive: 10.5281/zenodo.10031954
Docker archive: 10.5281/zenodo.10031960

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

@anirudhk686, 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 @agahkarakuzu 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 @anirudhk686

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 NeuroLibre 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 (@pbellec) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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?

[roboneuro]

Hello human, I'm @roboneuro, a robot that can help you with some common editorial tasks. @anirudhk686 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/neurolibre/neurolibre-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/neurolibre/neurolibre-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:

@roboneuro commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@roboneuro generate pdf

[roboneuro]

🌱  The PDF has been compiled!

• 📥  Download article proof
•   View article proof on GitHub

[roboneuro]

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

OK DOIs

- None

MISSING DOIs

- 10.1016/j.neuroimage.2017.11.063 may be a valid DOI for title: Neuroimage special issue on brain segmentation and parcellation - Editorial

INVALID DOIs

- None

[roboneuro]

👉📄 View built NeuroLibre Notebook 📄👈

[agahkarakuzu]

@pbellec can you please add DOI to your paper.bib as in:

@ARTICLE{Craddock2018-ou,
title    = "Neuroimage special issue on brain segmentation and parcellation -Editorial",
author   = "Craddock, R Cameron and Bellec, Pierre and Jbabdi, Saad",
journal  = "Neuroimage",
volume   =  170,
pages    = "1--4",
month    =  apr,
year     =  2018,
+ language = "en",
+ doi = "10.1016/j.neuroimage.2017.11.063"
}

[agahkarakuzu]

Also, the figures are really cool! Can you select your favourite one then add it to the root of you repository as featured.png, so that it shows up in the publication card?

[agahkarakuzu]

@anirudhk686 thank you for helping us out with the technical screening! A big chunk of the checklist above is coming from JOSS, as NeuroLibre is a fork of it. We will edit that section soon for relevance to the technical screening process. These test submissions are great for that!

As we are nearly finalizing our initial development phase, we may discover new bugs, missing features etc. during this review, so thank you for your patience in advance.

You can take a look at the technical screening guidelines of our documentation.

A good first step would be asking roboneuro to generate pdf after Pierre adds DOI to the paper.bib. Then you can ask it to check DOIs.

You can see the full list of commands by @roboneuro commands.

Once you ensure the functionality of the book, I will go ahead with archival and publishing steps as the handling editor of this submission.

[lunebellec]

thanks for getting @anirudhk686 started @agahkarakuzu ! I've created a thread with a few extra points to check: neurolibre/docs.neurolibre.org#39 Please add anything I missed, and @anirudhk686 please give feedback on ideas or issues you run into. Hopefully we can use this experience to improve the docs and replace the checklist above with something that actually matches the neurolibre process.

[lunebellec]

@agahkarakuzu I have added the DOI and a featured image.

@anirudhk686 please let me know if there is anything else.

[agahkarakuzu]

@anirudhk686 would you like to test the changes Pierre pushed by using some of the roboneuro commands I listed above?

[anirudhk686]

@roboneuro commands