[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

Status badge code:

HTML: <a href="http://neurolibre.herokuapp.com/papers/e62c9b30f9d1748c1e395c178b74a932"><img src="http://neurolibre.herokuapp.com/papers/e62c9b30f9d1748c1e395c178b74a932/status.svg"></a>
Markdown: [![status](http://neurolibre.herokuapp.com/papers/e62c9b30f9d1748c1e395c178b74a932/status.svg)](http://neurolibre.herokuapp.com/papers/e62c9b30f9d1748c1e395c178b74a932)

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.

[pbellec]

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.

[pbellec]

@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

[roboneuro]

Here are some things you can ask me to do:

# List RoboNeuro's capabilities
@roboneuro commands

# List of editor GitHub usernames
@roboneuro list editors

# List of reviewers together with programming language preferences and domain expertise
@roboneuro list reviewers

EDITORIAL TASKS

# Compile the paper
@roboneuro generate pdf

# Compile the paper from alternative branch
@roboneuro generate pdf from branch custom-branch-name

# Ask RoboNeuro to check the references for missing DOIs
@roboneuro check references

# Ask RoboNeuro to check repository statistics for the submitted software
@roboneuro check repository

[anirudhk686]

@roboneuro generate pdf

[roboneuro]

🌱  The PDF has been compiled!

• 📥  Download article proof
•   View article proof on GitHub

[agahkarakuzu]

@roboneuro check references

[roboneuro]

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

OK DOIs

- 10.1016/j.neuroimage.2017.11.063 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[agahkarakuzu]

OK this is on me, I messed up the TOC while adding Neurolibre specific parts. Book build should fail, will wait for a while and fix the problem.

[agahkarakuzu]

@roboneuro production start

[roboneuro]

⚡ ⚡ ⚡ Starting NeuroLibre production process. These are the steps I'll try to complete:

• Fork and config repository
• Book build for production
• Sync built book
• Sync built data
• BinderHub build for production

[roboneuro]

⚡ We are currently building your NeuroLibre notebook for production! 🔀 (fork)

[roboneuro]

🔁 Build was successful!

🧳 Next: Sending the book to our production server.

[roboneuro]

🍁 Your book is now on the NeuroLibre production server!
You may take a look at the the book (link below).

Book prod sync response

{"book_url": "http://neurolibre-data-prod.conp.cloud/book-artifacts/roboneurolibre/github.com/editorial_parcellation/82586fff0f449429f0af93eff10abd93402a03e5/_build/html/", "book_build_logs": "http://neurolibre-data-prod.conp.cloud/book-artifacts/roboneurolibre/github.com/editorial_parcellation/82586fff0f449429f0af93eff10abd93402a03e5/book-build.log", "download_link": "http://neurolibre-data-prod.conp.cloud/book-artifacts/roboneurolibre/github.com/editorial_parcellation/82586fff0f449429f0af93eff10abd93402a03e5.tar.gz", "notebook_list": ["http://neurolibre-data-prod.conp.cloud/book-artifacts/roboneurolibre/github.com/editorial_parcellation/82586fff0f449429f0af93eff10abd93402a03e5/_build/jupyter_execute/conclusion.ipynb", "http://neurolibre-data-prod.conp.cloud/book-artifacts/roboneurolibre/github.com/editorial_parcellation/82586fff0f449429f0af93eff10abd93402a03e5/_build/jupyter_execute/intro.ipynb", "http://neurolibre-data-prod.conp.cloud/book-artifacts/roboneurolibre/github.com/editorial_parcellation/82586fff0f449429f0af93eff10abd93402a03e5/_build/jupyter_execute/papers.ipynb"], "repo_link": "https://github.com/roboneurolibre/editorial_parcellation", "user_name": "roboneurolibre", "repo_name": "editorial_parcellation", "provider_name": "github.com", "commit_hash": "82586fff0f449429f0af93eff10abd93402a03e5", "time_added": "Fri Jul 29 17:30:35 2022"}

⚠️ Please do not execute this book, unless a (production) BinderHub image has been requested and completed by this technical screening.

[roboneuro]

🧳 Next: Sending the data to our production server.

[agahkarakuzu]

@roboneuro set 10.5281/zenodo.10031958 as data archive

[roboneuro]

Done, data archive is now 10.5281/zenodo.10031958

[agahkarakuzu]

@roboneuro set 10.5281/zenodo.10031960 as docker archive

[roboneuro]

Done, docker archive is now 10.5281/zenodo.10031960

[agahkarakuzu]

@roboneuro recommend-accept

[roboneuro]

Attempting dry run of processing paper acceptance...

[roboneuro]

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

OK DOIs

- 10.1016/j.neuroimage.2017.11.063 is OK
- 10.1007/978-3-319-33383-0_5 is OK
- 10.31219/osf.io/h89js is OK
- 10.1371/journal.pcbi.1009651 is OK
- 10.1371/journal.pcbi.1011230 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[roboneuro]

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

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in neurolibre/preprints#63, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[pbellec]

article looks good! All the asset links correctly resolve. Only DOI that's broken is for the preprint itself, but I assume it will become active once the book's published.

[agahkarakuzu]

@roboneuro production sync pdf

[roboneuro]

🌱♻️📄 Synced the summary PDF from the source, should be now available at https://preprint.neurolibre.org/10.55458/neurolibre.00010.pdf?no-cache

[agahkarakuzu]

@roboneuro accept

[roboneuro]

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

[roboneuro]

⚠️ Couldn't acccept/publish paper. An error happened. Could not deposit with Open Journals.

[agahkarakuzu]

@roboneuro accept

[roboneuro]

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

[roboneuro]

⚠️ Couldn't acccept/publish paper. An error happened. Could not deposit with Open Journals.

[agahkarakuzu]

@pbellec this is happening because the submission was created before the big migration, so there is database entry mismatches. I am manually fixing them, hopefully will resolve the issue.

[pbellec]

thanks so much for all your hard work on this.

[agahkarakuzu]

@roboneuro accept

[roboneuro]

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

[roboneuro]

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Bellec
  given-names: Pierre
  orcid: "https://orcid.org/0000-0002-9111-0699"
- family-names: Jbabdi
  given-names: Saâd
  orcid: "https://orcid.org/0000-0003-3234-5639"
- family-names: Craddock
  given-names: R. Cameron
  orcid: "https://orcid.org/0000-0002-4950-1303"
doi: 10.55458
message: To reference this work, please cite our reproducible preprint
  in NeuroLibre.
preferred-citation:
  authors:
  - family-names: Bellec
    given-names: Pierre
    orcid: "https://orcid.org/0000-0002-9111-0699"
  - family-names: Jbabdi
    given-names: Saâd
    orcid: "https://orcid.org/0000-0003-3234-5639"
  - family-names: Craddock
    given-names: R. Cameron
    orcid: "https://orcid.org/0000-0002-4950-1303"
  date-published: 2023-10-23
  doi: 10.55458/neurolibre.00010
  journal: NeuroLibre Reproducible Preprints
  publisher:
    name: NeuroLibre
  start: 10
  title: Parcellating the parcellation issue - a proof of concept for
    reproducible analyses using Neurolibre
  type: preprint
  url: "https://neurolibre.org/papers/10.55458/neurolibre.00010"
title: Parcellating the parcellation issue - a proof of concept for
  reproducible analyses using Neurolibre

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

[roboneuro]

🌰🌱🌺 THIS IS NOT A DRILL, YOU HAVE JUST PUBLISHED A NEUROLIBRE REPRODUCIBLE PREPRINT! 🌺🌸🍀

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.55458.neurolibre.00010 preprints#66
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/
2. If everything looks good, then close this review issue.
3. Party like you just published more than a PDF! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[agahkarakuzu]

@pbellec done!

https://doi.org/10.55458/neurolibre.00014

And it is on the main page https://neurolibre.org

[roboneuro]

🌰 🌱 🌺 Congratulations on your NeuroLibre Reproducible Preprint (NRP)! 🍀 🚀 ♻️

By publishing this NRP, you've gone beyond simply posting another traditional preprint, demonstrating your commitment to transparency and reproducibility in presenting your new findings. This achievement is certainly something to take pride in, and if you wish to showcase it in your repository:

Markdown:
[![DOI](https://neurolibre.org/papers/10.55458/neurolibre.00010/status.svg)](https://doi.org/10.55458/neurolibre.00010)

HTML:
<a style="border-width:0" href="https://doi.org/10.55458/neurolibre.00010">
  <img src="https://neurolibre.org/papers/10.55458/neurolibre.00010/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://neurolibre.org/papers/10.55458/neurolibre.00010/status.svg
   :target: https://doi.org/10.55458/neurolibre.00010

This is how it will look in your, e.g., README:

We need your help!

NeuroLibre is a community-run reproducible preprint server and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

• Volunteering to become a technical screener
• Contribute to the development

For details, please visit our documentation

[pbellec]

huge thanks Agâh for your patience and hard work! SO happy to see this preprint out :)