[REVIEW]: Analysis code for the paper "RF shimming in the cervical spinal cord at 7T"

roboneuro commented 9 months ago

Submitting author: !--author-handle-->@mathieuboudreau@pbellec@agahkarakuzu<!--end-reviewers-list-- Reproducible preprint: https://preprint.neurolibre.org/10.55458/neurolibre.00025 Repository archive: 10.5281/zenodo.10844540 Data archive: 10.5281/zenodo.10844542 Book archive: 10.5281/zenodo.10844538 Docker archive: 10.5281/zenodo.10844544

Status

Status badge code:

HTML: <a href="https://neurolibre.org/papers/5d2f9af7565d26f243c0d96effaf864a"><img src="https://neurolibre.org/papers/5d2f9af7565d26f243c0d96effaf864a/status.svg"></a>
Markdown: [![status](https://neurolibre.org/papers/5d2f9af7565d26f243c0d96effaf864a/status.svg)](https://neurolibre.org/papers/5d2f9af7565d26f243c0d96effaf864a)

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

@agahkarakuzu, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@roboneuro generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @pbellec 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 ✨

Checklists

@agahkarakuzu, please create your checklist typing: @roboneuro generate my checklist

roboneuro commented 8 months ago

Done, book archive is now 10.5281/zenodo.10844538

agahkarakuzu commented 8 months ago

@roboneuro set 10.5281/zenodo.10844540 as repository archive

roboneuro commented 8 months ago

Done, repository archive is now 10.5281/zenodo.10844540

agahkarakuzu commented 8 months ago

@roboneuro set 10.5281/zenodo.10844542 as data archive

roboneuro commented 8 months ago

Done, data archive is now 10.5281/zenodo.10844542

agahkarakuzu commented 8 months ago

@roboneuro set 10.5281/zenodo.10844544 as docker archive

roboneuro commented 8 months ago

Done, docker archive is now 10.5281/zenodo.10844544

agahkarakuzu commented 8 months ago

@roboneuro recommend-accept

roboneuro commented 8 months ago

Attempting dry run of processing paper acceptance...

roboneuro commented 8 months ago

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

OK DOIs

- 10.1002/mrm.29528 is OK
- 10.1016/j.neuroimage.2016.10.009 is OK
- 10.1038/nrneurol.2015.80 is OK
- 10.1038/s41582-019-0270-5 is OK
- 10.1016/S0730-725X(01)00300-9 is OK
- 10.1002/jmri.20245 is OK
- 10.1118/1.595995 is OK
- 10.1002/mrm.10137 is OK
- 10.1016/j.neuroimage.2017.10.041 is OK

MISSING DOIs

- None

INVALID DOIs

- None

roboneuro commented 8 months ago

:wave: @neurolibre/executable-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/neurolibre/preprints/pull/78, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

agahkarakuzu commented 8 months ago

@roboneuro commands

roboneuro commented 8 months ago

Hello @agahkarakuzu, here are the things you can ask me to do:


# List all available commands
@roboneuro commands

# Add to this issue's reviewers list
@roboneuro add @username as reviewer

# Remove from this issue's reviewers list
@roboneuro remove @username from reviewers

# Get a list of all editors's GitHub handles
@roboneuro list editors

# Assign a user as the editor of this submission
@roboneuro assign @username as editor

# Remove the editor assigned to this submission
@roboneuro remove editor

# Remind an author, a reviewer or the editor to return to a review after a 
# certain period of time (supported units days and weeks)
@roboneuro remind @reviewer in 2 weeks

# Check the references of the PDF for missing DOIs
@roboneuro check references

# Perform checks on the repository
@roboneuro check repository

# Adds a checklist for the reviewer using this command
@roboneuro generate my checklist

# Set a value for version
@roboneuro set v1.0.0 as version

# Set a value for branch
@roboneuro set neurolibre-paper as branch

# Set a value for repository
@roboneuro set https://github.com/organization/repo as repository

# Set a value for the archive DOI
@roboneuro set set 10.5281/zenodo.6861996 as archive

# Set a value for the (data/book/repository/docker) archive DOI.
@roboneuro set 10.5281/zenodo.6861996 as data archive

# Set executable book URI for the preprint.
@roboneuro set book uri

# Mention the EiCs for the correct track
@roboneuro ping track-eic

# Reject paper
@roboneuro reject

# Withdraw paper
@roboneuro withdraw

# Invite an editor to edit a submission (sending them an email)
@roboneuro invite @(.*) as editor

# Generates the pdf paper
@roboneuro generate pdf

# Recommends the submission for acceptance
@roboneuro recommend-accept

# Accept and publish the paper
@roboneuro accept

# Update data on an accepted/published paper
@roboneuro reaccept

# Generates a LaTeX preprint file
@roboneuro generate preprint

# Flag submission with questionable scope
@roboneuro query scope

# Get a link to the complete list of reviewers
@roboneuro list reviewers

# Creates a post-review checklist with editor and authors tasks
@roboneuro create post-review checklist

# Open the review issue
@roboneuro start review

# Check the status of the NeuroLibre preview server.
@roboneuro preview server status

# Check the status of the NeuroLibre preprint (production) server.
@roboneuro preprint server status

# Build a NeuroLibre reproducible preprint for technical screening.
@roboneuro build book

# After screening, build book from the forked reository.
@roboneuro production build book

# Transfer data from preview to the preprint (production) server.
@roboneuro production sync data

# Transfer the final preprint (forked repo) to the preprint (production) server (DOI URL).
@roboneuro production sync book

# Start the production process by forking repository and configuring it.
@roboneuro production start

# Creates Zenodo deposits (a.k.a buckets) for archiving reproducibility assets.
@roboneuro zenodo create buckets

# Status check for the archival of the reproducibility assets.
@roboneuro zenodo status

# Copy summary PDF from the preprints repository to the NeuroLibre production server.
@roboneuro production sync pdf

# Upload the latest Jupyter Book to Zenodo for archival.
@roboneuro zenodo upload book

# Upload the latest version of the book repository to Zenodo for archival.
@roboneuro zenodo upload repository

# Upload the latest version of the docker image to Zenodo for archival.
@roboneuro zenodo upload docker

# Upload the submission data to Zenodo for archival. Will not take effect if the data is already archived.
@roboneuro zenodo upload data

# DESTRUCTIVE ACTION: Deletes zenodo records and all the data that has been uploaded. Cannot perform after zenodo publish.
@roboneuro zenodo flush

# Publish reproducibility assets on Zenodo. Sets DOIs if successful.
@roboneuro zenodo publish

# Build an extended PDF for the target repository.
@roboneuro build extended pdf

# Download the submission data.
@roboneuro cache data

agahkarakuzu commented 8 months ago

@roboneuro production sync pdf

roboneuro commented 8 months ago

:seedling::recycle::page_facing_up: Synced the summary PDF from the source, should be now available at https://preprint.neurolibre.org/10.55458/neurolibre.00025.pdf?no-cache

agahkarakuzu commented 8 months ago

@roboneuro accept

roboneuro commented 8 months ago

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

roboneuro commented 8 months ago

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: Papp given-names: Daniel orcid: "https://orcid.org/0000-0003-1481-1413" - family-names: Gilbert given-names: Kyle M. orcid: "https://orcid.org/0000-0003-3026-5686" - family-names: Cereza given-names: Gaspard - family-names: D'Astous given-names: Alexandre orcid: "https://orcid.org/0000-0003-0381-7334" - family-names: Lopez-Rios given-names: Nibardo orcid: "https://orcid.org/0000-0002-4791-8260" - family-names: Boudreau given-names: Mathieu orcid: "https://orcid.org/0000-0002-7726-4456" - family-names: Couch given-names: Marcus orcid: "https://orcid.org/0000-0002-2732-8941" - family-names: Yazdanbakhsh given-names: Pedram orcid: "https://orcid.org/0000-0003-4456-5997" - family-names: Barry given-names: Robert L. - family-names: Ortiz given-names: Eva Alonso orcid: "https://orcid.org/0000-0001-6590-7234" - family-names: Cohen-Adad given-names: Julien orcid: "https://orcid.org/0000-0003-3662-9532" doi: 10.55458 message: To reference this work, please cite our reproducible preprint in NeuroLibre. preferred-citation: authors: - family-names: Papp given-names: Daniel orcid: "https://orcid.org/0000-0003-1481-1413" - family-names: Gilbert given-names: Kyle M. orcid: "https://orcid.org/0000-0003-3026-5686" - family-names: Cereza given-names: Gaspard - family-names: D'Astous given-names: Alexandre orcid: "https://orcid.org/0000-0003-0381-7334" - family-names: Lopez-Rios given-names: Nibardo orcid: "https://orcid.org/0000-0002-4791-8260" - family-names: Boudreau given-names: Mathieu orcid: "https://orcid.org/0000-0002-7726-4456" - family-names: Couch given-names: Marcus orcid: "https://orcid.org/0000-0002-2732-8941" - family-names: Yazdanbakhsh given-names: Pedram orcid: "https://orcid.org/0000-0003-4456-5997" - family-names: Barry given-names: Robert L. - family-names: Ortiz given-names: Eva Alonso orcid: "https://orcid.org/0000-0001-6590-7234" - family-names: Cohen-Adad given-names: Julien orcid: "https://orcid.org/0000-0003-3662-9532" date-published: 2024-04-04 doi: 10.55458/neurolibre.00025 journal: NeuroLibre Reproducible Preprints publisher: name: NeuroLibre start: 25 title: Analysis code for the paper "RF shimming in the cervical spinal cord at 7T" type: preprint url: "https://neurolibre.org/papers/10.55458/neurolibre.00025" title: Analysis code for the paper "RF shimming in the cervical spinal cord at 7T" ```

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 commented 8 months ago

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

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/neurolibre/preprints/pull/79
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.55458/neurolibre.00025
If everything looks good, then close this review issue.
Party like you just published more than a PDF! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

agahkarakuzu commented 8 months ago

@jcohenadad @mathieuboudreau congrats, this is now published! Sorry took a while as I was travelling.

https://doi.org/10.55458/neurolibre.00025

Feel free to add CITATION.cff above to the repository (or substitute entries with MRM DOIs :) ).

jcohenadad commented 8 months ago

amazing! thank you so much @agahkarakuzu and @mathieuboudreau

now we are doing the review of the submitted MRM paper, so the manuscript and the code and figure will have to change 😅

agahkarakuzu commented 6 months ago

@roboneuro build pdf

roboneuro commented 6 months ago

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@roboneuro commands

agahkarakuzu commented 6 months ago

@roboneuro generate pdf

roboneuro commented 6 months ago

:warning: An error happened when generating the pdf.

neurolibre / neurolibre-reviews