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

roboneuro commented 2 years ago

Submitting author: !--author-handle-->@pbellec@agahkarakuzu@agahkarakuzu<!--end-reviewers-list-- 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:

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 @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

[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 NeuroLibre 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 (@pbellec) 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?
[ ] 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?

roboneuro commented 2 years ago

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 :tada:.

:star: Important :star:

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:

Set yourself as 'Not watching' https://github.com/neurolibre/neurolibre-reviews:

watching

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

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 commented 2 years ago

:seedling: The PDF has been compiled!

:inbox_tray: Download article proof
:octocat: View article proof on GitHub

roboneuro commented 2 years ago

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 commented 2 years ago

:point_right::page_facing_up: View built NeuroLibre Notebook :page_facing_up::point_left:

agahkarakuzu commented 2 years ago

@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 commented 2 years ago

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 commented 2 years ago

@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 commented 2 years ago

thanks for getting @anirudhk686 started @agahkarakuzu ! I've created a thread with a few extra points to check: https://github.com/neurolibre/docs.neurolibre.org/issues/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 commented 2 years ago

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

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

agahkarakuzu commented 2 years ago

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

anirudhk686 commented 2 years ago

@roboneuro commands

roboneuro commented 2 years ago

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 commented 2 years ago

@roboneuro generate pdf

roboneuro commented 2 years ago

:seedling: The PDF has been compiled!

:inbox_tray: Download article proof
:octocat: View article proof on GitHub

agahkarakuzu commented 2 years ago

@roboneuro check references

roboneuro commented 2 years ago

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 commented 2 years ago

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 commented 2 years ago

@roboneuro production start

roboneuro commented 2 years ago

:zap: :zap: :zap: 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 commented 2 years ago

:zap: We are currently building your NeuroLibre notebook for production! :twisted_rightwards_arrows: (fork)

roboneuro commented 2 years ago

:repeat: Build was successful!

:luggage: Next: Sending the book to our production server.

roboneuro commented 2 years ago

:maple_leaf: 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"}

        <p>:warning: Please do not execute this book, unless a (production) BinderHub image has been requested and completed by this technical screening.</p>

roboneuro commented 2 years ago

:luggage: Next: Sending the data to our production server.

roboneuro commented 2 years ago

:maple_leaf: I have successfully moved your data to the production server!

Data prod sync response

{
  "reason": "200: Data sync succeeded."
}

roboneuro commented 2 years ago

:racing_car: :leaves: Next: Building the BinderHub image on our production server! :zap:

:hourglass_flowing_sand: :whale: Whale, whale, whale, this step may take some time depending on the cache status of Docker image layers on our registry. Sometimes builds are just over-whale-ming :bowtie:

roboneuro commented 2 years ago

Run into problem during production BinderHub build request for repo_url

This happens when the call is waiting, but dynos restart in between.

agahkarakuzu commented 2 years ago

@roboneuro production build-binderhub

roboneuro commented 2 years ago

:hibiscus: Your Binder is ready!

BinderHub prod build response

data: {"phase": "built", "imageName": "binder-registry.conp.cloud/binder-registry.conp.cloud/binder-roboneurolibre-2deditorial-5fparcellation-031f15:82586fff0f449429f0af93eff10abd93402a03e5", "message": "Found built image, launching...\n"}
data: {"phase": "launching", "message": "Launching server...\n"}
data: {"phase": "launching", "message": "Server requested\n"}
data: {"phase": "launching", "message": "2022-07-30T11:18:51.765169Z [Normal] Successfully assigned binderhub/jupyter-roboneurolibre-2d-2dal-5fparcellation-2dj0xj38sf to neurolibre-master\n"}
data: {"phase": "launching", "message": "2022-07-30T11:18:54Z [Normal] Container image \"jupyterhub/k8s-network-tools:1.1.2\" already present on machine\n"}
data: {"phase": "launching", "message": "2022-07-30T11:18:55Z [Normal] Created container block-cloud-metadata\n"}
data: {"phase": "launching", "message": "2022-07-30T11:18:55Z [Normal] Started container block-cloud-metadata\n"}
data: {"phase": "launching", "message": "2022-07-30T11:18:56Z [Normal] Container image \"binder-registry.conp.cloud/binder-registry.conp.cloud/binder-roboneurolibre-2deditorial-5fparcellation-031f15:82586fff0f449429f0af93eff10abd93402a03e5\" already present on machine\n"}
data: {"phase": "launching", "message": "2022-07-30T11:18:57Z [Normal] Created container notebook\n"}
data: {"phase": "launching", "message": "2022-07-30T11:18:58Z [Normal] Started container notebook\n"}
data: {"phase": "launching", "message": "Server ready at /jupyter/user/roboneurolibre--al_parcellation-j0xj38sf/\n"}
data: {"phase": "ready", "message": "server running at https://binder-mcgill.conp.cloud/jupyter/user/roboneurolibre--al_parcellation-j0xj38sf/\n", "image": "binder-registry.conp.cloud/binder-registry.conp.cloud/binder-roboneurolibre-2deditorial-5fparcellation-031f15:82586fff0f449429f0af93eff10abd93402a03e5", "repo_url": "https://github.com/roboneurolibre/editorial_parcellation", "token": "MdlWAKYmQImX6v6Ih-7svA", "binder_ref_url": "https://github.com/roboneurolibre/editorial_parcellation/tree/82586fff0f449429f0af93eff10abd93402a03e5", "binder_launch_host": "https://binder-mcgill.conp.cloud/", "binder_request": "v2/gh/roboneurolibre/editorial_parcellation.git/82586fff0f449429f0af93eff10abd93402a03e5", "binder_persistent_request": "v2/gh/roboneurolibre/editorial_parcellation/82586fff0f449429f0af93eff10abd93402a03e5", "url": "https://binder-mcgill.conp.cloud/jupyter/user/roboneurolibre--al_parcellation-j0xj38sf/"}

agahkarakuzu commented 2 years ago

@anirudhk686 can you please check that the book on the production server is working properly?

[x] The book pages look OK
[ ] BinderHub session is initiated on binder-mcgill.conp.cloud
[ ] The notebooks can load the data
[ ] Can execute all the cells & reproduce outputs on a BinderHub session.

If all looks good, I'll archive and publish this Jupyter Book!

anirudhk686 commented 2 years ago

@agahkarakuzu so i tried to run the notebook , for some reason it is not starting , it say starting and even after 5 min the kernel was not connected. sending pics on slack

agahkarakuzu commented 2 years ago

@roboneuro commands

roboneuro commented 2 years ago

Here are some things you can ask me to do:

# List all of RoboNeuro's capabilities
@roboneuro commands

# Assign a GitHub user as the sole reviewer of this submission
@roboneuro assign @username as reviewer

# Add a GitHub user to the reviewers of this submission
@roboneuro add @username as reviewer

# Re-invite a reviewer (if they can't update checklists)
@roboneuro re-invite @username as reviewer

# Remove a GitHub user from the reviewers of this submission
@roboneuro remove @username as reviewer

# List of editor GitHub usernames
@roboneuro list editors

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

# Change editorial assignment
@roboneuro assign @username as editor

# Set the software version at the top of the issue e.g.
@roboneuro set v1.0.1 as version

# Open the review issue
@roboneuro start review

EDITORIAL TASKS

# All commands can be run on a non-default branch, to do this pass a custom
# branch name by following the command with `from branch custom-branch-name`.
# For example:

# Compile the paper
@roboneuro generate pdf

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

# Build the NeuroLibre book (on the test server)
@roboneuro generate nl-notebook

# Build the NeuroLibre book from alternative branch (on the test server)
@roboneuro generate nl-notebook from branch custom-branch-name

PRODUCTION TASKS (Auth level editor)

# Start production sequence [fork-> config -> build (book and binder) -> sync (data and book)]
@roboneuro production start

# Production sequence processes can be called individually if `@roboneruo production start` is interrupted at some point.
@roboneuro production build-book
@roboneuro production sync-book
@roboneuro production sync-data
@roboneuro production build-binderhub

ARCHIVAL TASKS (Auth level editor)

# Displays Zenodo deposit, upload and publish status
@roboneuro zenodo status

# Create Zenodo records for archiving resources
@roboneuro zenodo deposit

# Uploads all resources to respective Zenodo deposits for archival
@roboneuro zenodo archive-all

# Zenodo uploads can be performed individually
@roboneuro zenodo archive-docker
@roboneuro zenodo archive-book
@roboneuro zenodo archive-repository
@roboneuro zenodo archive-data

# Destroy all the zenodo resources (cannot be called after publishing, cannot be performed for individual items)
@roboneuro zenodo flush

PUBLISHING TASKS

# Set the final book URL for publishing (Editor)
@roboneuro production set-book-url

# Publish all the Zenodo archives (EiC & zenodo status must be green for all types)
@roboneuro zenodo publish

# Set all the Zenodo DOIs for publishing (Editor)
@roboneuro production set-zenodo-dois

# Ask RoboNeuro to do a dry run of accepting the paper and depositing with Crossref (Editor)
@roboneuro accept

# 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

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

EiC TASKS

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

# Reject a paper
@roboneuro reject

# Withdraw a paper
@roboneuro withdraw

# Ask RoboNeuro to actually accept the paper and deposit with Crossref
@roboneuro accept deposit=true

agahkarakuzu commented 2 years ago

@roboneuro generate pdf

roboneuro commented 2 years ago

:seedling: The PDF has been compiled!

:inbox_tray: Download article proof
:octocat: View article proof on GitHub

pbellec commented 1 year ago

@anirudhk686 the issue is because you are using the "live code" link. It's using "thebe" which is broken in our workflow. This needs to be disabled from the submission. Please open an issue with the author (aka me :) ).

If you are using the binder link, it should start right away. From what I see the data is not cached, and redownloaded. This is an issue, and I am not sure at this stage how to fix it.

anirudhk686 commented 1 year ago

@roboneuro generate nl-notebook

anirudhk686 commented 1 year ago

@roboneuro generate pdf

roboneuro commented 1 year ago

:seedling: The PDF has been compiled!

:inbox_tray: Download article proof
:octocat: View article proof on GitHub

agahkarakuzu commented 1 year ago

@roboneuro generate nl-notebook

agahkarakuzu commented 1 year ago

@roboneuro generate nl-notebook

agahkarakuzu commented 1 year ago

@roboneuro commands

roboneuro commented 1 year ago

Here are some things you can ask me to do:

# List all of RoboNeuro's capabilities
@roboneuro commands

# Assign a GitHub user as the sole reviewer of this submission
@roboneuro assign @username as reviewer

# Add a GitHub user to the reviewers of this submission
@roboneuro add @username as reviewer

# Re-invite a reviewer (if they can't update checklists)
@roboneuro re-invite @username as reviewer

# Remove a GitHub user from the reviewers of this submission
@roboneuro remove @username as reviewer

# List of editor GitHub usernames
@roboneuro list editors

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

# Change editorial assignment
@roboneuro assign @username as editor

# Set the software version at the top of the issue e.g.
@roboneuro set v1.0.1 as version

# Open the review issue
@roboneuro start review

EDITORIAL TASKS

# All commands can be run on a non-default branch, to do this pass a custom
# branch name by following the command with `from branch custom-branch-name`.
# For example:

# Compile the paper
@roboneuro generate pdf

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

# Build the NeuroLibre book (on the test server)
@roboneuro generate nl-notebook

# Build the NeuroLibre book from alternative branch (on the test server)
@roboneuro generate nl-notebook from branch custom-branch-name

PRODUCTION TASKS (Auth level editor)

# Start production sequence [fork-> config -> build (book and binder) -> sync (data and book)]
@roboneuro production start

# Production sequence processes can be called individually if `@roboneruo production start` is interrupted at some point.
@roboneuro production build-book
@roboneuro production sync-book
@roboneuro production sync-data
@roboneuro production build-binderhub

ARCHIVAL TASKS (Auth level editor)

# Displays Zenodo deposit, upload and publish status
@roboneuro zenodo status

# Create Zenodo records for archiving resources
@roboneuro zenodo deposit

# Uploads all resources to respective Zenodo deposits for archival
@roboneuro zenodo archive-all

# Zenodo uploads can be performed individually
@roboneuro zenodo archive-docker
@roboneuro zenodo archive-book
@roboneuro zenodo archive-repository
@roboneuro zenodo archive-data

# Destroy all the zenodo resources (cannot be called after publishing, cannot be performed for individual items)
@roboneuro zenodo flush

PUBLISHING TASKS

# Set the final book URL for publishing (Editor)
@roboneuro production set-book-url

# Publish all the Zenodo archives (EiC & zenodo status must be green for all types)
@roboneuro zenodo publish

# Set all the Zenodo DOIs for publishing (Editor)
@roboneuro production set-zenodo-dois

# Ask RoboNeuro to do a dry run of accepting the paper and depositing with Crossref (Editor)
@roboneuro accept

# 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

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

EiC TASKS

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

# Reject a paper
@roboneuro reject

# Withdraw a paper
@roboneuro withdraw

# Ask RoboNeuro to actually accept the paper and deposit with Crossref
@roboneuro accept deposit=true

agahkarakuzu commented 1 year ago

@roboneuro generate nl-notebook

roboneuro commented 1 year ago

:point_right::page_facing_up: View built NeuroLibre Notebook :page_facing_up::point_left:

agahkarakuzu commented 1 year ago

@roboneuro commands

roboneuro commented 1 year 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

# 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

# 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

agahkarakuzu commented 11 months ago

@roboneuro commands

roboneuro commented 11 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

agahkarakuzu commented 11 months ago

@roboneuro build book

roboneuro commented 11 months ago

Can't perform this without reviewers

neurolibre / neurolibre-reviews