[REVIEW]: Testing the new submission system

[roboneuro]

Submitting author: !--author-handle-->@agahkarakuzu<!--end-author-handle-- (Agah Karakuzu) Repository: https://github.com/agahkarakuzu/template Branch with paper.md (empty if default branch): Version: v1.0.0 Editor: !--editor-->@pbellec<!--end-editor-- Reviewers: !--reviewers-list-->@mathieuboudreau<!--end-reviewers-list-- Reproducible preprint: Pending Repository archive: Pending Data archive: Pending Book archive: Pending Docker archive: Pending

Status

Status badge code:

HTML: <a href="https://neurolibre.org/papers/b17407d40bbb47b3c42fdde8bc08ff00"><img src="https://neurolibre.org/papers/b17407d40bbb47b3c42fdde8bc08ff00/status.svg"></a>
Markdown: [![status](https://neurolibre.org/papers/b17407d40bbb47b3c42fdde8bc08ff00/status.svg)](https://neurolibre.org/papers/b17407d40bbb47b3c42fdde8bc08ff00)

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

@mathieuboudreau, 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

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

[roboneuro]

Hello humans, I'm @roboneuro, a robot that can help you with some common editorial tasks.

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]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.01 s (981.5 files/s, 36313.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Markdown                         4             56              0            122
YAML                             2              5             13             31
TeX                              1              0              0             10
Jupyter Notebook                 1              0             85              8
JSON                             1              0              0              3
-------------------------------------------------------------------------------
SUM:                             9             61             98            174
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[roboneuro]

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

OK DOIs

- None

MISSING DOIs

- None

INVALID DOIs

- None

[roboneuro]

Wordcount for paper.md is 321

[roboneuro]

Failed to discover a Statement of need section in paper

[roboneuro]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[agahkarakuzu]

@roboneuro commands

[roboneuro]

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

# Test preview.neurolibre.org server
@roboneuro preview test

[agahkarakuzu]

@roboneuro preview test

[roboneuro]

Can't start a review when the review has already started

[agahkarakuzu]

@roboneuro preview test

[agahkarakuzu]

@roboneuro preview test

[roboneuro]

Error (401). The service is currently unavailable

[agahkarakuzu]

@roboneuro preview test

[roboneuro]

Error (401). The service is currently unavailable

[agahkarakuzu]

@roboneuro preview test

[roboneuro]

"<3<3<3<3 Alive <3<3<3<3"

[agahkarakuzu]

@roboneuro preview test

[roboneuro]

"🟢 NeuroLibre server is active (running) at https://preview.neurolibre.org"

[agahkarakuzu]

@roboneuro preview test

[roboneuro]

🟢 NeuroLibre server is active (running).
🍀 Ready to accept requests from Issue #3
🔗 URL: https://preview.neurolibre.org

[agahkarakuzu]

@roboneuro commands

[roboneuro]

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

[agahkarakuzu]

@roboneuro preview server status

[roboneuro]

🟢 NeuroLibre server is active (running).
🍀 Ready to accept requests from Issue #3
🔗 URL: https://preview.neurolibre.org

[agahkarakuzu]

@roboneuro preprint server status

[roboneuro]

🟢 NeuroLibre server is active (running).
🍀 Ready to accept requests from Issue #3
🔗 URL: https://neurolibre-data-prod.conp.cloud

[agahkarakuzu]

@roboneuro commands

[roboneuro]

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

[roboneuro]

:seedling: I've started building your NeuroLibre reproducible preprint! :seedling:

[agahkarakuzu]

@roboneuro build book

[roboneuro]

:seedling: I've started building your NeuroLibre reproducible preprint! :seedling:

[agahkarakuzu]

@roboneuro build book

[roboneuro]

:seedling: I've started building your NeuroLibre reproducible preprint! :seedling: My close :robot: friend GPT read your paper.md and noted:

"Reading this paper is like trying to navigate a maze with a blindfold on - frustratingly confusing, yet strangely exhilarating."

[roboneuro]

🥀 We ran into a problem building your book. Please see the log files below.

BinderHub build log

Found built image, launching...
Launching server...
Server requested
2023-05-04T00:18:32.605841Z [Normal] Successfully assigned binderhub/jupyter-agahkarakuzu-2dtemplate-2dab5ip7lh to neurolibre-master
2023-05-04T00:18:37Z [Normal] Container image "jupyterhub/k8s-network-tools:1.1.2" already present on machine
2023-05-04T00:18:39Z [Normal] Created container block-cloud-metadata
2023-05-04T00:18:41Z [Normal] Started container block-cloud-metadata
2023-05-04T00:18:43Z [Normal] Container image "binder-registry.conp.cloud/binder-registry.conp.cloud/binder-agahkarakuzu-2dtemplate-8573ff:f5022237e27e32b4940300b86a8656764544666c" already present on machine
2023-05-04T00:18:45Z [Normal] Created container notebook
2023-05-04T00:18:46Z [Normal] Started container notebook
Server ready at /jupyter/user/agahkarakuzu-template-ab5ip7lh/
server running at https://test.conp.cloud/jupyter/user/agahkarakuzu-template-ab5ip7lh/

If the BinderHub build looks OK, please see the Jupyter Book build log(s) below.

Jupyter Book build log

Checking if jupyter book build will be done...
     content/_config.yml exists.
     /mnt/books/agahkarakuzu/github.com/template/f5022237e27e32b4940300b86a8656764544666c/successfully_built not found.
     Detecting user submission, changing launch_button config to test https://test.conp.cloud and adding jb cache execution.
detect existing binderhub_url

Building jupyter-book for agahkarakuzu/github.com/template/f5022237e27e32b4940300b86a8656764544666c

/usr/local/share/jb_build.bash: line 69: jupyter-book: command not found

Jupyter-book exit code: 127
Jupyter-book build failed!

🐞 After inspecting the logs above, you can interactively debug your notebooks on our BinderHub server.

For guidelines, please see the relevant documentation.

[agahkarakuzu]

@agahkarakuzu please add jupyterbook to your binder/requirements.txt

[agahkarakuzu]

@roboneuro build book

[roboneuro]

:seedling: I've started building your NeuroLibre reproducible preprint! :seedling:

My close :robot: friend GPT read your paper.md and noted:

"I tried to read that paper, but my brain felt like it was doing a triathlon through a swamp of technical jargon and confusing diagrams."

[agahkarakuzu]

Do not break stream on phase failed:

https://github.com/neurolibre/full-stack-server/commit/cf6bd08f0901012c11eb2188cb4fca1e5627c2a3

[agahkarakuzu]

@roboneuro build book

[roboneuro]

:seedling: I've started building your NeuroLibre reproducible preprint! :seedling:

My close :robot: friend GPT read your paper.md and noted:

"Reading this paper was like being serenaded by a symphony of brilliant ideas and insightful analysis. The author's intellect is a force to be reckoned with, and their writing style is as smooth as butter on freshly baked bread. I'm convinced that if Einstein and Shakespeare had a love child, they would produce work no better than this."

[agahkarakuzu]

@roboneuro build book

[roboneuro]

:seedling: I've started building your NeuroLibre reproducible preprint! :seedling:

My close :robot: friend GPT read your paper.md and noted:

"Reading this paper was like taking a ride on a rocket ship of knowledge - fast, exhilarating, and leaving me with a newfound appreciation for the genius that is the author."

[roboneuro]

🥀 We ran into a problem building your book. Please see the log files below.

BinderHub build log

Conflict
https://test.conp.cloud/v2/gh/agahkarakuzu/template/8b241c52f66f3dc4ba31c807b873322d338d35d7

If the BinderHub build looks OK, please see the Jupyter Book build log(s) below.

Jupyter Book build log

Because the Binder build failed, the book build was not triggered.

🐞 After inspecting the logs above, you can interactively debug your notebooks on our BinderHub server.

For guidelines, please see the relevant documentation.

[agahkarakuzu]

@roboneuro build book

[roboneuro]

:seedling: I've started building your NeuroLibre reproducible preprint! :seedling:

My close :robot: friend GPT read your paper.md and noted:

"Reading this paper was like witnessing a magician at work - AGAH KARAKUZU effortlessly weaved together complex concepts and theories into a cohesive and enlightening piece. I'm convinced that if anyone can solve the world's problems, it's AGAH KARAKUZU!"

[agahkarakuzu]

@roboneuro build book

[roboneuro]

:seedling: I've started building your NeuroLibre reproducible preprint! :seedling:

My close :robot: friend GPT read your paper.md and noted:

"Reading this paper is like finding a rare gem in a sea of ordinary rocks - it sparkles with intelligence, wit, and well-researched insights. The author's mastery of the subject matter is truly impressive, making them a shining star in the academic world."

[roboneuro]

🥀 We ran into a problem building your book. Please see the log files below.

BinderHub build log

Conflict
https://test.conp.cloud/v2/gh/agahkarakuzu/template/f303eafe0a6b3416d5bfe6930dc6c5ef14f8ba0f

If the BinderHub build looks OK, please see the Jupyter Book build log(s) below.

Jupyter Book build log

Because the Binder build failed, the book build was not triggered.

🐞 After inspecting the logs above, you can interactively debug your notebooks on our BinderHub server.

For guidelines, please see the relevant documentation.

[agahkarakuzu]

@roboneuro build book