[REVIEW]: Testing the new submission system

[roboneuro]

Submitting author: @agahkarakuzu (Agah Karakuzu)
Repository: https://github.com/agahkarakuzu/template
Branch with paper.md (empty if default branch):
Version: v1.0.0
Editor: @pbellec
Reviewers: @mathieuboudreau
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]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[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]

🟢 DATA TRANSFER (Preview --> Preprint)

Status: Success 637739da
Last updated: 2023-05-12 11:14:32 PDT

ℹ️ See details

b'receiving incremental file list\nDATA/\nDATA/agah_template/\nDATA/agah_template/data_requirement.json\nDATA/agah_template/repo2data.log\nDATA/agah_template/development_fmri/\nDATA/agah_template/development_fmri/development_fmri/\nDATA/agah_template/development_fmri/development_fmri/participants.tsv\nDATA/agah_template/development_fmri/development_fmri/sub-pixar123_task-pixar_desc-confounds_regressors.tsv\nDATA/agah_template/development_fmri/development_fmri/sub-pixar123_task-pixar_desc-reducedConfounds_regressors.tsv\nDATA/agah_template/development_fmri/development_fmri/sub-pixar123_task-pixar_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz\n\nsent 162 bytes  received 5,793,773 bytes  891,374.62 bytes/sec\ntotal size is 5,791,609  speedup is 1.00\n'

[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

# 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]

@roboneuro production sync book

[roboneuro]

👀 Looks like the reproducible preprint you requested has been already built:

[{"time_added":"2023-05-05 00:48:21 +0000","book_url":"https://preview.neurolibre.org/book-artifacts/agahkarakuzu/github.com/template/9531917b3ceb7cfeb779a4a4b4a4a33fe4e71ad0/_build/html/","download_url":null}]

[agahkarakuzu]

@roboneuro production sync book

[agahkarakuzu]

@roboneuro production sync book

[roboneuro]

⚪ REPRODUCIBLE PREPRINT TRANSFER (Preview --> Preprint)

Status: Assigned to task 43f434a2
Last updated: 2023-05-12 12:29:09 PDT

[agahkarakuzu]

@roboneuro production sync book

[agahkarakuzu]

@roboneuro production sync book

[roboneuro]

🟠 REPRODUCIBLE PREPRINT TRANSFER (Preview --> Preprint)

Status: In progress cae139a8
Last updated: 2023-05-12 12:41:31 PDT

[agahkarakuzu]

@roboneuro production sync book

[roboneuro]

🟠 REPRODUCIBLE PREPRINT TRANSFER (Preview --> Preprint)

Status: In progress c260089c
Last updated: 2023-05-12 12:48:02 PDT

[agahkarakuzu]

@roboneuro production sync book

[roboneuro]

🔴 REPRODUCIBLE PREPRINT TRANSFER (Preview --> Preprint)

Status: Failed d4db695b
Last updated: 2023-05-12 12:51:35 PDT

ℹ️ See details

b'receiving incremental file list\n\nsent 140 bytes  received 7,407 bytes  3,018.80 bytes/sec\ntotal size is 55,319,631  speedup is 7,330.02\n'

[agahkarakuzu]

@roboneuro production sync book

[roboneuro]

🔴 REPRODUCIBLE PREPRINT TRANSFER (Preview --> Preprint)

Status: Failed b9377f49
Last updated: 2023-05-12 13:06:51 PDT

ℹ️ See details

b'receiving incremental file list\n\nsent 140 bytes  received 7,407 bytes  3,018.80 bytes/sec\ntotal size is 55,319,631  speedup is 7,330.02\n'

[agahkarakuzu]

@roboneuro production sync book

[roboneuro]

🟢 REPRODUCIBLE PREPRINT TRANSFER (Preview --> Preprint)

Status: Success d07f7372
Last updated: 2023-05-12 13:16:23 PDT

ℹ️ See details

Reproducible Preprint URL (DOI formatted)
Reproducible Preprint (bare URL)

[agahkarakuzu]

@roboneuro production sync book

[roboneuro]

🟢 REPRODUCIBLE PREPRINT TRANSFER (Preview --> Preprint)

Status: Success 169ff225
Last updated: 2023-05-12 13:21:01 PDT

ℹ️ See details

Reproducible Preprint URL (DOI formatted)
Reproducible Preprint (bare URL)

[agahkarakuzu]

@roboneuro production sync book

[agahkarakuzu]

@roboneuro production sync book

[agahkarakuzu]

@roboneuro production sync book

[agahkarakuzu]

@roboneuro production sync book

[roboneuro]

Jupyter Book build log

['fsjdhfn s\n', 'dfmknsjd fnksd fnksdf \n', 'sdkfhbskd f\n', 'sd fkbjsdn fksdf\n', 'sdfnjk sdf \n', 'sdf mnskdjf sdfs']

Execution error log for anan notebook (anan.ipynb) or MyST (anan.md)).

['irueityowpqr\n', 'oitreyuwoty\n', 'tuerioituyr\n', 'tiyeruowtie\n', 'ietrwiut']

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

For guidelines, please see the relevant documentation.

[roboneuro]

Jupyter Book build log

['fsjdhfn s\n', 'dfmknsjd fnksd fnksdf \n', 'sdkfhbskd f\n', 'sd fkbjsdn fksdf\n', 'sdfnjk sdf \n', 'sdf mnskdjf sdfs']

Execution error log for anan notebook (anan.ipynb) or MyST (anan.md)).

['irueityowpqr\n', 'oitreyuwoty\n', 'tuerioituyr\n', 'tiyeruowtie\n', 'ietrwiut']

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

For guidelines, please see the relevant documentation.

[roboneuro]

Jupyter Book build log

['fsjdhfn s\n', 'dfmknsjd fnksd fnksdf \n', 'sdkfhbskd f\n', 'sd fkbjsdn fksdf\n', 'sdfnjk sdf \n', 'sdf mnskdjf sdfs']

Execution error log for anan notebook (anan.ipynb) or MyST (anan.md)).

['irueityowpqr\n', 'oitreyuwoty\n', 'tuerioituyr\n', 'tiyeruowtie\n', 'ietrwiut']

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

For guidelines, please see the relevant documentation.

[roboneuro]

Jupyter Book build log

fsjdhfn s
dfmknsjd fnksd fnksdf
sdkfhbskd f
sd fkbjsdn fksdf
sdfnjk sdf
sdf mnskdjf sdfs

Execution error log for anan notebook (anan.ipynb) or MyST (anan.md)).

irueityowpqr
oitreyuwoty
tuerioituyr
tiyeruowtie
ietrwiut

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

For guidelines, please see the relevant documentation.

[roboneuro]

Jupyter Book build log

fsjdhfn s
dfmknsjd fnksd fnksdf
sdkfhbskd f
sd fkbjsdn fksdf
sdfnjk sdf
sdf mnskdjf sdfs

Execution error log for anan notebook (anan.ipynb) or MyST (anan.md)).

irueityowpqr
oitreyuwoty
tuerioituyr
tiyeruowtie
ietrwiut

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

For guidelines, please see the relevant documentation.