[REVIEW]: Little Science, Big Science, and Beyond: How Amateurs Shape the Scientific Landscape

[roboneuro]

Submitting author: @agahkarakuzu (Agah Karakuzu)
Repository: https://github.com/agahkarakuzu/amateur-science
Branch with paper.md (empty if default branch):
Version: v1.0.0
Editor: @mathieuboudreau
Reviewers: @pbellec
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/4525f4ab39fe89daedd9f31402485ffd"><img src="https://neurolibre.org/papers/4525f4ab39fe89daedd9f31402485ffd/status.svg"></a>
Markdown: [![status](https://neurolibre.org/papers/4525f4ab39fe89daedd9f31402485ffd/status.svg)](https://neurolibre.org/papers/4525f4ab39fe89daedd9f31402485ffd)

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

@pbellec, 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 @mathieuboudreau 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

@pbellec, 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 (726.8 files/s, 76770.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
TeX                              1              4              0            264
Markdown                         2             89              0            115
YAML                             3              3              9             91
Jupyter Notebook                 1              0            190             76
JSON                             1              0              0              4
-------------------------------------------------------------------------------
SUM:                             8             96            199            550
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[roboneuro]

Wordcount for paper.md is 5137

[roboneuro]

Failed to discover a Statement of need section in paper

[roboneuro]

⚠️ An error happened when generating the pdf.

[agahkarakuzu]

@pbellec error with pdf generation and ref check is expected as the current paper.md is not joss friendly yet.

[agahkarakuzu]

@roboneuro generate pdf

[roboneuro]

⚠️ An error happened when generating the pdf.

[agahkarakuzu]

@roboneuro generate pdf

[roboneuro]

⚠️ An error happened when generating the pdf.

[agahkarakuzu]

@roboneuro generate pdf

[roboneuro]

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

[agahkarakuzu]

@roboneuro generate pdf

[agahkarakuzu]

@roboneuro check references

[roboneuro]

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

OK DOIs

- 10.7312/pric91844 is OK
- 10.1126/science.284.5411.55 is OK
- 10.11126/stanford/9780804771856.003.0003 is OK
- 10.1093/acprof:osobl/9780199533091.003.0005 is OK
- 10.1126/science.1251554 is OK
- 10.7208/chicago/9780226365930.001.0001 is OK
- 10.1016/j.newideapsych.2021.100922 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

- 10.4324/9780203101612-9 may be a valid DOI for title: Plato

INVALID DOIs

- None

[agahkarakuzu]

@roboneuro build latest myst at runtime 5a23f6ee088d3d114ae98181b1a393c1aaf24ebc

[roboneuro]

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

[roboneuro]

🟢 Build MyST article

Status: Success fb357848
Last updated: 2024-12-03 09:11:43 PST

🌺 MyST build succeeded:

https://preview.neurolibre.org/myst/agahkarakuzu/amateur-science/4bd1ca10c9641dd423e22ec389f1dabd814de76a/_build/html/index.html

[agahkarakuzu]

@roboneuro build latest myst at runtime 5a23f6ee088d3d114ae98181b1a393c1aaf24ebc

[roboneuro]

🟢 Build MyST article

Status: Success aabfc7a0
Last updated: 2024-12-03 10:34:22 PST

🌺 MyST build succeeded:

https://preview.neurolibre.org/myst/agahkarakuzu/amateur-science/635293abd95e511e78bb56a68271e042763d932e/_build/html/index.html

None

[agahkarakuzu]

@roboneuro build latest myst at runtime 5a23f6ee088d3d114ae98181b1a393c1aaf24ebc

[roboneuro]

🟢 Build MyST article

Status: Success a7c53508
Last updated: 2024-12-03 11:16:24 PST

🌺 MyST build succeeded:

https://preview.neurolibre.org/myst/agahkarakuzu/amateur-science/d680766fa5010d9416af76bf1ec0a86729db7ac1/_build/html/index.html

[agahkarakuzu]

@roboneuro build latest myst at runtime 5a23f6ee088d3d114ae98181b1a393c1aaf24ebc

[roboneuro]

🟢 Build MyST article

Status: Success a69a9921
Last updated: 2024-12-03 11:23:20 PST

🌺 MyST build succeeded:

https://preview.neurolibre.org/myst/agahkarakuzu/amateur-science/9083c6a92c751f570cc6d325af9a9f011ba38e69/_build/html/index.html

[agahkarakuzu]

Now the builds not only can re-use a runtime from previous commits, but also can access the outputs of the latest successful build not to re-execute parts that already has been!

[2024-12-03 19:22:43,388: INFO/ForkPoolWorker-7] Jupyter hub is created
[2024-12-03 19:22:43,389: WARNING/ForkPoolWorker-7] ␤[Status]
[2024-12-03 19:22:43,389: WARNING/ForkPoolWorker-7]  ├─────── ⏺ running
[2024-12-03 19:22:43,389: WARNING/ForkPoolWorker-7]  └─────── Container 5df0c9c58478 sweet_khorana
[2024-12-03 19:22:43,389: WARNING/ForkPoolWorker-7]  ℹ Run the following commands in the terminal if you are debugging locally:
[2024-12-03 19:22:43,389: WARNING/ForkPoolWorker-7]  port="8888"
[2024-12-03 19:22:43,389: WARNING/ForkPoolWorker-7]  export JUPYTER_BASE_URL="http://localhost:8888"
[2024-12-03 19:22:43,389: WARNING/ForkPoolWorker-7]  export JUPYTER_TOKEN="e0b3a09115b3fc9e1c8ec96a0a17a5937b3db64c"
[2024-12-03 19:22:43,389: WARNING/ForkPoolWorker-7] ␤[Resources]
[2024-12-03 19:22:43,389: WARNING/ForkPoolWorker-7]  ├── MyST repository
[2024-12-03 19:22:43,389: WARNING/ForkPoolWorker-7]  │   ├───────── ✸ agahkarakuzu/amateur-science
[2024-12-03 19:22:43,389: WARNING/ForkPoolWorker-7]  │   ├───────── ⎌ 9083c6a92c751f570cc6d325af9a9f011ba38e69
[2024-12-03 19:22:43,389: WARNING/ForkPoolWorker-7]  │   └───────── ⏲ 2024-12-03 14:22:04-05:00: foo
+ [2024-12-03 19:22:43,390: WARNING/ForkPoolWorker-7]  └── Docker container
+ [2024-12-03 19:22:43,390: WARNING/ForkPoolWorker-7]      ├───────── ✸ binder-registry.conp.cloud/binder-registry.conp.cloud/binder-agahkarakuzu-2damateur-2dscience-3fc766
+ [2024-12-03 19:22:43,390: WARNING/ForkPoolWorker-7]      ├───────── ⎌ 5a23f6ee088d3d114ae98181b1a393c1aaf24ebc
+ [2024-12-03 19:22:43,390: WARNING/ForkPoolWorker-7]      ├───────── ⏲ 2024-12-02 18:13:29-05:00: fix mini
+ [2024-12-03 19:22:43,390: WARNING/ForkPoolWorker-7]      └───────── ℹ This image was built from REES-compliant agahkarakuzu/amateur-science repository at the commit above
[2024-12-03 19:22:47,670: WARNING/ForkPoolWorker-7] ␤[Preflight checks]
[2024-12-03 19:22:47,682: WARNING/ForkPoolWorker-7] ✓ Node.js is installed: v22.6.0
[2024-12-03 19:22:48,581: WARNING/ForkPoolWorker-7] ✓ mystmd is installed: v1.3.18
[2024-12-03 19:22:48,582: INFO/ForkPoolWorker-7] Found latest.txt
[2024-12-03 19:22:50,557: INFO/ForkPoolWorker-7] Previous commit: d680766fa5010d9416af76bf1ec0a86729db7ac1
[2024-12-03 19:22:57,951: WARNING/ForkPoolWorker-7] Starting MyST build http://localhost:8888
[2024-12-03 19:22:57,951: WARNING/ForkPoolWorker-7] --> Self env vars {'JUPYTER_BASE_URL': 'http://localhost:8888', 'JUPYTER_TOKEN': 'e0b3a09115b3fc9e1c8ec96a0a17a5937b3db64c', 'port': '8888', 'BASE_URL': '/myst/agahkarakuzu/amateur-science/9083c6a92c751f570cc6d325af9a9f011ba38e69/_build/html'}
[2024-12-03 19:22:57,951: WARNING/ForkPoolWorker-7] 🐞 Running command from directory: /DATA/myst/agahkarakuzu/amateur-science/9083c6a92c751f570cc6d325af9a9f011ba38e69
[2024-12-03 19:22:57,951: WARNING/ForkPoolWorker-7] 🐞 Set cwd to: /DATA/myst/agahkarakuzu/amateur-science/9083c6a92c751f570cc6d325af9a9f011ba38e69
[2024-12-03 19:22:57,951: WARNING/ForkPoolWorker-7] 🐞 Command: myst build --execute --html
[2024-12-03 19:23:00,033: WARNING/ForkPoolWorker-7] 🌎 Building MyST site
[2024-12-03 19:23:00,033: WARNING/ForkPoolWorker-7] ⚠️  _build/site/public/fig2stat-52e0b7016967982c1b342a4e98b33029.png Image is too large (3.45 MB) to convert to webp (build will be slow).
[2024-12-03 19:23:00,035: WARNING/ForkPoolWorker-7] BASE_URL environment overwrite is set
[2024-12-03 19:23:00,035: WARNING/ForkPoolWorker-7] ⚠️  _build/site/public/fig2stat-52e0b7016967982c1b342a4e98b33029.png Image is too large (3.45 MB) to convert to webp (build will be slow).
[2024-12-03 19:23:03,719: WARNING/ForkPoolWorker-7] Building the site with a baseurl of "/myst/agahkarakuzu/amateur-science/9083c6a92c751f570cc6d325af9a9f011ba38e69/_build/html"
+ [2024-12-03 19:23:03,719: WARNING/ForkPoolWorker-7] 💾 Adding Cached Notebook Outputs (content/figure_1.ipynb)
[2024-12-03 19:23:03,720: WARNING/ForkPoolWorker-7] 📖 Built content/index.md in 619 ms.
[2024-12-03 19:23:03,720: WARNING/ForkPoolWorker-7] 📖 Built content/figure_1.ipynb in 556 ms.
[2024-12-03 19:23:03,720: WARNING/ForkPoolWorker-7] 📚 Built 2 pages for project in 668 ms.
[2024-12-03 19:23:03,720: WARNING/ForkPoolWorker-7] 	✨✨✨  Starting Article Theme  ✨✨✨
[2024-12-03 19:23:03,720: WARNING/ForkPoolWorker-7] 🔌 Server started on port 3002!  🥳 🎉
[2024-12-03 19:23:03,720: WARNING/ForkPoolWorker-7] 	👉  http://localhost:3002  👈
[2024-12-03 19:23:03,721: WARNING/ForkPoolWorker-7] 💌 GET  /robots.txt 200 - - 4.646 ms
[2024-12-03 19:23:03,721: WARNING/ForkPoolWorker-7] 💌 GET  /myst-theme.css 200 - - 85.099 ms
[2024-12-03 19:23:03,721: WARNING/ForkPoolWorker-7] 💌 GET  /figure-1.json 200 - - 138.372 ms
[2024-12-03 19:23:03,721: WARNING/ForkPoolWorker-7] GET /index.json 200 - - 140.253 ms
[2024-12-03 19:23:03,721: WARNING/ForkPoolWorker-7] 💌 GET  /figure-1 200 - - 203.973 ms
[2024-12-03 19:23:03,721: WARNING/ForkPoolWorker-7] 💌 GET  /index 200 - - 317.307 ms
[2024-12-03 19:23:03,721: WARNING/ForkPoolWorker-7] 💌 GET  /favicon.ico 200 - - 282.407 ms
[2024-12-03 19:23:03,736: INFO/ForkPoolWorker-7] New active ports: {3002}
[2024-12-03 19:23:03,736: INFO/ForkPoolWorker-7] Attempting to close port 3002
[2024-12-03 19:23:03,748: INFO/ForkPoolWorker-7] Terminated process 1749780 using port 3002

[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

# 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

# Builds myst article. First argument is the commit hash, second is the binder hash.
@roboneuro build (\S+) myst at runtime (\S+)

# 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]

@roboneuro production sync data

[roboneuro]

🟢 DATA TRANSFER (Preview --> Preprint)

Status: Success 6567de40
Last updated: 2024-12-04 14:26:48 PST

ℹ️ See details

Success.

[agahkarakuzu]

@roboneuro production start

[roboneuro]

🔴 INITIATE PRODUCTION (Fork and Configure)

Status: Failed 262c1395
Last updated: 2024-12-04 14:33:34 PST

ℹ️ See details

Could not load [_config.yml and _toc.yml] under the content or myst.yml at the base of roboneurolibre/amateur-science

[agahkarakuzu]

@roboneuro production start

[roboneuro]

🟠 INITIATE PRODUCTION (Fork and Configure)

Status: In progress e820b8cd
Last updated: 2024-12-04 14:45:21 PST

ℹ️ See details

Forked repo has become available. Proceeding with configuration updates.

♻️ ♻️ Refresh

[agahkarakuzu]

@roboneuro production start

[roboneuro]

🟢 INITIATE PRODUCTION (Fork and Configure)

Status: Success f44a9806
Last updated: 2024-12-04 15:13:12 PST

ℹ️ See details

Please confirm that the forked repository is available and (myst.yml) properly configured.