[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

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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 1 year ago

🟢 Successfully built

Status: Success c9ff50b2 Last updated: 2023-10-21 18:52:36 PDT

:information_source: See details

:confetti_ball: Roboneuro will send you the book URL.

roboneuro commented 1 year ago

:robot::speech_balloon::confetti_ball::rocket: Congratulations to the authors for expertly navigating the intricate territories of parcellation and reproducible research with the creation of Neurolibre Reproducible Preprint (NRP) - a preprint that delivers brainy insights with a touch of avant-garde style, making neuroscience exploration a delightful journey.

:hibiscus: Take a loot at the latest version of your NRP! :hibiscus:

[!IMPORTANT] Please make sure the figures are displayed correctly, code cells are collapsible, and that BinderHub execution is successful.

pbellec commented 1 year ago

alright, so the book has built :tada: :tada: :tada:

But when I try to re-execute it, I run into an issue. After launching the server, I get a download of the md file.

I think this may be because I've set it up on the classic notebook interface. I've switched to jupyterlab instead.

agahkarakuzu commented 1 year ago

When the request url includes book path, it is doing the conversion automatically.

But,this is one issue hopefully future book builds will resolve. Because even when you get ipynb for one page, when you want to take a look at others, they remain as md.

Requesting another build.

agahkarakuzu commented 1 year ago

@roboneuro build book

roboneuro commented 1 year ago

🟢 Successfully built

Status: Success 62802c03 Last updated: 2023-10-21 19:07:19 PDT

:information_source: See details

:confetti_ball: Roboneuro will send you the book URL.

roboneuro commented 1 year ago

:robot::speech_balloon::confetti_ball::rocket: Congratulations to the authors on building the Neurolibre Reproducible Preprint (NRP)! With the power to parcellate the parcellation issue in neuroscience, this NRP proves that reproducibility can definitely be a piece of cake. Well done!

:hibiscus: Take a loot at the latest version of your NRP! :hibiscus:

[!IMPORTANT] Please make sure the figures are displayed correctly, code cells are collapsible, and that BinderHub execution is successful.

pbellec commented 1 year ago

alright so no luck :( I vaguely remember about struggling with that issue a long time ago, before finding a combo of versions which worked.

I've decided to give up, and converted everything to ipynb.

Also reverted to classic interface, as this was not the problem.

agahkarakuzu commented 1 year ago

@roboneuro build book

roboneuro commented 1 year ago

🟢 Successfully built

Status: Success d1eac603 Last updated: 2023-10-21 19:40:00 PDT

:information_source: See details

:confetti_ball: Roboneuro will send you the book URL.

roboneuro commented 1 year ago

:robot::speech_balloon::confetti_ball::rocket: Congratulations to the authors for masterfully parcellating the parcellation issue with Neurolibre! This reproducible preprint is a neuroscience gem that weaves together Jupyter Book magic and delivers a brain-tickling proof of concept.

:hibiscus: Take a loot at the latest version of your NRP! :hibiscus:

[!IMPORTANT] Please make sure the figures are displayed correctly, code cells are collapsible, and that BinderHub execution is successful.

pbellec commented 1 year ago

EVERYTHING LOOKS GOOD :tada: :tada: :tada:

in particular Info : ../data/editorial_parcellation already downloaded :)

agahkarakuzu commented 1 year ago

@pbellec great! I've just sent you a pull request, as now we can build extended pdf.

agahkarakuzu commented 1 year ago

@roboneuro build extended pdf

roboneuro commented 1 year ago

🟢 Successfully built

Status: Success a7716b91 Last updated: 2023-10-22 11:32:00 PDT

:information_source: See details

Roboneuro will post a new comment to share the results and provide an explanation of the next steps.

roboneuro commented 1 year ago

📑 Extended PDF has been compiled!

For the submitting author

👀 Please review the extended PDF and verify that all references are accurately included. If everything is correct, please proceed to the next steps. If not, please make the necessary adjustments in the source documents.
⬇️ Download the updated paper.md.
⬇️ Download the updated paper.bib.
ℹ️ Please read and confirm the following:

[!IMPORTANT]
We have added a note in the extended PDF to inform the readers that the narrative content from your notebook content has been automatically added to credit the referenced sources. This note includes citations to the articles explaining the NeuroLibre workflow, integrated research objects, and the Canadian Open Neuroscience Platform (CONP). If you prefer not to include them, please remove the respective citation directives in the updated paper.md before pushing the file to your repository.
- [x] I, the submitting author, confirm that I have read the note above.
♻️ Update the respective files in your source repository with the files you just downloaded and inform the screener.

For the technical screener

Once the submitting author has updated the repository with the paper.md and paper.bib, please confirm that the PDF successfully builds using the @roboneuro generate pdf.

:warning: However, DO NOT issue @roboneuro build extended pdf command after the submitting author has updated the paper.md and paper.bib.

pbellec commented 1 year ago

LGTM, I've incorporated the changes on the repo.

agahkarakuzu commented 1 year ago

Oh I thought you would merge the PR first, sorry:

I see that the PR is still open: https://github.com/pbellec/editorial_parcellation/pulls

If you can revert the changes to the paper.md and paper.bib, then merge PR, adding extended PDF content would be better after then.

I am sorry for the confusion.

pbellec commented 1 year ago

I've merged the PR.

From what I see it should work.

agahkarakuzu commented 1 year ago

We just need paper.md and paper.bib to be in their plain version, as the extended pdf build will append what is already there.

paper.md: https://raw.githubusercontent.com/pbellec/editorial_parcellation/babcd5efd94052e78a7002093a7dfb8bee4fc37b/paper.md

👆 You can get rid of the References section at the end

paper.bib:

https://raw.githubusercontent.com/pbellec/editorial_parcellation/babcd5efd94052e78a7002093a7dfb8bee4fc37b/paper.bib

pbellec commented 1 year ago

I see. I've cleaned up paper.(md, bib) as suggested. Should be ready for a new "extended pdf" generation.

agahkarakuzu commented 1 year ago

Thank you so much Pierre! I will add a "draft" version for this extended pdf build so that the instructions do not lead to confusion on every call.

agahkarakuzu commented 1 year ago

@roboneuro build extended pdf

roboneuro commented 1 year ago

🟢 Successfully built

Status: Success b20feb10 Last updated: 2023-10-22 12:00:02 PDT

:information_source: See details

Roboneuro will post a new comment to share the results and provide an explanation of the next steps.

roboneuro commented 1 year ago

📑 Extended PDF has been compiled!

For the submitting author

👀 Please review the extended PDF and verify that all references are accurately included. If everything is correct, please proceed to the next steps. If not, please make the necessary adjustments in the source documents.
⬇️ Download the updated paper.md.
⬇️ Download the updated paper.bib.
ℹ️ Please read and confirm the following:

[!IMPORTANT]
We have added a note in the extended PDF to inform the readers that the narrative content from your notebook content has been automatically added to credit the referenced sources. This note includes citations to the articles explaining the NeuroLibre workflow, integrated research objects, and the Canadian Open Neuroscience Platform (CONP). If you prefer not to include them, please remove the respective citation directives in the updated paper.md before pushing the file to your repository.
- [ ] I, the submitting author, confirm that I have read the note above.
♻️ Update the respective files in your source repository with the files you just downloaded and inform the screener.

For the technical screener

Once the submitting author has updated the repository with the paper.md and paper.bib, please confirm that the PDF successfully builds using the @roboneuro generate pdf.

:warning: However, DO NOT issue @roboneuro build extended pdf command after the submitting author has updated the paper.md and paper.bib.

agahkarakuzu commented 1 year ago

Can you add the following to your paper.bib:

@Inbook{Kramer2016,
author="Kramer, Oliver",
title="Scikit-Learn",
bookTitle="Machine Learning for Evolution Strategies",
year="2016",
publisher="Springer International Publishing",
address="Cham",
pages="45--53",
abstract="scikit-learn is an open source machine learning library written in Python.",
isbn="978-3-319-33383-0",
doi={10.1007/978-3-319-33383-0_5}
}

pbellec commented 1 year ago

done

agahkarakuzu commented 1 year ago

@roboneuro build extended pdf

roboneuro commented 1 year ago

🟢 Successfully built

Status: Success 5743aa96 Last updated: 2023-10-22 12:11:30 PDT

:information_source: See details

Roboneuro will post a new comment to share the results and provide an explanation of the next steps.

roboneuro commented 1 year ago

📑 Extended PDF has been compiled!

For the submitting author

👀 Please review the extended PDF and verify that all references are accurately included. If everything is correct, please proceed to the next steps. If not, please make the necessary adjustments in the source documents.
⬇️ Download the updated paper.md.
⬇️ Download the updated paper.bib.
ℹ️ Please read and confirm the following:

[!IMPORTANT]
We have added a note in the extended PDF to inform the readers that the narrative content from your notebook content has been automatically added to credit the referenced sources. This note includes citations to the articles explaining the NeuroLibre workflow, integrated research objects, and the Canadian Open Neuroscience Platform (CONP). If you prefer not to include them, please remove the respective citation directives in the updated paper.md before pushing the file to your repository.
- [x] I, the submitting author, confirm that I have read the note above.
♻️ Update the respective files in your source repository with the files you just downloaded and inform the screener.

For the technical screener

Once the submitting author has updated the repository with the paper.md and paper.bib, please confirm that the PDF successfully builds using the @roboneuro generate pdf.

:warning: However, DO NOT issue @roboneuro build extended pdf command after the submitting author has updated the paper.md and paper.bib.

agahkarakuzu commented 1 year ago

@pbellec if you are happy with https://preprint.neurolibre.org/10.55458/draft/00010/paper.pdf?no_cache, you can update the paper.md and paper.bib as described above, then I will publish this.

Thank you so much for your patience.

pbellec commented 1 year ago

LGTM !!

pbellec commented 1 year ago

extended pdf pushed on the repo :tada:

agahkarakuzu commented 1 year ago

@roboneuro recommend-accept

roboneuro commented 1 year ago

Attempting dry run of processing paper acceptance...

roboneuro commented 1 year ago

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

OK DOIs

- 10.1016/j.neuroimage.2017.11.063 is OK
- 10.1007/978-3-319-33383-0_5 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

- None

INVALID DOIs

- None

roboneuro commented 1 year ago

:wave: @openjournals/neurolibre-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/62, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

agahkarakuzu commented 1 year ago

@roboneuro production start

roboneuro commented 1 year ago

🔴 INITIATE PRODUCTION (Fork and Configure)

Status: Failed 07d7fa45 Last updated: 2023-10-22 12:26:58 PDT

[!WARNING] A book build could not be found at commit 13eeda9b56dc624d4a702774416f1ae89f4227a9 at https://github.com/pbellec/editorial_parcellation. Production process cannot be started.

agahkarakuzu commented 1 year ago

@roboneuro build book

roboneuro commented 1 year ago

🟢 Successfully built

Status: Success e0f2752c Last updated: 2023-10-22 12:31:56 PDT

:information_source: See details

:confetti_ball: Roboneuro will send you the book URL.

roboneuro commented 1 year ago

:robot::speech_balloon::confetti_ball::rocket: Congratulations to the authors on successfully parcellating the parcellation issue and delivering a neuroscientific masterpiece! Neurolibre's reproducible preprint is a true brainiac's guide, turning the concept of reproducibility into an irresistible neural adventure.

:hibiscus: Take a loot at the latest version of your NRP! :hibiscus:

[!IMPORTANT] Please make sure the figures are displayed correctly, code cells are collapsible, and that BinderHub execution is successful.

agahkarakuzu commented 1 year ago

I noticed a small issue and sent a PR for that.

pbellec commented 1 year ago

merged.

agahkarakuzu commented 1 year ago

@roboneuro build book

roboneuro commented 1 year ago

🟢 Successfully built

Status: Success d24225d9 Last updated: 2023-10-22 12:48:30 PDT

:information_source: See details

:confetti_ball: Roboneuro will send you the book URL.

roboneuro commented 1 year ago

:robot::speech_balloon::confetti_ball::rocket: Congratulations to the authors for expertly parcellating the parcellation issue and paving the way for reproducible analyses in neuroscience with their Neurolibre Reproducible Preprint (NRP)! With their Jupyter Book, they've interwoven reproducibility and readability, creating a brainy masterpiece.

:hibiscus: Take a loot at the latest version of your NRP! :hibiscus:

[!IMPORTANT] Please make sure the figures are displayed correctly, code cells are collapsible, and that BinderHub execution is successful.

agahkarakuzu commented 1 year ago

@roboneuro production start

roboneuro commented 1 year ago

🟢 INITIATE PRODUCTION (Fork and Configure)

Status: Success 87b455e7 Last updated: 2023-10-22 12:57:07 PDT

:information_source: See details

Please confirm that the forked repository is available and (_toc.yml and _config.ymlk) properly configured.

agahkarakuzu commented 1 year ago

@roboneuro production build book

neurolibre / neurolibre-reviews