editorialbot commented 1 year ago

Submitting author: !--author-handle-->@Mmasoud1@samhforbes<!--end-editor-- Reviewers: @mwegrzyn, @62442katieb, @richford Archive: 10.5281/zenodo.7735848

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/92e800c8ac3b0c431357adaad09cb677"><img src="https://joss.theoj.org/papers/92e800c8ac3b0c431357adaad09cb677/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/92e800c8ac3b0c431357adaad09cb677/status.svg)](https://joss.theoj.org/papers/92e800c8ac3b0c431357adaad09cb677)

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

@mwegrzyn & @62442katieb & @richford, 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:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @samhforbes 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

📝 Checklist for @mwegrzyn

📝 Checklist for @richford

📝 Checklist for @62442katieb

samhforbes commented 1 year ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

[x] Double check authors and affiliations (including ORCIDs)
[x] Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
[x] Archive the release on Zenodo/figshare/etc and post the DOI here.
[x] Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
[x] Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

[x] Read the text of the paper and offer comments/corrections (as either a list or a PR)
[x] Check the references in the paper for corrections (e.g. capitalization)
[x] Check that the archive title, author list, version tag, and the license are correct
[x] Set archive DOI with @editorialbot set <DOI here> as archive
[x] Set version with @editorialbot set <version here> as version
[x] Double check rendering of paper with @editorialbot generate pdf
[x] Specifically check the references with @editorialbot check references and ask author(s) to update as needed
[x] Recommend acceptance with @editorialbot recommend-accept

samhforbes commented 1 year ago

@editorialbot set 10.5281/zenodo.7735848 as archive

editorialbot commented 1 year ago

Done! Archive is now 10.5281/zenodo.7735848

samhforbes commented 1 year ago

@editorialbot set v2.1.0 as version

editorialbot commented 1 year ago

Done! version is now v2.1.0

samhforbes commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

OK DOIs

- 10.1109/IJCNN.2017.7966333 is OK
- 10.48550/arXiv.1511.07122 is OK
- 10.48550/arXiv.1901.05350 is OK
- 10.5281/zenodo.6430433 is OK
- 10.1016/j.neuroimage.2020.117012 is OK
- 10.1087/20150211 is OK
- 10.1002/hbm.460020402 is OK
- 10.1006/nimg.1998.0395 is OK

MISSING DOIs

- None

INVALID DOIs

- None

samhforbes commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

samhforbes commented 1 year ago

@Mmasoud1 Some minor things in the paper:

l27 and cross-platform operation, while
l73 Built-in models also are provided with Brainchop's live demo. (or with the Brainchop live demo)
Can you check the references - it feels like for example Papaya should link to the homepage http://rii-mango.github.io/Papaya/ rather than GitHub.
Likewise pyodide should probably cite the author list since they do in the Zenodo repo.

Mmasoud1 commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

OK DOIs

- 10.1109/IJCNN.2017.7966333 is OK
- 10.48550/arXiv.1511.07122 is OK
- 10.48550/arXiv.1901.05350 is OK
- 10.5281/zenodo.6430433 is OK
- 10.1016/j.neuroimage.2020.117012 is OK
- 10.1087/20150211 is OK
- 10.1002/hbm.460020402 is OK
- 10.1006/nimg.1998.0395 is OK

MISSING DOIs

- None

INVALID DOIs

- None

Mmasoud1 commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

Mmasoud1 commented 1 year ago

[x] Double check authors and affiliations (including ORCIDs)
[x] Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
[x] Archive the release on Zenodo/figshare/etc and post the DOI here.
[x] Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
[x] Make sure that the license listed for the archive is the same as the software license.

Dear @samhforbes , I double checked all items in the author post-review checklist. Thank you!

Mmasoud1 commented 1 year ago

Some minor things in the paper:

l27 and cross-platform operation, while
l73 Built-in models also are provided with Brainchop's live demo. (or with the Brainchop live demo)
Can you check the references - it feels like for example Papaya should link to the homepage http://rii-mango.github.io/Papaya/ rather than GitHub.
Likewise pyodide should probably cite the author list since they do in the Zenodo repo.

Thank you @samhforbes , I applied all suggested changes in the article.

samhforbes commented 1 year ago

Great! This is looking good @Mmasoud1 and I'm prepared to recommend acceptance to the EiC. Congrats on a really cool piece of software

samhforbes commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 year ago

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

OK DOIs

- 10.1109/IJCNN.2017.7966333 is OK
- 10.48550/arXiv.1511.07122 is OK
- 10.48550/arXiv.1901.05350 is OK
- 10.5281/zenodo.6430433 is OK
- 10.1016/j.neuroimage.2020.117012 is OK
- 10.1087/20150211 is OK
- 10.1002/hbm.460020402 is OK
- 10.1006/nimg.1998.0395 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 year ago

:wave: @openjournals/bcm-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/openjournals/joss-papers/pull/4076, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

Mmasoud1 commented 1 year ago

Thanks you @samhforbes, appreciate your time and valuable service.

Mmasoud1 commented 1 year ago

Dear @Kevin-Mattheus-Moerman let me know please if I can help with anything. I will be away for a while for traveling tomorrow, and I appreciate your pointing me out if there is anything still needed on my part before I go. Thank you!

Kevin-Mattheus-Moerman commented 1 year ago

@Mmasoud1 I reviewed the paper and archive and all seems in order. I only have the following minor comment:

[x] I suggest you rename the Statement of needs section to Statement of need

Mmasoud1 commented 1 year ago

Dear @Kevin-Mattheus-Moerman i applied the suggested change and pushed to brainchop master branch. Thank you!

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot accept

editorialbot commented 1 year ago

Doing it live! Attempting automated processing of paper acceptance...

editorialbot commented 1 year ago

:warning: Couldn't acccept/publish paper. An error happened.

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot accept

editorialbot commented 1 year ago

Doing it live! Attempting automated processing of paper acceptance...

editorialbot commented 1 year ago

:warning: Couldn't acccept/publish paper. An error happened.

Kevin-Mattheus-Moerman commented 1 year ago

@openjournals/dev can you see what is going wrong here?

xuanxu commented 1 year ago

The acceptance workflow has failed in a post-acceptance task, but the paper has been accepted and deposited correctly. This is the DOI: 10.21105/joss.05098

I'm going to try to run manually the missing steps.

editorialbot commented 1 year ago

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/4082
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05098
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

editorialbot commented 1 year ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot commented 1 year ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

Mmasoud1 commented 1 year ago

We are really delighted to have brainchop published with JOSS. Thank you all for your valuable comments and services.

Kevin-Mattheus-Moerman commented 1 year ago

@Mmasoud1 congratulations on this publication in JOSS!

Thanks for editing @samhforbes !

And a special thanks to the reviewers!!! @mwegrzyn, @62442katieb, @richford

editorialbot commented 1 year ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.05098/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05098/status.svg
   :target: https://doi.org/10.21105/joss.05098

This is how it will look in your documentation:

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openjournals / joss-reviews

[REVIEW]: Brainchop: In-browser MRI volumetric segmentation and rendering #5098

Status

Reviewer instructions & questions

Checklists

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance