[REVIEW]: MedPipe3D.jl: GPU accelerated medical image segmentation framework

[whedon]

Submitting author: @jakubMitura14 (Jakub Mitura)
Repository:
Branch with paper.md (empty if default branch):
Version:
Editor: @omlins
Reviewers: @jpsamaroo, @timholy
Archive: Pending

Status

Status badge code:

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Markdown: [![status](https://proceedings.juliacon.org/papers/0390a2e23fffde82f76752530635a68a/status.svg)](https://proceedings.juliacon.org/papers/0390a2e23fffde82f76752530635a68a)

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

@jpsamaroo & @timholy, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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✨ 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 @jpsamaroo

Conflict of interest

• As the reviewer I confirm that I have read the JuliaCon conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

• I confirm that I read and will adhere to the JuliaCon code of conduct.

General checks

• Repository: Is the source code for this software available at the repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Authorship: Has the submitting author (@jakubMitura14) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• 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

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
• 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

Paper format

• Authors: Does the paper.tex file include a list of authors with their affiliations?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?
• Page limit: Is the page limit for full papers respected by the submitted document?

Content

• Context: is the scientific context motivating the work correctly presented?
• Methodology: is the approach taken in the work justified, presented with enough details and reference to reproduce it?
• Results: are the results presented and compared to approaches with similar goals?

Review checklist for @timholy

Conflict of interest

• As the reviewer I confirm that I have read the JuliaCon conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

• I confirm that I read and will adhere to the JuliaCon code of conduct.

General checks

• Repository: Is the source code for this software available at the repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Authorship: Has the submitting author (@jakubMitura14) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• 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

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
• 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

Paper format

• Authors: Does the paper.tex file include a list of authors with their affiliations?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?
• Page limit: Is the page limit for full papers respected by the submitted document?

Content

• Context: is the scientific context motivating the work correctly presented?
• Methodology: is the approach taken in the work justified, presented with enough details and reference to reproduce it?
• Results: are the results presented and compared to approaches with similar goals?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @jpsamaroo, @timholy it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/JuliaCon/proceedings-review) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

1. Set yourself as 'Not watching' https://github.com/JuliaCon/proceedings-review:

2. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

For a list of things I can do to help you, just type:

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

[whedon]

PDF failed to compile for issue #127 with the following error:

 Can't find any papers to compile :-(

[jakubMitura14]

already compiled pdf is in paper folder
https://github.com/jakubMitura14/MedPipe3D.jl/blob/master/paper/test.pdf

[whedon]

👋 @timholy, please update us on how your review is going (this is an automated reminder).

[whedon]

👋 @jpsamaroo, please update us on how your review is going (this is an automated reminder).

[whedon]

👋 @jpsamaroo, please update us on how your review is going (this is an automated reminder).

[whedon]

👋 @timholy, please update us on how your review is going (this is an automated reminder).

[timholy]

I just tried to get started on this, but when I clicked on the invitation, it says

Sorry, we couldn't find that repository invitation. It is possible that the invitation was revoked or that you are not logged into the invited account.

I only have one GitHub account.

[matbesancon]

@whedon assign omlins as editor

[matbesancon]

@whedon generate pdf

[whedon]

PDF failed to compile for issue #127 with the following error:

 Can't find any papers to compile :-(

[matbesancon]

@jakubMitura14 did you modify something on the paper folder compared to the submission template?

[matbesancon]

@timholy are you able to tick the boxes on the first comment of the issue? If this is the case it will be sufficient to go through with the review

[matbesancon]

@jakubMitura14 please use the template paper folder form https://github.com/JuliaCon/JuliaConSubmission.jl, the submission should work then

[jakubMitura14]

Hello thanks for a tip, as I see there are some problems I had at least for that moment withdrawn the paper, still thank You!

[omlins]

@jakubMitura14, in order to avoid any misunderstandings, do we understand right that you would like to withdraw this submission (in which case this issue will be closed) and potentially resubmit anew at a later time?

[jakubMitura14]

Yes

[omlins]

@whedon assign @omlins as editor

[whedon]

I'm sorry @omlins, I'm afraid I can't do that. That's something only editors are allowed to do.

[matbesancon]

@whedon assign @omlins as editor

[luraess]

@whedon commands

[editorialbot]

My name is now @editorialbot

[luraess]

@editorialbot commands

[editorialbot]

Hello @luraess, here are the things you can ask me to do:

# List all available commands
@editorialbot commands

# Add to this issue's reviewers list
@editorialbot add @username as reviewer

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# certain period of time (supported units days and weeks)
@editorialbot remind @reviewer in 2 weeks

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for version
@editorialbot set v1.0.0 as version

# Set a value for branch
@editorialbot set juliacon-paper as branch

# Set a value for repository
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# Set a value for the archive DOI
@editorialbot set set 10.5281/zenodo.6861996 as archive

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@editorialbot generate pdf

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[luraess]

Yes

I am thus finalising the withdrawal of the paper.

[luraess]

@editorialbot withdraw

[editorialbot]

There was a problem withdrawing the paper.

[luraess]

@editorialbot reject

[editorialbot]

There was a problem rejecting the paper.

[luraess]

Closing this now manually given there are issues with the bot.

[lucaferranti]

@editorialbot reject

[editorialbot]

Paper rejected.