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[PRE REVIEW]: MNE-ICALabel: Automatically annotating ICA components with ICLabel in Python #4429

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editorialbot opened this issue May 26, 2022 · 47 comments
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[PRE REVIEW]: MNE-ICALabel: Automatically annotating ICA components with ICLabel in Python #4429

editorialbot opened this issue May 26, 2022 · 47 comments
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@TomDonoghue @hvgazula @emdupre
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editorialbot commented May 26, 2022 •
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Submitting author: @adam2392 (Adam Li)
Repository: https://github.com/mne-tools/mne-icalabel
Branch with paper.md (empty if default branch): main
Version: v0.1
Editor: @emdupre
Reviewers: @hvgazula, @TomDonoghue
Managing EiC: Arfon Smith

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/d91770e35a985ecda4f2e1f124977207"><img src="https://joss.theoj.org/papers/d91770e35a985ecda4f2e1f124977207/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/d91770e35a985ecda4f2e1f124977207/status.svg)](https://joss.theoj.org/papers/d91770e35a985ecda4f2e1f124977207)

Author instructions

Thanks for submitting your paper to JOSS @adam2392. Currently, there isn't an JOSS editor assigned to your paper.

The author's suggestion for the handling editor is @oliviaguest.

@adam2392 if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

Editor instructions

The JOSS submission bot @editorialbot is here to help you find and assign reviewers and start the main review. To find out what @editorialbot can do for you type:

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Hello human, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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

@editorialbot commands

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

@editorialbot generate pdf

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Couldn't check the bibtex because branch name is incorrect: mne-tools/mne-icalabel#61

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Couldn't check the bibtex because branch name is incorrect: mne-tools/mne-icalabel#61

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⚠️ An error happened when generating the pdf.

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arfon commented May 26, 2022

@adam2392 – JOSS can't compile a paper that's on a remote branch (adam2392:joss) sorry. Can you merge it please?

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@arfon done! Sorry about that. Wasn't aware of that limitation.

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@arfon do I have to do anything special to re-run the build for the PDF?

@Kevin-Mattheus-Moerman
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@editorialbot generate pdf

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@adam2392 you call @editorialbot generate pdf

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⚠️ An error happened when generating the pdf.

@Kevin-Mattheus-Moerman
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@editorialbot set main as branch

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Done! branch is now main

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@editorialbot generate pdf

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

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@editorialbot check repository

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@editorialbot commands

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Hello @adam2392, here are the things you can ask me to do:


# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

# Check the references of the paper for missing DOIs
@editorialbot check references

# Perform checks on the repository
@editorialbot check repository

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

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

# Generates the pdf paper
@editorialbot generate pdf

# Get a link to the complete list of reviewers
@editorialbot list reviewers

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@editorialbot check repository

trying again...

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Software report:

github.com/AlDanial/cloc v 1.88  T=0.08 s (781.3 files/s, 64614.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          28            498            896           1619
YAML                             5             59             22            479
Markdown                         7            134              0            263
make                             2             66             11            262
DOS Batch                        1             29              1            212
TeX                              2              8              1            151
reStructuredText                 8             93             70            113
HTML                             4              6              6             51
JavaScript                       1              3             10             50
Bourne Shell                     3              7              8             32
TOML                             1              3              0             21
CSS                              1              3              4             19
-------------------------------------------------------------------------------
SUM:                            63            909           1029           3272
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

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Wordcount for paper.md is 741

@danielskatz
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👋 @emdupre - would you be able to edit this submission?

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@editorialbot invite @emdupre as editor

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Invitation to edit this submission sent!

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emdupre commented Jun 2, 2022

Thank you for the invitation, @danielskatz ! I'm happy to edit this.

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emdupre commented Jun 2, 2022

@editorialbot assign @emdupre as editor

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Assigned! @emdupre is now the editor

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emdupre commented Jun 2, 2022

👋 Hi @adam2392, and thank you for your submission to JOSS !

If you have any suggestions for potential reviewers, please let me know by listing their names or GitHub handles (without the @, so they don't receive a notification) here.

You can suggest reviewers from any relevant project, though we often recommend starting with this list of people as they have already agreed to review for JOSS (please start at the bottom of the list).

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adam2392 commented Jun 2, 2022

Perhaps

vferat
hvgazula
Gabrock94
suhang96

I just picked ppl from the bottom starting that had "Neuro" related expertise?

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emdupre commented Jun 6, 2022

👋 Hi @hvgazula @jasmainak @martinagvilas @vferat !

Would you be willing to review MNE-ICALabel: Automatically annotating ICA components with ICLabel in Python for JOSS (the Journal of Open Source Software)?

You can learn more about reviewing for JOSS -- including our conflict of interest policy -- here.

The review takes place on GitHub and focuses on the software and this short paper:
https://github.com/openjournals/joss-papers/blob/joss.04429/joss.04429/10.21105.joss.04429.pdf

If you're available to review this work, please let me know and I'll add you as a reviewer. Once I have sufficient reviewers I'll open a dedicated review issue.

Thank you !

@hvgazula
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hvgazula commented Jun 6, 2022

Sure.

@vferat
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vferat commented Jun 7, 2022

Hey @emdupre

Thank you for this invitation to review, I would have been happy to participate in it, however I am currently working with some of the authors of this article on unpublished projects and having been employed by the same institution as some of them some years ago.
In view of these conflicts of interest, I prefer to decline your invitation.

I remain available for other reviews,
Hope the best for this article !

@martinagvilas
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Hi @emdupre 👋 Thank you for the invitation. Unfortunately, at the moment I'm lacking the time to review due to other commitments. I hope to be available for other reviews in the near future.

The article looks very interesting, all the best to the authors!

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jasmainak commented Jun 10, 2022 via email

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emdupre commented Jun 13, 2022

Hi everyone, and thanks for your responses !

@jasmainak since the co-authorship is within the last four years, it would count as a conflict of interest. Apologies for not catching that ! Thanks to both you and @vferat for letting me know about these concerns. I will, though, keep you (and @martinagvilas !) in mind for reviews in the future.

Thanks, too, to @hvgazula for agreeing to review ! I'll go ahead and add you on the submission now while I recruit additional reviewers 🚀

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emdupre commented Jun 13, 2022

@editorialbot add @hvgazula to reviewers

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@hvgazula added to the reviewers list!

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Hi @emdupre, sorry for the late response as I’m out of town currently. I’d be happy to review! I do have a COI with Adam Li on the mne-bids paper which was published in JOSS 3 years ago. Does that make me ineligible to review?

I actually wasn't a co-author on that publication :p

However, I did work with @jasmainak on the MNE-BIDs package a lot post-JOSS publication.

@adam2392
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Hi @emdupre are there any updates here, or action items needed from us?

Also just wanted to see if there was any insight into what we should expect and when for the JOSS process? Is there a summary you can point me to perhaps? Thanks!

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emdupre commented Jun 16, 2022

Hi @adam2392, thanks for following up !

The current action items are on my side to secure additional reviewers. I'm working on this now, but it's a difficult time of year as many folks are out-of-office. I'm sorry for the delay, and I appreciate your patience ! I hope I'll have more updates soon.

More generally, once we secure reviewers, I'll be able to open the review issue. You can see the reviewer checklist here, which is what reviewers will work through when evaluating the submission. You can also look at some previous JOSS reviews to see this in practice.

Hopefully that clarifies this process a bit, but please let me know if you have any other questions !

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emdupre commented Jun 16, 2022

👋 Hi @TomDonoghue, @rdgao, @ixjlyons !

Would you be willing to review MNE-ICALabel: Automatically annotating ICA components with ICLabel in Python for JOSS (the Journal of Open Source Software)?

You can learn more about reviewing for JOSS -- including our conflict of interest policy -- here.

The review takes place on GitHub and focuses on the software and this short paper:
https://github.com/openjournals/joss-papers/blob/joss.04429/joss.04429/10.21105.joss.04429.pdf

If you're available to review this work, please let me know and I'll add you as a reviewer. Once I have sufficient reviewers I'll open a dedicated review issue.

Thank you !

@TomDonoghue
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hey @emdupre - I'd be happy to review this submission!

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emdupre commented Jun 17, 2022

Thank you, @TomDonoghue ! I'll add you as a reviewer now and then give another 24h for any additional reviewer responses before opening the review issue ! 🚀

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emdupre commented Jun 17, 2022

@editorialbot add @TomDonoghue to reviewers

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@TomDonoghue added to the reviewers list!

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emdupre commented Jun 18, 2022

Thanks @rdgao, @ixjlyons for considering this invitation, but we'll go ahead and move forward as-is to get this submission under review !

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emdupre commented Jun 18, 2022

@editorialbot start review

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OK, I've started the review over in #4484.

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