Closed editorialbot closed 10 months ago
Hello humans, 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:
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For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:
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Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1038/sdata.2016.44 is OK
- 10.3389/fninf.2021.770608 is OK
- 10.1016/j.jneumeth.2016.03.001 is OK
MISSING DOIs
- None
INVALID DOIs
- None
Software report:
github.com/AlDanial/cloc v 1.88 T=0.13 s (718.8 files/s, 130337.4 lines/s)
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Language files blank comment code
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Python 72 1758 4769 7636
Markdown 10 398 0 1409
YAML 3 27 20 293
JSON 5 0 0 154
TeX 1 3 0 34
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SUM: 91 2186 4789 9526
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gitinspector failed to run statistical information for the repository
Wordcount for paper.md
is 1421
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π Hi @PeerHerholz and @TheChymera, and thank you again for agreeing to review this submission !
The review will take place in this issue, and you can generate your individual reviewer checklists by asking editorialbot directly with @editorialbot generate my checklist
.
In working through the checklist, you're likely to have specific feedback on Bidsme. Whenever possible, please open relevant issues on the linked software repository (and cross-link them with this issue) rather than discussing them here. This helps to make sure that feedback is translated into actionable items to improve the software !
If you aren't sure how to get started, please see the Reviewing for JOSS guide -- and, of course, feel free to ping me with any questions !
π Hi @PeerHerholz and @TheChymera, and happy Friday !
I just wanted to check whether you're having any issues in getting started with this review. Please let me know if so ; otherwise, thank you again for agreeing to review Bidsme !
Hi @emdupre,
sorry for the delay. I'm starting the review process now!
π Hi @TheChymera, I just wanted to check-in on how this review is going for you. Please let me know if you're encountering any issues in conducting this review, and thank you again !
@emdupre thanks for pinging me.
π Hi @nbeliy, and happy Monday !
I just wanted to note that you are welcome to start working on the issues raised by the reviewers, in case there was any confusion ! After you address this initial round of reviewer comments, please let me know.
I'll also be monitoring both this thread as well as the associated issues, so don't hesitate to tag me in either location if you have any difficulties in this process.
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@editorialbot generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
Hi @nbeliy , it looks like you're still working on addressing the issues currently raised by the reviewers.
Please let me know if you're encountering any issues in this process, either here in the main review thread or directly on the opened issues !
Hi @emdupre,
I think I've addressed the majority of issues of reviewers, and now waiting to their return.
Hi @nbeliy, thanks for confirming ! I noticed that you hadn't yet commented on https://github.com/CyclotronResearchCentre/bidsme/issues/5 and https://github.com/CyclotronResearchCentre/bidsme/issues/6 ; could you confirm if these have already been addressed ?
Hi everyone, and happy Monday ! π»
Just following up from my previous message : these remaining issues were subsequently discussed in their individual threads.
@TheChymera and @PeerHerholz, thank you again for your feedback on bidsme ! If you could please revisit your individual reviewer checklists now that @nbeliy has finished addressing your initial round of comments, that will help us to move the submission forward !
Hi @emdupre,
sorry for the slow response. I updated the checklist and I think all points are addressed now.
Thank you for the confirmation, @PeerHerholz !
Please let us know when you've had a chance to revisit your review checklist, @TheChymera. And thank you both again for your help in reviewing this submission for Bidsme !
π Hi @TheChymera, I just wanted to quickly follow-up to confirm if you've been able to review your review checklist in light of the recent changes to Bidsme. If you have any questions or concerns, please don't hesitate to let me know.
Hi @TheChymera, just another nudge on this. If you have any questions, please don't hesitate to let me know !
Just following up to note that I've also reached out to @TheChymera over email to check on the status of this. I've asked for confirmation within the next week that they will be able to finish this review.
Thanks for your patience, @nbeliy, and thank you @TheChymera and @PeerHerholz for your engagement in reviewing Bidsme to date !
@emdupre , thanks)
@emdupre sorry for the delay. I believe all points have been addressed, and I have updated the checklist.
Thank you for confirming, @TheChymera !
I'll perform a few editorial checks now that both reviewers have signed off.
@editorialbot generate pdf
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@editorialbot check references
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1038/sdata.2016.44 is OK
- 10.3389/fninf.2021.770608 is OK
- 10.1016/j.jneumeth.2016.03.001 is OK
MISSING DOIs
- None
INVALID DOIs
- None
A few editorial comments on the software paper :
Major comments
bidsme
relates to existing other BIDS-formatting tools such as Heudiconv and dcm2bids. This falls under the "State of the field" review criteria.Minor comments
Thanks, @emdupre , will do it asap
π Hi everyone, just a small note that I will be out-of-office 30 October - 10 November. I will answer any comments or questions as soon as I'm back, though, so please don't hesitate to ping this thread.
Hi @nbeliy, I'm back in office and just wanted to check in on this ! Have you had a chance to integrate the recommended changes for the software paper ?
Hi @emdupre ,
I did the smaller changes but got quite charged last weeks to compare tools. I'll regenerate the draft, can you check if the figure is readable now?
@editorialbot generate pdf
@editorialbot generate pdf
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Hi @nbeliy, the figure does look more legible, thank you ! Please let me know when you've finished making the other requested changes and I can continue processing the submission.
Also just to note: Editorial Bot only responds if the command is at the start of a GitHub comment. Apologies for any confusion !
@editorialbot generate pdf
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@emdupre
Major comments
* In the software paper _Statement of Need_, it would be useful to directly explain how `bidsme` relates to existing other BIDS-formatting tools such as [Heudiconv](https://heudiconv.readthedocs.io/en/latest/) and [dcm2bids](https://unfmontreal.github.io/Dcm2Bids/3.1.1/). This falls under the "State of the field" review criteria.
bidsme
addresses. I think it suits more the flow of paper. But if direct comparison is needed, I can rearrange these paragraphs.Minor comments
- Please capitalize BIDS when it appears as an acronym, outside of Bidsme. See L51, L62, etc.
bidsification
? BIDSification looks ugly for me, but I don't know the rules for derivative words from acronyms.* L7, L22: Please note that the correct name for BIDS is "Brain Imaging Data Structure" rather than "Brain Image Data Structure". Please update this throughout.
* L28: Please change ", i.e." should be updated to "; i.e.,". This update also holds for other abbreviations like "e.g." on L33, L37, L42,
i.e.
without comma.* L74. Please standardize "plug-in" to "plugin" as used on L75, or vice versa. Regardless, please review the text to ensure consistent spelling of this term.
* L99. "developed basing on" --> "developed based on"
done
* In Fig 1., the text under "source, "prepared," and "bidisifed" datasets listing the directory structures is difficult to read. Could you please increase the font size, likely by showing fewer files ?
done
Thank you, @nbeliy !
I capitalized BIDS, but should I also capitalize bidsification? BIDSification looks ugly for me, but I don't know the rules for derivative words from acronyms.
I would make these more explicit ; for example, "BIDS-ificiation" and "BIDS-ify." This is also more likely to avoid confusion e.g., with the bidsify
tool.
Just for myself, this comma is purely stylistic? I often seen i.e. without comma.
This is the correct in American style guides, which JOSS follows.
EDIT : And I did notice one additional small formatting issue, apologies. Could you please also correct Brain Imaging Data Structure (BIDS) (Gorgolewski et al., 2016)
to Brain Imaging Data Structure (BIDS; Gorgolewski et al., 2016)
? This should be possible by changing your text to [BIDS; @Gorgolewski2016]
in the Summary and Statement of Need.
After making these changes, could you then please:
@editorialbot generate pdf
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The tagged version: 1.5.0
The archived version on zenodo:
@editorialbot set 1.5.0 as version
Submitting author: !--author-handle-->@nbeliy<!--end-author-handle-- (Nikita Beliy) Repository: https://github.com/CyclotronResearchCentre/bidsme Branch with paper.md (empty if default branch): joss_paper Version: 1.5.0 Editor: !--editor-->@emdupre<!--end-editor-- Reviewers: @PeerHerholz, @TheChymera Archive: 10.5281/zenodo.10185300
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@PeerHerholz & @TheChymera, 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:
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