[REVIEW]: Bidsme: expandable bidsifier of brain imagery datasets

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@nbeliy@emdupre<!--end-editor-- Reviewers: @PeerHerholz, @TheChymera Archive: 10.5281/zenodo.10185300

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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

@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:

@editorialbot generate my checklist

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

📝 Checklist for @TheChymera

editorialbot commented 1 year ago

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editorialbot commented 1 year ago

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

editorialbot commented 1 year ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.13 s (718.8 files/s, 130337.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
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
-------------------------------------------------------------------------------
SUM:                            91           2186           4789           9526
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 1 year ago

Wordcount for paper.md is 1421

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:

emdupre commented 1 year ago

👋 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 !

emdupre commented 1 year ago

👋 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 !

PeerHerholz commented 1 year ago

Hi @emdupre,

sorry for the delay. I'm starting the review process now!

PeerHerholz commented 1 year ago

Review checklist for @PeerHerholz

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 JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/CyclotronResearchCentre/bidsme?
[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 (@nbeliy) 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
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] 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: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
[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?

emdupre commented 1 year ago

👋 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 !

TheChymera commented 1 year ago

@emdupre thanks for pinging me.

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest 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 JOSS 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 made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] 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: Does the paper have a section titled ‘Statement of need’ that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
[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?

emdupre commented 1 year ago

👋 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.

nbeliy 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:

nbeliy 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:

emdupre commented 1 year ago

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 !

nbeliy commented 1 year ago

Hi @emdupre,

I think I've addressed the majority of issues of reviewers, and now waiting to their return.

emdupre commented 1 year ago

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 ?

emdupre commented 1 year ago

Hi everyone, and happy Monday ! 🌻

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 !

PeerHerholz commented 1 year ago

Hi @emdupre,

sorry for the slow response. I updated the checklist and I think all points are addressed now.

emdupre commented 1 year ago

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 !

emdupre commented 1 year ago

👋 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.

emdupre commented 1 year ago

Hi @TheChymera, just another nudge on this. If you have any questions, please don't hesitate to let me know !

emdupre commented 1 year ago

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 !

nbeliy commented 1 year ago

@emdupre , thanks)

TheChymera commented 1 year ago

@emdupre sorry for the delay. I believe all points have been addressed, and I have updated the checklist.

emdupre commented 1 year ago

Thank you for confirming, @TheChymera !

I'll perform a few editorial checks now that both reviewers have signed off.

emdupre 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:

emdupre 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

- 10.1038/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

emdupre commented 1 year ago

A few editorial comments on the software paper :

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 and dcm2bids. This falls under the "State of the field" review criteria.

Minor comments

Please capitalize BIDS when it appears as an acronym, outside of Bidsme. See L51, L62, etc.
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,
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"
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 ?

nbeliy commented 12 months ago

Thanks, @emdupre , will do it asap

emdupre commented 12 months ago

👋 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.

emdupre commented 11 months ago

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 ?

nbeliy commented 11 months ago

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

emdupre commented 11 months ago

@editorialbot generate pdf

editorialbot commented 11 months ago

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

emdupre commented 11 months ago

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 !

nbeliy commented 11 months ago

@editorialbot generate pdf

editorialbot commented 11 months ago

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

nbeliy commented 11 months ago

@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.

Done, added reference to 3 tools (2 that you mentioned and one for PET). It's not direct comparison but statement of issues that 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.

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.

* 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.

done

* 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,

done. Just for myself, this comma is purely stylistic? I often seen 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.

done.

* 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

emdupre commented 11 months ago

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.

emdupre commented 11 months ago

After making these changes, could you then please:

[x] Make a tagged release of your software, and list the version tag of the archived version here.
[x] Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
[x] Check the archival deposit (e.g., in Zenodo) has the correct metadata (e.g., the JOSS paper and software archive have the same title and author listing)
[x] List the DOI of the archived version here.

nbeliy commented 11 months ago

Dear @emdupre,

I made a release 1.5.0, and uploaded on zendoo. Waiting the co-authors to check.

For the change of reference, I would need your help: changing to [BIDS; @Gorgolewski2016] made it appear in text as [BIDS; Gorgolewski(2016)], see here.

nbeliy commented 11 months ago

@editorialbot generate pdf

editorialbot commented 11 months ago

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

nbeliy commented 11 months ago

The tagged version: 1.5.0

The archived version on zenodo:

10.5281/zenodo.10185300 -- for 1.5.0;
10.5281/zenodo.7524615 -- for all versions.

emdupre commented 10 months ago

@editorialbot set 1.5.0 as version

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