[REVIEW]: BIDSonym - a BIDSapp for the pseudo-anonymization of neuroimaging datasets

[whedon]

Submitting author: @PeerHerholz (Peer Herholz)
Repository: https://github.com/PeerHerholz/BIDSonym/
Version: v0.0.5
Editor: @oliviaguest
Reviewer: @deep-introspection, @chrisgorgo, @neuromusic
Archive: 10.5281/zenodo.5301625

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Status

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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 @deep-introspection

Conflict of interest

• 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

• I confirm that I read and will adhere to the JOSS 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?
• Contribution and authorship: Has the submitting author (@PeerHerholz) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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 functionality 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

Software paper

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• 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 and who the target audience is?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• 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?

Review checklist for @chrisgorgo

Conflict of interest

• 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

• I confirm that I read and will adhere to the JOSS 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?
• Contribution and authorship: Has the submitting author (@PeerHerholz) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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 functionality 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

Software paper

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• 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 and who the target audience is?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• 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?

Review checklist for @neuromusic

Conflict of interest

• 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

• I confirm that I read and will adhere to the JOSS 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?
• Contribution and authorship: Has the submitting author (@PeerHerholz) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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 functionality 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

Software paper

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• 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 and who the target audience is?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• 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?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @deep-introspection, @chrisgorgo, @neuromusic 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/openjournals/joss-reviews) 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/openjournals/joss-reviews:

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]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.46 s (80.8 files/s, 12595.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                           9            617           1352           1843
reStructuredText                17            285            164            594
TeX                              2             31              0            450
Bourne Shell                     1              6              7             90
Dockerfile                       1             23              8             87
Markdown                         3             30              0             82
YAML                             2              3              4             33
DOS Batch                        1              8              1             27
make                             1              4              6             10
-------------------------------------------------------------------------------
SUM:                            37           1007           1542           3216
-------------------------------------------------------------------------------


Statistical information for the repository '9a988fc8cf4b9daac67b8233' was
gathered on 2021/04/12.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Peer Herholz                    16           981             43            8.59
PeerHerholz                     68          6882           4008           91.34
rxqx                             1             4              4            0.07

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
PeerHerholz                3812           55.4         17.5               13.93

[whedon]

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

OK DOIs

- 10.1002/hbm.20312 is OK
- 10.1038/sdata.2016.44 is OK
- 10.1371/journal.pcbi.1005209 is OK
- 10.1016/j.neuroimage.2015.05.073 is OK
- 10.3389/fninf.2013.00012 is OK
- 10.1038/nn.4500 is OK
- 10.3389/fninf.2012.00009 is OK
- 10.1016/j.neuroimage.2015.10.079 is OK
- 10.1016/j.neuroimage.2013.02.040 is OK
- 10.1038/nn.3818 is OK
- 10.31234/osf.io/f6mnp is OK
- 10.1371/journal.pmed.1001779 is OK
- 10.1016/j.neuroimage.2013.05.041 is OK
- 10.1038/mp.2013.78 is OK
- 10.1016/j.nic.2005.09.008 is OK
- 10.1371/journal.pone.0177459 is OK
- 10.5281/zenodo.3757992 is OK
- 10.3389/fninf.2011.00013 is OK
- 10.3389/fninf.2014.00014 is OK
- 10.21105/joss.01294 is OK

MISSING DOIs

- 10.25080/majora-92bf1922-00a may be a valid DOI for title: Data structures for statistical computing in python

INVALID DOIs

- None

[whedon]

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

[oliviaguest]

Hi all! 👋 Thank you so much, @deep-introspection, @chrisgorgo, @neuromusic for accepting to review this. Please read the instructions above. If you have trouble ticking things off in the list above, remember you need to click to "accept" here: https://github.com/openjournals/joss-reviews/invitations! Any questions, feedback on the paper, etc., please post here. Any very code-specific questions, suggestions, etc., please use the issues in the code repo and link to them from this thread, so we can all keep track of them.

For examples of how this process plays out feel free to skim previous reviews, such as: #2285 and #2348. ☺️

[oliviaguest]

Hey, @deep-introspection, @chrisgorgo, @neuromusic — when you get a sec, can you three please drop me your ETAs for your reviews here? Thanks! 🌸

[deep-introspection]

Hey! Was aiming at next Monday since got a bunch of deadlines for this Friday.

[whedon]

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

[whedon]

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

[whedon]

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

[chrisgorgo]

I recommend accepting the submissions as is. Many thanks to everyone who contributed to the package.

[deep-introspection]

Ok, same here! Congratulations to the team for this very nice contribution.

[oliviaguest]

Thank you @chrisgorgo and @deep-introspection — you two have been so speedy! @neuromusic let us know on a sensible/workable ETA for your review, please! 🌼

[neuromusic]

so sorry for the delay, I'll get me review in this week 😄

[oliviaguest]

@whedon remind @neuromusic in 1 week

[whedon]

Reminder set for @neuromusic in 1 week

[oliviaguest]

@neuromusic thanks! I set up a reminder as a soft ETA. 😊

[whedon]

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

[whedon]

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

OK DOIs

- 10.1002/hbm.20312 is OK
- 10.1038/sdata.2016.44 is OK
- 10.1371/journal.pcbi.1005209 is OK
- 10.1016/j.neuroimage.2015.05.073 is OK
- 10.3389/fninf.2013.00012 is OK
- 10.1038/nn.4500 is OK
- 10.3389/fninf.2012.00009 is OK
- 10.1016/j.neuroimage.2015.10.079 is OK
- 10.1016/j.neuroimage.2013.02.040 is OK
- 10.1038/nn.3818 is OK
- 10.31234/osf.io/f6mnp is OK
- 10.1371/journal.pmed.1001779 is OK
- 10.1016/j.neuroimage.2013.05.041 is OK
- 10.1038/mp.2013.78 is OK
- 10.1016/j.nic.2005.09.008 is OK
- 10.1371/journal.pone.0177459 is OK
- 10.5281/zenodo.3757992 is OK
- 10.3389/fninf.2011.00013 is OK
- 10.3389/fninf.2014.00014 is OK
- 10.21105/joss.01294 is OK

MISSING DOIs

- 10.25080/majora-92bf1922-00a may be a valid DOI for title: Data structures for statistical computing in python

INVALID DOIs

- None

[whedon]

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#2544

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2544, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[danielskatz]

@PeerHerholz - please add the missing DOI that whedon suggests, unless you think it's incorrect.

[danielskatz]

Also, please remove the abstract field from any references that do not have DOIs, as these get copied into unstructured metadata that is sent to crossref for for such references, which isn't needed.

[danielskatz]

Also, in the caption of Figure 1, there's one "meta-data" left that I missed - this should be changed to "metadata"

[danielskatz]

And for the McKinney reference in the bib file, please change the "Python" in the title to "{P}ython" to preserve the correct case for the P.

[PeerHerholz]

Hi @danielskatz,

sorry for all these missed little things.

I added the missing DOI, removed the abstract field from references that don't have a DOI, adapted the caption and changed the title of the McKinney reference. I hope everything is ok now.

Thanks again, best, Peer

[PeerHerholz]

@whedon generate pdf

[whedon]

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

[danielskatz]

@whedon recommend-accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1002/hbm.20312 is OK
- 10.1038/sdata.2016.44 is OK
- 10.1371/journal.pcbi.1005209 is OK
- 10.1016/j.neuroimage.2015.05.073 is OK
- 10.3389/fninf.2013.00012 is OK
- 10.1038/nn.4500 is OK
- 10.3389/fninf.2012.00009 is OK
- 10.1016/j.neuroimage.2015.10.079 is OK
- 10.1016/j.neuroimage.2013.02.040 is OK
- 10.1038/nn.3818 is OK
- 10.31234/osf.io/f6mnp is OK
- 10.1371/journal.pmed.1001779 is OK
- 10.1016/j.neuroimage.2013.05.041 is OK
- 10.1038/mp.2013.78 is OK
- 10.1016/j.nic.2005.09.008 is OK
- 10.1371/journal.pone.0177459 is OK
- 10.5281/zenodo.3757992 is OK
- 10.3389/fninf.2011.00013 is OK
- 10.3389/fninf.2014.00014 is OK
- 10.21105/joss.01294 is OK
- 10.25080/Majora-92bf1922-00a is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#2545

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2545, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[danielskatz]

@whedon accept deposit=true

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

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

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.03169 joss-papers#2546
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03169
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[danielskatz]

Congratulations to @PeerHerholz (Peer Herholz) and co-authors!!

And thanks to @oliviaguest for editing,
and @deep-introspection, @chrisgorgo, and @neuromusic for reviewing!

We couldn't do this without you!

[whedon]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.03169/status.svg)](https://doi.org/10.21105/joss.03169)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03169">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03169/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03169/status.svg
   :target: https://doi.org/10.21105/joss.03169

This is how it will look in your documentation:

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Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

• Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://joss.theoj.org/reviewer-signup.html
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[jbpoline]

Congratulations to @PeerHerholz (Peer Herholz) and co-authors!!

And thanks to @oliviaguest for editing,
and @deep-introspection, @chrisgorgo, and @neuromusic for reviewing!

We couldn't do this without you!

Thanks a lot @danielskatz !