[REVIEW]: MRdataset: A unified and user-friendly interface to medical imaging datasets

[editorialbot]

Submitting author: @sinhaharsh (Harsh Sinha)
Repository: https://github.com/Open-Minds-Lab/MRdataset
Branch with paper.md (empty if default branch): joss
Version: 0.4.4
Editor: @mstimberg
Reviewers: @htwangtw, @djmannion
Archive: 10.5281/zenodo.10805061

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/1b9ca51a9cc20b3e98f26e598c09c381/status.svg)](https://joss.theoj.org/papers/1b9ca51a9cc20b3e98f26e598c09c381)

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

@htwangtw & @djmannion, 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 @mstimberg 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 @htwangtw

📝 Checklist for @djmannion

[editorialbot]

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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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.13 s (379.7 files/s, 40617.2 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
Python                           22            574           1048           1719
XML                               1              0              0            389
reStructuredText                 11            141            100            189
TeX                               1             12              0            124
Jupyter Notebook                  1              0            399            120
make                              3             37              6            100
YAML                              2              7              9             77
JSON                              2              0              0             71
TOML                              1              8              0             56
Markdown                          2             25              0             53
INI                               1              5              3             30
DOS Batch                         1              8              1             27
Bourne Again Shell                1              5              0              5
HTML                              1              0              0              1
--------------------------------------------------------------------------------
SUM:                             50            822           1566           2961
--------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

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

OK DOIs

- 10.5281/zenodo.7795644 is OK
- 10.21105/joss.01294 is OK
- 10.3389/fninf.2017.00017 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

Wordcount for paper.md is 1022

[editorialbot]

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

[mstimberg]

👋🏼 @sinhaharsh, @raamana, @htwangtw, @djmannion, this is the review thread for the paper. All of our communications will happen here from now on. Looking forward to an enjoyable and constructive review 😊

As a reviewer, the first step is to create a checklist for your review by entering

@editorialbot generate my checklist

at the top of a new comment in this thread.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#6269 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them, instead of waiting until you've reviewed the entire package.
There are additional guidelines in the message at the start of this issue.

Please feel free to ping me (@mstimberg) if you have any questions/concerns.

[raamana]

thanks again everyone!

ignore my previous comment - I mistook # blank lines to be # blank files.

[htwangtw]

Review checklist for @htwangtw

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 https://github.com/Open-Minds-Lab/MRdataset?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@sinhaharsh) 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
• 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.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• 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

• 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, who the target audience is, and its relation to other work?
• 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?

[djmannion]

Review checklist for @djmannion

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 https://github.com/Open-Minds-Lab/MRdataset?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@sinhaharsh) 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
• 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.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• 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

• 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, who the target audience is, and its relation to other work?
• 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?

[mstimberg]

Many thanks @htwangtw for your feedback so far.
@djmannion could you give me a rough estimate when you will be able to have a look at the MRdataset software/paper? Of course, if there is anything unclear about the process, please don't hesitate to ask for help or clarifications!

[djmannion]

@mstimberg I'll likely get to it within the next few days - certainly within the next week.

[mstimberg]

@djmannion Great, thanks.

[mstimberg]

Dear @htwangtw and @djmannion, many thanks for your feedback and the issues that you opened. Do you feel that all your concerns have now been sufficiently addressed to recommend acceptance?
@sinhaharsh are you still working on any of the raised issues or are you only waiting for feedback from the reviewers before closing them? From what I can see, some of the "open" issues seem to have been resolved already.

[sinhaharsh]

Thank you @mstimberg . We have addressed the previous issues and we are planning to make a new release in the next few days incorporating all the feedback/issues from the reviewers.

The past issues/feedback by @djmannion and @htwangtw have helped us enhance our library. We kindly request the reviewers to report any new issues they may have, so that we can address them before the new release.

[htwangtw]

@sinhaharsh thank you for your patience - I will have time to have a closer look on the week commencing 4th of March the latest!

[djmannion]

I have had a look at the responses to the issues that I have raised and I am satisfied that they are either resolved in their current state or are fine to be left to the author's judgement. My review is complete and my concerns have been sufficiently addressed to recommend acceptance.

[raamana]

Thanks a lot Damien for your time and constructive feedback, and helping support the open source software ecosystem.

[htwangtw]

I am happy with the changes - the final comment is that you can omit the test data for basic installation to reduce the size of the package, and leave the data for a dev or full installation. It's up to you :)

[editorialbot]

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

[mstimberg]

@editorialbot set 10.5281/zenodo.10805061 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.10805061

[sinhaharsh]

Tags are now updated on Github

[mstimberg]

@editorialbot set 0.4.4 as version

[editorialbot]

Done! version is now 0.4.4

[mstimberg]

All looks good from my side, handing over things to an EiC for the final checks and publication steps 👋

[mstimberg]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1101/2023.07.17.548591 is OK
- 10.5281/zenodo.7795644 is OK
- 10.21105/joss.01294 is OK
- 10.3389/fninf.2017.00017 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#5118, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[Kevin-Mattheus-Moerman]

@sinhaharsh as AEiC I will now help process the final steps for acceptance in JOSS. I have checked this review, the repository, the paper, and the archive link. All seems in order so I will now proceed with acceptance in JOSS. However, I do have the below recommendations in relation to your repository (these are not required changes for JOSS, merely recommendations).

• I recommend that you edit your plain LICENSE file to confirm to the standard Apache text as I think currently this is causing GitHub not to recognise the license and render the name here properly:
  
• It may be good to extend your README.md file further, e.g. extend the description slightly, and consider adding short headings/sections on Documentation, Testing, Contributing (to link to your contributing file, although I see your documentation does too, I just expect this information in a README too), and the License (linking to the license file). On the documentation and the license, you could consider adding a license and a documentation badge as many projects do, this way these are clear at the top too. Again, just suggestions to make the README feel/look more complete especially to new users seeing your project.

[Kevin-Mattheus-Moerman]

@editorialbot accept

[editorialbot]

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

[editorialbot]

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Sinha
  given-names: Harsh
  orcid: "https://orcid.org/0000-0002-8498-8559"
- family-names: Raamana
  given-names: Pradeep Reddy
  orcid: "https://orcid.org/0000-0003-4662-0558"
doi: 10.5281/zenodo.10805061
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Sinha
    given-names: Harsh
    orcid: "https://orcid.org/0000-0002-8498-8559"
  - family-names: Raamana
    given-names: Pradeep Reddy
    orcid: "https://orcid.org/0000-0003-4662-0558"
  date-published: 2024-03-21
  doi: 10.21105/joss.06269
  issn: 2475-9066
  issue: 95
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6269
  title: "MRdataset : A unified and user-friendly interface to medical
    imaging datasets"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06269"
  volume: 9
title: "MRdataset : A unified and user-friendly interface to medical
  imaging datasets"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

[editorialbot]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

🚨🚨🚨 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.06269 joss-papers#5156
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06269
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...

[raamana]

Thank you Kevin - the old license text is likely a result of a template generator, and carried over through the years, just changed it. we will get the rest done.

[Kevin-Mattheus-Moerman]

@sinhaharsh @raamana congratulations on this JOSS publication!

Thanks for editing @mstimberg !!!
And a special thank you to the reviewers: @htwangtw, @djmannion !!!!

[editorialbot]

🎉🎉🎉 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.06269/status.svg)](https://doi.org/10.21105/joss.06269)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06269">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06269/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06269/status.svg
   :target: https://doi.org/10.21105/joss.06269

This is how it will look in your documentation:

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