[REVIEW]: AtlasReader: A Python package to generate coordinate tables, region labels, and informative figures from statistical MRI images

[whedon]

Submitting author: @miykael (Michael Philipp Notter)
Repository: https://github.com/miykael/atlasreader
Version: v0.1.0
Editor: @cMadan
Reviewer: @andrewheusser
Archive: 10.5281/zenodo.2575731

Status

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Reviewers and authors:

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Reviewer instructions & questions

@andrewheusser, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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The reviewer guidelines are available here: https://joss.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @cMadan know.

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @andrewheusser

Conflict of interest

• As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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?
• Version: v0.1.0
• Authorship: Has the submitting author (@miykael) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 function 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

• Authors: Does the paper.md file include a list of authors with their affiliations?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @andrewheusser it looks like you're currently assigned as the reviewer for this paper 🎉.

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

@whedon commands

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[andrewheusser]

hey @cMadan - I finished the review and the author sufficiently addressed all of my concerns (see here. The author implemented the changes on a branch, but they are not yet merged. What are the next steps?

[cMadan]

@andrewheusser, thank you for the prompt and thorough review! It looks like you're all done.

For @miykael, the next steps are to merge these changes and confirm that you think it's ready to be accepted. Then I'll look everything over and check that I agree. If that's the case, I'll then ask for the DOI of an archived copy of the code and what version of the software corresponds to the code after the revisions related to the review--and then we're all set!

[miykael]

Thank you @andrewheusser for the very nice and helpful feedback! Your comments were much appreciated and helped to improve the toolbox.

@cMadan - I've merged the changes, created a new GitHub release and a new PyPi release. So, the current version number is now v0.1.0. In my opinion (and this of the co-authors), the toolbox is ready to be accepted. Can I update the version number in the JOSS publication or is that up to you? Is there anything else that I can help with?

[miykael]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[miykael]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[miykael]

I apologize for the repeated @whedon commands, but I try to get the paper output to the right format. But the next "PDF generation" should be the last.

[miykael]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[miykael]

Sorry, found a small typo in the references. But otherwise, everything is good to go.

[miykael]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[andrewheusser]

my pleasure, nice job on the package!

[cMadan]

@whedon set v0.1.0 as version

[whedon]

OK. v0.1.0 is the version.

[cMadan]

@whedon set 10.5281/zenodo.2575731 as archive

[whedon]

OK. 10.5281/zenodo.2575731 is the archive.

[cMadan]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Check final proof 👉 openjournals/joss-papers#518

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#518, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[whedon]

OK DOIs

- http://doi.org/10.1109/MCSE.2007.55 is OK
- http://doi.org/10.1016/j.neuroimage.2010.07.033 is OK
- http://doi.org/10.5281/zenodo.1287921 is OK
- http://doi.org/10.3389/fninf.2014.00014 is OK
- http://doi.org/10.1109/MCSE.2007.58 is OK
- http://doi.org/10.7717/peerj.453 is OK

MISSING DOIs

- https://doi.org/10.1017/cbo9781139871754.008 may be missing for title: SciPy: Open source scientific tools for Python
- https://doi.org/10.3389/fninf.2014.00014 may be missing for title: Scikit-learn: Machine learning in Python

INVALID DOIs

- None

[cMadan]

I think those missing DOIs aren't correct here, they are related but more tutorial to the packages than for the packages per se. As discussed in the review (miykael/atlasreader#105), I think there aren't DOIs for those references.

@miykael, you're all set congratulations! @andrewheusser, thank you again for the thorough review.

@arfon, can you do the honors?

[arfon]

@arfon, can you do the honors?

Done. The proof I generated locally ended up doing a slightly better job with figure layout so I processed the paper manually.

@andrewheusser - many thanks for your review here and to @cMadan for editing this submission ✨

@miykael - your paper is now accepted into JOSS ⚡🚀💥

[whedon]

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

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HTML:
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  <img src="http://joss.theoj.org/papers/10.21105/joss.01257/status.svg" alt="DOI badge" >
</a>

reStructuredText:
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   :target: https://doi.org/10.21105/joss.01257

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[miykael]

@andrewheusser - thank you again for your great review!

@cMadan - thank you for your work and accepting the paper.

@arfon - thank you for changing the figure layout. It's now exactly how I wanted it.

[andrewheusser]

👍 my pleasure