Joss-reviews: [REVIEW]: 3D ultrasound file reading and coordinate transformations

[whedon]

Submitting author: @plooney (Padraig Looney)
Repository: https://github.com/plooney/kretz
Version: v1.1
Editor: @cMadan
Reviewer: @thewtex
Archive: 10.5281/zenodo.2537876

Status

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Markdown: [![status](http://joss.theoj.org/papers/7a2fedfa7961977f015743ad287542b6/status.svg)](http://joss.theoj.org/papers/7a2fedfa7961977f015743ad287542b6)

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) 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

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

1. Make sure you're logged in to your GitHub account
2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

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 @thewtex

Conflict of interest

• [x] 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

• [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] Version: v1.1
• [x] Authorship: Has the submitting author (@plooney) 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 function 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] Authors: Does the paper.md file include a list of authors with their affiliations?
• [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] 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. @thewtex it looks like you're currently assigned as the reviewer for this paper :tada:.

:star: Important :star:

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:

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[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[thewtex]

License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?

https://github.com/plooney/kretz/issues/1 created to clarify / standardize the license file.

[thewtex]

Version: Does the release version given match the GitHub release (0.01)?

https://github.com/plooney/kretz/issues/2 created to create a GitHub release. It may be desirable to address other review items before creating this release.

[thewtex]

Installation: Does installation proceed as outlined in the documentation?

Generally, yes, but a few minor issues identified:

• https://github.com/plooney/kretz/issues/4
• https://github.com/plooney/kretz/issues/5

[thewtex]

Functionality: Have the functional claims of the software been confirmed?

Testing functionality, it works very well. I ran the tests, and I also tried on a non-test local dataset. Some screenshots of the result created with itk-vtk-viewer

[thewtex]

Functionality: Have the functional claims of the software been confirmed?

https://github.com/plooney/kretz/issues/8 created to enable use as a library.

[thewtex]

Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?

There is Doxygen documentation and the naming of classes and methods are information.

A few items to improve with the command line programs:

• https://github.com/plooney/kretz/issues/6
• https://github.com/plooney/kretz/issues/7

[thewtex]

References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

• Minor correction required: https://github.com/plooney/kretz/issues/10

[thewtex]

@cMadan @plooney review complete.

I apologize again for the tardiness of the review.

@plooney the code looks outstanding, and this is a valuable contribution for ultrasound research. Thank you for sharing this work.

[cMadan]

@thewtex, thank you for the thorough review!

@plooney, please let us know after you have have revised the project based on the reviewer feedback.

[plooney]

@cMadan

Thanks for the comments @thewtex. I have tried to address all the points, I struggled to get the two of the issues resolved fully; ITK Module and CI.

[thewtex]

@plooney looking good.

Please review and fix up this PR as required:

https://github.com/plooney/kretz/pulls/12

which should how to format as an ITK Module to use as a library and adds CI configuration.

One other item is to tag the repository.

[thewtex]

@cMadan I believe all review items are now complete!

[cMadan]

@thewtex, great, thank you for all your work in reviewing this!

@plooney, I will do a final proof to make sure everything looks good and comment again shortly.

[cMadan]

@whedon set v1.0 as version

[whedon]

OK. v1.0 is the version.

[cMadan]

@plooney, can you deposit the current code on Zenodo or figshare and tell me the corresponding doi?

[plooney]

@cMadan I have deposited it on Zenodo. The DOI is

DOI: 10.5281/zenodo.2537876

https://zenodo.org/account/settings/github/repository/plooney/kretz

[plooney]

I changed the tag to v1.1 to include the latest commit with all the responses to the review.

[cMadan]

@whedon set v1.1 as version

[whedon]

OK. v1.1 is the version.

[cMadan]

@whedon set 10.5281/zenodo.2537876 as archive

[whedon]

OK. 10.5281/zenodo.2537876 is the archive.

[cMadan]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/429

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/429, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true

[cMadan]

@whedon accept deposit=true

[whedon]

I'm sorry @cMadan, I'm afraid I can't do that. That's something only editor-in-chiefs are allowed to do.

[cMadan]

@arfon @danielskatz, we're all set to accept here!

[arfon]

@whedon accept deposit=true

[whedon]

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

[whedon]

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

Here's what you must now do:

1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/430
2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01063
3. If everything looks good, then close this review issue.

4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

   Any issues? notify your editorial technical team...

[arfon]

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

@plooney - your paper is now accepted into JOSS :zap::rocket::boom:

[whedon]

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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