Joss-reviews: [REVIEW]: medical image visualization library in python

[whedon]

Submitting author: @raamana (Pradeep Reddy Raamana)
Repository: https://github.com/raamana/mrivis
Version: 0.3
Editor: @arokem
Reviewer: @miykael
Archive: 10.5281/zenodo.1450944

Status

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Markdown: [![status](http://joss.theoj.org/papers/06f56034fa3b4c012f96dcba17167b69/status.svg)](http://joss.theoj.org/papers/06f56034fa3b4c012f96dcba17167b69)

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

@miykael, 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 @arokem know.

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

Review checklist for @miykael

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: Does the release version given match the GitHub release (0.3)?
• [x] Authorship: Has the submitting author (@raamana) 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. @miykael 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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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 :page_facing_up: <--

[raamana]

Hi @miykael, the docs website is ready for you to provide a sense of what it is. I am finalizing the implementation for one another class Carpet, but what it is now should give you a very good sense of what's happening.

[raamana]

It should be ready now, I believe.

[miykael]

Perfect! I have a conference and workshop coming up in the next 10 days but will start reviewing in the time between and finalize the review shortly after.

[raamana]

No problem. I plan to add an example notebook for Carpet class shortly, the docs already (API etc) should give you a good idea.

[arokem]

@raamana : is this ready for a review? It seems like you are still working on some things?

[raamana]

Yes it is. Sorry I should have made that explicit.

[arokem]

@miykael: have you had a chance to take a look?

[miykael]

@arokem and @raamana I apologize for my late reply, I had an unforeseen hectic two weeks. But the review has now my full attention!

The software looks very good and useful and I will write my full review in the issue tracker of https://github.com/raamana/mrivis. But I think the repo is missing a paper.md file (as mentioned
in the author guidlines), or is this optional?

[raamana]

thanks - looking fwd to learn your comments.

its in the docs folder, as required : https://github.com/raamana/mrivis/blob/master/docs/paper.md

[miykael]

@raamana and @arokem - my review can be found under https://github.com/raamana/mrivis/issues/11. @raamana, don't hesitate to ask for clarification!

[miykael]

@arokem - the review under https://github.com/raamana/mrivis/issues/11 is finished. @raamana corrected all relevant issues and the software is in my opinion ready for publication. What are the next steps?

[raamana]

Thanks Michael for a thorough and a helpful review, appreciate it.

Ariel, this is the final DOI for this version: 10.5281/zenodo.1443427

[raamana]

Just pushed the latest code to pypi also! :)

[arokem]

Thanks @miykael for the excellent review! 👏 Your work is done here...

[arokem]

@whedon set 10.5281/zenodo.1443427 as archive

[whedon]

OK. 10.5281/zenodo.1443427 is the archive.

[arokem]

@raamana : sorry - a couple of things I noticed about your article just now:

• The title is not capitalized. I don't think that you want every word in the title to be capitalized, but the very first word probably should be. Also, the title currently doesn't include the name of the software library. I would recommend adding that.

• The references do not have DOIs. Please add these.

[raamana]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[raamana]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[raamana]

Good catch - fixed them now.

[arokem]

Thanks for doing that. Would you mind creating a new Zenodo DOI?

[raamana]

Sure - it is 10.5281/zenodo.1450944

[arokem]

@whedon set 10.5281/zenodo.1450944 as archive

[whedon]

OK. 10.5281/zenodo.1450944 is the archive.

[arokem]

@arfon : I believe that this paper is ready to be accepted!

[arfon]

@miykael - many thanks for your review here and to @arokem for editing this submission ✨

@raamana - your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00897 :zap: :rocket: :boom:

[whedon]

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

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

Markdown:
[![DOI](http://joss.theoj.org/papers/10.21105/joss.00897/status.svg)](https://doi.org/10.21105/joss.00897)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.00897">
  <img src="http://joss.theoj.org/papers/10.21105/joss.00897/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.00897/status.svg
   :target: https://doi.org/10.21105/joss.00897

This is how it will look in your documentation:

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