[REVIEW]: medical image visualization library in python

whedon commented 6 years ago

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

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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 commented 6 years ago

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:.

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whedon commented 6 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 6 years ago

--> Check article proof :page_facing_up: <--

raamana commented 6 years ago

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 commented 6 years ago

It should be ready now, I believe.

miykael commented 6 years ago

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 commented 6 years ago

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 commented 6 years ago

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

raamana commented 6 years ago

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

arokem commented 6 years ago

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

miykael commented 6 years ago

@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 commented 6 years ago

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 commented 6 years ago

@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 commented 6 years ago

@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 commented 6 years ago

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 commented 6 years ago

Just pushed the latest code to pypi also! :)

arokem commented 6 years ago

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

arokem commented 6 years ago

@whedon set 10.5281/zenodo.1443427 as archive

whedon commented 6 years ago

OK. 10.5281/zenodo.1443427 is the archive.

arokem commented 6 years ago

@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 commented 6 years ago

@whedon generate pdf

whedon commented 6 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 6 years ago

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

raamana commented 6 years ago

@whedon generate pdf

whedon commented 6 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 6 years ago

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

raamana commented 6 years ago

Good catch - fixed them now.

arokem commented 6 years ago

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

raamana commented 6 years ago

Sure - it is 10.5281/zenodo.1450944

arokem commented 6 years ago

@whedon set 10.5281/zenodo.1450944 as archive

whedon commented 6 years ago

OK. 10.5281/zenodo.1450944 is the archive.

arokem commented 6 years ago

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

arfon commented 6 years ago

@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 commented 6 years ago

: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:
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  <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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