Joss-reviews: [REVIEW]: mbir: Magnitude-Based Inferences

[whedon]

Submitting author: @kdpeterson51 (Kyle Peterson)
Repository: https://github.com/kdpeterson51/mbir
Version: 1.3
Editor: @arfon
Reviewer: @kellieotto
Archive: 10.5281/zenodo.2546910

Status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/ff46731883f6f27042a27fc970f3b150"><img src="http://joss.theoj.org/papers/ff46731883f6f27042a27fc970f3b150/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/ff46731883f6f27042a27fc970f3b150/status.svg)](http://joss.theoj.org/papers/ff46731883f6f27042a27fc970f3b150)

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

@kellieotto, 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 @leeper know.

Review checklist for @kellieotto

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 (1.3)?
• [x] Authorship: Has the submitting author (@kdpeterson51) 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. I'm here to help you with some common editorial tasks. @kellieotto 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:

1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

1. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

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: <--

[kellieotto]

I've done a first review. The version and automated tests need attention. I'm leaving detailed feedback in the repository issues.

[leeper]

Excellent. Thank you, @kellieotto!

[leeper]

@kdpeterson51 Please address the issues raised in the review and then let me know once your updates are ready. I'll then take a look and decide if further review is needed.

[kdpeterson51]

Thank you for your patience, @leeper. One of the two issues raised by @kellieotto has been addressed.

To address the second, I am currently in progress of pairing up Travis CI and will update you immediately upon successful integration.

[kdpeterson51]

@leeper Both issues raised by @kellieotto have now been addressed.

Please inform me if there is anything else you may need form me. Thank you very much.

[kellieotto]

The version issue has been addressed. The package still needs unit tests.

[leeper]

Yes, please add unit tests as suggested here: https://github.com/kdpeterson51/mbir/issues/2

[leeper]

@kdpeterson51 I see you've started adding tests. Let me know when you feel the package is ready for me to take another, more thorough look. Thanks!

[kdpeterson51]

@leeper @kellieotto we have added more comprehensive unit tests and would like your feedback on the matter. Thank you for all that you do.

[leeper]

Thanks, @kdpeterson51. @kellieotto can you take a final look?

[kellieotto]

I'm very sorry for such a long delay. This got buried in my inbox. The tests are a good start, but I'd still like to see more comprehensive ones. See my comment.

Might be useful to have a look at this resource or other tutorials on unit testing. This tutorial is Python specific, but there are some good conceptual things in there that apply to R packages too.

[arfon]

@kdpeterson51 - how are you getting along here?

[kdpeterson51]

All but 1 function is left for required tests. I apologize for how long this process has been and appreciate your patience.

[arfon]

👋 @kdpeterson51 - how are you getting along here?

[arfon]

@whedon assign @arfon as editor

[labarba]

👋 @kdpeterson51 — We haven't heard from you in a while... it looks like there remained only some work to do with the tests. Will you be able to finish this up soon?

[kdpeterson51]

@arfon @labarba All tests are finished. Thank you for all your help.

[arfon]

:wave: @kellieotto - would you be able to take another look at this submission now that @kdpeterson51 has made their updates?

[kellieotto]

@arfon @kdpeterson51 Looks like the functions with missing unit tests have them now. I've closed the issue on it. Great! I recommend to accept.

[arfon]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[arfon]

@kdpeterson51 - At this point could you make an archive of the reviewed software in Zenodo/figshare/other service and update this thread with the DOI of the archive? I can then move forward with accepting the submission.

[kdpeterson51]

@arfon Zenodo archive has been made.

[arfon]

@whedon set 10.5281/zenodo.2546910 as archive

[whedon]

OK. 10.5281/zenodo.2546910 is the archive.

[arfon]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/451

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/451, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true

[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/452
2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.00746
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]

@kellieotto - many thanks for your review here and to @leeper for editing this submission :sparkles:

@kdpeterson51 - your paper is now accepted into JOSS :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.00746/status.svg)](https://doi.org/10.21105/joss.00746)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.00746">
  <img src="http://joss.theoj.org/papers/10.21105/joss.00746/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.00746/status.svg
   :target: https://doi.org/10.21105/joss.00746

This is how it will look in your documentation:

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