search

openjournals / joss-reviews

Reviews for the Journal of Open Source Software
Creative Commons Zero v1.0 Universal
712 stars 38 forks source link

[REVIEW]: mbir: Magnitude-Based Inferences #746

Closed whedon closed 5 years ago

whedon commented 6 years ago

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

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

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented 6 years ago

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:

watching

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

notifications

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

@whedon commands
whedon commented 6 years ago 
Attempting PDF compilation. Reticulating splines etc...
whedon commented 6 years ago

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

kellieotto commented 6 years ago

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

leeper commented 6 years ago

Excellent. Thank you, @kellieotto!

leeper commented 6 years ago

@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 commented 6 years ago

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 commented 6 years ago

@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 commented 6 years ago

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

leeper commented 6 years ago

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

leeper commented 6 years ago

@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 commented 6 years ago

@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 commented 6 years ago

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

kellieotto commented 6 years ago

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 commented 6 years ago

@kdpeterson51 - how are you getting along here?

kdpeterson51 commented 6 years ago

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

arfon commented 5 years ago

👋 @kdpeterson51 - how are you getting along here?

arfon commented 5 years ago

@whedon assign @arfon as editor

labarba commented 5 years ago

👋 @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 commented 5 years ago

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

arfon commented 5 years ago

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

kellieotto commented 5 years ago

@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 commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago 
Attempting PDF compilation. Reticulating splines etc...
whedon commented 5 years ago

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

arfon commented 5 years ago

@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 commented 5 years ago

@arfon Zenodo archive has been made.

arfon commented 5 years ago

@whedon set 10.5281/zenodo.2546910 as archive

whedon commented 5 years ago

OK. 10.5281/zenodo.2546910 is the archive.

arfon commented 5 years ago

@whedon accept

whedon commented 5 years ago 
Attempting dry run of processing paper acceptance...
whedon commented 5 years ago

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 commented 5 years ago

@whedon accept deposit=true

whedon commented 5 years ago 
Doing it live! Attempting automated processing of paper acceptance...
whedon commented 5 years ago

🚨🚨🚨 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 commented 5 years ago

@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 commented 5 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.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:

DOI

We need your help!

Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following: