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[REVIEW]: ggvoronoi: Voronoi Diagrams and Heatmaps with ggplot2 #1096

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whedon opened this issue Nov 25, 2018 · 30 comments
Closed
36 tasks done

[REVIEW]: ggvoronoi: Voronoi Diagrams and Heatmaps with ggplot2 #1096

whedon opened this issue Nov 25, 2018 · 30 comments
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accepted published Papers published in JOSS recommend-accept Papers recommended for acceptance in JOSS. review

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@whedon
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whedon commented Nov 25, 2018

Submitting author: @garretrc (Robert Garrett)
Repository: https://github.com/garretrc/ggvoronoi
Version: v0.8.2
Editor: @yochannah
Reviewer: @trinker, @corybrunson
Archive: 10.5281/zenodo.1933346

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/7e294d1043804b4b36ce6dca29db7999"><img src="http://joss.theoj.org/papers/7e294d1043804b4b36ce6dca29db7999/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/7e294d1043804b4b36ce6dca29db7999/status.svg)](http://joss.theoj.org/papers/7e294d1043804b4b36ce6dca29db7999)

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

@trinker & @corybrunson, 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 @yochannah know.

Please try and complete your review in the next two weeks

Review checklist for @trinker

Conflict of interest

Code of Conduct

General checks

  • Repository: Is the source code for this software available at the repository url?
  • License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • Version: Does the release version given match the GitHub release (v0.8.2)?
  • Authorship: Has the submitting author (@garretrc) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

  • Installation: Does installation proceed as outlined in the documentation?
  • Functionality: Have the functional claims of the software been confirmed?
  • 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

  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
  • Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
  • Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
  • Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
  • 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

  • Authors: Does the paper.md file include a list of authors with their affiliations?
  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @corybrunson

Conflict of interest

Code of Conduct

General checks

  • Repository: Is the source code for this software available at the repository url?
  • License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • Version: Does the release version given match the GitHub release (v0.8.2)?
  • Authorship: Has the submitting author (@garretrc) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

  • Installation: Does installation proceed as outlined in the documentation?
  • Functionality: Have the functional claims of the software been confirmed?
  • 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

  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
  • Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
  • Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
  • Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
  • 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

  • Authors: Does the paper.md file include a list of authors with their affiliations?
  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?
@whedon
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whedon commented Nov 25, 2018

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @trinker, it looks like you're currently assigned as the reviewer for this paper 🎉.

⭐ Important ⭐

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
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whedon commented Nov 25, 2018

Attempting PDF compilation. Reticulating splines etc...

@whedon
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whedon commented Nov 25, 2018

👉 Check article proof 📄 👈

@corybrunson
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Thanks @garretrc for this elegant Voronoi extension! I'll start raising issues at the code repo momentarily. As you address the issues, i'll check off the related items on my review checklist. If you think some of my issues aren't really problematic, or if you think my suggestions are not great, then please let me know in the issue thread and handle them as you see fit—i'll probably then better understand the issue and check it off for reviewing purposes.

@garretrc
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Thanks for the feedback! I've started to go through the issues on the ggvoronoi repository. I'll close issues on that repo if I'm confident the issue is resolved and comment if I have any questions.

@garretrc
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@corybrunson I've addressed each issue, one is still open and I've left a comment as justification. If you accept that reasoning you can close the issue, otherwise leave a comment and I can make further changes. Feel free to re-open any of the other issues if you feel my solutions aren't acceptable! Thank you.

@corybrunson
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@whedon commands

@whedon
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whedon commented Nov 26, 2018

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

# Compile the paper
@whedon generate pdf

🚧 🚧 🚧 Experimental Whedon features 🚧 🚧 🚧

# Compile the paper from a custom git branch
@whedon generate pdf from branch custom-branch-name

@corybrunson
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@whedon generate pdf

@whedon
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whedon commented Nov 26, 2018

Attempting PDF compilation. Reticulating splines etc...

@whedon
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whedon commented Nov 26, 2018

@corybrunson
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@garretrc thanks for addressing all of the issues! You've resolved or explained them to my satisfaction.

@yochannah i have completed my review and, conditional on my co-reviewer's feedback, recommend acceptance of the current GitHub version (garretrc/ggvoronoi@2b2821c).

@trinker
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trinker commented Dec 3, 2018

@garretrc Thanks for addressing the couple of GitHub issues. These have been addressed/resolved.

@yochannah I have also completed my review and also recommend acceptance of the current GitHub version (garretrc/ggvoronoi@c9ba48f).

@yochannah
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@whedon generate pdf

@whedon
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whedon commented Dec 4, 2018

Attempting PDF compilation. Reticulating splines etc...

@whedon
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whedon commented Dec 4, 2018

@yochannah
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@corybrunson @trinker Thanks for the speedy reviews! 💯

@garretrc - 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?

@garretrc
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garretrc commented Dec 4, 2018

DOI: 10.5281/zenodo.1933346

@garretrc
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garretrc commented Dec 4, 2018

Thanks @yochannah @trinker @corybrunson for all your swift work and wonderful feedback!

@yochannah
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@whedon set 10.5281/zenodo.1933346 as archive

@whedon
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whedon commented Dec 4, 2018

OK. 10.5281/zenodo.1933346 is the archive.

@yochannah
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@arfon Okay, we're ready to accept! 🏆

Nice work, @garretrc and great job reviewing @trinker @corybrunson!

@arfon
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arfon commented Dec 5, 2018

@whedon accept

@whedon
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whedon commented Dec 5, 2018

Attempting dry run of processing paper acceptance...

@whedon
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whedon commented Dec 5, 2018

Check final proof 👉 openjournals/joss-papers#101

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#101, 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
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arfon commented Dec 5, 2018

@whedon accept deposit=true

@whedon whedon added the accepted label Dec 5, 2018
@whedon
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whedon commented Dec 5, 2018

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

@whedon
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whedon commented Dec 5, 2018

🚨🚨🚨 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 👉 Creating pull request for 10.21105.joss.01096 joss-papers#102
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01096
  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
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arfon commented Dec 5, 2018

@trinker, @corybrunson - many thanks for your reviews here and to @yochannah for editing this submission ✨

@garretrc - your paper is now accepted into JOSS ⚡🚀💥

@arfon arfon closed this as completed Dec 5, 2018
@whedon
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whedon commented Dec 5, 2018

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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.01096/status.svg)](https://doi.org/10.21105/joss.01096)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01096">
  <img src="http://joss.theoj.org/papers/10.21105/joss.01096/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01096/status.svg
   :target: https://doi.org/10.21105/joss.01096

This is how it will look in your documentation:

DOI

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