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[REVIEW]: greta: simple and scalable statistical modelling in R #1601

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whedon opened this issue Jul 27, 2019 · 51 comments

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@whedon
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commented Jul 27, 2019

Submitting author: @goldingn (Nick Golding)
Repository: https://github.com/greta-dev/greta
Version: 0.3.1
Editor: @terrytangyuan
Reviewers: @lionel68, @joethorley, @lionel68
Archive: 10.5281/zenodo.819476

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/62e62338d8ba44ff9e5dc295cf631477"><img src="http://joss.theoj.org/papers/62e62338d8ba44ff9e5dc295cf631477/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/62e62338d8ba44ff9e5dc295cf631477/status.svg)](http://joss.theoj.org/papers/62e62338d8ba44ff9e5dc295cf631477)

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) by leaving comments 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

@lionel68 @joethorley, 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.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @terrytangyuan know.

Please try and complete your review in the next two weeks

Review checklist for @joethorley

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: 0.3.1
  • Authorship: Has the submitting author (@goldingn) 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 @lionel68

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: 0.3.1
  • Authorship: Has the submitting author (@goldingn) 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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commented Jul 27, 2019

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @lionel68 @joethorley it looks like you're currently assigned to review 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

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf
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commented Jul 27, 2019

Attempting PDF compilation. Reticulating splines etc...
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commented Jul 27, 2019

@joethorley

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commented Jul 30, 2019

@goldingn greta is a fantastic piece of software. I just have three minor issues that need to be addressed

greta-dev/greta#295
greta-dev/greta#296
greta-dev/greta#297

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commented Jul 31, 2019

@whedon generate pdf

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commented Jul 31, 2019

Attempting PDF compilation. Reticulating splines etc...
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commented Jul 31, 2019

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commented Jul 31, 2019

Thanks @joethorley!

Resolved two of those issues now. The last formatting issue (#297) doesn't seem to be present in the article proof, but I may have misunderstood.

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commented Jul 31, 2019

Nice job @goldingn and thanks @joethorley for the review!
👋 @lionel68 Have you got a chance to review this paper yet?

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commented Jul 31, 2019

On my agenda for this friday :) @terrytangyuan

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commented Aug 1, 2019

Thanks for the review @joethorley! There's one item (references) still unchecked in your review list. I think that's resolved now.

@lionel68

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commented Aug 2, 2019

@whedon @terrytangyuan I am starting the review but I can't seem to be able to update the review checklist above. Am I missing something?

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commented Aug 2, 2019

It looks like you are not a collaborator of this repo, @kyleniemeyer could you help take a look?

@lionel68

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commented Aug 2, 2019

greta is a very promising software and is likely to become a very handy tool in the data scientist toolbox.

I opened three issues:

greta-dev/greta#299 (example R code not running on my laptop)
greta-dev/greta#300 (python warnings when running greta::model)
greta-dev/greta#301 (minor textual comments)

Looking forward to using the capacities of greta.

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commented Aug 2, 2019

@whedon add @lionel68 as reviewer

@joethorley

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commented Aug 9, 2019

I am happy

@terrytangyuan

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commented Aug 9, 2019

@whedon set 0.3.1 as version

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commented Aug 9, 2019

OK. 0.3.1 is the version.

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commented Aug 9, 2019

@whedon check references

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commented Aug 9, 2019

Attempting to check references...
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commented Aug 9, 2019


OK DOIs

- 10.1080/10618600.2016.1172487 is OK
- 10.18637/jss.v076.i01 is OK
- 10.7717/peerj-cs.55 is OK

MISSING DOIs

- None

INVALID DOIs

- None
@terrytangyuan

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commented Aug 9, 2019

Thank you!

@goldingn - At this point could you make a new release of this software that includes the changes that have resulted from this review. Then, please make an archive of the software in Zenodo/figshare/other service and update this thread with the DOI of the archive? For the Zenodo/figshare archive, please make sure that:

  • The title of the archive is the same as the JOSS paper title
  • That the authors of the archive are the same as the JOSS paper authors
    I can then move forward with accepting the submission.

@openjournals openjournals deleted a comment from whedon Aug 9, 2019

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commented Aug 10, 2019

This version of the software is now released on GitHub and on CRAN. Here's a figshare archive of this version of the software:
https://doi.org/10.6084/m9.figshare.9461447.v1
Title and authors are the same as this paper.

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commented Aug 11, 2019

@whedon set 10.5281/zenodo.819476 as archive

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commented Aug 11, 2019

OK. 10.5281/zenodo.819476 is the archive.

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commented Aug 11, 2019

@whedon generate pdf

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commented Aug 11, 2019

Attempting PDF compilation. Reticulating splines etc...
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commented Aug 11, 2019

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commented Aug 11, 2019

@whedon check references

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commented Aug 11, 2019

Attempting to check references...
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commented Aug 11, 2019


OK DOIs

- 10.1080/10618600.2016.1172487 is OK
- 10.18637/jss.v076.i01 is OK
- 10.7717/peerj-cs.55 is OK

MISSING DOIs

- None

INVALID DOIs

- None
@terrytangyuan

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commented Aug 11, 2019

@whedon accept

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commented Aug 11, 2019

Attempting dry run of processing paper acceptance...
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commented Aug 11, 2019

Check final proof 👉 openjournals/joss-papers#892

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#892, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
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commented Aug 11, 2019

The paper looks good to me. I am handing this over to our editors-in-chief now. @openjournals/joss-eics

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commented Aug 11, 2019

Thanks @terrytangyuan!

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commented Aug 12, 2019

@whedon accept deposit=true

@whedon whedon added the accepted label Aug 12, 2019

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commented Aug 12, 2019

Doing it live! Attempting automated processing of paper acceptance...
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commented Aug 12, 2019

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

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commented Aug 12, 2019

🚨🚨🚨 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 👉 openjournals/joss-papers#895
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01601
  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...

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commented Aug 12, 2019

@lionel68, @joethorley - many thanks for your reviews and to @terrytangyuan for editing this submission.

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

@arfon arfon closed this Aug 12, 2019

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commented Aug 12, 2019

🎉🎉🎉 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](https://joss.theoj.org/papers/10.21105/joss.01601/status.svg)](https://doi.org/10.21105/joss.01601)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01601">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01601/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01601/status.svg
   :target: https://doi.org/10.21105/joss.01601

This is how it will look in your documentation:

DOI

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