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[REVIEW]: Prest: Open-Source Software for Computational Revealed Preference Analysis #1015

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whedon opened this Issue Oct 14, 2018 · 28 comments

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whedon commented Oct 14, 2018

Submitting author: @georgiosgerasimou (Georgios Gerasimou)
Repository: https://github.com/prestsoftware/prest
Version: v.0.9.7
Editor: @arfon
Reviewer: @HaoZeke
Archive: 10.5281/zenodo.1466984

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/f3b70136a43eb28b9327ec1ce42533c2"><img src="http://joss.theoj.org/papers/f3b70136a43eb28b9327ec1ce42533c2/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/f3b70136a43eb28b9327ec1ce42533c2/status.svg)](http://joss.theoj.org/papers/f3b70136a43eb28b9327ec1ce42533c2)

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

@HaoZeke, 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 @arfon know.

Please try and complete your review in the next two weeks

Review checklist for @HaoZeke

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 (v.0.9.7)?
  • Authorship: Has the submitting author (@georgiosgerasimou) 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)?
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whedon commented Oct 14, 2018

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @HaoZeke 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
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whedon commented Oct 14, 2018

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Oct 14, 2018

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arfon commented Oct 14, 2018

@HaoZeke - please carry out your review in this issue by updating the checklist above and giving feedback in this issue. The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html

Any questions/concerns please let me know.

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HaoZeke commented Oct 14, 2018

Sure, I will have the review finished in a few days.

@georgiosgerasimou I will be opening pull requests (like prestsoftware/prest#2) like to discuss issues on the prest tracker (eg. prestsoftware/prest#1), but I will also mention them here.

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georgiosgerasimou commented Oct 14, 2018

@HaoZeke Sure, thank you.

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HaoZeke commented Oct 16, 2018

@georgiosgerasimou I have raised some concerns regarding the installation procedure in prestsoftware/prest#3.

Since there are multiple possible ways of resolving them, please discuss them on the appropriate issue.

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HaoZeke commented Oct 18, 2018

@whedon generate pdf

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whedon commented Oct 18, 2018

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Oct 18, 2018

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HaoZeke commented Oct 18, 2018

@arfon This is now fully compliant with the JOSS guidelines IMO.

@georgiosgerasimou and @ziman, thank you so much for being prompt and accommodative of my many queries and clarifications. It's an amazing software, with great docs and code architecture, and I am glad I got the chance to review it! Also, thanks for taking the time to ensure JOSS compliance.

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georgiosgerasimou commented Oct 19, 2018

@HaoZeke Thank you very much for reviewing Prest, and for your kind words!

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arfon commented Oct 19, 2018

@georgiosgerasimou - 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.

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georgiosgerasimou commented Oct 19, 2018

@whedon generate pdf

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whedon commented Oct 19, 2018

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Oct 19, 2018

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georgiosgerasimou commented Oct 19, 2018

@arfon the archive is 10.5281/zenodo.1466984

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arfon commented Oct 20, 2018

@whedon set 10.5281/zenodo.1466984 as archive

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whedon commented Oct 20, 2018

OK. 10.5281/zenodo.1466984 is the archive.

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arfon commented Oct 20, 2018

@whedon accept

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whedon commented Oct 20, 2018

Attempting dry run of processing paper acceptance...

@whedon whedon added the accepted label Oct 20, 2018

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whedon commented Oct 20, 2018

Check final proof 👉 openjournals/joss-papers#24

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#24, 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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arfon commented Oct 20, 2018

I'm going to try accepting this automatically here (this is new fucntionality for Whedon). If this goes wrong I will have to fix this up tomorrow evening my time (currently typing this from my phone) 😬

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arfon commented Oct 20, 2018

@whedon accept deposit=true

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whedon commented Oct 20, 2018

Doing it live! Attempting automated processing of paper acceptance...
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whedon commented Oct 20, 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 👉 openjournals/joss-papers#25
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01015
  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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arfon commented Oct 20, 2018

@HaoZeke - many thanks for your review here!
If
@georgiosgerasimou - your paper is now accepted into JOSS and your DOI is
https://doi.org/10.21105/joss.01015 ⚡️🚀💥

@arfon arfon closed this Oct 20, 2018

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whedon commented Oct 20, 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.01015/status.svg)](https://doi.org/10.21105/joss.01015)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01015">
  <img src="http://joss.theoj.org/papers/10.21105/joss.01015/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01015/status.svg
   :target: https://doi.org/10.21105/joss.01015

This is how it will look in your documentation:

DOI

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