Joss-reviews: [REVIEW]: Prest: Open-Source Software for Computational Revealed Preference Analysis

[whedon]

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 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

• [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 (v.0.9.7)?
• [x] Authorship: Has the submitting author (@georgiosgerasimou) 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, 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 :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]

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

[arfon]

@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.

[HaoZeke]

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

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

[georgiosgerasimou]

@HaoZeke Sure, thank you.

[HaoZeke]

@georgiosgerasimou I have raised some concerns regarding the installation procedure in https://github.com/prestsoftware/prest/issues/3.

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

[HaoZeke]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[HaoZeke]

@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.

[georgiosgerasimou]

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

[arfon]

@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.

[georgiosgerasimou]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[georgiosgerasimou]

@arfon the archive is 10.5281/zenodo.1466984

[arfon]

@whedon set 10.5281/zenodo.1466984 as archive

[whedon]

OK. 10.5281/zenodo.1466984 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/24

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/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

[arfon]

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) 😬

[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/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...

[arfon]

@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 ⚡️🚀💥

[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.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:

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