Joss-reviews: [REVIEW]: hei: Calculate Healthy Eating Index (HEI) Scores

[whedon]

Submitting author: @timfolsom (Timothy Folsom)
Repository: https://github.com/timfolsom/hei
Version: v0.1.0
Editor: @leeper
Reviewer: @maelle
Archive: 10.6084/m9.figshare.5469208

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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 questions

@maelle, please carry out your review in this issue by updating the checklist below (please make sure you're logged in to GitHub). The reviewer guidelines are available here: http://joss.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @leeper know.

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 (v0.1.0)?
• [x] Authorship: Has the submitting author (@timfolsom) 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).
• [ ] 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. I'm here to help you with some common editorial tasks for JOSS. @maelle it looks like you're currently assigned as the reviewer for this paper :tada:.

:star: Important :star:

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To fix this do the following two things:

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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:

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[maelle]

I'm done with the review, nice package! You'll see I've opened many issues but nearly everything in the review list is crossed.

• I think the installation instructions could be made a bit clearer, see this issue

• I've made some suggestions for the documentation https://github.com/timfolsom/hei/issues/9, https://github.com/timfolsom/hei/issues/11, https://github.com/timfolsom/hei/issues/16, https://github.com/timfolsom/hei/issues/17, https://github.com/timfolsom/hei/issues/20, https://github.com/timfolsom/hei/issues/21.

• I've also made some suggestions regarding the paper. https://github.com/timfolsom/hei/issues/14, https://github.com/timfolsom/hei/issues/19, https://github.com/timfolsom/hei/issues/23.

• I found a (really easy to fix) bug in a vignette https://github.com/timfolsom/hei/issues/18 so this one is an important issue.

• Some other issues are really more suggestions! https://github.com/timfolsom/hei/issues/12, https://github.com/timfolsom/hei/issues/13, https://github.com/timfolsom/hei/issues/15, https://github.com/timfolsom/hei/issues/16, https://github.com/timfolsom/hei/issues/22.

Happy to discuss further if something is unclear.

[leeper]

@maelle Thank you so much for your thorough and prompt review!

@timfolsom Can you please address the issues Maëlle has raised and ping me when you're done?

[maelle]

I'm happy with the changes that @timfolsom's coauthor @vpnagraj made. Nearly all issues I've opened are closed, now everything in the checklist is checked. ✅

[timfolsom]

Thank you for the review and the feedback. @vpnagraj and I have incorporated almost all of your suggestions. If it is all the same to you, we would prefer to leave the pkgdown issue open for now.

[leeper]

Thanks, all. This looks good to me. @arfon - over to you.

[vpnagraj]

@leeper @maelle thank you both so much for the comprehensive review ... i think this helped make the package a lot better 👍 👍

let us know if there's anything else you need on our end to wrap up the submission

[arfon]

@vpnagraj - please merge this pull request https://github.com/timfolsom/hei/pull/24
and then 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.

[vpnagraj]

@arfon thanks for following up ... i've merged the pull request and published an archive of the package in figshare with the following following DOI:

10.6084/m9.figshare.5469208

[arfon]

@whedon set 10.6084/m9.figshare.5469208 as archive

[whedon]

OK. 10.6084/m9.figshare.5469208 is the archive.

[arfon]

@maelle - many thanks for your review and to @leeper for editing this one ✨

@timfolsom @vpnagraj - your paper is now accepted into JOSS and your DOI is http://dx.doi.org/10.21105/joss.00417 ⚡️ 🚀 💥