[REVIEW]: hmis: A python tool to visualize and analyze HMIS data

[whedon]

Submitting author: @mattbellis (Matthew Bellis)
Repository: https://github.com/mattbellis/hmis
Version: 1.0
Editor: @leeper
Reviewer: @alexhanna
Archive: 10.5281/zenodo.1002225

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Reviewers and authors:

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Reviewer questions

@alexhanna, 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

• As the reviewer I confirm that there are no conflicts of interest for me to review this work (such as being a major contributor to the software).

Code of Conduct

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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 (1.0)?
• Authorship: Has the submitting author (@mattbellis) 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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[alexhanna]

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[whedon]

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[alexhanna]

This project meets the requirements for acceptance with a few exceptions.

• I was not able to get the visualizations to work
• The examples do not work on Python 2.7 due to pickling issues. The README.md says it can work on 2.7, but the docs do not.
• Example code in the README.md references a file which does not exist.
• Needs a release.

Otherwise, this package seems straightforward and meets all the other requirements.

[alexhanna]

@leeper Not sure what I do next!

[leeper]

@alexhanna Thanks for your review!

@mattbellis Can you try to address the new issues that Alex opened and then ping me when they're complete?

[alexhanna]

All issues have been resolved. Happy to approve this.

[leeper]

Thanks, @alexhanna! Your work is very much appreciated!

[leeper]

@arfon I think this one is ready for you. Let me know if there's anything else I need to do.

[arfon]

@mattbellis - Could you please cite the entries you have in the paper.bib file directly in your paper please? (You can read how to do that here)

[mattbellis]

Done! However, one of my entries (2017) when I try to build it on my desktop using the commands from whedon, prints a dashed line "----" for the authors. The first entry is totally fine. I've spend some time now trying to debug it and I'm not sure the issue. I thought maybe it was because it is a website that I'm citing there, but that doesn't seem to be it. It could also be that I'm not executing the whedon command properly? The citations appear fine in the text though.

Just a heads up. I'm happy to fix this, but for the life of me, I can't figure out what the issue is.