[REVIEW]: Hickle: A HDF5-based Python pickle replacement

[whedon]

Submitting author: @telegraphic (Danny Price)
Repository: https://github.com/telegraphic/hickle
Version: v3.2.2
Editor: @arfon
Reviewer: @betteridiot
Archive: 10.5281/zenodo.2345649

Status

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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 instructions & questions

@betteridiot, 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 @betteridiot

Conflict of interest

• 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

• I confirm that I read and will adhere to the JOSS 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 (v3.2.2)?
• Authorship: Has the submitting author (@telegraphic) 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]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @betteridiot it looks like you're currently assigned as the reviewer for this paper 🎉.

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[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[betteridiot]

Thank you. I see the checklist and proof. I will get back to you as soon as possible.

[betteridiot]

@telegraphic, there is a DOI available for Raffel 2016: https://doi.org/10.7916/D8N58MHV

[telegraphic]

Thanks @betteridiot -- I've added contribution guidelines and the DOI for Raffel 2016

[betteridiot]

Both telegraphic/hickle#79 and telegraphic/hickle#80 appear to be addressed by the author. These issues can be closed now.

I opened Issues telegraphic/hickle#82 and telegraphic/hickle#83 to address some specific items. I request your input @arfon on telegraphic/hickle#82 specifically though.

I also made a PR at telegraphic/hickle#81 to address some very minor compatibility issues.

Lastly, I would like to point @telegraphic towards https://github.com/conda-forge/staged-recipes for a very simple way of adding hickle to conda-forge. This is what I did with bamnostic, and it works great.

If you need any help or guidance, I am available. I believe that once these items are addressed, hickle should be good on my end.

[telegraphic]

Thanks @betteridiot, I very much appreciate your time on this! I've tried to address all the issues and improved the documentation in the README.md. Working on the conda recipe now

[telegraphic]

conda recipe is working! conda-forge/staged-recipes#7268

[betteridiot]

@arfon Looks good on my end.

[arfon]

@arfon Looks good on my end.

Great, thanks @betteridiot.

I opened Issues telegraphic/hickle#82 and telegraphic/hickle#83 to address some specific items. I request your input @arfon on telegraphic/hickle#82 specifically though.

I think where we've got to here is good with me.

[arfon]

@telegraphic - 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.

[telegraphic]

Hi @arfon -- record is https://zenodo.org/record/2345649, and DOI is 10.5281/zenodo.2345649.

@betteridiot -- after some fiddling I've gotten a conda-forge recipe too, waiting on checks (conda-forge/staged-recipes#7268)

[arfon]

@whedon set 10.5281/zenodo.2345649 as archive

[whedon]

OK. 10.5281/zenodo.2345649 is the archive.

[arfon]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Check final proof 👉 openjournals/joss-papers#121

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#121, 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]

@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:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.01115 joss-papers#122
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01115
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

[arfon]

@betteridiot - many thanks for your review here ✨

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

[whedon]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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[telegraphic]

Fantastic! Thanks @arfon and @betteridiot! 🎈 🎈