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[REVIEW]: Hickle: A HDF5-based Python pickle replacement #1115

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whedon opened this Issue Dec 4, 2018 · 24 comments

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whedon commented Dec 4, 2018

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

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/0c6638f84a1a574913ed7c6dd1051847"><img src="http://joss.theoj.org/papers/0c6638f84a1a574913ed7c6dd1051847/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/0c6638f84a1a574913ed7c6dd1051847/status.svg)](http://joss.theoj.org/papers/0c6638f84a1a574913ed7c6dd1051847)

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

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)?
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whedon commented Dec 4, 2018

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 🎉.

⭐️ 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

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For a list of things I can do to help you, just type:

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whedon commented Dec 4, 2018

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Dec 4, 2018

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betteridiot commented Dec 4, 2018

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

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betteridiot commented Dec 5, 2018

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

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telegraphic commented Dec 10, 2018

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

betteridiot added a commit to betteridiot/joss_reviews that referenced this issue Dec 12, 2018

Preliminary review document for openjournals/joss-reviews#1115
@telegraphic, @arfon: Some basic results and insights for the review process of `hickle` for JoSS
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betteridiot commented Dec 12, 2018

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.

betteridiot added a commit to betteridiot/joss_reviews that referenced this issue Dec 12, 2018

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telegraphic commented Dec 13, 2018

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

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telegraphic commented Dec 14, 2018

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

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betteridiot commented Dec 14, 2018

@arfon Looks good on my end.

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arfon commented Dec 14, 2018

@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.

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arfon commented Dec 14, 2018

@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.

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telegraphic commented Dec 17, 2018

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)

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arfon commented Dec 17, 2018

@whedon set 10.5281/zenodo.2345649 as archive

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whedon commented Dec 17, 2018

OK. 10.5281/zenodo.2345649 is the archive.

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arfon commented Dec 17, 2018

@whedon accept

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whedon commented Dec 17, 2018

Attempting dry run of processing paper acceptance...
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whedon commented Dec 17, 2018

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
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arfon commented Dec 17, 2018

@whedon accept deposit=true

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whedon commented Dec 17, 2018

Doing it live! Attempting automated processing of paper acceptance...

@whedon whedon added the accepted label Dec 17, 2018

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whedon commented Dec 17, 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#122
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01115
  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 Dec 17, 2018

@betteridiot - many thanks for your review here

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

@arfon arfon closed this Dec 17, 2018

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whedon commented Dec 17, 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.01115/status.svg)](https://doi.org/10.21105/joss.01115)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01115">
  <img src="http://joss.theoj.org/papers/10.21105/joss.01115/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01115/status.svg
   :target: https://doi.org/10.21105/joss.01115

This is how it will look in your documentation:

DOI

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telegraphic commented Dec 17, 2018

Fantastic! Thanks @arfon and @betteridiot! 🎈 🎈

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