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[REVIEW]: OnlineStats.jl: A Julia package for statistics on data streams #1816

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whedon opened this issue Oct 16, 2019 · 65 comments
Closed

[REVIEW]: OnlineStats.jl: A Julia package for statistics on data streams #1816

whedon opened this issue Oct 16, 2019 · 65 comments
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@whedon whedon commented Oct 16, 2019

Submitting author: @joshday (Josh Day)
Repository: https://github.com/joshday/OnlineStats.jl
Version: v1.0.3
Editor: @karthik
Reviewers: @pkofod, @ahwillia
Archive: 10.5281/zenodo.3659245

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/306085f555d2f0015aa1a131e41c491c"><img src="https://joss.theoj.org/papers/306085f555d2f0015aa1a131e41c491c/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/306085f555d2f0015aa1a131e41c491c/status.svg)](https://joss.theoj.org/papers/306085f555d2f0015aa1a131e41c491c)

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) by leaving comments 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

@pkofod & @ahwillia, 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.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @karthik know.

Please try and complete your review in the next two weeks

Review checklist for @pkofod

Conflict of interest

  • I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

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?
  • Contribution and authorship: Has the submitting author (@joshday) 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 functionality 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

  • Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • State of the field: Do the authors describe how this software compares to other commonly-used packages?
  • Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
  • References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

Review checklist for @ahwillia

Conflict of interest

  • I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

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?
  • Contribution and authorship: Has the submitting author (@joshday) 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 functionality 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

  • Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • State of the field: Do the authors describe how this software compares to other commonly-used packages?
  • Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
  • References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?
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@whedon whedon commented Oct 16, 2019

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @vchuravy, @ahwillia it looks like you're currently assigned to review 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:

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf
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@whedon whedon commented Oct 16, 2019

Attempting PDF compilation. Reticulating splines etc...
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@karthik karthik commented Oct 16, 2019

Editor note: @ahwillia will start review in November.

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@whedon whedon commented Oct 16, 2019

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@ahwillia ahwillia commented Nov 6, 2019

This looks good to me -- I went ahead and checked all my boxes. The documentation is really nice, and the functionality of the package is clear.

My only feedback is that it would be nice to show more full-fledged examples or tutorials, since the operations performed by this particular package are nice building blocks for more complex models/applications. Are there any examples of other repos using OnlineStats.jl to do impressive things? Can these be mentioned in the documentation or the README?

Other than this suggestion, I am happy to see this accepted and published as is.

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@ahwillia ahwillia commented Nov 6, 2019

Also one area the documentation could use more work is the StatLearn object (e.g. for online fitting of GLMs). An example showing how to take multiple passes over the same dataset (i.e. multiple epochs) could be useful.

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@karthik karthik commented Nov 12, 2019

@vchuravy Quick ping to check in. Can you give us a sense for when you might complete this review? 🙏

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@karthik karthik commented Nov 22, 2019

/ooo November 21 until December 2

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@ooo ooo bot commented Nov 22, 2019

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@karthik karthik commented Dec 7, 2019

@vchuravy Another ping to check in. Can you give us a sense for when you might complete this review?

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@karthik karthik commented Dec 16, 2019

@vchuravy Pinging one more time. Are you still able to complete the review?

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@karthik karthik commented Dec 21, 2019

@joshday Apologies for the delays with this submission. I'm still trying to get a response from reviewer 2. I'll look for a reviewer in the new year. I'll be out of office for the next few weeks.

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@karthik karthik commented Dec 21, 2019

/ooo December 22 2019 until January 10 2020

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@ooo ooo bot commented Dec 21, 2019

@openjournals openjournals deleted a comment from ooo bot Dec 21, 2019
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@karthik karthik commented Jan 28, 2020

@joshday I am still looking for reviewers without much success. Are you able to recommend anyone that can review without any conflict of interest?

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@pkofod pkofod commented Jan 28, 2020

@karthik I can review but I do have to disclose that we are both employed by Julia Computing. Though, we do live 7000km from each other, and have never worked on projects together. I have never used OnlineStats.jl either, although I'm aware of it's existence.

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@karthik karthik commented Jan 28, 2020

@pkofod That's totally fine! In fact I've tried to get a few people from Julia Computing to review. Thanks so much for stepping in, assigning you now.

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@karthik karthik commented Jan 28, 2020

@whedon remove @vchuravy as reviewer

@whedon whedon assigned ahwillia and karthik and unassigned karthik, vchuravy and ahwillia Jan 28, 2020
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@whedon whedon commented Jan 28, 2020

OK, @vchuravy is no longer a reviewer

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@arfon arfon commented Feb 7, 2020

If the software doesn't have a DOI, I think we can skip it but I'll tag @arfon in case he can help.

This sounds fine. The DOI search/recommender is just using the Crossref API looking for similar titles.

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@karthik karthik commented Feb 7, 2020

@whedon generate pdf

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@whedon whedon commented Feb 7, 2020

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@karthik karthik commented Feb 7, 2020

LGTM

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@karthik karthik commented Feb 7, 2020

Ready to accept. Over you to @openjournals/joss-eics

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@kthyng kthyng commented Feb 8, 2020

@joshday Hi! I'll take over from here.

What version number do you want associated with this publication?

Also, can you create an archive of your code at, for example, Zenodo, and report the doi back here? Please be sure that the title and author list match your paper exactly, which might requires editing the metadata.

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@karthik karthik commented Feb 9, 2020

@kthyng Yikes, sorry I forget about Zenodo and versions. doh.

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@joshday joshday commented Feb 10, 2020

@kthyng The version I'd like to use is is v1.0.3 and the DOI is 10.5281/zenodo.3659245. Let me know if there's anything else I can do to help!

A big thank you to @ahwillia and @pkofod for reviewing and @karthik for keeping this thing moving along!

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@kthyng kthyng commented Feb 10, 2020

@whedon set v1.0.3 as version

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@whedon whedon commented Feb 10, 2020

OK. v1.0.3 is the version.

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@kthyng kthyng commented Feb 10, 2020

@whedon set 10.5281/zenodo.3659245 as archive

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@whedon whedon commented Feb 10, 2020

OK. 10.5281/zenodo.3659245 is the archive.

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@kthyng kthyng commented Feb 10, 2020

@whedon accept

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@whedon whedon commented Feb 10, 2020

Attempting dry run of processing paper acceptance...
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@whedon whedon commented Feb 10, 2020

Reference check summary:

OK DOIs

- 10.1137/141000671 is OK

MISSING DOIs

- https://doi.org/10.1007/978-1-4842-3579-9_6 may be missing for title: Spark Streaming

INVALID DOIs

- None
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@whedon whedon commented Feb 10, 2020

Check final proof 👉 openjournals/joss-papers#1292

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1292, 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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@kthyng kthyng commented Feb 10, 2020

@whedon accept deposit=true

@whedon whedon added the accepted label Feb 10, 2020
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@whedon whedon commented Feb 10, 2020

Doing it live! Attempting automated processing of paper acceptance...
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@whedon whedon commented Feb 10, 2020

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

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@whedon whedon commented Feb 10, 2020

🚨🚨🚨 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#1293
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01816
  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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@kthyng kthyng commented Feb 10, 2020

Congratulations on your new publication to @joshday!! Thank to editor @karthik and to reviewers @pkofod and @ahwillia — without your time and expertise we couldn't have done this!

@kthyng kthyng closed this Feb 10, 2020
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@whedon whedon commented Feb 10, 2020

🎉🎉🎉 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](https://joss.theoj.org/papers/10.21105/joss.01816/status.svg)](https://doi.org/10.21105/joss.01816)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01816">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01816/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01816/status.svg
   :target: https://doi.org/10.21105/joss.01816

This is how it will look in your documentation:

DOI

We need your help!

Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

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@joshday joshday commented Feb 11, 2020

My apologies for missing this in the proof, but a unicode character (μ) fails to render in the example at the end of the paper. Is it possible to revise the paper? I can simply change the problem character to ASCII.

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@danielskatz danielskatz commented Feb 11, 2020

Please make the change in the .md or .bib file, than let us know - @arfon will have to manually propagate the change it at this point

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@joshday joshday commented Feb 11, 2020

Thanks @danielskatz, I've made the change.

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@danielskatz danielskatz commented Feb 11, 2020

👋 @arfon - over to you...

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@arfon arfon commented Feb 11, 2020

👋 @arfon - over to you...

OK this should be updated now. The PDF might take a few hours to show up as modified as there's caching in place for the papers.

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@joshday joshday commented Feb 11, 2020

Much appreciated! Thank you!

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