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[REVIEW]: Flux: Seamless machine learning with Julia #602

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whedon opened this issue Mar 5, 2018 · 36 comments
Closed
18 tasks done

[REVIEW]: Flux: Seamless machine learning with Julia #602

whedon opened this issue Mar 5, 2018 · 36 comments
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accepted published Papers published in JOSS recommend-accept Papers recommended for acceptance in JOSS. review

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@whedon
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whedon commented Mar 5, 2018

Submitting author: @MikeInnes (Michael Innes)
Repository: https://github.com/FluxML/Flux.jl
Version: v0.4.1
Editor: @Kevin-Mattheus-Moerman
Reviewer: @ysimillides
Archive: 10.5281/zenodo.1240350

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/6b550f67bdfaf97a1851c8f4bad96513"><img src="http://joss.theoj.org/papers/6b550f67bdfaf97a1851c8f4bad96513/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/6b550f67bdfaf97a1851c8f4bad96513/status.svg)](http://joss.theoj.org/papers/6b550f67bdfaf97a1851c8f4bad96513)

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


@ysimillides, 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 @Kevin-Mattheus-Moerman know.

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 (v0.4.1)?
  • Authorship: Has the submitting author (@MikeInnes) 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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whedon commented Mar 5, 2018

Hello human, I'm @whedon. I'm here to help you with some common editorial tasks. @ysimillides 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

notifications

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

@whedon commands

@whedon
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whedon commented Mar 5, 2018

Attempting PDF compilation. Reticulating splines etc...

@whedon
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whedon commented Mar 5, 2018

@Kevin-Mattheus-Moerman
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@MikeInnes this is where the review takes place.

@Kevin-Mattheus-Moerman
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@ysimillides @vchuravy thanks for reviewing this submission 🚀 I've created tick boxes for the both of you at the top of this issue. You can leave review comments here but for larger items we suggest you open an issue on the project repo and link to it here.
Here are our reviewer guidelines: http://joss.theoj.org/about#reviewer_guidelines

Let me know if you have questions.

Let the reviewing begin 🎉

@Kevin-Mattheus-Moerman
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@davidbarber @taheris are you interested in reviewing this submission for JOSS as well? Review is focused largely on the software and also a short paper 🔖

@MikeInnes
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MikeInnes commented Mar 5, 2018

@ChrisRackauckas also mentioned an interest in reviewing, if we're going for 3.

@Kevin-Mattheus-Moerman
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Kevin-Mattheus-Moerman commented Mar 5, 2018

Great the more the better. @ChrisRackauckas I've created a check list for you at the top of this issue as well.

@ChrisRackauckas
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The invitation seems to not have worked.

@arfon
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arfon commented Mar 7, 2018

The invitation seems to not have worked.

@ChrisRackauckas - I just re-invited you.

@ChrisRackauckas
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I think I will need to step down after reading the conflict of interests policy. I am currently (well just started) working with @MikeInnes on a publication which utilizes Flux.jl and so someone with less experience of the software, it's community, and its authors can probably do a more impartial scientific assessment, though I will still go through and open docs PRs where I see fit.

@Kevin-Mattheus-Moerman
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Thanks @ChrisRackauckas that sounds good

@vchuravy
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vchuravy commented Mar 9, 2018

I also have to report a potential COI, @MikeInnes and I recently co-authored a (publication)[http://www.sysml.cc/doc/37.pdf].
I will leave it to the editors to decide whether or not I should step down.

@MikeInnes
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I've tried to address @ysimillides comments, he can say if that's sufficient.

As no other reviewers have stepped up over a month, seems like it might be challenging to get more review on this. Is there any chance of moving forward with the one review?

@ysimillides
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@MikeInnes Thanks! Everything looks good on my end now.

@Kevin-Mattheus-Moerman
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@whedon generate pdf

@whedon
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whedon commented Mar 27, 2018

Attempting PDF compilation. Reticulating splines etc...

@whedon
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whedon commented Mar 27, 2018

@Kevin-Mattheus-Moerman
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@MikeInnes I've reviewed the paper. About the statement

Flux has been used heavily for natural language processing...

would you be able to add one or more references for this?

@MikeInnes
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I've updated the paper a little to reference some of the NLP work that's out there via Minibatch.jl and the model zoo. It's a bit tricky that a lot of the really neat stuff is either industrial or in preparation / review right now (indeed a big part of the motivation for this submission is so that they can cite us :)

@ysimillides
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@whedon generate pdf

@whedon
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whedon commented Apr 14, 2018

Attempting PDF compilation. Reticulating splines etc...

@whedon
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whedon commented Apr 14, 2018

@Kevin-Mattheus-Moerman
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@MikeInnes thanks for updating the paper. BTW if works are in submission and you'd like to cite them you could cite the DOI of a pre-print for instance.

@MikeInnes
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I'll poke those folks in case there are any public DOIs around that I can cite, but if this paper can go through before then I'm equally happy to leave it.

@MikeInnes
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No luck on the DOIs, is there anything else blocking this at this point?

@Kevin-Mattheus-Moerman
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@MikeInnes thanks, all boxes are ticked and it looks like we are all set. I recommend acceptance of this submission.
At this point, can you please make an archive of the final reviewed software in Zenodo, or figshare, or another service, and update this thread with the DOI of the archive? Once we have that available we can process acceptance.

@Kevin-Mattheus-Moerman
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@ysimillides thanks for reviewing this submission! 🚀

@MikeInnes
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Alright, that's up! https://zenodo.org/record/1240350

@Kevin-Mattheus-Moerman
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@arfon over to you. We are all set.

@arfon
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arfon commented May 3, 2018

@whedon set 10.5281/zenodo.1240350 as archive

@whedon
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whedon commented May 3, 2018

OK. 10.5281/zenodo.1240350 is the archive.

@arfon arfon added the accepted label May 3, 2018
@MikeInnes
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Awesome, thanks @arfon and @Kevin-Mattheus-Moerman, and @ysimillides for the review!

@arfon
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arfon commented May 3, 2018

@ysimillides - many thanks for your review and to @Kevin-Mattheus-Moerman for editing this one ✨

@MikeInnes - your paper is now accepted and your DOI is https://doi.org/10.21105/joss.00602 ⚡ 🚀 💥

@arfon arfon closed this as completed May 3, 2018
@whedon
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whedon commented May 3, 2018

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

If you would like to include a link to your paper from your README use the following code snippet:

[![DOI](http://joss.theoj.org/papers/10.21105/joss.00602/status.svg)](https://doi.org/10.21105/joss.00602)

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:

@Kevin-Mattheus-Moerman
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Congratulations @MikeInnes 🍰

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