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[REVIEW]: Embeddings.jl: easy access to pretrained word embeddings from julia #1013

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whedon opened this Issue Oct 10, 2018 · 74 comments

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whedon commented Oct 10, 2018

Submitting author: @oxinabox (Lyndon White)
Repository: https://github.com/JuliaText/Embeddings.jl/
Version: 0.3.1
Editor: @Kevin-Mattheus-Moerman
Reviewer: @aviks
Archive: 10.5281/zenodo.2633789

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/fed0b7d1db22a7fe0d5933a7b6b81e81"><img src="http://joss.theoj.org/papers/fed0b7d1db22a7fe0d5933a7b6b81e81/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/fed0b7d1db22a7fe0d5933a7b6b81e81/status.svg)](http://joss.theoj.org/papers/fed0b7d1db22a7fe0d5933a7b6b81e81)

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

@aviks, 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.

Please try and complete your review in the next two weeks

Review checklist for @aviks

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: 0.3.1
  • Authorship: Has the submitting author (@oxinabox) 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 Oct 10, 2018

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @aviks 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
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whedon commented Oct 10, 2018

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Oct 10, 2018

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Kevin-Mattheus-Moerman commented Oct 30, 2018

@aviks thanks again for being a reviewer for this submission. How are you getting on? Let me know if you have questions.

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Kevin-Mattheus-Moerman commented Nov 20, 2018

@aviks can you give an update as to how you are getting on with the review process? Thanks.

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Kevin-Mattheus-Moerman commented Jan 4, 2019

@aviks we'd like to move on with this submission. If you are still able to review this work please do so at your earliest convenience. If you are no longer able to do so please let us know. Thanks.

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oxinabox commented Jan 4, 2019

I'm honestly happy to wait. I am in no hurry for this one. @aviks is a pretty ideal reviewer.

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Kevin-Mattheus-Moerman commented Jan 4, 2019

@oxinabox thanks for letting us know. We can of course be flexible regarding timing.

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labarba commented Feb 13, 2019

I have just sent a follow-up message via email to the reviewer to ask if they still plan on doing this (copied @Kevin-Mattheus-Moerman).

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aviks commented Feb 13, 2019

Sorry for delaying this folks. I will get on this now.

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aviks commented Feb 26, 2019

Everything looks good apart from a couple of documentation nits that I've raised on the repo.

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Kevin-Mattheus-Moerman commented Mar 1, 2019

@oxinabox I see you have a short contributing section in your readme. Would you be okay with expanding your community guidelines (last unticked box above) a bit, e.g. using the steps/info below?

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Kevin-Mattheus-Moerman commented Mar 1, 2019

The other unticked box is installation instructions.
@oxinabox can you also expand your installation instructions. @aviks if you have more feedback on this to point @oxinabox in the right direction (i.e. what you feel is missing) that would be great. Thanks again for your review work.

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oxinabox commented Mar 1, 2019

I added an Installation section the other day. https://github.com/JuliaText/Embeddings.jl/blob/master/README.md#installation
I do not think there are more instructions I can give.

I have further expanded the Contributing section, and added reference to the Julia Community Standards.
I'm not sure if moving this section of the document to a CONTRIBUTING.md would make it more, or less likely to be read.

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Kevin-Mattheus-Moerman commented Mar 13, 2019

@whedon check references

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whedon commented Mar 13, 2019

Attempting to check references...
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whedon commented Mar 13, 2019


OK DOIs

- 10.21105/joss.00602 is OK

MISSING DOIs

- https://doi.org/10.1137/141000671 may be missing for title: Julia: A Fresh Approach to Numerical Computing
- https://doi.org/10.1108/09504121211251880 may be missing for title: DataDeps.jl: Repeatable Data Setup for Replicable Data Science
- https://doi.org/10.1162/tacl_a_00051 may be missing for title: Enriching Word Vectors with Subword Information
- https://doi.org/10.1162/tacl_a_00051 may be missing for title: Learning Word Vectors for 157 Languages
- https://doi.org/10.2172/1209543 may be missing for title: Efficient estimation of word representations in vector space
- https://doi.org/10.3115/v1/d14-1162 may be missing for title: GloVe: Global Vectors for Word Representation

INVALID DOIs

- None
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Kevin-Mattheus-Moerman commented Mar 13, 2019

@oxinabox can you check those DOI's?

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oxinabox commented Mar 13, 2019

  • correct: https://doi.org/10.1137/141000671 may be missing for title: Julia: A Fresh Approach to Numerical Computing
  • Incorrect: https://doi.org/10.1108/09504121211251880 may be missing for title: DataDeps.jl: Repeatable Data Setup for Replicable Data Science
    • this paper has been stuck in some review hole for almost a year, so the citation is for the preprint. idk where this DOI is from.
  • correct: https://doi.org/10.1162/tacl_a_00051 may be missing for title: Enriching Word Vectors with Subword Information
  • Incorrect: https://doi.org/10.1162/tacl_a_00051 may be missing for title: Learning Word Vectors for 157 Languages
    • This is the same DOI as above so it can't be for this paper too.
  • Incorrect: https://doi.org/10.2172/1209543 may be missing for title: Efficient estimation of word representations in vector space
  • correct: https://doi.org/10.3115/v1/d14-1162 may be missing for title: GloVe: Global Vectors for Word Representation

I should update the bibliography to use these DOIs that are correct?

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labarba commented Mar 14, 2019

Please update your bibliography, yes.

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Kevin-Mattheus-Moerman commented Mar 20, 2019

@oxinabox any luck updaring the .bib file? Let me know if you need help or have questions.

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oxinabox commented Mar 20, 2019

No, sorry i've been away. Will see to it soon

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oxinabox commented Mar 21, 2019

Done

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Kevin-Mattheus-Moerman commented Mar 21, 2019

@whedon generate pdf

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whedon commented Mar 21, 2019

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Mar 21, 2019

PDF failed to compile for issue #1013 with the following error:

% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed

0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 14 0 14 0 0 176 0 --:--:-- --:--:-- --:--:-- 177
Error reading bibliography ./paper.bib (line 40, column 3):
unexpected "d"
expecting space, ",", white space or "}"
Error running filter pandoc-citeproc:
Filter returned error status 1
Looks like we failed to compile the PDF

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Kevin-Mattheus-Moerman commented Mar 21, 2019

@oxinabox can you trouble shoot the above a bit? Feel free to call @whedon generate pdf yourself here to attempt to recreate the paper.

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whedon commented Mar 25, 2019

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oxinabox commented Mar 25, 2019

Done

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oxinabox commented Apr 8, 2019

@Kevin-Mattheus-Moerman his this good to go now?
I am submitting my final corrected version of my thesis soon, and it would be nice to be able to switch this from "Under Review" to "Published".

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Kevin-Mattheus-Moerman commented Apr 8, 2019

@oxinabox apologies for the delay. I'll get to this now.

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Kevin-Mattheus-Moerman commented Apr 8, 2019

@oxinabox looks good.

One minor thing. Currently it says "an long", this should be "a long". Also, since now you do not reuse the acronym LSTM, consider removing it all together, or if the acronym is used more often than the spelled out form use: "LSTM (long short term memory)" rather than "long short term memory (LSTM)".

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Kevin-Mattheus-Moerman commented Apr 8, 2019

@whedon check references

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whedon commented Apr 8, 2019

Attempting to check references...
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whedon commented Apr 8, 2019


OK DOIs

- 10.1137/141000671 is OK
- 10.1162/tacl_a_00051 is OK
- 10.3115/v1/d14-1162 is OK
- 10.21105/joss.00602 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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oxinabox commented Apr 8, 2019

if the acronym is used more often than the spelled out form use: "LSTM (long short term memory)" rather than "long short term memory (LSTM)

That is indeed the case.
I have made this change

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Kevin-Mattheus-Moerman commented Apr 8, 2019

@whedon generate pdf

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whedon commented Apr 8, 2019

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Apr 8, 2019

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Kevin-Mattheus-Moerman commented Apr 9, 2019

Great. Thanks @oxinabox. At this point can you provide a DOI to an archived version of the final reviewed software through a service like ZENODO (some find these steps useful)? Once you've done that can you provide the version tag of the final version of the reviewed software?

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oxinabox commented Apr 9, 2019

Thanks:
DOI: 10.5281/zenodo.2633789
Version: 0.3.1

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Kevin-Mattheus-Moerman commented Apr 9, 2019

@whedon set 10.5281/zenodo.2633789 as archive

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whedon commented Apr 9, 2019

OK. 10.5281/zenodo.2633789 is the archive.

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Kevin-Mattheus-Moerman commented Apr 9, 2019

@whedon set 0.3.1 as version

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whedon commented Apr 9, 2019

OK. 0.3.1 is the version.

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Kevin-Mattheus-Moerman commented Apr 9, 2019

@openjournals/joss-eics I recommend this work is accepted in JOSS

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labarba commented Apr 10, 2019

@whedon accept

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whedon commented Apr 10, 2019

Attempting dry run of processing paper acceptance...
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whedon commented Apr 10, 2019


OK DOIs

- 10.1137/141000671 is OK
- 10.1162/tacl_a_00051 is OK
- 10.3115/v1/d14-1162 is OK
- 10.21105/joss.00602 is OK

MISSING DOIs

- None

INVALID DOIs

- None
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whedon commented Apr 10, 2019

Check final proof 👉 openjournals/joss-papers#615

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#615, 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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labarba commented Apr 10, 2019

@whedon accept deposit=true

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whedon commented Apr 10, 2019

Doing it live! Attempting automated processing of paper acceptance...
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whedon commented Apr 10, 2019

🚨🚨🚨 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#616
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01013
  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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labarba commented Apr 10, 2019

Congratulations, @oxinabox, your JOSS paper is published!

Big thanks to our editor: @Kevin-Mattheus-Moerman, and the reviewer: @aviks — Merci, danke, gracias 🙏

@labarba labarba closed this Apr 10, 2019

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whedon commented Apr 10, 2019

🎉🎉🎉 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.01013/status.svg)](https://doi.org/10.21105/joss.01013)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01013">
  <img src="http://joss.theoj.org/papers/10.21105/joss.01013/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01013/status.svg
   :target: https://doi.org/10.21105/joss.01013

This is how it will look in your documentation:

DOI

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