Joss-reviews: [REVIEW]: A Hyperbolic "Crystal Ball"

[whedon]

Submitting author: @benjaminwilson (Benjamin Wilson)
Repository: https://github.com/lateral/crystal-ball
Version: v1.0.1
Editor: @poulson
Reviewer: @HaoZeke
Archive: 10.5281/zenodo.2573958

Status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/033b265ce2f8562dc1148b534a09275c"><img src="http://joss.theoj.org/papers/033b265ce2f8562dc1148b534a09275c/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/033b265ce2f8562dc1148b534a09275c/status.svg)](http://joss.theoj.org/papers/033b265ce2f8562dc1148b534a09275c)

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

@HaoZeke, 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 @poulson know.

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @HaoZeke

Conflict of interest

• [x] 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

• [x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• [x] Repository: Is the source code for this software available at the repository url?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Version: v1.0.1
• [x] Authorship: Has the submitting author (@benjaminwilson) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] 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

• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• [x] Automated tests: Are there automated tests or manual steps described so that the function of the software can be verified?
• [x] 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

• [x] Authors: Does the paper.md file include a list of authors with their affiliations?
• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] 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. @HaoZeke it looks like you're currently assigned as the reviewer for this paper :tada:.

:star: Important :star:

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:

1. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

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

@whedon commands

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[benjaminwilson]

@HaoZeke thanks for your initial feedback over on the other issue. I'll address that today!

[benjaminwilson]

Hi @HaoZeke , I've added a section that gives a high-level view of the algorithms for computing the updates to the point configurations to paper.md, and added a small note about the performance to README.md.

I think this addresses the bulk of your points from previously - but not all of them - I'm afraid I'll have to leave those until Monday.

Thanks already for the comments to date!

[HaoZeke]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[HaoZeke]

@benjaminwilson, thank you for the extensions, I will check when your additions are completed. In general, for the review process I will be opening issues on the project tracker, or where the solution is unambiguous, I shall be opening pull requests. Also, please check the references of the article.

[HaoZeke]

@whedon check references

[whedon]

Attempting to check references...

[whedon]

```Reference check summary:

OK DOIs

• None

MISSING DOIs

• https://doi.org/10.2172/1209543 may be missing for title: Neural Embeddings of Graphs in Hyperbolic Space
• https://doi.org/10.2172/963444 may be missing for title: Hyperbolic Neural Networks

INVALID DOIs

• None
  ```

[benjaminwilson]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[benjaminwilson]

@whedon check references

[whedon]

Attempting to check references...

[whedon]

```Reference check summary:

OK DOIs

• None

MISSING DOIs

• https://doi.org/10.1039/c5cc90276b may be missing for title: Neural Embeddings of Graphs in Hyperbolic Space
• https://doi.org/10.1016/0893-6080(88)90120-7 may be missing for title: Hyperbolic Neural Networks

INVALID DOIs

• None
  ```

[benjaminwilson]

@whedon check references

[whedon]

Attempting to check references...

[whedon]

```Reference check summary:

OK DOIs

• None

MISSING DOIs

• None

INVALID DOIs

• None
  ```

[benjaminwilson]

@HaoZeke thanks for your patience! I think I've now addressed all issues raised in the pre-review.

[HaoZeke]

Excellent work @benjaminwilson, I believe this is ready for submission now, @poulson .

[poulson]

@benjaminwilson It seems that the DOIs were removed rather than fixed. Would you mind making sure that each of the references has a DOI?

[benjaminwilson]

Hi @poulson, I've indeed removed some entries from the .bib file that I wasn't using. For all but one of the remainder, I am afraid that I am really stumped on getting DOIs for any of them. I was surprised that I couldn't find either on the paper itself or in published BibTeX or on crossref.org. I don't know if this is because they are all either arXiv (1) or conference proceedings (rest). Do you know of somewhere else I can look?

[poulson]

@benjaminwilson Hi Benjamin, I am still relatively new to whedon's check references, but you might try mirroring the DOI formatting of a recently completed review, such as https://github.com/sivaramambikasaran/HODLR/blob/master/docs/paper/paper.bib.

The DOI links are surrounded by curly braces and only contain the latter part of the address. Could you try this approach to see if the DOI's are picked up?

[benjaminwilson]

Hi! The problem is rather that I can't find the DOIs for those articles anywhere.

[benjaminwilson]

@whedon check references

[whedon]

Attempting to check references...

[whedon]

```Reference check summary:

OK DOIs

• None

MISSING DOIs

• https://doi.org/10.4414/saez.2013.01498 may be missing for title: Skip-gram word embeddings in hyperbolic space

INVALID DOIs

• None
  ```

[benjaminwilson]

whedon sure does come up with some crazy suggestions for what the missing DOI might be!

[poulson]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[poulson]

Thanks @benjaminwilson; I proofread and everything looks great. Would you mind creating a Zenodo archive and reporting the DOI here?

[benjaminwilson]

Hi @poulson , I think I've got that done now: DOI: 10.5281/zenodo.2573958

[poulson]

@whedon set 10.5281/zenodo.2573958 as archive

[whedon]

OK. 10.5281/zenodo.2573958 is the archive.

[poulson]

@whedon set v1.0.1 as version

[whedon]

OK. v1.0.1 is the version.

[poulson]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[poulson]

@benjaminwilson Thank you for your contribution!

@HaoZeke Thank you for providing your time and expertise for this review!

@arfon This paper should be ready for submission; I am forwarding it over to you (please excuse me, I think there is a rotating editorial board but am not sure who that lands on right now).

[benjaminwilson]

Thanks very much both @poulson and @HaoZeke for your comments and your patience!

[arfon]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

```Reference check summary:

OK DOIs

• None

MISSING DOIs

• https://doi.org/10.4414/saez.2013.01498 may be missing for title: Skip-gram word embeddings in hyperbolic space

INVALID DOIs

• None
  ```

[whedon]

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/511

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/511, 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]

@arfon This paper should be ready for submission; I am forwarding it over to you (please excuse me, I think there is a rotating editorial board but am not sure who that lands on right now).

@poulson - yep it's me this week. In the future you can ping @openjournals/joss-eics to get the editor on rotation.

[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:

1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/512
2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01240
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...

[arfon]

@HaoZeke - many thanks for your review here and to @poulson for editing this submission ✨

@benjaminwilson - your paper is now accepted into JOSS :zap::rocket::boom:

[whedon]

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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.01240/status.svg)](https://doi.org/10.21105/joss.01240)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01240">
  <img src="http://joss.theoj.org/papers/10.21105/joss.01240/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01240/status.svg
   :target: https://doi.org/10.21105/joss.01240

This is how it will look in your documentation:

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[arfon]

P.S. Congratulations to @poulson for editing his first JOSS paper ⚡️