Joss-reviews: [REVIEW]: ivis: dimensionality reduction in very large datasets using Siamese Networks

[whedon]

Submitting author: @beringresearch (Ignat Drozdov)
Repository: https://github.com/beringresearch/ivis
Version: v1.2.4
Editor: @lpantano
Reviewer: @SaskiaFreytag, @kevinrue
Archive: 10.5281/zenodo.3360634

Status

Status badge code:

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Markdown: [![status](http://joss.theoj.org/papers/b498439c2585ddc954d80a89427b96e2/status.svg)](http://joss.theoj.org/papers/b498439c2585ddc954d80a89427b96e2)

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

@SaskiaFreytag & @kevinrue, 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 @lpantano know.

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

Review checklist for @SaskiaFreytag

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: v1.2.4
• [x] Authorship: Has the submitting author (@beringresearch) 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)?

Review checklist for @kevinrue

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: v1.2.4
• [x] Authorship: Has the submitting author (@beringresearch) 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. @SaskiaFreytag, @kevinrue it looks like you're currently assigned to review 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

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

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[kevinrue]

General checks

For the record, the submitting author (@beringresearch) is an institutional account representative of the affiliation of the authors who made major contributions to the software.
This is frequent practice and absolutely fine.

[SaskiaFreytag]

@whedon commands

[whedon]

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Ask Whedon to check the references for missing DOIs
@whedon check references

[SaskiaFreytag]

@whedon check references

[whedon]

Attempting to check references...

[whedon]

```Reference check summary:

OK DOIs

• 10.1038/s41598-019-45301-0 is OK

MISSING DOIs

• None

INVALID DOIs

• None
  ```

[kevinrue]

@lpantano Both reviewers have ticked all our respective boxes. Let us know if you need anything else from us!

[lpantano]

Thank you so much, @kevinrue and @SaskiaFreytag!, I’ll move to final steps then.

[lpantano]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[lpantano]

Hi @beringresearch, can you create a Zenodo archive from your github and make sure it matches the title and authors of the paper?, thanks

[idroz]

Hi @lpantano , Zenodo archive should have already been created - https://zenodo.org/record/3268357#.XUguXi2ZPOQ

[lpantano]

@whedon set 10.5281/zenodo.3360569 as archive

[whedon]

OK. 10.5281/zenodo.3360569 is the archive.

[lpantano]

@openjournals/joss-eics, reviewers are done, please, let us know if this is ready to go. Thanks everybody!

[kevinrue]

Argh, @lpantano was too fast for me. Here is what I was just typing:

As flattered as I am to be listed as a co-author on the citation in ZENODO

Cite as:
Ignat Drozdov, Benjamin Szubert, beringresearch, & Kevin Rue-Albrecht. (2019, August 5). beringresearch/ivis 1.2.3-joss (Version 1.2.3-joss). Zenodo. http://doi.org/10.5281/zenodo.3360569

I think what Lorena needs would be to only have " Ignat Drozdov & Benjamin Szubert" as authors.
Also, "beringresearch" is an affiliation rather than an author.
To be honest, I don't know if that is possible, when creating a ZENODO archive from GitHub. That said, if it's possible, I think it would be more appropriate (which now depends if Lorena can run again the command to set the archive to a new version).

With regards to my contributions to the R package during the review process, I think the fairest approach would be to add this to the R package DESCRIPTION file:

c(person("Kevin", "Rue-Albrecht", role = "ctb", email = "[email protected]", comment = c(ORCID = "0000-0003-3899-3872"))

It declares that I contributed to, rather than authored, the package.
See http://r-pkgs.had.co.nz/description.html#author

[lpantano]

Good catch, I checked the previous version. @idroz, if you could update the metadata, please? or if you create a new version let me know, I can update both references. Thanks

[idroz]

Still getting to know my way around Zenodo! Author list should now be fixed. I have also modified R package DESCRIPTION file to acknowledge @kevinrue contribution. Thanks again!

[lpantano]

Thank you @idroz, but you may need to bump the version and get another zenodo. Right now DESCRIPTION in master has @kevinrue as author, but not the zenodo archive file. It would be possible to create a v 1.2.4 to make sure we point to the final version and the zenodo points to the final version? Thanks!

[idroz]

v 1.2.4 released and author details synced across zenodo and GitHub.

[lpantano]

@whedon set v1.2.4 as version

[whedon]

OK. v1.2.4 is the version.

[lpantano]

Thanks, version looks good, and zenode as well, just need to update the title of the zenodo archive. The title should match the title of your paper (ivis: dimensionality reduction in very large datasets using Siamese Networks). thanks.

[idroz]

Done.

[lpantano]

@whedon set 10.5281/zenodo.3360634 as archive

[whedon]

OK. 10.5281/zenodo.3360634 is the archive.

[lpantano]

thanks!

ok, @openjournals/joss-eics , this time for real. I think all makes sense now. Sorry about the noise.

[arfon]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/886

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/886, 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]

@whedon accept deposit=true

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[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/887
2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01596
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]

@SaskiaFreytag, @kevinrue - many thanks for your reviews here and to @lpantano for editing this submission ✨

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

[whedon]

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

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