Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

[REVIEW]: ivis: dimensionality reduction in very large datasets using Siamese Networks #1596

Closed
whedon opened this issue Jul 25, 2019 · 40 comments

Comments

@whedon
Copy link
Collaborator

commented Jul 25, 2019

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

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/b498439c2585ddc954d80a89427b96e2"><img src="http://joss.theoj.org/papers/b498439c2585ddc954d80a89427b96e2/status.svg"></a>
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

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

Review checklist for @kevinrue

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: v1.2.4
  • Authorship: Has the submitting author (@beringresearch) 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

This comment has been minimized.

Copy link
Collaborator Author

commented Jul 25, 2019

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 🎉.

⭐️ 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

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

@whedon generate pdf
@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Jul 25, 2019

Attempting PDF compilation. Reticulating splines etc...
@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Jul 25, 2019

@kevinrue

This comment has been minimized.

Copy link

commented Jul 28, 2019

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

This comment has been minimized.

Copy link

commented Aug 3, 2019

@whedon commands

@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Aug 3, 2019

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

This comment has been minimized.

Copy link

commented Aug 3, 2019

@whedon check references

@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Aug 3, 2019

Attempting to check references...
@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Aug 3, 2019


OK DOIs

- 10.1038/s41598-019-45301-0 is OK

MISSING DOIs

- None

INVALID DOIs

- None
@kevinrue

This comment has been minimized.

Copy link

commented Aug 3, 2019

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

@lpantano

This comment has been minimized.

Copy link

commented Aug 4, 2019

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

@lpantano

This comment has been minimized.

Copy link

commented Aug 5, 2019

@whedon generate pdf

@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Aug 5, 2019

Attempting PDF compilation. Reticulating splines etc...
@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Aug 5, 2019

@lpantano

This comment has been minimized.

Copy link

commented Aug 5, 2019

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

This comment has been minimized.

Copy link

commented Aug 5, 2019

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

@lpantano

This comment has been minimized.

Copy link

commented Aug 5, 2019

@whedon set 10.5281/zenodo.3360569 as archive

@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Aug 5, 2019

OK. 10.5281/zenodo.3360569 is the archive.

@lpantano

This comment has been minimized.

Copy link

commented Aug 5, 2019

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

@kevinrue

This comment has been minimized.

Copy link

commented Aug 5, 2019

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 = "kevin.rue-albrecht@kennedy.ox.ac.uk", 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

This comment has been minimized.

Copy link

commented Aug 5, 2019

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

This comment has been minimized.

Copy link

commented Aug 5, 2019

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

This comment has been minimized.

Copy link

commented Aug 5, 2019

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

This comment has been minimized.

Copy link

commented Aug 5, 2019

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

@lpantano

This comment has been minimized.

Copy link

commented Aug 5, 2019

@whedon set v1.2.4 as version

@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Aug 5, 2019

OK. v1.2.4 is the version.

@lpantano

This comment has been minimized.

Copy link

commented Aug 5, 2019

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

This comment has been minimized.

Copy link

commented Aug 5, 2019

Done.

@lpantano

This comment has been minimized.

Copy link

commented Aug 5, 2019

@whedon set 10.5281/zenodo.3360634 as archive

@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Aug 5, 2019

OK. 10.5281/zenodo.3360634 is the archive.

@lpantano

This comment has been minimized.

Copy link

commented Aug 5, 2019

thanks!

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

@arfon

This comment has been minimized.

Copy link
Member

commented Aug 6, 2019

@whedon accept

@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Aug 6, 2019

Attempting dry run of processing paper acceptance...
@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Aug 6, 2019

Check final proof 👉 openjournals/joss-papers#886

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#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

This comment has been minimized.

Copy link
Member

commented Aug 6, 2019

@whedon accept deposit=true

@whedon whedon added the accepted label Aug 6, 2019

@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Aug 6, 2019

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

This comment has been minimized.

Copy link
Collaborator Author

commented Aug 6, 2019

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Aug 6, 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#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

This comment has been minimized.

Copy link
Member

commented Aug 6, 2019

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

@beringresearch - your paper is now accepted into JOSS ⚡️🚀💥

@arfon arfon closed this Aug 6, 2019

@whedon

This comment has been minimized.

Copy link
Collaborator Author

commented Aug 6, 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](https://joss.theoj.org/papers/10.21105/joss.01596/status.svg)](https://doi.org/10.21105/joss.01596)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01596">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01596/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01596/status.svg
   :target: https://doi.org/10.21105/joss.01596

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:

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Projects
None yet
6 participants
You can’t perform that action at this time.