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[REVIEW]: MaterialNet: A web-based graph explorer for materials science data #2105

Closed whedon closed 4 years ago

whedon commented 4 years ago

Submitting author: @waxlamp (Roni Choudhury) Repository: https://github.com/ToyotaResearchInstitute/materialnet Version: v1.0.0 Editor: @danielskatz Reviewer: @Luthaf, @rcannood Archive: 10.5281/zenodo.3701759

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/7e663b9196c523b88d2de24fb20ecdac"><img src="https://joss.theoj.org/papers/7e663b9196c523b88d2de24fb20ecdac/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/7e663b9196c523b88d2de24fb20ecdac/status.svg)](https://joss.theoj.org/papers/7e663b9196c523b88d2de24fb20ecdac)

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

@Luthaf & @rcannood, 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 @danielskatz know.

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

Review checklist for @Luthaf

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @rcannood

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented 4 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @Luthaf, @rcannood 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:

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  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 commented 4 years ago 
Reference check summary:

OK DOIs

- 10.1038/npjcompumats.2015.10 is OK
- 10.1063/1.4812323 is OK
- 10.1016/j.commatsci.2012.02.002 is OK
- 10.1038/s41467-019-10030-5 is OK
- 10.1016/j.matt.2019.10.024 is OK
- 10.1021/cm503507h is OK
- 10.1109/TVCG.2013.173 is OK
- 10.1103/PhysRevB.96.024104 is OK
- 10.1021/acs.jcim.9b00470 is OK
- 10.1038/s41586-019-1335-8 is OK

MISSING DOIs

- None

INVALID DOIs

- None
whedon commented 4 years ago

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

danielskatz commented 4 years ago

👋 @Luthaf & @rcannood - thanks for agreeing to review - here's where the action happens.

Please read the comments above carefully, particularly in terms of accepting the invitation to be able to use the checkboxes, and in terms of not getting unwanted JOSS notifications.

Your job now is to examine the paper and the software, and to check off the items on your list that you can, and to explain what blocks you from checking off other items, either here if they are brief, or in new issues in the source repo if they are more complex. (If you do open issues in the source repo, please mention this review issue in those issues so that we can see them here as well.)

We expect that the review will be done in a couple of weeks, at most, or at least it will get to a list of blocking items in that timeframe.

Luthaf commented 4 years ago

@danielskatz, are they JOSS guideline for documentation concerning SaaS/Online tools? Is user documentation/developer reference/separate installation information something that is required?

danielskatz commented 4 years ago

are they JOSS guideline for documentation concerning SaaS/Online tools? Is user documentation/developer reference/separate installation information something that is required?

JOSS doesn't really provide detailed guidance here. You should probably consider this from the point of view of a user who wants to use the SaaS as well as a developer who wants to understand and potentially contribute to the underlying software.

waxlamp commented 4 years ago

are they JOSS guideline for documentation concerning SaaS/Online tools? Is user documentation/developer reference/separate installation information something that is required?

JOSS doesn't really provide detailed guidance here. You should probably consider this from the point of view of a user who wants to use the SaaS as well as a developer who wants to understand and potentially contribute to the underlying software.

Thanks for this insight. Creating detailed developer documentation is currently out of scope for our project, but of course I can see how it would enrich our open source offering here.

danielskatz commented 4 years ago

I think that's a reasonable answer, as long as the community guidelines match - expectations for community contributions will depend on developer documentation to some extent.

waxlamp commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

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

rcannood commented 4 years ago

Would be nice if @whedon could also generate a diff :)

Here are the changes w.r.t. the original proof.

rcannood commented 4 years ago

@danielskatz I believe @Luthaf and I have ticked all the checkboxes :)

danielskatz commented 4 years ago

great, thanks very much to both of you

danielskatz commented 4 years ago

@whedon generate pdf

danielskatz commented 4 years ago

@whedon check references

whedon commented 4 years ago

PDF failed to compile for issue #2105 with the following error:

/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in block in find': No such file or directory - tmp/2105 (Errno::ENOENT) from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:incollect!' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in find' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-45a043c4bfc2/lib/whedon/processor.rb:61:infind_paper_paths' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-45a043c4bfc2/bin/whedon:50:in prepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:inrun' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in invoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:indispatch' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:in start' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-45a043c4bfc2/bin/whedon:116:in<top (required)>' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in load' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in

'

whedon commented 4 years ago 
Reference check summary:

OK DOIs

- 10.1038/npjcompumats.2015.10 is OK
- 10.1063/1.4812323 is OK
- 10.1016/j.commatsci.2012.02.002 is OK
- 10.1038/s41467-019-10030-5 is OK
- 10.1016/j.matt.2019.10.024 is OK
- 10.1021/cm503507h is OK
- 10.1109/TVCG.2013.173 is OK
- 10.1103/PhysRevB.96.024104 is OK
- 10.1021/acs.jcim.9b00470 is OK
- 10.1038/s41586-019-1335-8 is OK

MISSING DOIs

- None

INVALID DOIs

- None
danielskatz commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

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

danielskatz commented 4 years ago

👋 @waxlamp - please check the references, particular the cases (upper vs lower) for title and journal names. Add {}s in the .bib file to protect cases through compilation, and then use @whedon generate pdf to generate a new PDF. The immediate thing I see is that voronoi should be Voronoi, but please check for anything else as well.

danielskatz commented 4 years ago

I've also created https://github.com/ToyotaResearchInstitute/materialnet/pull/175 with a few more changes in the paper, and a question about wording.

waxlamp commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

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

danielskatz commented 4 years ago

Thanks - looks good. At this point could you:

I can then move forward with accepting the submission.

waxlamp commented 4 years ago

Here's the requested information:

Please let me know if these look ok.

danielskatz commented 4 years ago

@whedon set v1.0.0 as version

whedon commented 4 years ago

OK. v1.0.0 is the version.

danielskatz commented 4 years ago

@whedon set 10.5281/zenodo.3701759 as archive

whedon commented 4 years ago

OK. 10.5281/zenodo.3701759 is the archive.

danielskatz commented 4 years ago

@whedon accept

whedon commented 4 years ago 
Attempting dry run of processing paper acceptance...
whedon commented 4 years ago

:wave: @openjournals/joss-eics, this paper is ready to be accepted and published

. Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1364

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1364, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true
danielskatz commented 4 years ago

@whedon accept deposit=true

whedon commented 4 years ago 
Doing it live! Attempting automated processing of paper acceptance...
whedon commented 4 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 4 years ago

🚨🚨🚨 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/1365
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02105
  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...

danielskatz commented 4 years ago

Thanks to @Luthaf and @rcannood for reviewing, and congratulations to @waxlamp and coauthors!

whedon commented 4 years ago

: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](https://joss.theoj.org/papers/10.21105/joss.02105/status.svg)](https://doi.org/10.21105/joss.02105)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02105">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02105/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02105/status.svg
   :target: https://doi.org/10.21105/joss.02105

This is how it will look in your documentation:

DOI

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waxlamp commented 4 years ago

Thanks to @Luthaf and @rcannood for reviewing, and congratulations to @waxlamp and coauthors!

Thank you, reviewers! And thank you @danielskatz for your support during this very first JOSS paper submission experience for me!