[REVIEW]: osfr: An R Interface to the Open Science Framework

[whedon]

Submitting author: @aaronwolen (Aaron R Wolen)
Repository: https://github.com/ropensci/osfr
Version: v0.2.7
Editor: @kthyng
Reviewer: @kthyng
Archive: 10.5281/zenodo.3625248

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/d5398fc36ea92794a20914143d3fcdc4"><img src="https://joss.theoj.org/papers/d5398fc36ea92794a20914143d3fcdc4/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/d5398fc36ea92794a20914143d3fcdc4/status.svg)](https://joss.theoj.org/papers/d5398fc36ea92794a20914143d3fcdc4)

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

@kthyng, 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 @kthyng know.

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

Review checklist for @kthyng

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS 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?
• Contribution and authorship: Has the submitting author (@aaronwolen) 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 functionality 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

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[whedon]

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

2. 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]

Reference check summary:

OK DOIs

- 10.1371/journal.pcbi.1003285 is OK
- 10.1002/cpet.32 is OK
- 10.1371/journal.pcbi.1005510 is OK

MISSING DOIs

- https://doi.org/10.1186/1751-0473-8-7 may be missing for title: Git can facilitate greater reproducibility and increased transparency in science

INVALID DOIs

- None

[whedon]

👉 Check article proof 📄 👈

[kthyng]

This has already been reviewed and accepted by rOpenSci. Issue #279

[kthyng]

@aaronwolen and @maelle I can't find your paper on a quick glance so I'll just ask you — what is with the "AND" in a bunch of the references? Is it meant to be that way or is that incorrectly forced capitalization?

[aaronwolen]

The latter. I'm not sure how/why it happened but I'll fix in the repo. Thanks for catching it, @kthyng!

Also, the paper is located here.

[aaronwolen]

@whedon generate pdf

[whedon]

👉 Check article proof 📄 👈

[aaronwolen]

I fixed the capitalization issue in ropensci/osfr@d03f5bc.

[kthyng]

@aaronwolen ok great!

[kthyng]

Also, the paper is located here.

The paper is being found correctly by whedon right? As in, the last proof shows up the way you want? It looks good to me.

[kthyng]

Do you have a Zenodo archive yet? If not, please make that now and report the doi here.

[aaronwolen]

Thanks, @kthyng. The Zenodo archive for osfr is here: https://zenodo.org/record/3625248#.XjrSDhdMF24.

I just made a small tweak to my affiliation in the paper but otherwise the proof looks good to me 👍.

[kthyng]

@aaronwolen Great! Can you update the metadata in the Zenodo archive to exactly match the title and authors of your paper?

[aaronwolen]

Thanks, I updated the info but Zenodo throws the following error when I attempt to publish:

Internal Server Error Error ID: f7916d075dfa44e993b9f48d0203b19e

I'm looking into it.

[aaronwolen]

Okay, I was able to update and publish the new metadata on Zenodo.

[kthyng]

@whedon accept

[whedon]

No archive DOI set. Exiting...

[kthyng]

@whedon set 10.5281/zenodo.3625248 as archive

[whedon]

OK. 10.5281/zenodo.3625248 is the archive.

[kthyng]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

PDF failed to compile for issue #2071 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/2071 (Errno::ENOENT) from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/find.rb:43:in collect!'
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-9847f98e9ec6/lib/whedon/processor.rb:61:in find_paper_paths'
from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-9847f98e9ec6/bin/whedon:73:in compile' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:in run'
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:in dispatch'
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-9847f98e9ec6/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]

Reference check summary:

OK DOIs

- 10.1186/1751-0473-8-7 is OK
- 10.1371/journal.pcbi.1003285 is OK
- 10.1002/cpet.32 is OK
- 10.1371/journal.pcbi.1005510 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[kthyng]

Sorry @openjournals/dev but I guess it is happening here too? Please let me know if I am doing something wrong.

[arfon]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Reference check summary:

OK DOIs

- 10.1186/1751-0473-8-7 is OK
- 10.1371/journal.pcbi.1003285 is OK
- 10.1002/cpet.32 is OK
- 10.1371/journal.pcbi.1005510 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

Check final proof 👉 openjournals/joss-papers#1274

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1274, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[aaronwolen]

Proof looks good to me 👍

[aaronwolen]

One question: should the Reviewers list also include the ROpenSci reviewers?

cc/@maelle

[arfon]

@aaronwolen on the paper you mean? Currently the JOSS papers simply include the JOSS reviewers, including the rOpenSci reviewers in the PDF isn't supported sorry.

[aaronwolen]

Okay, just wanted to verify. Thanks!

[kthyng]

thanks @arfon!

[kthyng]

@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:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.02071 joss-papers#1275
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02071
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

[kthyng]

@aaronwolen congrats on your new publication!! 🎉

[whedon]

🎉🎉🎉 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.02071/status.svg)](https://doi.org/10.21105/joss.02071)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02071">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02071/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02071/status.svg
   :target: https://doi.org/10.21105/joss.02071

This is how it will look in your documentation:

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[aaronwolen]

Awesome! Thanks so much @kthyng.